scripts/GMXRC.* !filter
scripts/make_gromos_rtp.py !filter
share/template/README.cmakein !filter
-share/template/template.cpp filter=copyright
src/contrib/* -filter -gmx-doxygen
src/gromacs/gmxlib/nonbonded/preprocessor/gmxpreprocess.py !filter
src/gromacs/linearalgebra/gmx_blas/* !filter
/lib
*~
#*
-*.pyc
-*.o
*.a
+*.cache
+*.DS_Store
+*.egg-info
*.exe
+*.gch
*.lib
-*.cache
+*.o
+*.pyc
+*.so
+*.swp
+.eggs
+.idea
Makefile
lib*.pc
.project
+.tox
.cproject
+build
+_build
CMakeLists.txt.user
/VersionInfo*.cmake
Testing
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-cmake_minimum_required(VERSION 2.8.8)
-# When we require cmake >= 2.8.12, it will provide
-# CMAKE_MINIMUM_REQUIRED_VERSION automatically, but in the meantime we
-# need to set a variable, and it must have a different name.
-set(GMX_CMAKE_MINIMUM_REQUIRED_VERSION "2.8.8")
+cmake_minimum_required(VERSION 3.4.3)
# CMake modules/macros are in a subdirectory to keep this file cleaner
# This needs to be set before project() in order to pick up toolchain files
include(gmxBuildTypeReleaseWithAssert)
if(NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile." FORCE)
- # There's no need to offer a user the choice of ThreadSanitizer
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile TSAN ASAN MSAN." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
- "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile")
+ "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile" "TSAN" "ASAN" "MSAN")
endif()
if(CMAKE_CONFIGURATION_TYPES)
# Add appropriate GROMACS-specific build types for the Visual
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
-# Set a default valgrind suppression file.
-# This unfortunately needs to duplicate information from CTest to work as
-# expected...
-set(MEMORYCHECK_SUPPRESSIONS_FILE
- "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
- CACHE FILEPATH
- "File that contains suppressions for the memory checker")
-include(CTest)
+include(gmxCTestUtilities)
+gmx_ctest_init()
include(gmxCPackUtilities)
gmx_cpack_init()
set(INSTALLED_HEADER_INCLUDE_DIRS "")
set(INSTALLED_HEADER_DEFINITIONS "")
+########################################################################
+# Global non-cache variables for implementing the build system
+########################################################################
+
+# These variables collect libraries that GROMACS requires for
+# linking. They should be appended to with list(APPEND ${name}
+# new-library) calls. They are:
+# - Libraries that are required for libgromacs (only)
+set(GMX_EXTRA_LIBRARIES "")
+# - Libraries that are required for all code in the repository
+set(GMX_COMMON_LIBRARIES "")
+# - Libraries that all code linked against libgromacs needs
+# (i.e., something that is exposed in installed headers).
+set(GMX_PUBLIC_LIBRARIES "")
+
########################################################################
# Check and warn if cache generated on a different host is being reused
########################################################################
option(GMX_USE_OPENCL "Enable OpenCL acceleration" OFF)
-# Decide on GPU settings based on user-settings and GPU/CUDA detection.
-# GCC 4.6 requires CUDA 5.0 and VS2015 requires CUDA 8.0
+# Decide on GPU settings based on user-settings and GPU/CUDA
+# detection. GCC 4.8 requires CUDA 6.0 (but we choose 6.5 for the
+# preliminary C++11 support), icc 15 requires CUDA 7.0, and VS2015
+# requires CUDA 8.0
if(MSVC)
set(REQUIRED_CUDA_VERSION 8.0)
+elseif(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+ set(REQUIRED_CUDA_VERSION 7.0)
else()
- set(REQUIRED_CUDA_VERSION 5.0)
+ set(REQUIRED_CUDA_VERSION 6.5)
endif()
set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
endif()
endif()
-include(gmxDetectSimd)
-gmx_detect_simd(GMX_SUGGESTED_SIMD)
-
gmx_option_multichoice(
GMX_SIMD
"SIMD instruction set for CPU kernels and compiler optimization"
- "${GMX_SUGGESTED_SIMD}"
- None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD IBM_QPX IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
+ "AUTO"
+ AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD IBM_QPX IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
if(GMX_TARGET_MIC)
set(GMX_FFT_LIBRARY_DEFAULT "mkl")
# Run through a number of tests for buggy compilers and other issues
include(gmxTestCompilerProblems)
gmx_test_compiler_problems()
-# GMX_SIMD will not be set automatically until the second
-# pass (which is not strictly guaranteed to occur), so putting this
-# check here among logically-related tests is inefficient, but the
-# potential loss is likely zero.
-if(GMX_SIMD STREQUAL "AVX_256"
- AND CMAKE_COMPILER_IS_GNUCC
- AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
- OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
- message(FATAL_ERROR "gcc 4.6.1 has buggy support for AVX, and GROMACS mdrun will not work. If you want simulation performance, use a more recent compiler. Otherwise, use GMX_SIMD=SSE4.1")
- # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
-endif()
# Implement double-precision option. This is complicated because we
# need installed headers to use the precision mode of the build that
# Find external packages #
########################################################################
-# TNG wants zlib if it is available. And static libxml2 might have a dependency
-find_package(ZLIB QUIET)
-include(gmxTestZLib)
-gmx_test_zlib(HAVE_ZLIB)
-
# Unconditionally find the package, as it is also required for unit
# tests. This exports LIBXML2_FOUND, which we should not use because
# it does not tell us that linking will succeed. Instead, we test that
option(GMX_HWLOC "Add support for hwloc Portable Hardware locality library" ${GMX_HWLOC_DEFAULT})
if(GMX_HWLOC)
if(HWLOC_FOUND)
- include_directories(${HWLOC_INCLUDE_DIRS})
+ include_directories(SYSTEM ${HWLOC_INCLUDE_DIRS})
list(APPEND GMX_EXTRA_LIBRARIES ${HWLOC_LIBRARIES})
else()
message(FATAL_ERROR "Hwloc package support requested, but not found.")
add_definitions(-DTMPI_ATOMICS_DISABLED)
endif()
-# Note this relies on zlib detection having already run
include(gmxManageTNG)
include(gmxManageLmfit)
if(GMX_GPU)
# now that we have detected the dependencies, do the second configure pass
gmx_gpu_setup()
-else()
- mark_as_advanced(CUDA_HOST_COMPILER)
endif()
if(CYGWIN)
add_definitions( -DHAVE_CONFIG_H )
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
-include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
+# TODO required at high level because both libgromacs and progs/mdrun
+# require it, both for thread-MPI and its atomics and mutexes.
+include_directories(BEFORE SYSTEM ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
include(gmxSetBuildInformation)
gmx_set_build_information()
-# Turn on RDTSCP if:
-# - the build system's CPU supports it
-# - the acceleration is set to AVX as all AVX-capable CPUs support AVX (which
-# at this point means that the user set it).
-# Note: it's better to not use the later set value of GMX_SIMD because
-# it reflects the system's capability of both compiling and running AVX code.
-# TODO: After merge with 5.0 one could implement a cache variable dependency
-# such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
-# after the first cmake pass.
-if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
- set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
-else()
- set(GMX_USE_RDTSCP_DEFAULT_VALUE OFF)
-endif()
-option(GMX_USE_RDTSCP "Use RDTSCP for better CPU-based timers (available on recent x86 CPUs; might need to be off when compiling for heterogeneous environments)" ${GMX_USE_RDTSCP_DEFAULT_VALUE})
+
+gmx_option_multichoice(
+ GMX_USE_RDTSCP
+ "Use low-latency RDTSCP instruction for CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments)"
+ "AUTO"
+ OFF ON AUTO DETECT)
mark_as_advanced(GMX_USE_RDTSCP)
-if(GMX_USE_RDTSCP)
+
+macro(gmx_check_rdtscp)
+ if (CPU_DETECTION_FEATURES MATCHES "rdtscp")
+ set(HAVE_RDTSCP 1)
+ set(RDTSCP_DETECTION_MESSAGE " - detected on the build host")
+ else()
+ set(RDTSCP_DETECTION_MESSAGE " - not detected on the build host")
+ endif()
+endmacro()
+
+set(HAVE_RDTSCP 0)
+if (GMX_USE_RDTSCP STREQUAL "ON")
set(HAVE_RDTSCP 1)
+elseif(GMX_USE_RDTSCP STREQUAL "DETECT")
+ gmx_check_rdtscp()
+elseif(GMX_USE_RDTSCP STREQUAL "AUTO")
+ # If the user specified automated SIMD selection, that the choice
+ # is made based on detection on the build host. If so, then RDTSCP
+ # should be chosen the same way.
+ #
+ # If the user specified an AVX SIMD level (e.g. when
+ # cross-compiling GROMACS) then they will get our best guess, ie
+ # that in practice AVX mostly correlates with rdtscp (and anyway
+ # is only relevant in rather old x86 hardware).
+ if (GMX_SIMD STREQUAL "AUTO")
+ gmx_check_rdtscp()
+ elseif (GMX_SIMD MATCHES "AVX")
+ set(HAVE_RDTSCP 1)
+ endif()
+endif()
+gmx_check_if_changed(HAVE_RDTSCP_CHANGED HAVE_RDTSCP)
+if (HAVE_RDTSCP_CHANGED)
+ if (HAVE_RDTSCP)
+ message(STATUS "Enabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
+ else()
+ message(STATUS "Disabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
+ endif()
endif()
include(gmxTestLargeFiles)
endif()
# Math and thread libraries must often come after all others when linking...
-if(HAVE_LIBM)
- list(APPEND GMX_EXTRA_LIBRARIES m)
+if (HAVE_LIBM)
+ list(APPEND GMX_PUBLIC_LIBRARIES m)
endif()
option(GMX_NACL "Configure for Native Client builds" OFF)
message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
- message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
+ message("CMAKE_SHARED_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
endif()
if(NOT GMX_OPENMP)
################################################################
# Shared library load path settings
################################################################
-# CMake supports RPATH on OS X only from 2.8.12 upwards.
-# CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
-# was added.
-
if(NOT GMX_BUILD_SHARED_EXE)
# No rpath
set(CMAKE_SKIP_RPATH TRUE)
set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) # remove -Wl,-Bdynamic
set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
-elseif((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
- ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
+else()
# The build folder always has bin/ and lib/; if we are also going to
# install to lib/, then the installation RPATH works also in the build
# tree. This makes installation slightly faster (no need to rewrite the
endif()
# Set the RPATH as relative to the executable location to make the
# binaries relocatable.
- if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
+ if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") #Assume OS X >=10.5
set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
else()
set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
endif()
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
set(CMAKE_MACOSX_RPATH 1)
-else()
- # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
- if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
- # Set the RPATH options manually.
- set(CMAKE_INSTALL_NAME_DIR "@rpath")
- set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
- else()
- # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
- set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
- endif()
endif()
#COPYING file: Only necessary for binary distributions.
endif()
if (BUILD_TESTING)
- # "tests" target builds all the separate test binaries.
- add_custom_target(tests)
- # "run-ctest" is an internal target that actually runs the tests.
- # This is necessary to be able to add separate targets that execute as part
- # of 'make check', but are ensured to be executed after the actual tests.
- add_custom_target(run-ctest
- COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
- COMMENT "Running all tests"
- VERBATIM)
- add_dependencies(run-ctest tests)
- # "check" target builds and runs all tests.
- add_custom_target(check DEPENDS run-ctest)
+ include(tests/CheckTarget.cmake)
endif()
if (NOT GMX_BUILD_MDRUN_ONLY)
--- /dev/null
+The GROMACS developers generally suggest you install GROMACS for
+production scientific use only from a tarball from an official
+source-code release.
+
+However, if you have a special need and wish to build and/or install a
+version from a git repository, please see
+docs/install-guide/index.rst in this repository, or (if applicable)
+the latest master branch documentation found via
+http://manual.gromacs.org/documentation/.
+
+Note for GROMACS developers
+---------------------------
+This file is excluded from the GROMACS source packages made with CPack,
+and not included into binary packages made with CPack. Source packages
+do include an INSTALL file containing the installation instructions, which
+has been compiled into plain text by Sphinx from docs/install-guide.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-build_options = ['clang-3.8', 'clang-static-analyzer-3.8']
+# These options need to match Jenkins labels on the slave where the
+# analysis is intended to run.
+build_options = ['clang-4', 'clang-static-analyzer-4']
def do_build(context):
cmake_opts = {
'GMX_GPU': 'OFF',
'GMX_OPENMP': 'OFF',
'GMX_SIMD': 'None',
+ 'GMX_USE_RDTSCP': 'OFF',
'GMX_FFT_LIBRARY': 'fftpack'
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
import os.path
-build_options = ['gcc-4.6']
+build_options = ['gcc-6', 'gcov-6']
extra_projects = [Project.REGRESSIONTESTS]
def do_build(context):
# Ideally, this would be Reference, but running the regression tests is way
# too slow that way (and also with None)...
cmake_opts['GMX_SIMD'] = 'SSE4.1'
+ cmake_opts['GMX_USE_RDTSCP'] = 'DETECT'
context.env.set_env_var('GMX_NO_TERM', '1')
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# TODO: Make the XMLs go directly to the desired folder.
# xml_dir = context.workspace.get_log_dir(category='cppcheck')
cmake_opts = {
- 'CPPCHECK_EXECUTABLE': context.env.get_cppcheck_command(version='1.72'),
+ 'CPPCHECK_EXECUTABLE': context.env.get_cppcheck_command(version='1.76.1'),
'CPPCHECK_XML_OUTPUT': 'ON',
- 'GMX_SIMD': 'Reference'
+ 'GMX_SIMD': 'Reference',
+ 'GMX_USE_RDTSCP': 'OFF'
}
context.run_cmake(cmake_opts)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'CMAKE_BUILD_TYPE': 'Debug',
'GMX_GPU': 'OFF',
'GMX_OPENMP': 'OFF',
- 'GMX_SIMD': 'None'
+ 'GMX_SIMD': 'None',
+ 'GMX_USE_RDTSCP': 'OFF'
}
release = (context.job_type == JobType.RELEASE)
if release:
cmake_opts['GMX_COMPILER_WARNINGS'] = 'ON'
cmake_opts['GMX_DEFAULT_SUFFIX'] = 'OFF'
cmake_opts['CMAKE_BUILD_TYPE'] = 'Debug'
+ cmake_opts['GMX_USE_RDTSCP'] = 'DETECT'
if context.opts.reference:
cmake_opts['CMAKE_BUILD_TYPE'] = 'Reference'
if context.opts.x11:
cmake_opts['GMX_X11'] = 'ON'
+ # At least hwloc on Jenkins produces a massive amount of reports about
+ # memory leaks, which cannot be reasonably suppressed because ASAN cannot
+ # produce a reasonable stack trace for them.
+ if context.opts.asan:
+ cmake_opts['GMX_HWLOC'] = 'OFF'
+
regressiontests_path = context.workspace.get_project_dir(Project.REGRESSIONTESTS)
if context.job_type == JobType.RELEASE:
else:
context.build_target(target='tests', keep_going=True)
- context.run_ctest(args=['--output-on-failure'])
+ context.run_ctest(args=['--output-on-failure'], memcheck=context.opts.asan)
context.build_target(target='install')
# TODO: Consider what could be tested about the installed binaries.
use_tmpi = not context.opts.mpi and context.opts.thread_mpi is not False
cmd = 'perl gmxtest.pl -mpirun mpirun -xml -nosuffix all'
- if context.opts.asan:
- cmd+=' -parse asan_symbolize.py'
# setting this stuff below is just a temporary solution,
# it should all be passed as a proper the runconf from outside
cmd += ' -nt ' + nranks
if context.opts.double:
cmd += ' -double'
+ if context.opts.asan:
+ context.env.set_env_var('ASAN_OPTIONS', 'detect_leaks=0')
context.run_cmd(cmd, shell=True, failure_message='Regression tests failed to execute')
# configuration syntax, so that the configurations are stable even
# if the defaults change in future.
+# Test on ARM v7
+# Test ARM_NEON SIMD
+gcc-4.8 simd=ARM_NEON release
+
+# Test on ARM v8
+# Test ARM_NEON_ASIMD SIMD
+gcc-5 simd=ARM_NEON_ASIMD release
+
# Test the mdrun-only build
# TODO In combination with gmx from another build, arrange to run regressiontests
clang-3.7 double mpi no-openmp fftpack mdrun-only
# Test MPMD PME with thread-MPI
# TODO Add double to this configuration if/when we stablize the essentialdynamics tests
-gcc-5 npme=1 nranks=2 no-openmp fftpack simd=avx_128_fma release
+gcc-7 npme=1 nranks=2 no-openmp fftpack release
# Test non-default GMX_PREFER_STATIC_LIBS behavior
# TODO enable this
# Test SSE4.1 SIMD
# Test single-rank GPU
-gcc-4.8 nranks=1 gpu cuda-7.5 simd=sse4.1
+# TODO Test clang + OpenMP + CUDA
+# TODO change to clang-4 and cuda-8.0
+gcc-4.8 openmp nranks=1 gpu cuda-7.5 simd=sse4.1
# Test MPMD PME with library MPI
-clang-3.4 npme=1 nranks=2 mpi
+# Test clang + OpenMP
+clang-4 openmp simd=avx_128_fma npme=1 nranks=2 mpi
# Test non-default use of mdrun -gpu_id
# Test SSE2 SIMD
# Test own-fftw build (from local copy of the file)
# Test mdrun -tunepme (e.g. with relaxed tolerances, for now)
# Consider testing of other CMake option paths
-# Consider adding our ARM dev boards as slaves to improve cross-platform portability testing.
# once, and for the intent to be reflected precisely in the
# configuration syntax, so that the configurations are stable even
# if the defaults change in future.
+#
+# The phrase "at time of release" refers to either the initial
+# GROMACS release from that branch, or the next expected release
+# from that branch. (We will tend not to retroactively support
+# newer infrastructure in CI, unless it's either easy or of
+# high impact.)
# Test older gcc
# Test oldest supported CUDA
-# Test oldest supported cmake
# Test oldest supported Ubuntu
-# Test X11 build
# Test MPI with CUDA
# Test MPMD PME with library MPI
-gcc-4.6 gpu cuda-5.0 mpi npme=1 nranks=2 openmp x11 cmake-2.8.8
-
-# Test newest gcc supported by newest CUDA shortly after the release
-# Test SIMD implementation of pair search for GPU code-path
-gcc-5 gpu cuda-8.0 openmp simd=avx2_256
+# Test cmake FindCUDA functionality introduced in 3.8
+gcc-4.8 gpu cuda-6.5 cmake-3.8.1 mpi npme=1 nranks=2 openmp
# Test newest gcc supported by newest CUDA at time of release
# Test thread-MPI with CUDA
-gcc-4.8 gpu thread-mpi cuda-7.5 openmp release
+# Test cmake version from before new FindCUDA support (in 3.8)
+# Test SIMD implementation of pair search for GPU code-path
+gcc-5 gpu cuda-8.0 thread-mpi openmp cmake-3.6.1 release simd=avx2_256
-# Test with ThreadSanitizer
-# Test AVX2_256 SIMD
+# Test with ThreadSanitizer (compiled without OpenMP, even though
+# this gcc was configured with --disable-linux-futex, because
+# Redmine #1850 is unresolved, which causes more suspected
+# false positives than races detected)
# Test fftpack fallback
-gcc-4.9 tsan fftpack simd=avx2_256
+gcc-7 tsan no-openmp fftpack
# Test newest gcc at time of release
+gcc-7 mpi
+
# Test on MacOS (because gcc-6 is only available there)
-gcc-6 double
+# Test X11 build
+gcc-6 double x11
+# Test oldest supported cmake
# Test older clang
# Test double precision
-# Test with AddressSanitizer
# Test without OpenMP
# Test thread-MPI
-clang-3.4 double thread-mpi no-openmp fftpack asan
+clang-3.4 double thread-mpi no-openmp fftpack cmake-3.4.3
+
+# Test newest clang at time of release
+# Test with AddressSanitizer (without OpenMP, see below)
+clang-4 no-openmp asan
# Test oldest supported MSVC on Windows
# Test newest supported MSVC on Windows
# Test MKL
# Test without any MPI
# Test on CentOS (because icc-16.0 is only available there)
-icc-16.0 no-thread-mpi openmp mkl cmake-3.3.2 simd=avx_256
-
-# Test AVX_128_FMA SIMD
-gcc-5 mpi openmp simd=avx_128_fma
+icc-16.0 no-thread-mpi openmp mkl cmake-3.8.1 simd=avx_256
# Test NVIDIA OpenCL
# Test MPI + OpenCL
-gcc-4.8 openmp opencl cuda-7.5 mpi release
+# Test AVX2_256 SIMD
+gcc-4.8 openmp opencl cuda-7.5 mpi release simd=avx2_256
# Test AMD OpenCL
-gcc-5 openmp opencl amdappsdk-3.0
+# Test AVX_128_FMA SIMD
+gcc-5 openmp simd=avx_128_fma opencl amdappsdk-3.0
# TODO
+# Add OpenMP support to ASAN build (but libomp.so in clang-4 reports leaks, so might need a suitable build or suppression)
# Test hwloc support
-# Test newest supported Ubuntu
-# Migrate ThreadSanitizer test off GPU build slave
+# Test newest supported LTS Ubuntu
+# Update gpu testing specifiers per https://redmine.gromacs.org/issues/2161
+# Resolve Redmine #1850 so that ThreadSanitizer can test our OpenMP code
import os.path
-# TODO when merging this to master, update gcc to 4.8
-build_options = ['gcc-4.7', 'cmake-3.4.3']
+build_options = ['gcc-4.8', 'cmake-3.4.3']
extra_projects = [Project.REGRESSIONTESTS]
def run_build(context, cmake_opts):
# These configurations will be used to build and test the tarballs
# before the release.
gcc-4.8 mpi mdrun-only
-gcc-4.6 static
-gcc-4.7 double
+gcc-6 static
+gcc-5 double
clang-3.4 static double
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'GMX_BUILD_HELP': 'ON',
'CMAKE_BUILD_TYPE': 'Debug',
'GMX_SIMD': 'None',
+ 'GMX_USE_RDTSCP': 'OFF',
'GMX_THREAD_MPI': 'OFF',
'GMX_OPENMP': 'OFF',
'GMX_GPU': 'OFF'
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
endif()
endif()
+include(FindPackageHandleStandardArgs)
find_package_handle_standard_args(Hwloc
REQUIRED_VARS HWLOC_LIBRARIES HWLOC_INCLUDE_DIRS
VERSION_VAR HWLOC_VERSION)
+++ /dev/null
-#include<immintrin.h>
-int main()
-{
- __m256d a;
- __m256i mask;
- double d[4]={1,2,3,4};
-
- a = _mm256_setzero_pd();
- mask = _mm256_castpd_si256(a);
-
-#if GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
- a = _mm256_maskload_pd(d,_mm256_castsi256_pd(mask));
-#else
- a = _mm256_maskload_pd(d,mask);
-#endif
- return 0;
-}
-
+++ /dev/null
-int main()
-{
-/* This detects 3.0 versions for both C and C++ clang. It detects the
- * version of the LLVM back end, and not (for example) the Apple clang
- * version number (which might be 4.1 or some number based on its
- * "compatibility with gcc 4.2.1," even though the LLVM back end is
- * 3.0!).
- *
- * If/when we have time or user complaints, we can maybe ban earlier
- * versions of clang, but we don't actually know there's a problem
- * with them at the time of this commit.
- */
-#if (__clang_major__ == 3) && (__clang_minor__ == 0)
- return 0;
-#else
-#error clang version information not found
-#endif
-}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(CMAKE_${_language}_FLAGS_ASAN ${_flags} CACHE STRING "${_human_readable_language} flags for address sanitizer")
mark_as_advanced(CMAKE_${_language}_FLAGS_ASAN)
endforeach()
-
-string(TOUPPER "${CMAKE_BUILD_TYPE}" _cmake_build_type)
-if (APPLE AND _cmake_build_type STREQUAL ASAN) #https://code.google.com/p/address-sanitizer/issues/detail?id=210
- set(BUILD_SHARED_LIBS OFF CACHE BOOL "Disabled for ASAN builds" FORCE)
-endif()
-
set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Disabled for regressiontests reference builds" FORCE)
set(GMX_THREAD_MPI OFF CACHE BOOL "Disabled for regressiontests reference builds" FORCE)
- if(NOT "${CMAKE_C_COMPILER_ID}" STREQUAL "GNU" OR NOT "${CMAKE_C_COMPILER_VERSION}" MATCHES "4.7")
+ if(NOT "${CMAKE_C_COMPILER_ID}" STREQUAL "GNU" OR NOT "${CMAKE_C_COMPILER_VERSION}" MATCHES "4.8")
message(WARNING "Reference values for regressiontests should use GROMACS compiled with "
- "gcc 4.7, but your configuration is using ${CMAKE_C_COMPILER_ID}-${CMAKE_C_COMPILER_VERSION}.")
+ "gcc 4.8, but your configuration is using ${CMAKE_C_COMPILER_ID}-${CMAKE_C_COMPILER_VERSION}.")
endif()
endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
string(TOUPPER "${CMAKE_BUILD_TYPE}" _cmake_build_type)
if (_cmake_build_type STREQUAL TSAN)
set(TMPI_ATOMICS_DISABLED 1)
- set(TMPI_ATOMICS 0)
if (NOT((CMAKE_${_language}_COMPILER_ID MATCHES "Clang" AND
CMAKE_${_language}_COMPILER_VERSION VERSION_GREATER 3.2.999)
OR (CMAKE_${_language}_COMPILER_ID MATCHES "GNU" AND
GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CXXFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall -Wno-unused-function" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall" GMXC_CXXFLAGS)
# Problematic with CUDA
# GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EFFCXX "-Wnon-virtual-dtor" GMXC_CXXFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra -Wno-missing-field-initializers -Wpointer-arith" GMXC_CXXFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_UNDEF "-Wundef" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-declarations" GMXC_CXXFLAGS)
+ # CUDA versions prior to 7.5 come with a header (math_functions.h) which uses the _MSC_VER macro
+ # unconditionally, so we don't use -Wundef for earlier CUDA versions.
+ if(NOT(GMX_GPU AND CUDA_VERSION VERSION_LESS "7.5"))
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN_UNDEF "-Wundef" GMXC_CXXFLAGS)
+ endif()
GMX_TEST_CFLAG(CXXFLAGS_WARN_REL "-Wno-array-bounds" GMXC_CXXFLAGS_RELEASE_ONLY)
endif()
# new in gcc 4.5
if (CMAKE_C_COMPILER_ID MATCHES "Intel")
if (NOT WIN32)
if(NOT GMX_OPENMP)
- if(CMAKE_C_COMPILER_VERSION VERSION_GREATER 13.99.99)
# 3180: unrecognized OpenMP #pragma
- GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd3180" GMXC_CFLAGS)
- else()
-# 161: unrecognized #pragma
- GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd161" GMXC_CFLAGS)
- endif()
+ GMX_TEST_CFLAG(CFLAGS_PRAGMA "-wd3180" GMXC_CFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- if(CMAKE_C_COMPILER_VERSION VERSION_LESS 15.00.00)
-# 193: zero used for undefined preprocessing identifier ".."
- GMX_TEST_CFLAG(CFLAGS_WARN_OLD -wd193 GMXC_CFLAGS)
- endif()
# 177: function/variable ".." was declared but never referenced
-# 271: trailing comma is nonstandard
-# 304: access control not specified ("public" by default)
-# 383: value copied to temporary, reference to temporary used
-# 424: extra ";" ignored
-# 444: destructor for base class ".." is not virtual
-# 522: function ".." redeclared "inline" after being called
+# 411: class defines no constructor to initialize the following (incorrect for struct, initializer list works)
# 593: variable ".." was set but never used
-# 869: parameter ".." was never referenced
# 981: operands are evaluated in unspecified order
#1418: external function definition with no prior declaration
#1419: external declaration in primary source file
#2547: ".." was specified as both a system and non-system include directory
#2557: comparison between signed and unsigned operands
#3280: declaration hides member ".."
-#3346: dynamic exception specifications are deprecated
#11074: Inlining inhibited by limit max-size(/max-total-size)
#11076: To get full report use -opt-report=3 -opt-report-phase ipo (shown for previous remark)
- GMX_TEST_CFLAG(CFLAGS_WARN "-w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076" GMXC_CFLAGS)
+ GMX_TEST_CFLAG(CFLAGS_WARN "-w3 -wd177 -wd411 -wd593 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd11074 -wd11076" GMXC_CFLAGS)
endif()
GMX_TEST_CFLAG(CFLAGS_STDGNU "-std=gnu99" GMXC_CFLAGS)
- GMX_TEST_CFLAG(CFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias" GMXC_CFLAGS_RELEASE)
+ GMX_TEST_CFLAG(CFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14" GMXC_CFLAGS_RELEASE)
GMX_TEST_CFLAG(CFLAGS_DEBUG "-O0" GMXC_CFLAGS_DEBUG) #icc defaults to -O2 even with -g
GMX_TEST_CFLAG(CFLAGS_FP_RELASSERT "-fp-model except -fp-model precise" GMXC_CFLAGS_RELWITHASSERT)
else()
if(NOT GMX_OPENMP)
- if(CMAKE_C_COMPILER_VERSION VERSION_GREATER 13.99.99)
- GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
- else()
- GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd161" GMXC_CFLAGS)
- endif()
+ GMX_TEST_CFLAG(CFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- if(CMAKE_C_COMPILER_VERSION VERSION_LESS 15.00.00)
- GMX_TEST_CFLAG(CFLAGS_WARN_OLD /wd193 GMXC_CFLAGS)
- endif()
- GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346" GMXC_CFLAGS)
+GMX_TEST_CFLAG(CFLAGS_WARN "/W3 /wd177 /wd411 /wd593 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280" GMXC_CFLAGS)
endif()
GMX_TEST_CFLAG(CFLAGS_OPT "/Qip" GMXC_CFLAGS_RELEASE)
endif()
if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
if (NOT WIN32)
if(NOT GMX_OPENMP)
- if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 13.99.99)
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-wd3180" GMXC_CXXFLAGS)
- else()
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-wd161" GMXC_CXXFLAGS)
- endif()
+ GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-wd3180" GMXC_CXXFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.00.00)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_OLD -wd193 GMXC_CXXFLAGS)
+ if (GMX_GPU)
+# Suppress warnings from CUDA headers
+# 7: unrecognized token
+# 82: storage class is not first
+# The below are also required for math_functions.h / math_functions.hpp at least until CUDA 8.0-RC
+# 193: zero used for undefined preprocessing identifer
+# 3346:dynamic exception specifiers are deprecated
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN_OLD_GPU "-wd7 -wd82 -wd193 -wd3346" GMXC_CXXFLAGS)
endif()
#All but the following warnings are identical for the C-compiler (see above)
-#1782: #pragma once is obsolete
+# 383: value copied to temporary, reference to temporary used
+# 444: destructor for base class ".." is not virtual
#2282: unrecognized GCC pragma
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3 -wd177 -wd271 -wd304 -wd383 -wd424 -wd444 -wd522 -wd593 -wd869 -wd981 -wd1418 -wd1419 -wd1572 -wd1599 -wd2259 -wd2415 -wd2547 -wd2557 -wd3280 -wd3346 -wd11074 -wd11076 -wd1782 -wd2282" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-w3 -wd177 -wd383 -wd411 -wd444 -wd981 -wd1418 -wd1572 -wd1599 -wd2259 -wd3280 -wd11074 -wd11076 -wd2282" GMXC_CXXFLAGS)
endif()
- GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias" GMXC_CXXFLAGS_RELEASE)
+ GMX_TEST_CXXFLAG(CXXFLAGS_OPT "-ip -funroll-all-loops -alias-const -ansi-alias -no-prec-div -fimf-domain-exclusion=14" GMXC_CXXFLAGS_RELEASE)
GMX_TEST_CXXFLAG(CXXFLAGS_DEBUG "-O0" GMXC_CXXFLAGS_DEBUG)
GMX_TEST_CXXFLAG(CXXFLAGS_FP_RELASSERT "-fp-model except -fp-model precise" GMXC_CXXFLAGS_RELWITHASSERT)
else()
if(NOT GMX_OPENMP)
- if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 13.99.99)
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
- else()
- GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd161" GMXC_CXXFLAGS)
- endif()
+ GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "/wd3180" GMXC_CFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.00.00)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_OLD /wd193 GMXC_CXXFLAGS)
- endif()
#809: exception specification for virtual function X is incompatible with that of overridden function
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd177 /wd271 /wd304 /wd383 /wd424 /wd444 /wd522 /wd593 /wd809 /wd869 /wd981 /wd1418 /wd1419 /wd1572 /wd1599 /wd2259 /wd2415 /wd2547 /wd2557 /wd3280 /wd3346 /wd1782 /wd2282" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "/W3 /wd177 /wd383 /wd411 /wd444 /wd809 /wd981 /wd1418 /wd1572 /wd1599 /wd2259 /wd3280 /wd11074 /wd11076 /wd2282" GMXC_CXXFLAGS)
endif()
GMX_TEST_CXXFLAG(CXXFLAGS_OPT "/Qip" GMXC_CXXFLAGS_RELEASE)
endif()
GMX_TEST_CXXFLAG(CXXFLAGS_PRAGMA "-Wno-unknown-pragmas" GMXC_CXXFLAGS)
endif()
if (GMX_COMPILER_WARNINGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall -Wno-unused-function" GMXC_CXXFLAGS)
- GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra -Wno-missing-field-initializers -Wpointer-arith" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN "-Wall" GMXC_CXXFLAGS)
+ GMX_TEST_CXXFLAG(CXXFLAGS_WARN_EXTRA "-Wextra -Wno-missing-field-initializers -Wpointer-arith -Wmissing-prototypes" GMXC_CXXFLAGS)
GMX_TEST_CXXFLAG(CXXFLAGS_DEPRECATED "-Wdeprecated" GMXC_CXXFLAGS)
endif()
endif()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(CPACK_SOURCE_GENERATOR TGZ)
set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
set(CPACK_SOURCE_IGNORE_FILES
- "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
+ "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;INSTALL-dev;")
# Get the list of directories added with gmx_cpack_add_generated_source_directory()
get_property(CPACK_SOURCE_INSTALLED_DIRECTORIES
GLOBAL PROPERTY GMX_CPACK_SOURCE_INSTALLED_DIRECTORIES)
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2016, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# Helper macros to encapsulate some usage of CTest
+#
+# This file is intended to contain CTest workarounds and such.
+include(CMakeParseArguments)
+
+macro (gmx_ctest_init)
+ # Set a default valgrind suppression file.
+ # This unfortunately needs to duplicate information from CTest to work as
+ # expected...
+ #set(MEMORYCHECK_SUPPRESSIONS_FILE
+ # "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
+ # CACHE FILEPATH
+ # "File that contains suppressions for the memory checker")
+ string(TOUPPER "${CMAKE_BUILD_TYPE}" _cmake_build_type)
+ if (_cmake_build_type STREQUAL "ASAN")
+ set(MEMORYCHECK_TYPE "AddressSanitizer")
+ endif()
+ include(CTest)
+ # At least with CMake 3.4.1 on OS X, AddressSanitizer support in CTest
+ # does not work without this...
+ set(_ctest_config_file "${PROJECT_BINARY_DIR}/DartConfiguration.tcl")
+ file(STRINGS ${_ctest_config_file} _existing REGEX "^CMakeCommand: ")
+ if (NOT _existing)
+ file(APPEND ${_ctest_config_file} "\nCMakeCommand: ${CMAKE_COMMAND}\n")
+ endif()
+endmacro()
+
+function (gmx_get_test_prefix_cmd VAR)
+ set(_options IGNORE_LEAKS)
+ cmake_parse_arguments(ARG "${_options}" "" "" ${ARGN})
+ set(_opts "")
+ if (ARG_IGNORE_LEAKS OR APPLE)
+ list(APPEND _opts "detect_leaks=0")
+ endif()
+ set(_cmd "")
+ if (MEMORYCHECK_TYPE STREQUAL "AddressSanitizer")
+ string(REPLACE ";" " " _opts "${_opts}")
+ set(_cmd ${PROJECT_SOURCE_DIR}/cmake/with_asan_opts.sh ${_opts} --)
+ endif()
+ set(${VAR} "${_cmd}" PARENT_SCOPE)
+endfunction()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# More flexible alternative to add_custom_command() and add_custom_target()
# for dependent custom commands. It adds a few convenience features:
-# - Support for custom commands that always run (like add_custom_target()),
-# but still have the ability to act as dependencies of other custom
-# commands (such that the dependent commands run only if the output
-# has been updated) also for Ninja.
# - Adds file-level dependencies between custom targets added with this
# command such that if there is a target-level dependency, it also implies
# that the custom command should always be run if the output file of the
# [WORKING_DIRECTORY <dir>]
# [DEPENDS <deps...>]
# [DEPENDS_FILE_LIST <list>]
-# [COMMENT <comment>])
+# [COMMENT <comment>] [USES_TERMINAL])
#
# <target>
# - Name of the custom target to create.
# RUN_ALWAYS
-# - Create the command such that it always runs.
-# This takes care of differences between the Ninja generator and others,
-# which require different rules to make this happen such that
-# dependencies on the output of the target work correctly, also in the
-# case the command does not always update the timestamp of the output.
+# - Create the command such that it always runs, and may update the output
+# file in the process.
# The dependencies listed with DEPENDS are ignored in this case.
# ADD_FAST_TARGET
# - In addition to creating <target>, create a secondary target
# - Passed to add_custom_command()/add_custom_target()
# COMMENT
# - Passed to add_custom_command()/add_custom_target()
+# USES_TERMINAL
+# - Passed to add_custom_command()/add_custom_target()
# DEPENDS
# - Dependencies passed to add_custom_command(). Any targets in this list
# that have been created with gmx_add_custom_output_target() are
set(_add_fast ON)
elseif ("x${_arg}" MATCHES "^x(OUTPUT|DEPENDS|DEPENDS_FILE_LIST)$")
set(_option ${_arg})
- elseif ("x${_arg}" MATCHES "^x(COMMAND|COMMENT|WORKING_DIRECTORY)$")
+ elseif ("x${_arg}" MATCHES "^x(COMMAND|COMMENT|WORKING_DIRECTORY|USES_TERMINAL)$")
set(_option "PASS")
list(APPEND _command_args "${_arg}")
elseif ("x${_option}" STREQUAL "xDEPENDS")
endif()
# Create the actual command as requested.
if (NOT _always)
- # If the command does not need to run always, the standard CMake
- # mechanism is sufficient.
add_custom_command(OUTPUT ${_output}
${_command_args} DEPENDS ${_deps} VERBATIM)
add_custom_target(${targetname} DEPENDS ${_output})
- elseif (CMAKE_GENERATOR STREQUAL "Ninja")
- # Ninja requires all generated files mentioned in dependencies of custom
- # commands to be actually mentioned in the build system, and luckily
- # add_custom_command() makes that possible.
- # But it seems impossible to create a robust custom command that would be
- # always run, so other generators that do not have this constraint simply
- # use an add_custom_target().
- #
- # The second, phony file is never created, so the rule is always
- # triggered again. TODO: Figure out why this works, even though ninja
- # very eagerly complains about missing files.
- # This unfortunately does not work with the make generator, as
- # the non-existent second file causes some part of the generated system
- # erase the first file at the beginning of every build, causing a full
- # rebuild of the dependencies.
- add_custom_command(OUTPUT ${_output} ${targetname}-phony
- ${_command_args} VERBATIM)
- # The generated Ninja build system would probably work fine even
- # without this target, but CMake requires all custom commands to belong
- # to a target in the same CMakeLists.txt to generate anything for them.
- add_custom_target(${targetname} DEPENDS ${_output})
else()
- # For other generators, a target-level dependency on the custom target
- # ensures that the output is created before the dependent targets'
- # dependencies are even evaluated.
- add_custom_target(${targetname} ${_command_args} VERBATIM)
+ add_custom_target(${targetname} BYPRODUCTS ${_output}
+ ${_command_args} VERBATIM)
endif()
# Store the output file name in a custom property to be used in dependency
# resolution later.
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+include(gmxTestInlineASM)
+
+# Ensure things like GMX_TARGET_X86 are available
+include(gmxDetectTargetArchitecture)
+gmx_detect_target_architecture()
+
+# gmx_run_cpu_detection()
+#
+# Try to detect information about the CPU of the build host by
+# building and running the same detection code used by mdrun. This
+# works on all architectures where we are not cross-compiling;
+# depending on the architecture the detection will either use special
+# assembly instructions (like cpuid), preprocessor defines, or probing
+# /proc/cpuinfo on Linux.
+#
+# The TYPE argument is passed as a command-line argument to the
+# detection program, and the terminal output is captured and stored in
+# the cache variable CPU_DETECTION_${TYPE} as the result. If the detection
+# program fails to compile, or fails to run, no value is stored.
+#
+# The function caches information about whether the detection program
+# has already been built or run with this TYPE, so this function
+# should be called freely, even if the call might be repeated within
+# or across invocations of cmake.
+#
+function(gmx_run_cpu_detection TYPE)
+ string(TOUPPER ${TYPE} UPPERTYPE)
+ string(TOLOWER ${TYPE} LOWERTYPE)
+
+ set(OUTPUT_VAR "")
+ # We need to execute the binary, so this only works if not
+ # cross-compiling. However, note that we are NOT limited to x86.
+ if(CMAKE_CROSSCOMPILING)
+ # TODO Need we explain that we're not detecting because we are cross compiling?
+ else()
+ set(CPU_DETECTION_BINARY "${PROJECT_BINARY_DIR}/CMakeFiles/GmxDetectCpu${CMAKE_EXECUTABLE_SUFFIX}")
+ if(NOT CPU_DETECTION_COMPILED)
+ # Compile the detection program
+ set(GMX_TARGET_X86_VALUE 0)
+ if(GMX_TARGET_X86)
+ set(GMX_TARGET_X86_VALUE 1)
+ endif()
+
+ # for x86 we need inline assembly to use cpuid
+ gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
+ if(GMX_X86_GCC_INLINE_ASM)
+ set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=1")
+ else()
+ set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=0")
+ endif()
+
+ set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${PROJECT_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}")
+ set(LINK_LIBRARIES "${GMX_STDLIB_LIBRARIES}")
+ try_compile(CPU_DETECTION_COMPILED
+ "${PROJECT_BINARY_DIR}"
+ "${PROJECT_SOURCE_DIR}/src/gromacs/hardware/cpuinfo.cpp"
+ COMPILE_DEFINITIONS "${_compile_definitions}"
+ CMAKE_FLAGS "-DLINK_LIBRARIES=${LINK_LIBRARIES}"
+ OUTPUT_VARIABLE CPU_DETECTION_COMPILED_OUTPUT
+ COPY_FILE ${CPU_DETECTION_BINARY})
+ if(NOT CPU_DETECTION_COMPILED AND NOT RUN_CPU_DETECTION_COMPILATION_QUIETLY)
+ message(STATUS "Did not detect build CPU ${LOWERTYPE} - detection program did not compile")
+ endif()
+ set(RUN_CPU_DETECTION_COMPILATION_QUIETLY TRUE CACHE INTERNAL "Keep quiet on any future compilation attempts")
+ endif()
+
+ if(CPU_DETECTION_COMPILED)
+ # Run the detection program with -type as the argument.
+
+ if(NOT DEFINED CPU_DETECTION_${UPPERTYPE})
+ execute_process(COMMAND ${CPU_DETECTION_BINARY} "-${LOWERTYPE}"
+ RESULT_VARIABLE RESULT_VAR
+ OUTPUT_VARIABLE OUTPUT_VAR_TEMP
+ ERROR_QUIET)
+ if (RESULT_VAR EQUAL 0)
+ string(STRIP "${OUTPUT_VAR_TEMP}" OUTPUT_VAR)
+ message(STATUS "Detected build CPU ${LOWERTYPE} - ${OUTPUT_VAR}")
+ set(CPU_DETECTION_${UPPERTYPE} "${OUTPUT_VAR}" CACHE INTERNAL "Result of running cpu detection code with argument -${LOWERTYPE}")
+ else()
+ message(STATUS "Did not detect build CPU ${LOWERTYPE} - detection program did not run successfully")
+ endif()
+ endif()
+ endif()
+ endif()
+endfunction()
# - Check the username performing the build, as well as date and time
#
-# gmx_detect_simd(GMX_SUGGESTED_SIMD)
+# gmx_detect_simd(_suggested_simd_)
#
-# Try to detect CPU information and suggest SIMD instruction set
+# Try to detect CPU features and suggest a SIMD instruction set
# that fits the current CPU. This should work on all architectures
# where we are not cross-compiling; depending on the architecture the
# detection will either use special assembly instructions (like cpuid),
# preprocessor defines, or probing /proc/cpuinfo on Linux.
#
-# This assumes gmx_detect_target_architecture() has already been run,
-# so that things like GMX_TARGET_X86 are already available.
-# (otherwise we cannot use inline ASM on x86).
-#
-# Sets ${GMX_SUGGESTED_SIMD} in the parent scope if
-# GMX_SIMD is not set (e.g. by the user, or a previous run
-# of CMake).
+# Sets ${suggested_simd} in the parent scope if GMX_SIMD is not set
+# (e.g. by the user, or a previous run of CMake).
#
# we rely on inline asm support for GNU!
include(gmxTestInlineASM)
+# Ensure things like GMX_TARGET_X86 are available
+include(gmxDetectTargetArchitecture)
+gmx_detect_target_architecture()
+include(gmxDetectCpu)
function(gmx_suggest_simd _suggested_simd)
- if(${_suggested_simd})
- # There's already been a suggestion made, which can't change
- return()
- endif()
-
- # for x86 we need inline asm to use cpuid
- gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
-
- if(GMX_X86_GCC_INLINE_ASM)
- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=1")
- else()
- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=0")
+ if (NOT SUGGEST_SIMD_QUIETLY)
+ message(STATUS "Detecting best SIMD instructions for this CPU")
endif()
- message(STATUS "Detecting best SIMD instructions for this CPU")
-
- # Get CPU SIMD properties information
- if(GMX_TARGET_X86)
- set(GMX_TARGET_X86_VALUE 1)
- else()
- set(GMX_TARGET_X86_VALUE 0)
- endif()
- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}")
-
# Prepare a default suggestion
set(OUTPUT_SIMD "None")
- # We need to execute the binary, so this only works if not cross-compiling.
- # However, note that we are NOT limited to x86.
- if(NOT CMAKE_CROSSCOMPILING)
- # TODO Extract this try_compile to a helper function, because
- # it duplicates code in gmxSetBuildInformation.cmake
- set(GMX_DETECTSIMD_BINARY "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/GmxDetectSimd${CMAKE_EXECUTABLE_SUFFIX}")
- set(LINK_LIBRARIES "${GMX_STDLIB_LIBRARIES}")
- try_compile(GMX_DETECTSIMD_COMPILED
- "${CMAKE_CURRENT_BINARY_DIR}"
- "${CMAKE_CURRENT_SOURCE_DIR}/src/gromacs/hardware/cpuinfo.cpp"
- COMPILE_DEFINITIONS "${_compile_definitions}"
- CMAKE_FLAGS "-DLINK_LIBRARIES=${LINK_LIBRARIES}"
- OUTPUT_VARIABLE GMX_DETECTSIMD_COMPILED_OUTPUT
- COPY_FILE ${GMX_DETECTSIMD_BINARY})
- unset(_compile_definitions)
+ # Detect CPU features and place the string in CPU_DETECTION_FEATURES
+ # Note that we are NOT limited to x86.
+ gmx_run_cpu_detection(features)
+
+ if (DEFINED CPU_DETECTION_FEATURES)
+ # Make a concrete suggestion of SIMD level if a feature flag
+ # matches. Make sure that the match strings below work even if
+ # the feature is first or last.
+ set(CPU_DETECTION_FEATURES " ${CPU_DETECTION_FEATURES} ")
- if(GMX_DETECTSIMD_COMPILED)
- if(NOT DEFINED GMX_DETECTSIMD_RUN)
- execute_process(COMMAND ${GMX_DETECTSIMD_BINARY} "-features"
- RESULT_VARIABLE GMX_DETECTSIMD_RUN
- OUTPUT_VARIABLE OUTPUT_TMP
- ERROR_QUIET)
- set(GMX_DETECTSIMD_RUN "${GMX_DETECTSIMD_RUN}" CACHE INTERNAL "Result of running cpuinfo code to detect SIMD support")
- if(GMX_DETECTSIMD_RUN EQUAL 0)
- # Make a concrete suggestion of SIMD level
- if(GMX_TARGET_X86)
- if(OUTPUT_TMP MATCHES " avx512er ")
- set(OUTPUT_SIMD "AVX_512_KNL")
- elseif(OUTPUT_TMP MATCHES " avx512f ")
- set(OUTPUT_SIMD "AVX_512")
- elseif(OUTPUT_TMP MATCHES " avx2 ")
- set(OUTPUT_SIMD "AVX2_256")
- elseif(OUTPUT_TMP MATCHES " avx ")
- if(OUTPUT_TMP MATCHES " fma4 ")
- # AMD that works better with avx-128-fma
- set(OUTPUT_SIMD "AVX_128_FMA")
- else()
- # Intel
- set(OUTPUT_SIMD "AVX_256")
- endif()
- elseif(OUTPUT_TMP MATCHES " sse4.1 ")
- set(OUTPUT_SIMD "SSE4.1")
- elseif(OUTPUT_TMP MATCHES " sse2 ")
- set(OUTPUT_SIMD "SSE2")
- endif()
- else()
- if(OUTPUT_TMP MATCHES " vsx ")
- set(OUTPUT_SIMD "IBM_VSX")
- elseif(OUTPUT_TMP MATCHES " vmx ")
- set(OUTPUT_SIMD "IBM_VMX")
- elseif(OUTPUT_TMP MATCHES " qpx ")
- set(OUTPUT_SIMD "IBM_QPX")
- elseif(OUTPUT_TMP MATCHES " neon_asimd ")
- set(OUTPUT_SIMD "ARM_NEON_ASIMD")
- elseif(OUTPUT_TMP MATCHES " neon " AND NOT GMX_DOUBLE)
- set(OUTPUT_SIMD "ARM_NEON")
- endif()
- endif()
- message(STATUS "Detected best SIMD instructions for this CPU - ${OUTPUT_SIMD}")
+ if(GMX_TARGET_X86)
+ if(CPU_DETECTION_FEATURES MATCHES " avx512er ")
+ set(OUTPUT_SIMD "AVX_512_KNL")
+ elseif(CPU_DETECTION_FEATURES MATCHES " avx512f ")
+ set(OUTPUT_SIMD "AVX_512")
+ elseif(CPU_DETECTION_FEATURES MATCHES " avx2 ")
+ if(CPU_DETECTION_FEATURES MATCHES " amd ")
+ set(OUTPUT_SIMD "AVX2_128")
+ else()
+ set(OUTPUT_SIMD "AVX2_256")
+ endif()
+ elseif(CPU_DETECTION_FEATURES MATCHES " avx ")
+ if(CPU_DETECTION_FEATURES MATCHES " fma4 ")
+ # AMD that works better with avx-128-fma
+ set(OUTPUT_SIMD "AVX_128_FMA")
else()
- message(WARNING "Cannot run cpuinfo code, which means no SIMD suggestion can be made.")
- message(STATUS "Run output: ${OUTPUT_TMP}")
+ # Intel
+ set(OUTPUT_SIMD "AVX_256")
endif()
+ elseif(CPU_DETECTION_FEATURES MATCHES " sse4.1 ")
+ set(OUTPUT_SIMD "SSE4.1")
+ elseif(CPU_DETECTION_FEATURES MATCHES " sse2 ")
+ set(OUTPUT_SIMD "SSE2")
endif()
else()
- message(WARNING "Cannot compile cpuinfo code, which means no SIMD instructions.")
- message(STATUS "Compile output: ${GMX_DETECTSIMD_COMPILED_OUTPUT}")
+ if(CPU_DETECTION_FEATURES MATCHES " vsx ")
+ set(OUTPUT_SIMD "IBM_VSX")
+ elseif(CPU_DETECTION_FEATURES MATCHES " vmx ")
+ set(OUTPUT_SIMD "IBM_VMX")
+ elseif(CPU_DETECTION_FEATURES MATCHES " qpx ")
+ set(OUTPUT_SIMD "IBM_QPX")
+ elseif(CPU_DETECTION_FEATURES MATCHES " neon_asimd ")
+ set(OUTPUT_SIMD "ARM_NEON_ASIMD")
+ elseif(CPU_DETECTION_FEATURES MATCHES " neon " AND NOT GMX_DOUBLE)
+ set(OUTPUT_SIMD "ARM_NEON")
+ endif()
+ endif()
+ if (NOT SUGGEST_SIMD_QUIETLY)
+ message(STATUS "Detected best SIMD instructions for this CPU - ${OUTPUT_SIMD}")
endif()
else()
- message(WARNING "Cannot detect SIMD architecture for this cross-compile; you should check it manually.")
+ if (NOT SUGGEST_SIMD_QUIETLY)
+ message(STATUS "Detection for best SIMD instructions failed, using SIMD - ${OUTPUT_SIMD}")
+ endif()
endif()
- set(${_suggested_simd} "${OUTPUT_SIMD}" CACHE INTERNAL "Suggested SIMD")
+ set(${_suggested_simd} "${OUTPUT_SIMD}" PARENT_SCOPE)
+ set(SUGGEST_SIMD_QUIETLY TRUE CACHE INTERNAL "Be quiet during future construction of SIMD suggestions")
endfunction()
function(gmx_detect_simd _suggested_simd)
- if(NOT DEFINED GMX_SIMD)
+ if(GMX_SIMD STREQUAL "AUTO")
if(GMX_TARGET_BGQ)
+ # BG/Q requires cross-compilation, so needs this
+ # logic. While the qpx feature flag in cpuinfo works, it
+ # can't be returned by cpuinfo running on the build host.
set(${_suggested_simd} "IBM_QPX")
elseif(GMX_TARGET_FUJITSU_SPARC64)
# HPC-ACE is always present. In the future we
set(PKG_FFT "${${FFTW}_PKG}")
include_directories(SYSTEM ${${FFTW}_INCLUDE_DIRS})
- if ((${GMX_SIMD} MATCHES "SSE" OR ${GMX_SIMD} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
+ if ((${GMX_SIMD_ACTIVE} MATCHES "SSE" OR ${GMX_SIMD_ACTIVE} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
else()
- if(${GMX_SIMD} MATCHES "AVX" AND NOT (${FFTW}_HAVE_SSE OR ${FFTW}_HAVE_SSE2))
+ if(${GMX_SIMD_ACTIVE} MATCHES "AVX" AND NOT (${FFTW}_HAVE_SSE OR ${FFTW}_HAVE_SSE2))
# If we end up here we have an AVX Gromacs build, and
# FFTW with SIMD.
message(WARNING "The FFTW library was compiled with neither --enable-sse nor --enable-sse2; those would have enabled SSE(2) SIMD instructions. This will give suboptimal performance. You should (re)compile the FFTW library with --enable-sse2 and --enable-avx (and --enable-avx2 or --enable-avx512 if supported).")
gmx_detect_gpu()
endif()
-# CMake 3.0-3.1 has a bug in the following case, which breaks
-# configuration on at least BlueGene/Q. Fixed in 3.1.1
-if ((NOT CMAKE_VERSION VERSION_LESS "3.0.0") AND
- (CMAKE_VERSION VERSION_LESS "3.1.1") AND
- (CMAKE_CROSSCOMPILING AND NOT CMAKE_SYSTEM_PROCESSOR))
- message(STATUS "Cannot search for CUDA because the CMake find package has a bug. Set a valid CMAKE_SYSTEM_PROCESSOR if you need to detect CUDA")
-else()
- set(CAN_RUN_CUDA_FIND_PACKAGE 1)
-endif()
-
# We need to call find_package even when we've already done the detection/setup
-if(GMX_GPU OR GMX_GPU_AUTO AND CAN_RUN_CUDA_FIND_PACKAGE)
+if(GMX_GPU OR GMX_GPU_AUTO)
if(NOT GMX_GPU AND NOT GMX_DETECT_GPU_AVAILABLE)
# Stay quiet when detection has occured and found no GPU.
# Noise is acceptable when there is a GPU or the user required one.
endif()
find_package(CUDA ${REQUIRED_CUDA_VERSION} ${FIND_CUDA_QUIETLY})
-
- # Cmake 2.8.12 (and CMake 3.0) introduced a new bug where the cuda
- # library dir is added twice as an rpath on APPLE, which in turn causes
- # the install_name_tool to wreck the binaries when it tries to remove this
- # path. Since this is set inside the cuda module, we remove the extra rpath
- # added in the library string - an rpath is not a library anyway, and at
- # least for Gromacs this works on all CMake versions. This should be
- # reasonably future-proof, since newer versions of CMake appear to handle
- # the rpath automatically based on the provided library path, meaning
- # the explicit rpath specification is no longer needed.
- if(APPLE AND (CMAKE_VERSION VERSION_GREATER 2.8.11))
- foreach(elem ${CUDA_LIBRARIES})
- if(elem MATCHES "-Wl,.*")
- list(REMOVE_ITEM CUDA_LIBRARIES ${elem})
- endif()
- endforeach(elem)
- endif()
endif()
# Depending on the current vale of GMX_GPU and GMX_GPU_AUTO:
# We need to mark these advanced outside the conditional, otherwise, if the
# user turns GMX_GPU=OFF after a failed cmake pass, these variables will be
# left behind in the cache.
-mark_as_advanced(CUDA_BUILD_CUBIN CUDA_BUILD_EMULATION CUDA_SDK_ROOT_DIR CUDA_VERBOSE_BUILD # cmake 2.8.9 still spews these, check again when requirements change
- CUDA_SEPARABLE_COMPILATION # not present at least with cmake 3.2, remove when required
- CUDA_USE_STATIC_CUDA_RUNTIME # since cmake 3.3
- CUDA_dl_LIBRARY CUDA_rt_LIBRARY # - || -
+mark_as_advanced(CUDA_SDK_ROOT_DIR
+ CUDA_USE_STATIC_CUDA_RUNTIME
+ CUDA_dl_LIBRARY CUDA_rt_LIBRARY
)
if(NOT GMX_GPU)
mark_as_advanced(CUDA_TOOLKIT_ROOT_DIR)
+ mark_as_advanced(CUDA_HOST_COMPILER)
endif()
# Try to execute ${CUDA_NVCC_EXECUTABLE} --version and set the output
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
# This may also not work correctly if the user changes
# MKL_LIBRARIES after the first run. However,
- # MKL_LIBRARIES is only needed for icc version < 11, or
+ # MKL_LIBRARIES is only needed
# for trying to use MKL with a non-Intel compiler, and we
# can live with that for now.
check_function_exists(${function_in_library} _${name}_mkl_works)
if (NOT _library_was_found)
set(${name}_FIND_QUIETLY ${_find_quietly})
# Note that this finds all kinds of system libraries,
- # including Apple's Accelerate Framework (and perhaps MKL for
- # icc < 11).
+ # including Apple's Accelerate Framework
find_package(${name})
if (${name}_FOUND)
set(_libraries_to_link ${${name}_LIBRARIES})
set(MPI_COMPILE_FLAGS ${MPI_C_COMPILE_FLAGS})
set(MPI_LINKER_FLAGS ${MPI_C_LINK_FLAGS})
include_directories(SYSTEM ${MPI_C_INCLUDE_PATH})
- list(APPEND GMX_EXTRA_LIBRARIES ${MPI_C_LIBRARIES})
+ list(APPEND GMX_COMMON_LIBRARIES ${MPI_C_LIBRARIES})
endif()
set(MPI_FOUND ${MPI_C_FOUND})
else()
endif()
endif()
unset(MPINAME_BIN CACHE)
-
- # Using find_file() runs the CMake standard module
- # GetPrerequisites.cmake, which adds the file_cmd
- # variable to the top-level CMake namespace. This is
- # fixed in CMake 2.8.10. Meanwhile, clean up for it.
- if(CMAKE_VERSION VERSION_LESS "2.8.10")
- mark_as_advanced(file_cmd)
- endif()
-
else()
message(FATAL_ERROR
"MPI support requested, but no MPI compiler found. Either set the "
# pain as much as possible:
# - use the CUDA_HOST_COMPILER if defined by the user, otherwise
# - auto-detect compatible nvcc host compiler and set nvcc -ccbin (if not MPI wrapper)
-# - set icc compatibility mode to gcc 4.6
+# - set icc compatibility mode to gcc 4.8.1
# - (advanced) variables set:
# * CUDA_HOST_COMPILER - the host compiler for nvcc (only with cmake <2.8.10)
# * CUDA_HOST_COMPILER_OPTIONS - the full host-compiler related option list passed to nvcc
unset(CUDA_HOST_COMPILER_AUTOSET CACHE)
endif()
-# Set the host compiler for nvcc if this is not set by CMake (v<=2.8.9)
-#
-# Note that even though nvcc compiles host code as C++, we use the
-# CMAKE_C_COMPILER as host compiler. We do this because CUDA versions
-# preceding 5.0 only recognize icc, but not icpc. However, both gcc and icc
-# (i.e. all supported compilers) happily compile C++ code.
-#
-# Also note that with MSVC nvcc sets the -compiler-bindir option behind the
-# scenes; to avoid conflicts we don't set -ccbin automatically.
-#
-# TODO: remove this when CMAke >=v2.8.10 is required.
-if (NOT DEFINED CUDA_HOST_COMPILER AND NOT MSVC)
- set(CUDA_HOST_COMPILER "${CMAKE_C_COMPILER}")
- set(CUDA_HOST_COMPILER_AUTOSET TRUE CACHE INTERNAL
- "True if CUDA_HOST_COMPILER is automatically set")
-endif()
-
# glibc 2.23 changed string.h in a way that breaks CUDA compilation in
# many projects, but which has a trivial workaround. It would be nicer
# to compile with nvcc and see that the workaround is necessary and
# set up host compiler and its options
if(CUDA_HOST_COMPILER_CHANGED)
- # FindCUDA in CMake 2.8.10 sets the host compiler internally
- if (CMAKE_VERSION VERSION_LESS "2.8.10")
- set(CUDA_HOST_COMPILER ${CUDA_HOST_COMPILER}
- CACHE PATH "Host compiler for nvcc")
- endif()
-
- # On *nix force icc in gcc 4.6 compatibility mode. This is needed
- # as even with icc used as host compiler, when icc's gcc compatibility
- # mode is higher than the max gcc version officially supported by CUDA,
- # nvcc will freak out.
set(CUDA_HOST_COMPILER_OPTIONS "")
- if (UNIX AND
- ((CMAKE_C_COMPILER_ID MATCHES "Intel" AND
- (CUDA_HOST_COMPILER_AUTOSET OR CMAKE_C_COMPILER STREQUAL CUDA_HOST_COMPILER)) OR
- (CMAKE_CXX_COMPILER_ID MATCHES "Intel" AND CMAKE_CXX_COMPILER STREQUAL CUDA_HOST_COMPILER))
- )
- message(STATUS "Setting Intel Compiler compatibity mode to gcc 4.6 for nvcc host compilation")
- list(APPEND CUDA_HOST_COMPILER_OPTIONS "-Xcompiler;-gcc-version=460")
- endif()
if(APPLE AND CMAKE_C_COMPILER_ID MATCHES "GNU")
# Some versions of gcc-4.8 and gcc-4.9 produce errors (in particular on OS X)
endif()
endif()
-gmx_dependent_cache_variable(GMX_CUDA_TARGET_SM "List of CUDA GPU architecture codes to compile for (without the sm_ prefix)" STRING "" GMX_CUDA_TARGET_SM)
-gmx_dependent_cache_variable(GMX_CUDA_TARGET_COMPUTE "List of CUDA virtual architecture codes to compile for (without the compute_ prefix)" STRING "" GMX_CUDA_TARGET_COMPUTE)
+if (GMX_CUDA_TARGET_SM)
+ set_property(CACHE GMX_CUDA_TARGET_SM PROPERTY HELPSTRING "List of CUDA GPU architecture codes to compile for (without the sm_ prefix)")
+ set_property(CACHE GMX_CUDA_TARGET_SM PROPERTY TYPE STRING)
+endif()
+if (GMX_CUDA_TARGET_COMPUTE)
+ set_property(CACHE GMX_CUDA_TARGET_COMPUTE PROPERTY HELPSTRING "List of CUDA virtual architecture codes to compile for (without the compute_ prefix)")
+ set_property(CACHE GMX_CUDA_TARGET_COMPUTE PROPERTY TYPE STRING)
+endif()
# assemble the CUDA flags
list(APPEND GMX_CUDA_NVCC_FLAGS "${GMX_CUDA_NVCC_GENCODE_FLAGS}")
endif()
# assemble the CUDA host compiler flags
-# with CMake <2.8.10 the host compiler needs to be set on the nvcc command line
-if (CMAKE_VERSION VERSION_LESS "2.8.10")
- list(APPEND GMX_CUDA_NVCC_FLAGS "-ccbin=${CUDA_HOST_COMPILER}")
-endif()
list(APPEND GMX_CUDA_NVCC_FLAGS "${CUDA_HOST_COMPILER_OPTIONS}")
# The flags are set as local variables which shadow the cache variables. The cache variables
# (can be set by the user) are appended. This is done in a macro to set the flags when all
# host compiler flags are already set.
macro(GMX_SET_CUDA_NVCC_FLAGS)
- if(CUDA_PROPAGATE_HOST_FLAGS)
- set(CUDA_PROPAGATE_HOST_FLAGS OFF)
-
- # When CUDA 6.5 is required we should use C++11 also for CUDA and also propagate
- # the C++11 flag to CUDA. Then we can use the solution implemented in FindCUDA
- # (starting with 3.3 - can be backported). For now we need to remove the C++11
- # flag which means we need to manually propagate all other flags.
- string(REGEX REPLACE "[-]+std=c\\+\\+0x" "" _CMAKE_CXX_FLAGS_SANITIZED "${CMAKE_CXX_FLAGS}")
-
- # The IBM xlc compiler chokes if we use both altivec and Cuda. Solve
- # this by not propagating the flag in this case.
- if(CMAKE_CXX_COMPILER_ID MATCHES "XL")
- string(REGEX REPLACE "-qaltivec" "" _CMAKE_CXX_FLAGS_SANITIZED "${_CMAKE_CXX_FLAGS_SANITIZED}")
- endif()
-
- # CUDA versions prior to 7.5 come with a header (math_functions.h) which uses the _MSC_VER macro
- # unconditionally, so we strip -Wundef from the propagatest flags for earlier CUDA versions.
- if (CUDA_VERSION VERSION_LESS "7.5")
- string(REGEX REPLACE "-Wundef" "" _CMAKE_CXX_FLAGS_SANITIZED "${_CMAKE_CXX_FLAGS_SANITIZED}")
- endif()
-
- string(REPLACE " " "," _flags "${_CMAKE_CXX_FLAGS_SANITIZED}")
- set(CUDA_NVCC_FLAGS "${GMX_CUDA_NVCC_FLAGS};${CUDA_NVCC_FLAGS};-Xcompiler;${_flags}")
-
- # Create list of all possible configurations. For multi-configuration this is CMAKE_CONFIGURATION_TYPES
- # and for single configuration CMAKE_BUILD_TYPE. Not sure why to add the default ones, but FindCUDA
- # claims one should.
- set(CUDA_configuration_types ${CMAKE_CONFIGURATION_TYPES} ${CMAKE_BUILD_TYPE} Debug MinSizeRel Release RelWithDebInfo)
- list(REMOVE_DUPLICATES CUDA_configuration_types)
-
- foreach(_config ${CUDA_configuration_types})
- string(TOUPPER ${_config} _config_upper)
- string(REPLACE " " "," _flags "${CMAKE_CXX_FLAGS_${_config_upper}}")
- set(CUDA_NVCC_FLAGS_${_config_upper} "${CUDA_NVCC_FLAGS_${_config_upper}};-Xcompiler;${_flags}")
- endforeach()
- else()
- set(CUDA_NVCC_FLAGS "${GMX_CUDA_NVCC_FLAGS};${CUDA_NVCC_FLAGS}")
- endif()
+ set(CUDA_NVCC_FLAGS "${GMX_CUDA_NVCC_FLAGS};${CUDA_NVCC_FLAGS}")
endmacro()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# and then does some additional tests for flags afterwards.
if(GMX_OPENMP)
- if(CMAKE_C_COMPILER_ID MATCHES "Cray" AND CMAKE_VERSION VERSION_LESS 3)
- message(STATUS "OpenMP multithreading is not detected correctly for the Cray compiler with CMake before version 3.0 (see http://public.kitware.com/Bug/view.php?id=14567)")
- set(GMX_OPENMP OFF CACHE BOOL
- "OpenMP multithreading is not detected correctly for the Cray compiler with CMake before version 3.0 (see http://public.kitware.com/Bug/view.php?id=14567)" FORCE)
- else()
- # We should do OpenMP detection if we get here
- # OpenMP check must come before other CFLAGS!
- find_package(OpenMP)
- if(OPENMP_FOUND)
- # CMake on Windows doesn't support linker flags passed to target_link_libraries
- # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
- if(NOT (WIN32 AND NOT MINGW))
- if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
- set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
- set(OpenMP_SHARED_LINKER_FLAGS "")
- else()
- # Only set a linker flag if the user didn't set them manually
- if(NOT DEFINED OpenMP_LINKER_FLAGS)
- set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
- endif()
- if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
- set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
- endif()
+ # We should do OpenMP detection if we get here
+ # OpenMP check must come before other CFLAGS!
+ find_package(OpenMP)
+ if(OPENMP_FOUND)
+ # CMake on Windows doesn't support linker flags passed to target_link_libraries
+ # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
+ if(NOT (WIN32 AND NOT MINGW))
+ if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
+ set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
+ set(OpenMP_SHARED_LINKER_FLAGS "")
+ else()
+ # Only set a linker flag if the user didn't set them manually
+ if(NOT DEFINED OpenMP_LINKER_FLAGS)
+ set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
+ endif()
+ if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
+ set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
endif()
endif()
- if(MINGW)
- #GCC Bug 48659
- set(OpenMP_C_FLAGS "${OpenMP_C_FLAGS} -mstackrealign")
- endif()
- else()
- message(WARNING
- "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.")
- set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
endif()
+ if(MINGW)
+ #GCC Bug 48659
+ set(OpenMP_C_FLAGS "${OpenMP_C_FLAGS} -mstackrealign")
+ endif()
+ else()
+ message(WARNING
+ "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.")
+ set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
endif()
endif()
gmx_dependent_cache_variable(GMX_OPENMP_MAX_THREADS
"Maximum number of OpenMP Threads supported. Has to be 32 or a multiple of 64."
- STRING 32 GMX_OPENMP)
+ STRING 64 GMX_OPENMP)
mark_as_advanced(GMX_OPENMP_MAX_THREADS)
math(EXPR MAX_THREAD_MOD "${GMX_OPENMP_MAX_THREADS} % 64")
if (NOT GMX_OPENMP_MAX_THREADS EQUAL 32 AND NOT ${MAX_THREAD_MOD} EQUAL 0)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2016, by the GROMACS development team, led by
+# Copyright (c) 2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# include avx test source, used if the AVX flags are set below
-include(gmxTestAVXMaskload)
+include(gmxDetectCpu)
include(gmxFindFlagsForSource)
# Macro that manages setting the respective C and C++ toolchain
# VSX uses the same function API as Altivec/VMX, so make sure we tune for the current CPU and not VMX.
# By putting these flags here rather than in the general compiler flags file we can safely assume
# that we are at least on Power7 since that is when VSX appeared.
- if(BUILD_CPU_BRAND MATCHES "POWER7")
+ gmx_run_cpu_detection(brand)
+ if(CPU_DETECTION_BRAND MATCHES "POWER7")
gmx_test_cflag(GNU_C_VSX_POWER7 "-mcpu=power7 -mtune=power7" ${TOOLCHAIN_C_FLAGS_VARIABLE})
gmx_test_cflag(GNU_CXX_VSX_POWER7 "-mcpu=power7 -mtune=power7" ${TOOLCHAIN_CXX_FLAGS_VARIABLE})
else()
#
# Section to set (and test) compiler flags for SIMD.
#
-# The flags will be set based on the GMX_SIMD choice provided by the user.
-# Automatic detection of the architecture on the build host is done prior to
-# calling this macro.
+# If the user chose the (default) automatic behaviour, then detection
+# is run to suggest a SIMD choice suitable for the build
+# host. Otherwise, the users's choice is always honoured. The compiler
+# flags will be set based on that choice.
#
-if(GMX_SIMD STREQUAL "NONE")
+set(GMX_SIMD_ACTIVE ${GMX_SIMD})
+if(GMX_SIMD STREQUAL "AUTO")
+ include(gmxDetectSimd)
+ gmx_detect_simd(GMX_SUGGESTED_SIMD)
+ set(GMX_SIMD_ACTIVE ${GMX_SUGGESTED_SIMD})
+endif()
+
+if(GMX_SIMD_ACTIVE STREQUAL "NONE")
# nothing to do configuration-wise
set(SIMD_STATUS_MESSAGE "SIMD instructions disabled")
-elseif(GMX_SIMD STREQUAL "SSE2")
+elseif(GMX_SIMD_ACTIVE STREQUAL "SSE2")
gmx_find_flags(
"#include<xmmintrin.h>
int main(){__m128 x=_mm_set1_ps(0.5);x=_mm_rsqrt_ps(x);return _mm_movemask_ps(x);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-msse2" "/arch:SSE2" "-hgnu")
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("SSE2" "disable SIMD support (slow)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_X86_${GMX_SIMD} 1)
+ set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling SSE2 SIMD instructions")
-elseif(GMX_SIMD STREQUAL "SSE4.1")
+elseif(GMX_SIMD_ACTIVE STREQUAL "SSE4.1")
# Note: MSVC enables SSE4.1 with the SSE2 flag, so we include that in testing.
gmx_find_flags(
set(GMX_SIMD_X86_SSE4_1 1)
set(SIMD_STATUS_MESSAGE "Enabling SSE4.1 SIMD instructions")
-elseif(GMX_SIMD STREQUAL "AVX_128_FMA")
+elseif(GMX_SIMD_ACTIVE STREQUAL "AVX_128_FMA")
prepare_x86_toolchain(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
${INCLUDE_INTRIN_H}
int main(){__m128 x=_mm_set1_ps(0.5);x=_mm_macc_ps(x,x,x);return _mm_movemask_ps(x);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-mfma4" "-hgnu")
# We only need to check the last (FMA) test; that will always fail if the generic AVX test failed
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("128-bit AVX with FMA support" "choose SSE4.1 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_X86_${GMX_SIMD} 1)
+ set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 128-bit AVX SIMD GROMACS SIMD (with fused-multiply add)")
- gmx_test_avx_gcc_maskload_bug(GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG "${SIMD_C_FLAGS}")
-
-elseif(GMX_SIMD STREQUAL "AVX_256")
+elseif(GMX_SIMD_ACTIVE STREQUAL "AVX_256")
prepare_x86_toolchain(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
"#include<immintrin.h>
int main(){__m256 x=_mm256_set1_ps(0.5);x=_mm256_add_ps(x,x);return _mm256_movemask_ps(x);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-mavx" "/arch:AVX" "-hgnu")
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("AVX" "choose SSE4.1 SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_X86_${GMX_SIMD} 1)
+ set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 256-bit AVX SIMD instructions")
- gmx_test_avx_gcc_maskload_bug(GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG "${SIMD_C_FLAGS}")
-
-elseif(GMX_SIMD STREQUAL "AVX2_256")
+elseif(GMX_SIMD_ACTIVE MATCHES "AVX2_")
prepare_x86_toolchain(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
"#include<immintrin.h>
int main(){__m256i x=_mm256_set1_epi32(5);x=_mm256_add_epi32(x,x);return _mm256_movemask_epi8(x);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-march=core-avx2" "-mavx2" "/arch:AVX" "-hgnu") # no AVX2-specific flag for MSVC yet
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("AVX2" "choose AVX SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_X86_${GMX_SIMD} 1)
- set(SIMD_STATUS_MESSAGE "Enabling 256-bit AVX2 SIMD instructions")
+ set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
- # No need to test for Maskload bug - it was fixed before gcc added AVX2 support
+ if(GMX_SIMD_ACTIVE STREQUAL "AVX2_128")
+ set(SIMD_STATUS_MESSAGE "Enabling 128-bit AVX2 SIMD instructions")
+ else()
+ set(SIMD_STATUS_MESSAGE "Enabling 256-bit AVX2 SIMD instructions")
+ endif()
-elseif(GMX_SIMD STREQUAL "MIC")
+elseif(GMX_SIMD_ACTIVE STREQUAL "MIC")
# No flags needed. Not testing.
set(GMX_SIMD_X86_MIC 1)
set(SIMD_STATUS_MESSAGE "Enabling MIC (Xeon Phi) SIMD instructions")
-elseif(GMX_SIMD STREQUAL "AVX_512")
+elseif(GMX_SIMD_ACTIVE STREQUAL "AVX_512")
prepare_x86_toolchain(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
"#include<immintrin.h>
int main(){__m512 y,x=_mm512_set1_ps(0.5);y=_mm512_fmadd_ps(x,x,x);return (int)_mm512_cmp_ps_mask(x,y,_CMP_LT_OS);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-xCORE-AVX512" "-mavx512f -mfma" "-mavx512f" "/arch:AVX" "-hgnu") # no AVX_512F flags known for MSVC yet
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("AVX 512F" "choose a lower level of SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_X86_${GMX_SIMD} 1)
+ set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 512-bit AVX-512 SIMD instructions")
-elseif(GMX_SIMD STREQUAL "AVX_512_KNL")
+elseif(GMX_SIMD_ACTIVE STREQUAL "AVX_512_KNL")
prepare_x86_toolchain(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
"#include<immintrin.h>
int main(){__m512 y,x=_mm512_set1_ps(0.5);y=_mm512_rsqrt28_ps(x);return (int)_mm512_cmp_ps_mask(x,y,_CMP_LT_OS);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-xMIC-AVX512" "-mavx512er -mfma" "-mavx512er" "/arch:AVX" "-hgnu") # no AVX_512ER flags known for MSVC yet
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("AVX 512ER" "choose a lower level of SIMD (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_X86_${GMX_SIMD} 1)
+ set(GMX_SIMD_X86_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 512-bit AVX-512-KNL SIMD instructions")
-elseif(GMX_SIMD STREQUAL "ARM_NEON")
+elseif(GMX_SIMD_ACTIVE STREQUAL "ARM_NEON")
if (GMX_DOUBLE)
message(FATAL_ERROR "ARM_NEON SIMD support is not available for a double precision build because the architecture lacks double-precision support")
"#include<arm_neon.h>
int main(){float32x4_t x=vdupq_n_f32(0.5);x=vmlaq_f32(x,x,x);return vgetq_lane_f32(x,0)>0;}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-mfpu=neon-vfpv4" "-mfpu=neon" "")
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("ARM NEON" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_${GMX_SIMD} 1)
+ set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling 32-bit ARM NEON SIMD instructions")
-elseif(GMX_SIMD STREQUAL "ARM_NEON_ASIMD")
+elseif(GMX_SIMD_ACTIVE STREQUAL "ARM_NEON_ASIMD")
gmx_find_flags(
"#include<arm_neon.h>
int main(){float64x2_t x=vdupq_n_f64(0.5);x=vfmaq_f64(x,x,x);x=vrndnq_f64(x);return vgetq_lane_f64(x,0)>0;}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"")
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("ARM (AArch64) NEON Advanced SIMD" "particularly gcc version 4.9 or later, or disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_${GMX_SIMD} 1)
+ set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling ARM (AArch64) NEON Advanced SIMD instructions")
-elseif(GMX_SIMD STREQUAL "IBM_QPX")
+elseif(GMX_SIMD_ACTIVE STREQUAL "IBM_QPX")
try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
"${CMAKE_SOURCE_DIR}/cmake/TestQPX.c")
if (TEST_QPX)
message(WARNING "IBM QPX SIMD instructions selected. This will work, but SIMD kernels are only available for the Verlet cut-off scheme. The plain C kernels that are used for the group cut-off scheme kernels will be slow, so please consider using the Verlet cut-off scheme.")
- set(GMX_SIMD_${GMX_SIMD} 1)
+ set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling IBM QPX SIMD instructions")
else()
- gmx_give_fatal_error_when_simd_support_not_found("IBM QPX" "or 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-CXX' to set up the tool chain" "${SUGGEST_BINUTILS_UPDATE}")
+ gmx_give_fatal_error_when_simd_support_not_found("IBM QPX" "or 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-bgclang-CXX' to set up the tool chain" "${SUGGEST_BINUTILS_UPDATE}")
endif()
-elseif(GMX_SIMD STREQUAL "IBM_VMX")
+elseif(GMX_SIMD_ACTIVE STREQUAL "IBM_VMX")
gmx_find_flags(
"#include<altivec.h>
int main(){vector float x,y=vec_ctf(vec_splat_s32(1),0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
- if(NOT SIMD_${GMX_SIMD}_C_FLAGS OR NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS OR NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("IBM VMX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_${GMX_SIMD} 1)
+ set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling IBM VMX SIMD instructions")
-elseif(GMX_SIMD STREQUAL "IBM_VSX")
+elseif(GMX_SIMD_ACTIVE STREQUAL "IBM_VSX")
prepare_power_vsx_toolchain(TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS)
"#include<altivec.h>
int main(){vector double x,y=vec_splats(1.0);x=vec_madd(y,y,y);return vec_all_ge(y,x);}"
TOOLCHAIN_C_FLAGS TOOLCHAIN_CXX_FLAGS
- SIMD_${GMX_SIMD}_C_FLAGS SIMD_${GMX_SIMD}_CXX_FLAGS
+ SIMD_${GMX_SIMD_ACTIVE}_C_FLAGS SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS
"-mvsx" "-maltivec -mabi=altivec" "-qarch=auto -qaltivec")
# Usually we check also for the C compiler here, but a C compiler
# at least version 3.7 cannot pass this check with the C compiler
# in the latest xlc 13.1.5, but the C++ compiler has different
# behaviour and is OK. See Redmine #2102.
- if(NOT SIMD_${GMX_SIMD}_CXX_FLAGS)
+ if(NOT SIMD_${GMX_SIMD_ACTIVE}_CXX_FLAGS)
gmx_give_fatal_error_when_simd_support_not_found("IBM VSX" "disable SIMD support (slower)" "${SUGGEST_BINUTILS_UPDATE}")
endif()
set(SIMD_C_FLAGS "${TOOLCHAIN_C_FLAGS}")
set(SIMD_CXX_FLAGS "${TOOLCHAIN_CXX_FLAGS}")
- set(GMX_SIMD_${GMX_SIMD} 1)
+ set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling IBM VSX SIMD instructions")
-elseif(GMX_SIMD STREQUAL "SPARC64_HPC_ACE")
+elseif(GMX_SIMD_ACTIVE STREQUAL "SPARC64_HPC_ACE")
# Note that GMX_RELAXED_DOUBLE_PRECISION is enabled by default in the top-level CMakeLists.txt
- set(GMX_SIMD_${GMX_SIMD} 1)
+ set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling Sparc64 HPC-ACE SIMD instructions")
-elseif(GMX_SIMD STREQUAL "REFERENCE")
+elseif(GMX_SIMD_ACTIVE STREQUAL "REFERENCE")
# NB: This file handles settings for the SIMD module, so in the interest
# of proper modularization, please do NOT put any verlet kernel settings in this file.
add_definitions(-DGMX_SIMD_REF_DOUBLE_WIDTH=${GMX_SIMD_REF_DOUBLE_WIDTH})
endif()
- set(GMX_SIMD_${GMX_SIMD} 1)
+ set(GMX_SIMD_${GMX_SIMD_ACTIVE} 1)
set(SIMD_STATUS_MESSAGE "Enabling reference (emulated) SIMD instructions.")
else()
- gmx_invalid_option_value(GMX_SIMD)
+ gmx_invalid_option_value(GMX_SIMD_ACTIVE)
endif()
-gmx_check_if_changed(SIMD_CHANGED GMX_SIMD)
+gmx_check_if_changed(SIMD_CHANGED GMX_SIMD_ACTIVE)
if (SIMD_CHANGED AND DEFINED SIMD_STATUS_MESSAGE)
message(STATUS "${SIMD_STATUS_MESSAGE}")
endif()
if(NOT DEFINED GMX_SIMD_CALLING_CONVENTION)
if(GMX_TARGET_BGQ)
set(CALLCONV_LIST " ")
- elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND GMX_SIMD STREQUAL "REFERENCE")
+ elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND GMX_SIMD_ACTIVE STREQUAL "REFERENCE")
set(CALLCONV_LIST __regcall " ")
elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
set(CALLCONV_LIST " ")
endforeach()
endif()
+if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+ # GCC bug 49001, 54412 on Windows (just warn, since it might be fixed in later versions)
+ if((CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.9.0" OR CMAKE_SIZEOF_VOID_P EQUAL 8)
+ AND (WIN32 OR CYGWIN)
+ AND (GMX_SIMD_ACTIVE MATCHES "AVX") AND NOT (GMX_SIMD_ACTIVE STREQUAL "AVX_128_FMA"))
+ message(WARNING "GCC on Windows (GCC older than 4.9 in 32-bit mode, or any version in 64-bit mode) with 256-bit AVX will probably crash. You might want to choose a different GMX_SIMD or a different compiler.")
+ endif()
+endif()
+
endmacro()
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-set(GMX_TNG_MINIMUM_REQUIRED_VERSION "1.7.6")
-set(BUNDLED_TNG_LOCATION "${CMAKE_SOURCE_DIR}/src/external/tng_io")
-if(GMX_USE_TNG)
- option(GMX_EXTERNAL_TNG "Use external TNG instead of compiling the version shipped with GROMACS." OFF)
+set(GMX_TNG_MINIMUM_REQUIRED_VERSION "1.7.10")
+
+gmx_dependent_option(
+ GMX_EXTERNAL_TNG
+ "Use external TNG instead of compiling the version shipped with GROMACS."
+ OFF
+ GMX_USE_TNG)
+gmx_dependent_option(
+ GMX_EXTERNAL_ZLIB
+ "Use external ZLIB instead of compiling the version shipped with GROMACS as part of TNG."
+ OFF
+ "NOT GMX_EXTERNAL_TNG")
+if(GMX_USE_TNG)
# Detect TNG if GMX_EXTERNAL_TNG is explicitly ON
if(GMX_EXTERNAL_TNG)
find_package(TNG_IO ${GMX_TNG_MINIMUM_REQUIRED_VERSION})
if(NOT TNG_IO_FOUND)
message(FATAL_ERROR "TNG >= ${GMX_TNG_MINIMUM_REQUIRED_VERSION} not found. You can set GMX_EXTERNAL_TNG=OFF to compile the TNG bundled with GROMACS.")
endif()
- include_directories(SYSTEM ${TNG_IO_INCLUDE_DIRS})
else()
- include(${BUNDLED_TNG_LOCATION}/BuildTNG.cmake)
- tng_get_source_list(TNG_SOURCES TNG_IO_DEFINITIONS)
-
- if (HAVE_ZLIB)
- list(APPEND GMX_EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(SYSTEM ${ZLIB_INCLUDE_DIRS})
+ # Detect zlib if the user requires us to use an external
+ # version. If found, it can be used by TNG.
+ if(GMX_EXTERNAL_ZLIB)
+ find_package(ZLIB)
+ if(NOT ZLIB_FOUND)
+ message(FATAL_ERROR "External zlib compression library was required but could not be found. Set GMX_EXTERNAL_ZLIB=OFF to compile zlib as part of GROMACS.")
+ endif()
+ include(gmxTestZLib)
+ gmx_test_zlib(HAVE_ZLIB)
+ if(NOT HAVE_ZLIB)
+ message(FATAL_ERROR "External zlib compression library was required but could not compile and link. Set GMX_EXTERNAL_ZLIB=OFF to compile zlib as part of GROMACS.")
+ endif()
endif()
endif()
-else()
- # We still need to get tng/tng_io_fwd.h from somewhere!
- include_directories(BEFORE ${BUNDLED_TNG_LOCATION}/include)
endif()
+function(gmx_setup_tng_for_libgromacs)
+ set(BUNDLED_TNG_LOCATION "${CMAKE_SOURCE_DIR}/src/external/tng_io")
+ if (GMX_USE_TNG)
+ if (GMX_EXTERNAL_TNG)
+ target_link_libraries(libgromacs PRIVATE tng_io::tng_io)
+ else()
+ set(_zlib_arg)
+ if (NOT GMX_EXTERNAL_ZLIB)
+ set(_zlib_arg OWN_ZLIB)
+ endif()
+ include(${BUNDLED_TNG_LOCATION}/BuildTNG.cmake)
+ add_tng_io_library(tng_io OBJECT ${_zlib_arg})
+ add_library(tng_io::tng_io ALIAS tng_io)
+ target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:tng_io::tng_io>)
+ endif()
+ endif()
+endfunction()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(${NAME} ${${NAME}} PARENT_SCOPE)
endfunction()
-# Checks if one or more cache variables have changed
+# Checks if one or more variables have changed since last call to this function
#
# Usage:
# gmx_check_if_changed(RESULT VAR1 VAR2 ... VARN)
#
-# Sets RESULT to true if any of the given cache variables VAR1 ... VARN has
-# changes since the last call to this function for that variable.
+# Sets RESULT to true if any of the given variables VAR1 ... VARN has
+# changed since the last call to this function for that variable.
# Changes are tracked also across CMake runs.
function(GMX_CHECK_IF_CHANGED RESULT)
set(_result FALSE)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-# - Check the username performing the build, as well as date and time
+# Check the username performing the build, as well as date, time, and
+# build CPU features.
#
-# gmx_set_build_information()
-#
-# The macro variables will be set to the user/host/cpu used for configuration,
-# or anonymous/unknown if it cannot be detected (windows)
+# The following variables will be set to the user/host/cpu used for
+# configuration, or anonymous/unknown if it cannot be detected
+# (Windows).
#
# BUILD_TIME
# BUILD_USER
# BUILD_CPU_FEATURES
#
-# we rely on inline asm support for GNU!
-include(gmxTestInlineASM)
-
-macro(gmx_set_build_information)
- IF(NOT DEFINED BUILD_USER)
+include(gmxDetectCpu)
- gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
+function(gmx_set_build_information)
+ if(NOT BUILD_USER)
+ if(CMAKE_HOST_UNIX)
+ execute_process( COMMAND whoami OUTPUT_VARIABLE TMP_USER OUTPUT_STRIP_TRAILING_WHITESPACE)
+ execute_process( COMMAND hostname OUTPUT_VARIABLE TMP_HOSTNAME OUTPUT_STRIP_TRAILING_WHITESPACE)
+ else()
+ set(TMP_USER "Anonymous")
+ set(TMP_HOSTNAME "unknown")
+ endif()
+ set(BUILD_USER "${TMP_USER}\@${TMP_HOSTNAME} [CMAKE]" CACHE INTERNAL "Build user")
+ message(STATUS "Setting build user - ${BUILD_USER}")
+ endif()
- if(GMX_X86_GCC_INLINE_ASM)
- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=1")
- else()
- set(GCC_INLINE_ASM_DEFINE "-DGMX_X86_GCC_INLINE_ASM=0")
+ if(NOT BUILD_TIME)
+ STRING(TIMESTAMP TMP_TIME "%Y-%m-%d %H:%M:%S" UTC)
+ set(BUILD_TIME "${TMP_TIME}" CACHE INTERNAL "Build date & time")
+ message(STATUS "Setting build time - ${BUILD_TIME}")
endif()
- message(STATUS "Setting build user/date/host/cpu information")
- if(CMAKE_HOST_UNIX)
- execute_process( COMMAND date OUTPUT_VARIABLE TMP_TIME OUTPUT_STRIP_TRAILING_WHITESPACE)
- execute_process( COMMAND whoami OUTPUT_VARIABLE TMP_USER OUTPUT_STRIP_TRAILING_WHITESPACE)
- execute_process( COMMAND hostname OUTPUT_VARIABLE TMP_HOSTNAME OUTPUT_STRIP_TRAILING_WHITESPACE)
- set(BUILD_USER "${TMP_USER}\@${TMP_HOSTNAME} [CMAKE]" CACHE INTERNAL "Build user")
- set(BUILD_TIME "${TMP_TIME}" CACHE INTERNAL "Build date & time")
- execute_process( COMMAND uname -srm OUTPUT_VARIABLE TMP_HOST OUTPUT_STRIP_TRAILING_WHITESPACE)
- set(BUILD_HOST "${TMP_HOST}" CACHE INTERNAL "Build host & architecture")
- message(STATUS "Setting build user & time - OK")
- else()
- set(BUILD_USER "Anonymous\@unknown [CMAKE]" CACHE INTERNAL "Build user")
- set(BUILD_TIME "Unknown date" CACHE INTERNAL "Build date & time")
- set(BUILD_HOST "${CMAKE_HOST_SYSTEM} ${CMAKE_HOST_SYSTEM_PROCESSOR}" CACHE INTERNAL "Build host & architecture")
- message(STATUS "Setting build user & time - not on Unix, using anonymous")
+ if(NOT BUILD_HOST)
+ if(CMAKE_HOST_UNIX)
+ execute_process( COMMAND uname -srm OUTPUT_VARIABLE TMP_HOST OUTPUT_STRIP_TRAILING_WHITESPACE)
+ else()
+ set(TMP_HOST "${CMAKE_HOST_SYSTEM} ${CMAKE_HOST_SYSTEM_PROCESSOR}")
+ endif()
+ set(BUILD_HOST "${TMP_HOST}" CACHE INTERNAL "Build host & architecture")
+ message(STATUS "Setting build host - ${BUILD_HOST}")
endif()
- # Set up some defaults that will usually be overridden
+ # Set up some defaults that will usually be overwritten
if(CMAKE_CROSSCOMPILING)
set(_reason ", cross-compiled")
endif()
- set(OUTPUT_CPU_VENDOR "Unknown${_reason}")
- set(OUTPUT_CPU_BRAND "Unknown${_reason}")
- set(OUTPUT_CPU_FAMILY "0")
- set(OUTPUT_CPU_MODEL "0")
- set(OUTPUT_CPU_STEPPING "0")
- set(OUTPUT_CPU_FEATURES "Unknown${_reason}")
- unset(_reason)
-
- if(NOT CMAKE_CROSSCOMPILING)
- # Get CPU information, e.g. for deciding what SIMD support probably exists
- if(GMX_TARGET_X86)
- set(GMX_TARGET_X86_VALUE 1)
- else()
- set(GMX_TARGET_X86_VALUE 0)
- endif()
- set(_compile_definitions "${GCC_INLINE_ASM_DEFINE} -I${CMAKE_SOURCE_DIR}/src -DGMX_CPUINFO_STANDALONE ${GMX_STDLIB_CXX_FLAGS} -DGMX_TARGET_X86=${GMX_TARGET_X86_VALUE}")
- set(GMX_BUILDINFORMATION_BINARY "${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/GmxBuildInformation${CMAKE_EXECUTABLE_SUFFIX}")
- set(LINK_LIBRARIES "${GMX_STDLIB_LIBRARIES}")
- # TODO Extract this try_compile to a helper function, because
- # it duplicates code in gmxDetectSimd.cmake
- try_compile(GMX_BUILDINFORMATION_COMPILED
- "${CMAKE_CURRENT_BINARY_DIR}"
- "${CMAKE_CURRENT_SOURCE_DIR}/src/gromacs/hardware/cpuinfo.cpp"
- COMPILE_DEFINITIONS "${_compile_definitions}"
- CMAKE_FLAGS "-DLINK_LIBRARIES=${LINK_LIBRARIES}"
- OUTPUT_VARIABLE GMX_BUILDINFORMATION_COMPILED_OUTPUT
- COPY_FILE ${GMX_BUILDINFORMATION_BINARY})
- unset(_compile_definitions)
+ # Run the cpu detection. If it produces an empty output, set a
+ # local value in the parent scope with a suitable fallback (which
+ # hides the cached value).
- if(GMX_BUILDINFORMATION_COMPILED)
- # TODO Extract this duplication to a helper function (also
- # from gmxDetectSimd.cmake)
- if(NOT DEFINED GMX_BUILDINFORMATION_RUN_VENDOR)
- execute_process(COMMAND ${GMX_BUILDINFORMATION_BINARY} "-vendor"
- RESULT_VARIABLE GMX_BUILDINFORMATION_RUN_VENDOR
- OUTPUT_VARIABLE OUTPUT_TMP
- ERROR_QUIET)
- set(GMX_BUILDINFORMATION_RUN_VENDOR "${GMX_BUILDINFORMATION_RUN_VENDOR}" CACHE INTERNAL "Result of running cpuinfo code with arg -vendor")
- if(GMX_BUILDINFORMATION_RUN_VENDOR EQUAL 0)
- string(STRIP "${OUTPUT_TMP}" OUTPUT_CPU_VENDOR)
- endif()
- endif()
- if(NOT DEFINED GMX_BUILDINFORMATION_RUN_BRAND)
- execute_process(COMMAND ${GMX_BUILDINFORMATION_BINARY} "-brand"
- RESULT_VARIABLE GMX_BUILDINFORMATION_RUN_BRAND
- OUTPUT_VARIABLE OUTPUT_TMP
- ERROR_QUIET)
- set(GMX_BUILDINFORMATION_RUN_BRAND "${GMX_BUILDINFORMATION_RUN_BRAND}" CACHE INTERNAL "Result of running cpuinfo code with arg -brand")
- if(GMX_BUILDINFORMATION_RUN_BRAND EQUAL 0)
- string(STRIP "${OUTPUT_TMP}" OUTPUT_CPU_BRAND)
- endif()
- endif()
- if(NOT DEFINED GMX_BUILDINFORMATION_RUN_FAMILY)
- execute_process(COMMAND ${GMX_BUILDINFORMATION_BINARY} "-family"
- RESULT_VARIABLE GMX_BUILDINFORMATION_RUN_FAMILY
- OUTPUT_VARIABLE OUTPUT_TMP
- ERROR_QUIET)
- set(GMX_BUILDINFORMATION_RUN_FAMILY "${GMX_BUILDINFORMATION_RUN_FAMILY}" CACHE INTERNAL "Result of running cpuinfo code with arg -family")
- if(GMX_BUILDINFORMATION_RUN_FAMILY EQUAL 0)
- string(STRIP "${OUTPUT_TMP}" OUTPUT_CPU_FAMILY)
- endif()
- endif()
- if(NOT DEFINED GMX_BUILDINFORMATION_RUN_MODEL)
- execute_process(COMMAND ${GMX_BUILDINFORMATION_BINARY} "-model"
- RESULT_VARIABLE GMX_BUILDINFORMATION_RUN_MODEL
- OUTPUT_VARIABLE OUTPUT_TMP
- ERROR_QUIET)
- set(GMX_BUILDINFORMATION_RUN_MODEL "${GMX_BUILDINFORMATION_RUN_MODEL}" CACHE INTERNAL "Result of running cpuinfo code with arg -model")
- if(GMX_BUILDINFORMATION_RUN_MODEL EQUAL 0)
- string(STRIP "${OUTPUT_TMP}" OUTPUT_CPU_MODEL)
- endif()
- endif()
- if(NOT DEFINED GMX_BUILDINFORMATION_RUN_STEPPING)
- execute_process(COMMAND ${GMX_BUILDINFORMATION_BINARY} "-stepping"
- RESULT_VARIABLE GMX_BUILDINFORMATION_RUN_STEPPING
- OUTPUT_VARIABLE OUTPUT_TMP
- ERROR_QUIET)
- set(GMX_BUILDINFORMATION_RUN_STEPPING "${GMX_BUILDINFORMATION_RUN_STEPPING}" CACHE INTERNAL "Result of running cpuinfo code with arg -stepping")
- if(GMX_BUILDINFORMATION_RUN_STEPPING EQUAL 0)
- string(STRIP "${OUTPUT_TMP}" OUTPUT_CPU_STEPPING)
- endif()
- endif()
- if(NOT DEFINED GMX_BUILDINFORMATION_RUN_FEATURES)
- execute_process(COMMAND ${GMX_BUILDINFORMATION_BINARY} "-features"
- RESULT_VARIABLE GMX_BUILDINFORMATION_RUN_FEATURES
- OUTPUT_VARIABLE OUTPUT_TMP
- ERROR_QUIET)
- set(GMX_BUILDINFORMATION_RUN_FEATURES "${GMX_BUILDINFORMATION_RUN_FEATURES}" CACHE INTERNAL "Result of running cpuinfo code with arg -features")
- if(GMX_BUILDINFORMATION_RUN_FEATURES EQUAL 0)
- string(STRIP "${OUTPUT_TMP}" OUTPUT_CPU_FEATURES)
- endif()
- endif()
+ macro(gmx_get_build_cpu_string TYPE DEFAULT_VALUE)
+ string(TOUPPER ${TYPE} UPPERTYPE)
+ gmx_run_cpu_detection(${TYPE})
+ set(OUTPUT_VALUE "${DEFAULT_VALUE}")
+ if (CPU_DETECTION_${UPPERTYPE})
+ set(OUTPUT_VALUE ${CPU_DETECTION_${UPPERTYPE}})
endif()
- endif()
-
- set(BUILD_CPU_VENDOR "${OUTPUT_CPU_VENDOR}" CACHE INTERNAL "Build CPU vendor")
- set(BUILD_CPU_BRAND "${OUTPUT_CPU_BRAND}" CACHE INTERNAL "Build CPU brand")
- set(BUILD_CPU_FAMILY "${OUTPUT_CPU_FAMILY}" CACHE INTERNAL "Build CPU family")
- set(BUILD_CPU_MODEL "${OUTPUT_CPU_MODEL}" CACHE INTERNAL "Build CPU model")
- set(BUILD_CPU_STEPPING "${OUTPUT_CPU_STEPPING}" CACHE INTERNAL "Build CPU stepping")
- set(BUILD_CPU_FEATURES "${OUTPUT_CPU_FEATURES}" CACHE INTERNAL "Build CPU features")
+ set(BUILD_CPU_${UPPERTYPE} ${OUTPUT_VALUE} PARENT_SCOPE)
+ endmacro()
- ENDIF(NOT DEFINED BUILD_USER)
-endmacro(gmx_set_build_information)
+ gmx_get_build_cpu_string(vendor "Unknown${_reason}")
+ gmx_get_build_cpu_string(brand "Unknown${_reason}")
+ gmx_get_build_cpu_string(family "0")
+ gmx_get_build_cpu_string(model "0")
+ gmx_get_build_cpu_string(stepping "0")
+ gmx_get_build_cpu_string(features "Unknown${_reason}")
+endfunction()
+++ /dev/null
-#
-# This file is part of the GROMACS molecular simulation package.
-#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
-# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
-# and including many others, as listed in the AUTHORS file in the
-# top-level source directory and at http://www.gromacs.org.
-#
-# GROMACS is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public License
-# as published by the Free Software Foundation; either version 2.1
-# of the License, or (at your option) any later version.
-#
-# GROMACS is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
-#
-# You should have received a copy of the GNU Lesser General Public
-# License along with GROMACS; if not, see
-# http://www.gnu.org/licenses, or write to the Free Software Foundation,
-# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-#
-# If you want to redistribute modifications to GROMACS, please
-# consider that scientific software is very special. Version
-# control is crucial - bugs must be traceable. We will be happy to
-# consider code for inclusion in the official distribution, but
-# derived work must not be called official GROMACS. Details are found
-# in the README & COPYING files - if they are missing, get the
-# official version at http://www.gromacs.org.
-#
-# To help us fund GROMACS development, we humbly ask that you cite
-# the research papers on the package. Check out http://www.gromacs.org.
-
-# GMX_TEST_AVX_GCC_MASKLOAD_BUG(VARIABLE AVX_CFLAGS)
-#
-# VARIABLE will be set if the compiler is a buggy version
-# of GCC (prior to 4.5.3, and maybe 4.6) that has an incorrect second
-# argument to the AVX _mm256_maskload_ps() intrinsic.
-#
-# You need to use this variable in a cmakedefine, and then handle
-# the case separately in your code - no automatic cure, unfortunately.
-#
-MACRO(GMX_TEST_AVX_GCC_MASKLOAD_BUG VARIABLE AVX_CFLAGS)
- IF(NOT DEFINED ${VARIABLE})
- MESSAGE(STATUS "Checking for gcc AVX maskload bug")
- # some compilers like clang accept both cases,
- # so first try a normal compile to avoid flagging those as buggy.
- TRY_COMPILE(${VARIABLE}_COMPILEOK "${CMAKE_BINARY_DIR}"
- "${CMAKE_SOURCE_DIR}/cmake/TestAVXMaskload.c"
- COMPILE_DEFINITIONS "${AVX_CFLAGS} -DGMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG=0" )
- IF(${VARIABLE}_COMPILEOK)
- SET(${VARIABLE} 0 CACHE INTERNAL "Work around GCC bug in AVX maskload argument" FORCE)
- MESSAGE(STATUS "Checking for gcc AVX maskload bug - not present")
- ELSE()
- TRY_COMPILE(${VARIABLE}_COMPILEOK "${CMAKE_BINARY_DIR}"
- "${CMAKE_SOURCE_DIR}/cmake/TestAVXMaskload.c"
- COMPILE_DEFINITIONS "${AVX_CFLAGS} -DGMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG=1" )
- IF(${VARIABLE}_COMPILEOK)
- SET(${VARIABLE} 1 CACHE INTERNAL "Work around GCC bug in AVX maskload argument" FORCE)
- MESSAGE(STATUS "Checking for gcc AVX maskload bug - found, will try to work around")
- ELSE()
- MESSAGE(WARNING "Cannot compile AVX code - assuming gcc AVX maskload bug not present." )
- MESSAGE(STATUS "Checking for gcc AVX maskload bug - not present")
- ENDIF()
- ENDIF()
- ENDIF()
-ENDMACRO()
# First check that the compiler is OK, and find the appropriate flag.
if(WIN32 AND NOT MINGW)
- set(CXX11_CXX_FLAG "/Qstd=c++0x")
+ set(CXX11_CXX_FLAG "/Qstd=c++11")
elseif(CYGWIN)
- set(CXX11_CXX_FLAG "-std=gnu++0x") #required for strdup
+ set(CXX11_CXX_FLAG "-std=gnu++11") #required for strdup
else()
- set(CXX11_CXX_FLAG "-std=c++0x")
+ set(CXX11_CXX_FLAG "-std=c++11")
endif()
CHECK_CXX_COMPILER_FLAG("${CXX11_CXX_FLAG}" CXXFLAG_STD_CXX0X)
if(NOT CXXFLAG_STD_CXX0X)
b bTest() {
return b();
}
-// Early patch versions of icc 16 (and perhaps earlier versions)
-// have an issue with this test, but the GROMACS tests pass,
-// so we disable this test in that sub-case.
-#if (defined __INTEL_COMPILER && __INTEL_COMPILER >= 1700) || (defined __ICL && __ICL >= 1700) || (defined __INTEL_COMPILER_UDPATE && __INTEL_COMPILER_UPDATE >= 3)
+// ICC requires that a suitable GCC is available. It is using its standard library and emulates
+// GCC behaviour based on its version. Relevant here it emulates the implementation of the move
+// constructor. This compiler check should only fail based on the compiler not GCC. The GCC version
+// is checked by the following STL check. It is known that all ICC>=15 have the proper move
+// constructor. Thus this check is disabled for ICC.
+#if !((defined __INTEL_COMPILER && __INTEL_COMPILER >= 1500) || (defined __ICL && __ICL >= 1500))
// Test that a subclass has a proper move constructor
struct c {
c() {};
int array[5] = { 1, 2, 3, 4, 5 };
for (int& x : array)
x *= 2;
+ // Test alignas
+ alignas(4*sizeof(int)) int y;
}" CXX11_SUPPORTED)
+ if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
+ if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "4.8.1")
+ message(FATAL_ERROR "GROMACS requires version 4.8.1 or later of the GNU C++ compiler for complete C++11 support")
+ endif()
+ elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+ if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "3.3")
+ message(FATAL_ERROR "GROMACS requires version 3.3 or later of the Clang C++ compiler for complete C++11 support")
+ endif()
+ elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
+ if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "15.0")
+ message(FATAL_ERROR "GROMACS requires version 15.0 or later of the Intel C++ compiler for complete C++11 support")
+ endif()
+ elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
+ if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS "19.0.23026")
+ message(FATAL_ERROR "GROMACS requires version 2015 (19.0.23026) or later of the MSVC C++ compiler for complete C++11 support")
+ endif()
+ endif()
if(CXX11_SUPPORTED)
set(${CXX11_CXX_FLAG_NAME} ${CXX11_CXX_FLAG} PARENT_SCOPE)
else()
intPointer p(new int(10));
std::map<int, std::unique_ptr<int>> m;
m.insert(std::make_pair(5, std::move(p)));
- auto start = std::chrono::system_clock::now();
- if (std::chrono::system_clock::now() - start < std::chrono::seconds(2))
+ auto start = std::chrono::steady_clock::now();
+ if (std::chrono::steady_clock::now() - start < std::chrono::seconds(2))
{
std::thread t;
}
}" CXX11_STDLIB_PRESENT)
if(NOT CXX11_STDLIB_PRESENT)
- message(FATAL_ERROR "This version of GROMACS requires C++11-compatible standard library. Please use a newer compiler, or a newer standard library, or use the GROMACS 5.1.x release. See the installation guide for details.")
+ message(FATAL_ERROR "This version of GROMACS requires C++11-compatible standard library. Several compilers (e.g. Clang and Intel) use GCC. For those make sure to have GCC 4.8.1 or later. Please use a newer compiler, or a newer standard library, or use the GROMACS 5.1.x release. See the installation guide for details.")
endif()
endfunction()
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
message(WARNING "The versions of the C and C++ compilers do not match (${CMAKE_C_COMPILER_VERSION} and ${CMAKE_CXX_COMPILER_VERSION}, respectively). Mixing different C/C++ compilers can cause problems.")
endif()
- # clang 3.0 is buggy for some unknown reason detected during adding
- # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
- # that is, we should replace these tests with a compiler feature test,
- # update GROMACS Redmine task #1039 and perhaps report a clang bug.
- #
- # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
- # the compiler version for us. So we need a manual check for clang 3.0.
- include(gmxDetectClang30)
- gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
- if(COMPILER_IS_CLANG_3_0)
- message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
- endif()
-
- if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
- message(WARNING "Currently tested PGI compiler versions (up to 15.7) generate binaries that do not pass all regression test, and the generated binaries are significantly slower than with GCC, ICC or Clang. For now we do not recommend PGI beyond development testing - make sure to run the regressiontests.")
- endif()
-
- if(CMAKE_COMPILER_IS_GNUCC AND
- (CMAKE_C_COMPILER_VERSION VERSION_LESS "4.9.0" OR CMAKE_SIZEOF_VOID_P EQUAL 8)
- AND (WIN32 OR CYGWIN)
- AND GMX_SIMD MATCHES "AVX" AND NOT GMX_SIMD STREQUAL AVX_128_FMA)
- message(WARNING "GCC on Windows (GCC older than 4.9 or any version when compiling for 64bit) with AVX (other than AVX_128_FMA) crashes. Choose a different GMX_SIMD or a different compiler.") # GCC bug 49001, 54412.
- endif()
-
- if(CMAKE_C_COMPILER_ID MATCHES "Clang" AND WIN32)
- if(CMAKE_VERSION VERSION_LESS 3.0.0)
- message(WARNING "Clang on Windows requires cmake 3.0.0")
- endif()
- if(CMAKE_C_COMPILER_VERSION VERSION_LESS 3.5.0)
- message(WARNING "Clang on Windows requires clang 3.5.0")
+ # Note that we've already tested that the compiler works with C++11
+ if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
+ if(WIN32 AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS "3.5.0")
+ message(WARNING "Using Clang on Windows requires Clang 3.5.0")
endif()
+ elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "PGI")
+ message(WARNING "Currently tested PGI compiler versions (up to 15.7) generate binaries that do not pass all regression test, and the generated binaries are significantly slower than with GCC, ICC or Clang. For now we do not recommend PGI beyond development testing - make sure to run the regressiontests.")
endif()
endmacro(gmx_test_compiler_problems)
# The main interface to this machinery is the gmx_configure_version_file()
# CMake function. The signature is
# gmx_configure_version_file(<input> <output>
-# [REMOTE_HASH] [SOURCE_FILE]
+# [REMOTE_HASH]
# [TARGET <target>]
# [COMMENT <comment>])
# <input> Specify the input and output files as for configure_file().
# This variable is much more expensive to initialize than the
# others, so this allows local changes in this file to only
# compute that value when required if that becomes necessary.
-# SOURCE_FILE Signals that <output> will be used as a source file.
-# The function will set properties for the source file
-# appropriately to signify that it is generated.
# TARGET By default, this function uses add_custom_command() to
# generate the output file. If TARGET is specified, then
# add_custom_target() is used to create a target with the given
# The GROMACS convention is that these are the version number of the next
# release that is going to be made from this branch.
-set(GMX_VERSION_MAJOR 2016)
-set(GMX_VERSION_PATCH 4)
+set(GMX_VERSION_MAJOR 2017)
+set(GMX_VERSION_PATCH 0)
# The suffix, on the other hand, is used mainly for betas and release
# candidates, where it signifies the most recent such release from
# this branch; it will be empty before the first such release, as well
# here. The important thing is to minimize the chance of third-party
# code being able to dynamically link with a version of libgromacs
# that might not work.
-set(LIBRARY_SOVERSION_MAJOR 2)
-set(LIBRARY_SOVERSION_MINOR 3)
+set(LIBRARY_SOVERSION_MAJOR 3)
+set(LIBRARY_SOVERSION_MINOR 0)
set(LIBRARY_VERSION ${LIBRARY_SOVERSION_MAJOR}.${LIBRARY_SOVERSION_MINOR}.0)
#####################################################################
endif()
set(REGRESSIONTEST_VERSION "${GMX_VERSION_STRING}")
-set(REGRESSIONTEST_BRANCH "refs/heads/release-2016")
-set(REGRESSIONTEST_MD5SUM "bed92d1d9cdca66fbd2efa142b6e0dd3" CACHE INTERNAL "MD5 sum of the regressiontests tarball")
+set(REGRESSIONTEST_BRANCH "refs/heads/master")
+set(REGRESSIONTEST_MD5SUM "366438549270d005fa6def6e56ca0256")
math(EXPR GMX_VERSION_NUMERIC
"${GMX_VERSION_MAJOR}*10000 + ${GMX_VERSION_PATCH}")
# See documentation at the top of the script.
function (gmx_configure_version_file INFILE OUTFILE)
include(CMakeParseArguments)
- set(_options REMOTE_HASH SOURCE_FILE)
+ set(_options REMOTE_HASH)
set(_one_value_args COMMENT TARGET)
set(_multi_value_args EXTRA_VARS)
cmake_parse_arguments(
add_custom_target(${ARG_TARGET} DEPENDS ${OUTFILE} VERBATIM)
gmx_set_custom_target_output(${ARG_TARGET} ${OUTFILE})
endif()
- if (ARG_SOURCE_FILE)
- set_source_files_properties(${OUTFILE} PROPERTIES GENERATED true)
- endif()
endfunction()
...
fun:gmx_fio_fopen
}
-{
- bTimeSet/tMPI_Thread_mutex_init_once
- Memcheck:Leak
- ...
- fun:tMPI_Thread_mutex_init_once
- fun:tMPI_Thread_mutex_lock
- fun:bTimeSet
-}
-{
- gmx_ffclose/tMPI_Thread_mutex_init_once
- Memcheck:Leak
- ...
- fun:tMPI_Thread_mutex_init_once
- fun:tMPI_Thread_mutex_lock
- fun:gmx_ffclose
-}
{
mdrun
--- /dev/null
+#!/bin/bash
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2016, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+while [[ "$1" != "--" ]] ; do
+ extra_opts="$extra_opts $1"
+ shift
+done
+for opt in $ASAN_OPTIONS ; do
+ if [[ "$opt" == log_path=* ]] ; then
+ # CTest gives errors if the file does not exist, but AddressSanitizer
+ # only produces it if it finds issues...
+ log_path="${opt#log_path=}"
+ log_path="${log_path%\"}"
+ log_path="${log_path#\"}"
+ touch ${log_path}.99999
+ fi
+done
+# Suppressions are not currently necessary, but can be introduced like this.
+#path=`dirname $0`
+#export LSAN_OPTIONS="suppressions=$path/../admin/lsan-suppressions.txt"
+export ASAN_OPTIONS="$ASAN_OPTIONS $extra_opts"
+exec "$@"
EXTRA_VARS
SPHINX_EXTENSION_PATH RELENG_PATH
EXPECTED_DOXYGEN_VERSION
- GMX_CMAKE_MINIMUM_REQUIRED_VERSION REQUIRED_CUDA_VERSION
+ CMAKE_MINIMUM_REQUIRED_VERSION REQUIRED_CUDA_VERSION
REQUIRED_OPENCL_MIN_VERSION
REQUIRED_CUDA_COMPUTE_CAPABILITY REGRESSIONTEST_VERSION
SOURCE_MD5SUM REGRESSIONTEST_MD5SUM_STRING
regressiontest_version = '@REGRESSIONTEST_VERSION@'
variables = [
('EXPECTED_DOXYGEN_VERSION', '@EXPECTED_DOXYGEN_VERSION@'),
- ('GMX_CMAKE_MINIMUM_REQUIRED_VERSION', '@GMX_CMAKE_MINIMUM_REQUIRED_VERSION@'),
+ ('CMAKE_MINIMUM_REQUIRED_VERSION', '@CMAKE_MINIMUM_REQUIRED_VERSION@'),
('REQUIRED_CUDA_VERSION', '@REQUIRED_CUDA_VERSION@'),
('REQUIRED_CUDA_COMPUTE_CAPABILITY', '@REQUIRED_CUDA_COMPUTE_CAPABILITY@'),
('REQUIRED_OPENCL_MIN_VERSION', '@REQUIRED_OPENCL_MIN_VERSION@'),
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
.. _LAM-MPI: http://www.lam-mpi.org
.. _OpenMP: http://en.wikipedia.org/wiki/OpenMP
.. _CMake installation page: http://www.cmake.org/install/
+.. _Ubuntu toolchain ppa page: https://launchpad.net/~ubuntu-toolchain-r/+archive/ubuntu/test
+.. _EPEL page: https://fedoraproject.org/wiki/EPEL
.. _running CMake: http://www.cmake.org/runningcmake/
.. _CMake environment variables: http://cmake.org/Wiki/CMake_Useful_Variables#Environment_Variables
.. _FFTW: http://www.fftw.org
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
-execfile('conf-man.py')
+if tags.has('do_man'):
+ execfile('conf-man.py')
# If true, show URL addresses after external links.
#man_show_urls = False
=====================
The |Gromacs| build system uses CMake (version
-|GMX_CMAKE_MINIMUM_REQUIRED_VERSION| or newer is required) to generate the
+|CMAKE_MINIMUM_REQUIRED_VERSION| or newer is required) to generate the
actual build system for the build tool choosen by the user. See CMake
documentation for general introduction to CMake and how to use it. This
documentation focuses on how the |Gromacs| build system is organized and
Documentation flavors
---------------------
-The |Gromacs| source tree is set up to produce three different levels of Doxygen
+The |Gromacs| source tree is set up to produce several different levels of Doxygen
documentation:
1. Public API documentation (suffix ``-user``), which documents functions and
developers.
3. Full documentation (suffix ``-full``), which includes (nearly) all (documented)
functions and classes in the source tree.
+4. Maximally verbose documentation (suffix ``-dev``) with everything doxygen can
+ extract as well as additional internal links.
Each subsequent level of documentation includes all the documentation from the
levels above it. The suffixes above refer to the suffixes of Doxygen input and
result is what you want, and that you do not produce any warnings.
For local work, it is generally a good idea to set ``GMX_COMPACT_DOXYGEN=ON``
CMake option, which removes some large generated graphs from the documentation
-and speeds up the process significantly.
+and speeds up the process significantly. There are also "fast" versions
+of the ``make`` targets that skip the additional diagrams built for the ``lib``
+level and lower.
All files related to Doxygen reside in the ``docs/doxygen/`` subdirectory in the source
and build trees. In a freshly checked out source tree, this directory contains
various ``Doxyfile-*.cmakein`` files. When you run CMake, corresponding files
-``Doxyfile-user``, ``Doxyfile-lib``, and ``Doxyfile-full`` are generated at the
+``Doxyfile-user``, ``Doxyfile-lib``, ``Doxyfile-full``, ``Doxyfile-dev`` are generated at the
corresponding location in the build tree. There is also a
``Doxyfile-common.cmakein``, which is used to produce ``Doxyfile-common``.
This file contains settings that are shared between all the input files.
You can run Doxygen directly with one of the generated files (all output will
be produced under the current working directory), or build one of the
-``doxygen-user``, ``doxygen-lib``, and ``doxygen-full`` targets. The targets run
+``doxygen-user``, ``doxygen-lib``, ``doxygen-full``, ``doxygen-dev`` targets. The targets run
Doxygen in a quieter mode and only show the warnings if there were any, and put
the output under ``docs/html/doxygen/`` in the build tree, so that the Doxygen
build cooperates with the broader ``webpage`` target.
The ``doxygen-all`` target builds all three targets with less typing.
-The generated documentation is put under ``html-user/``, ``html-lib/``, and/or
-``html-full/``. Open ``index.xhtml`` file from one of
+The generated documentation is put under ``html-user/``, ``html-lib/``,
+``html-full/``, and/or ``html-dev/``. Open ``index.xhtml`` file from one of
these subdirectories to start browsing (for |Gromacs| developers, the
``html-lib/`` is a reasonable starting point). Log files with all Doxygen
warnings are also produced as ``docs/doxygen/doxygen-*.log``, so you can inspect them after
* MSVC supports only a subset of C99 and work-arounds are required in those cases.
* Before 7.0 (partial support in 6.5) CUDA didn't support C++11. Therefore any
- header file which is needed (or likly will be nedded) by CUDA should not use C++11.
-* C++11 features which are not widely implemented (including in MSVC 2015 and GCC 4.6)
- should not be used.
+ header file which is needed (or likely will be nedded) by CUDA should not use C++11.
+* We should be able to use virtually all C++ features outside of the header files
+ required by CUDA code (and OpenCL kernels), since we have gradually moved to
+ compilers that have full support for C++11.
.. TODO: Copy important points from http://www.gromacs.org/index.php?title=Developer_Zone/Programming_Guide/Allowed_C%2B%2B_Features
+
+C++ Standard Library
+--------------------
+
+|Gromacs| code must support the lowest common denominator of C++11 standard library
+features available on supported platforms.
+Some modern features are useful enough to warrant back-porting.
+Consistent and forward-compatible headers are provided in ``src/gromacs/compat/``
+as described in the `Library documentation <../doxygen/html-lib/group__group__compatibility.xhtml>`_
+
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(DOXYGEN_EXTRA_SETTINGS "@INCLUDE = ${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile-compact")
endif()
configure_file(Doxyfile-common.cmakein Doxyfile-common)
+ configure_file(Doxyfile-dev.cmakein Doxyfile-dev)
configure_file(Doxyfile-full.cmakein Doxyfile-full)
configure_file(Doxyfile-lib.cmakein Doxyfile-lib)
configure_file(Doxyfile-user.cmakein Doxyfile-user)
COMMAND ${CMAKE_COMMAND} -DDOCTYPE=${TYPE} -P RunDoxygen.cmake
DEPENDS ${_deps}
WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
- COMMENT "${COMMENT}")
+ COMMENT "${COMMENT}" USES_TERMINAL)
if (_fast_arg)
add_dependencies(${TARGET}-fast doxygen-version)
endif()
${CMAKE_CURRENT_SOURCE_DIR}/gmxtree.py
${CMAKE_CURRENT_SOURCE_DIR}/graphbuilder.py
${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt
- COMMENT "Generating include dependency graphs for dot")
+ COMMENT "Generating include dependency graphs for dot"
+ USES_TERMINAL)
# Add separate targets for converting the .dot files to .png.
# These are not needed by the Doxygen targets, but are useful for
add_doxygen_target(doxygen-full full "Generating full documentation with Doxygen" DEPGRAPHS)
add_doxygen_target(doxygen-lib lib "Generating library documentation with Doxygen" DEPGRAPHS)
add_doxygen_target(doxygen-user user "Generating public API documentation with Doxygen")
+ add_doxygen_target(doxygen-dev dev "Generating verbose developer docs with Doxygen" DEPGRAPHS)
# Convenience targets to build all the documentation flavors.
add_custom_target(doxygen-all)
add_custom_target(doxygen-all-fast)
--ignore ${CMAKE_CURRENT_SOURCE_DIR}/suppressions.txt
--ignore-cycles ${CMAKE_CURRENT_SOURCE_DIR}/cycle-suppressions.txt)
add_custom_target(check-source COMMAND ${check_source_command}
- COMMENT "Checking source code for various issues" VERBATIM)
+ COMMENT "Checking source code for various issues" VERBATIM USES_TERMINAL)
add_custom_target(check-source-fast COMMAND ${check_source_command}
- COMMENT "Checking source code for various issues" VERBATIM)
+ COMMENT "Checking source code for various issues" VERBATIM USES_TERMINAL)
add_dependencies(check-source doxygen-xml)
endif()
else()
CLASS_DIAGRAMS = NO
CLASS_GRAPH = NO
COLLABORATION_GRAPH = NO
+GROUP_GRAPHS = NO
+TEMPLATE_RELATIONS = NO
INCLUDE_GRAPH = NO
INCLUDED_BY_GRAPH = NO
+CALL_GRAPH = NO
+CALLER_GRAPH = NO
+GRAPHICAL_HIERARCHY = NO
+DIRECTORY_GRAPH = NO
--- /dev/null
+@INCLUDE = Doxyfile-common
+
+PREDEFINED += F77_FUNC(name,NAME)=name
+
+ENABLED_SECTIONS += libapi internal
+INTERNAL_DOCS = YES
+EXTRACT_LOCAL_CLASSES = YES
+EXTRACT_LOCAL_METHODS = YES
+EXTRACT_ANON_NSPACES = YES
+SOURCE_BROWSER = YES
+HIDE_UNDOC_CLASSES = NO
+HIDE_UNDOC_MEMBERS = NO
+REFERENCED_BY_RELATION = YES
+REFERENCES_RELATION = YES
+VERBATIM_HEADERS = YES # restore default overridden by Doxyfile-common
+
+WARN_LOGFILE = doxygen-dev.log
+HTML_OUTPUT = html-dev
+
+ALIASES += inpublicapi="\ingroup group_publicapi"
+ALIASES += inlibraryapi="\ingroup group_libraryapi"
+ALIASES += libinternal=
simd -> hardware
gpu_utils -> hardware
topology -> listed-forces
-pbcutil -> mdtypes
listed-forces -> mdlib
\ingroup module_commandline
*/
+/*! \libinternal
+\dir src/gromacs/compat
+\brief \ref group_compatibility
+
+\ingroup group_compatibility
+ */
+
+/*! \internal
+\dir src/gromacs/compat/tests
+\brief Tests for \ref group_compatibility
+
+\ingroup group_compatibility
+ */
+
/*! \libinternal
\dir src/gromacs/onlinehelp
\brief \ref module_onlinehelp
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
self._module = None
self._is_test_dir = False
if parent and parent.is_test_directory() or \
- self._name in ('tests', 'legacytests'):
+ self._name == 'tests':
self._is_test_dir = True
self._is_external = False
if parent and parent.is_external() or self._name == 'external':
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
'time.h']
_std_c_cpp_headers = ['c' + x[:-2] for x in _std_c_headers]
_std_cpp_headers = ['algorithm', 'array', 'chrono', 'deque', 'exception', 'fstream',
- 'functional', 'iomanip', 'ios', 'iosfwd', 'iostream', 'istream', 'iterator',
- 'limits', 'list', 'map', 'memory', 'new', 'numeric', 'ostream', 'random',
+ 'functional', 'initializer_list', 'iomanip', 'ios', 'iosfwd',
+ 'iostream', 'istream', 'iterator',
+ 'limits', 'list', 'map', 'memory', 'mutex',
+ 'new', 'numeric', 'ostream', 'random',
'regex', 'set', 'sstream', 'stdexcept', 'streambuf', 'string', 'strstream',
'thread', 'tuple', 'type_traits', 'typeindex', 'typeinfo', 'vector', 'utility']
--- /dev/null
+Logging {#page_logging}
+=======
+
+Currently, mdrun is using a combination of direct C-style I/O into `fplog` and
+`stderr`, and the facilities described here. However, more and more should get
+moved to this interface in the future.
+
+The parts that make up the logging system are shown below.
+
+\dot
+ digraph logging_overview {
+ builder [label="LoggerBuilder", URL="\ref gmx::LoggerBuilder"]
+ owner [label="LoggerOwner", URL="\ref gmx::LoggerOwner"]
+ logger [label="MDLogger", URL="\ref gmx::MDLogger"]
+ target [label="ILogTarget", URL="\ref gmx::ILogTarget"]
+ user [label="using code"]
+
+ builder -> owner [label="builds"]
+ owner -> logger
+ owner -> target [label="owns"]
+ logger -> target [label="references"]
+ user -> builder [label="set logging targets"]
+ user -> logger [label="write with\nGMX_LOG()"]
+ }
+\enddot
+
+To initialize the logging system, the using code creates an instance of
+gmx::LoggerBuilder, and sets the desired logging targets with provided methods.
+Once all targets have been initialized, the code calls
+gmx::LoggerBuilder::build() and gets a gmx::LoggerOwner, which is responsible
+of managing the memory allocated for the logger.
+
+To log information, the using code uses an gmx::MDLogger returned by
+gmx::LoggerOwner::logger() with the ::GMX_LOG macro. Code that writes to the
+log only needs to know of this class (and helper classes used to implement the
+macro), which is a relatively simple container for references to the logging
+targets. If there is no log target that would consume the information written
+with ::GMX_LOG, the whole statement evaluates to a conditional that reads the
+log target from a member variable and compares it against `nullptr`. All the
+code that formats the output is skipped in this case.
+
+Currently the implementation is geared to making ::GMX_LOG behavior stable, and
+to be relatively extensible. However, using any other approach than ::GMX_LOG
+for writing to the log should first think about how the API could be best
+organized for that.
+
+All information written to the log is composed of _log entries_. Each
+::GMX_LOG statement writes a single log entry, meaning that newlines are
+automatically added.
+
+The logging methods are not thread-safe, so it is the responsibility of the
+calling code to only use them from a single thread or otherwise synchronize
+access.
--- /dev/null
+mdrun modules {#page_mdmodules}
+=============
+
+Currently, most of mdrun is constructed as a set of C routines calling each
+other, and sharing data through a couple of common data structures (t_inputrec,
+t_forcerec, t_state etc.) that flow throughout the code.
+
+The electric field code (in `src/gromacs/applied-forces/`) implements an
+alternative concept that allows keeping everything related to the electric
+field functionality in a single place. At least for most special-purpose
+functionality, this would hopefully provide a more maintainable approach that
+would also support more easily adding new functionality. Some core features
+may still need stronger coupling than this provides.
+
+The rest of the page documents those parts of the modularity mechanism that
+have taken a clear form. Generalizing and designing other parts may require
+more code to be converted to modules to have clearer requirements on what the
+mechanism needs to support and what is the best way to express that in a
+generally usable form.
+
+Structure of a module
+---------------------
+
+Each module implements a factory that returns an instance of gmx::IMDModule.
+This interface has methods that in turn refer to other interfaces:
+gmx::IMdpOptionProvider, gmx::IMDOutputProvider, and gmx::IForceProvider.
+The module also implements these interfaces (or a subset of them), and code
+outside the module only calls methods in these interfaces.
+
+See documentation of the individual interfaces for details of what they
+support.
+
+Implementation of a module
+--------------------------
+
+Modules are constructed by composition of interfaces (i.e. abstract classes,
+general with pure virtual methods lacking implementations), so that e.g.
+trajectory-writing code can loop over containers of pointers to
+gmx::IMDOutputProvider without needing to know about all the concrete types
+that might implement that interface.
+
+The module classes should not be extended by using them as a base
+class, which is expressed with the final keyword in the class
+definition. Generally, modules will implement different flavours of
+functionality, perhaps based on user choices, or available computing
+resources. This should generally be implemented by providing variable
+behaviour for the methods that are called through the above
+interfaces. Either code should branch at run time upon some data
+contained by the module (e.g. read from the mdp options), or that the
+module class should contain a pointer to an internal interface class
+whose concrete type might be chosen during setup from the set of
+implementations of that internal interface. Such an approach keeps
+separate the set of interfaces characteristic of "MD modules" from
+those that are particular to flavours of any specific module.
+
+The virtual methods that the module classes inherit from their
+interfaces should be declared as `override`, to express the intent
+that they implement a virtual function from the interface. This
+permits the compiler to check that this is true, e.g. if the interface
+class changes. The `virtual` keyword should not be specified,
+because this is redundant when `override` is used. This follows
+the Cpp Core Guidelines (guideline C.128).
+
+Handling mdp input
+------------------
+
+To accept parameters from an mdp file, a module needs to implement
+gmx::IMdpOptionProvider.
+
+initMdpOptions() should declare the required input parameters using the options
+module. In most cases, the parameters should be declared as nested sections
+instead of a flat set of options. The structure used should be such that in
+the future, we can get the input values from a structured mdp file (e.g., JSON
+or XML), where the structure matches the declared options. As with other uses
+of the options module, the module needs to declare local variables where the
+values from the options will be assigned. The defined structure will also be
+used for storing in the tpr file (see below).
+
+initMdpTransform() should declare the mapping from current flat mdp format to
+the structured format defined in initMdpOptions(). For now, this makes it
+possible to have an internal forward-looking structured representation while
+the input is still a flat list of values, but in the future it also allows
+supporting both formats side-by-side as long as that is deemed necessary.
+
+On the implementation side, the framework (and other code that interacts with
+the modules) will do the following things to make mdp input work:
+
+* When grompp reads the mdp file, it will first construct a flat
+ KeyValueTreeObject, where each input option is set as a property.
+
+ It then calls initMdpTransform() for the module(s), and uses the produced
+ transform to convert the flat tree into a structured tree, performing any
+ defined conversions in the process. This transformation is one-way only,
+ although the framework keeps track of the origin of each value to provide
+ sensible error messages that have the original mdp option name included.
+
+ It calls initMdpOptions() for the module(s), initializing a single Options
+ object that has the input options.
+
+ It processes the structured tree using the options in two steps:
+
+ * For any option that is not specified in the input, it adds a property to
+ the tree with a default value. For options specified in the input, the
+ values in the tree are converted to native values for the options (e.g.,
+ from string to int for integer options).
+ * It assigns the values from the tree to the Options object. This will make
+ the values available in the local variables the module defined in
+ initMdpOptions().
+
+ Note that currently, the module(s) cannot use storeIsSet() in options to know
+ whether a particular option has been provided from the mdp file. This will
+ always return true for all the options. This is a limitation in the current
+ implementation, but it also, in part, enforces that the mdp file written out
+ by `gmx grompp -po` cannot produce different behavior because of set/not-set
+ differences.
+
+* grompp -po writes an mdp file that was equivalent to the input,
+ which is implemented by calling buildMdpOutput() for each module, to
+ prepare a builder object that is used with writeKeyValueTreeAsMdp().
+ As with the old flat tree, the values given by the user's input are
+ preserved, but not the ordering of options, or their formatting.
+
+* When grompp writes the tpr file, it writes the structured tree (after the
+ default value and native value conversion) into the tpr file.
+
+* When mdrun reads the tpr file, it reads the structured tree.
+ It then broadcasts the structure to all ranks. Each rank calls
+ initMdpOptions() for the modules, and assigns the values from the tree to the
+ Options object. After this, the modules will be exactly in the same state as
+ in grompp.
+
+* When other tools (gmx dump or gmx check in particular) read the tpr file,
+ they read the structured tree. In principle, they could operate directly on
+ this tree (and `gmx dump` in particular does, with the `-orgir` option).
+ However, in the future with proper tpr backward compatibility support, they
+ need to call to the modules to ensure that the tree has the structure that
+ this version expects, instead of what the original version that wrote the
+ file had. Currently, these tools only call initMdpOptions() and do the basic
+ default+native value conversion.
+
+* Any code that is not interested in the parameters for these modules can just
+ read the t_inputrec from the tpr file and ignore the tree.
+
+* For compatibility with old tpr files that did not yet have the structured
+ tree, the I/O code converts old values for the modules to parameters in the
+ structured tree (in tpxio.cpp).
+
+Currently, there is no mechanism for changing the mdp input parameters (adding
+new or removing old ones) that would maintain tpr and mdp backward
+compatibility. The vision for this is to use the same transformation engine as
+for initMdpTransform() to support specifying version-to-version conversions for
+any changed options, and applying the necessary conversions in sequence. The
+main challenge is keeping track of the versions to know which conversions to
+apply.
test. The test can naturally also use its own test assertions for additional
checks, but any mismatch will automatically also fail the test.
+It is also possible to read values of the reference data items using
+gmx::test::TestReferenceChecker, so that they can be used programmatically.
+For this to work, those items should first be written in the same test.
+This supports tests that want to both check data against a reference, and use
+that reference as a persistence layer for storing information. This is useful
+at least for serialization tests.
+This is currently not supported for all use cases, but with some caveats, it is
+possible to use this for testing.
+
When using floating-point values in reference data, the tolerance for the
comparison can be influenced with
gmx::test::TestReferenceChecker::setDefaultTolerance().
in `gromacs/simd/simd.h` and requires that files using those symbols
do the correct include. Similar checking is done for higher-level
SIMD-management headers, e.g. `gromacs/ewald/pme-simd.h`.
+
+
+The SIMD math library
+=====================
+
+In addition to the low-level SIMD instructions, \Gromacs comes with a fairly
+extensive SIMD math library in `gromacs/simd/simd_math.h` to support various
+mathematical functions. The functions are available both in single and
+double precision (overloaded on the usual math function names), and we also
+provide a special version of functions that use double precision arguments,
+but that only evaluate the result to single precision accuracy. This is
+useful when you don’t need highly accurate results, but you want to avoid
+the overhead of doing multiple single/double conversions, or if the hardware
+architecture only provides a double precision SIMD implementation.
+
+For a few functions such as the square root and exponential that are
+performance-critical, we provide additional tempate parameters where the
+default choice is to execute the normal function version, but it is also
+possible to choose an unsafe execution path that completely bypass all
+argument checking. Make absolutely sure your arguments always fulfil the
+restrictions listed in the documentation of such a function before using it,
+and it might even be a good idea to add a note before each call to an unsafe
+function justifying why that flavor is fine to use here.
in public headers because of implementation reasons.
*/
+/*!
+\libinternal
+\namespace gmx::compat
+\brief Compatibility aliases for standard library features.
+
+Provide consistent naming for standard library features that must be back-ported
+on some platforms.
+gmx::compat::some_feature may map to back-ported code or to a feature provided by
+the STL available on a given build platform, but by including the compatibility
+header and using the gmx::compat namespace, forward and backward compatible code
+is cleaner and clearer. In the future, when a feature is determined to be provided
+by the system on all supported platforms, references to gmx::compat::some_feature
+can be replaced, e.g. with std::some_feature, and gmx::compat::some_feature
+deprecated.
+
+Since compatibility headers are likely to be included by other
+headers, there is a risk of ambiguity if code in the gmx namespace refers to an
+unqualified name in the std namespace. To reduce ambiguity, symbol names from
+gmx::compat should not be imported into scopes that are shared between multiple
+translation units (e.g. via `using` statements in header files).
+
+\ingroup group_compatibility
+*/
+
+/*!
+\libinternal
+\defgroup group_compatibility C++ standard library compatibility helpers.
+\brief Provide uniform interface to selected C++ standard library features.
+
+For some features not available on all platforms supported by \Gromacs,
+provide back-ports or mappings to available standard library implementations
+as appropriate.
+*/
+
/*!
\file share/template/template.cpp
\brief Template code for writing analysis programs.
src/gromacs/gmxlib/nonbonded/nb_kernel_sparc64_hpc_ace_double/kernelutil_sparc64_hpc_ace_double.h: warning: should include "config.h"
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.cpp: warning: includes "config.h" unnecessarily
src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.cpp: warning: includes "config.h" unnecessarily
-src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.cpp: warning: includes "config.h" unnecessarily
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h: warning: should include "config.h"
src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h: warning: should include "nbnxn_simd.h"
-src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.cpp: warning: includes "config.h" unnecessarily
src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h: warning: should include "nbnxn_simd.h"
# Temporary while we change the SIMD implementation
src/gromacs/simd/tests/scalar.cpp: warning: includes "simd.h" unnecessarily
src/gromacs/simd/tests/scalar_math.cpp: warning: includes "simd.h" unnecessarily
src/gromacs/simd/tests/scalar_util.cpp: warning: includes "simd.h" unnecessarily
+src/gromacs/tables/cubicsplinetable.h: warning: includes "simd.h" unnecessarily
+src/gromacs/tables/quadraticsplinetable.h: warning: includes "simd.h" unnecessarily
# These are specific to Folding@Home, and easiest to suppress here
*: warning: includes non-local file as "corewrap.h"
density and not limited by the cutoff.
- Transparent fallback to a simple all-pairs search if the cutoff is too long
for the algorithm or grid searching is not otherwise supported.
+ - Support for either N-vs-M pair search with two sets of coordinates, or for
+ all pairs within a single set of coordinates.
- Support for computing all distances in the XY plane only (and still
grid-based).
- Convenience functions for finding the shortest distance or the nearest pair
falls back automatically to an all-pairs search. For correct operation, the
grid algorithm needs three cells in each dimension, but the code can fall
back to a non-gridded search for each dimension separately.
- - If the resulting grid has so few cells that the search would anyways
- consider all (or nearly all) cell pairs, the search falls back to a
- simple search.
- The initialization also pre-calculates the shifts required across the
periodic boundaries for triclinic cells, i.e., the fractional number of
cells that the grid origin is shifted when crossing the periodic boundary in
Y or Z directions.
- Finally, all the reference positions are mapped to the grid cells.
-There are a few heuristic numbers in the above logic: the average number of
-particles within a cell, and the cutover point from grid to an all-pairs
-search. These have not been particularly optimized for best performance.
+The average number of particles within a cell is somewhat heuristic in the
+above logic. This has not been particularly optimized for best performance.
When doing the search for test positions, each test position is considered
independently:
\if libapi
- \subpage page_wrapperbinary <br/>
Provides an overview of how the `gmx` wrapper binary is implemented.
+ - \subpage page_logging <br/>
+ Documentation for logging and status output (for now, within mdrun).
- \subpage page_simd <br/>
Documentation about the new SIMD module that makes it possible to write
highly accelerated CPU code that is still portable.
+ - \subpage page_mdmodules <br/>
+ Documentation for work-in-progress modularization of parts of mdrun, that
+ should make it easier to implement additional features as add-ons on top of
+ a common interface.
- \subpage page_refdata <br/>
Documentation for writing tests that use reference data generated by the
same test.
Quick and dirty installation
----------------------------
1. Get the latest version of your C and C++ compilers.
-2. Check that you have CMake version |GMX_CMAKE_MINIMUM_REQUIRED_VERSION| or later.
+2. Check that you have CMake version |CMAKE_MINIMUM_REQUIRED_VERSION| or later.
3. Get and unpack the latest version of the |Gromacs| tarball.
4. Make a separate build directory and change to it.
5. Run ``cmake`` with the path to the source as an argument
frequently provides the best performance.
You should strive to use the most recent version of your
-compiler. Minimum supported compiler versions are
+compiler. Since we require full C++11 support the minimum supported
+compiler versions are
-* GNU (gcc) 4.6
-* Intel (icc) 14
-* LLVM (clang) 3.4
+* GNU (gcc) 4.8.1
+* Intel (icc) 15.0
+* LLVM (clang) 3.3
* Microsoft (MSVC) 2015
Other compilers may work (Cray, Pathscale, older clang) but do
On Linux, both the Intel and clang compiler use the libstdc++ which
comes with gcc as the default C++ library. For |Gromacs|, we require
-the compiler to support libstc++ version 4.6.1 or higher. To select a
+the compiler to support libstc++ version 4.8.1 or higher. To select a
particular libstdc++ library, use:
* For Intel: ``-DGMX_STDLIB_CXX_FLAGS=-gcc-name=/path/to/gcc/binary``
the vendor's default or recommended compiler, and check for
specialized information below.
+For updated versions of gcc to add to your Linux OS, see
+
+* Ubuntu: `Ubuntu toolchain ppa page`_
+* RHEL/CentOS: `EPEL page`_ or the RedHat Developer Toolset
+
Compiling with parallelization options
--------------------------------------
GPU support
^^^^^^^^^^^
|Gromacs| has excellent support for NVIDIA GPUs supported via CUDA.
-NVIDIA's CUDA_ version |REQUIRED_CUDA_VERSION| software development kit is required,
-and the latest version is strongly encouraged. NVIDIA GPUs with at
+On Linux with gcc, NVIDIA's CUDA_ version |REQUIRED_CUDA_VERSION|
+software development kit is required, and the latest
+version is strongly encouraged. Using Intel or Microsoft compilers
+requires version 7.0 and 8.0, respectively. NVIDIA GPUs with at
least NVIDIA compute capability |REQUIRED_CUDA_COMPUTE_CAPABILITY| are
required, e.g. Fermi, Kepler, Maxwell or Pascal cards. You are strongly recommended to
get the latest CUDA version and driver supported by your hardware, but
-----
|Gromacs| builds with the CMake build system, requiring at least
-version |GMX_CMAKE_MINIMUM_REQUIRED_VERSION|. You can check whether
+version |CMAKE_MINIMUM_REQUIRED_VERSION|. You can check whether
CMake is installed, and what version it is, with ``cmake
--version``. If you need to install CMake, then first check whether
your platform's package management system provides a suitable version,
it works because we have tested it. We do test on Linux, Windows, and
Mac with a range of compilers and libraries for a range of our
configuration options. Every commit in our git source code repository
-is currently tested on x86 with gcc versions ranging from 4.6 through
-5.2, and versions 16 of the Intel compiler as well as Clang
-version 3.4 through 3.8. For this, we use a variety of GNU/Linux
+is currently tested on x86 with a number of gcc versions ranging from 4.8.1
+through 6.1, versions 16 of the Intel compiler, and Clang
+versions 3.4 through 3.8. For this, we use a variety of GNU/Linux
flavors and versions as well as recent versions of Windows. Under
Windows, we test both MSVC 2015 and version 16 of the Intel compiler.
For details, you can
are much faster than the kernels used in the group scheme for most
types of systems, particularly on newer hardware.
+Additionally, when the list buffer is determined automatically as
+described below, we also apply dynamic pair list pruning. The pair list
+can be constructed infrequently, but that can lead to a lot of pairs
+in the list that are outside the cut-off range for all or most of
+the life time of this pair list. Such pairs can be pruned out by
+applying a cluster-pair kernel that only determines which clusters
+are in range. Because of the way the non-bonded data is regularized
+in {\gromacs}, this kernel is an order of magnitude faster than
+the search and the interaction kernel. On the GPU this pruning is
+overlapped with the integration on the CPU, so it is free in most
+cases. Therefore we can prune every 4-10 integration steps with
+little overhead and significantly reduce the number of cluster pairs
+in the interaction kernel. This procedure is applied automatically,
+unless the user set the pair-list buffer size manually.
+
\ifthenelse{\equal{\gmxlite}{1}}{}{
\subsubsection{Energy drift and pair-list buffering}
For a canonical (NVT) ensemble, the average energy error caused by
of zero mean and variance $\sigma^2 = t^2 k_B T/m$. For the distance
between two particles, the variance changes to $\sigma^2 = \sigma_{12}^2 =
t^2 k_B T(1/m_1+1/m_2)$. Note that in practice particles usually
-interact with other particles over time $t$ and therefore the real
+interact with (bump into) other particles over time $t$ and therefore the real
displacement distribution is much narrower. Given a non-bonded
interaction cut-off distance of $r_c$ and a pair-list cut-off
$r_\ell=r_c+r_b$ for $r_b$ the Verlet buffer size, we can then
comprehensive comparisons have been carried out, and some caution must
be taking in interpreting the results.
+When using temperature and/or pressure coupling the total energy is
+no longer conserved. Instead there is a \normindex{conserved energy quantity}
+the formula of which will depend on the combination or temperature and
+pressure coupling algorithm used. For all coupling algorithms, except
+for Andersen temperature coupling and Parrinello-Rahman pressure coupling
+combined with shear stress, the conserved energy quantity is computed
+and stored in the energy and log file. Note that this quantity will not
+be conserved when external forces are applied to the system, such as
+pulling on group with a changing distance or an electric field.
+Furthermore, how well the energy is conserved depends on the accuracy
+of all algorithms involved in the simulation. Usually the algorithms that
+cause most drift are constraints and the pair-list buffer, depending
+on the parameters used.
+
\subsubsection{Berendsen temperature coupling\pawsindexquiet{Berendsen}{temperature coupling}\index{weak coupling}}
The Berendsen algorithm mimics weak coupling with first-order
kinetics to an external heat bath with given temperature $T_0$.
numbers which may crash the simulation. In normal use,
$\lambda$ will always be much closer to 1.0.
+The thermostat modifies the kinetic energy at each scaling step by:
+\beq
+\Delta E_k = (\lambda - 1)^2 E_k
+\eeq
+The sum of these changes over the run needs to subtracted from the total energy
+to obtain the conserved energy quantity.
+
\subsubsection{Velocity-rescaling temperature coupling\pawsindexquiet{velocity-rescaling}{temperature coupling}}
The velocity-rescaling thermostat~\cite{Bussi2007a} is essentially a Berendsen
thermostat (see above) with an additional stochastic term that ensures
This thermostat produces a correct canonical ensemble and still has
the advantage of the Berendsen thermostat: first order decay of
temperature deviations and no oscillations.
-When an $NVT$ ensemble is used, the conserved energy quantity
-is written to the energy and log file.
\subsubsection{\normindex{Andersen thermostat}}
One simple way to maintain a thermostatted ensemble is to take an
\end{array}\right).
\eeq
The velocities are neither scaled nor rotated.
+Since the equations of motion are modified by pressure coupling, the conserved
+energy quantity also needs to be modified. For first order pressure coupling,
+the work the barostat applies to the system every step needs to
+be subtracted from the total energy to obtain the conserved energy quantity:
+\beq
+- \sum_{i,j} (\mu_{ij} -\delta_{ij}) P_{ij} V =
+\sum_{i,j} 2(\mu_{ij} -\delta_{ij}) \Xi_{ij}
+\eeq
+where $\delta_{ij}$ is the Kronecker delta and ${\bf \Xi}$ is the virial.
+Note that the factor 2 originates from the factor $\frac{1}{2}$
+in the virial definition (\eqnref{Xi}).
+
In {\gromacs}, the Berendsen scaling can also be done isotropically,
which means that instead of $\ve{P}$ a diagonal matrix with elements of size
for the Nos{\'e}-Hoover coupling. In most cases you would combine the
Parrinello-Rahman barostat with the Nos{\'e}-Hoover
thermostat, but to keep it simple we only show the Parrinello-Rahman
-modification here:
-
+modification here. The modified Hamiltonian, which will be conserved, is:
+\beq
+E_\mathrm{pot} + E_\mathrm{kin} + \sum_i P_{ii} V +
+\sum_{i,j} \frac{1}{2} W_{ij} \left( \frac{\de b_{ij}}{\de t} \right)^2
+\eeq
+The equations of motion for the atoms, obtained from the Hamiltonian are:
\bea \frac {\de^2\ve{r}_i}{\de t^2} & = & \frac{\ve{F}_i}{m_i} -
\ve{M} \frac{\de \ve{r}_i}{\de t} , \\ \ve{M} & = & \ve{b}^{-1} \left[
\ve{b} \frac{\de \ve{b}'}{\de t} + \frac{\de \ve{b}}{\de t} \ve{b}'
%
% This file is part of the GROMACS molecular simulation package.
%
-% Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+% Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
% Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
% and including many others, as listed in the AUTHORS file in the
% top-level source directory and at http://www.gromacs.org.
\item {\em Restraints}: position restraints, angle restraints,
distance restraints, orientation restraints and dihedral restraints, all
based on fixed lists.
+%\ifthenelse{\equal{\gmxlite}{1}}{}{
+\item {\em Applied Forces}:
+externally applied forces, see \chref{special}.
+%}
\end{enumerate}
\section{Non-bonded interactions}
\subsubsection{Proper dihedrals: Fourier function}
\label{subsec:Fourierdihedral}
The OPLS potential function is given as the first three
-or four~\cite{Jorgensen2005a} cosine terms of a Fourier series.
+~\cite{Jorgensen1996} or four~\cite{Robertson2015a} cosine terms of a Fourier series.
In {\gromacs} the four term function is implemented:
\beq
V_{F} (\phi_{ijkl}) ~=~ \frac{1}{2} \left[C_1(1+\cos(\phi)) + C_2(
each time step in order to remain on the Born-Oppenheimer surface.
\subsection{Simple polarization}
-This is merely a harmonic potential with equilibrium distance 0.
+This is implemented as a harmonic potential with equilibrium distance
+0.
+The input given in the topology file is the polarizability $\alpha$ (in
+{\gromacs} units) as follows:
+\begin{verbatim}
+[ polarization ]
+; Atom i j type alpha
+1 2 1 0.001
+\end{verbatim}
+in this case the polarizability volume is 0.001 nm$^3$ (or 1
+{\AA$^3$}). In order to compute the harmonic force constant $k_{cs}$
+(where $cs$ stands for core-shell), the
+following is used~\cite{Maaren2001a}:
+\begin{equation}
+k_{cs} ~=~ \frac{q_s^2}{\alpha}
+\end{equation}
+where $q_s$ is the charge on the shell particle.
+
+\subsection{Anharmonic polarization}
+For the development of the Drude force field by Roux and McKerell~\cite{Lopes2013a}
+it was found
+that some particles can overpolarize and this was fixed by introducing
+a higher order term in the polarization energy:
+\begin{eqnarray}
+V_{pol} ~=& \frac{k_{cs}}{2} r_{cs}^2 & r_{cs} \le \delta \\
+ =& \frac{k_{cs}}{2} r_{cs}^2 + k_{hyp} (r_{cs}-\delta)^4 & r_{cs} > \delta
+\end{eqnarray}
+where $\delta$ is a user-defined constant that is set to 0.02 nm for
+anions in the Drude force field~\cite{HYu2010}. Since this original introduction it
+has also been used in other atom types~\cite{Lopes2013a}.
+\begin{verbatim}
+[ polarization ]
+;Atom i j type alpha (nm^3) delta khyp
+1 2 2 0.001786 0.02 16.736e8
+\end{verbatim}
+The above force constant $k_{hyp}$ corresponds to 4$\cdot$10$^8$
+kcal/mol/nm$^4$, hence the strange number.
\subsection{Water polarization}
A special potential for water that allows anisotropic polarization of
pages = "294--305",
}
+@ARTICLE{HYu2010,
+ author = {Yu, Haibo and Whitfield, Troy W and Harder, Edward and Lamoureux,
+ Guillaume and Vorobyov, Igor and Anisimov, Victor M and {MacKerell,
+ Jr.}, Alexander D and Roux, Benoit},
+ title = {{Simulating Monovalent and Divalent Ions in Aqueous Solution Using
+ a Drude Polarizable Force Field}},
+ journal = BTjctc,
+ year = {2010},
+ volume = {6},
+ pages = {774--786},
+}
+
@Article{Zettlmeissl83,
author = "Gerd Zettlmeissl and Rainer Rudolph and Rainer
Jaenicke",
pages = {1986--1994}
}
+@article{Caleman2008a,
+ author = {Caleman, C and van der Spoel, D},
+ title = {{Picosecond Melting of Ice by an Infrared Laser Pulse - A simulation
+ study}},
+ journal = {Angew. Chem., Int. Ed. Engl.},
+ year = {2008},
+ volume = {47},
+ pages = {1417--1420}
+}
+
@article{Wolf2010,
author = {Wolf, M.G. and Hoefling, M. and Aponte-Santamar\'{i}a, C. and Grubm\"{u}ller, H. and Groenhof, G.},
title = {{g\_membed}: Efficient insertion of a membrane protein into an equilibrated lipid bilayer with minimal perturbation},
volume = {31},
pages = {2169--2174}
}
+
+@Article{Lopes2013a,
+ author = {Lopes, Pedro E. M. and Huang, Jing and Shim, Jihyun and Luo, Yun and Li, Hui and Roux, Benoit and MacKerell, Alexander D., Jr.},
+ title = {Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator},
+ journal = {J. Chem. Theory Comput},
+ year = 2013,
+ volume = 9,
+ pages = {5430-5449}}
+
+@Article{Robertson2015a,
+ author = {Michael J. Robertson and Julian Tirado-Rives and William L. Jorgensen},
+ title = {Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force Field},
+ journal = BTjctc,
+ year = 2015,
+ volume = 11,
+ pages = {3499-3509}}
+
--- /dev/null
+%!PS-Adobe-3.0 EPSF-3.0
+%%BoundingBox: 5 8 769 591
+%%LanguageLevel: 2
+%%Creator: Grace-5.1.25
+%%CreationDate: Tue Jul 5 08:32:47 2016
+%%DocumentData: Clean8Bit
+%%Orientation: Portrait
+%%Title: field.xvg
+%%For: spoel
+%%DocumentNeededResources: (atend)
+%%EndComments
+%%BeginProlog
+/m {moveto} def
+/l {lineto} def
+/s {stroke} def
+/n {newpath} def
+/c {closepath} def
+/RL {rlineto} def
+/SLW {setlinewidth} def
+/GS {gsave} def
+/GR {grestore} def
+/SC {setcolor} def
+/SGRY {setgray} def
+/SRGB {setrgbcolor} def
+/SD {setdash} def
+/SLC {setlinecap} def
+/SLJ {setlinejoin} def
+/SCS {setcolorspace} def
+/FFSF {findfont setfont} def
+/CC {concat} def
+/PXL {n m 0 0 RL s} def
+/Color0 {1.0000 1.0000 1.0000} def
+/Color1 {0.0000 0.0000 0.0000} def
+/Color2 {1.0000 0.0000 0.0000} def
+/Color3 {0.0000 1.0000 0.0000} def
+/Color4 {0.0000 0.0000 1.0000} def
+/Color5 {1.0000 1.0000 0.0000} def
+/Color6 {0.7373 0.5608 0.5608} def
+/Color7 {0.8627 0.8627 0.8627} def
+/Color8 {0.5804 0.0000 0.8275} def
+/Color9 {0.0000 1.0000 1.0000} def
+/Color10 {1.0000 0.0000 1.0000} def
+/Color11 {1.0000 0.6471 0.0000} def
+/Color12 {0.4471 0.1294 0.7373} def
+/Color13 {0.4039 0.0275 0.2824} def
+/Color14 {0.2510 0.8784 0.8157} def
+/Color15 {0.0000 0.5451 0.0000} def
+/Color16 {0.7529 0.7529 0.7529} def
+/Color17 {0.5059 0.5059 0.5059} def
+/Color18 {0.2588 0.2588 0.2588} def
+/PTRN {
+ /pat_bits exch def
+ <<
+ /PaintType 2
+ /PatternType 1 /TilingType 1
+ /BBox[0 0 16 16]
+ /XStep 16 /YStep 16
+ /PaintProc {
+ pop
+ 16 16 true [-1 0 0 -1 16 16] pat_bits imagemask
+ }
+ >>
+ [0.0016 0 0 0.0016 0 0]
+ makepattern
+} def
+/Pattern0 {<0000000000000000000000000000000000000000000000000000000000000000> PTRN} bind def
+/Pattern1 {<ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff> PTRN} bind def
+/Pattern2 {<eeeeffffbbbbffffeeeeffffbbbbffffeeeeffffbbbbffffeeeeffffbbbbffff> PTRN} bind def
+/Pattern3 {<eeeebbbbeeeebbbbeeeebbbbeeeebbbbeeeebbbbeeeebbbbeeeebbbbeeeebbbb> PTRN} bind def
+/Pattern4 {<5555aaaa5555aaaa5555aaaa5555aaaa5555aaaa5555aaaa5555aaaa5555aaaa> PTRN} bind def
+/Pattern5 {<1111444411114444111144441111444411114444111144441111444411114444> PTRN} bind def
+/Pattern6 {<1111000044440000111100004444000011110000444400001111000044440000> PTRN} bind def
+/Pattern7 {<1010000000000000010100000000000010100000000000000101000000000000> PTRN} bind def
+/Pattern8 {<0000000000000000000000000000000000000000000000000000000000000000> PTRN} bind def
+/Pattern9 {<1e1e0f0f8787c3c3e1e1f0f078783c3c1e1e0f0f8787c3c3e1e1f0f078783c3c> PTRN} bind def
+/Pattern10 {<7878f0f0e1e1c3c387870f0f1e1e3c3c7878f0f0e1e1c3c387870f0f1e1e3c3c> PTRN} bind def
+/Pattern11 {<3333333333333333333333333333333333333333333333333333333333333333> PTRN} bind def
+/Pattern12 {<ffffffff00000000ffffffff00000000ffffffff00000000ffffffff00000000> PTRN} bind def
+/Pattern13 {<8181424224241818181824244242818181814242242418181818242442428181> PTRN} bind def
+/Pattern14 {<8080404020201010080804040202010180804040202010100808040402020101> PTRN} bind def
+/Pattern15 {<0101020204040808101020204040808001010202040408081010202040408080> PTRN} bind def
+/Pattern16 {<2222222222222222222222222222222222222222222222222222222222222222> PTRN} bind def
+/Pattern17 {<0000ffff000000000000ffff000000000000ffff000000000000ffff00000000> PTRN} bind def
+/Pattern18 {<2222ffff222222222222ffff222222222222ffff222222222222ffff22222222> PTRN} bind def
+/Pattern19 {<ffffffff33333333ffffffff33333333ffffffff33333333ffffffff33333333> PTRN} bind def
+/Pattern20 {<0f0f0f0f0f0f0f0ff0f0f0f0f0f0f0f00f0f0f0f0f0f0f0ff0f0f0f0f0f0f0f0> PTRN} bind def
+/Pattern21 {<ff00ff00ff00ff00ff00ff00ff00ff0000ff00ff00ff00ff00ff00ff00ff00ff> PTRN} bind def
+/Pattern22 {<8001800180018001800180018001ffffffff8001800180018001800180018001> PTRN} bind def
+/Pattern23 {<c003c003c003c003c003c003ffffffffffffffffc003c003c003c003c003c003> PTRN} bind def
+/Pattern24 {<040404040404ffff404040404040ffff040404040404ffff404040404040ffff> PTRN} bind def
+/Pattern25 {<180018001800180018001800ffffffff001800180018001800180018ffffffff> PTRN} bind def
+/Pattern26 {<1111b8b87c7c3a3a1111a3a3c7c78b8b1111b8b87c7c3a3a1111a3a3c7c78b8b> PTRN} bind def
+/Pattern27 {<101010102828c7c70101010182827c7c101010102828c7c70101010182827c7c> PTRN} bind def
+/Pattern28 {<1c1c121211112121c1c12121111112121c1c121211112121c1c1212111111212> PTRN} bind def
+/Pattern29 {<3e3e414180808080e3e31414080808083e3e414180808080e3e3141408080808> PTRN} bind def
+/Pattern30 {<4848888884848383848488884848383848488888848483838484888848483838> PTRN} bind def
+/Pattern31 {<03030404080808080c0c12122121c0c003030404080808080c0c12122121c0c0> PTRN} bind def
+/ellipsedict 8 dict def
+ellipsedict /mtrx matrix put
+/EARC {
+ ellipsedict begin
+ /endangle exch def
+ /startangle exch def
+ /yrad exch def
+ /xrad exch def
+ /y exch def
+ /x exch def
+ /savematrix mtrx currentmatrix def
+ x y translate
+ xrad yrad scale
+ 0 0 1 startangle endangle arc
+ savematrix setmatrix
+ end
+} def
+/TL {
+ /kcomp exch def
+ /linewidth exch def
+ /offset exch def
+ GS
+ 0 offset rmoveto
+ linewidth SLW
+ dup stringwidth exch kcomp add exch RL s
+ GR
+} def
+/KINIT
+{
+ /kvector exch def
+ /kid 0 def
+} def
+/KPROC
+{
+ pop pop
+ kvector kid get
+ 0 rmoveto
+ /kid 1 kid add def
+} def
+/DefEncoding [
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /space
+ /exclam
+ /quotedbl
+ /numbersign
+ /dollar
+ /percent
+ /ampersand
+ /quoteright
+ /parenleft
+ /parenright
+ /asterisk
+ /plus
+ /comma
+ /hyphen
+ /period
+ /slash
+ /zero
+ /one
+ /two
+ /three
+ /four
+ /five
+ /six
+ /seven
+ /eight
+ /nine
+ /colon
+ /semicolon
+ /less
+ /equal
+ /greater
+ /question
+ /at
+ /A
+ /B
+ /C
+ /D
+ /E
+ /F
+ /G
+ /H
+ /I
+ /J
+ /K
+ /L
+ /M
+ /N
+ /O
+ /P
+ /Q
+ /R
+ /S
+ /T
+ /U
+ /V
+ /W
+ /X
+ /Y
+ /Z
+ /bracketleft
+ /backslash
+ /bracketright
+ /asciicircum
+ /underscore
+ /grave
+ /a
+ /b
+ /c
+ /d
+ /e
+ /f
+ /g
+ /h
+ /i
+ /j
+ /k
+ /l
+ /m
+ /n
+ /o
+ /p
+ /q
+ /r
+ /s
+ /t
+ /u
+ /v
+ /w
+ /x
+ /y
+ /z
+ /braceleft
+ /bar
+ /braceright
+ /asciitilde
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /.notdef
+ /space
+ /exclamdown
+ /cent
+ /sterling
+ /currency
+ /yen
+ /brokenbar
+ /section
+ /dieresis
+ /copyright
+ /ordfeminine
+ /guillemotleft
+ /logicalnot
+ /hyphen
+ /registered
+ /macron
+ /degree
+ /plusminus
+ /twosuperior
+ /threesuperior
+ /acute
+ /mu
+ /paragraph
+ /periodcentered
+ /cedilla
+ /onesuperior
+ /ordmasculine
+ /guillemotright
+ /onequarter
+ /onehalf
+ /threequarters
+ /questiondown
+ /Agrave
+ /Aacute
+ /Acircumflex
+ /Atilde
+ /Adieresis
+ /Aring
+ /AE
+ /Ccedilla
+ /Egrave
+ /Eacute
+ /Ecircumflex
+ /Edieresis
+ /Igrave
+ /Iacute
+ /Icircumflex
+ /Idieresis
+ /Eth
+ /Ntilde
+ /Ograve
+ /Oacute
+ /Ocircumflex
+ /Otilde
+ /Odieresis
+ /multiply
+ /Oslash
+ /Ugrave
+ /Uacute
+ /Ucircumflex
+ /Udieresis
+ /Yacute
+ /Thorn
+ /germandbls
+ /agrave
+ /aacute
+ /acircumflex
+ /atilde
+ /adieresis
+ /aring
+ /ae
+ /ccedilla
+ /egrave
+ /eacute
+ /ecircumflex
+ /edieresis
+ /igrave
+ /iacute
+ /icircumflex
+ /idieresis
+ /eth
+ /ntilde
+ /ograve
+ /oacute
+ /ocircumflex
+ /otilde
+ /odieresis
+ /divide
+ /oslash
+ /ugrave
+ /uacute
+ /ucircumflex
+ /udieresis
+ /yacute
+ /thorn
+ /ydieresis
+] def
+%%EndProlog
+%%BeginSetup
+%%EndSetup
+612.00 612.00 scale
+n
+0.0000 0.0000 m
+0.0000 1.0000 l
+1.2941 1.0000 l
+1.2941 0.0000 l
+c
+[/DeviceRGB] SCS
+Color0 SC
+fill
+[/DeviceRGB] SCS
+Color1 SC
+[] 0 SD
+0.0015 SLW
+0 SLC
+0 SLJ
+n
+0.1000 0.5250 m
+0.1003 0.5250 l
+0.1006 0.5250 l
+0.1009 0.5250 l
+0.1011 0.5250 l
+0.1014 0.5250 l
+0.1017 0.5250 l
+0.1020 0.5250 l
+0.1023 0.5250 l
+0.1026 0.5250 l
+0.1029 0.5250 l
+0.1031 0.5250 l
+0.1034 0.5250 l
+0.1037 0.5250 l
+0.1040 0.5250 l
+0.1043 0.5250 l
+0.1046 0.5250 l
+0.1049 0.5250 l
+0.1052 0.5250 l
+0.1054 0.5250 l
+0.1057 0.5250 l
+0.1060 0.5250 l
+0.1063 0.5250 l
+0.1066 0.5250 l
+0.1069 0.5250 l
+0.1072 0.5250 l
+0.1074 0.5250 l
+0.1077 0.5250 l
+0.1080 0.5250 l
+0.1083 0.5250 l
+0.1086 0.5250 l
+0.1089 0.5250 l
+0.1092 0.5250 l
+0.1094 0.5250 l
+0.1097 0.5250 l
+0.1100 0.5250 l
+0.1103 0.5250 l
+0.1106 0.5250 l
+0.1109 0.5250 l
+0.1112 0.5250 l
+0.1114 0.5250 l
+0.1117 0.5250 l
+0.1120 0.5250 l
+0.1123 0.5250 l
+0.1126 0.5250 l
+0.1129 0.5250 l
+0.1132 0.5250 l
+0.1135 0.5250 l
+0.1137 0.5250 l
+0.1140 0.5250 l
+0.1143 0.5250 l
+0.1146 0.5250 l
+0.1149 0.5250 l
+0.1152 0.5250 l
+0.1155 0.5250 l
+0.1157 0.5250 l
+0.1160 0.5250 l
+0.1163 0.5250 l
+0.1166 0.5250 l
+0.1169 0.5250 l
+0.1172 0.5250 l
+0.1175 0.5250 l
+0.1177 0.5250 l
+0.1180 0.5250 l
+0.1183 0.5250 l
+0.1186 0.5250 l
+0.1189 0.5250 l
+0.1192 0.5250 l
+0.1195 0.5250 l
+0.1197 0.5250 l
+0.1200 0.5250 l
+0.1203 0.5250 l
+0.1206 0.5250 l
+0.1209 0.5250 l
+0.1212 0.5250 l
+0.1215 0.5250 l
+0.1218 0.5250 l
+0.1220 0.5250 l
+0.1223 0.5250 l
+0.1226 0.5250 l
+0.1229 0.5250 l
+0.1232 0.5250 l
+0.1235 0.5250 l
+0.1238 0.5250 l
+0.1240 0.5250 l
+0.1243 0.5250 l
+0.1246 0.5250 l
+0.1249 0.5250 l
+0.1252 0.5250 l
+0.1255 0.5250 l
+0.1258 0.5250 l
+0.1260 0.5250 l
+0.1263 0.5250 l
+0.1266 0.5250 l
+0.1269 0.5250 l
+0.1272 0.5250 l
+0.1275 0.5250 l
+0.1278 0.5250 l
+0.1281 0.5250 l
+0.1283 0.5250 l
+0.1286 0.5250 l
+0.1289 0.5250 l
+0.1292 0.5250 l
+0.1295 0.5250 l
+0.1298 0.5250 l
+0.1301 0.5250 l
+0.1303 0.5250 l
+0.1306 0.5250 l
+0.1309 0.5250 l
+0.1312 0.5250 l
+0.1315 0.5250 l
+0.1318 0.5250 l
+0.1321 0.5250 l
+0.1323 0.5250 l
+0.1326 0.5250 l
+0.1329 0.5250 l
+0.1332 0.5250 l
+0.1335 0.5250 l
+0.1338 0.5250 l
+0.1341 0.5250 l
+0.1343 0.5250 l
+0.1346 0.5250 l
+0.1349 0.5250 l
+0.1352 0.5250 l
+0.1355 0.5250 l
+0.1358 0.5250 l
+0.1361 0.5250 l
+0.1364 0.5250 l
+0.1366 0.5250 l
+0.1369 0.5250 l
+0.1372 0.5250 l
+0.1375 0.5250 l
+0.1378 0.5250 l
+0.1381 0.5250 l
+0.1384 0.5250 l
+0.1386 0.5250 l
+0.1389 0.5250 l
+0.1392 0.5250 l
+0.1395 0.5250 l
+0.1398 0.5250 l
+0.1401 0.5250 l
+0.1404 0.5250 l
+0.1406 0.5250 l
+0.1409 0.5250 l
+0.1412 0.5250 l
+0.1415 0.5250 l
+0.1418 0.5250 l
+0.1421 0.5250 l
+0.1424 0.5250 l
+0.1426 0.5250 l
+0.1429 0.5250 l
+0.1432 0.5250 l
+0.1435 0.5250 l
+0.1438 0.5250 l
+0.1441 0.5250 l
+0.1444 0.5250 l
+0.1447 0.5250 l
+0.1449 0.5250 l
+0.1452 0.5250 l
+0.1455 0.5250 l
+0.1458 0.5250 l
+0.1461 0.5250 l
+0.1464 0.5250 l
+0.1467 0.5250 l
+0.1469 0.5250 l
+0.1472 0.5250 l
+0.1475 0.5250 l
+0.1478 0.5250 l
+0.1481 0.5250 l
+0.1484 0.5250 l
+0.1487 0.5250 l
+0.1489 0.5250 l
+0.1492 0.5250 l
+0.1495 0.5250 l
+0.1498 0.5250 l
+0.1501 0.5250 l
+0.1504 0.5250 l
+0.1507 0.5250 l
+0.1509 0.5250 l
+0.1512 0.5250 l
+0.1515 0.5250 l
+0.1518 0.5250 l
+0.1521 0.5250 l
+0.1524 0.5250 l
+0.1527 0.5250 l
+0.1530 0.5250 l
+0.1532 0.5250 l
+0.1535 0.5250 l
+0.1538 0.5250 l
+0.1541 0.5250 l
+0.1544 0.5250 l
+0.1547 0.5250 l
+0.1550 0.5250 l
+0.1552 0.5250 l
+0.1555 0.5250 l
+0.1558 0.5250 l
+0.1561 0.5250 l
+0.1564 0.5250 l
+0.1567 0.5250 l
+0.1570 0.5250 l
+0.1572 0.5250 l
+0.1575 0.5250 l
+0.1578 0.5250 l
+0.1581 0.5250 l
+0.1584 0.5250 l
+0.1587 0.5250 l
+0.1590 0.5250 l
+0.1592 0.5250 l
+0.1595 0.5250 l
+0.1598 0.5250 l
+0.1601 0.5250 l
+0.1604 0.5250 l
+0.1607 0.5250 l
+0.1610 0.5250 l
+0.1613 0.5250 l
+0.1615 0.5250 l
+0.1618 0.5250 l
+0.1621 0.5250 l
+0.1624 0.5250 l
+0.1627 0.5250 l
+0.1630 0.5250 l
+0.1633 0.5250 l
+0.1635 0.5250 l
+0.1638 0.5250 l
+0.1641 0.5250 l
+0.1644 0.5250 l
+0.1647 0.5250 l
+0.1650 0.5250 l
+0.1653 0.5250 l
+0.1655 0.5250 l
+0.1658 0.5250 l
+0.1661 0.5250 l
+0.1664 0.5250 l
+0.1667 0.5250 l
+0.1670 0.5250 l
+0.1673 0.5250 l
+0.1675 0.5250 l
+0.1678 0.5250 l
+0.1681 0.5250 l
+0.1684 0.5250 l
+0.1687 0.5250 l
+0.1690 0.5250 l
+0.1693 0.5250 l
+0.1696 0.5250 l
+0.1698 0.5250 l
+0.1701 0.5250 l
+0.1704 0.5250 l
+0.1707 0.5250 l
+0.1710 0.5250 l
+0.1713 0.5250 l
+0.1716 0.5250 l
+0.1718 0.5250 l
+0.1721 0.5250 l
+0.1724 0.5250 l
+0.1727 0.5250 l
+0.1730 0.5250 l
+0.1733 0.5250 l
+0.1736 0.5250 l
+0.1738 0.5250 l
+0.1741 0.5250 l
+0.1744 0.5250 l
+0.1747 0.5250 l
+0.1750 0.5250 l
+0.1753 0.5250 l
+0.1756 0.5250 l
+0.1758 0.5250 l
+0.1761 0.5250 l
+0.1764 0.5250 l
+0.1767 0.5250 l
+0.1770 0.5250 l
+0.1773 0.5250 l
+0.1776 0.5250 l
+0.1779 0.5250 l
+0.1781 0.5250 l
+0.1784 0.5250 l
+0.1787 0.5250 l
+0.1790 0.5250 l
+0.1793 0.5250 l
+0.1796 0.5250 l
+0.1799 0.5250 l
+0.1801 0.5250 l
+0.1804 0.5250 l
+0.1807 0.5250 l
+0.1810 0.5250 l
+0.1813 0.5250 l
+0.1816 0.5250 l
+0.1819 0.5250 l
+0.1821 0.5250 l
+0.1824 0.5250 l
+0.1827 0.5250 l
+0.1830 0.5250 l
+0.1833 0.5250 l
+0.1836 0.5250 l
+0.1839 0.5250 l
+0.1842 0.5250 l
+0.1844 0.5250 l
+0.1847 0.5250 l
+0.1850 0.5250 l
+0.1853 0.5250 l
+0.1856 0.5250 l
+0.1859 0.5250 l
+0.1862 0.5250 l
+0.1864 0.5250 l
+0.1867 0.5250 l
+0.1870 0.5250 l
+0.1873 0.5250 l
+0.1876 0.5250 l
+0.1879 0.5250 l
+0.1882 0.5250 l
+0.1884 0.5250 l
+0.1887 0.5250 l
+0.1890 0.5250 l
+0.1893 0.5250 l
+0.1896 0.5250 l
+0.1899 0.5250 l
+0.1902 0.5250 l
+0.1904 0.5250 l
+0.1907 0.5251 l
+0.1910 0.5251 l
+0.1913 0.5251 l
+0.1916 0.5251 l
+0.1919 0.5251 l
+0.1922 0.5251 l
+0.1925 0.5251 l
+0.1927 0.5251 l
+0.1930 0.5251 l
+0.1933 0.5251 l
+0.1936 0.5251 l
+0.1939 0.5251 l
+0.1942 0.5251 l
+0.1945 0.5251 l
+0.1947 0.5251 l
+0.1950 0.5251 l
+0.1953 0.5251 l
+0.1956 0.5251 l
+0.1959 0.5251 l
+0.1962 0.5250 l
+0.1965 0.5250 l
+0.1967 0.5250 l
+0.1970 0.5250 l
+0.1973 0.5250 l
+0.1976 0.5250 l
+0.1979 0.5250 l
+0.1982 0.5250 l
+0.1985 0.5250 l
+0.1987 0.5250 l
+0.1990 0.5250 l
+0.1993 0.5250 l
+0.1996 0.5250 l
+0.1999 0.5250 l
+0.2002 0.5250 l
+0.2005 0.5250 l
+0.2008 0.5250 l
+0.2010 0.5250 l
+0.2013 0.5249 l
+0.2016 0.5249 l
+0.2019 0.5249 l
+0.2022 0.5249 l
+0.2025 0.5249 l
+0.2028 0.5249 l
+0.2030 0.5249 l
+0.2033 0.5249 l
+0.2036 0.5249 l
+0.2039 0.5249 l
+0.2042 0.5249 l
+0.2045 0.5249 l
+0.2048 0.5249 l
+0.2050 0.5249 l
+0.2053 0.5249 l
+0.2056 0.5249 l
+0.2059 0.5249 l
+0.2062 0.5249 l
+0.2065 0.5249 l
+0.2068 0.5249 l
+0.2070 0.5249 l
+0.2073 0.5249 l
+0.2076 0.5249 l
+0.2079 0.5249 l
+0.2082 0.5249 l
+0.2085 0.5249 l
+0.2088 0.5249 l
+0.2091 0.5249 l
+0.2093 0.5250 l
+0.2096 0.5250 l
+0.2099 0.5250 l
+0.2102 0.5250 l
+0.2105 0.5250 l
+0.2108 0.5250 l
+0.2111 0.5250 l
+0.2113 0.5250 l
+0.2116 0.5250 l
+0.2119 0.5250 l
+0.2122 0.5250 l
+0.2125 0.5251 l
+0.2128 0.5251 l
+0.2131 0.5251 l
+0.2133 0.5251 l
+0.2136 0.5251 l
+0.2139 0.5251 l
+0.2142 0.5251 l
+0.2145 0.5251 l
+0.2148 0.5251 l
+0.2151 0.5251 l
+0.2153 0.5251 l
+0.2156 0.5251 l
+0.2159 0.5251 l
+0.2162 0.5251 l
+0.2165 0.5252 l
+0.2168 0.5252 l
+0.2171 0.5252 l
+0.2174 0.5252 l
+0.2176 0.5252 l
+0.2179 0.5252 l
+0.2182 0.5252 l
+0.2185 0.5251 l
+0.2188 0.5251 l
+0.2191 0.5251 l
+0.2194 0.5251 l
+0.2196 0.5251 l
+0.2199 0.5251 l
+0.2202 0.5251 l
+0.2205 0.5251 l
+0.2208 0.5251 l
+0.2211 0.5251 l
+0.2214 0.5251 l
+0.2216 0.5251 l
+0.2219 0.5250 l
+0.2222 0.5250 l
+0.2225 0.5250 l
+0.2228 0.5250 l
+0.2231 0.5250 l
+0.2234 0.5250 l
+0.2236 0.5250 l
+0.2239 0.5249 l
+0.2242 0.5249 l
+0.2245 0.5249 l
+0.2248 0.5249 l
+0.2251 0.5249 l
+0.2254 0.5249 l
+0.2257 0.5249 l
+0.2259 0.5248 l
+0.2262 0.5248 l
+0.2265 0.5248 l
+0.2268 0.5248 l
+0.2271 0.5248 l
+0.2274 0.5248 l
+0.2277 0.5248 l
+0.2279 0.5248 l
+0.2282 0.5248 l
+0.2285 0.5248 l
+0.2288 0.5248 l
+0.2291 0.5248 l
+0.2294 0.5248 l
+0.2297 0.5248 l
+0.2299 0.5248 l
+0.2302 0.5248 l
+0.2305 0.5248 l
+0.2308 0.5248 l
+0.2311 0.5248 l
+0.2314 0.5248 l
+0.2317 0.5248 l
+0.2320 0.5248 l
+0.2322 0.5248 l
+0.2325 0.5248 l
+0.2328 0.5249 l
+0.2331 0.5249 l
+0.2334 0.5249 l
+0.2337 0.5249 l
+0.2340 0.5249 l
+0.2342 0.5250 l
+0.2345 0.5250 l
+0.2348 0.5250 l
+0.2351 0.5250 l
+0.2354 0.5250 l
+0.2357 0.5251 l
+0.2360 0.5251 l
+0.2362 0.5251 l
+0.2365 0.5251 l
+0.2368 0.5252 l
+0.2371 0.5252 l
+0.2374 0.5252 l
+0.2377 0.5252 l
+0.2380 0.5252 l
+0.2382 0.5252 l
+0.2385 0.5253 l
+0.2388 0.5253 l
+0.2391 0.5253 l
+0.2394 0.5253 l
+0.2397 0.5253 l
+0.2400 0.5253 l
+0.2403 0.5253 l
+0.2405 0.5253 l
+0.2408 0.5253 l
+0.2411 0.5254 l
+0.2414 0.5254 l
+0.2417 0.5253 l
+0.2420 0.5253 l
+0.2423 0.5253 l
+0.2425 0.5253 l
+0.2428 0.5253 l
+0.2431 0.5253 l
+0.2434 0.5253 l
+0.2437 0.5253 l
+0.2440 0.5253 l
+0.2443 0.5252 l
+0.2445 0.5252 l
+0.2448 0.5252 l
+0.2451 0.5252 l
+0.2454 0.5251 l
+0.2457 0.5251 l
+0.2460 0.5251 l
+0.2463 0.5251 l
+0.2465 0.5250 l
+0.2468 0.5250 l
+0.2471 0.5250 l
+0.2474 0.5249 l
+0.2477 0.5249 l
+0.2480 0.5249 l
+0.2483 0.5248 l
+0.2486 0.5248 l
+0.2488 0.5248 l
+0.2491 0.5247 l
+0.2494 0.5247 l
+0.2497 0.5247 l
+0.2500 0.5247 l
+0.2503 0.5246 l
+0.2506 0.5246 l
+0.2508 0.5246 l
+0.2511 0.5246 l
+0.2514 0.5245 l
+0.2517 0.5245 l
+0.2520 0.5245 l
+0.2523 0.5245 l
+0.2526 0.5245 l
+0.2528 0.5245 l
+0.2531 0.5245 l
+0.2534 0.5245 l
+0.2537 0.5245 l
+0.2540 0.5245 l
+0.2543 0.5245 l
+0.2546 0.5245 l
+0.2548 0.5245 l
+0.2551 0.5245 l
+0.2554 0.5246 l
+0.2557 0.5246 l
+0.2560 0.5246 l
+0.2563 0.5246 l
+0.2566 0.5247 l
+0.2569 0.5247 l
+0.2571 0.5247 l
+0.2574 0.5248 l
+0.2577 0.5248 l
+0.2580 0.5249 l
+0.2583 0.5249 l
+0.2586 0.5250 l
+0.2589 0.5250 l
+0.2591 0.5251 l
+0.2594 0.5251 l
+0.2597 0.5251 l
+0.2600 0.5252 l
+0.2603 0.5252 l
+0.2606 0.5253 l
+0.2609 0.5253 l
+0.2611 0.5254 l
+0.2614 0.5254 l
+0.2617 0.5255 l
+0.2620 0.5255 l
+0.2623 0.5255 l
+0.2626 0.5256 l
+0.2629 0.5256 l
+0.2631 0.5256 l
+0.2634 0.5257 l
+0.2637 0.5257 l
+0.2640 0.5257 l
+0.2643 0.5257 l
+0.2646 0.5257 l
+0.2649 0.5258 l
+0.2652 0.5258 l
+0.2654 0.5258 l
+0.2657 0.5258 l
+0.2660 0.5257 l
+0.2663 0.5257 l
+0.2666 0.5257 l
+0.2669 0.5257 l
+0.2672 0.5257 l
+0.2674 0.5256 l
+0.2677 0.5256 l
+0.2680 0.5256 l
+0.2683 0.5255 l
+0.2686 0.5255 l
+0.2689 0.5254 l
+0.2692 0.5254 l
+0.2694 0.5253 l
+0.2697 0.5252 l
+0.2700 0.5252 l
+0.2703 0.5251 l
+0.2706 0.5251 l
+0.2709 0.5250 l
+0.2712 0.5249 l
+0.2714 0.5248 l
+0.2717 0.5248 l
+0.2720 0.5247 l
+0.2723 0.5246 l
+0.2726 0.5246 l
+0.2729 0.5245 l
+0.2732 0.5244 l
+0.2735 0.5244 l
+0.2737 0.5243 l
+0.2740 0.5243 l
+0.2743 0.5242 l
+0.2746 0.5242 l
+0.2749 0.5241 l
+0.2752 0.5241 l
+0.2755 0.5240 l
+0.2757 0.5240 l
+0.2760 0.5240 l
+0.2763 0.5239 l
+0.2766 0.5239 l
+0.2769 0.5239 l
+0.2772 0.5239 l
+0.2775 0.5239 l
+0.2777 0.5239 l
+0.2780 0.5239 l
+0.2783 0.5240 l
+0.2786 0.5240 l
+0.2789 0.5240 l
+0.2792 0.5241 l
+0.2795 0.5241 l
+0.2797 0.5242 l
+0.2800 0.5242 l
+0.2803 0.5243 l
+0.2806 0.5243 l
+0.2809 0.5244 l
+0.2812 0.5245 l
+0.2815 0.5246 l
+0.2818 0.5247 l
+0.2820 0.5248 l
+0.2823 0.5248 l
+0.2826 0.5249 l
+0.2829 0.5250 l
+0.2832 0.5251 l
+0.2835 0.5252 l
+0.2838 0.5253 l
+0.2840 0.5254 l
+0.2843 0.5255 l
+0.2846 0.5256 l
+0.2849 0.5257 l
+0.2852 0.5258 l
+0.2855 0.5259 l
+0.2858 0.5260 l
+0.2860 0.5261 l
+0.2863 0.5262 l
+0.2866 0.5262 l
+0.2869 0.5263 l
+0.2872 0.5263 l
+0.2875 0.5264 l
+0.2878 0.5264 l
+0.2881 0.5265 l
+0.2883 0.5265 l
+0.2886 0.5265 l
+0.2889 0.5266 l
+0.2892 0.5266 l
+0.2895 0.5266 l
+0.2898 0.5265 l
+0.2901 0.5265 l
+0.2903 0.5265 l
+0.2906 0.5264 l
+0.2909 0.5264 l
+0.2912 0.5263 l
+0.2915 0.5263 l
+0.2918 0.5262 l
+0.2921 0.5261 l
+0.2923 0.5260 l
+0.2926 0.5259 l
+0.2929 0.5258 l
+0.2932 0.5257 l
+0.2935 0.5256 l
+0.2938 0.5255 l
+0.2941 0.5253 l
+0.2943 0.5252 l
+0.2946 0.5251 l
+0.2949 0.5249 l
+0.2952 0.5248 l
+0.2955 0.5247 l
+0.2958 0.5245 l
+0.2961 0.5244 l
+0.2964 0.5242 l
+0.2966 0.5241 l
+0.2969 0.5240 l
+0.2972 0.5238 l
+0.2975 0.5237 l
+0.2978 0.5236 l
+0.2981 0.5235 l
+0.2984 0.5234 l
+0.2986 0.5233 l
+0.2989 0.5232 l
+0.2992 0.5231 l
+0.2995 0.5230 l
+0.2998 0.5229 l
+0.3001 0.5229 l
+0.3004 0.5229 l
+0.3006 0.5228 l
+0.3009 0.5228 l
+0.3012 0.5228 l
+0.3015 0.5228 l
+0.3018 0.5228 l
+0.3021 0.5229 l
+0.3024 0.5229 l
+0.3026 0.5230 l
+0.3029 0.5230 l
+0.3032 0.5231 l
+0.3035 0.5232 l
+0.3038 0.5233 l
+0.3041 0.5234 l
+0.3044 0.5236 l
+0.3047 0.5237 l
+0.3049 0.5239 l
+0.3052 0.5240 l
+0.3055 0.5242 l
+0.3058 0.5244 l
+0.3061 0.5245 l
+0.3064 0.5247 l
+0.3067 0.5249 l
+0.3069 0.5251 l
+0.3072 0.5253 l
+0.3075 0.5255 l
+0.3078 0.5257 l
+0.3081 0.5259 l
+0.3084 0.5261 l
+0.3087 0.5263 l
+0.3089 0.5265 l
+0.3092 0.5267 l
+0.3095 0.5268 l
+0.3098 0.5270 l
+0.3101 0.5272 l
+0.3104 0.5273 l
+0.3107 0.5275 l
+0.3109 0.5276 l
+0.3112 0.5277 l
+0.3115 0.5278 l
+0.3118 0.5279 l
+0.3121 0.5280 l
+0.3124 0.5280 l
+0.3127 0.5280 l
+0.3130 0.5281 l
+0.3132 0.5281 l
+0.3135 0.5281 l
+0.3138 0.5280 l
+0.3141 0.5280 l
+0.3144 0.5279 l
+0.3147 0.5278 l
+0.3150 0.5277 l
+0.3152 0.5276 l
+0.3155 0.5275 l
+0.3158 0.5273 l
+0.3161 0.5272 l
+0.3164 0.5270 l
+0.3167 0.5268 l
+0.3170 0.5266 l
+0.3172 0.5263 l
+0.3175 0.5261 l
+0.3178 0.5259 l
+0.3181 0.5256 l
+0.3184 0.5253 l
+0.3187 0.5251 l
+0.3190 0.5248 l
+0.3192 0.5245 l
+0.3195 0.5243 l
+0.3198 0.5240 l
+0.3201 0.5237 l
+0.3204 0.5234 l
+0.3207 0.5232 l
+0.3210 0.5229 l
+0.3213 0.5227 l
+0.3215 0.5224 l
+0.3218 0.5222 l
+0.3221 0.5220 l
+0.3224 0.5218 l
+0.3227 0.5216 l
+0.3230 0.5214 l
+0.3233 0.5213 l
+0.3235 0.5211 l
+0.3238 0.5210 l
+0.3241 0.5209 l
+0.3244 0.5208 l
+0.3247 0.5208 l
+0.3250 0.5208 l
+0.3253 0.5208 l
+0.3255 0.5208 l
+0.3258 0.5208 l
+0.3261 0.5209 l
+0.3264 0.5210 l
+0.3267 0.5211 l
+0.3270 0.5213 l
+0.3273 0.5214 l
+0.3275 0.5216 l
+0.3278 0.5218 l
+0.3281 0.5221 l
+0.3284 0.5223 l
+0.3287 0.5226 l
+0.3290 0.5229 l
+0.3293 0.5232 l
+0.3296 0.5235 l
+0.3298 0.5239 l
+0.3301 0.5242 l
+0.3304 0.5246 l
+0.3307 0.5249 l
+0.3310 0.5253 l
+0.3313 0.5257 l
+0.3316 0.5261 l
+0.3318 0.5264 l
+0.3321 0.5268 l
+0.3324 0.5272 l
+0.3327 0.5275 l
+0.3330 0.5279 l
+0.3333 0.5282 l
+0.3336 0.5286 l
+0.3338 0.5289 l
+0.3341 0.5292 l
+0.3344 0.5295 l
+0.3347 0.5297 l
+0.3350 0.5299 l
+0.3353 0.5302 l
+0.3356 0.5303 l
+0.3359 0.5305 l
+0.3361 0.5306 l
+0.3364 0.5307 l
+0.3367 0.5308 l
+0.3370 0.5308 l
+0.3373 0.5308 l
+0.3376 0.5308 l
+0.3379 0.5307 l
+0.3381 0.5306 l
+0.3384 0.5305 l
+0.3387 0.5303 l
+0.3390 0.5301 l
+0.3393 0.5298 l
+0.3396 0.5296 l
+0.3399 0.5293 l
+0.3401 0.5290 l
+0.3404 0.5286 l
+0.3407 0.5282 l
+0.3410 0.5278 l
+0.3413 0.5274 l
+0.3416 0.5270 l
+0.3419 0.5265 l
+0.3421 0.5260 l
+0.3424 0.5255 l
+0.3427 0.5250 l
+0.3430 0.5245 l
+0.3433 0.5240 l
+0.3436 0.5235 l
+0.3439 0.5230 l
+0.3442 0.5225 l
+0.3444 0.5220 l
+0.3447 0.5215 l
+0.3450 0.5210 l
+0.3453 0.5206 l
+0.3456 0.5201 l
+0.3459 0.5197 l
+0.3462 0.5193 l
+0.3464 0.5189 l
+0.3467 0.5186 l
+0.3470 0.5183 l
+0.3473 0.5180 l
+0.3476 0.5178 l
+0.3479 0.5176 l
+0.3482 0.5174 l
+0.3484 0.5173 l
+0.3487 0.5172 l
+0.3490 0.5172 l
+0.3493 0.5172 l
+0.3496 0.5172 l
+0.3499 0.5173 l
+0.3502 0.5175 l
+0.3504 0.5177 l
+0.3507 0.5179 l
+0.3510 0.5182 l
+0.3513 0.5185 l
+0.3516 0.5189 l
+0.3519 0.5193 l
+0.3522 0.5197 l
+0.3525 0.5202 l
+0.3527 0.5207 l
+0.3530 0.5212 l
+0.3533 0.5218 l
+0.3536 0.5224 l
+0.3539 0.5230 l
+0.3542 0.5237 l
+0.3545 0.5243 l
+0.3547 0.5250 l
+0.3550 0.5257 l
+0.3553 0.5264 l
+0.3556 0.5271 l
+0.3559 0.5278 l
+0.3562 0.5284 l
+0.3565 0.5291 l
+0.3567 0.5298 l
+0.3570 0.5304 l
+0.3573 0.5310 l
+0.3576 0.5316 l
+0.3579 0.5322 l
+0.3582 0.5327 l
+0.3585 0.5332 l
+0.3587 0.5336 l
+0.3590 0.5341 l
+0.3593 0.5344 l
+0.3596 0.5347 l
+0.3599 0.5350 l
+0.3602 0.5352 l
+0.3605 0.5353 l
+0.3608 0.5354 l
+0.3610 0.5355 l
+0.3613 0.5355 l
+0.3616 0.5354 l
+0.3619 0.5352 l
+0.3622 0.5350 l
+0.3625 0.5348 l
+0.3628 0.5344 l
+0.3630 0.5341 l
+0.3633 0.5336 l
+0.3636 0.5331 l
+0.3639 0.5326 l
+0.3642 0.5320 l
+0.3645 0.5313 l
+0.3648 0.5306 l
+0.3650 0.5299 l
+0.3653 0.5291 l
+0.3656 0.5283 l
+0.3659 0.5275 l
+0.3662 0.5266 l
+0.3665 0.5258 l
+0.3668 0.5249 l
+0.3670 0.5240 l
+0.3673 0.5230 l
+0.3676 0.5221 l
+0.3679 0.5212 l
+0.3682 0.5203 l
+0.3685 0.5194 l
+0.3688 0.5186 l
+0.3691 0.5177 l
+0.3693 0.5169 l
+0.3696 0.5161 l
+0.3699 0.5154 l
+0.3702 0.5147 l
+0.3705 0.5141 l
+0.3708 0.5135 l
+0.3711 0.5129 l
+0.3713 0.5125 l
+0.3716 0.5121 l
+0.3719 0.5117 l
+0.3722 0.5115 l
+0.3725 0.5113 l
+0.3728 0.5112 l
+0.3731 0.5111 l
+0.3733 0.5112 l
+0.3736 0.5113 l
+0.3739 0.5115 l
+0.3742 0.5118 l
+0.3745 0.5121 l
+0.3748 0.5126 l
+0.3751 0.5131 l
+0.3753 0.5137 l
+0.3756 0.5144 l
+0.3759 0.5151 l
+0.3762 0.5159 l
+0.3765 0.5167 l
+0.3768 0.5177 l
+0.3771 0.5186 l
+0.3774 0.5197 l
+0.3776 0.5207 l
+0.3779 0.5218 l
+0.3782 0.5230 l
+0.3785 0.5241 l
+0.3788 0.5253 l
+0.3791 0.5265 l
+0.3794 0.5277 l
+0.3796 0.5289 l
+0.3799 0.5301 l
+0.3802 0.5313 l
+0.3805 0.5324 l
+0.3808 0.5336 l
+0.3811 0.5347 l
+0.3814 0.5357 l
+0.3816 0.5367 l
+0.3819 0.5377 l
+0.3822 0.5386 l
+0.3825 0.5394 l
+0.3828 0.5402 l
+0.3831 0.5409 l
+0.3834 0.5415 l
+0.3836 0.5420 l
+0.3839 0.5424 l
+0.3842 0.5427 l
+0.3845 0.5430 l
+0.3848 0.5431 l
+0.3851 0.5431 l
+0.3854 0.5431 l
+0.3857 0.5429 l
+0.3859 0.5426 l
+0.3862 0.5422 l
+0.3865 0.5417 l
+0.3868 0.5411 l
+0.3871 0.5404 l
+0.3874 0.5397 l
+0.3877 0.5388 l
+0.3879 0.5378 l
+0.3882 0.5368 l
+0.3885 0.5356 l
+0.3888 0.5344 l
+0.3891 0.5331 l
+0.3894 0.5318 l
+0.3897 0.5304 l
+0.3899 0.5290 l
+0.3902 0.5275 l
+0.3905 0.5260 l
+0.3908 0.5244 l
+0.3911 0.5229 l
+0.3914 0.5213 l
+0.3917 0.5198 l
+0.3920 0.5182 l
+0.3922 0.5167 l
+0.3925 0.5152 l
+0.3928 0.5137 l
+0.3931 0.5123 l
+0.3934 0.5109 l
+0.3937 0.5096 l
+0.3940 0.5084 l
+0.3942 0.5072 l
+0.3945 0.5062 l
+0.3948 0.5052 l
+0.3951 0.5044 l
+0.3954 0.5036 l
+0.3957 0.5029 l
+0.3960 0.5024 l
+0.3962 0.5020 l
+0.3965 0.5017 l
+0.3968 0.5016 l
+0.3971 0.5016 l
+0.3974 0.5017 l
+0.3977 0.5019 l
+0.3980 0.5023 l
+0.3982 0.5028 l
+0.3985 0.5035 l
+0.3988 0.5043 l
+0.3991 0.5052 l
+0.3994 0.5062 l
+0.3997 0.5073 l
+0.4000 0.5086 l
+0.4003 0.5100 l
+0.4005 0.5115 l
+0.4008 0.5130 l
+0.4011 0.5147 l
+0.4014 0.5164 l
+0.4017 0.5182 l
+0.4020 0.5201 l
+0.4023 0.5220 l
+0.4025 0.5240 l
+0.4028 0.5260 l
+0.4031 0.5280 l
+0.4034 0.5300 l
+0.4037 0.5320 l
+0.4040 0.5340 l
+0.4043 0.5359 l
+0.4045 0.5378 l
+0.4048 0.5397 l
+0.4051 0.5415 l
+0.4054 0.5433 l
+0.4057 0.5449 l
+0.4060 0.5465 l
+0.4063 0.5479 l
+0.4065 0.5493 l
+0.4068 0.5505 l
+0.4071 0.5516 l
+0.4074 0.5525 l
+0.4077 0.5533 l
+0.4080 0.5540 l
+0.4083 0.5545 l
+0.4086 0.5548 l
+0.4088 0.5550 l
+0.4091 0.5550 l
+0.4094 0.5548 l
+0.4097 0.5545 l
+0.4100 0.5539 l
+0.4103 0.5533 l
+0.4106 0.5524 l
+0.4108 0.5514 l
+0.4111 0.5502 l
+0.4114 0.5489 l
+0.4117 0.5474 l
+0.4120 0.5457 l
+0.4123 0.5440 l
+0.4126 0.5421 l
+0.4128 0.5400 l
+0.4131 0.5379 l
+0.4134 0.5357 l
+0.4137 0.5334 l
+0.4140 0.5310 l
+0.4143 0.5285 l
+0.4146 0.5260 l
+0.4148 0.5235 l
+0.4151 0.5210 l
+0.4154 0.5184 l
+0.4157 0.5159 l
+0.4160 0.5133 l
+0.4163 0.5108 l
+0.4166 0.5084 l
+0.4169 0.5060 l
+0.4171 0.5038 l
+0.4174 0.5016 l
+0.4177 0.4995 l
+0.4180 0.4975 l
+0.4183 0.4957 l
+0.4186 0.4940 l
+0.4189 0.4925 l
+0.4191 0.4912 l
+0.4194 0.4900 l
+0.4197 0.4890 l
+0.4200 0.4882 l
+0.4203 0.4876 l
+0.4206 0.4872 l
+0.4209 0.4870 l
+0.4211 0.4871 l
+0.4214 0.4873 l
+0.4217 0.4878 l
+0.4220 0.4885 l
+0.4223 0.4894 l
+0.4226 0.4905 l
+0.4229 0.4918 l
+0.4231 0.4934 l
+0.4234 0.4951 l
+0.4237 0.4970 l
+0.4240 0.4991 l
+0.4243 0.5013 l
+0.4246 0.5038 l
+0.4249 0.5063 l
+0.4252 0.5090 l
+0.4254 0.5119 l
+0.4257 0.5148 l
+0.4260 0.5178 l
+0.4263 0.5209 l
+0.4266 0.5241 l
+0.4269 0.5272 l
+0.4272 0.5305 l
+0.4274 0.5337 l
+0.4277 0.5369 l
+0.4280 0.5400 l
+0.4283 0.5431 l
+0.4286 0.5462 l
+0.4289 0.5491 l
+0.4292 0.5520 l
+0.4294 0.5547 l
+0.4297 0.5573 l
+0.4300 0.5597 l
+0.4303 0.5620 l
+0.4306 0.5641 l
+0.4309 0.5659 l
+0.4312 0.5676 l
+0.4314 0.5690 l
+0.4317 0.5702 l
+0.4320 0.5712 l
+0.4323 0.5719 l
+0.4326 0.5723 l
+0.4329 0.5725 l
+0.4332 0.5724 l
+0.4335 0.5721 l
+0.4337 0.5714 l
+0.4340 0.5705 l
+0.4343 0.5694 l
+0.4346 0.5679 l
+0.4349 0.5662 l
+0.4352 0.5643 l
+0.4355 0.5621 l
+0.4357 0.5597 l
+0.4360 0.5570 l
+0.4363 0.5542 l
+0.4366 0.5511 l
+0.4369 0.5479 l
+0.4372 0.5445 l
+0.4375 0.5410 l
+0.4377 0.5373 l
+0.4380 0.5335 l
+0.4383 0.5297 l
+0.4386 0.5257 l
+0.4389 0.5218 l
+0.4392 0.5178 l
+0.4395 0.5138 l
+0.4397 0.5098 l
+0.4400 0.5059 l
+0.4403 0.5020 l
+0.4406 0.4982 l
+0.4409 0.4946 l
+0.4412 0.4911 l
+0.4415 0.4877 l
+0.4418 0.4845 l
+0.4420 0.4816 l
+0.4423 0.4788 l
+0.4426 0.4762 l
+0.4429 0.4740 l
+0.4432 0.4720 l
+0.4435 0.4702 l
+0.4438 0.4688 l
+0.4440 0.4676 l
+0.4443 0.4668 l
+0.4446 0.4663 l
+0.4449 0.4662 l
+0.4452 0.4663 l
+0.4455 0.4668 l
+0.4458 0.4677 l
+0.4460 0.4688 l
+0.4463 0.4703 l
+0.4466 0.4721 l
+0.4469 0.4743 l
+0.4472 0.4767 l
+0.4475 0.4795 l
+0.4478 0.4825 l
+0.4481 0.4858 l
+0.4483 0.4894 l
+0.4486 0.4932 l
+0.4489 0.4972 l
+0.4492 0.5014 l
+0.4495 0.5058 l
+0.4498 0.5104 l
+0.4501 0.5150 l
+0.4503 0.5198 l
+0.4506 0.5246 l
+0.4509 0.5295 l
+0.4512 0.5345 l
+0.4515 0.5394 l
+0.4518 0.5442 l
+0.4521 0.5491 l
+0.4523 0.5538 l
+0.4526 0.5584 l
+0.4529 0.5629 l
+0.4532 0.5672 l
+0.4535 0.5712 l
+0.4538 0.5751 l
+0.4541 0.5787 l
+0.4543 0.5821 l
+0.4546 0.5852 l
+0.4549 0.5879 l
+0.4552 0.5903 l
+0.4555 0.5924 l
+0.4558 0.5941 l
+0.4561 0.5954 l
+0.4564 0.5964 l
+0.4566 0.5969 l
+0.4569 0.5971 l
+0.4572 0.5968 l
+0.4575 0.5961 l
+0.4578 0.5950 l
+0.4581 0.5935 l
+0.4584 0.5916 l
+0.4586 0.5894 l
+0.4589 0.5867 l
+0.4592 0.5836 l
+0.4595 0.5802 l
+0.4598 0.5764 l
+0.4601 0.5724 l
+0.4604 0.5680 l
+0.4606 0.5633 l
+0.4609 0.5583 l
+0.4612 0.5532 l
+0.4615 0.5478 l
+0.4618 0.5422 l
+0.4621 0.5365 l
+0.4624 0.5307 l
+0.4626 0.5248 l
+0.4629 0.5188 l
+0.4632 0.5128 l
+0.4635 0.5068 l
+0.4638 0.5009 l
+0.4641 0.4951 l
+0.4644 0.4893 l
+0.4647 0.4838 l
+0.4649 0.4784 l
+0.4652 0.4732 l
+0.4655 0.4683 l
+0.4658 0.4636 l
+0.4661 0.4593 l
+0.4664 0.4552 l
+0.4667 0.4516 l
+0.4669 0.4483 l
+0.4672 0.4455 l
+0.4675 0.4430 l
+0.4678 0.4410 l
+0.4681 0.4395 l
+0.4684 0.4384 l
+0.4687 0.4378 l
+0.4689 0.4377 l
+0.4692 0.4381 l
+0.4695 0.4390 l
+0.4698 0.4404 l
+0.4701 0.4423 l
+0.4704 0.4447 l
+0.4707 0.4475 l
+0.4709 0.4508 l
+0.4712 0.4546 l
+0.4715 0.4588 l
+0.4718 0.4634 l
+0.4721 0.4684 l
+0.4724 0.4737 l
+0.4727 0.4794 l
+0.4730 0.4854 l
+0.4732 0.4917 l
+0.4735 0.4983 l
+0.4738 0.5050 l
+0.4741 0.5119 l
+0.4744 0.5189 l
+0.4747 0.5261 l
+0.4750 0.5333 l
+0.4752 0.5405 l
+0.4755 0.5477 l
+0.4758 0.5548 l
+0.4761 0.5618 l
+0.4764 0.5687 l
+0.4767 0.5753 l
+0.4770 0.5818 l
+0.4772 0.5879 l
+0.4775 0.5938 l
+0.4778 0.5994 l
+0.4781 0.6045 l
+0.4784 0.6093 l
+0.4787 0.6136 l
+0.4790 0.6174 l
+0.4792 0.6208 l
+0.4795 0.6236 l
+0.4798 0.6259 l
+0.4801 0.6277 l
+0.4804 0.6289 l
+0.4807 0.6295 l
+0.4810 0.6295 l
+0.4813 0.6289 l
+0.4815 0.6278 l
+0.4818 0.6260 l
+0.4821 0.6237 l
+0.4824 0.6208 l
+0.4827 0.6173 l
+0.4830 0.6132 l
+0.4833 0.6086 l
+0.4835 0.6036 l
+0.4838 0.5980 l
+0.4841 0.5919 l
+0.4844 0.5855 l
+0.4847 0.5786 l
+0.4850 0.5714 l
+0.4853 0.5638 l
+0.4855 0.5560 l
+0.4858 0.5480 l
+0.4861 0.5397 l
+0.4864 0.5313 l
+0.4867 0.5228 l
+0.4870 0.5142 l
+0.4873 0.5056 l
+0.4875 0.4971 l
+0.4878 0.4886 l
+0.4881 0.4803 l
+0.4884 0.4722 l
+0.4887 0.4643 l
+0.4890 0.4566 l
+0.4893 0.4494 l
+0.4896 0.4424 l
+0.4898 0.4359 l
+0.4901 0.4299 l
+0.4904 0.4243 l
+0.4907 0.4193 l
+0.4910 0.4148 l
+0.4913 0.4109 l
+0.4916 0.4076 l
+0.4918 0.4050 l
+0.4921 0.4030 l
+0.4924 0.4017 l
+0.4927 0.4011 l
+0.4930 0.4012 l
+0.4933 0.4020 l
+0.4936 0.4035 l
+0.4938 0.4057 l
+0.4941 0.4086 l
+0.4944 0.4121 l
+0.4947 0.4164 l
+0.4950 0.4212 l
+0.4953 0.4267 l
+0.4956 0.4329 l
+0.4959 0.4395 l
+0.4961 0.4467 l
+0.4964 0.4545 l
+0.4967 0.4626 l
+0.4970 0.4712 l
+0.4973 0.4802 l
+0.4976 0.4895 l
+0.4979 0.4990 l
+0.4981 0.5088 l
+0.4984 0.5187 l
+0.4987 0.5288 l
+0.4990 0.5389 l
+0.4993 0.5490 l
+0.4996 0.5590 l
+0.4999 0.5690 l
+0.5001 0.5787 l
+0.5004 0.5882 l
+0.5007 0.5975 l
+0.5010 0.6064 l
+0.5013 0.6149 l
+0.5016 0.6229 l
+0.5019 0.6305 l
+0.5021 0.6375 l
+0.5024 0.6440 l
+0.5027 0.6498 l
+0.5030 0.6549 l
+0.5033 0.6594 l
+0.5036 0.6631 l
+0.5039 0.6661 l
+0.5042 0.6683 l
+0.5044 0.6697 l
+0.5047 0.6702 l
+0.5050 0.6700 l
+0.5053 0.6690 l
+0.5056 0.6671 l
+0.5059 0.6644 l
+0.5062 0.6609 l
+0.5064 0.6566 l
+0.5067 0.6515 l
+0.5070 0.6457 l
+0.5073 0.6391 l
+0.5076 0.6319 l
+0.5079 0.6240 l
+0.5082 0.6155 l
+0.5084 0.6064 l
+0.5087 0.5967 l
+0.5090 0.5866 l
+0.5093 0.5761 l
+0.5096 0.5652 l
+0.5099 0.5541 l
+0.5102 0.5426 l
+0.5104 0.5310 l
+0.5107 0.5193 l
+0.5110 0.5075 l
+0.5113 0.4957 l
+0.5116 0.4841 l
+0.5119 0.4725 l
+0.5122 0.4612 l
+0.5125 0.4502 l
+0.5127 0.4395 l
+0.5130 0.4292 l
+0.5133 0.4194 l
+0.5136 0.4101 l
+0.5139 0.4014 l
+0.5142 0.3934 l
+0.5145 0.3860 l
+0.5147 0.3794 l
+0.5150 0.3735 l
+0.5153 0.3685 l
+0.5156 0.3643 l
+0.5159 0.3610 l
+0.5162 0.3586 l
+0.5165 0.3571 l
+0.5167 0.3566 l
+0.5170 0.3570 l
+0.5173 0.3584 l
+0.5176 0.3607 l
+0.5179 0.3640 l
+0.5182 0.3682 l
+0.5185 0.3733 l
+0.5187 0.3793 l
+0.5190 0.3862 l
+0.5193 0.3939 l
+0.5196 0.4024 l
+0.5199 0.4116 l
+0.5202 0.4216 l
+0.5205 0.4322 l
+0.5208 0.4434 l
+0.5210 0.4551 l
+0.5213 0.4674 l
+0.5216 0.4800 l
+0.5219 0.4929 l
+0.5222 0.5062 l
+0.5225 0.5196 l
+0.5228 0.5331 l
+0.5230 0.5467 l
+0.5233 0.5602 l
+0.5236 0.5737 l
+0.5239 0.5869 l
+0.5242 0.5999 l
+0.5245 0.6126 l
+0.5248 0.6248 l
+0.5250 0.6365 l
+0.5253 0.6477 l
+0.5256 0.6583 l
+0.5259 0.6682 l
+0.5262 0.6773 l
+0.5265 0.6856 l
+0.5268 0.6931 l
+0.5270 0.6997 l
+0.5273 0.7053 l
+0.5276 0.7100 l
+0.5279 0.7136 l
+0.5282 0.7162 l
+0.5285 0.7177 l
+0.5288 0.7181 l
+0.5291 0.7175 l
+0.5293 0.7157 l
+0.5296 0.7129 l
+0.5299 0.7090 l
+0.5302 0.7040 l
+0.5305 0.6980 l
+0.5308 0.6909 l
+0.5311 0.6829 l
+0.5313 0.6740 l
+0.5316 0.6641 l
+0.5319 0.6534 l
+0.5322 0.6419 l
+0.5325 0.6297 l
+0.5328 0.6168 l
+0.5331 0.6033 l
+0.5333 0.5892 l
+0.5336 0.5748 l
+0.5339 0.5599 l
+0.5342 0.5448 l
+0.5345 0.5295 l
+0.5348 0.5140 l
+0.5351 0.4985 l
+0.5353 0.4831 l
+0.5356 0.4678 l
+0.5359 0.4528 l
+0.5362 0.4380 l
+0.5365 0.4237 l
+0.5368 0.4099 l
+0.5371 0.3966 l
+0.5374 0.3840 l
+0.5376 0.3721 l
+0.5379 0.3610 l
+0.5382 0.3507 l
+0.5385 0.3414 l
+0.5388 0.3331 l
+0.5391 0.3258 l
+0.5394 0.3196 l
+0.5396 0.3145 l
+0.5399 0.3105 l
+0.5402 0.3078 l
+0.5405 0.3063 l
+0.5408 0.3060 l
+0.5411 0.3069 l
+0.5414 0.3091 l
+0.5416 0.3125 l
+0.5419 0.3171 l
+0.5422 0.3229 l
+0.5425 0.3300 l
+0.5428 0.3381 l
+0.5431 0.3473 l
+0.5434 0.3577 l
+0.5436 0.3690 l
+0.5439 0.3812 l
+0.5442 0.3944 l
+0.5445 0.4083 l
+0.5448 0.4230 l
+0.5451 0.4383 l
+0.5454 0.4543 l
+0.5457 0.4707 l
+0.5459 0.4875 l
+0.5462 0.5046 l
+0.5465 0.5219 l
+0.5468 0.5394 l
+0.5471 0.5568 l
+0.5474 0.5742 l
+0.5477 0.5914 l
+0.5479 0.6083 l
+0.5482 0.6248 l
+0.5485 0.6408 l
+0.5488 0.6563 l
+0.5491 0.6711 l
+0.5494 0.6852 l
+0.5497 0.6985 l
+0.5499 0.7108 l
+0.5502 0.7222 l
+0.5505 0.7325 l
+0.5508 0.7417 l
+0.5511 0.7497 l
+0.5514 0.7565 l
+0.5517 0.7620 l
+0.5520 0.7662 l
+0.5522 0.7690 l
+0.5525 0.7705 l
+0.5528 0.7706 l
+0.5531 0.7694 l
+0.5534 0.7667 l
+0.5537 0.7627 l
+0.5540 0.7573 l
+0.5542 0.7505 l
+0.5545 0.7425 l
+0.5548 0.7332 l
+0.5551 0.7226 l
+0.5554 0.7109 l
+0.5557 0.6981 l
+0.5560 0.6842 l
+0.5562 0.6694 l
+0.5565 0.6537 l
+0.5568 0.6371 l
+0.5571 0.6199 l
+0.5574 0.6020 l
+0.5577 0.5836 l
+0.5580 0.5648 l
+0.5582 0.5456 l
+0.5585 0.5263 l
+0.5588 0.5068 l
+0.5591 0.4873 l
+0.5594 0.4680 l
+0.5597 0.4489 l
+0.5600 0.4301 l
+0.5603 0.4118 l
+0.5605 0.3940 l
+0.5608 0.3769 l
+0.5611 0.3605 l
+0.5614 0.3450 l
+0.5617 0.3304 l
+0.5620 0.3168 l
+0.5623 0.3044 l
+0.5625 0.2931 l
+0.5628 0.2831 l
+0.5631 0.2744 l
+0.5634 0.2671 l
+0.5637 0.2612 l
+0.5640 0.2568 l
+0.5643 0.2538 l
+0.5645 0.2524 l
+0.5648 0.2525 l
+0.5651 0.2542 l
+0.5654 0.2574 l
+0.5657 0.2621 l
+0.5660 0.2683 l
+0.5663 0.2760 l
+0.5665 0.2852 l
+0.5668 0.2957 l
+0.5671 0.3076 l
+0.5674 0.3207 l
+0.5677 0.3351 l
+0.5680 0.3506 l
+0.5683 0.3672 l
+0.5686 0.3847 l
+0.5688 0.4032 l
+0.5691 0.4223 l
+0.5694 0.4422 l
+0.5697 0.4626 l
+0.5700 0.4834 l
+0.5703 0.5046 l
+0.5706 0.5260 l
+0.5708 0.5475 l
+0.5711 0.5689 l
+0.5714 0.5902 l
+0.5717 0.6112 l
+0.5720 0.6319 l
+0.5723 0.6520 l
+0.5726 0.6715 l
+0.5728 0.6902 l
+0.5731 0.7081 l
+0.5734 0.7250 l
+0.5737 0.7409 l
+0.5740 0.7556 l
+0.5743 0.7691 l
+0.5746 0.7813 l
+0.5748 0.7921 l
+0.5751 0.8014 l
+0.5754 0.8092 l
+0.5757 0.8154 l
+0.5760 0.8200 l
+0.5763 0.8230 l
+0.5766 0.8243 l
+0.5769 0.8239 l
+0.5771 0.8218 l
+0.5774 0.8180 l
+0.5777 0.8126 l
+0.5780 0.8055 l
+0.5783 0.7968 l
+0.5786 0.7866 l
+0.5789 0.7748 l
+0.5791 0.7616 l
+0.5794 0.7469 l
+0.5797 0.7310 l
+0.5800 0.7138 l
+0.5803 0.6955 l
+0.5806 0.6762 l
+0.5809 0.6559 l
+0.5811 0.6348 l
+0.5814 0.6130 l
+0.5817 0.5906 l
+0.5820 0.5678 l
+0.5823 0.5446 l
+0.5826 0.5213 l
+0.5829 0.4978 l
+0.5831 0.4744 l
+0.5834 0.4513 l
+0.5837 0.4284 l
+0.5840 0.4060 l
+0.5843 0.3842 l
+0.5846 0.3631 l
+0.5849 0.3428 l
+0.5852 0.3235 l
+0.5854 0.3052 l
+0.5857 0.2881 l
+0.5860 0.2723 l
+0.5863 0.2578 l
+0.5866 0.2448 l
+0.5869 0.2334 l
+0.5872 0.2235 l
+0.5874 0.2153 l
+0.5877 0.2088 l
+0.5880 0.2041 l
+0.5883 0.2012 l
+0.5886 0.2000 l
+0.5889 0.2008 l
+0.5892 0.2033 l
+0.5894 0.2077 l
+0.5897 0.2139 l
+0.5900 0.2218 l
+0.5903 0.2315 l
+0.5906 0.2429 l
+0.5909 0.2559 l
+0.5912 0.2705 l
+0.5914 0.2866 l
+0.5917 0.3040 l
+0.5920 0.3228 l
+0.5923 0.3428 l
+0.5926 0.3639 l
+0.5929 0.3860 l
+0.5932 0.4089 l
+0.5935 0.4325 l
+0.5937 0.4568 l
+0.5940 0.4815 l
+0.5943 0.5066 l
+0.5946 0.5319 l
+0.5949 0.5572 l
+0.5952 0.5824 l
+0.5955 0.6073 l
+0.5957 0.6319 l
+0.5960 0.6560 l
+0.5963 0.6794 l
+0.5966 0.7020 l
+0.5969 0.7237 l
+0.5972 0.7444 l
+0.5975 0.7638 l
+0.5977 0.7820 l
+0.5980 0.7988 l
+0.5983 0.8141 l
+0.5986 0.8279 l
+0.5989 0.8399 l
+0.5992 0.8502 l
+0.5995 0.8588 l
+0.5998 0.8654 l
+0.6000 0.8702 l
+0.6003 0.8731 l
+0.6006 0.8739 l
+0.6009 0.8729 l
+0.6012 0.8698 l
+0.6015 0.8648 l
+0.6018 0.8579 l
+0.6020 0.8491 l
+0.6023 0.8384 l
+0.6026 0.8259 l
+0.6029 0.8117 l
+0.6032 0.7958 l
+0.6035 0.7783 l
+0.6038 0.7594 l
+0.6040 0.7391 l
+0.6043 0.7175 l
+0.6046 0.6948 l
+0.6049 0.6710 l
+0.6052 0.6464 l
+0.6055 0.6210 l
+0.6058 0.5949 l
+0.6060 0.5684 l
+0.6063 0.5416 l
+0.6066 0.5146 l
+0.6069 0.4876 l
+0.6072 0.4608 l
+0.6075 0.4342 l
+0.6078 0.4080 l
+0.6081 0.3825 l
+0.6083 0.3576 l
+0.6086 0.3337 l
+0.6089 0.3107 l
+0.6092 0.2889 l
+0.6095 0.2684 l
+0.6098 0.2492 l
+0.6101 0.2316 l
+0.6103 0.2156 l
+0.6106 0.2012 l
+0.6109 0.1887 l
+0.6112 0.1780 l
+0.6115 0.1693 l
+0.6118 0.1625 l
+0.6121 0.1577 l
+0.6123 0.1550 l
+0.6126 0.1544 l
+0.6129 0.1559 l
+0.6132 0.1595 l
+0.6135 0.1651 l
+0.6138 0.1728 l
+0.6141 0.1825 l
+0.6143 0.1941 l
+0.6146 0.2076 l
+0.6149 0.2230 l
+0.6152 0.2401 l
+0.6155 0.2588 l
+0.6158 0.2791 l
+0.6161 0.3008 l
+0.6164 0.3239 l
+0.6166 0.3481 l
+0.6169 0.3734 l
+0.6172 0.3996 l
+0.6175 0.4266 l
+0.6178 0.4542 l
+0.6181 0.4823 l
+0.6184 0.5106 l
+0.6186 0.5391 l
+0.6189 0.5676 l
+0.6192 0.5960 l
+0.6195 0.6240 l
+0.6198 0.6515 l
+0.6201 0.6783 l
+0.6204 0.7044 l
+0.6206 0.7295 l
+0.6209 0.7535 l
+0.6212 0.7763 l
+0.6215 0.7977 l
+0.6218 0.8176 l
+0.6221 0.8359 l
+0.6224 0.8525 l
+0.6226 0.8673 l
+0.6229 0.8802 l
+0.6232 0.8911 l
+0.6235 0.9000 l
+0.6238 0.9068 l
+0.6241 0.9114 l
+0.6244 0.9139 l
+0.6247 0.9142 l
+0.6249 0.9123 l
+0.6252 0.9082 l
+0.6255 0.9020 l
+0.6258 0.8936 l
+0.6261 0.8831 l
+0.6264 0.8706 l
+0.6267 0.8561 l
+0.6269 0.8397 l
+0.6272 0.8215 l
+0.6275 0.8016 l
+0.6278 0.7801 l
+0.6281 0.7571 l
+0.6284 0.7328 l
+0.6287 0.7072 l
+0.6289 0.6806 l
+0.6292 0.6530 l
+0.6295 0.6247 l
+0.6298 0.5958 l
+0.6301 0.5664 l
+0.6304 0.5367 l
+0.6307 0.5069 l
+0.6309 0.4771 l
+0.6312 0.4476 l
+0.6315 0.4184 l
+0.6318 0.3898 l
+0.6321 0.3619 l
+0.6324 0.3349 l
+0.6327 0.3089 l
+0.6330 0.2841 l
+0.6332 0.2606 l
+0.6335 0.2385 l
+0.6338 0.2180 l
+0.6341 0.1992 l
+0.6344 0.1822 l
+0.6347 0.1671 l
+0.6350 0.1540 l
+0.6352 0.1430 l
+0.6355 0.1341 l
+0.6358 0.1274 l
+0.6361 0.1229 l
+0.6364 0.1207 l
+0.6367 0.1208 l
+0.6370 0.1231 l
+0.6372 0.1277 l
+0.6375 0.1345 l
+0.6378 0.1436 l
+0.6381 0.1548 l
+0.6384 0.1681 l
+0.6387 0.1835 l
+0.6390 0.2008 l
+0.6392 0.2199 l
+0.6395 0.2408 l
+0.6398 0.2633 l
+0.6401 0.2874 l
+0.6404 0.3128 l
+0.6407 0.3394 l
+0.6410 0.3671 l
+0.6413 0.3958 l
+0.6415 0.4252 l
+0.6418 0.4552 l
+0.6421 0.4857 l
+0.6424 0.5164 l
+0.6427 0.5472 l
+0.6430 0.5779 l
+0.6433 0.6083 l
+0.6435 0.6384 l
+0.6438 0.6678 l
+0.6441 0.6964 l
+0.6444 0.7242 l
+0.6447 0.7508 l
+0.6450 0.7762 l
+0.6453 0.8002 l
+0.6455 0.8227 l
+0.6458 0.8436 l
+0.6461 0.8626 l
+0.6464 0.8798 l
+0.6467 0.8950 l
+0.6470 0.9082 l
+0.6473 0.9192 l
+0.6475 0.9280 l
+0.6478 0.9345 l
+0.6481 0.9388 l
+0.6484 0.9407 l
+0.6487 0.9402 l
+0.6490 0.9375 l
+0.6493 0.9324 l
+0.6496 0.9250 l
+0.6498 0.9153 l
+0.6501 0.9035 l
+0.6504 0.8895 l
+0.6507 0.8734 l
+0.6510 0.8554 l
+0.6513 0.8354 l
+0.6516 0.8137 l
+0.6518 0.7904 l
+0.6521 0.7656 l
+0.6524 0.7393 l
+0.6527 0.7119 l
+0.6530 0.6833 l
+0.6533 0.6539 l
+0.6536 0.6237 l
+0.6538 0.5929 l
+0.6541 0.5617 l
+0.6544 0.5303 l
+0.6547 0.4988 l
+0.6550 0.4675 l
+0.6553 0.4364 l
+0.6556 0.4058 l
+0.6559 0.3759 l
+0.6561 0.3468 l
+0.6564 0.3187 l
+0.6567 0.2917 l
+0.6570 0.2660 l
+0.6573 0.2417 l
+0.6576 0.2191 l
+0.6579 0.1981 l
+0.6581 0.1790 l
+0.6584 0.1618 l
+0.6587 0.1466 l
+0.6590 0.1336 l
+0.6593 0.1227 l
+0.6596 0.1141 l
+0.6599 0.1079 l
+0.6601 0.1039 l
+0.6604 0.1024 l
+0.6607 0.1032 l
+0.6610 0.1064 l
+0.6613 0.1119 l
+0.6616 0.1198 l
+0.6619 0.1299 l
+0.6621 0.1423 l
+0.6624 0.1569 l
+0.6627 0.1735 l
+0.6630 0.1921 l
+0.6633 0.2126 l
+0.6636 0.2349 l
+0.6639 0.2588 l
+0.6642 0.2842 l
+0.6644 0.3110 l
+0.6647 0.3390 l
+0.6650 0.3680 l
+0.6653 0.3979 l
+0.6656 0.4286 l
+0.6659 0.4598 l
+0.6662 0.4914 l
+0.6664 0.5232 l
+0.6667 0.5550 l
+0.6670 0.5867 l
+0.6673 0.6180 l
+0.6676 0.6488 l
+0.6679 0.6789 l
+0.6682 0.7081 l
+0.6684 0.7363 l
+0.6687 0.7634 l
+0.6690 0.7891 l
+0.6693 0.8133 l
+0.6696 0.8359 l
+0.6699 0.8567 l
+0.6702 0.8757 l
+0.6704 0.8927 l
+0.6707 0.9076 l
+0.6710 0.9204 l
+0.6713 0.9310 l
+0.6716 0.9393 l
+0.6719 0.9452 l
+0.6722 0.9488 l
+0.6725 0.9500 l
+0.6727 0.9488 l
+0.6730 0.9452 l
+0.6733 0.9393 l
+0.6736 0.9310 l
+0.6739 0.9204 l
+0.6742 0.9076 l
+0.6745 0.8927 l
+0.6747 0.8757 l
+0.6750 0.8567 l
+0.6753 0.8359 l
+0.6756 0.8133 l
+0.6759 0.7891 l
+0.6762 0.7634 l
+0.6765 0.7363 l
+0.6767 0.7081 l
+0.6770 0.6789 l
+0.6773 0.6488 l
+0.6776 0.6180 l
+0.6779 0.5867 l
+0.6782 0.5550 l
+0.6785 0.5232 l
+0.6787 0.4914 l
+0.6790 0.4598 l
+0.6793 0.4286 l
+0.6796 0.3979 l
+0.6799 0.3680 l
+0.6802 0.3390 l
+0.6805 0.3110 l
+0.6808 0.2842 l
+0.6810 0.2588 l
+0.6813 0.2349 l
+0.6816 0.2126 l
+0.6819 0.1921 l
+0.6822 0.1735 l
+0.6825 0.1569 l
+0.6828 0.1423 l
+0.6830 0.1299 l
+0.6833 0.1198 l
+0.6836 0.1119 l
+0.6839 0.1064 l
+0.6842 0.1032 l
+0.6845 0.1024 l
+0.6848 0.1039 l
+0.6850 0.1079 l
+0.6853 0.1141 l
+0.6856 0.1227 l
+0.6859 0.1336 l
+0.6862 0.1466 l
+0.6865 0.1618 l
+0.6868 0.1790 l
+0.6870 0.1981 l
+0.6873 0.2191 l
+0.6876 0.2417 l
+0.6879 0.2660 l
+0.6882 0.2917 l
+0.6885 0.3187 l
+0.6888 0.3468 l
+0.6891 0.3759 l
+0.6893 0.4058 l
+0.6896 0.4364 l
+0.6899 0.4675 l
+0.6902 0.4988 l
+0.6905 0.5303 l
+0.6908 0.5617 l
+0.6911 0.5929 l
+0.6913 0.6237 l
+0.6916 0.6539 l
+0.6919 0.6833 l
+0.6922 0.7119 l
+0.6925 0.7393 l
+0.6928 0.7656 l
+0.6931 0.7904 l
+0.6933 0.8137 l
+0.6936 0.8354 l
+0.6939 0.8554 l
+0.6942 0.8734 l
+0.6945 0.8895 l
+0.6948 0.9035 l
+0.6951 0.9153 l
+0.6953 0.9250 l
+0.6956 0.9324 l
+0.6959 0.9375 l
+0.6962 0.9402 l
+0.6965 0.9407 l
+0.6968 0.9388 l
+0.6971 0.9345 l
+0.6974 0.9280 l
+0.6976 0.9192 l
+0.6979 0.9082 l
+0.6982 0.8950 l
+0.6985 0.8798 l
+0.6988 0.8626 l
+0.6991 0.8436 l
+0.6994 0.8227 l
+0.6996 0.8002 l
+0.6999 0.7762 l
+0.7002 0.7508 l
+0.7005 0.7242 l
+0.7008 0.6964 l
+0.7011 0.6678 l
+0.7014 0.6384 l
+0.7016 0.6083 l
+0.7019 0.5779 l
+0.7022 0.5472 l
+0.7025 0.5164 l
+0.7028 0.4857 l
+0.7031 0.4552 l
+0.7034 0.4252 l
+0.7037 0.3958 l
+0.7039 0.3671 l
+0.7042 0.3394 l
+0.7045 0.3128 l
+0.7048 0.2874 l
+0.7051 0.2633 l
+0.7054 0.2408 l
+0.7057 0.2199 l
+0.7059 0.2008 l
+0.7062 0.1835 l
+0.7065 0.1681 l
+0.7068 0.1548 l
+0.7071 0.1436 l
+0.7074 0.1345 l
+0.7077 0.1277 l
+0.7079 0.1231 l
+0.7082 0.1208 l
+0.7085 0.1207 l
+0.7088 0.1229 l
+0.7091 0.1274 l
+0.7094 0.1341 l
+0.7097 0.1430 l
+0.7099 0.1540 l
+0.7102 0.1671 l
+0.7105 0.1822 l
+0.7108 0.1992 l
+0.7111 0.2180 l
+0.7114 0.2385 l
+0.7117 0.2606 l
+0.7120 0.2841 l
+0.7122 0.3089 l
+0.7125 0.3349 l
+0.7128 0.3619 l
+0.7131 0.3898 l
+0.7134 0.4184 l
+0.7137 0.4476 l
+0.7140 0.4771 l
+0.7142 0.5069 l
+0.7145 0.5367 l
+0.7148 0.5664 l
+0.7151 0.5958 l
+0.7154 0.6247 l
+0.7157 0.6530 l
+0.7160 0.6806 l
+0.7162 0.7072 l
+0.7165 0.7328 l
+0.7168 0.7571 l
+0.7171 0.7801 l
+0.7174 0.8016 l
+0.7177 0.8215 l
+0.7180 0.8397 l
+0.7182 0.8561 l
+0.7185 0.8706 l
+0.7188 0.8831 l
+0.7191 0.8936 l
+0.7194 0.9020 l
+0.7197 0.9082 l
+0.7200 0.9123 l
+0.7203 0.9142 l
+0.7205 0.9139 l
+0.7208 0.9114 l
+0.7211 0.9068 l
+0.7214 0.9000 l
+0.7217 0.8911 l
+0.7220 0.8802 l
+0.7223 0.8673 l
+0.7225 0.8525 l
+0.7228 0.8359 l
+0.7231 0.8176 l
+0.7234 0.7977 l
+0.7237 0.7763 l
+0.7240 0.7535 l
+0.7243 0.7295 l
+0.7245 0.7044 l
+0.7248 0.6783 l
+0.7251 0.6515 l
+0.7254 0.6240 l
+0.7257 0.5960 l
+0.7260 0.5676 l
+0.7263 0.5391 l
+0.7265 0.5106 l
+0.7268 0.4823 l
+0.7271 0.4542 l
+0.7274 0.4266 l
+0.7277 0.3996 l
+0.7280 0.3734 l
+0.7283 0.3481 l
+0.7286 0.3239 l
+0.7288 0.3008 l
+0.7291 0.2791 l
+0.7294 0.2588 l
+0.7297 0.2401 l
+0.7300 0.2230 l
+0.7303 0.2076 l
+0.7306 0.1941 l
+0.7308 0.1825 l
+0.7311 0.1728 l
+0.7314 0.1651 l
+0.7317 0.1595 l
+0.7320 0.1559 l
+0.7323 0.1544 l
+0.7326 0.1550 l
+0.7328 0.1577 l
+0.7331 0.1625 l
+0.7334 0.1693 l
+0.7337 0.1780 l
+0.7340 0.1887 l
+0.7343 0.2012 l
+0.7346 0.2156 l
+0.7348 0.2316 l
+0.7351 0.2492 l
+0.7354 0.2684 l
+0.7357 0.2889 l
+0.7360 0.3107 l
+0.7363 0.3337 l
+0.7366 0.3576 l
+0.7369 0.3825 l
+0.7371 0.4080 l
+0.7374 0.4342 l
+0.7377 0.4608 l
+0.7380 0.4876 l
+0.7383 0.5146 l
+0.7386 0.5416 l
+0.7389 0.5684 l
+0.7391 0.5949 l
+0.7394 0.6210 l
+0.7397 0.6464 l
+0.7400 0.6710 l
+0.7403 0.6948 l
+0.7406 0.7175 l
+0.7409 0.7391 l
+0.7411 0.7594 l
+0.7414 0.7783 l
+0.7417 0.7958 l
+0.7420 0.8117 l
+0.7423 0.8259 l
+0.7426 0.8384 l
+0.7429 0.8491 l
+0.7431 0.8579 l
+0.7434 0.8648 l
+0.7437 0.8698 l
+0.7440 0.8729 l
+0.7443 0.8739 l
+0.7446 0.8731 l
+0.7449 0.8702 l
+0.7452 0.8654 l
+0.7454 0.8588 l
+0.7457 0.8502 l
+0.7460 0.8399 l
+0.7463 0.8279 l
+0.7466 0.8141 l
+0.7469 0.7988 l
+0.7472 0.7820 l
+0.7474 0.7638 l
+0.7477 0.7444 l
+0.7480 0.7237 l
+0.7483 0.7020 l
+0.7486 0.6794 l
+0.7489 0.6560 l
+0.7492 0.6319 l
+0.7494 0.6073 l
+0.7497 0.5824 l
+0.7500 0.5572 l
+0.7503 0.5319 l
+0.7506 0.5066 l
+0.7509 0.4815 l
+0.7512 0.4568 l
+0.7514 0.4325 l
+0.7517 0.4089 l
+0.7520 0.3859 l
+0.7523 0.3639 l
+0.7526 0.3428 l
+0.7529 0.3228 l
+0.7532 0.3040 l
+0.7535 0.2866 l
+0.7537 0.2705 l
+0.7540 0.2559 l
+0.7543 0.2429 l
+0.7546 0.2315 l
+0.7549 0.2218 l
+0.7552 0.2139 l
+0.7555 0.2077 l
+0.7557 0.2033 l
+0.7560 0.2008 l
+0.7563 0.2000 l
+0.7566 0.2012 l
+0.7569 0.2041 l
+0.7572 0.2088 l
+0.7575 0.2153 l
+0.7577 0.2235 l
+0.7580 0.2334 l
+0.7583 0.2448 l
+0.7586 0.2578 l
+0.7589 0.2723 l
+0.7592 0.2881 l
+0.7595 0.3052 l
+0.7598 0.3235 l
+0.7600 0.3428 l
+0.7603 0.3631 l
+0.7606 0.3842 l
+0.7609 0.4060 l
+0.7612 0.4284 l
+0.7615 0.4513 l
+0.7618 0.4744 l
+0.7620 0.4978 l
+0.7623 0.5213 l
+0.7626 0.5446 l
+0.7629 0.5678 l
+0.7632 0.5906 l
+0.7635 0.6130 l
+0.7638 0.6348 l
+0.7640 0.6559 l
+0.7643 0.6762 l
+0.7646 0.6955 l
+0.7649 0.7138 l
+0.7652 0.7310 l
+0.7655 0.7469 l
+0.7658 0.7616 l
+0.7660 0.7748 l
+0.7663 0.7866 l
+0.7666 0.7968 l
+0.7669 0.8055 l
+0.7672 0.8126 l
+0.7675 0.8180 l
+0.7678 0.8218 l
+0.7681 0.8239 l
+0.7683 0.8243 l
+0.7686 0.8230 l
+0.7689 0.8200 l
+0.7692 0.8154 l
+0.7695 0.8092 l
+0.7698 0.8014 l
+0.7701 0.7921 l
+0.7703 0.7813 l
+0.7706 0.7691 l
+0.7709 0.7556 l
+0.7712 0.7409 l
+0.7715 0.7250 l
+0.7718 0.7081 l
+0.7721 0.6902 l
+0.7723 0.6715 l
+0.7726 0.6520 l
+0.7729 0.6319 l
+0.7732 0.6112 l
+0.7735 0.5902 l
+0.7738 0.5689 l
+0.7741 0.5475 l
+0.7743 0.5260 l
+0.7746 0.5046 l
+0.7749 0.4834 l
+0.7752 0.4626 l
+0.7755 0.4422 l
+0.7758 0.4223 l
+0.7761 0.4032 l
+0.7764 0.3847 l
+0.7766 0.3672 l
+0.7769 0.3506 l
+0.7772 0.3351 l
+0.7775 0.3207 l
+0.7778 0.3076 l
+0.7781 0.2957 l
+0.7784 0.2852 l
+0.7786 0.2760 l
+0.7789 0.2683 l
+0.7792 0.2621 l
+0.7795 0.2574 l
+0.7798 0.2542 l
+0.7801 0.2525 l
+0.7804 0.2524 l
+0.7806 0.2538 l
+0.7809 0.2568 l
+0.7812 0.2612 l
+0.7815 0.2671 l
+0.7818 0.2744 l
+0.7821 0.2831 l
+0.7824 0.2931 l
+0.7826 0.3044 l
+0.7829 0.3168 l
+0.7832 0.3304 l
+0.7835 0.3450 l
+0.7838 0.3605 l
+0.7841 0.3769 l
+0.7844 0.3940 l
+0.7847 0.4118 l
+0.7849 0.4301 l
+0.7852 0.4489 l
+0.7855 0.4680 l
+0.7858 0.4873 l
+0.7861 0.5068 l
+0.7864 0.5263 l
+0.7867 0.5456 l
+0.7869 0.5648 l
+0.7872 0.5836 l
+0.7875 0.6020 l
+0.7878 0.6199 l
+0.7881 0.6371 l
+0.7884 0.6537 l
+0.7887 0.6694 l
+0.7889 0.6842 l
+0.7892 0.6981 l
+0.7895 0.7109 l
+0.7898 0.7226 l
+0.7901 0.7332 l
+0.7904 0.7425 l
+0.7907 0.7505 l
+0.7909 0.7573 l
+0.7912 0.7627 l
+0.7915 0.7667 l
+0.7918 0.7694 l
+0.7921 0.7706 l
+0.7924 0.7705 l
+0.7927 0.7690 l
+0.7930 0.7662 l
+0.7932 0.7620 l
+0.7935 0.7565 l
+0.7938 0.7497 l
+0.7941 0.7417 l
+0.7944 0.7325 l
+0.7947 0.7222 l
+0.7950 0.7108 l
+0.7952 0.6985 l
+0.7955 0.6852 l
+0.7958 0.6711 l
+0.7961 0.6563 l
+0.7964 0.6408 l
+0.7967 0.6248 l
+0.7970 0.6083 l
+0.7972 0.5914 l
+0.7975 0.5742 l
+0.7978 0.5568 l
+0.7981 0.5394 l
+0.7984 0.5219 l
+0.7987 0.5046 l
+0.7990 0.4875 l
+0.7992 0.4707 l
+0.7995 0.4543 l
+0.7998 0.4383 l
+0.8001 0.4230 l
+0.8004 0.4083 l
+0.8007 0.3944 l
+0.8010 0.3812 l
+0.8013 0.3690 l
+0.8015 0.3577 l
+0.8018 0.3473 l
+0.8021 0.3381 l
+0.8024 0.3300 l
+0.8027 0.3229 l
+0.8030 0.3171 l
+0.8033 0.3125 l
+0.8035 0.3091 l
+0.8038 0.3069 l
+0.8041 0.3060 l
+0.8044 0.3063 l
+0.8047 0.3078 l
+0.8050 0.3105 l
+0.8053 0.3145 l
+0.8055 0.3196 l
+0.8058 0.3258 l
+0.8061 0.3331 l
+0.8064 0.3414 l
+0.8067 0.3507 l
+0.8070 0.3610 l
+0.8073 0.3721 l
+0.8076 0.3840 l
+0.8078 0.3966 l
+0.8081 0.4099 l
+0.8084 0.4237 l
+0.8087 0.4380 l
+0.8090 0.4528 l
+0.8093 0.4678 l
+0.8096 0.4831 l
+0.8098 0.4985 l
+0.8101 0.5140 l
+0.8104 0.5295 l
+0.8107 0.5448 l
+0.8110 0.5599 l
+0.8113 0.5748 l
+0.8116 0.5892 l
+0.8118 0.6033 l
+0.8121 0.6168 l
+0.8124 0.6297 l
+0.8127 0.6419 l
+0.8130 0.6534 l
+0.8133 0.6641 l
+0.8136 0.6740 l
+0.8138 0.6829 l
+0.8141 0.6909 l
+0.8144 0.6980 l
+0.8147 0.7040 l
+0.8150 0.7090 l
+0.8153 0.7129 l
+0.8156 0.7157 l
+0.8159 0.7175 l
+0.8161 0.7181 l
+0.8164 0.7177 l
+0.8167 0.7162 l
+0.8170 0.7136 l
+0.8173 0.7100 l
+0.8176 0.7053 l
+0.8179 0.6997 l
+0.8181 0.6931 l
+0.8184 0.6856 l
+0.8187 0.6773 l
+0.8190 0.6682 l
+0.8193 0.6583 l
+0.8196 0.6477 l
+0.8199 0.6365 l
+0.8201 0.6248 l
+0.8204 0.6126 l
+0.8207 0.5999 l
+0.8210 0.5869 l
+0.8213 0.5737 l
+0.8216 0.5602 l
+0.8219 0.5467 l
+0.8221 0.5331 l
+0.8224 0.5196 l
+0.8227 0.5062 l
+0.8230 0.4929 l
+0.8233 0.4800 l
+0.8236 0.4674 l
+0.8239 0.4551 l
+0.8242 0.4434 l
+0.8244 0.4322 l
+0.8247 0.4216 l
+0.8250 0.4116 l
+0.8253 0.4024 l
+0.8256 0.3939 l
+0.8259 0.3862 l
+0.8262 0.3793 l
+0.8264 0.3733 l
+0.8267 0.3682 l
+0.8270 0.3640 l
+0.8273 0.3607 l
+0.8276 0.3584 l
+0.8279 0.3570 l
+0.8282 0.3566 l
+0.8284 0.3571 l
+0.8287 0.3586 l
+0.8290 0.3610 l
+0.8293 0.3643 l
+0.8296 0.3685 l
+0.8299 0.3735 l
+0.8302 0.3794 l
+0.8304 0.3860 l
+0.8307 0.3934 l
+0.8310 0.4014 l
+0.8313 0.4101 l
+0.8316 0.4194 l
+0.8319 0.4292 l
+0.8322 0.4395 l
+0.8325 0.4502 l
+0.8327 0.4612 l
+0.8330 0.4725 l
+0.8333 0.4841 l
+0.8336 0.4957 l
+0.8339 0.5075 l
+0.8342 0.5193 l
+0.8345 0.5310 l
+0.8347 0.5426 l
+0.8350 0.5541 l
+0.8353 0.5652 l
+0.8356 0.5761 l
+0.8359 0.5866 l
+0.8362 0.5967 l
+0.8365 0.6064 l
+0.8367 0.6155 l
+0.8370 0.6240 l
+0.8373 0.6319 l
+0.8376 0.6391 l
+0.8379 0.6457 l
+0.8382 0.6515 l
+0.8385 0.6566 l
+0.8387 0.6609 l
+0.8390 0.6644 l
+0.8393 0.6671 l
+0.8396 0.6690 l
+0.8399 0.6700 l
+0.8402 0.6702 l
+0.8405 0.6697 l
+0.8408 0.6683 l
+0.8410 0.6661 l
+0.8413 0.6631 l
+0.8416 0.6594 l
+0.8419 0.6549 l
+0.8422 0.6498 l
+0.8425 0.6440 l
+0.8428 0.6375 l
+0.8430 0.6305 l
+0.8433 0.6229 l
+0.8436 0.6149 l
+0.8439 0.6064 l
+0.8442 0.5975 l
+0.8445 0.5882 l
+0.8448 0.5787 l
+0.8450 0.5690 l
+0.8453 0.5590 l
+0.8456 0.5490 l
+0.8459 0.5389 l
+0.8462 0.5288 l
+0.8465 0.5187 l
+0.8468 0.5088 l
+0.8470 0.4990 l
+0.8473 0.4895 l
+0.8476 0.4802 l
+0.8479 0.4712 l
+0.8482 0.4626 l
+0.8485 0.4545 l
+0.8488 0.4467 l
+0.8491 0.4395 l
+0.8493 0.4329 l
+0.8496 0.4267 l
+0.8499 0.4212 l
+0.8502 0.4164 l
+0.8505 0.4121 l
+0.8508 0.4086 l
+0.8511 0.4057 l
+0.8513 0.4035 l
+0.8516 0.4020 l
+0.8519 0.4012 l
+0.8522 0.4011 l
+0.8525 0.4017 l
+0.8528 0.4030 l
+0.8531 0.4050 l
+0.8533 0.4076 l
+0.8536 0.4109 l
+0.8539 0.4148 l
+0.8542 0.4193 l
+0.8545 0.4243 l
+0.8548 0.4299 l
+0.8551 0.4359 l
+0.8553 0.4424 l
+0.8556 0.4494 l
+0.8559 0.4566 l
+0.8562 0.4643 l
+0.8565 0.4722 l
+0.8568 0.4803 l
+0.8571 0.4886 l
+0.8574 0.4971 l
+0.8576 0.5056 l
+0.8579 0.5142 l
+0.8582 0.5228 l
+0.8585 0.5313 l
+0.8588 0.5397 l
+0.8591 0.5480 l
+0.8594 0.5560 l
+0.8596 0.5638 l
+0.8599 0.5714 l
+0.8602 0.5786 l
+0.8605 0.5855 l
+0.8608 0.5919 l
+0.8611 0.5980 l
+0.8614 0.6036 l
+0.8616 0.6086 l
+0.8619 0.6132 l
+0.8622 0.6173 l
+0.8625 0.6208 l
+0.8628 0.6237 l
+0.8631 0.6260 l
+0.8634 0.6278 l
+0.8637 0.6289 l
+0.8639 0.6295 l
+0.8642 0.6295 l
+0.8645 0.6289 l
+0.8648 0.6277 l
+0.8651 0.6259 l
+0.8654 0.6236 l
+0.8657 0.6208 l
+0.8659 0.6174 l
+0.8662 0.6136 l
+0.8665 0.6093 l
+0.8668 0.6045 l
+0.8671 0.5994 l
+0.8674 0.5938 l
+0.8677 0.5880 l
+0.8679 0.5818 l
+0.8682 0.5753 l
+0.8685 0.5687 l
+0.8688 0.5618 l
+0.8691 0.5548 l
+0.8694 0.5477 l
+0.8697 0.5405 l
+0.8699 0.5333 l
+0.8702 0.5261 l
+0.8705 0.5189 l
+0.8708 0.5119 l
+0.8711 0.5050 l
+0.8714 0.4983 l
+0.8717 0.4917 l
+0.8720 0.4854 l
+0.8722 0.4794 l
+0.8725 0.4737 l
+0.8728 0.4684 l
+0.8731 0.4634 l
+0.8734 0.4588 l
+0.8737 0.4546 l
+0.8740 0.4508 l
+0.8742 0.4475 l
+0.8745 0.4447 l
+0.8748 0.4423 l
+0.8751 0.4404 l
+0.8754 0.4390 l
+0.8757 0.4381 l
+0.8760 0.4377 l
+0.8762 0.4378 l
+0.8765 0.4384 l
+0.8768 0.4395 l
+0.8771 0.4410 l
+0.8774 0.4430 l
+0.8777 0.4455 l
+0.8780 0.4483 l
+0.8782 0.4516 l
+0.8785 0.4552 l
+0.8788 0.4593 l
+0.8791 0.4636 l
+0.8794 0.4683 l
+0.8797 0.4732 l
+0.8800 0.4784 l
+0.8803 0.4838 l
+0.8805 0.4893 l
+0.8808 0.4951 l
+0.8811 0.5009 l
+0.8814 0.5068 l
+0.8817 0.5128 l
+0.8820 0.5188 l
+0.8823 0.5248 l
+0.8825 0.5307 l
+0.8828 0.5365 l
+0.8831 0.5422 l
+0.8834 0.5478 l
+0.8837 0.5532 l
+0.8840 0.5583 l
+0.8843 0.5633 l
+0.8845 0.5680 l
+0.8848 0.5724 l
+0.8851 0.5764 l
+0.8854 0.5802 l
+0.8857 0.5836 l
+0.8860 0.5867 l
+0.8863 0.5894 l
+0.8865 0.5916 l
+0.8868 0.5935 l
+0.8871 0.5950 l
+0.8874 0.5961 l
+0.8877 0.5968 l
+0.8880 0.5971 l
+0.8883 0.5969 l
+0.8886 0.5964 l
+0.8888 0.5954 l
+0.8891 0.5941 l
+0.8894 0.5924 l
+0.8897 0.5903 l
+0.8900 0.5879 l
+0.8903 0.5852 l
+0.8906 0.5821 l
+0.8908 0.5787 l
+0.8911 0.5751 l
+0.8914 0.5712 l
+0.8917 0.5672 l
+0.8920 0.5629 l
+0.8923 0.5584 l
+0.8926 0.5538 l
+0.8928 0.5491 l
+0.8931 0.5442 l
+0.8934 0.5394 l
+0.8937 0.5345 l
+0.8940 0.5295 l
+0.8943 0.5246 l
+0.8946 0.5198 l
+0.8948 0.5150 l
+0.8951 0.5104 l
+0.8954 0.5058 l
+0.8957 0.5014 l
+0.8960 0.4972 l
+0.8963 0.4932 l
+0.8966 0.4894 l
+0.8969 0.4858 l
+0.8971 0.4825 l
+0.8974 0.4795 l
+0.8977 0.4767 l
+0.8980 0.4743 l
+0.8983 0.4721 l
+0.8986 0.4703 l
+0.8989 0.4688 l
+0.8991 0.4677 l
+0.8994 0.4668 l
+0.8997 0.4663 l
+0.9000 0.4662 l
+0.9003 0.4663 l
+0.9006 0.4668 l
+0.9009 0.4676 l
+0.9011 0.4688 l
+0.9014 0.4702 l
+0.9017 0.4720 l
+0.9020 0.4740 l
+0.9023 0.4762 l
+0.9026 0.4788 l
+0.9029 0.4816 l
+0.9031 0.4845 l
+0.9034 0.4877 l
+0.9037 0.4911 l
+0.9040 0.4946 l
+0.9043 0.4982 l
+0.9046 0.5020 l
+0.9049 0.5059 l
+0.9052 0.5098 l
+0.9054 0.5138 l
+0.9057 0.5178 l
+0.9060 0.5218 l
+0.9063 0.5257 l
+0.9066 0.5297 l
+0.9069 0.5335 l
+0.9072 0.5373 l
+0.9074 0.5410 l
+0.9077 0.5445 l
+0.9080 0.5479 l
+0.9083 0.5511 l
+0.9086 0.5542 l
+0.9089 0.5570 l
+0.9092 0.5597 l
+0.9094 0.5621 l
+0.9097 0.5643 l
+0.9100 0.5662 l
+0.9103 0.5679 l
+0.9106 0.5694 l
+0.9109 0.5705 l
+0.9112 0.5714 l
+0.9115 0.5721 l
+0.9117 0.5724 l
+0.9120 0.5725 l
+0.9123 0.5723 l
+0.9126 0.5719 l
+0.9129 0.5712 l
+0.9132 0.5702 l
+0.9135 0.5690 l
+0.9137 0.5676 l
+0.9140 0.5659 l
+0.9143 0.5641 l
+0.9146 0.5620 l
+0.9149 0.5597 l
+0.9152 0.5573 l
+0.9155 0.5547 l
+0.9157 0.5520 l
+0.9160 0.5491 l
+0.9163 0.5462 l
+0.9166 0.5431 l
+0.9169 0.5400 l
+0.9172 0.5369 l
+0.9175 0.5337 l
+0.9177 0.5305 l
+0.9180 0.5272 l
+0.9183 0.5241 l
+0.9186 0.5209 l
+0.9189 0.5178 l
+0.9192 0.5148 l
+0.9195 0.5119 l
+0.9198 0.5090 l
+0.9200 0.5063 l
+0.9203 0.5038 l
+0.9206 0.5013 l
+0.9209 0.4991 l
+0.9212 0.4970 l
+0.9215 0.4951 l
+0.9218 0.4934 l
+0.9220 0.4918 l
+0.9223 0.4905 l
+0.9226 0.4894 l
+0.9229 0.4885 l
+0.9232 0.4878 l
+0.9235 0.4873 l
+0.9238 0.4871 l
+0.9240 0.4870 l
+0.9243 0.4872 l
+0.9246 0.4876 l
+0.9249 0.4882 l
+0.9252 0.4890 l
+0.9255 0.4900 l
+0.9258 0.4912 l
+0.9260 0.4925 l
+0.9263 0.4940 l
+0.9266 0.4957 l
+0.9269 0.4975 l
+0.9272 0.4995 l
+0.9275 0.5016 l
+0.9278 0.5038 l
+0.9281 0.5060 l
+0.9283 0.5084 l
+0.9286 0.5108 l
+0.9289 0.5133 l
+0.9292 0.5159 l
+0.9295 0.5184 l
+0.9298 0.5210 l
+0.9301 0.5235 l
+0.9303 0.5260 l
+0.9306 0.5285 l
+0.9309 0.5310 l
+0.9312 0.5334 l
+0.9315 0.5357 l
+0.9318 0.5379 l
+0.9321 0.5400 l
+0.9323 0.5421 l
+0.9326 0.5440 l
+0.9329 0.5457 l
+0.9332 0.5474 l
+0.9335 0.5489 l
+0.9338 0.5502 l
+0.9341 0.5514 l
+0.9343 0.5524 l
+0.9346 0.5533 l
+0.9349 0.5539 l
+0.9352 0.5545 l
+0.9355 0.5548 l
+0.9358 0.5550 l
+0.9361 0.5550 l
+0.9364 0.5548 l
+0.9366 0.5545 l
+0.9369 0.5540 l
+0.9372 0.5533 l
+0.9375 0.5525 l
+0.9378 0.5516 l
+0.9381 0.5505 l
+0.9384 0.5493 l
+0.9386 0.5479 l
+0.9389 0.5465 l
+0.9392 0.5449 l
+0.9395 0.5433 l
+0.9398 0.5415 l
+0.9401 0.5397 l
+0.9404 0.5378 l
+0.9406 0.5359 l
+0.9409 0.5340 l
+0.9412 0.5320 l
+0.9415 0.5300 l
+0.9418 0.5280 l
+0.9421 0.5260 l
+0.9424 0.5240 l
+0.9426 0.5220 l
+0.9429 0.5201 l
+0.9432 0.5182 l
+0.9435 0.5164 l
+0.9438 0.5147 l
+0.9441 0.5130 l
+0.9444 0.5115 l
+0.9447 0.5100 l
+0.9449 0.5086 l
+0.9452 0.5073 l
+0.9455 0.5062 l
+0.9458 0.5052 l
+0.9461 0.5043 l
+0.9464 0.5035 l
+0.9467 0.5028 l
+0.9469 0.5023 l
+0.9472 0.5019 l
+0.9475 0.5017 l
+0.9478 0.5016 l
+0.9481 0.5016 l
+0.9484 0.5017 l
+0.9487 0.5020 l
+0.9489 0.5024 l
+0.9492 0.5029 l
+0.9495 0.5036 l
+0.9498 0.5044 l
+0.9501 0.5052 l
+0.9504 0.5062 l
+0.9507 0.5072 l
+0.9509 0.5084 l
+0.9512 0.5096 l
+0.9515 0.5109 l
+0.9518 0.5123 l
+0.9521 0.5137 l
+0.9524 0.5152 l
+0.9527 0.5167 l
+0.9530 0.5182 l
+0.9532 0.5198 l
+0.9535 0.5213 l
+0.9538 0.5229 l
+0.9541 0.5244 l
+0.9544 0.5260 l
+0.9547 0.5275 l
+0.9550 0.5290 l
+0.9552 0.5304 l
+0.9555 0.5318 l
+0.9558 0.5331 l
+0.9561 0.5344 l
+0.9564 0.5356 l
+0.9567 0.5368 l
+0.9570 0.5378 l
+0.9572 0.5388 l
+0.9575 0.5397 l
+0.9578 0.5404 l
+0.9581 0.5411 l
+0.9584 0.5417 l
+0.9587 0.5422 l
+0.9590 0.5426 l
+0.9592 0.5429 l
+0.9595 0.5431 l
+0.9598 0.5431 l
+0.9601 0.5431 l
+0.9604 0.5430 l
+0.9607 0.5427 l
+0.9610 0.5424 l
+0.9613 0.5420 l
+0.9615 0.5415 l
+0.9618 0.5409 l
+0.9621 0.5402 l
+0.9624 0.5394 l
+0.9627 0.5386 l
+0.9630 0.5377 l
+0.9633 0.5367 l
+0.9635 0.5357 l
+0.9638 0.5347 l
+0.9641 0.5336 l
+0.9644 0.5324 l
+0.9647 0.5313 l
+0.9650 0.5301 l
+0.9653 0.5289 l
+0.9655 0.5277 l
+0.9658 0.5265 l
+0.9661 0.5253 l
+0.9664 0.5241 l
+0.9667 0.5230 l
+0.9670 0.5218 l
+0.9673 0.5207 l
+0.9676 0.5197 l
+0.9678 0.5186 l
+0.9681 0.5177 l
+0.9684 0.5167 l
+0.9687 0.5159 l
+0.9690 0.5151 l
+0.9693 0.5144 l
+0.9696 0.5137 l
+0.9698 0.5131 l
+0.9701 0.5126 l
+0.9704 0.5121 l
+0.9707 0.5118 l
+0.9710 0.5115 l
+0.9713 0.5113 l
+0.9716 0.5112 l
+0.9718 0.5111 l
+0.9721 0.5112 l
+0.9724 0.5113 l
+0.9727 0.5115 l
+0.9730 0.5117 l
+0.9733 0.5121 l
+0.9736 0.5125 l
+0.9738 0.5129 l
+0.9741 0.5135 l
+0.9744 0.5141 l
+0.9747 0.5147 l
+0.9750 0.5154 l
+0.9753 0.5161 l
+0.9756 0.5169 l
+0.9759 0.5177 l
+0.9761 0.5186 l
+0.9764 0.5194 l
+0.9767 0.5203 l
+0.9770 0.5212 l
+0.9773 0.5221 l
+0.9776 0.5230 l
+0.9779 0.5240 l
+0.9781 0.5249 l
+0.9784 0.5258 l
+0.9787 0.5266 l
+0.9790 0.5275 l
+0.9793 0.5283 l
+0.9796 0.5291 l
+0.9799 0.5299 l
+0.9801 0.5306 l
+0.9804 0.5313 l
+0.9807 0.5320 l
+0.9810 0.5326 l
+0.9813 0.5331 l
+0.9816 0.5336 l
+0.9819 0.5341 l
+0.9821 0.5344 l
+0.9824 0.5348 l
+0.9827 0.5350 l
+0.9830 0.5352 l
+0.9833 0.5354 l
+0.9836 0.5355 l
+0.9839 0.5355 l
+0.9842 0.5354 l
+0.9844 0.5353 l
+0.9847 0.5352 l
+0.9850 0.5350 l
+0.9853 0.5347 l
+0.9856 0.5344 l
+0.9859 0.5341 l
+0.9862 0.5336 l
+0.9864 0.5332 l
+0.9867 0.5327 l
+0.9870 0.5322 l
+0.9873 0.5316 l
+0.9876 0.5310 l
+0.9879 0.5304 l
+0.9882 0.5298 l
+0.9884 0.5291 l
+0.9887 0.5284 l
+0.9890 0.5278 l
+0.9893 0.5271 l
+0.9896 0.5264 l
+0.9899 0.5257 l
+0.9902 0.5250 l
+0.9904 0.5243 l
+0.9907 0.5237 l
+0.9910 0.5230 l
+0.9913 0.5224 l
+0.9916 0.5218 l
+0.9919 0.5212 l
+0.9922 0.5207 l
+0.9925 0.5202 l
+0.9927 0.5197 l
+0.9930 0.5193 l
+0.9933 0.5189 l
+0.9936 0.5185 l
+0.9939 0.5182 l
+0.9942 0.5179 l
+0.9945 0.5177 l
+0.9947 0.5175 l
+0.9950 0.5173 l
+0.9953 0.5172 l
+0.9956 0.5172 l
+0.9959 0.5172 l
+0.9962 0.5172 l
+0.9965 0.5173 l
+0.9967 0.5174 l
+0.9970 0.5176 l
+0.9973 0.5178 l
+0.9976 0.5180 l
+0.9979 0.5183 l
+0.9982 0.5186 l
+0.9985 0.5189 l
+0.9987 0.5193 l
+0.9990 0.5197 l
+0.9993 0.5201 l
+0.9996 0.5206 l
+0.9999 0.5210 l
+1.0002 0.5215 l
+1.0005 0.5220 l
+1.0008 0.5225 l
+1.0010 0.5230 l
+1.0013 0.5235 l
+1.0016 0.5240 l
+1.0019 0.5245 l
+1.0022 0.5250 l
+1.0025 0.5255 l
+1.0028 0.5260 l
+1.0030 0.5265 l
+1.0033 0.5270 l
+1.0036 0.5274 l
+1.0039 0.5278 l
+1.0042 0.5282 l
+1.0045 0.5286 l
+1.0048 0.5290 l
+1.0050 0.5293 l
+1.0053 0.5296 l
+1.0056 0.5298 l
+1.0059 0.5301 l
+1.0062 0.5303 l
+1.0065 0.5305 l
+1.0068 0.5306 l
+1.0070 0.5307 l
+1.0073 0.5308 l
+1.0076 0.5308 l
+1.0079 0.5308 l
+1.0082 0.5308 l
+1.0085 0.5307 l
+1.0088 0.5306 l
+1.0091 0.5305 l
+1.0093 0.5303 l
+1.0096 0.5302 l
+1.0099 0.5299 l
+1.0102 0.5297 l
+1.0105 0.5295 l
+1.0108 0.5292 l
+1.0111 0.5289 l
+1.0113 0.5286 l
+1.0116 0.5282 l
+1.0119 0.5279 l
+1.0122 0.5275 l
+1.0125 0.5272 l
+1.0128 0.5268 l
+1.0131 0.5264 l
+1.0133 0.5261 l
+1.0136 0.5257 l
+1.0139 0.5253 l
+1.0142 0.5249 l
+1.0145 0.5246 l
+1.0148 0.5242 l
+1.0151 0.5239 l
+1.0153 0.5235 l
+1.0156 0.5232 l
+1.0159 0.5229 l
+1.0162 0.5226 l
+1.0165 0.5223 l
+1.0168 0.5221 l
+1.0171 0.5218 l
+1.0174 0.5216 l
+1.0176 0.5214 l
+1.0179 0.5213 l
+1.0182 0.5211 l
+1.0185 0.5210 l
+1.0188 0.5209 l
+1.0191 0.5208 l
+1.0194 0.5208 l
+1.0196 0.5208 l
+1.0199 0.5208 l
+1.0202 0.5208 l
+1.0205 0.5208 l
+1.0208 0.5209 l
+1.0211 0.5210 l
+1.0214 0.5211 l
+1.0216 0.5213 l
+1.0219 0.5214 l
+1.0222 0.5216 l
+1.0225 0.5218 l
+1.0228 0.5220 l
+1.0231 0.5222 l
+1.0234 0.5224 l
+1.0237 0.5227 l
+1.0239 0.5229 l
+1.0242 0.5232 l
+1.0245 0.5234 l
+1.0248 0.5237 l
+1.0251 0.5240 l
+1.0254 0.5243 l
+1.0257 0.5245 l
+1.0259 0.5248 l
+1.0262 0.5251 l
+1.0265 0.5253 l
+1.0268 0.5256 l
+1.0271 0.5259 l
+1.0274 0.5261 l
+1.0277 0.5263 l
+1.0279 0.5266 l
+1.0282 0.5268 l
+1.0285 0.5270 l
+1.0288 0.5272 l
+1.0291 0.5273 l
+1.0294 0.5275 l
+1.0297 0.5276 l
+1.0299 0.5277 l
+1.0302 0.5278 l
+1.0305 0.5279 l
+1.0308 0.5280 l
+1.0311 0.5280 l
+1.0314 0.5281 l
+1.0317 0.5281 l
+1.0320 0.5281 l
+1.0322 0.5280 l
+1.0325 0.5280 l
+1.0328 0.5280 l
+1.0331 0.5279 l
+1.0334 0.5278 l
+1.0337 0.5277 l
+1.0340 0.5276 l
+1.0342 0.5275 l
+1.0345 0.5273 l
+1.0348 0.5272 l
+1.0351 0.5270 l
+1.0354 0.5268 l
+1.0357 0.5267 l
+1.0360 0.5265 l
+1.0362 0.5263 l
+1.0365 0.5261 l
+1.0368 0.5259 l
+1.0371 0.5257 l
+1.0374 0.5255 l
+1.0377 0.5253 l
+1.0380 0.5251 l
+1.0382 0.5249 l
+1.0385 0.5247 l
+1.0388 0.5245 l
+1.0391 0.5244 l
+1.0394 0.5242 l
+1.0397 0.5240 l
+1.0400 0.5239 l
+1.0403 0.5237 l
+1.0405 0.5236 l
+1.0408 0.5234 l
+1.0411 0.5233 l
+1.0414 0.5232 l
+1.0417 0.5231 l
+1.0420 0.5230 l
+1.0423 0.5230 l
+1.0425 0.5229 l
+1.0428 0.5229 l
+1.0431 0.5228 l
+1.0434 0.5228 l
+1.0437 0.5228 l
+1.0440 0.5228 l
+1.0443 0.5228 l
+1.0445 0.5229 l
+1.0448 0.5229 l
+1.0451 0.5229 l
+1.0454 0.5230 l
+1.0457 0.5231 l
+1.0460 0.5232 l
+1.0463 0.5233 l
+1.0465 0.5234 l
+1.0468 0.5235 l
+1.0471 0.5236 l
+1.0474 0.5237 l
+1.0477 0.5238 l
+1.0480 0.5240 l
+1.0483 0.5241 l
+1.0486 0.5242 l
+1.0488 0.5244 l
+1.0491 0.5245 l
+1.0494 0.5247 l
+1.0497 0.5248 l
+1.0500 0.5249 l
+1.0503 0.5251 l
+1.0506 0.5252 l
+1.0508 0.5253 l
+1.0511 0.5255 l
+1.0514 0.5256 l
+1.0517 0.5257 l
+1.0520 0.5258 l
+1.0523 0.5259 l
+1.0526 0.5260 l
+1.0528 0.5261 l
+1.0531 0.5262 l
+1.0534 0.5263 l
+1.0537 0.5263 l
+1.0540 0.5264 l
+1.0543 0.5264 l
+1.0546 0.5265 l
+1.0548 0.5265 l
+1.0551 0.5265 l
+1.0554 0.5266 l
+1.0557 0.5266 l
+1.0560 0.5266 l
+1.0563 0.5265 l
+1.0566 0.5265 l
+1.0569 0.5265 l
+1.0571 0.5264 l
+1.0574 0.5264 l
+1.0577 0.5263 l
+1.0580 0.5263 l
+1.0583 0.5262 l
+1.0586 0.5262 l
+1.0589 0.5261 l
+1.0591 0.5260 l
+1.0594 0.5259 l
+1.0597 0.5258 l
+1.0600 0.5257 l
+1.0603 0.5256 l
+1.0606 0.5255 l
+1.0609 0.5254 l
+1.0611 0.5253 l
+1.0614 0.5252 l
+1.0617 0.5251 l
+1.0620 0.5250 l
+1.0623 0.5249 l
+1.0626 0.5248 l
+1.0629 0.5248 l
+1.0631 0.5247 l
+1.0634 0.5246 l
+1.0637 0.5245 l
+1.0640 0.5244 l
+1.0643 0.5243 l
+1.0646 0.5243 l
+1.0649 0.5242 l
+1.0652 0.5242 l
+1.0654 0.5241 l
+1.0657 0.5241 l
+1.0660 0.5240 l
+1.0663 0.5240 l
+1.0666 0.5240 l
+1.0669 0.5239 l
+1.0672 0.5239 l
+1.0674 0.5239 l
+1.0677 0.5239 l
+1.0680 0.5239 l
+1.0683 0.5239 l
+1.0686 0.5239 l
+1.0689 0.5240 l
+1.0692 0.5240 l
+1.0694 0.5240 l
+1.0697 0.5241 l
+1.0700 0.5241 l
+1.0703 0.5242 l
+1.0706 0.5242 l
+1.0709 0.5243 l
+1.0712 0.5243 l
+1.0715 0.5244 l
+1.0717 0.5244 l
+1.0720 0.5245 l
+1.0723 0.5246 l
+1.0726 0.5246 l
+1.0729 0.5247 l
+1.0732 0.5248 l
+1.0735 0.5248 l
+1.0737 0.5249 l
+1.0740 0.5250 l
+1.0743 0.5251 l
+1.0746 0.5251 l
+1.0749 0.5252 l
+1.0752 0.5252 l
+1.0755 0.5253 l
+1.0757 0.5254 l
+1.0760 0.5254 l
+1.0763 0.5255 l
+1.0766 0.5255 l
+1.0769 0.5256 l
+1.0772 0.5256 l
+1.0775 0.5256 l
+1.0777 0.5257 l
+1.0780 0.5257 l
+1.0783 0.5257 l
+1.0786 0.5257 l
+1.0789 0.5257 l
+1.0792 0.5258 l
+1.0795 0.5258 l
+1.0798 0.5258 l
+1.0800 0.5258 l
+1.0803 0.5257 l
+1.0806 0.5257 l
+1.0809 0.5257 l
+1.0812 0.5257 l
+1.0815 0.5257 l
+1.0818 0.5256 l
+1.0820 0.5256 l
+1.0823 0.5256 l
+1.0826 0.5255 l
+1.0829 0.5255 l
+1.0832 0.5255 l
+1.0835 0.5254 l
+1.0838 0.5254 l
+1.0840 0.5253 l
+1.0843 0.5253 l
+1.0846 0.5252 l
+1.0849 0.5252 l
+1.0852 0.5251 l
+1.0855 0.5251 l
+1.0858 0.5251 l
+1.0860 0.5250 l
+1.0863 0.5250 l
+1.0866 0.5249 l
+1.0869 0.5249 l
+1.0872 0.5248 l
+1.0875 0.5248 l
+1.0878 0.5247 l
+1.0881 0.5247 l
+1.0883 0.5247 l
+1.0886 0.5246 l
+1.0889 0.5246 l
+1.0892 0.5246 l
+1.0895 0.5246 l
+1.0898 0.5245 l
+1.0901 0.5245 l
+1.0903 0.5245 l
+1.0906 0.5245 l
+1.0909 0.5245 l
+1.0912 0.5245 l
+1.0915 0.5245 l
+1.0918 0.5245 l
+1.0921 0.5245 l
+1.0923 0.5245 l
+1.0926 0.5245 l
+1.0929 0.5245 l
+1.0932 0.5245 l
+1.0935 0.5245 l
+1.0938 0.5246 l
+1.0941 0.5246 l
+1.0943 0.5246 l
+1.0946 0.5246 l
+1.0949 0.5247 l
+1.0952 0.5247 l
+1.0955 0.5247 l
+1.0958 0.5247 l
+1.0961 0.5248 l
+1.0964 0.5248 l
+1.0966 0.5248 l
+1.0969 0.5249 l
+1.0972 0.5249 l
+1.0975 0.5249 l
+1.0978 0.5250 l
+1.0981 0.5250 l
+1.0984 0.5250 l
+1.0986 0.5251 l
+1.0989 0.5251 l
+1.0992 0.5251 l
+1.0995 0.5251 l
+1.0998 0.5252 l
+1.1001 0.5252 l
+1.1004 0.5252 l
+1.1006 0.5252 l
+1.1009 0.5253 l
+1.1012 0.5253 l
+1.1015 0.5253 l
+1.1018 0.5253 l
+1.1021 0.5253 l
+1.1024 0.5253 l
+1.1026 0.5253 l
+1.1029 0.5253 l
+1.1032 0.5253 l
+1.1035 0.5254 l
+1.1038 0.5254 l
+1.1041 0.5253 l
+1.1044 0.5253 l
+1.1047 0.5253 l
+1.1049 0.5253 l
+1.1052 0.5253 l
+1.1055 0.5253 l
+1.1058 0.5253 l
+1.1061 0.5253 l
+1.1064 0.5253 l
+1.1067 0.5252 l
+1.1069 0.5252 l
+1.1072 0.5252 l
+1.1075 0.5252 l
+1.1078 0.5252 l
+1.1081 0.5252 l
+1.1084 0.5251 l
+1.1087 0.5251 l
+1.1089 0.5251 l
+1.1092 0.5251 l
+1.1095 0.5250 l
+1.1098 0.5250 l
+1.1101 0.5250 l
+1.1104 0.5250 l
+1.1107 0.5250 l
+1.1109 0.5249 l
+1.1112 0.5249 l
+1.1115 0.5249 l
+1.1118 0.5249 l
+1.1121 0.5249 l
+1.1124 0.5248 l
+1.1127 0.5248 l
+1.1130 0.5248 l
+1.1132 0.5248 l
+1.1135 0.5248 l
+1.1138 0.5248 l
+1.1141 0.5248 l
+1.1144 0.5248 l
+1.1147 0.5248 l
+1.1150 0.5248 l
+1.1152 0.5248 l
+1.1155 0.5248 l
+1.1158 0.5248 l
+1.1161 0.5248 l
+1.1164 0.5248 l
+1.1167 0.5248 l
+1.1170 0.5248 l
+1.1172 0.5248 l
+1.1175 0.5248 l
+1.1178 0.5248 l
+1.1181 0.5248 l
+1.1184 0.5248 l
+1.1187 0.5248 l
+1.1190 0.5248 l
+1.1192 0.5249 l
+1.1195 0.5249 l
+1.1198 0.5249 l
+1.1201 0.5249 l
+1.1204 0.5249 l
+1.1207 0.5249 l
+1.1210 0.5249 l
+1.1213 0.5250 l
+1.1215 0.5250 l
+1.1218 0.5250 l
+1.1221 0.5250 l
+1.1224 0.5250 l
+1.1227 0.5250 l
+1.1230 0.5250 l
+1.1233 0.5251 l
+1.1235 0.5251 l
+1.1238 0.5251 l
+1.1241 0.5251 l
+1.1244 0.5251 l
+1.1247 0.5251 l
+1.1250 0.5251 l
+1.1253 0.5251 l
+1.1255 0.5251 l
+1.1258 0.5251 l
+1.1261 0.5251 l
+1.1264 0.5251 l
+1.1267 0.5252 l
+1.1270 0.5252 l
+1.1273 0.5252 l
+1.1276 0.5252 l
+1.1278 0.5252 l
+1.1281 0.5252 l
+1.1284 0.5252 l
+1.1287 0.5251 l
+1.1290 0.5251 l
+1.1293 0.5251 l
+1.1296 0.5251 l
+1.1298 0.5251 l
+1.1301 0.5251 l
+1.1304 0.5251 l
+1.1307 0.5251 l
+1.1310 0.5251 l
+1.1313 0.5251 l
+1.1316 0.5251 l
+1.1318 0.5251 l
+1.1321 0.5251 l
+1.1324 0.5251 l
+1.1327 0.5250 l
+1.1330 0.5250 l
+1.1333 0.5250 l
+1.1336 0.5250 l
+1.1338 0.5250 l
+1.1341 0.5250 l
+1.1344 0.5250 l
+1.1347 0.5250 l
+1.1350 0.5250 l
+1.1353 0.5250 l
+1.1356 0.5250 l
+1.1359 0.5249 l
+1.1361 0.5249 l
+1.1364 0.5249 l
+1.1367 0.5249 l
+1.1370 0.5249 l
+1.1373 0.5249 l
+1.1376 0.5249 l
+1.1379 0.5249 l
+1.1381 0.5249 l
+1.1384 0.5249 l
+1.1387 0.5249 l
+1.1390 0.5249 l
+1.1393 0.5249 l
+1.1396 0.5249 l
+1.1399 0.5249 l
+1.1401 0.5249 l
+1.1404 0.5249 l
+1.1407 0.5249 l
+1.1410 0.5249 l
+1.1413 0.5249 l
+1.1416 0.5249 l
+1.1419 0.5249 l
+1.1421 0.5249 l
+1.1424 0.5249 l
+1.1427 0.5249 l
+1.1430 0.5249 l
+1.1433 0.5249 l
+1.1436 0.5249 l
+1.1439 0.5250 l
+1.1442 0.5250 l
+1.1444 0.5250 l
+1.1447 0.5250 l
+1.1450 0.5250 l
+1.1453 0.5250 l
+1.1456 0.5250 l
+1.1459 0.5250 l
+1.1462 0.5250 l
+1.1464 0.5250 l
+1.1467 0.5250 l
+1.1470 0.5250 l
+1.1473 0.5250 l
+1.1476 0.5250 l
+1.1479 0.5250 l
+1.1482 0.5250 l
+1.1484 0.5250 l
+1.1487 0.5250 l
+1.1490 0.5251 l
+1.1493 0.5251 l
+1.1496 0.5251 l
+1.1499 0.5251 l
+1.1502 0.5251 l
+1.1504 0.5251 l
+1.1507 0.5251 l
+1.1510 0.5251 l
+1.1513 0.5251 l
+1.1516 0.5251 l
+1.1519 0.5251 l
+1.1522 0.5251 l
+1.1525 0.5251 l
+1.1527 0.5251 l
+1.1530 0.5251 l
+1.1533 0.5251 l
+1.1536 0.5251 l
+1.1539 0.5251 l
+1.1542 0.5251 l
+1.1545 0.5250 l
+1.1547 0.5250 l
+1.1550 0.5250 l
+1.1553 0.5250 l
+1.1556 0.5250 l
+1.1559 0.5250 l
+1.1562 0.5250 l
+1.1565 0.5250 l
+1.1567 0.5250 l
+1.1570 0.5250 l
+1.1573 0.5250 l
+1.1576 0.5250 l
+1.1579 0.5250 l
+1.1582 0.5250 l
+1.1585 0.5250 l
+1.1587 0.5250 l
+1.1590 0.5250 l
+1.1593 0.5250 l
+1.1596 0.5250 l
+1.1599 0.5250 l
+1.1602 0.5250 l
+1.1605 0.5250 l
+1.1608 0.5250 l
+1.1610 0.5250 l
+1.1613 0.5250 l
+1.1616 0.5250 l
+1.1619 0.5250 l
+1.1622 0.5250 l
+1.1625 0.5250 l
+1.1628 0.5250 l
+1.1630 0.5250 l
+1.1633 0.5250 l
+1.1636 0.5250 l
+1.1639 0.5250 l
+1.1642 0.5250 l
+1.1645 0.5250 l
+1.1648 0.5250 l
+1.1650 0.5250 l
+1.1653 0.5250 l
+1.1656 0.5250 l
+1.1659 0.5250 l
+1.1662 0.5250 l
+1.1665 0.5250 l
+1.1668 0.5250 l
+1.1670 0.5250 l
+1.1673 0.5250 l
+1.1676 0.5250 l
+1.1679 0.5250 l
+1.1682 0.5250 l
+1.1685 0.5250 l
+1.1688 0.5250 l
+1.1691 0.5250 l
+1.1693 0.5250 l
+1.1696 0.5250 l
+1.1699 0.5250 l
+1.1702 0.5250 l
+1.1705 0.5250 l
+1.1708 0.5250 l
+1.1711 0.5250 l
+1.1713 0.5250 l
+1.1716 0.5250 l
+1.1719 0.5250 l
+1.1722 0.5250 l
+1.1725 0.5250 l
+1.1728 0.5250 l
+1.1731 0.5250 l
+1.1733 0.5250 l
+1.1736 0.5250 l
+1.1739 0.5250 l
+1.1742 0.5250 l
+1.1745 0.5250 l
+1.1748 0.5250 l
+1.1751 0.5250 l
+1.1754 0.5250 l
+1.1756 0.5250 l
+1.1759 0.5250 l
+1.1762 0.5250 l
+1.1765 0.5250 l
+1.1768 0.5250 l
+1.1771 0.5250 l
+1.1774 0.5250 l
+1.1776 0.5250 l
+1.1779 0.5250 l
+1.1782 0.5250 l
+1.1785 0.5250 l
+1.1788 0.5250 l
+1.1791 0.5250 l
+1.1794 0.5250 l
+1.1796 0.5250 l
+1.1799 0.5250 l
+1.1802 0.5250 l
+1.1805 0.5250 l
+1.1808 0.5250 l
+1.1811 0.5250 l
+1.1814 0.5250 l
+1.1816 0.5250 l
+1.1819 0.5250 l
+1.1822 0.5250 l
+1.1825 0.5250 l
+1.1828 0.5250 l
+1.1831 0.5250 l
+1.1834 0.5250 l
+1.1837 0.5250 l
+1.1839 0.5250 l
+1.1842 0.5250 l
+1.1845 0.5250 l
+1.1848 0.5250 l
+1.1851 0.5250 l
+1.1854 0.5250 l
+1.1857 0.5250 l
+1.1859 0.5250 l
+1.1862 0.5250 l
+1.1865 0.5250 l
+1.1868 0.5250 l
+1.1871 0.5250 l
+1.1874 0.5250 l
+1.1877 0.5250 l
+1.1879 0.5250 l
+1.1882 0.5250 l
+1.1885 0.5250 l
+1.1888 0.5250 l
+1.1891 0.5250 l
+1.1894 0.5250 l
+1.1897 0.5250 l
+1.1899 0.5250 l
+1.1902 0.5250 l
+1.1905 0.5250 l
+1.1908 0.5250 l
+1.1911 0.5250 l
+1.1914 0.5250 l
+1.1917 0.5250 l
+1.1920 0.5250 l
+1.1922 0.5250 l
+1.1925 0.5250 l
+1.1928 0.5250 l
+1.1931 0.5250 l
+1.1934 0.5250 l
+1.1937 0.5250 l
+1.1940 0.5250 l
+1.1942 0.5250 l
+1.1945 0.5250 l
+1.1948 0.5250 l
+1.1951 0.5250 l
+1.1954 0.5250 l
+1.1957 0.5250 l
+1.1960 0.5250 l
+1.1962 0.5250 l
+1.1965 0.5250 l
+1.1968 0.5250 l
+1.1971 0.5250 l
+1.1974 0.5250 l
+1.1977 0.5250 l
+1.1980 0.5250 l
+1.1982 0.5250 l
+1.1985 0.5250 l
+1.1988 0.5250 l
+1.1991 0.5250 l
+1.1994 0.5250 l
+1.1997 0.5250 l
+1.2000 0.5250 l
+1.2003 0.5250 l
+1.2005 0.5250 l
+1.2008 0.5250 l
+1.2011 0.5250 l
+1.2014 0.5250 l
+1.2017 0.5250 l
+1.2020 0.5250 l
+1.2023 0.5250 l
+1.2025 0.5250 l
+1.2028 0.5250 l
+1.2031 0.5250 l
+1.2034 0.5250 l
+1.2037 0.5250 l
+1.2040 0.5250 l
+1.2043 0.5250 l
+1.2045 0.5250 l
+1.2048 0.5250 l
+1.2051 0.5250 l
+1.2054 0.5250 l
+1.2057 0.5250 l
+1.2060 0.5250 l
+1.2063 0.5250 l
+1.2065 0.5250 l
+1.2068 0.5250 l
+1.2071 0.5250 l
+1.2074 0.5250 l
+1.2077 0.5250 l
+1.2080 0.5250 l
+1.2083 0.5250 l
+1.2086 0.5250 l
+1.2088 0.5250 l
+1.2091 0.5250 l
+1.2094 0.5250 l
+1.2097 0.5250 l
+1.2100 0.5250 l
+1.2103 0.5250 l
+1.2106 0.5250 l
+1.2108 0.5250 l
+1.2111 0.5250 l
+1.2114 0.5250 l
+1.2117 0.5250 l
+1.2120 0.5250 l
+1.2123 0.5250 l
+1.2126 0.5250 l
+1.2128 0.5250 l
+1.2131 0.5250 l
+1.2134 0.5250 l
+1.2137 0.5250 l
+1.2140 0.5250 l
+1.2143 0.5250 l
+1.2146 0.5250 l
+1.2148 0.5250 l
+1.2151 0.5250 l
+1.2154 0.5250 l
+1.2157 0.5250 l
+1.2160 0.5250 l
+1.2163 0.5250 l
+1.2166 0.5250 l
+1.2169 0.5250 l
+1.2171 0.5250 l
+1.2174 0.5250 l
+1.2177 0.5250 l
+1.2180 0.5250 l
+1.2183 0.5250 l
+1.2186 0.5250 l
+1.2189 0.5250 l
+1.2191 0.5250 l
+1.2194 0.5250 l
+1.2197 0.5250 l
+1.2200 0.5250 l
+1.2203 0.5250 l
+1.2206 0.5250 l
+1.2209 0.5250 l
+1.2211 0.5250 l
+1.2214 0.5250 l
+1.2217 0.5250 l
+1.2220 0.5250 l
+1.2223 0.5250 l
+1.2226 0.5250 l
+1.2229 0.5250 l
+1.2231 0.5250 l
+1.2234 0.5250 l
+1.2237 0.5250 l
+1.2240 0.5250 l
+1.2243 0.5250 l
+1.2246 0.5250 l
+1.2249 0.5250 l
+1.2252 0.5250 l
+1.2254 0.5250 l
+1.2257 0.5250 l
+1.2260 0.5250 l
+1.2263 0.5250 l
+1.2266 0.5250 l
+1.2269 0.5250 l
+1.2272 0.5250 l
+1.2274 0.5250 l
+1.2277 0.5250 l
+1.2280 0.5250 l
+1.2283 0.5250 l
+1.2286 0.5250 l
+1.2289 0.5250 l
+1.2292 0.5250 l
+1.2294 0.5250 l
+1.2297 0.5250 l
+1.2300 0.5250 l
+1.2303 0.5250 l
+1.2306 0.5250 l
+1.2309 0.5250 l
+1.2312 0.5250 l
+1.2315 0.5250 l
+1.2317 0.5250 l
+1.2320 0.5250 l
+1.2323 0.5250 l
+1.2326 0.5250 l
+1.2329 0.5250 l
+1.2332 0.5250 l
+1.2335 0.5250 l
+1.2337 0.5250 l
+1.2340 0.5250 l
+1.2343 0.5250 l
+1.2346 0.5250 l
+1.2349 0.5250 l
+1.2352 0.5250 l
+1.2355 0.5250 l
+1.2357 0.5250 l
+1.2360 0.5250 l
+1.2363 0.5250 l
+1.2366 0.5250 l
+1.2369 0.5250 l
+1.2372 0.5250 l
+1.2375 0.5250 l
+1.2377 0.5250 l
+1.2380 0.5250 l
+1.2383 0.5250 l
+1.2386 0.5250 l
+1.2389 0.5250 l
+1.2392 0.5250 l
+1.2395 0.5250 l
+1.2398 0.5250 l
+1.2400 0.5250 l
+1.2403 0.5250 l
+1.2406 0.5250 l
+1.2409 0.5250 l
+1.2412 0.5250 l
+1.2415 0.5250 l
+1.2418 0.5250 l
+1.2420 0.5250 l
+1.2423 0.5250 l
+1.2426 0.5250 l
+1.2429 0.5250 l
+1.2432 0.5250 l
+1.2435 0.5250 l
+1.2438 0.5250 l
+1.2440 0.5250 l
+1.2443 0.5250 l
+1.2446 0.5250 l
+1.2449 0.5250 l
+s
+n
+0.1000 0.1000 m
+1.2449 0.1000 l
+s
+n
+0.1000 0.9500 m
+1.2449 0.9500 l
+s
+n
+0.2431 0.1000 m
+0.2431 0.1100 l
+s
+n
+0.2431 0.9500 m
+0.2431 0.9400 l
+s
+n
+0.5293 0.1000 m
+0.5293 0.1100 l
+s
+n
+0.5293 0.9500 m
+0.5293 0.9400 l
+s
+n
+0.8156 0.1000 m
+0.8156 0.1100 l
+s
+n
+0.8156 0.9500 m
+0.8156 0.9400 l
+s
+n
+1.1018 0.1000 m
+1.1018 0.1100 l
+s
+n
+1.1018 0.9500 m
+1.1018 0.9400 l
+s
+n
+0.1000 0.1000 m
+0.1000 0.1200 l
+s
+n
+0.1000 0.9500 m
+0.1000 0.9300 l
+s
+n
+0.3862 0.1000 m
+0.3862 0.1200 l
+s
+n
+0.3862 0.9500 m
+0.3862 0.9300 l
+s
+n
+0.6725 0.1000 m
+0.6725 0.1200 l
+s
+n
+0.6725 0.9500 m
+0.6725 0.9300 l
+s
+n
+0.9587 0.1000 m
+0.9587 0.1200 l
+s
+n
+0.9587 0.9500 m
+0.9587 0.9300 l
+s
+n
+1.2449 0.1000 m
+1.2449 0.1200 l
+s
+n
+1.2449 0.9500 m
+1.2449 0.9300 l
+s
+/Helvetica findfont
+dup length dict begin
+ {1 index /FID ne {def} {pop pop} ifelse} forall
+ /Encoding DefEncoding def
+ currentdict
+end
+/Font4 exch definefont pop
+/Font4 FFSF
+0.0912 0.0653 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(0) show
+GR
+/Font4 FFSF
+0.3627 0.0653 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(0.5) show
+GR
+/Font4 FFSF
+0.6664 0.0653 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(1) show
+GR
+/Font4 FFSF
+0.9351 0.0653 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(1.5) show
+GR
+/Font4 FFSF
+1.2359 0.0653 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(2) show
+GR
+/Font4 FFSF
+0.5854 0.0239 m
+GS
+[0.0420 0.0000 0.0000 0.0420 0 0] CC
+(Time \(ps\)) show
+GR
+n
+0.1000 0.1000 m
+0.1000 0.9500 l
+s
+n
+1.2449 0.1000 m
+1.2449 0.9500 l
+s
+n
+0.1000 0.2063 m
+0.1100 0.2063 l
+s
+n
+1.2449 0.2063 m
+1.2349 0.2063 l
+s
+n
+0.1000 0.4188 m
+0.1100 0.4188 l
+s
+n
+1.2449 0.4188 m
+1.2349 0.4188 l
+s
+n
+0.1000 0.6312 m
+0.1100 0.6312 l
+s
+n
+1.2449 0.6312 m
+1.2349 0.6312 l
+s
+n
+0.1000 0.8438 m
+0.1100 0.8438 l
+s
+n
+1.2449 0.8438 m
+1.2349 0.8438 l
+s
+n
+0.1000 0.1000 m
+0.1200 0.1000 l
+s
+n
+1.2449 0.1000 m
+1.2249 0.1000 l
+s
+n
+0.1000 0.3125 m
+0.1200 0.3125 l
+s
+n
+1.2449 0.3125 m
+1.2249 0.3125 l
+s
+n
+0.1000 0.5250 m
+0.1200 0.5250 l
+s
+n
+1.2449 0.5250 m
+1.2249 0.5250 l
+s
+n
+0.1000 0.7375 m
+0.1200 0.7375 l
+s
+n
+1.2449 0.7375 m
+1.2249 0.7375 l
+s
+n
+0.1000 0.9500 m
+0.1200 0.9500 l
+s
+n
+1.2449 0.9500 m
+1.2249 0.9500 l
+s
+/Font4 FFSF
+0.0602 0.0878 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(-2) show
+GR
+/Font4 FFSF
+0.0661 0.3001 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(-1) show
+GR
+/Font4 FFSF
+0.0724 0.5130 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(0) show
+GR
+/Font4 FFSF
+0.0778 0.7251 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(1) show
+GR
+/Font4 FFSF
+0.0720 0.9378 m
+GS
+[0.0350 0.0000 0.0000 0.0350 0 0] CC
+(2) show
+GR
+/Font4 FFSF
+0.0412 0.3446 m
+GS
+[0.0000 0.0420 -0.0420 0.0000 0 0] CC
+(Electric field \(V/nm\)) show
+GR
+n
+0.1000 0.1000 m
+0.1000 0.9500 l
+1.2449 0.9500 l
+1.2449 0.1000 l
+0.1000 0.1000 l
+c
+s
+%%Trailer
+%%DocumentNeededResources: font Helvetica
+%%EOF
--- /dev/null
+# Grace project file
+#
+@version 50125
+@page size 792, 612
+@page scroll 5%
+@page inout 5%
+@link page off
+@map font 0 to "Times-Roman", "Times-Roman"
+@map font 1 to "Times-Italic", "Times-Italic"
+@map font 2 to "Times-Bold", "Times-Bold"
+@map font 3 to "Times-BoldItalic", "Times-BoldItalic"
+@map font 4 to "Helvetica", "Helvetica"
+@map font 5 to "Helvetica-Oblique", "Helvetica-Oblique"
+@map font 6 to "Helvetica-Bold", "Helvetica-Bold"
+@map font 7 to "Helvetica-BoldOblique", "Helvetica-BoldOblique"
+@map font 8 to "Courier", "Courier"
+@map font 9 to "Courier-Oblique", "Courier-Oblique"
+@map font 10 to "Courier-Bold", "Courier-Bold"
+@map font 11 to "Courier-BoldOblique", "Courier-BoldOblique"
+@map font 12 to "Symbol", "Symbol"
+@map font 13 to "ZapfDingbats", "ZapfDingbats"
+@map color 0 to (255, 255, 255), "white"
+@map color 1 to (0, 0, 0), "black"
+@map color 2 to (255, 0, 0), "red"
+@map color 3 to (0, 255, 0), "green"
+@map color 4 to (0, 0, 255), "blue"
+@map color 5 to (255, 255, 0), "yellow"
+@map color 6 to (188, 143, 143), "brown"
+@map color 7 to (220, 220, 220), "grey"
+@map color 8 to (148, 0, 211), "violet"
+@map color 9 to (0, 255, 255), "cyan"
+@map color 10 to (255, 0, 255), "magenta"
+@map color 11 to (255, 165, 0), "orange"
+@map color 12 to (114, 33, 188), "indigo"
+@map color 13 to (103, 7, 72), "maroon"
+@map color 14 to (64, 224, 208), "turquoise"
+@map color 15 to (0, 139, 0), "green4"
+@reference date 0
+@date wrap off
+@date wrap year 1950
+@default linewidth 1.0
+@default linestyle 1
+@default color 1
+@default pattern 1
+@default font 0
+@default char size 1.000000
+@default symbol size 1.000000
+@default sformat "%.8g"
+@background color 0
+@page background fill on
+@timestamp off
+@timestamp 0.03, 0.03
+@timestamp color 1
+@timestamp rot 0
+@timestamp font 0
+@timestamp char size 1.000000
+@timestamp def "Tue Jul 5 08:29:55 2016"
+@r0 off
+@link r0 to g0
+@r0 type above
+@r0 linestyle 1
+@r0 linewidth 1.0
+@r0 color 1
+@r0 line 0, 0, 0, 0
+@r1 off
+@link r1 to g0
+@r1 type above
+@r1 linestyle 1
+@r1 linewidth 1.0
+@r1 color 1
+@r1 line 0, 0, 0, 0
+@r2 off
+@link r2 to g0
+@r2 type above
+@r2 linestyle 1
+@r2 linewidth 1.0
+@r2 color 1
+@r2 line 0, 0, 0, 0
+@r3 off
+@link r3 to g0
+@r3 type above
+@r3 linestyle 1
+@r3 linewidth 1.0
+@r3 color 1
+@r3 line 0, 0, 0, 0
+@r4 off
+@link r4 to g0
+@r4 type above
+@r4 linestyle 1
+@r4 linewidth 1.0
+@r4 color 1
+@r4 line 0, 0, 0, 0
+@g0 on
+@g0 hidden false
+@g0 type XY
+@g0 stacked false
+@g0 bar hgap 0.000000
+@g0 fixedpoint off
+@g0 fixedpoint type 0
+@g0 fixedpoint xy 0.000000, 0.000000
+@g0 fixedpoint format general general
+@g0 fixedpoint prec 6, 6
+@with g0
+@ world 0, -2, 2, 2
+@ stack world 0, 0, 0, 0
+@ znorm 1
+@ view 0.100000, 0.100000, 1.244903, 0.950000
+@ title ""
+@ title font 0
+@ title size 1.500000
+@ title color 1
+@ subtitle ""
+@ subtitle font 0
+@ subtitle size 1.000000
+@ subtitle color 1
+@ xaxes scale Normal
+@ yaxes scale Normal
+@ xaxes invert off
+@ yaxes invert off
+@ xaxis on
+@ xaxis type zero false
+@ xaxis offset 0.000000 , 0.000000
+@ xaxis bar on
+@ xaxis bar color 1
+@ xaxis bar linestyle 1
+@ xaxis bar linewidth 1.0
+@ xaxis label "Time (ps)"
+@ xaxis label layout para
+@ xaxis label place auto
+@ xaxis label char size 1.500000
+@ xaxis label font 4
+@ xaxis label color 1
+@ xaxis label place normal
+@ xaxis tick on
+@ xaxis tick major 0.5
+@ xaxis tick minor ticks 1
+@ xaxis tick default 6
+@ xaxis tick place rounded true
+@ xaxis tick in
+@ xaxis tick major size 1.000000
+@ xaxis tick major color 1
+@ xaxis tick major linewidth 1.0
+@ xaxis tick major linestyle 1
+@ xaxis tick major grid off
+@ xaxis tick minor color 1
+@ xaxis tick minor linewidth 1.0
+@ xaxis tick minor linestyle 1
+@ xaxis tick minor grid off
+@ xaxis tick minor size 0.500000
+@ xaxis ticklabel on
+@ xaxis ticklabel format general
+@ xaxis ticklabel prec 5
+@ xaxis ticklabel formula ""
+@ xaxis ticklabel append ""
+@ xaxis ticklabel prepend ""
+@ xaxis ticklabel angle 0
+@ xaxis ticklabel skip 0
+@ xaxis ticklabel stagger 0
+@ xaxis ticklabel place normal
+@ xaxis ticklabel offset auto
+@ xaxis ticklabel offset 0.000000 , 0.010000
+@ xaxis ticklabel start type auto
+@ xaxis ticklabel start 0.000000
+@ xaxis ticklabel stop type auto
+@ xaxis ticklabel stop 0.000000
+@ xaxis ticklabel char size 1.250000
+@ xaxis ticklabel font 4
+@ xaxis ticklabel color 1
+@ xaxis tick place both
+@ xaxis tick spec type none
+@ yaxis on
+@ yaxis type zero false
+@ yaxis offset 0.000000 , 0.000000
+@ yaxis bar on
+@ yaxis bar color 1
+@ yaxis bar linestyle 1
+@ yaxis bar linewidth 1.0
+@ yaxis label "Electric field (V/nm)"
+@ yaxis label layout para
+@ yaxis label place auto
+@ yaxis label char size 1.500000
+@ yaxis label font 4
+@ yaxis label color 1
+@ yaxis label place normal
+@ yaxis tick on
+@ yaxis tick major 1
+@ yaxis tick minor ticks 1
+@ yaxis tick default 6
+@ yaxis tick place rounded true
+@ yaxis tick in
+@ yaxis tick major size 1.000000
+@ yaxis tick major color 1
+@ yaxis tick major linewidth 1.0
+@ yaxis tick major linestyle 1
+@ yaxis tick major grid off
+@ yaxis tick minor color 1
+@ yaxis tick minor linewidth 1.0
+@ yaxis tick minor linestyle 1
+@ yaxis tick minor grid off
+@ yaxis tick minor size 0.500000
+@ yaxis ticklabel on
+@ yaxis ticklabel format general
+@ yaxis ticklabel prec 5
+@ yaxis ticklabel formula ""
+@ yaxis ticklabel append ""
+@ yaxis ticklabel prepend ""
+@ yaxis ticklabel angle 0
+@ yaxis ticklabel skip 0
+@ yaxis ticklabel stagger 0
+@ yaxis ticklabel place normal
+@ yaxis ticklabel offset auto
+@ yaxis ticklabel offset 0.000000 , 0.010000
+@ yaxis ticklabel start type auto
+@ yaxis ticklabel start 0.000000
+@ yaxis ticklabel stop type auto
+@ yaxis ticklabel stop 0.000000
+@ yaxis ticklabel char size 1.250000
+@ yaxis ticklabel font 4
+@ yaxis ticklabel color 1
+@ yaxis tick place both
+@ yaxis tick spec type none
+@ altxaxis off
+@ altyaxis off
+@ legend on
+@ legend loctype view
+@ legend 0.85, 0.8
+@ legend box color 1
+@ legend box pattern 1
+@ legend box linewidth 1.0
+@ legend box linestyle 1
+@ legend box fill color 0
+@ legend box fill pattern 1
+@ legend font 0
+@ legend char size 1.000000
+@ legend color 1
+@ legend length 4
+@ legend vgap 1
+@ legend hgap 1
+@ legend invert false
+@ frame type 0
+@ frame linestyle 1
+@ frame linewidth 1.0
+@ frame color 1
+@ frame pattern 1
+@ frame background color 0
+@ frame background pattern 0
+@ s0 hidden false
+@ s0 type xy
+@ s0 symbol 0
+@ s0 symbol size 1.000000
+@ s0 symbol color 1
+@ s0 symbol pattern 1
+@ s0 symbol fill color 1
+@ s0 symbol fill pattern 0
+@ s0 symbol linewidth 1.0
+@ s0 symbol linestyle 1
+@ s0 symbol char 65
+@ s0 symbol char font 0
+@ s0 symbol skip 0
+@ s0 line type 1
+@ s0 line linestyle 1
+@ s0 line linewidth 1.0
+@ s0 line color 1
+@ s0 line pattern 1
+@ s0 baseline type 0
+@ s0 baseline off
+@ s0 dropline off
+@ s0 fill type 0
+@ s0 fill rule 0
+@ s0 fill color 1
+@ s0 fill pattern 1
+@ s0 avalue off
+@ s0 avalue type 2
+@ s0 avalue char size 1.000000
+@ s0 avalue font 0
+@ s0 avalue color 1
+@ s0 avalue rot 0
+@ s0 avalue format general
+@ s0 avalue prec 3
+@ s0 avalue prepend ""
+@ s0 avalue append ""
+@ s0 avalue offset 0.000000 , 0.000000
+@ s0 errorbar on
+@ s0 errorbar place both
+@ s0 errorbar color 1
+@ s0 errorbar pattern 1
+@ s0 errorbar size 1.000000
+@ s0 errorbar linewidth 1.0
+@ s0 errorbar linestyle 1
+@ s0 errorbar riser linewidth 1.0
+@ s0 errorbar riser linestyle 1
+@ s0 errorbar riser clip off
+@ s0 errorbar riser clip length 0.100000
+@ s0 comment "field.xvg"
+@ s0 legend ""
+@target G0.S0
+@type xy
+0 5.21174e-06
+0.0005 4.8582e-06
+0.001 4.46725e-06
+0.0015 4.04017e-06
+0.002 3.57871e-06
+0.0025 3.08465e-06
+0.003 2.56005e-06
+0.0035 2.0072e-06
+0.004 1.42855e-06
+0.0045 8.27051e-07
+0.005 2.0556e-07
+0.0055 -4.3279e-07
+0.006 -1.08468e-06
+0.0065 -1.74674e-06
+0.007 -2.4151e-06
+0.0075 -3.08612e-06
+0.008 -3.75593e-06
+0.0085 -4.42057e-06
+0.009 -5.07613e-06
+0.0095 -5.7183e-06
+0.01 -6.34309e-06
+0.0105 -6.94642e-06
+0.011 -7.52419e-06
+0.0115 -8.07249e-06
+0.012 -8.58716e-06
+0.0125 -9.06443e-06
+0.013 -9.5006e-06
+0.0135 -9.89205e-06
+0.014 -1.02354e-05
+0.0145 -1.05275e-05
+0.015 -1.07651e-05
+0.0155 -1.09458e-05
+0.016 -1.10668e-05
+0.0165 -1.11262e-05
+0.017 -1.11219e-05
+0.0175 -1.10524e-05
+0.018 -1.09166e-05
+0.0185 -1.07135e-05
+0.019 -1.04426e-05
+0.0195 -1.01039e-05
+0.02 -9.69779e-06
+0.0205 -9.22485e-06
+0.021 -8.68609e-06
+0.0215 -8.0833e-06
+0.022 -7.41831e-06
+0.0225 -6.69347e-06
+0.023 -5.91155e-06
+0.0235 -5.07554e-06
+0.024 -4.18956e-06
+0.0245 -3.25681e-06
+0.025 -2.28218e-06
+0.0255 -1.27017e-06
+0.026 -2.25546e-07
+0.0265 8.45705e-07
+0.027 1.93884e-06
+0.0275 3.04734e-06
+0.028 4.1653e-06
+0.0285 5.28662e-06
+0.029 6.40417e-06
+0.0295 7.51217e-06
+0.03 8.60324e-06
+0.0305 9.67081e-06
+0.031 1.07082e-05
+0.0315 1.17081e-05
+0.032 1.26644e-05
+0.0325 1.357e-05
+0.033 1.44184e-05
+0.0335 1.52034e-05
+0.034 1.59185e-05
+0.0345 1.65582e-05
+0.035 1.71168e-05
+0.0355 1.75889e-05
+0.036 1.79698e-05
+0.0365 1.82549e-05
+0.037 1.84404e-05
+0.0375 1.85226e-05
+0.038 1.84986e-05
+0.0385 1.83658e-05
+0.039 1.81227e-05
+0.0395 1.77676e-05
+0.04 1.73001e-05
+0.0405 1.67203e-05
+0.041 1.60287e-05
+0.0415 1.52266e-05
+0.042 1.4316e-05
+0.0425 1.32999e-05
+0.043 1.21814e-05
+0.0435 1.09648e-05
+0.044 9.65433e-06
+0.0445 8.2561e-06
+0.045 6.77585e-06
+0.0455 5.22026e-06
+0.046 3.59662e-06
+0.0465 1.91244e-06
+0.047 1.76813e-07
+0.0475 -1.60169e-06
+0.048 -3.4137e-06
+0.0485 -5.24943e-06
+0.049 -7.09906e-06
+0.0495 -8.95136e-06
+0.05 -1.0796e-05
+0.0505 -1.26218e-05
+0.051 -1.44179e-05
+0.0515 -1.61733e-05
+0.052 -1.7876e-05
+0.0525 -1.95152e-05
+0.053 -2.10797e-05
+0.0535 -2.25588e-05
+0.054 -2.39418e-05
+0.0545 -2.52179e-05
+0.055 -2.63773e-05
+0.0555 -2.74107e-05
+0.056 -2.83084e-05
+0.0565 -2.90627e-05
+0.057 -2.96652e-05
+0.0575 -3.0109e-05
+0.058 -3.03877e-05
+0.0585 -3.04957e-05
+0.059 -3.04283e-05
+0.0595 -3.01817e-05
+0.06 -2.97532e-05
+0.0605 -2.9141e-05
+0.061 -2.83441e-05
+0.0615 -2.73627e-05
+0.062 -2.61986e-05
+0.0625 -2.48541e-05
+0.063 -2.33327e-05
+0.0635 -2.16391e-05
+0.064 -1.97788e-05
+0.0645 -1.77594e-05
+0.065 -1.55887e-05
+0.0655 -1.32758e-05
+0.066 -1.08307e-05
+0.0665 -8.26413e-06
+0.067 -5.58933e-06
+0.0675 -2.8188e-06
+0.068 3.3503e-08
+0.0685 2.95285e-06
+0.069 5.92437e-06
+0.0695 8.93009e-06
+0.07 1.19557e-05
+0.0705 1.49822e-05
+0.071 1.79924e-05
+0.0715 2.09691e-05
+0.072 2.38928e-05
+0.0725 2.67458e-05
+0.073 2.95098e-05
+0.0735 3.21666e-05
+0.074 3.46986e-05
+0.0745 3.70872e-05
+0.075 3.93155e-05
+0.0755 4.13667e-05
+0.076 4.32248e-05
+0.0765 4.48746e-05
+0.077 4.63011e-05
+0.0775 4.74911e-05
+0.078 4.8432e-05
+0.0785 4.91127e-05
+0.079 4.95229e-05
+0.0795 4.96542e-05
+0.08 4.94991e-05
+0.0805 4.90519e-05
+0.081 4.83086e-05
+0.0815 4.72662e-05
+0.082 4.59245e-05
+0.0825 4.4284e-05
+0.083 4.23475e-05
+0.0835 4.01187e-05
+0.084 3.76052e-05
+0.0845 3.48143e-05
+0.085 3.1756e-05
+0.0855 2.8442e-05
+0.086 2.48848e-05
+0.0865 2.11021e-05
+0.087 1.71074e-05
+0.0875 1.29217e-05
+0.088 8.5642e-06
+0.0885 4.05536e-06
+0.089 -5.79145e-07
+0.0895 -5.31895e-06
+0.09 -1.01359e-05
+0.0905 -1.50047e-05
+0.091 -1.98991e-05
+0.0915 -2.47881e-05
+0.092 -2.96471e-05
+0.0925 -3.44439e-05
+0.093 -3.91504e-05
+0.0935 -4.37376e-05
+0.094 -4.81737e-05
+0.0945 -5.24325e-05
+0.095 -5.64828e-05
+0.0955 -6.02969e-05
+0.096 -6.38478e-05
+0.0965 -6.7107e-05
+0.097 -7.00511e-05
+0.0975 -7.26541e-05
+0.098 -7.48937e-05
+0.0985 -7.67485e-05
+0.099 -7.81986e-05
+0.0995 -7.92268e-05
+0.1 -7.98172e-05
+0.1005 -7.99564e-05
+0.101 -7.96334e-05
+0.1015 -7.884e-05
+0.102 -7.75691e-05
+0.1025 -7.58184e-05
+0.103 -7.35867e-05
+0.1035 -7.08762e-05
+0.104 -6.76919e-05
+0.1045 -6.40408e-05
+0.105 -5.99352e-05
+0.1055 -5.53879e-05
+0.106 -5.04157e-05
+0.1065 -4.50365e-05
+0.107 -3.92749e-05
+0.1075 -3.31549e-05
+0.108 -2.67039e-05
+0.1085 -1.9952e-05
+0.109 -1.2932e-05
+0.1095 -5.67709e-06
+0.11 1.77265e-06
+0.1105 9.37968e-06
+0.111 1.71032e-05
+0.1115 2.49024e-05
+0.112 3.27304e-05
+0.1125 4.05437e-05
+0.113 4.82966e-05
+0.1135 5.59424e-05
+0.114 6.34357e-05
+0.1145 7.07264e-05
+0.115 7.77691e-05
+0.1155 8.45172e-05
+0.116 9.09248e-05
+0.1165 9.69478e-05
+0.117 0.000102541
+0.1175 0.000107662
+0.118 0.000112273
+0.1185 0.000116332
+0.119 0.000119806
+0.1195 0.000122661
+0.12 0.000124867
+0.1205 0.000126395
+0.121 0.000127223
+0.1215 0.00012733
+0.122 0.000126699
+0.1225 0.000125318
+0.123 0.000123178
+0.1235 0.000120274
+0.124 0.000116606
+0.1245 0.00011218
+0.125 0.000107004
+0.1255 0.000101092
+0.126 9.44624e-05
+0.1265 8.71353e-05
+0.127 7.91416e-05
+0.1275 7.05119e-05
+0.128 6.12822e-05
+0.1285 5.14929e-05
+0.129 4.11867e-05
+0.1295 3.04165e-05
+0.13 1.92326e-05
+0.1305 7.69112e-06
+0.131 -4.14868e-06
+0.1315 -1.62269e-05
+0.132 -2.8471e-05
+0.1325 -4.08232e-05
+0.133 -5.32067e-05
+0.1335 -6.55524e-05
+0.134 -7.77902e-05
+0.1345 -8.98416e-05
+0.135 -0.000101635
+0.1355 -0.000113095
+0.136 -0.000124152
+0.1365 -0.000134726
+0.137 -0.000144748
+0.1375 -0.00015415
+0.138 -0.000162861
+0.1385 -0.000170816
+0.139 -0.000177954
+0.1395 -0.000184212
+0.14 -0.000189537
+0.1405 -0.000193877
+0.141 -0.000197186
+0.1415 -0.000199421
+0.142 -0.000200548
+0.1425 -0.000200535
+0.143 -0.000199357
+0.1435 -0.000196997
+0.144 -0.000193441
+0.1445 -0.000188686
+0.145 -0.000182733
+0.1455 -0.000175591
+0.146 -0.000167273
+0.1465 -0.000157807
+0.147 -0.000147221
+0.1475 -0.000135553
+0.148 -0.000122847
+0.1485 -0.000109154
+0.149 -9.45312e-05
+0.1495 -7.90457e-05
+0.15 -6.27703e-05
+0.1505 -4.57812e-05
+0.151 -2.816e-05
+0.1515 -9.9992e-06
+0.152 8.61086e-06
+0.1525 2.75697e-05
+0.153 4.67707e-05
+0.1535 6.61152e-05
+0.154 8.54878e-05
+0.1545 0.000104781
+0.155 0.000123874
+0.1555 0.00014266
+0.156 0.000161019
+0.1565 0.000178834
+0.157 0.000195993
+0.1575 0.00021238
+0.158 0.000227882
+0.1585 0.000242394
+0.159 0.000255808
+0.1595 0.000268024
+0.16 0.000278943
+0.1605 0.000288479
+0.161 0.000296543
+0.1615 0.000303058
+0.162 0.000307954
+0.1625 0.000311168
+0.163 0.000312645
+0.1635 0.00031234
+0.164 0.000310218
+0.1645 0.000306253
+0.165 0.000300429
+0.1655 0.00029274
+0.166 0.000283191
+0.1665 0.0002718
+0.167 0.000258592
+0.1675 0.000243609
+0.168 0.000226898
+0.1685 0.000208519
+0.169 0.000188545
+0.1695 0.000167064
+0.17 0.000144158
+0.1705 0.00011994
+0.171 9.45162e-05
+0.1715 6.8015e-05
+0.172 4.0565e-05
+0.1725 1.23028e-05
+0.173 -1.66184e-05
+0.1735 -4.60506e-05
+0.174 -7.58303e-05
+0.1745 -0.000105786
+0.175 -0.000135759
+0.1755 -0.00016557
+0.176 -0.00019504
+0.1765 -0.000223991
+0.177 -0.000252251
+0.1775 -0.000279638
+0.178 -0.00030597
+0.1785 -0.000331079
+0.179 -0.000354791
+0.1795 -0.000376935
+0.18 -0.000397359
+0.1805 -0.000415904
+0.181 -0.000432421
+0.1815 -0.000446777
+0.182 -0.00045884
+0.1825 -0.000468496
+0.183 -0.000475638
+0.1835 -0.000480172
+0.184 -0.000482019
+0.1845 -0.000481113
+0.185 -0.000477401
+0.1855 -0.000470848
+0.186 -0.000461434
+0.1865 -0.000449155
+0.187 -0.000434021
+0.1875 -0.000416065
+0.188 -0.000395332
+0.1885 -0.000371882
+0.189 -0.000345801
+0.1895 -0.000317184
+0.19 -0.000286141
+0.1905 -0.000252807
+0.191 -0.000217334
+0.1915 -0.000179872
+0.192 -0.000140603
+0.1925 -9.97231e-05
+0.193 -5.7428e-05
+0.1935 -1.39473e-05
+0.194 3.05086e-05
+0.1945 7.56883e-05
+0.195 0.000121353
+0.1955 0.000167245
+0.196 0.000213091
+0.1965 0.000258644
+0.197 0.000303625
+0.1975 0.000347756
+0.198 0.000390773
+0.1985 0.0004324
+0.199 0.000472359
+0.1995 0.000510397
+0.2 0.000546255
+0.2005 0.000579676
+0.201 0.000610412
+0.2015 0.000638241
+0.202 0.000662939
+0.2025 0.000684297
+0.203 0.000702128
+0.2035 0.000716255
+0.204 0.000726522
+0.2045 0.000732793
+0.205 0.000734951
+0.2055 0.0007329
+0.206 0.000726571
+0.2065 0.000715911
+0.207 0.000700895
+0.2075 0.000681526
+0.208 0.000657829
+0.2085 0.00062985
+0.209 0.000597673
+0.2095 0.000561393
+0.21 0.000521145
+0.2105 0.000477082
+0.211 0.000429382
+0.2115 0.000378243
+0.212 0.000323899
+0.2125 0.000266607
+0.213 0.000206634
+0.2135 0.000144268
+0.214 7.98362e-05
+0.2145 1.36575e-05
+0.215 -5.39127e-05
+0.2155 -0.000122496
+0.216 -0.000191745
+0.2165 -0.000261247
+0.217 -0.000330622
+0.2175 -0.000399443
+0.218 -0.000467329
+0.2185 -0.000533853
+0.219 -0.000598597
+0.2195 -0.000661164
+0.22 -0.000721143
+0.2205 -0.000778123
+0.221 -0.000831738
+0.2215 -0.000881594
+0.222 -0.000927342
+0.2225 -0.00096862
+0.223 -0.00100512
+0.2235 -0.00103652
+0.224 -0.00106255
+0.2245 -0.00108295
+0.225 -0.00109749
+0.2255 -0.00110598
+0.226 -0.00110824
+0.2265 -0.00110414
+0.227 -0.00109358
+0.2275 -0.0010765
+0.228 -0.00105286
+0.2285 -0.00102268
+0.229 -0.000986009
+0.2295 -0.000942923
+0.23 -0.000893556
+0.2305 -0.000838068
+0.231 -0.000776655
+0.2315 -0.000709563
+0.232 -0.000637087
+0.2325 -0.00055951
+0.233 -0.000477207
+0.2335 -0.000390545
+0.234 -0.000299961
+0.2345 -0.000205893
+0.235 -0.000108808
+0.2355 -9.23019e-06
+0.236 9.23325e-05
+0.2365 0.000195321
+0.237 0.000299144
+0.2375 0.000403262
+0.238 0.000507054
+0.2385 0.000609903
+0.239 0.000711199
+0.2395 0.000810355
+0.24 0.000906734
+0.2405 0.000999717
+0.241 0.00108872
+0.2415 0.00117314
+0.242 0.00125239
+0.2425 0.00132595
+0.243 0.00139325
+0.2435 0.00145379
+0.244 0.0015071
+0.2445 0.00155272
+0.245 0.00159025
+0.2455 0.00161932
+0.246 0.0016396
+0.2465 0.00165079
+0.247 0.00165268
+0.2475 0.00164506
+0.248 0.0016278
+0.2485 0.00160082
+0.249 0.0015641
+0.2495 0.00151765
+0.25 0.00146156
+0.2505 0.00139598
+0.251 0.0013211
+0.2515 0.00123719
+0.252 0.00114455
+0.2525 0.00104356
+0.253 0.000934631
+0.2535 0.000818285
+0.254 0.000695002
+0.2545 0.000565389
+0.255 0.000430088
+0.2555 0.000289763
+0.256 0.000145101
+0.2565 -3.06876e-06
+0.257 -0.000154016
+0.2575 -0.000306921
+0.258 -0.000460919
+0.2585 -0.000615112
+0.259 -0.000768673
+0.2595 -0.000920672
+0.26 -0.00107018
+0.2605 -0.00121633
+0.261 -0.00135819
+0.2615 -0.00149484
+0.262 -0.00162542
+0.2625 -0.00174908
+0.263 -0.00186495
+0.2635 -0.0019722
+0.264 -0.00207009
+0.2645 -0.00215786
+0.265 -0.00223481
+0.2655 -0.00230031
+0.266 -0.00235376
+0.2665 -0.00239462
+0.267 -0.00242243
+0.2675 -0.0024368
+0.268 -0.00243738
+0.2685 -0.00242393
+0.269 -0.00239625
+0.2695 -0.00235424
+0.27 -0.0022979
+0.2705 -0.00222727
+0.271 -0.0021425
+0.2715 -0.00204382
+0.272 -0.00193154
+0.2725 -0.00180607
+0.273 -0.00166791
+0.2735 -0.00151759
+0.274 -0.00135576
+0.2745 -0.00118314
+0.275 -0.00100057
+0.2755 -0.000808891
+0.276 -0.000609027
+0.2765 -0.000402025
+0.277 -0.000188906
+0.2775 2.91893e-05
+0.278 0.000251046
+0.2785 0.00047552
+0.279 0.000701385
+0.2795 0.000927272
+0.28 0.0011519
+0.2805 0.00137402
+0.281 0.00159225
+0.2815 0.00180524
+0.282 0.00201172
+0.2825 0.00221035
+0.283 0.0023998
+0.2835 0.00257887
+0.284 0.00274636
+0.2845 0.00290102
+0.285 0.00304176
+0.2855 0.00316753
+0.286 0.00327733
+0.2865 0.00337022
+0.287 0.00344538
+0.2875 0.00350205
+0.288 0.00353956
+0.2885 0.00355737
+0.289 0.00355501
+0.2895 0.00353213
+0.29 0.00348852
+0.2905 0.00342402
+0.291 0.00333865
+0.2915 0.00323254
+0.292 0.00310591
+0.2925 0.00295915
+0.293 0.00279274
+0.2935 0.00260726
+0.294 0.00240346
+0.2945 0.00218224
+0.295 0.0019445
+0.2955 0.00169129
+0.296 0.0014239
+0.2965 0.00114356
+0.297 0.000851664
+0.2975 0.000549661
+0.298 0.000239175
+0.2985 -7.82175e-05
+0.299 -0.000400775
+0.2995 -0.000726663
+0.3 -0.00105419
+0.3005 -0.00138144
+0.301 -0.00170647
+0.3015 -0.00202738
+0.302 -0.00234234
+0.3025 -0.00264937
+0.303 -0.00294652
+0.3035 -0.00323196
+0.304 -0.00350382
+0.3045 -0.00376024
+0.305 -0.00399958
+0.3055 -0.00422009
+0.306 -0.00442015
+0.3065 -0.00459828
+0.307 -0.00475312
+0.3075 -0.00488328
+0.308 -0.00498762
+0.3085 -0.0050651
+0.309 -0.00511479
+0.3095 -0.00513592
+0.31 -0.00512787
+0.3105 -0.00509018
+0.311 -0.00502256
+0.3115 -0.00492488
+0.312 -0.00479717
+0.3125 -0.00463965
+0.313 -0.00445273
+0.3135 -0.00423693
+0.314 -0.00399306
+0.3145 -0.003722
+0.315 -0.00342483
+0.3155 -0.00310282
+0.316 -0.00275748
+0.3165 -0.00239025
+0.317 -0.00200295
+0.3175 -0.0015975
+0.318 -0.00117589
+0.3185 -0.000740179
+0.319 -0.000292861
+0.3195 0.000163868
+0.32 0.000627539
+0.3205 0.00109555
+0.321 0.00156519
+0.3215 0.00203396
+0.322 0.00249906
+0.3225 0.0029577
+0.323 0.00340721
+0.3235 0.0038448
+0.324 0.00426768
+0.3245 0.00467327
+0.325 0.00505895
+0.3255 0.0054221
+0.326 0.00576021
+0.3265 0.00607101
+0.327 0.0063522
+0.3275 0.00660161
+0.328 0.00681734
+0.3285 0.00699752
+0.329 0.00714054
+0.3295 0.00724495
+0.33 0.00730949
+0.3305 0.00733311
+0.331 0.007315
+0.3315 0.00725454
+0.332 0.00715136
+0.3325 0.00700537
+0.333 0.00681668
+0.3335 0.00658563
+0.334 0.00631287
+0.3345 0.00599924
+0.335 0.00564587
+0.3355 0.00525422
+0.336 0.00482578
+0.3365 0.00436241
+0.337 0.00386622
+0.3375 0.00333958
+0.338 0.00278496
+0.3385 0.00220503
+0.339 0.00160282
+0.3395 0.000981312
+0.34 0.000343815
+0.3405 -0.00030613
+0.341 -0.000965188
+0.3415 -0.00162979
+0.342 -0.00229592
+0.3425 -0.00295985
+0.343 -0.00361791
+0.3435 -0.0042661
+0.344 -0.00490045
+0.3445 -0.0055172
+0.345 -0.00611246
+0.3455 -0.00668234
+0.346 -0.0072233
+0.3465 -0.00773181
+0.347 -0.00820419
+0.3475 -0.0086372
+0.348 -0.00902783
+0.3485 -0.00937304
+0.349 -0.00967006
+0.3495 -0.00991647
+0.35 -0.01011
+0.3505 -0.0102486
+0.351 -0.0103306
+0.3515 -0.0103547
+0.352 -0.0103198
+0.3525 -0.010225
+0.353 -0.01007
+0.3535 -0.00985468
+0.354 -0.00957927
+0.3545 -0.00924437
+0.355 -0.008851
+0.3555 -0.00840043
+0.356 -0.00789427
+0.3565 -0.00733459
+0.357 -0.00672387
+0.3575 -0.00606459
+0.358 -0.00535969
+0.3585 -0.00461278
+0.359 -0.00382731
+0.3595 -0.00300721
+0.36 -0.00215651
+0.3605 -0.00127982
+0.361 -0.000381554
+0.3615 0.000533364
+0.362 0.00145975
+0.3625 0.00239285
+0.363 0.00332721
+0.3635 0.00425738
+0.364 0.00517796
+0.3645 0.00608377
+0.365 0.00696918
+0.3655 0.00782868
+0.366 0.00865711
+0.3665 0.00944909
+0.367 0.0101994
+0.3675 0.0109033
+0.368 0.0115558
+0.3685 0.0121524
+0.369 0.0126887
+0.3695 0.013161
+0.37 0.0135651
+0.3705 0.0138979
+0.371 0.0141563
+0.3715 0.0143375
+0.372 0.0144394
+0.3725 0.0144601
+0.373 0.0143982
+0.3735 0.0142527
+0.374 0.0140233
+0.3745 0.0137097
+0.375 0.0133127
+0.3755 0.012833
+0.376 0.0122722
+0.3765 0.0116322
+0.377 0.0109155
+0.3775 0.0101249
+0.378 0.00926381
+0.3785 0.00833631
+0.379 0.00734629
+0.3795 0.00629867
+0.38 0.00519866
+0.3805 0.00405167
+0.381 0.00286331
+0.3815 0.00164037
+0.382 0.000388846
+0.3825 -0.000884521
+0.383 -0.00217263
+0.3835 -0.00346804
+0.384 -0.00476396
+0.3845 -0.00605269
+0.385 -0.00732657
+0.3855 -0.00857832
+0.386 -0.00980029
+0.3865 -0.0109847
+0.387 -0.0121247
+0.3875 -0.0132128
+0.388 -0.0142421
+0.3885 -0.0152053
+0.389 -0.0160965
+0.3895 -0.0169092
+0.39 -0.0176373
+0.3905 -0.0182757
+0.391 -0.018819
+0.3915 -0.0192629
+0.392 -0.0196032
+0.3925 -0.0198365
+0.393 -0.0199596
+0.3935 -0.0199703
+0.394 -0.0198667
+0.3945 -0.0196477
+0.395 -0.0193128
+0.3955 -0.0188622
+0.396 -0.0182966
+0.3965 -0.0176176
+0.397 -0.0168273
+0.3975 -0.0159286
+0.398 -0.0149253
+0.3985 -0.0138211
+0.399 -0.0126209
+0.3995 -0.0113302
+0.4 -0.0099553
+0.4005 -0.00850257
+0.401 -0.00697904
+0.4015 -0.00539271
+0.402 -0.00375142
+0.4025 -0.00206392
+0.403 -0.000339552
+0.4035 0.00141286
+0.404 0.00318388
+0.4045 0.00496288
+0.405 0.00673997
+0.4055 0.00850546
+0.406 0.0102487
+0.4065 0.0119591
+0.407 0.0136268
+0.4075 0.0152414
+0.408 0.0167925
+0.4085 0.0182707
+0.409 0.0196666
+0.4095 0.0209704
+0.41 0.0221735
+0.4105 0.0232677
+0.411 0.0242449
+0.4115 0.0250978
+0.412 0.0258196
+0.4125 0.0264044
+0.413 0.0268466
+0.4135 0.0271417
+0.414 0.0272858
+0.4145 0.0272758
+0.415 0.0271096
+0.4155 0.0267857
+0.416 0.0263037
+0.4165 0.0256642
+0.417 0.0248683
+0.4175 0.0239184
+0.418 0.0228178
+0.4185 0.0215703
+0.419 0.0201811
+0.4195 0.0186564
+0.42 0.0170024
+0.4205 0.0152267
+0.421 0.0133383
+0.4215 0.011346
+0.422 0.00925979
+0.4225 0.00709001
+0.423 0.00484833
+0.4235 0.00254611
+0.424 0.000195897
+0.4245 -0.00218904
+0.425 -0.0045965
+0.4255 -0.00701253
+0.426 -0.00942313
+0.4265 -0.0118144
+0.427 -0.0141732
+0.4275 -0.0164848
+0.428 -0.0187353
+0.4285 -0.0209112
+0.429 -0.0229988
+0.4295 -0.0249845
+0.43 -0.0268561
+0.4305 -0.028601
+0.431 -0.0302072
+0.4315 -0.0316634
+0.432 -0.0329599
+0.4325 -0.034086
+0.433 -0.0350334
+0.4335 -0.0357939
+0.434 -0.0363606
+0.4345 -0.0367274
+0.435 -0.0368894
+0.4355 -0.0368427
+0.436 -0.0365846
+0.4365 -0.0361138
+0.437 -0.0354296
+0.4375 -0.0345333
+0.438 -0.0334268
+0.4385 -0.0321134
+0.439 -0.0305979
+0.4395 -0.0288861
+0.44 -0.0269848
+0.4405 -0.0249024
+0.441 -0.0226488
+0.4415 -0.0202334
+0.442 -0.0176684
+0.4425 -0.0149667
+0.443 -0.0121414
+0.4435 -0.00920658
+0.444 -0.00617889
+0.4445 -0.00307319
+0.445 9.38279e-05
+0.4455 0.00330456
+0.446 0.00654057
+0.4465 0.00978498
+0.447 0.0130187
+0.4475 0.0162226
+0.448 0.0193787
+0.4485 0.0224679
+0.449 0.025471
+0.4495 0.0283705
+0.45 0.0311483
+0.4505 0.0337865
+0.451 0.0362676
+0.4515 0.0385763
+0.452 0.0406963
+0.4525 0.0426129
+0.453 0.0443125
+0.4535 0.0457821
+0.454 0.0470104
+0.4545 0.0479869
+0.455 0.0487028
+0.4555 0.0491501
+0.456 0.0493228
+0.4565 0.049216
+0.457 0.0488265
+0.4575 0.0481527
+0.458 0.0471947
+0.4585 0.0459539
+0.459 0.0444338
+0.4595 0.0426389
+0.46 0.040576
+0.4605 0.0382538
+0.461 0.0356813
+0.4615 0.0328698
+0.462 0.0298324
+0.4625 0.0265838
+0.463 0.0231394
+0.4635 0.0195159
+0.464 0.0157324
+0.4645 0.0118076
+0.465 0.00776245
+0.4655 0.00361934
+0.466 -0.000600586
+0.4665 -0.00487467
+0.467 -0.00917742
+0.4675 -0.0134851
+0.468 -0.0177743
+0.4685 -0.0220194
+0.469 -0.0261952
+0.4695 -0.0302776
+0.47 -0.0342415
+0.4705 -0.0380621
+0.471 -0.0417166
+0.4715 -0.0451823
+0.472 -0.0484354
+0.4725 -0.0514549
+0.473 -0.0542213
+0.4735 -0.0567147
+0.474 -0.0589172
+0.4745 -0.0608126
+0.475 -0.0623858
+0.4755 -0.0636236
+0.476 -0.0645146
+0.4765 -0.065049
+0.477 -0.065219
+0.4775 -0.0650191
+0.478 -0.0644453
+0.4785 -0.0634961
+0.479 -0.0621721
+0.4795 -0.0604757
+0.48 -0.058412
+0.4805 -0.055988
+0.481 -0.0532125
+0.4815 -0.0500969
+0.482 -0.0466555
+0.4825 -0.0429026
+0.483 -0.0388552
+0.4835 -0.0345342
+0.484 -0.0299599
+0.4845 -0.0251554
+0.485 -0.0201444
+0.4855 -0.014954
+0.486 -0.00961063
+0.4865 -0.00414326
+0.487 0.00141726
+0.4875 0.00704261
+0.488 0.0127003
+0.4885 0.0183578
+0.489 0.0239829
+0.4895 0.0295446
+0.49 0.0350091
+0.4905 0.0403434
+0.491 0.0455165
+0.4915 0.0504961
+0.492 0.0552504
+0.4925 0.0597511
+0.493 0.0639685
+0.4935 0.0678742
+0.494 0.0714423
+0.4945 0.0746493
+0.495 0.0774705
+0.4955 0.0798857
+0.496 0.081876
+0.4965 0.0834246
+0.497 0.0845167
+0.4975 0.0851407
+0.498 0.0852869
+0.4985 0.0849485
+0.499 0.0841214
+0.4995 0.082804
+0.5 0.0809979
+0.5005 0.0787068
+0.501 0.0759384
+0.5015 0.0727022
+0.502 0.0690109
+0.5025 0.0648793
+0.503 0.060326
+0.5035 0.0553728
+0.504 0.0500409
+0.5045 0.0443576
+0.505 0.03835
+0.5055 0.0320489
+0.506 0.0254881
+0.5065 0.018699
+0.507 0.011719
+0.5075 0.00458631
+0.508 -0.00266161
+0.5085 -0.00998256
+0.509 -0.0173386
+0.5095 -0.0246866
+0.51 -0.0319838
+0.5105 -0.0391894
+0.511 -0.0462588
+0.5115 -0.0531529
+0.512 -0.0598287
+0.5125 -0.0662447
+0.513 -0.0723624
+0.5135 -0.0781414
+0.514 -0.0835468
+0.5145 -0.088542
+0.515 -0.0930931
+0.5155 -0.0971695
+0.516 -0.100741
+0.5165 -0.103783
+0.517 -0.106269
+0.5175 -0.108181
+0.518 -0.109499
+0.5185 -0.110208
+0.519 -0.110299
+0.5195 -0.109762
+0.52 -0.108593
+0.5205 -0.106791
+0.521 -0.104358
+0.5215 -0.101302
+0.522 -0.0976316
+0.5225 -0.093361
+0.523 -0.0885072
+0.5235 -0.0830903
+0.524 -0.0771355
+0.5245 -0.0706694
+0.525 -0.0637239
+0.5255 -0.0563325
+0.526 -0.0485311
+0.5265 -0.040361
+0.527 -0.0318629
+0.5275 -0.0230839
+0.528 -0.0140672
+0.5285 -0.00486342
+0.529 0.00447629
+0.5295 0.0139021
+0.53 0.0233583
+0.5305 0.0327951
+0.531 0.0421565
+0.5315 0.0513873
+0.532 0.060435
+0.5325 0.0692449
+0.533 0.0777623
+0.5335 0.0859384
+0.534 0.0937202
+0.5345 0.10106
+0.535 0.10791
+0.5355 0.114225
+0.536 0.119964
+0.5365 0.125086
+0.537 0.129556
+0.5375 0.133339
+0.538 0.136408
+0.5385 0.138735
+0.539 0.140299
+0.5395 0.141083
+0.54 0.141072
+0.5405 0.140258
+0.541 0.138635
+0.5415 0.136205
+0.542 0.132971
+0.5425 0.128943
+0.543 0.124134
+0.5435 0.118563
+0.544 0.112252
+0.5445 0.105232
+0.545 0.0975308
+0.5455 0.0891869
+0.546 0.080239
+0.5465 0.0707321
+0.547 0.0607162
+0.5475 0.0502385
+0.548 0.0393566
+0.5485 0.028126
+0.549 0.0166077
+0.5495 0.00486666
+0.55 -0.00703746
+0.5505 -0.019035
+0.551 -0.031061
+0.5515 -0.0430459
+0.552 -0.0549185
+0.5525 -0.0666147
+0.553 -0.0780621
+0.5535 -0.0891951
+0.554 -0.0999452
+0.5545 -0.110245
+0.555 -0.120035
+0.5555 -0.12925
+0.556 -0.137834
+0.5565 -0.145729
+0.557 -0.152881
+0.5575 -0.159244
+0.558 -0.164772
+0.5585 -0.169423
+0.559 -0.173161
+0.5595 -0.175956
+0.56 -0.177781
+0.5605 -0.178614
+0.561 -0.17844
+0.5615 -0.177249
+0.562 -0.175036
+0.5625 -0.171803
+0.563 -0.167556
+0.5635 -0.162311
+0.564 -0.156084
+0.5645 -0.148901
+0.565 -0.140792
+0.5655 -0.131792
+0.566 -0.121947
+0.5665 -0.111299
+0.567 -0.0999022
+0.5675 -0.0878121
+0.568 -0.075091
+0.5685 -0.0618074
+0.569 -0.0480254
+0.5695 -0.0338208
+0.57 -0.0192717
+0.5705 -0.00445414
+0.571 0.0105456
+0.5715 0.0256502
+0.572 0.0407716
+0.5725 0.0558222
+0.573 0.0707186
+0.5735 0.0853704
+0.574 0.0996952
+0.5745 0.113607
+0.575 0.12702
+0.5755 0.139855
+0.576 0.152031
+0.5765 0.163472
+0.577 0.174107
+0.5775 0.183863
+0.578 0.192678
+0.5785 0.20049
+0.579 0.207245
+0.5795 0.212894
+0.58 0.217391
+0.5805 0.2207
+0.581 0.222789
+0.5815 0.223633
+0.582 0.223215
+0.5825 0.221523
+0.583 0.218554
+0.5835 0.214311
+0.584 0.208806
+0.5845 0.202055
+0.585 0.194086
+0.5855 0.18493
+0.586 0.174627
+0.5865 0.163225
+0.587 0.150776
+0.5875 0.137342
+0.588 0.122986
+0.5885 0.107783
+0.589 0.0918109
+0.5895 0.0751504
+0.59 0.0578935
+0.5905 0.0401271
+0.591 0.0219507
+0.5915 0.00346363
+0.592 -0.0152348
+0.5925 -0.0340354
+0.593 -0.052838
+0.5935 -0.0715316
+0.594 -0.0900087
+0.5945 -0.108164
+0.595 -0.12589
+0.5955 -0.143078
+0.596 -0.159631
+0.5965 -0.175443
+0.597 -0.190419
+0.5975 -0.204465
+0.598 -0.21749
+0.5985 -0.229412
+0.599 -0.24015
+0.5995 -0.249631
+0.6 -0.257791
+0.6005 -0.264566
+0.601 -0.269907
+0.6015 -0.273767
+0.602 -0.276112
+0.6025 -0.27691
+0.603 -0.276144
+0.6035 -0.2738
+0.604 -0.269879
+0.6045 -0.264384
+0.605 -0.257333
+0.6055 -0.248751
+0.606 -0.23867
+0.6065 -0.227132
+0.607 -0.214193
+0.6075 -0.199906
+0.608 -0.184346
+0.6085 -0.167583
+0.609 -0.149704
+0.6095 -0.1308
+0.61 -0.110965
+0.6105 -0.0903091
+0.611 -0.0689348
+0.6115 -0.0469612
+0.612 -0.0245075
+0.6125 -0.0016946
+0.613 0.0213488
+0.6135 0.0444974
+0.614 0.0676168
+0.6145 0.0905752
+0.615 0.113243
+0.6155 0.135485
+0.616 0.157174
+0.6165 0.178181
+0.617 0.198376
+0.6175 0.21764
+0.618 0.235853
+0.6185 0.252901
+0.619 0.268678
+0.6195 0.283078
+0.62 0.29601
+0.6205 0.307385
+0.621 0.317121
+0.6215 0.325151
+0.622 0.33141
+0.6225 0.335848
+0.623 0.338421
+0.6235 0.339096
+0.624 0.337853
+0.6245 0.33468
+0.625 0.329577
+0.6255 0.322554
+0.626 0.313636
+0.6265 0.302851
+0.627 0.290249
+0.6275 0.275878
+0.628 0.259807
+0.6285 0.242113
+0.629 0.222877
+0.6295 0.2022
+0.63 0.18018
+0.6305 0.156932
+0.631 0.132581
+0.6315 0.107248
+0.632 0.0810733
+0.6325 0.0541978
+0.633 0.0267653
+0.6335 -0.00107051
+0.634 -0.0291593
+0.6345 -0.0573394
+0.635 -0.0854513
+0.6355 -0.113337
+0.636 -0.140834
+0.6365 -0.167785
+0.637 -0.19403
+0.6375 -0.219411
+0.638 -0.243779
+0.6385 -0.266984
+0.639 -0.288886
+0.6395 -0.309349
+0.64 -0.328238
+0.6405 -0.345438
+0.641 -0.360832
+0.6415 -0.374318
+0.642 -0.385802
+0.6425 -0.395198
+0.643 -0.402438
+0.6435 -0.407459
+0.644 -0.410213
+0.6445 -0.410665
+0.645 -0.408791
+0.6455 -0.40458
+0.646 -0.398036
+0.6465 -0.389178
+0.647 -0.378031
+0.6475 -0.364643
+0.648 -0.349066
+0.6485 -0.33137
+0.649 -0.311641
+0.6495 -0.289968
+0.65 -0.266463
+0.6505 -0.241235
+0.651 -0.21442
+0.6515 -0.186154
+0.652 -0.156582
+0.6525 -0.125868
+0.653 -0.0941679
+0.6535 -0.0616588
+0.654 -0.0285188
+0.6545 0.00507432
+0.655 0.0389249
+0.6555 0.072853
+0.656 0.10666
+0.6565 0.140152
+0.657 0.17314
+0.6575 0.205431
+0.658 0.236831
+0.6585 0.267161
+0.659 0.296234
+0.6595 0.323877
+0.66 0.349921
+0.6605 0.374199
+0.661 0.396566
+0.6615 0.416873
+0.662 0.434989
+0.6625 0.450793
+0.663 0.464172
+0.6635 0.475035
+0.664 0.483295
+0.6645 0.488885
+0.665 0.49175
+0.6655 0.491851
+0.666 0.489164
+0.6665 0.483681
+0.667 0.47541
+0.6675 0.464374
+0.668 0.450615
+0.6685 0.434184
+0.669 0.415155
+0.6695 0.393617
+0.67 0.369666
+0.6705 0.343425
+0.671 0.315015
+0.6715 0.284587
+0.672 0.252296
+0.6725 0.218306
+0.673 0.182804
+0.6735 0.145969
+0.674 0.108006
+0.6745 0.0691231
+0.675 0.0295283
+0.6755 -0.0105549
+0.676 -0.0509088
+0.6765 -0.0913003
+0.677 -0.1315
+0.6775 -0.171283
+0.678 -0.210415
+0.6785 -0.248673
+0.679 -0.285832
+0.6795 -0.321666
+0.68 -0.355968
+0.6805 -0.388526
+0.681 -0.419146
+0.6815 -0.447636
+0.682 -0.473813
+0.6825 -0.497519
+0.683 -0.518593
+0.6835 -0.536893
+0.684 -0.552299
+0.6845 -0.564696
+0.685 -0.573993
+0.6855 -0.58011
+0.686 -0.582988
+0.6865 -0.582586
+0.687 -0.57888
+0.6875 -0.571864
+0.688 -0.561552
+0.6885 -0.547981
+0.689 -0.531196
+0.6895 -0.511273
+0.69 -0.488295
+0.6905 -0.462372
+0.691 -0.433632
+0.6915 -0.402208
+0.692 -0.368267
+0.6925 -0.331972
+0.693 -0.293516
+0.6935 -0.253107
+0.694 -0.210947
+0.6945 -0.167271
+0.695 -0.122314
+0.6955 -0.0763184
+0.696 -0.0295412
+0.6965 0.017765
+0.697 0.0653285
+0.6975 0.112881
+0.698 0.160158
+0.6985 0.206883
+0.699 0.252793
+0.6995 0.29762
+0.7 0.341094
+0.7005 0.382966
+0.701 0.422982
+0.7015 0.460905
+0.702 0.496502
+0.7025 0.529549
+0.703 0.559849
+0.7035 0.5872
+0.704 0.611431
+0.7045 0.63238
+0.705 0.649901
+0.7055 0.663873
+0.706 0.674188
+0.7065 0.680762
+0.707 0.683529
+0.7075 0.682445
+0.708 0.677489
+0.7085 0.66866
+0.709 0.655982
+0.7095 0.639494
+0.71 0.619269
+0.7105 0.595386
+0.711 0.567958
+0.7115 0.537121
+0.712 0.503014
+0.7125 0.465818
+0.713 0.42571
+0.7135 0.382906
+0.714 0.337628
+0.7145 0.290109
+0.715 0.240615
+0.7155 0.189396
+0.716 0.136743
+0.7165 0.0829431
+0.717 0.0282854
+0.7175 -0.0269121
+0.718 -0.082357
+0.7185 -0.137725
+0.719 -0.192702
+0.7195 -0.246978
+0.72 -0.300241
+0.7205 -0.35217
+0.721 -0.402478
+0.7215 -0.450854
+0.722 -0.49702
+0.7225 -0.540695
+0.723 -0.581609
+0.7235 -0.61952
+0.724 -0.654184
+0.7245 -0.685388
+0.725 -0.712929
+0.7255 -0.736621
+0.726 -0.756311
+0.7265 -0.771853
+0.727 -0.783135
+0.7275 -0.790062
+0.728 -0.792565
+0.7285 -0.790599
+0.729 -0.784146
+0.7295 -0.773211
+0.73 -0.757825
+0.7305 -0.73805
+0.731 -0.71396
+0.7315 -0.685668
+0.732 -0.653309
+0.7325 -0.617031
+0.733 -0.577025
+0.7335 -0.533478
+0.734 -0.486624
+0.7345 -0.436707
+0.735 -0.38398
+0.7355 -0.328739
+0.736 -0.271263
+0.7365 -0.211874
+0.737 -0.150897
+0.7375 -0.0886603
+0.738 -0.0255159
+0.7385 0.0381943
+0.739 0.102103
+0.7395 0.165849
+0.74 0.229077
+0.7405 0.291418
+0.741 0.352519
+0.7415 0.412025
+0.742 0.469581
+0.7425 0.524855
+0.743 0.577514
+0.7435 0.627249
+0.744 0.673757
+0.7445 0.716746
+0.745 0.755962
+0.7455 0.791153
+0.746 0.822087
+0.7465 0.848573
+0.747 0.870424
+0.7475 0.887493
+0.748 0.89965
+0.7485 0.906793
+0.749 0.908853
+0.7495 0.905786
+0.75 0.897576
+0.7505 0.884236
+0.751 0.865815
+0.7515 0.842379
+0.752 0.814037
+0.7525 0.780909
+0.753 0.743159
+0.7535 0.700979
+0.754 0.654566
+0.7545 0.604174
+0.755 0.550046
+0.7555 0.492474
+0.756 0.431774
+0.7565 0.368251
+0.757 0.302261
+0.7575 0.234163
+0.758 0.164323
+0.7585 0.0931338
+0.759 0.0209795
+0.7595 -0.0517257
+0.76 -0.124573
+0.7605 -0.197158
+0.761 -0.269061
+0.7615 -0.339877
+0.762 -0.409198
+0.7625 -0.476612
+0.763 -0.541736
+0.7635 -0.604181
+0.764 -0.663583
+0.7645 -0.719588
+0.765 -0.771847
+0.7655 -0.820057
+0.766 -0.86391
+0.7665 -0.903139
+0.767 -0.937492
+0.7675 -0.966741
+0.768 -0.9907
+0.7685 -1.00919
+0.769 -1.02209
+0.7695 -1.02929
+0.77 -1.0307
+0.7705 -1.0263
+0.771 -1.01607
+0.7715 -1.00004
+0.772 -0.978266
+0.7725 -0.950838
+0.773 -0.917875
+0.7735 -0.879534
+0.774 -0.836011
+0.7745 -0.787509
+0.775 -0.734289
+0.7755 -0.67661
+0.776 -0.614785
+0.7765 -0.549141
+0.777 -0.480018
+0.7775 -0.407807
+0.778 -0.332877
+0.7785 -0.255652
+0.779 -0.176557
+0.7795 -0.0960186
+0.78 -0.0145043
+0.7805 0.0675539
+0.781 0.149678
+0.7815 0.231402
+0.782 0.312271
+0.7825 0.391821
+0.783 0.469578
+0.7835 0.545116
+0.784 0.617976
+0.7845 0.687743
+0.785 0.754002
+0.7855 0.816349
+0.786 0.874426
+0.7865 0.927868
+0.787 0.976356
+0.7875 1.01959
+0.788 1.05728
+0.7885 1.08921
+0.789 1.11515
+0.7895 1.13492
+0.79 1.14839
+0.7905 1.15544
+0.791 1.15599
+0.7915 1.15002
+0.792 1.13752
+0.7925 1.11853
+0.793 1.09312
+0.7935 1.0614
+0.794 1.02352
+0.7945 0.979661
+0.795 0.930041
+0.7955 0.874917
+0.796 0.814559
+0.7965 0.749293
+0.797 0.679468
+0.7975 0.605441
+0.798 0.527627
+0.7985 0.44643
+0.799 0.362298
+0.7995 0.275707
+0.8 0.187114
+0.8005 0.0970296
+0.801 0.00593733
+0.8015 -0.0856452
+0.802 -0.177186
+0.8025 -0.268193
+0.803 -0.358125
+0.8035 -0.446487
+0.804 -0.532762
+0.8045 -0.616443
+0.805 -0.697062
+0.8055 -0.774127
+0.806 -0.847206
+0.8065 -0.915853
+0.807 -0.979653
+0.8075 -1.03824
+0.808 -1.09124
+0.8085 -1.13833
+0.809 -1.17921
+0.8095 -1.21364
+0.81 -1.24137
+0.8105 -1.26223
+0.811 -1.27605
+0.8115 -1.28273
+0.812 -1.28221
+0.8125 -1.27443
+0.813 -1.25943
+0.8135 -1.23724
+0.814 -1.20796
+0.8145 -1.17173
+0.815 -1.1287
+0.8155 -1.07911
+0.816 -1.02319
+0.8165 -0.961235
+0.817 -0.893574
+0.8175 -0.820547
+0.818 -0.742554
+0.8185 -0.660021
+0.819 -0.573377
+0.8195 -0.483101
+0.82 -0.389702
+0.8205 -0.293667
+0.821 -0.195555
+0.8215 -0.0958884
+0.822 0.00476546
+0.8225 0.105831
+0.823 0.206761
+0.8235 0.306957
+0.824 0.405877
+0.8245 0.50294
+0.825 0.59758
+0.8255 0.689271
+0.826 0.777462
+0.8265 0.86166
+0.827 0.941356
+0.8275 1.01608
+0.828 1.08539
+0.8285 1.14887
+0.829 1.20614
+0.8295 1.25685
+0.83 1.30068
+0.8305 1.33735
+0.831 1.36663
+0.8315 1.38831
+0.832 1.40226
+0.8325 1.40834
+0.833 1.4065
+0.8335 1.39672
+0.834 1.37901
+0.8345 1.35344
+0.835 1.32013
+0.8355 1.27922
+0.836 1.23093
+0.8365 1.1755
+0.837 1.11319
+0.8375 1.04436
+0.838 0.969344
+0.8385 0.888553
+0.839 0.802429
+0.8395 0.71142
+0.84 0.616039
+0.8405 0.51679
+0.841 0.414224
+0.8415 0.308925
+0.842 0.201454
+0.8425 0.0924322
+0.843 -0.0175529
+0.8435 -0.127874
+0.844 -0.23789
+0.8445 -0.347009
+0.845 -0.454593
+0.8455 -0.560018
+0.846 -0.662701
+0.8465 -0.762031
+0.847 -0.857454
+0.8475 -0.948402
+0.848 -1.03434
+0.8485 -1.11477
+0.849 -1.18921
+0.8495 -1.25723
+0.85 -1.31841
+0.8505 -1.37238
+0.851 -1.41881
+0.8515 -1.4574
+0.852 -1.48792
+0.8525 -1.51015
+0.853 -1.52394
+0.8535 -1.52919
+0.854 -1.52583
+0.8545 -1.51384
+0.855 -1.49327
+0.8555 -1.46421
+0.856 -1.42677
+0.8565 -1.38115
+0.857 -1.32758
+0.8575 -1.26632
+0.858 -1.1977
+0.8585 -1.12207
+0.859 -1.03985
+0.8595 -0.951477
+0.86 -0.857418
+0.8605 -0.758201
+0.861 -0.654351
+0.8615 -0.546444
+0.862 -0.435094
+0.8625 -0.320894
+0.863 -0.204502
+0.8635 -0.0865447
+0.864 0.0323067
+0.8645 0.151363
+0.865 0.269987
+0.8655 0.387474
+0.866 0.503183
+0.8665 0.616442
+0.867 0.726591
+0.8675 0.833022
+0.868 0.935092
+0.8685 1.03224
+0.869 1.12388
+0.8695 1.20948
+0.87 1.28854
+0.8705 1.36059
+0.871 1.42519
+0.8715 1.48197
+0.872 1.53057
+0.8725 1.5707
+0.873 1.60209
+0.8735 1.62455
+0.874 1.63792
+0.8745 1.64209
+0.875 1.63701
+0.8755 1.62268
+0.876 1.59916
+0.8765 1.56655
+0.877 1.525
+0.8775 1.47472
+0.878 1.41597
+0.8785 1.34906
+0.879 1.27433
+0.8795 1.1922
+0.88 1.10309
+0.8805 1.00748
+0.881 0.905927
+0.8815 0.798947
+0.882 0.687141
+0.8825 0.571147
+0.883 0.451574
+0.8835 0.329119
+0.884 0.204439
+0.8845 0.0782435
+0.885 -0.048745
+0.8855 -0.17584
+0.886 -0.302289
+0.8865 -0.427414
+0.887 -0.55048
+0.8875 -0.670779
+0.888 -0.787646
+0.8885 -0.900389
+0.889 -1.00838
+0.8895 -1.11099
+0.89 -1.2076
+0.8905 -1.29769
+0.891 -1.38069
+0.8915 -1.45615
+0.892 -1.5236
+0.8925 -1.58263
+0.893 -1.63291
+0.8935 -1.67411
+0.894 -1.70599
+0.8945 -1.72833
+0.895 -1.74098
+0.8955 -1.74386
+0.896 -1.73691
+0.8965 -1.72015
+0.897 -1.69365
+0.8975 -1.65754
+0.898 -1.61198
+0.8985 -1.55722
+0.899 -1.49355
+0.8995 -1.42129
+0.9 -1.34085
+0.9005 -1.25264
+0.901 -1.15714
+0.9015 -1.0549
+0.902 -0.946445
+0.9025 -0.832403
+0.903 -0.713377
+0.9035 -0.590041
+0.904 -0.463096
+0.9045 -0.333221
+0.905 -0.201171
+0.9055 -0.0676599
+0.906 0.06655
+0.9065 0.200685
+0.907 0.334018
+0.9075 0.465778
+0.908 0.595203
+0.9085 0.721587
+0.909 0.844177
+0.9095 0.962304
+0.91 1.07527
+0.9105 1.18243
+0.911 1.28316
+0.9115 1.37688
+0.912 1.46306
+0.9125 1.54118
+0.913 1.61078
+0.9135 1.67146
+0.914 1.72285
+0.9145 1.76464
+0.915 1.79657
+0.9155 1.81845
+0.916 1.83012
+0.9165 1.83151
+0.917 1.82257
+0.9175 1.80335
+0.918 1.77392
+0.9185 1.73444
+0.919 1.6851
+0.9195 1.62617
+0.92 1.55795
+0.9205 1.48082
+0.921 1.39519
+0.9215 1.30152
+0.922 1.20035
+0.9225 1.0922
+0.923 0.977703
+0.9235 0.857461
+0.924 0.732157
+0.9245 0.602506
+0.925 0.469198
+0.9255 0.333013
+0.926 0.19468
+0.9265 0.0549945
+0.927 -0.085242
+0.9275 -0.22527
+0.928 -0.364266
+0.9285 -0.501477
+0.929 -0.636108
+0.9295 -0.767377
+0.93 -0.89457
+0.9305 -1.01693
+0.931 -1.13379
+0.9315 -1.24446
+0.932 -1.3483
+0.9325 -1.44473
+0.933 -1.53318
+0.9335 -1.61313
+0.934 -1.68414
+0.9345 -1.74577
+0.935 -1.79767
+0.9355 -1.83952
+0.936 -1.87108
+0.9365 -1.89215
+0.937 -1.90259
+0.9375 -1.90233
+0.938 -1.89135
+0.9385 -1.8697
+0.939 -1.83749
+0.9395 -1.79487
+0.94 -1.74208
+0.9405 -1.67939
+0.941 -1.60715
+0.9415 -1.52575
+0.942 -1.43564
+0.9425 -1.33731
+0.943 -1.2313
+0.9435 -1.11821
+0.944 -0.998652
+0.9445 -0.8733
+0.945 -0.74287
+0.9455 -0.608061
+0.946 -0.46966
+0.9465 -0.328409
+0.947 -0.185118
+0.9475 -0.0406129
+0.948 0.104329
+0.9485 0.248854
+0.949 0.39218
+0.9495 0.53348
+0.95 0.671937
+0.9505 0.8068
+0.951 0.937269
+0.9515 1.06263
+0.952 1.18217
+0.9525 1.29517
+0.953 1.40103
+0.9535 1.4991
+0.954 1.58886
+0.9545 1.66978
+0.955 1.74137
+0.9555 1.80324
+0.956 1.85502
+0.9565 1.89642
+0.957 1.92718
+0.9575 1.94711
+0.958 1.95611
+0.9585 1.95409
+0.959 1.94107
+0.9595 1.9171
+0.96 1.88232
+0.9605 1.83689
+0.961 1.78108
+0.9615 1.71518
+0.962 1.63956
+0.9625 1.55464
+0.963 1.46088
+0.9635 1.3588
+0.964 1.24899
+0.9645 1.13203
+0.965 1.00861
+0.9655 0.879391
+0.966 0.745105
+0.9665 0.606525
+0.967 0.464396
+0.9675 0.319552
+0.968 0.172774
+0.9685 0.0249056
+0.969 -0.123203
+0.9695 -0.270749
+0.97 -0.416884
+0.9705 -0.560763
+0.971 -0.701608
+0.9715 -0.838588
+0.972 -0.97096
+0.9725 -1.09796
+0.973 -1.21884
+0.9735 -1.33297
+0.974 -1.43964
+0.9745 -1.5383
+0.975 -1.62835
+0.9755 -1.70928
+0.976 -1.78065
+0.9765 -1.84203
+0.977 -1.89308
+0.9775 -1.9335
+0.978 -1.96305
+0.9785 -1.98156
+0.979 -1.98893
+0.9795 -1.98511
+0.98 -1.97011
+0.9805 -1.94401
+0.981 -1.90695
+0.9815 -1.85913
+0.982 -1.80084
+0.9825 -1.73237
+0.983 -1.65412
+0.9835 -1.56653
+0.984 -1.47007
+0.9845 -1.36531
+0.985 -1.25282
+0.9855 -1.13324
+0.986 -1.00722
+0.9865 -0.87549
+0.987 -0.738802
+0.9875 -0.597895
+0.988 -0.453594
+0.9885 -0.306679
+0.989 -0.157996
+0.9895 -0.00839989
+0.99 0.141301
+0.9905 0.290225
+0.991 0.437569
+0.9915 0.582483
+0.992 0.724131
+0.9925 0.861749
+0.993 0.994525
+0.9935 1.12174
+0.994 1.24266
+0.9945 1.3566
+0.995 1.46292
+0.9955 1.56102
+0.996 1.65034
+0.9965 1.73039
+0.997 1.80069
+0.9975 1.86087
+0.998 1.91058
+0.9985 1.94953
+0.999 1.97752
+0.9995 1.99437
+1 2
+1.0005 1.99437
+1.001 1.97752
+1.0015 1.94953
+1.002 1.91058
+1.0025 1.86086
+1.003 1.80069
+1.0035 1.73039
+1.004 1.65035
+1.0045 1.56101
+1.005 1.46292
+1.0055 1.35661
+1.006 1.24265
+1.0065 1.12174
+1.007 0.994541
+1.0075 0.861733
+1.008 0.724131
+1.0085 0.582483
+1.009 0.437587
+1.0095 0.290225
+1.01 0.141301
+1.0105 -0.00838203
+1.011 -0.158014
+1.0115 -0.306679
+1.012 -0.453577
+1.0125 -0.597912
+1.013 -0.738802
+1.0135 -0.87549
+1.014 -1.00724
+1.0145 -1.13324
+1.015 -1.25282
+1.0155 -1.3653
+1.016 -1.47008
+1.0165 -1.56653
+1.017 -1.65411
+1.0175 -1.73238
+1.018 -1.80084
+1.0185 -1.85913
+1.019 -1.90695
+1.0195 -1.94401
+1.02 -1.97011
+1.0205 -1.98511
+1.021 -1.98893
+1.0215 -1.98156
+1.022 -1.96305
+1.0225 -1.93349
+1.023 -1.89308
+1.0235 -1.84203
+1.024 -1.78064
+1.0245 -1.70928
+1.025 -1.62835
+1.0255 -1.53829
+1.026 -1.43964
+1.0265 -1.33297
+1.027 -1.21886
+1.0275 -1.09794
+1.028 -0.97096
+1.0285 -0.838605
+1.029 -0.701591
+1.0295 -0.560763
+1.03 -0.416884
+1.0305 -0.270731
+1.031 -0.123203
+1.0315 0.0249056
+1.032 0.172756
+1.0325 0.319552
+1.033 0.464396
+1.0335 0.606508
+1.034 0.745122
+1.0345 0.879391
+1.035 1.0086
+1.0355 1.13205
+1.036 1.24899
+1.0365 1.3588
+1.037 1.46087
+1.0375 1.55464
+1.038 1.63956
+1.0385 1.71518
+1.039 1.78108
+1.0395 1.83689
+1.04 1.88231
+1.0405 1.91711
+1.041 1.94107
+1.0415 1.95409
+1.042 1.95611
+1.0425 1.94711
+1.043 1.92718
+1.0435 1.89642
+1.044 1.85502
+1.0445 1.80324
+1.045 1.74138
+1.0455 1.66977
+1.046 1.58886
+1.0465 1.49911
+1.047 1.40101
+1.0475 1.29517
+1.048 1.18217
+1.0485 1.06265
+1.049 0.937269
+1.0495 0.8068
+1.05 0.671954
+1.0505 0.533463
+1.051 0.39218
+1.0515 0.24887
+1.052 0.104311
+1.0525 -0.0406129
+1.053 -0.185118
+1.0535 -0.328425
+1.054 -0.46966
+1.0545 -0.608061
+1.055 -0.742855
+1.0555 -0.873315
+1.056 -0.998652
+1.0565 -1.1182
+1.057 -1.23131
+1.0575 -1.33731
+1.058 -1.43563
+1.0585 -1.52576
+1.059 -1.60715
+1.0595 -1.67939
+1.06 -1.74207
+1.0605 -1.79487
+1.061 -1.83749
+1.0615 -1.8697
+1.062 -1.89135
+1.0625 -1.90233
+1.063 -1.90259
+1.0635 -1.89215
+1.064 -1.87108
+1.0645 -1.83952
+1.065 -1.79766
+1.0655 -1.74577
+1.066 -1.68414
+1.0665 -1.61314
+1.067 -1.53317
+1.0675 -1.44473
+1.068 -1.34831
+1.0685 -1.24445
+1.069 -1.13379
+1.0695 -1.01695
+1.07 -0.894556
+1.0705 -0.767377
+1.071 -0.636108
+1.0715 -0.501493
+1.072 -0.364266
+1.0725 -0.22527
+1.073 -0.0852581
+1.0735 0.0550105
+1.074 0.19468
+1.0745 0.332995
+1.075 0.469215
+1.0755 0.602506
+1.076 0.732157
+1.0765 0.857477
+1.077 0.977703
+1.0775 1.0922
+1.078 1.20033
+1.0785 1.30153
+1.079 1.39519
+1.0795 1.48081
+1.08 1.55796
+1.0805 1.62617
+1.081 1.6851
+1.0815 1.73444
+1.082 1.77392
+1.0825 1.80335
+1.083 1.82257
+1.0835 1.83151
+1.084 1.83012
+1.0845 1.81845
+1.085 1.79657
+1.0855 1.76464
+1.086 1.72285
+1.0865 1.67145
+1.087 1.61078
+1.0875 1.54118
+1.088 1.46305
+1.0885 1.37688
+1.089 1.28316
+1.0895 1.18244
+1.09 1.07526
+1.0905 0.962304
+1.091 0.844192
+1.0915 0.721572
+1.092 0.595203
+1.0925 0.465778
+1.093 0.334002
+1.0935 0.200685
+1.094 0.06655
+1.0945 -0.0676429
+1.095 -0.201171
+1.0955 -0.333221
+1.096 -0.463082
+1.0965 -0.590057
+1.097 -0.713377
+1.0975 -0.832389
+1.098 -0.946458
+1.0985 -1.0549
+1.099 -1.15714
+1.0995 -1.25262
+1.1 -1.34085
+1.1005 -1.42129
+1.101 -1.49354
+1.1015 -1.55723
+1.102 -1.61198
+1.1025 -1.65753
+1.103 -1.69365
+1.1035 -1.72015
+1.104 -1.73691
+1.1045 -1.74386
+1.105 -1.74098
+1.1055 -1.72833
+1.106 -1.70599
+1.1065 -1.67411
+1.107 -1.63291
+1.1075 -1.58264
+1.108 -1.52359
+1.1085 -1.45615
+1.109 -1.3807
+1.1095 -1.29768
+1.11 -1.2076
+1.1105 -1.11099
+1.111 -1.00839
+1.1115 -0.900389
+1.112 -0.787646
+1.1125 -0.670794
+1.113 -0.550468
+1.1135 -0.427414
+1.114 -0.302305
+1.1145 -0.175824
+1.115 -0.048745
+1.1155 0.0782435
+1.116 0.204455
+1.1165 0.329119
+1.117 0.451574
+1.1175 0.571132
+1.118 0.687155
+1.1185 0.798947
+1.119 0.905916
+1.1195 1.0075
+1.12 1.10309
+1.1205 1.19219
+1.121 1.27434
+1.1215 1.34906
+1.122 1.41597
+1.1225 1.47471
+1.123 1.525
+1.1235 1.56655
+1.124 1.59916
+1.1245 1.62268
+1.125 1.63701
+1.1255 1.64209
+1.126 1.63791
+1.1265 1.62455
+1.127 1.60209
+1.1275 1.57069
+1.128 1.53057
+1.1285 1.48197
+1.129 1.4252
+1.1295 1.36058
+1.13 1.28854
+1.1305 1.20949
+1.131 1.12387
+1.1315 1.03224
+1.132 0.935104
+1.1325 0.833009
+1.133 0.726591
+1.1335 0.616442
+1.134 0.503198
+1.1345 0.387474
+1.135 0.269987
+1.1355 0.151378
+1.136 0.0322916
+1.1365 -0.0865447
+1.137 -0.20449
+1.1375 -0.320908
+1.138 -0.435094
+1.1385 -0.546444
+1.139 -0.654361
+1.1395 -0.758201
+1.14 -0.857418
+1.1405 -0.951468
+1.141 -1.03986
+1.1415 -1.12207
+1.142 -1.19769
+1.1425 -1.26632
+1.143 -1.32758
+1.1435 -1.38115
+1.144 -1.42678
+1.1445 -1.46421
+1.145 -1.49327
+1.1455 -1.51384
+1.146 -1.52583
+1.1465 -1.52919
+1.147 -1.52395
+1.1475 -1.51015
+1.148 -1.48792
+1.1485 -1.4574
+1.149 -1.4188
+1.1495 -1.37238
+1.15 -1.31841
+1.1505 -1.25722
+1.151 -1.18921
+1.1515 -1.11477
+1.152 -1.03435
+1.1525 -0.948391
+1.153 -0.857454
+1.1535 -0.762043
+1.154 -0.662691
+1.1545 -0.560018
+1.155 -0.454593
+1.1555 -0.346996
+1.156 -0.23789
+1.1565 -0.127874
+1.157 -0.0175669
+1.1575 0.0924322
+1.158 0.201454
+1.1585 0.308915
+1.159 0.414237
+1.1595 0.51679
+1.16 0.616027
+1.1605 0.711432
+1.161 0.802429
+1.1615 0.888553
+1.162 0.969336
+1.1625 1.04436
+1.163 1.11319
+1.1635 1.17549
+1.164 1.23094
+1.1645 1.27922
+1.165 1.32012
+1.1655 1.35344
+1.166 1.37901
+1.1665 1.39672
+1.167 1.40651
+1.1675 1.40834
+1.168 1.40226
+1.1685 1.38832
+1.169 1.36663
+1.1695 1.33735
+1.17 1.30068
+1.1705 1.25684
+1.171 1.20614
+1.1715 1.14888
+1.172 1.08538
+1.1725 1.01608
+1.173 0.941356
+1.1735 0.861668
+1.174 0.777462
+1.1745 0.689271
+1.175 0.597592
+1.1755 0.50293
+1.176 0.405877
+1.1765 0.306969
+1.177 0.206749
+1.1775 0.105831
+1.178 0.00476546
+1.1785 -0.0959011
+1.179 -0.195555
+1.1795 -0.293667
+1.18 -0.38969
+1.1805 -0.483112
+1.181 -0.573377
+1.1815 -0.660012
+1.182 -0.742564
+1.1825 -0.820547
+1.183 -0.893564
+1.1835 -0.961242
+1.184 -1.02319
+1.1845 -1.07911
+1.185 -1.1287
+1.1855 -1.17173
+1.186 -1.20796
+1.1865 -1.23724
+1.187 -1.25943
+1.1875 -1.27443
+1.188 -1.28221
+1.1885 -1.28273
+1.189 -1.27605
+1.1895 -1.26223
+1.19 -1.24137
+1.1905 -1.21364
+1.191 -1.17921
+1.1915 -1.13833
+1.192 -1.09123
+1.1925 -1.03824
+1.193 -0.979661
+1.1935 -0.915846
+1.194 -0.847206
+1.1945 -0.774136
+1.195 -0.697052
+1.1955 -0.616443
+1.196 -0.532762
+1.1965 -0.446498
+1.197 -0.358125
+1.1975 -0.268193
+1.198 -0.177197
+1.1985 -0.0856335
+1.199 0.00593733
+1.1995 0.0970204
+1.2 0.187126
+1.2005 0.275707
+1.201 0.362298
+1.2015 0.446438
+1.202 0.527627
+1.2025 0.605441
+1.203 0.67946
+1.2035 0.749302
+1.204 0.814559
+1.2045 0.874909
+1.205 0.930046
+1.2055 0.979661
+1.206 1.02352
+1.2065 1.0614
+1.207 1.09312
+1.2075 1.11853
+1.208 1.13752
+1.2085 1.15002
+1.209 1.15599
+1.2095 1.15544
+1.21 1.14839
+1.2105 1.13492
+1.211 1.11515
+1.2115 1.0892
+1.212 1.05728
+1.2125 1.01959
+1.213 0.976351
+1.2135 0.927868
+1.214 0.874426
+1.2145 0.816358
+1.215 0.753996
+1.2155 0.687743
+1.216 0.617984
+1.2165 0.545109
+1.217 0.469578
+1.2175 0.391821
+1.218 0.312263
+1.2185 0.231402
+1.219 0.149678
+1.2195 0.0675623
+1.22 -0.0145043
+1.2205 -0.0960186
+1.221 -0.176549
+1.2215 -0.25566
+1.222 -0.332877
+1.2225 -0.407799
+1.223 -0.480029
+1.2235 -0.549141
+1.224 -0.614785
+1.2245 -0.676604
+1.225 -0.734289
+1.2255 -0.787509
+1.226 -0.836007
+1.2265 -0.879541
+1.227 -0.917875
+1.2275 -0.950834
+1.228 -0.97827
+1.2285 -1.00004
+1.229 -1.01607
+1.2295 -1.0263
+1.23 -1.0307
+1.2305 -1.02929
+1.231 -1.02209
+1.2315 -1.00919
+1.232 -0.9907
+1.2325 -0.966745
+1.233 -0.937489
+1.2335 -0.903139
+1.234 -0.863915
+1.2345 -0.820053
+1.235 -0.771847
+1.2355 -0.719588
+1.236 -0.663592
+1.2365 -0.604181
+1.237 -0.541736
+1.2375 -0.476619
+1.238 -0.409191
+1.2385 -0.339877
+1.239 -0.269068
+1.2395 -0.197151
+1.24 -0.124573
+1.2405 -0.0517257
+1.241 0.0209906
+1.2415 0.0931338
+1.242 0.164323
+1.2425 0.234156
+1.243 0.302268
+1.2435 0.368251
+1.244 0.431768
+1.2445 0.492483
+1.245 0.550046
+1.2455 0.604168
+1.246 0.654574
+1.2465 0.700979
+1.247 0.743159
+1.2475 0.780906
+1.248 0.814037
+1.2485 0.842379
+1.249 0.865813
+1.2495 0.884239
+1.25 0.897576
+1.2505 0.905785
+1.251 0.908853
+1.2515 0.906793
+1.252 0.89965
+1.2525 0.887492
+1.253 0.870424
+1.2535 0.848573
+1.254 0.822092
+1.2545 0.791149
+1.255 0.755962
+1.2555 0.716752
+1.256 0.673753
+1.2565 0.627249
+1.257 0.57752
+1.2575 0.52485
+1.258 0.469581
+1.2585 0.412025
+1.259 0.352528
+1.2595 0.291418
+1.26 0.229077
+1.2605 0.165856
+1.261 0.102097
+1.2615 0.0381943
+1.262 -0.0255094
+1.2625 -0.0886667
+1.263 -0.150897
+1.2635 -0.211874
+1.264 -0.271271
+1.2645 -0.328739
+1.265 -0.38398
+1.2655 -0.436701
+1.266 -0.486629
+1.2665 -0.533478
+1.267 -0.57702
+1.2675 -0.617037
+1.268 -0.653309
+1.2685 -0.685668
+1.269 -0.713963
+1.2695 -0.73805
+1.27 -0.757825
+1.2705 -0.77321
+1.271 -0.784146
+1.2715 -0.790599
+1.272 -0.792564
+1.2725 -0.790061
+1.273 -0.783135
+1.2735 -0.771855
+1.274 -0.756309
+1.2745 -0.736621
+1.275 -0.712929
+1.2755 -0.685385
+1.276 -0.654184
+1.2765 -0.61952
+1.277 -0.581615
+1.2775 -0.540691
+1.278 -0.49702
+1.2785 -0.450859
+1.279 -0.402473
+1.2795 -0.35217
+1.28 -0.300241
+1.2805 -0.246972
+1.281 -0.192702
+1.2815 -0.137725
+1.282 -0.0823626
+1.2825 -0.0269121
+1.283 0.0282854
+1.2835 0.0829376
+1.284 0.136749
+1.2845 0.189396
+1.285 0.24061
+1.2855 0.290116
+1.286 0.337628
+1.2865 0.382906
+1.287 0.425706
+1.2875 0.465818
+1.288 0.503014
+1.2885 0.537117
+1.289 0.567963
+1.2895 0.595386
+1.29 0.619265
+1.2905 0.639497
+1.291 0.655982
+1.2915 0.66866
+1.292 0.67749
+1.2925 0.682445
+1.293 0.683529
+1.2935 0.680762
+1.294 0.674188
+1.2945 0.663873
+1.295 0.649903
+1.2955 0.632378
+1.296 0.611431
+1.2965 0.587203
+1.297 0.559846
+1.2975 0.529549
+1.298 0.496502
+1.2985 0.46091
+1.299 0.422982
+1.2995 0.382966
+1.3 0.341098
+1.3005 0.297615
+1.301 0.252793
+1.3015 0.206888
+1.302 0.160153
+1.3025 0.112881
+1.303 0.0653285
+1.3035 0.0177578
+1.304 -0.0295412
+1.3045 -0.0763184
+1.305 -0.12231
+1.3055 -0.167275
+1.306 -0.210947
+1.3065 -0.253103
+1.307 -0.293522
+1.3075 -0.331972
+1.308 -0.368263
+1.3085 -0.402213
+1.309 -0.433632
+1.3095 -0.462372
+1.31 -0.488293
+1.3105 -0.511273
+1.311 -0.531196
+1.3115 -0.547979
+1.312 -0.561554
+1.3125 -0.571864
+1.313 -0.578879
+1.3135 -0.582586
+1.314 -0.582988
+1.3145 -0.58011
+1.315 -0.573992
+1.3155 -0.564696
+1.316 -0.552299
+1.3165 -0.536896
+1.317 -0.518591
+1.3175 -0.497519
+1.318 -0.473817
+1.3185 -0.447633
+1.319 -0.419146
+1.3195 -0.38853
+1.32 -0.355965
+1.3205 -0.321666
+1.321 -0.285832
+1.3215 -0.248678
+1.322 -0.210415
+1.3225 -0.171283
+1.323 -0.131504
+1.3235 -0.0912962
+1.324 -0.0509088
+1.3245 -0.010559
+1.325 0.0295323
+1.3255 0.0691231
+1.326 0.108006
+1.3265 0.145975
+1.327 0.182804
+1.3275 0.218306
+1.328 0.252293
+1.3285 0.28459
+1.329 0.315015
+1.3295 0.343422
+1.33 0.36967
+1.3305 0.393617
+1.331 0.415155
+1.3315 0.434186
+1.332 0.450615
+1.3325 0.464374
+1.333 0.475409
+1.3335 0.483681
+1.334 0.489164
+1.3345 0.491851
+1.335 0.49175
+1.3355 0.488885
+1.336 0.483296
+1.3365 0.475034
+1.337 0.464172
+1.3375 0.450793
+1.338 0.434987
+1.3385 0.416873
+1.339 0.396566
+1.3395 0.374203
+1.34 0.349919
+1.3405 0.323877
+1.341 0.296237
+1.3415 0.267158
+1.342 0.236831
+1.3425 0.205431
+1.343 0.173136
+1.3435 0.140152
+1.344 0.10666
+1.3445 0.0728565
+1.345 0.0389249
+1.3455 0.00507432
+1.346 -0.0285154
+1.3465 -0.0616621
+1.347 -0.0941679
+1.3475 -0.125865
+1.348 -0.156587
+1.3485 -0.186154
+1.349 -0.21442
+1.3495 -0.241233
+1.35 -0.266463
+1.3505 -0.289968
+1.351 -0.311639
+1.3515 -0.331373
+1.352 -0.349066
+1.3525 -0.364641
+1.353 -0.378033
+1.3535 -0.389178
+1.354 -0.398036
+1.3545 -0.404581
+1.355 -0.408791
+1.3555 -0.410665
+1.356 -0.410214
+1.3565 -0.407459
+1.357 -0.402438
+1.3575 -0.395199
+1.358 -0.385801
+1.3585 -0.374318
+1.359 -0.360833
+1.3595 -0.345436
+1.36 -0.328238
+1.3605 -0.309349
+1.361 -0.28889
+1.3615 -0.266984
+1.362 -0.243779
+1.3625 -0.219413
+1.363 -0.194027
+1.3635 -0.167785
+1.364 -0.140837
+1.3645 -0.113335
+1.365 -0.0854513
+1.3655 -0.0573394
+1.366 -0.029155
+1.3665 -0.00107051
+1.367 0.0267653
+1.3675 0.0541951
+1.368 0.081076
+1.3685 0.107248
+1.369 0.132578
+1.3695 0.156935
+1.37 0.18018
+1.3705 0.202198
+1.371 0.22288
+1.3715 0.242113
+1.372 0.259807
+1.3725 0.275877
+1.373 0.290249
+1.3735 0.302851
+1.374 0.313635
+1.3745 0.322555
+1.375 0.329577
+1.3755 0.334679
+1.376 0.337853
+1.3765 0.339096
+1.377 0.338421
+1.3775 0.335848
+1.378 0.33141
+1.3785 0.325151
+1.379 0.317123
+1.3795 0.307384
+1.38 0.29601
+1.3805 0.28308
+1.381 0.268677
+1.3815 0.252901
+1.382 0.235854
+1.3825 0.217638
+1.383 0.198376
+1.3835 0.178181
+1.384 0.157178
+1.3845 0.135485
+1.385 0.113243
+1.3855 0.0905775
+1.386 0.0676144
+1.3865 0.0444974
+1.387 0.0213512
+1.3875 -0.00169693
+1.388 -0.0245075
+1.3885 -0.0469612
+1.389 -0.0689382
+1.3895 -0.0903091
+1.39 -0.110965
+1.3905 -0.130798
+1.391 -0.149706
+1.3915 -0.167583
+1.392 -0.184345
+1.3925 -0.199909
+1.393 -0.214193
+1.3935 -0.227132
+1.394 -0.238671
+1.3945 -0.248751
+1.395 -0.257333
+1.3955 -0.264384
+1.396 -0.269879
+1.3965 -0.2738
+1.397 -0.276143
+1.3975 -0.27691
+1.398 -0.276112
+1.3985 -0.273768
+1.399 -0.269907
+1.3995 -0.264566
+1.4 -0.257791
+1.4005 -0.24963
+1.401 -0.24015
+1.4015 -0.229412
+1.402 -0.217492
+1.4025 -0.204464
+1.403 -0.190419
+1.4035 -0.175444
+1.404 -0.159629
+1.4045 -0.143078
+1.405 -0.12589
+1.4055 -0.108162
+1.406 -0.0900087
+1.4065 -0.0715316
+1.407 -0.0528399
+1.4075 -0.0340354
+1.408 -0.0152348
+1.4085 0.00346174
+1.409 0.0219525
+1.4095 0.0401271
+1.41 0.0578917
+1.4105 0.075153
+1.411 0.0918109
+1.4115 0.107783
+1.412 0.122984
+1.4125 0.137342
+1.413 0.150776
+1.4135 0.163224
+1.414 0.174628
+1.4145 0.18493
+1.415 0.194085
+1.4155 0.202056
+1.416 0.208806
+1.4165 0.214311
+1.417 0.218554
+1.4175 0.221523
+1.418 0.223215
+1.4185 0.223633
+1.419 0.222789
+1.4195 0.2207
+1.42 0.217392
+1.4205 0.212893
+1.421 0.207245
+1.4215 0.200491
+1.422 0.192677
+1.4225 0.183863
+1.423 0.174107
+1.4235 0.163474
+1.424 0.152031
+1.4245 0.139855
+1.425 0.127022
+1.4255 0.113606
+1.426 0.0996952
+1.4265 0.0853719
+1.427 0.0707171
+1.4275 0.0558222
+1.428 0.0407716
+1.4285 0.0256487
+1.429 0.0105456
+1.4295 -0.00445414
+1.43 -0.0192702
+1.4305 -0.0338223
+1.431 -0.0480254
+1.4315 -0.0618046
+1.432 -0.0750923
+1.4325 -0.0878121
+1.433 -0.099901
+1.4335 -0.1113
+1.434 -0.121947
+1.4345 -0.131792
+1.435 -0.140791
+1.4355 -0.148901
+1.436 -0.156084
+1.4365 -0.16231
+1.437 -0.167557
+1.4375 -0.171803
+1.438 -0.175036
+1.4385 -0.177249
+1.439 -0.17844
+1.4395 -0.178614
+1.44 -0.17778
+1.4405 -0.175956
+1.441 -0.173161
+1.4415 -0.169423
+1.442 -0.164771
+1.4425 -0.159244
+1.443 -0.152881
+1.4435 -0.145727
+1.444 -0.137834
+1.4445 -0.129251
+1.445 -0.120034
+1.4455 -0.110245
+1.446 -0.0999452
+1.4465 -0.0891962
+1.447 -0.0780621
+1.4475 -0.0666147
+1.448 -0.0549197
+1.4485 -0.0430435
+1.449 -0.031061
+1.4495 -0.0190362
+1.45 -0.00703624
+1.4505 0.00486666
+1.451 0.0166077
+1.4515 0.0281271
+1.452 0.0393566
+1.4525 0.0502385
+1.453 0.0607141
+1.4535 0.0707331
+1.454 0.080239
+1.4545 0.089186
+1.455 0.0975316
+1.4555 0.105232
+1.456 0.112252
+1.4565 0.118563
+1.457 0.124134
+1.4575 0.128943
+1.458 0.132971
+1.4585 0.136205
+1.459 0.138635
+1.4595 0.140258
+1.46 0.141072
+1.4605 0.141083
+1.461 0.140299
+1.4615 0.138735
+1.462 0.136408
+1.4625 0.133339
+1.463 0.129555
+1.4635 0.125086
+1.464 0.119964
+1.4645 0.114225
+1.465 0.107909
+1.4655 0.10106
+1.466 0.093721
+1.4665 0.0859376
+1.467 0.0777623
+1.4675 0.0692449
+1.468 0.0604341
+1.4685 0.0513873
+1.469 0.0421565
+1.4695 0.0327961
+1.47 0.0233583
+1.4705 0.0139021
+1.471 0.00447725
+1.4715 -0.00486436
+1.472 -0.0140672
+1.4725 -0.023082
+1.473 -0.0318637
+1.4735 -0.040361
+1.474 -0.0485311
+1.4745 -0.0563309
+1.475 -0.0637239
+1.4755 -0.0706694
+1.476 -0.0771349
+1.4765 -0.0830908
+1.477 -0.0885072
+1.4775 -0.0933606
+1.478 -0.097632
+1.4785 -0.101302
+1.479 -0.104358
+1.4795 -0.106791
+1.48 -0.108593
+1.4805 -0.109762
+1.481 -0.110299
+1.4815 -0.110208
+1.482 -0.109499
+1.4825 -0.108181
+1.483 -0.106269
+1.4835 -0.103783
+1.484 -0.100741
+1.4845 -0.0971687
+1.485 -0.0930931
+1.4855 -0.088542
+1.486 -0.0835474
+1.4865 -0.0781414
+1.487 -0.0723624
+1.4875 -0.0662454
+1.488 -0.059828
+1.4885 -0.0531529
+1.489 -0.0462602
+1.4895 -0.0391887
+1.49 -0.0319838
+1.4905 -0.0246866
+1.491 -0.0173379
+1.4915 -0.00998256
+1.492 -0.00266161
+1.4925 0.00458557
+1.493 0.0117197
+1.4935 0.018699
+1.494 0.0254867
+1.4945 0.0320496
+1.495 0.03835
+1.4955 0.044357
+1.496 0.0500414
+1.4965 0.0553728
+1.497 0.060326
+1.4975 0.0648789
+1.498 0.0690109
+1.4985 0.0727022
+1.499 0.0759381
+1.4995 0.0787071
+1.5 0.0809979
+1.5005 0.082804
+1.501 0.0841215
+1.5015 0.0849485
+1.502 0.0852869
+1.5025 0.0851406
+1.503 0.0845167
+1.5035 0.0834246
+1.504 0.0818762
+1.5045 0.0798857
+1.505 0.0774705
+1.5055 0.0746493
+1.506 0.0714423
+1.5065 0.0678742
+1.507 0.0639685
+1.5075 0.0597507
+1.508 0.0552504
+1.5085 0.0504961
+1.509 0.045517
+1.5095 0.0403434
+1.51 0.0350091
+1.5105 0.0295451
+1.511 0.0239829
+1.5115 0.0183578
+1.512 0.0127003
+1.5125 0.00704203
+1.513 0.00141726
+1.5135 -0.00414326
+1.514 -0.00961118
+1.5145 -0.014954
+1.515 -0.0201444
+1.5155 -0.0251543
+1.516 -0.0299599
+1.5165 -0.0345342
+1.517 -0.0388552
+1.5175 -0.0429026
+1.518 -0.0466555
+1.5185 -0.0500969
+1.519 -0.0532128
+1.5195 -0.055988
+1.52 -0.058412
+1.5205 -0.0604755
+1.521 -0.0621721
+1.5215 -0.0634961
+1.522 -0.0644453
+1.5225 -0.0650191
+1.523 -0.065219
+1.5235 -0.065049
+1.524 -0.0645145
+1.5245 -0.0636236
+1.525 -0.0623858
+1.5255 -0.0608123
+1.526 -0.0589172
+1.5265 -0.0567147
+1.527 -0.0542215
+1.5275 -0.0514549
+1.528 -0.0484354
+1.5285 -0.0451823
+1.529 -0.0417166
+1.5295 -0.0380621
+1.53 -0.0342415
+1.5305 -0.0302771
+1.531 -0.0261952
+1.5315 -0.0220194
+1.532 -0.0177747
+1.5325 -0.0134851
+1.533 -0.00917742
+1.5335 -0.00487467
+1.534 -0.000600586
+1.5345 0.00361934
+1.535 0.00776245
+1.5355 0.011808
+1.536 0.0157324
+1.5365 0.0195159
+1.537 0.0231387
+1.5375 0.0265838
+1.538 0.0298324
+1.5385 0.0328695
+1.539 0.0356813
+1.5395 0.0382538
+1.54 0.040576
+1.5405 0.0426391
+1.541 0.0444338
+1.5415 0.0459539
+1.542 0.0471948
+1.5425 0.0481527
+1.543 0.0488265
+1.5435 0.0492159
+1.544 0.0493228
+1.5445 0.0491501
+1.545 0.0487028
+1.5455 0.0479869
+1.546 0.0470104
+1.5465 0.0457821
+1.547 0.0443122
+1.5475 0.0426129
+1.548 0.0406963
+1.5485 0.0385765
+1.549 0.0362676
+1.5495 0.0337865
+1.55 0.0311486
+1.5505 0.0283705
+1.551 0.025471
+1.5515 0.0224679
+1.552 0.0193784
+1.5525 0.0162226
+1.553 0.0130187
+1.5535 0.00978465
+1.554 0.00654057
+1.5545 0.00330456
+1.555 9.41526e-05
+1.5555 -0.00307319
+1.556 -0.00617889
+1.5565 -0.00920658
+1.557 -0.0121414
+1.5575 -0.0149667
+1.558 -0.0176684
+1.5585 -0.0202337
+1.559 -0.0226488
+1.5595 -0.0249024
+1.56 -0.0269846
+1.5605 -0.0288861
+1.561 -0.0305979
+1.5615 -0.0321132
+1.562 -0.0334268
+1.5625 -0.0345333
+1.563 -0.0354296
+1.5635 -0.0361138
+1.564 -0.0365846
+1.5645 -0.0368427
+1.565 -0.0368893
+1.5655 -0.0367274
+1.566 -0.0363606
+1.5665 -0.035794
+1.567 -0.0350334
+1.5675 -0.034086
+1.568 -0.0329599
+1.5685 -0.0316634
+1.569 -0.0302072
+1.5695 -0.028601
+1.57 -0.026856
+1.5705 -0.0249845
+1.571 -0.0229988
+1.5715 -0.0209114
+1.572 -0.0187353
+1.5725 -0.0164848
+1.573 -0.0141734
+1.5735 -0.0118144
+1.574 -0.00942313
+1.5745 -0.00701253
+1.575 -0.00459626
+1.5755 -0.00218904
+1.576 0.000195897
+1.5765 0.00254635
+1.577 0.00484833
+1.5775 0.00709001
+1.578 0.00925935
+1.5785 0.011346
+1.579 0.0133383
+1.5795 0.0152267
+1.58 0.0170024
+1.5805 0.0186564
+1.581 0.0201811
+1.5815 0.0215704
+1.582 0.0228178
+1.5825 0.0239184
+1.583 0.0248682
+1.5835 0.0256642
+1.584 0.0263037
+1.5845 0.0267857
+1.585 0.0271096
+1.5855 0.0272758
+1.586 0.0272858
+1.5865 0.0271417
+1.587 0.0268466
+1.5875 0.0264044
+1.588 0.0258195
+1.5885 0.0250978
+1.589 0.0242449
+1.5895 0.0232678
+1.59 0.0221735
+1.5905 0.0209704
+1.591 0.0196666
+1.5915 0.0182707
+1.592 0.0167925
+1.5925 0.0152414
+1.593 0.0136266
+1.5935 0.0119591
+1.594 0.0102487
+1.5945 0.00850564
+1.595 0.00673997
+1.5955 0.00496288
+1.596 0.00318388
+1.5965 0.00141286
+1.597 -0.000339552
+1.5975 -0.00206392
+1.598 -0.00375159
+1.5985 -0.00539271
+1.599 -0.00697904
+1.5995 -0.00850226
+1.6 -0.0099553
+1.6005 -0.0113302
+1.601 -0.0126208
+1.6015 -0.0138211
+1.602 -0.0149253
+1.6025 -0.0159286
+1.603 -0.0168274
+1.6035 -0.0176176
+1.604 -0.0182966
+1.6045 -0.0188622
+1.605 -0.0193128
+1.6055 -0.0196477
+1.606 -0.0198667
+1.6065 -0.0199703
+1.607 -0.0199596
+1.6075 -0.0198365
+1.608 -0.0196032
+1.6085 -0.0192629
+1.609 -0.018819
+1.6095 -0.0182756
+1.61 -0.0176373
+1.6105 -0.0169092
+1.611 -0.0160966
+1.6115 -0.0152053
+1.612 -0.0142421
+1.6125 -0.0132129
+1.613 -0.0121247
+1.6135 -0.0109847
+1.614 -0.00980029
+1.6145 -0.0085782
+1.615 -0.00732657
+1.6155 -0.00605269
+1.616 -0.00476383
+1.6165 -0.00346804
+1.617 -0.00217263
+1.6175 -0.000884652
+1.618 0.000388846
+1.6185 0.00164037
+1.619 0.00286331
+1.6195 0.00405167
+1.62 0.00519866
+1.6205 0.00629867
+1.621 0.0073464
+1.6215 0.00833631
+1.622 0.00926381
+1.6225 0.0101248
+1.623 0.0109155
+1.6235 0.0116322
+1.624 0.0122721
+1.6245 0.012833
+1.625 0.0133127
+1.6255 0.0137097
+1.626 0.0140233
+1.6265 0.0142527
+1.627 0.0143982
+1.6275 0.0144601
+1.628 0.0144394
+1.6285 0.0143375
+1.629 0.0141563
+1.6295 0.0138979
+1.63 0.0135651
+1.6305 0.013161
+1.631 0.0126887
+1.6315 0.0121524
+1.632 0.0115558
+1.6325 0.0109032
+1.633 0.0101994
+1.6335 0.00944909
+1.634 0.00865719
+1.6345 0.00782868
+1.635 0.00696918
+1.6355 0.00608386
+1.636 0.00517796
+1.6365 0.00425738
+1.637 0.00332721
+1.6375 0.00239276
+1.638 0.00145975
+1.6385 0.000533364
+1.639 -0.000381646
+1.6395 -0.00127982
+1.64 -0.00215651
+1.6405 -0.00300703
+1.641 -0.00382731
+1.6415 -0.00461278
+1.642 -0.00535969
+1.6425 -0.00606459
+1.643 -0.00672387
+1.6435 -0.00733459
+1.644 -0.00789433
+1.6445 -0.00840043
+1.645 -0.008851
+1.6455 -0.00924433
+1.646 -0.00957927
+1.6465 -0.00985468
+1.647 -0.01007
+1.6475 -0.010225
+1.648 -0.0103198
+1.6485 -0.0103547
+1.649 -0.0103306
+1.6495 -0.0102486
+1.65 -0.01011
+1.6505 -0.00991643
+1.651 -0.00967006
+1.6515 -0.00937304
+1.652 -0.00902787
+1.6525 -0.0086372
+1.653 -0.00820419
+1.6535 -0.00773181
+1.654 -0.0072233
+1.6545 -0.00668234
+1.655 -0.00611246
+1.6555 -0.00551714
+1.656 -0.00490045
+1.6565 -0.0042661
+1.657 -0.00361798
+1.6575 -0.00295985
+1.658 -0.00229592
+1.6585 -0.00162979
+1.659 -0.000965188
+1.6595 -0.00030613
+1.66 0.000343815
+1.6605 0.000981375
+1.661 0.00160282
+1.6615 0.00220503
+1.662 0.00278484
+1.6625 0.00333958
+1.663 0.00386622
+1.6635 0.00436236
+1.664 0.00482578
+1.6645 0.00525422
+1.665 0.00564587
+1.6655 0.00599927
+1.666 0.00631287
+1.6665 0.00658563
+1.667 0.0068167
+1.6675 0.00700537
+1.668 0.00715136
+1.6685 0.00725453
+1.669 0.007315
+1.6695 0.00733311
+1.67 0.00730949
+1.6705 0.00724495
+1.671 0.00714054
+1.6715 0.00699752
+1.672 0.0068173
+1.6725 0.00660161
+1.673 0.0063522
+1.6735 0.00607104
+1.674 0.00576021
+1.6745 0.0054221
+1.675 0.00505899
+1.6755 0.00467327
+1.676 0.00426768
+1.6765 0.0038448
+1.677 0.00340716
+1.6775 0.0029577
+1.678 0.00249906
+1.6785 0.00203391
+1.679 0.00156519
+1.6795 0.00109555
+1.68 0.000627586
+1.6805 0.000163868
+1.681 -0.000292861
+1.6815 -0.000740179
+1.682 -0.00117589
+1.6825 -0.0015975
+1.683 -0.00200295
+1.6835 -0.00239029
+1.684 -0.00275748
+1.6845 -0.00310282
+1.685 -0.00342479
+1.6855 -0.003722
+1.686 -0.00399306
+1.6865 -0.00423691
+1.687 -0.00445273
+1.6875 -0.00463965
+1.688 -0.00479717
+1.6885 -0.00492489
+1.689 -0.00502256
+1.6895 -0.00509018
+1.69 -0.00512787
+1.6905 -0.00513592
+1.691 -0.00511479
+1.6915 -0.00506511
+1.692 -0.00498762
+1.6925 -0.00488328
+1.693 -0.00475312
+1.6935 -0.00459828
+1.694 -0.00442015
+1.6945 -0.00422009
+1.695 -0.00399955
+1.6955 -0.00376024
+1.696 -0.00350382
+1.6965 -0.00323199
+1.697 -0.00294652
+1.6975 -0.00264937
+1.698 -0.00234237
+1.6985 -0.00202738
+1.699 -0.00170647
+1.6995 -0.00138144
+1.7 -0.00105416
+1.7005 -0.000726663
+1.701 -0.000400775
+1.7015 -7.81849e-05
+1.702 0.000239175
+1.7025 0.000549661
+1.703 0.000851603
+1.7035 0.00114356
+1.704 0.0014239
+1.7045 0.00169129
+1.705 0.0019445
+1.7055 0.00218224
+1.706 0.00240346
+1.7065 0.00260728
+1.707 0.00279274
+1.7075 0.00295915
+1.708 0.0031059
+1.7085 0.00323254
+1.709 0.00333865
+1.7095 0.00342401
+1.71 0.00348852
+1.7105 0.00353213
+1.711 0.00355501
+1.7115 0.00355737
+1.712 0.00353956
+1.7125 0.00350205
+1.713 0.00344537
+1.7135 0.00337022
+1.714 0.00327733
+1.7145 0.00316754
+1.715 0.00304176
+1.7155 0.00290102
+1.716 0.00274636
+1.7165 0.00257887
+1.717 0.0023998
+1.7175 0.00221035
+1.718 0.0020117
+1.7185 0.00180524
+1.719 0.00159225
+1.7195 0.00137404
+1.72 0.0011519
+1.7205 0.000927272
+1.721 0.000701385
+1.7215 0.00047552
+1.722 0.000251046
+1.7225 2.91893e-05
+1.723 -0.000188927
+1.7235 -0.000402025
+1.724 -0.000609027
+1.7245 -0.000808851
+1.725 -0.00100057
+1.7255 -0.00118314
+1.726 -0.00135574
+1.7265 -0.00151759
+1.727 -0.00166791
+1.7275 -0.00180607
+1.728 -0.00193156
+1.7285 -0.00204382
+1.729 -0.0021425
+1.7295 -0.00222728
+1.73 -0.0022979
+1.7305 -0.00235424
+1.731 -0.00239625
+1.7315 -0.00242393
+1.732 -0.00243738
+1.7325 -0.0024368
+1.733 -0.00242243
+1.7335 -0.00239462
+1.734 -0.00235376
+1.7345 -0.0023003
+1.735 -0.00223481
+1.7355 -0.00215786
+1.736 -0.0020701
+1.7365 -0.0019722
+1.737 -0.00186495
+1.7375 -0.00174909
+1.738 -0.00162542
+1.7385 -0.00149484
+1.739 -0.00135819
+1.7395 -0.00121632
+1.74 -0.00107018
+1.7405 -0.000920672
+1.741 -0.000768657
+1.7415 -0.000615112
+1.742 -0.000460919
+1.7425 -0.000306936
+1.743 -0.000154016
+1.7435 -3.06876e-06
+1.744 0.000145101
+1.7445 0.000289763
+1.745 0.000430088
+1.7455 0.000565389
+1.746 0.000695016
+1.7465 0.000818285
+1.747 0.000934631
+1.7475 0.00104354
+1.748 0.00114455
+1.7485 0.00123719
+1.749 0.00132109
+1.7495 0.00139598
+1.75 0.00146156
+1.7505 0.00151765
+1.751 0.0015641
+1.7515 0.00160082
+1.752 0.0016278
+1.7525 0.00164506
+1.753 0.00165268
+1.7535 0.00165079
+1.754 0.0016396
+1.7545 0.00161932
+1.755 0.00159025
+1.7555 0.00155272
+1.756 0.00150709
+1.7565 0.00145379
+1.757 0.00139325
+1.7575 0.00132594
+1.758 0.00125239
+1.7585 0.00117314
+1.759 0.00108873
+1.7595 0.000999717
+1.76 0.000906734
+1.7605 0.000810364
+1.761 0.000711199
+1.7615 0.000609903
+1.762 0.000507054
+1.7625 0.000403251
+1.763 0.000299144
+1.7635 0.000195321
+1.764 9.23221e-05
+1.7645 -9.23019e-06
+1.765 -0.000108808
+1.7655 -0.000205873
+1.766 -0.000299961
+1.7665 -0.000390545
+1.767 -0.000477198
+1.7675 -0.000559518
+1.768 -0.000637087
+1.7685 -0.000709563
+1.769 -0.000776661
+1.7695 -0.000838068
+1.77 -0.000893556
+1.7705 -0.000942918
+1.771 -0.000986009
+1.7715 -0.00102268
+1.772 -0.00105286
+1.7725 -0.0010765
+1.773 -0.00109358
+1.7735 -0.00110414
+1.774 -0.00110824
+1.7745 -0.00110598
+1.775 -0.00109749
+1.7755 -0.00108295
+1.776 -0.00106255
+1.7765 -0.00103652
+1.777 -0.00100512
+1.7775 -0.00096862
+1.778 -0.000927342
+1.7785 -0.0008816
+1.779 -0.000831732
+1.7795 -0.000778123
+1.78 -0.000721143
+1.7805 -0.000661158
+1.781 -0.000598597
+1.7815 -0.000533853
+1.782 -0.000467336
+1.7825 -0.000399443
+1.783 -0.000330622
+1.7835 -0.000261255
+1.784 -0.000191737
+1.7845 -0.000122496
+1.785 -5.39127e-05
+1.7855 1.36643e-05
+1.786 7.98362e-05
+1.7865 0.000144268
+1.787 0.000206621
+1.7875 0.000266607
+1.788 0.000323899
+1.7885 0.000378238
+1.789 0.000429382
+1.7895 0.000477082
+1.79 0.000521141
+1.7905 0.000561396
+1.791 0.000597673
+1.7915 0.00062985
+1.792 0.000657832
+1.7925 0.000681526
+1.793 0.000700895
+1.7935 0.000715909
+1.794 0.000726571
+1.7945 0.0007329
+1.795 0.000734951
+1.7955 0.000732793
+1.796 0.000726522
+1.7965 0.000716255
+1.797 0.000702125
+1.7975 0.000684297
+1.798 0.000662939
+1.7985 0.000638244
+1.799 0.000610412
+1.7995 0.000579676
+1.8 0.000546258
+1.8005 0.000510397
+1.801 0.000472359
+1.8015 0.0004324
+1.802 0.000390768
+1.8025 0.000347756
+1.803 0.000303625
+1.8035 0.00025864
+1.804 0.000213091
+1.8045 0.000167245
+1.805 0.000121358
+1.8055 7.56883e-05
+1.806 3.05086e-05
+1.8065 -1.39384e-05
+1.807 -5.74324e-05
+1.8075 -9.97231e-05
+1.808 -0.000140603
+1.8085 -0.000179876
+1.809 -0.000217334
+1.8095 -0.000252807
+1.81 -0.000286138
+1.8105 -0.000317184
+1.811 -0.000345801
+1.8115 -0.000371879
+1.812 -0.000395332
+1.8125 -0.000416065
+1.813 -0.000434021
+1.8135 -0.000449157
+1.814 -0.000461434
+1.8145 -0.000470848
+1.815 -0.000477401
+1.8155 -0.000481113
+1.816 -0.000482019
+1.8165 -0.000480173
+1.817 -0.000475638
+1.8175 -0.000468496
+1.818 -0.000458841
+1.8185 -0.000446775
+1.819 -0.000432421
+1.8195 -0.000415904
+1.82 -0.000397357
+1.8205 -0.000376935
+1.821 -0.000354791
+1.8215 -0.000331082
+1.822 -0.00030597
+1.8225 -0.000279638
+1.823 -0.000252254
+1.8235 -0.000223991
+1.824 -0.00019504
+1.8245 -0.00016557
+1.825 -0.000135756
+1.8255 -0.000105786
+1.826 -7.58303e-05
+1.8265 -4.60475e-05
+1.827 -1.66184e-05
+1.8275 1.23028e-05
+1.828 4.05593e-05
+1.8285 6.8015e-05
+1.829 9.45162e-05
+1.8295 0.000119937
+1.83 0.000144161
+1.8305 0.000167064
+1.831 0.000188545
+1.8315 0.000208521
+1.832 0.000226898
+1.8325 0.000243609
+1.833 0.000258591
+1.8335 0.0002718
+1.834 0.000283191
+1.8345 0.000292739
+1.835 0.00030043
+1.8355 0.000306253
+1.836 0.000310218
+1.8365 0.000312341
+1.837 0.000312645
+1.8375 0.000311168
+1.838 0.000307953
+1.8385 0.000303058
+1.839 0.000296543
+1.8395 0.00028848
+1.84 0.000278943
+1.8405 0.000268024
+1.841 0.000255809
+1.8415 0.000242393
+1.842 0.000227882
+1.8425 0.00021238
+1.843 0.000195991
+1.8435 0.000178834
+1.844 0.000161019
+1.8445 0.000142662
+1.845 0.000123874
+1.8455 0.000104781
+1.846 8.54898e-05
+1.8465 6.61132e-05
+1.847 4.67707e-05
+1.8475 2.75697e-05
+1.848 8.60894e-06
+1.8485 -9.9992e-06
+1.849 -2.816e-05
+1.8495 -4.57777e-05
+1.85 -6.27703e-05
+1.8505 -7.90457e-05
+1.851 -9.45297e-05
+1.8515 -0.000109154
+1.852 -0.000122847
+1.8525 -0.000135552
+1.853 -0.000147222
+1.8535 -0.000157807
+1.854 -0.000167273
+1.8545 -0.00017559
+1.855 -0.000182733
+1.8555 -0.000188686
+1.856 -0.000193441
+1.8565 -0.000196997
+1.857 -0.000199357
+1.8575 -0.000200535
+1.858 -0.000200548
+1.8585 -0.000199421
+1.859 -0.000197186
+1.8595 -0.000193877
+1.86 -0.000189537
+1.8605 -0.000184212
+1.861 -0.000177954
+1.8615 -0.000170816
+1.862 -0.000162861
+1.8625 -0.000154151
+1.863 -0.000144748
+1.8635 -0.000134726
+1.864 -0.000124152
+1.8645 -0.000113095
+1.865 -0.000101635
+1.8655 -8.98416e-05
+1.866 -7.77878e-05
+1.8665 -6.55524e-05
+1.867 -5.32067e-05
+1.8675 -4.08257e-05
+1.868 -2.8471e-05
+1.8685 -1.62269e-05
+1.869 -4.15112e-06
+1.8695 7.69111e-06
+1.87 1.92326e-05
+1.8705 3.04165e-05
+1.871 4.11889e-05
+1.8715 5.14929e-05
+1.872 6.12822e-05
+1.8725 7.051e-05
+1.873 7.91416e-05
+1.8735 8.71353e-05
+1.874 9.44609e-05
+1.8745 0.000101092
+1.875 0.000107004
+1.8755 0.00011218
+1.876 0.000116607
+1.8765 0.000120274
+1.877 0.000123178
+1.8775 0.000125318
+1.878 0.000126699
+1.8785 0.00012733
+1.879 0.000127223
+1.8795 0.000126395
+1.88 0.000124867
+1.8805 0.000122661
+1.881 0.000119806
+1.8815 0.000116332
+1.882 0.000112273
+1.8825 0.000107661
+1.883 0.000102541
+1.8835 9.69478e-05
+1.884 9.0926e-05
+1.8845 8.45172e-05
+1.885 7.77691e-05
+1.8855 7.07265e-05
+1.886 6.34342e-05
+1.8865 5.59424e-05
+1.887 4.82981e-05
+1.8875 4.05437e-05
+1.888 3.27304e-05
+1.8885 2.49024e-05
+1.889 1.71032e-05
+1.8895 9.37968e-06
+1.89 1.77265e-06
+1.8905 -5.67709e-06
+1.891 -1.2932e-05
+1.8915 -1.9952e-05
+1.892 -2.67025e-05
+1.8925 -3.31548e-05
+1.893 -3.92749e-05
+1.8935 -4.50365e-05
+1.894 -5.04156e-05
+1.8945 -5.53879e-05
+1.895 -5.99352e-05
+1.8955 -6.40408e-05
+1.896 -6.76919e-05
+1.8965 -7.08762e-05
+1.897 -7.35861e-05
+1.8975 -7.58183e-05
+1.898 -7.75691e-05
+1.8985 -7.88397e-05
+1.899 -7.96335e-05
+1.8995 -7.99564e-05
+1.9 -7.98172e-05
+1.9005 -7.92267e-05
+1.901 -7.81986e-05
+1.9015 -7.67485e-05
+1.902 -7.4894e-05
+1.9025 -7.26541e-05
+1.903 -7.00511e-05
+1.9035 -6.71076e-05
+1.904 -6.38472e-05
+1.9045 -6.02969e-05
+1.905 -5.64828e-05
+1.9055 -5.24317e-05
+1.906 -4.81737e-05
+1.9065 -4.37376e-05
+1.907 -3.91513e-05
+1.9075 -3.44439e-05
+1.908 -2.96471e-05
+1.9085 -2.47891e-05
+1.909 -1.98981e-05
+1.9095 -1.50047e-05
+1.91 -1.01359e-05
+1.9105 -5.31799e-06
+1.911 -5.79145e-07
+1.9115 4.05536e-06
+1.912 8.56329e-06
+1.9125 1.29217e-05
+1.913 1.71074e-05
+1.9135 2.11013e-05
+1.914 2.48856e-05
+1.9145 2.8442e-05
+1.915 3.1756e-05
+1.9155 3.48149e-05
+1.916 3.76052e-05
+1.9165 4.01187e-05
+1.917 4.23474e-05
+1.9175 4.4284e-05
+1.918 4.59245e-05
+1.9185 4.72662e-05
+1.919 4.83086e-05
+1.9195 4.90519e-05
+1.92 4.94991e-05
+1.9205 4.96542e-05
+1.921 4.95229e-05
+1.9215 4.91127e-05
+1.922 4.8432e-05
+1.9225 4.74911e-05
+1.923 4.63011e-05
+1.9235 4.48746e-05
+1.924 4.32248e-05
+1.9245 4.13667e-05
+1.925 3.93155e-05
+1.9255 3.70868e-05
+1.926 3.46986e-05
+1.9265 3.21671e-05
+1.927 2.95098e-05
+1.9275 2.67458e-05
+1.928 2.38928e-05
+1.9285 2.09685e-05
+1.929 1.79924e-05
+1.9295 1.49822e-05
+1.93 1.19563e-05
+1.9305 8.93009e-06
+1.931 5.92437e-06
+1.9315 2.95345e-06
+1.932 3.35029e-08
+1.9325 -2.8188e-06
+1.933 -5.58933e-06
+1.9335 -8.26467e-06
+1.934 -1.08307e-05
+1.9345 -1.32758e-05
+1.935 -1.55883e-05
+1.9355 -1.77594e-05
+1.936 -1.97788e-05
+1.9365 -2.16387e-05
+1.937 -2.33327e-05
+1.9375 -2.48541e-05
+1.938 -2.61987e-05
+1.9385 -2.7363e-05
+1.939 -2.83441e-05
+1.9395 -2.9141e-05
+1.94 -2.97534e-05
+1.9405 -3.01817e-05
+1.941 -3.04283e-05
+1.9415 -3.04957e-05
+1.942 -3.03877e-05
+1.9425 -3.0109e-05
+1.943 -2.96653e-05
+1.9435 -2.90626e-05
+1.944 -2.83084e-05
+1.9445 -2.74107e-05
+1.945 -2.63771e-05
+1.9455 -2.52179e-05
+1.946 -2.39418e-05
+1.9465 -2.2559e-05
+1.947 -2.10797e-05
+1.9475 -1.95152e-05
+1.948 -1.7876e-05
+1.9485 -1.61729e-05
+1.949 -1.44179e-05
+1.9495 -1.26222e-05
+1.95 -1.07959e-05
+1.9505 -8.95136e-06
+1.951 -7.09906e-06
+1.9515 -5.24942e-06
+1.952 -3.4137e-06
+1.9525 -1.60169e-06
+1.953 1.76813e-07
+1.9535 1.91279e-06
+1.954 3.59662e-06
+1.9545 5.21993e-06
+1.955 6.77584e-06
+1.9555 8.2561e-06
+1.956 9.65433e-06
+1.9565 1.09648e-05
+1.957 1.21814e-05
+1.9575 1.32999e-05
+1.958 1.4316e-05
+1.9585 1.52266e-05
+1.959 1.60287e-05
+1.9595 1.67201e-05
+1.96 1.73001e-05
+1.9605 1.77676e-05
+1.961 1.81226e-05
+1.9615 1.83659e-05
+1.962 1.84986e-05
+1.9625 1.85226e-05
+1.963 1.84404e-05
+1.9635 1.82549e-05
+1.964 1.79698e-05
+1.9645 1.7589e-05
+1.965 1.71167e-05
+1.9655 1.65582e-05
+1.966 1.59186e-05
+1.9665 1.52032e-05
+1.967 1.44184e-05
+1.9675 1.357e-05
+1.968 1.26642e-05
+1.9685 1.17081e-05
+1.969 1.07082e-05
+1.9695 9.67102e-06
+1.97 8.60324e-06
+1.9705 7.51217e-06
+1.971 6.40439e-06
+1.9715 5.2864e-06
+1.972 4.1653e-06
+1.9725 3.04734e-06
+1.973 1.93862e-06
+1.9735 8.45705e-07
+1.974 -2.25546e-07
+1.9745 -1.26996e-06
+1.975 -2.28218e-06
+1.9755 -3.25681e-06
+1.976 -4.18937e-06
+1.9765 -5.07572e-06
+1.977 -5.91155e-06
+1.9775 -6.69348e-06
+1.978 -7.41846e-06
+1.9785 -8.0833e-06
+1.979 -8.68609e-06
+1.9795 -9.22484e-06
+1.98 -9.69779e-06
+1.9805 -1.01039e-05
+1.981 -1.04426e-05
+1.9815 -1.07135e-05
+1.982 -1.09166e-05
+1.9825 -1.10524e-05
+1.983 -1.11219e-05
+1.9835 -1.11262e-05
+1.984 -1.10668e-05
+1.9845 -1.09457e-05
+1.985 -1.07651e-05
+1.9855 -1.05275e-05
+1.986 -1.02355e-05
+1.9865 -9.89205e-06
+1.987 -9.5006e-06
+1.9875 -9.06445e-06
+1.988 -8.58707e-06
+1.9885 -8.07249e-06
+1.989 -7.5243e-06
+1.9895 -6.94641e-06
+1.99 -6.34309e-06
+1.9905 -5.7183e-06
+1.991 -5.07601e-06
+1.9915 -4.42057e-06
+1.992 -3.75593e-06
+1.9925 -3.08625e-06
+1.993 -2.41497e-06
+1.9935 -1.74674e-06
+1.994 -1.08481e-06
+1.9945 -4.32789e-07
+1.995 2.0556e-07
+1.9955 8.27053e-07
+1.996 1.42867e-06
+1.9965 2.0072e-06
+1.997 2.56005e-06
+1.9975 3.08454e-06
+1.998 3.57871e-06
+1.9985 4.04017e-06
+1.999 4.46717e-06
+1.9995 4.85819e-06
+2 5.21174e-06
+&
local rotation axis of the slab and the Gaussian-weighted positions.
+\section{\normindex{Electric fields}}
+A pulsed and oscillating electric field can be applied according to:
+\begin{equation}
+E(t) = E_0 \exp\left[-\frac{(t-t_0)^2}{2\sigma^2}\right]\cos\left[\omega (t-t_0)\right]
+\label{eq_efield}
+\end{equation}
+where $E_0$ is the field strength, the angular frequency \mbox{$\omega = 2\pi c/\lambda$}, $t_0$ is
+the time at of the peak in the field strength and $\sigma$ is the with
+of the pulse. Special cases occur when $\sigma$ = 0 (non-pulsed field)
+and for $\omega$ is 0 (static field).
+
+This simulated \normindex{laser}-pulse was applied to
+simulations of melting ice~\cite{Caleman2008a}. A pulsed electric field may
+look ike Fig.~\ref{fig:field}. In the supporting
+information of that paper the impact of an applied electric field on a
+system under periodic boundary conditions is analyzed. It is described
+that the effective electric field under PBC is larger than the applied
+field, by a factor depending on the size of the box and the dielectric
+properties of molecules in the box. For a system with static dielectric
+properties this factor can be corrected for. But for a system where
+the dielectric varies over time, for example a membrane protein with
+a pore that opens and closes during the simulatippn, this way of applying
+an electric field is not useful. In such cases one can use the computational
+electrophysiology protocol described in the next section (\secref{compel}).
+\begin{figure}[ht]
+\centerline{\includegraphics[width=8cm]{plots/field}}
+\caption {A simulated laser pulse in GROMACS.}
+\label{fig:field}
+\end{figure}
+
+Electric fields are applied when the following options are specified
+in the {\tt grompp.mdp} file. You specify, in order, $E_0$, $\omega$,
+$t_0$ and $\sigma$:
+\begin{verbatim}
+ElectricField-x = 0.04 0 0 0
+\end{verbatim}
+yields a static field with $E_0$ = 0.04 V/nm in the X-direction. In contrast,
+\begin{verbatim}
+ElectricField-x = 2.0 150 5 0
+\end{verbatim}
+yields an oscillating electric field with $E_0$ = 2 V/nm, $\omega$ = 150/ps and
+$t_0$ = 5 ps. Finally
+\begin{verbatim}
+ElectricField-x = 2.0 150 5 1
+\end{verbatim}
+yields an pulsed-oscillating electric field with $E_0$ = 2 V/nm, $\omega$ = 150/ps and
+$t_0$ = 5 ps and $\sigma$ = 1 ps. Read more in ref.~\cite{Caleman2008a}.
+Note that the input file format is changed from the undocumented older
+version. A figure like Fig.~\ref{fig:field} may be produced by passing
+the {\tt -field} option to {\tt gmx mdrun}.
+
+
\section{\normindex{Computational Electrophysiology}}
\label{sec:compel}
This section lists only major changes; minor changes like additional/removed
options or bug fixes are not typically included.
+Version 2017
+^^^^^^^^^^^^
+
+gmx trajectory
+..............
+
+**new**
+
+:ref:`gmx trajectory` has been introduced as a selection-enabled version of
+:ref:`gmx traj`. It supports output of coordinates, velocities, and/or forces
+for positions calculated for selections.
+
Version 2016
^^^^^^^^^^^^
``GMX_EMULATE_GPU``
emulate GPU runs by using algorithmically equivalent CPU reference code instead of
GPU-accelerated functions. As the CPU code is slow, it is intended to be used only for debugging purposes.
- The behavior is automatically triggered if non-bonded calculations are turned off using ``GMX_NO_NONBONDED``
- case in which the non-bonded calculations will not be called, but the CPU-GPU transfer will also be skipped.
``GMX_ENX_NO_FATAL``
disable exiting upon encountering a corrupted frame in an :ref:`edr`
skip non-bonded calculations; can be used to estimate the possible
performance gain from adding a GPU accelerator to the current hardware setup -- assuming that this is
fast enough to complete the non-bonded calculations while the CPU does bonded force and PME computation.
+ Freezing the particles will be required to stop the system blowing up.
``GMX_NO_PULLVIR``
when set, do not add virial contribution to COM pull forces.
``MDRUN``
the :ref:`gmx mdrun` command used by :ref:`gmx tune_pme`.
-``GMX_NSTLIST``
- sets the default value for :mdp:`nstlist`, preventing it from being tuned during
- :ref:`gmx mdrun` startup when using the Verlet cutoff scheme.
+``GMX_DISABLE_DYNAMICPRUNING``
+ disables dynamic pair-list pruning. Note that :ref:`gmx mdrun` will
+ still tune nstlist to the optimal value picked assuming dynamic pruning. Thus
+ for good performance the -nstlist option should be used.
+
+``GMX_NSTLIST_DYNAMICPRUNING``
+ overrides the dynamic pair-list pruning interval chosen heuristically
+ by mdrun. Values should be between the pruning frequency value
+ (1 for CPU and 2 for GPU) and :mdp:`nstlist - 1`.
``GMX_USE_TREEREDUCE``
use tree reduction for nbnxn force reduction. Potentially faster for large number of
override |Gromacs| default behavior, or if you want to test
your own kernels.
+``GMX_OCL_DISABLE_COMPATIBILITY_CHECK``
+ Disables the hardware compatibility check. Useful for developers
+ and allows testing the OpenCL kernels on non-supported platforms
+ (like Intel iGPUs) without source code modification.
+
Analysis and Core Functions
---------------------------
``GMX_QM_ACCURACY``
-cmake_minimum_required(VERSION 2.8.8)
+cmake_minimum_required(VERSION 3.4.3)
project(template CXX)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
add_subdirectory(external/gmock-1.7.0)
endif()
include(testutils/TestMacros.cmake)
- if (GMX_BUILD_UNITTESTS)
- add_subdirectory(testutils)
- else()
- add_custom_target(unittests-notice
- ${CMAKE_COMMAND} -E echo "NOTE: Unit tests have not been run. You need to set GMX_BUILD_UNITTESTS=ON if you want to build and run them."
- DEPENDS run-ctest
- COMMENT "Unit tests disabled" VERBATIM)
- add_dependencies(check unittests-notice)
- endif()
+ add_subdirectory(testutils)
endif()
add_subdirectory(gromacs)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/** Define if we are building for Cygwin */
#cmakedefine01 GMX_CYGWIN
-/* GCC bug in AVX maskload/maskstore arguments - worked around internally */
-#cmakedefine01 GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
-
/* SSE2 was selected for SIMD instruction set level */
#cmakedefine01 GMX_SIMD_X86_SSE2
/* AVX2 256-bit SIMD instruction set level was selected */
#cmakedefine01 GMX_SIMD_X86_AVX2_256
+/* AVX2 128-bit SIMD instruction set level was selected */
+#cmakedefine01 GMX_SIMD_X86_AVX2_128
+
/* MIC (Xeon Phi) SIMD instruction set level was selected */
#cmakedefine01 GMX_SIMD_X86_MIC
#cmakedefine01 GMX_SIMD_REFERENCE
/* String for SIMD instruction choice (for writing to log files and stdout) */
-#define GMX_SIMD_STRING "@GMX_SIMD@"
+#define GMX_SIMD_STRING "@GMX_SIMD_ACTIVE@"
/* Calling convention string (if any) for routines with SIMD variable args */
#define gmx_simdcall @GMX_SIMD_CALLING_CONVENTION@
/* Define when Windows threads are used */
#cmakedefine THREAD_WINDOWS
-/* Define native atomic operations are found */
-#cmakedefine TMPI_ATOMICS
-
/* Define for busy wait option */
/* See gmxpre-config.h.cmakein for explanation for the #ifdef */
#ifndef TMPI_WAIT_FOR_NO_ONE
#cmakedefine01 HAVE_GETTIMEOFDAY
/* Define to 1 if you have the rdtscp instruction. */
-#cmakedefine HAVE_RDTSCP
+#cmakedefine01 HAVE_RDTSCP
/* Define to 1 if you have the fsync() function. */
#cmakedefine01 HAVE_FSYNC
/* Define if we have feenableexcept */
#cmakedefine01 HAVE_FEENABLEEXCEPT
-/* Define if we have zlib */
-#cmakedefine01 HAVE_ZLIB
-
/*! \endcond */
#endif
gmx_ffclose(fo);
gmx_ffclose(frc);
fprintf(stderr,"\n");
- close_trj(status);
+ close_trx(status);
if (trxout != NULL) {
close_trx(trxout);
}
nframe++;
}
} while(read_next_x(status,&t,natoms,x,box));
- close_trj(status);
+ close_trx(status);
gmx_ffclose(out);
gmx_thanx(stderr);
# Set library optimizations
set(_fftw_simd_support_level "")
-if(${GMX_SIMD} MATCHES "^(SSE|AVX)" AND APPLE)
+if(${GMX_SIMD_ACTIVE} MATCHES "^(SSE|AVX)" AND APPLE)
# OS X and --enable-avx causes compilation issues (fftw always picks gcc by default). It's
# not an important enough performance loss to bother warning the
# user about.
set(_fftw_simd_support_level "--enable-sse2")
-elseif(${GMX_SIMD} MATCHES "^(SSE)")
+elseif(${GMX_SIMD_ACTIVE} MATCHES "^(SSE)")
set(_fftw_simd_support_level "--enable-sse2")
-elseif(${GMX_SIMD} MATCHES "^(AVX)")
+elseif(${GMX_SIMD_ACTIVE} MATCHES "^(AVX)")
# Testing shows FFTW configured with --enable-sse2 --enable-avx is
# slightly faster on most architectures than --enable-sse2 alone.
# Support for --enable-avx2 was only added in 3.3.5, but
else()
set(_fftw_simd_support_level --enable-sse2;--enable-avx;--enable-avx2;--enable-avx512)
endif()
-elseif(${GMX_SIMD} MATCHES "^(VSX)")
+elseif(${GMX_SIMD_ACTIVE} MATCHES "^(VSX)")
set(_fftw_simd_support_level --enable-vsx)
endif()
set(GMX_BUILD_OWN_FFTW_OPTIMIZATION_CONFIGURATION ${_fftw_simd_support_level} CACHE INTERNAL "Optimization flags for FFTW compilation")
gmx_rmpbc_done(gpbc);
- close_trj(status);
+ close_trx(status);
sfree(x);
set(PTHREADS_LIBRARIES)
if (CMAKE_USE_PTHREADS_INIT)
set(PTHREADS_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
+ list(APPEND GMOCK_COMPILE_DEFINITIONS "GTEST_HAS_PTHREAD=1")
+ set(GTEST_IS_THREADSAFE 1)
+else()
+ list(APPEND GMOCK_COMPILE_DEFINITIONS "GTEST_HAS_PTHREAD=0")
+ set(GTEST_IS_THREADSAFE 0)
endif()
# Skip variadic implementation of matchers if using GCC < 4.7 due to
set(GTEST_INCLUDE_DIRS ${GTEST_INCLUDE_DIRS} PARENT_SCOPE)
set(GMOCK_COMPILE_DEFINITIONS ${GMOCK_COMPILE_DEFINITIONS} PARENT_SCOPE)
set(GMOCK_COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}" PARENT_SCOPE)
+set(GTEST_IS_THREADSAFE "${GTEST_IS_THREADSAFE}" PARENT_SCOPE)
void GTEST_TEST_CLASS_NAME_(test_case_name, test_name)::TestBody()
# define INSTANTIATE_TEST_CASE_P(prefix, test_case_name, generator) \
- ::testing::internal::ParamGenerator<test_case_name::ParamType> \
+ static ::testing::internal::ParamGenerator<test_case_name::ParamType> \
gtest_##prefix##test_case_name##_EvalGenerator_() { return generator; } \
int gtest_##prefix##test_case_name##_dummy_ = \
::testing::UnitTest::GetInstance()->parameterized_test_registry(). \
/*! \brief The try_lock function.
- Throws a tMPI::system_error exception upon failure.
- \return true if the lock was locked successfully, false if not*/
+ \return true if the lock was locked successfully, false if
+ another thread owned it, and implementation-specific if
+ already held by this thread. Do not rely on the return code
+ if the calling thread could already hold this lock. */
bool try_lock()
{
if (tMPI_Thread_mutex_trylock(&handle_))
/** Try to lock a mutex, return if busy
*
- * This routine always return directly. If the mutex was available and
- * we successfully locked it we return 0, otherwise a non-zero
- * return code (usually meaning the mutex was already locked).
+ * This routine always returns directly.
*
* \param mtx Pointer to the mutex to try and lock
- * \return 0 if locked, non-zero if not locked or an error occurred.
+ * \return If the mutex was available and we successfully locked it,
+ * we return 0. If the mutex was unavailable because it was
+ * already locked by another thread, we return non-zero. If the
+ * mutex was already held by this thread, the return value is
+ * implementation-defined (pthreads non-zero, winthreads zero).
*/
TMPI_EXPORT
int tMPI_Thread_mutex_trylock(tMPI_Thread_mutex_t *mtx);
This source code file is part of thread_mpi.
Written by Sander Pronk, Erik Lindahl, and possibly others.
- Copyright (c) 2009, Sander Pronk, Erik Lindahl.
+ Copyright (c) 2009,2016, Sander Pronk, Erik Lindahl.
All rights reserved.
Redistribution and use in source and binary forms, with or without
\param[in] comm The shared communicator.
\return TMPI_SUCCESS on success, TMPI_FAILURE on failure. */
TMPI_EXPORT
-int tMPI_Send(void* buf, int count, tMPI_Datatype datatype, int dest,
+int tMPI_Send(const void* buf, int count, tMPI_Datatype datatype, int dest,
int tag, tMPI_Comm comm);
/** Receive message; blocks until buf is filled.
\param[out] status The received message status.
\return TMPI_SUCCESS on success, TMPI_FAILURE on failure. */
TMPI_EXPORT
-int tMPI_Sendrecv(void *sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Sendrecv(const void *sendbuf, int sendcount, tMPI_Datatype sendtype,
int dest, int sendtag, void *recvbuf, int recvcount,
tMPI_Datatype recvtype, int source, int recvtag,
tMPI_Comm comm, tMPI_Status *status);
tMPI_Test, etc.
\return TMPI_SUCCESS on success, TMPI_FAILURE on failure. */
TMPI_EXPORT
-int tMPI_Isend(void* buf, int count, tMPI_Datatype datatype, int dest,
+int tMPI_Isend(const void* buf, int count, tMPI_Datatype datatype, int dest,
int tag, tMPI_Comm comm, tMPI_Request *request);
/** Initiate receiving a message.
\return TMPI_SUCCESS on success, TMPI_FAILURE on failure. */
TMPI_EXPORT
-int tMPI_Gather(void* sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Gather(const void* sendbuf, int sendcount, tMPI_Datatype sendtype,
void* recvbuf, int recvcount, tMPI_Datatype recvtype, int root,
tMPI_Comm comm);
\return TMPI_SUCCESS on success, TMPI_FAILURE on failure. */
TMPI_EXPORT
-int tMPI_Gatherv(void* sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Gatherv(const void* sendbuf, int sendcount, tMPI_Datatype sendtype,
void* recvbuf, int *recvcounts, int *displs,
tMPI_Datatype recvtype, int root, tMPI_Comm comm);
\return TMPI_SUCCESS on success, TMPI_FAILURE on failure. */
TMPI_EXPORT
-int tMPI_Scatter(void* sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Scatter(const void* sendbuf, int sendcount, tMPI_Datatype sendtype,
void* recvbuf, int recvcount, tMPI_Datatype recvtype, int root,
tMPI_Comm comm);
\return TMPI_SUCCESS on success, TMPI_FAILURE on failure. */
TMPI_EXPORT
-int tMPI_Scatterv(void* sendbuf, int *sendcounts, int *displs,
+int tMPI_Scatterv(const void* sendbuf, int *sendcounts, int *displs,
tMPI_Datatype sendtype, void* recvbuf, int recvcount,
tMPI_Datatype recvtype, int root, tMPI_Comm comm);
This source code file is part of thread_mpi.
Written by Sander Pronk, Erik Lindahl, and possibly others.
- Copyright (c) 2009, Sander Pronk, Erik Lindahl.
+ Copyright (c) 2009,2016, Sander Pronk, Erik Lindahl.
All rights reserved.
Redistribution and use in source and binary forms, with or without
#include "collective.h"
-int tMPI_Gather(void* sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Gather(const void* sendbuf, int sendcount, tMPI_Datatype sendtype,
void* recvbuf, int recvcount, tMPI_Datatype recvtype,
int root, tMPI_Comm comm)
{
tMPI_Coll_root_xfer(comm, sendtype, recvtype,
sendtype->size*sendcount,
recvtype->size*recvcount,
- sendbuf,
+ (void*)sendbuf,
(char*)recvbuf+myrank*recvcount*recvtype->size,
&ret);
}
/* first set up the data just to root. */
ret = tMPI_Post_multi(cev, myrank, 0, TMPI_GATHER_TAG, sendtype,
- sendcount*sendtype->size, sendbuf, 1, synct, root);
+ sendcount*sendtype->size, (void*)sendbuf, 1, synct, root);
if (ret != TMPI_SUCCESS)
{
return ret;
-int tMPI_Gatherv(void* sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Gatherv(const void* sendbuf, int sendcount, tMPI_Datatype sendtype,
void* recvbuf, int *recvcounts, int *displs,
tMPI_Datatype recvtype, int root, tMPI_Comm comm)
{
tMPI_Coll_root_xfer(comm, sendtype, recvtype,
sendtype->size*sendcount,
recvtype->size*recvcounts[myrank],
- sendbuf,
+ (void*)sendbuf,
(char*)recvbuf+displs[myrank]*recvtype->size,
&ret);
}
/* first set up the data just to root. */
ret = tMPI_Post_multi(cev, myrank, 0, TMPI_GATHERV_TAG, sendtype,
- sendcount*sendtype->size, sendbuf, 1, synct, root);
+ sendcount*sendtype->size, (void*)sendbuf, 1, synct, root);
if (ret != TMPI_SUCCESS)
{
return ret;
This source code file is part of thread_mpi.
Written by Sander Pronk, Erik Lindahl, and possibly others.
- Copyright (c) 2009, Sander Pronk, Erik Lindahl.
+ Copyright (c) 2009,2016, Sander Pronk, Erik Lindahl.
All rights reserved.
Redistribution and use in source and binary forms, with or without
/* point-to-point communication exported functions */
-int tMPI_Send(void* buf, int count, tMPI_Datatype datatype, int dest,
+int tMPI_Send(const void* buf, int count, tMPI_Datatype datatype, int dest,
int tag, tMPI_Comm comm)
{
struct envelope *sev;
return tMPI_Error(comm, TMPI_ERR_SEND_DEST);
}
- sev = tMPI_Post_send(cur, comm, send_dst, buf, count, datatype, tag, FALSE);
+ sev = tMPI_Post_send(cur, comm, send_dst, (void*)buf, count, datatype, tag, FALSE);
if (sev == NULL)
{
return TMPI_ERR_ENVELOPES;
-int tMPI_Sendrecv(void *sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Sendrecv(const void *sendbuf, int sendcount, tMPI_Datatype sendtype,
int dest, int sendtag, void *recvbuf, int recvcount,
tMPI_Datatype recvtype, int source, int recvtag,
tMPI_Comm comm, tMPI_Status *status)
}
/* we first prepare to send */
- sev = tMPI_Post_send(cur, comm, send_dst, sendbuf, sendcount,
+ sev = tMPI_Post_send(cur, comm, send_dst, (void*)sendbuf, sendcount,
sendtype, sendtag, FALSE);
if (sev == NULL)
{
/* async */
-int tMPI_Isend(void* buf, int count, tMPI_Datatype datatype, int dest,
+int tMPI_Isend(const void* buf, int count, tMPI_Datatype datatype, int dest,
int tag, tMPI_Comm comm, tMPI_Request *request)
{
struct tmpi_thread *cur = tMPI_Get_current();
tMPI_Return_req(rql, rq);
return tMPI_Error(comm, TMPI_ERR_SEND_DEST);
}
- ev = tMPI_Post_send(cur, comm, send_dst, buf, count, datatype, tag, TRUE);
+ ev = tMPI_Post_send(cur, comm, send_dst, (void*)buf, count, datatype, tag, TRUE);
if (ev == NULL)
{
return TMPI_ERR_ENVELOPES;
}
ret = pthread_mutex_trylock(&(mtx->mutex->mtx));
+ /* ret is zero when the lock was available and is now held, and
+ non-zero when any thread (including this one) held the lock
+ already. This is because the default pthreads mutex is not
+ re-entrant. */
return ret;
}
This source code file is part of thread_mpi.
Written by Sander Pronk, Erik Lindahl, and possibly others.
- Copyright (c) 2009, Sander Pronk, Erik Lindahl.
+ Copyright (c) 2009,2016, Sander Pronk, Erik Lindahl.
All rights reserved.
Redistribution and use in source and binary forms, with or without
-int tMPI_Scatter(void* sendbuf, int sendcount, tMPI_Datatype sendtype,
+int tMPI_Scatter(const void* sendbuf, int sendcount, tMPI_Datatype sendtype,
void* recvbuf, int recvcount, tMPI_Datatype recvtype,
int root, tMPI_Comm comm)
{
-int tMPI_Scatterv(void* sendbuf, int *sendcounts, int *displs,
+int tMPI_Scatterv(const void* sendbuf, int *sendcounts, int *displs,
tMPI_Datatype sendtype, void* recvbuf, int recvcount,
tMPI_Datatype recvtype, int root, tMPI_Comm comm)
{
/* The mutex is now guaranteed to be valid. */
ret = TryEnterCriticalSection( &(mtx->mutex->cs) );
-
- return (ret != 0);
+ /* ret is zero if another thread owns the critical section, and
+ non-zero when the critical section was available and is now
+ held OR the critical section was already owned by this
+ thread. By default Windows critical sections are re-entrant. */
+ return (ret == 0);
}
# include <cstddef>
#endif
+#if defined(__GNUC__) && __GNUC__>=7
+#pragma GCC diagnostic ignored "-Wimplicit-fallthrough"
+#endif
+
static const char LINE_FEED = (char)0x0a; // all line endings are normalized to LF
static const char LF = LINE_FEED;
static const char CARRIAGE_RETURN = (char)0x0d; // CR gets filtered out
set(TNG_ROOT_SOURCE_DIR ${CMAKE_CURRENT_LIST_DIR})
file(RELATIVE_PATH TNG_ROOT_BINARY_DIR ${CMAKE_SOURCE_DIR} ${TNG_ROOT_SOURCE_DIR})
+if ("${TNG_ROOT_BINARY_DIR}" MATCHES "^\.\.")
+ set(TNG_ROOT_BINARY_DIR tng)
+endif()
set(TNG_ROOT_BINARY_DIR ${CMAKE_BINARY_DIR}/${TNG_ROOT_BINARY_DIR})
function (TNG_GENERATE_VERSION_H)
set(TNG_MAJOR_VERSION "1")
- set(TNG_MINOR_VERSION "7")
- set(TNG_VERSION_PATCH_LEVEL "6")
+ set(TNG_MINOR_VERSION "8")
+ set(TNG_VERSION_PATCH_LEVEL "0")
set(TNG_IO_VERSION "${TNG_MAJOR_VERSION}.${TNG_MINOR_VERSION}.${TNG_VERSION_PATCH_LEVEL}")
- set(TNG_API_VERSION "7")
+ set(TNG_API_VERSION "8")
configure_file(${TNG_ROOT_SOURCE_DIR}/include/tng/version.h.in
${TNG_ROOT_BINARY_DIR}/include/tng/version.h)
set(TNG_IO_VERSION ${TNG_IO_VERSION} PARENT_SCOPE)
endfunction()
-tng_generate_version_h()
-
include(TestBigEndian)
test_big_endian(TNG_INTEGER_BIG_ENDIAN)
include(CheckIncludeFile)
check_include_file(inttypes.h TNG_HAVE_INTTYPES_H)
+include(CMakeParseArguments)
+
+function(add_tng_io_library NAME)
+ tng_generate_version_h()
-macro(TNG_GET_SOURCE_LIST TNG_SOURCELIST TNG_COMPILEDEFS)
- include_directories(BEFORE ${TNG_ROOT_SOURCE_DIR}/include)
- include_directories(BEFORE ${TNG_ROOT_BINARY_DIR}/include)
- set(_tng_compression_sources bwlzh.c bwt.c coder.c dict.c fixpoint.c huffman.c huffmem.c lz77.c merge_sort.c mtf.c rle.c tng_compress.c vals16.c warnmalloc.c widemuldiv.c xtc2.c xtc3.c)
+ set(_tng_compression_sources
+ bwlzh.c bwt.c coder.c dict.c fixpoint.c huffman.c huffmem.c
+ lz77.c merge_sort.c mtf.c rle.c tng_compress.c vals16.c
+ warnmalloc.c widemuldiv.c xtc2.c xtc3.c)
set(_tng_io_sources tng_io.c md5.c)
- set(${TNG_SOURCELIST})
- set(${TNG_COMPILEDEFS})
+ set(_sources)
foreach(_file ${_tng_compression_sources})
- list(APPEND ${TNG_SOURCELIST} ${TNG_ROOT_SOURCE_DIR}/src/compression/${_file})
+ list(APPEND _sources ${TNG_ROOT_SOURCE_DIR}/src/compression/${_file})
endforeach()
foreach(_file ${_tng_io_sources})
- list(APPEND ${TNG_SOURCELIST} ${TNG_ROOT_SOURCE_DIR}/src/lib/${_file})
+ list(APPEND _sources ${TNG_ROOT_SOURCE_DIR}/src/lib/${_file})
endforeach()
if(TNG_BUILD_FORTRAN)
- list(APPEND ${TNG_SOURCELIST} ${TNG_ROOT_SOURCE_DIR}/src/lib/tng_io_fortran.c)
+ list(APPEND _sources ${TNG_ROOT_SOURCE_DIR}/src/lib/tng_io_fortran.c)
endif()
- if (TNG_HAVE_INTTYPES_H)
- list(APPEND ${TNG_COMPILEDEFS} USE_STD_INTTYPES_H)
+
+ set(_options OBJECT OWN_ZLIB)
+ cmake_parse_arguments(ARG "${_options}" "" "" ${ARGN})
+
+ set(_build_target ${NAME})
+ set(_link_type PRIVATE)
+ if (ARG_OBJECT)
+ set(_build_target tng_io_obj)
+ set(_link_type INTERFACE)
+ add_library(${_build_target} OBJECT ${_sources})
+ # PIC is only on by default for SHARED libraries, but in case the
+ # object library is going to get used in such a library, the objects
+ # should be compiled with PIC as well.
+ if (BUILD_SHARED_LIBS)
+ set_target_properties(${_build_target} PROPERTIES POSITION_INDEPENDENT_CODE ON)
+ endif()
+ add_library(${NAME} INTERFACE)
+ target_sources(${NAME} INTERFACE $<TARGET_OBJECTS:tng_io_obj>)
+ else()
+ add_library(${NAME} ${_sources})
+ set_target_properties(${NAME} PROPERTIES
+ VERSION ${TNG_IO_VERSION}
+ SOVERSION ${TNG_MAJOR_VERSION})
+ target_include_directories(${NAME} INTERFACE $<INSTALL_INTERFACE:include>)
endif()
-endmacro()
+ target_include_directories(${_build_target} PRIVATE
+ $<BUILD_INTERFACE:${TNG_ROOT_SOURCE_DIR}/include>
+ $<BUILD_INTERFACE:${TNG_ROOT_BINARY_DIR}/include>)
+ target_include_directories(${NAME} INTERFACE
+ $<BUILD_INTERFACE:${TNG_ROOT_SOURCE_DIR}/include>
+ $<BUILD_INTERFACE:${TNG_ROOT_BINARY_DIR}/include>)
-macro(TNG_SET_SOURCE_PROPERTIES)
- set(_tng_with_zlib OFF)
- set(_curr_var)
- foreach (_arg ${ARGN})
- if (_arg STREQUAL "WITH_ZLIB")
- set(_curr_var with_zlib)
- elseif (_curr_var)
- set(_tng_${_curr_var} ${_arg})
- set(_curr_var "")
- else()
- message(FATAL_ERROR "Invalid argument ${_arg} to TNG_SET_SOURCE_PROPERTIES")
+ if (UNIX)
+ target_link_libraries(${NAME} ${_link_type} m)
+ endif()
+
+ if (ARG_OWN_ZLIB)
+ set(_zlib_dir ${TNG_ROOT_SOURCE_DIR}/external/zlib)
+ set(_zlib_sources)
+ # Add minimal necessary number of TNG source files
+ foreach(_file adler32.c compress.c crc32.c deflate.c inffast.c inflate.c inftrees.c trees.c uncompr.c zutil.c)
+ list(APPEND _zlib_sources ${_zlib_dir}/${_file})
+ endforeach()
+ add_library(tng_io_zlib OBJECT ${_zlib_sources})
+ if (BUILD_SHARED_LIBS)
+ set_target_properties(tng_io_zlib PROPERTIES POSITION_INDEPENDENT_CODE ON)
endif()
- endforeach()
- if (_tng_with_zlib)
- set_property(SOURCE ${TNG_ROOT_SOURCE_DIR}/src/lib/tng_io.c
- APPEND PROPERTY COMPILE_DEFINITIONS USE_ZLIB)
+ target_include_directories(tng_io_zlib PUBLIC ${_zlib_dir})
+ target_include_directories(${_build_target} PRIVATE ${_zlib_dir})
+ target_sources(${NAME} ${_link_type} $<TARGET_OBJECTS:tng_io_zlib>)
+ else()
+ target_link_libraries(${NAME} ${_link_type} ZLIB::ZLIB)
endif()
+
if (TNG_HAVE_INTTYPES_H)
+ target_compile_definitions(${NAME} INTERFACE USE_STD_INTTYPES_H)
set_property(SOURCE ${TNG_ROOT_SOURCE_DIR}/src/lib/tng_io.c
APPEND PROPERTY COMPILE_DEFINITIONS USE_STD_INTTYPES_H)
endif()
set_property(SOURCE ${TNG_ROOT_SOURCE_DIR}/src/lib/md5.c
APPEND PROPERTY COMPILE_DEFINITIONS TNG_INTEGER_BIG_ENDIAN)
endif()
-endmacro()
+endfunction()
-cmake_minimum_required(VERSION 2.8.8)
+cmake_minimum_required(VERSION 3.1)
project(TNG_IO)
-
if("${CMAKE_C_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_C_FLAGS_DEBUG "${CMAKE_C_FLAGS_DEBUG} -Wall")
elseif(WIN32)
endif()
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
option(BUILD_SHARED_LIBS "Enable shared libraries" ON)
option(TNG_BUILD_TEST "Build TNG testing binary." ON)
option(TNG_BUILD_COMPRESSION_TESTS "Build tests of the TNG compression library" OFF)
-find_package(ZLIB QUIET)
-option(TNG_BUILD_WITH_ZLIB "Build TNG with zlib compression" ${ZLIB_FOUND})
+option(TNG_BUILD_OWN_ZLIB "Build and use the internal zlib library" OFF)
+if(NOT TNG_BUILD_OWN_ZLIB)
+ find_package(ZLIB QUIET)
+endif()
include(CheckIncludeFile)
check_include_file(inttypes.h HAVE_INTTYPES_H)
include(BuildTNG.cmake)
-tng_get_source_list(TNG_SOURCES TNG_COMPILE_DEFS)
-
-tng_set_source_properties(WITH_ZLIB ${ZLIB_FOUND})
-
-add_library(tng_io ${TNG_SOURCES})
-
-if (ZLIB_FOUND)
- list(APPEND EXTRA_LIBRARIES ${ZLIB_LIBRARIES})
- include_directories(${ZLIB_INCLUDE_DIRS})
-endif()
-
-if (UNIX)
- list(APPEND EXTRA_LIBRARIES m)
+if (ZLIB_FOUND AND NOT TNG_BUILD_OWN_ZLIB)
+ add_tng_io_library(tng_io)
+else()
+ add_tng_io_library(tng_io OWN_ZLIB)
endif()
-target_link_libraries(tng_io ${EXTRA_LIBRARIES})
-
-set_target_properties(tng_io PROPERTIES VERSION ${TNG_IO_VERSION} SOVERSION ${TNG_MAJOR_VERSION})
+# Use GNUInstallDirs to set paths on multiarch systems
+include(GNUInstallDirs)
# Create the tng_ioConfig.cmake and tng_ioConfigVersion.cmake files for the install tree
-set(CONF_INCLUDE_DIRS "${CMAKE_INSTALL_PREFIX}/include")
configure_file( src/lib/tng_io-config.cmake.in
"${CMAKE_CURRENT_BINARY_DIR}/cmake/tng_io-config.cmake" @ONLY)
configure_file( src/lib/tng_io-configVersion.cmake.in
"${CMAKE_CURRENT_BINARY_DIR}/cmake/tng_io-configVersion.cmake" @ONLY)
-# Use GNUInstallDirst to set paths on multiarch systems
-include(GNUInstallDirs)
+install(TARGETS tng_io
+ EXPORT tng_io
+ LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+ ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}")
-# Install the tng_ioConfig.cmake and tng_ioConfigVersion.cmake
-install(FILES
- "${CMAKE_CURRENT_BINARY_DIR}/cmake/tng_io-config.cmake"
- "${CMAKE_CURRENT_BINARY_DIR}/cmake/tng_io-configVersion.cmake"
- DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/tng_io")
+install(EXPORT tng_io FILE tng_io.cmake
+ NAMESPACE tng_io::
+ DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/tng_io")
-install(TARGETS tng_io
- LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
- ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+install(FILES
+ "${CMAKE_CURRENT_BINARY_DIR}/cmake/tng_io-config.cmake"
+ "${CMAKE_CURRENT_BINARY_DIR}/cmake/tng_io-configVersion.cmake"
+ DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/tng_io")
-install(FILES include/tng/tng_io.h include/tng/tng_io_fwd.h ${CMAKE_CURRENT_BINARY_DIR}/include/tng/version.h
+install(FILES
+ include/tng/tng_io.h include/tng/tng_io_fwd.h
+ ${CMAKE_CURRENT_BINARY_DIR}/include/tng/version.h
DESTINATION include/tng)
#-- Add an Option to toggle the generation of the API documentation
endif()
add_subdirectory(src)
-
--- /dev/null
+The libraries included in the external directory are not supported by the TNG developers.
+
+zlib: version 1.2.8, with content not necessary for TNG build removed.
+
+Modifications within source files were
+* minor refactoring in crc32.c to make clear that some code should sometimes be unreachable
+* replacing some undefined behaviour (-1L << 16) with well defined value (~0xFFFFL) in inflate.c
+* commenting out unused zlibCompileFlags() declaration and definition
+* removing unnecessary configurability from zconf.h
+* removing #include of unused gzguts.h
--- /dev/null
+ZLIB DATA COMPRESSION LIBRARY
+
+zlib 1.2.8 is a general purpose data compression library. All the code is
+thread safe. The data format used by the zlib library is described by RFCs
+(Request for Comments) 1950 to 1952 in the files
+http://tools.ietf.org/html/rfc1950 (zlib format), rfc1951 (deflate format) and
+rfc1952 (gzip format).
+
+All functions of the compression library are documented in the file zlib.h
+(volunteer to write man pages welcome, contact zlib@gzip.org). A usage example
+of the library is given in the file test/example.c which also tests that
+the library is working correctly. Another example is given in the file
+test/minigzip.c. The compression library itself is composed of all source
+files in the root directory.
+
+To compile all files and run the test program, follow the instructions given at
+the top of Makefile.in. In short "./configure; make test", and if that goes
+well, "make install" should work for most flavors of Unix. For Windows, use
+one of the special makefiles in win32/ or contrib/vstudio/ . For VMS, use
+make_vms.com.
+
+Questions about zlib should be sent to <zlib@gzip.org>, or to Gilles Vollant
+<info@winimage.com> for the Windows DLL version. The zlib home page is
+http://zlib.net/ . Before reporting a problem, please check this site to
+verify that you have the latest version of zlib; otherwise get the latest
+version and check whether the problem still exists or not.
+
+PLEASE read the zlib FAQ http://zlib.net/zlib_faq.html before asking for help.
+
+Mark Nelson <markn@ieee.org> wrote an article about zlib for the Jan. 1997
+issue of Dr. Dobb's Journal; a copy of the article is available at
+http://marknelson.us/1997/01/01/zlib-engine/ .
+
+The changes made in version 1.2.8 are documented in the file ChangeLog.
+
+Unsupported third party contributions are provided in directory contrib/ .
+
+zlib is available in Java using the java.util.zip package, documented at
+http://java.sun.com/developer/technicalArticles/Programming/compression/ .
+
+A Perl interface to zlib written by Paul Marquess <pmqs@cpan.org> is available
+at CPAN (Comprehensive Perl Archive Network) sites, including
+http://search.cpan.org/~pmqs/IO-Compress-Zlib/ .
+
+A Python interface to zlib written by A.M. Kuchling <amk@amk.ca> is
+available in Python 1.5 and later versions, see
+http://docs.python.org/library/zlib.html .
+
+zlib is built into tcl: http://wiki.tcl.tk/4610 .
+
+An experimental package to read and write files in .zip format, written on top
+of zlib by Gilles Vollant <info@winimage.com>, is available in the
+contrib/minizip directory of zlib.
+
+
+Notes for some targets:
+
+- For Windows DLL versions, please see win32/DLL_FAQ.txt
+
+- For 64-bit Irix, deflate.c must be compiled without any optimization. With
+ -O, one libpng test fails. The test works in 32 bit mode (with the -n32
+ compiler flag). The compiler bug has been reported to SGI.
+
+- zlib doesn't work with gcc 2.6.3 on a DEC 3000/300LX under OSF/1 2.1 it works
+ when compiled with cc.
+
+- On Digital Unix 4.0D (formely OSF/1) on AlphaServer, the cc option -std1 is
+ necessary to get gzprintf working correctly. This is done by configure.
+
+- zlib doesn't work on HP-UX 9.05 with some versions of /bin/cc. It works with
+ other compilers. Use "make test" to check your compiler.
+
+- gzdopen is not supported on RISCOS or BEOS.
+
+- For PalmOs, see http://palmzlib.sourceforge.net/
+
+
+Acknowledgments:
+
+ The deflate format used by zlib was defined by Phil Katz. The deflate and
+ zlib specifications were written by L. Peter Deutsch. Thanks to all the
+ people who reported problems and suggested various improvements in zlib; they
+ are too numerous to cite here.
+
+Copyright notice:
+
+ (C) 1995-2013 Jean-loup Gailly and Mark Adler
+
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+
+ Jean-loup Gailly Mark Adler
+ jloup@gzip.org madler@alumni.caltech.edu
+
+If you use the zlib library in a product, we would appreciate *not* receiving
+lengthy legal documents to sign. The sources are provided for free but without
+warranty of any kind. The library has been entirely written by Jean-loup
+Gailly and Mark Adler; it does not include third-party code.
+
+If you redistribute modified sources, we would appreciate that you include in
+the file ChangeLog history information documenting your changes. Please read
+the FAQ for more information on the distribution of modified source versions.
--- /dev/null
+/* adler32.c -- compute the Adler-32 checksum of a data stream
+ * Copyright (C) 1995-2011 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#include "zutil.h"
+
+#define local static
+
+local uLong adler32_combine_ OF((uLong adler1, uLong adler2, z_off64_t len2));
+
+#define BASE 65521 /* largest prime smaller than 65536 */
+#define NMAX 5552
+/* NMAX is the largest n such that 255n(n+1)/2 + (n+1)(BASE-1) <= 2^32-1 */
+
+#define DO1(buf,i) {adler += (buf)[i]; sum2 += adler;}
+#define DO2(buf,i) DO1(buf,i); DO1(buf,i+1);
+#define DO4(buf,i) DO2(buf,i); DO2(buf,i+2);
+#define DO8(buf,i) DO4(buf,i); DO4(buf,i+4);
+#define DO16(buf) DO8(buf,0); DO8(buf,8);
+
+/* use NO_DIVIDE if your processor does not do division in hardware --
+ try it both ways to see which is faster */
+#ifdef NO_DIVIDE
+/* note that this assumes BASE is 65521, where 65536 % 65521 == 15
+ (thank you to John Reiser for pointing this out) */
+# define CHOP(a) \
+ do { \
+ unsigned long tmp = a >> 16; \
+ a &= 0xffffUL; \
+ a += (tmp << 4) - tmp; \
+ } while (0)
+# define MOD28(a) \
+ do { \
+ CHOP(a); \
+ if (a >= BASE) a -= BASE; \
+ } while (0)
+# define MOD(a) \
+ do { \
+ CHOP(a); \
+ MOD28(a); \
+ } while (0)
+# define MOD63(a) \
+ do { /* this assumes a is not negative */ \
+ z_off64_t tmp = a >> 32; \
+ a &= 0xffffffffL; \
+ a += (tmp << 8) - (tmp << 5) + tmp; \
+ tmp = a >> 16; \
+ a &= 0xffffL; \
+ a += (tmp << 4) - tmp; \
+ tmp = a >> 16; \
+ a &= 0xffffL; \
+ a += (tmp << 4) - tmp; \
+ if (a >= BASE) a -= BASE; \
+ } while (0)
+#else
+# define MOD(a) a %= BASE
+# define MOD28(a) a %= BASE
+# define MOD63(a) a %= BASE
+#endif
+
+/* ========================================================================= */
+uLong ZEXPORT adler32(adler, buf, len)
+ uLong adler;
+ const Bytef *buf;
+ uInt len;
+{
+ unsigned long sum2;
+ unsigned n;
+
+ /* split Adler-32 into component sums */
+ sum2 = (adler >> 16) & 0xffff;
+ adler &= 0xffff;
+
+ /* in case user likes doing a byte at a time, keep it fast */
+ if (len == 1) {
+ adler += buf[0];
+ if (adler >= BASE)
+ adler -= BASE;
+ sum2 += adler;
+ if (sum2 >= BASE)
+ sum2 -= BASE;
+ return adler | (sum2 << 16);
+ }
+
+ /* initial Adler-32 value (deferred check for len == 1 speed) */
+ if (buf == Z_NULL)
+ return 1L;
+
+ /* in case short lengths are provided, keep it somewhat fast */
+ if (len < 16) {
+ while (len--) {
+ adler += *buf++;
+ sum2 += adler;
+ }
+ if (adler >= BASE)
+ adler -= BASE;
+ MOD28(sum2); /* only added so many BASE's */
+ return adler | (sum2 << 16);
+ }
+
+ /* do length NMAX blocks -- requires just one modulo operation */
+ while (len >= NMAX) {
+ len -= NMAX;
+ n = NMAX / 16; /* NMAX is divisible by 16 */
+ do {
+ DO16(buf); /* 16 sums unrolled */
+ buf += 16;
+ } while (--n);
+ MOD(adler);
+ MOD(sum2);
+ }
+
+ /* do remaining bytes (less than NMAX, still just one modulo) */
+ if (len) { /* avoid modulos if none remaining */
+ while (len >= 16) {
+ len -= 16;
+ DO16(buf);
+ buf += 16;
+ }
+ while (len--) {
+ adler += *buf++;
+ sum2 += adler;
+ }
+ MOD(adler);
+ MOD(sum2);
+ }
+
+ /* return recombined sums */
+ return adler | (sum2 << 16);
+}
+
+/* ========================================================================= */
+local uLong adler32_combine_(adler1, adler2, len2)
+ uLong adler1;
+ uLong adler2;
+ z_off64_t len2;
+{
+ unsigned long sum1;
+ unsigned long sum2;
+ unsigned rem;
+
+ /* for negative len, return invalid adler32 as a clue for debugging */
+ if (len2 < 0)
+ return 0xffffffffUL;
+
+ /* the derivation of this formula is left as an exercise for the reader */
+ MOD63(len2); /* assumes len2 >= 0 */
+ rem = (unsigned)len2;
+ sum1 = adler1 & 0xffff;
+ sum2 = rem * sum1;
+ MOD(sum2);
+ sum1 += (adler2 & 0xffff) + BASE - 1;
+ sum2 += ((adler1 >> 16) & 0xffff) + ((adler2 >> 16) & 0xffff) + BASE - rem;
+ if (sum1 >= BASE) sum1 -= BASE;
+ if (sum1 >= BASE) sum1 -= BASE;
+ if (sum2 >= (BASE << 1)) sum2 -= (BASE << 1);
+ if (sum2 >= BASE) sum2 -= BASE;
+ return sum1 | (sum2 << 16);
+}
+
+/* ========================================================================= */
+uLong ZEXPORT adler32_combine(adler1, adler2, len2)
+ uLong adler1;
+ uLong adler2;
+ z_off_t len2;
+{
+ return adler32_combine_(adler1, adler2, len2);
+}
+
+uLong ZEXPORT adler32_combine64(adler1, adler2, len2)
+ uLong adler1;
+ uLong adler2;
+ z_off64_t len2;
+{
+ return adler32_combine_(adler1, adler2, len2);
+}
--- /dev/null
+/* compress.c -- compress a memory buffer
+ * Copyright (C) 1995-2005 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#define ZLIB_INTERNAL
+#include "zlib.h"
+
+/* ===========================================================================
+ Compresses the source buffer into the destination buffer. The level
+ parameter has the same meaning as in deflateInit. sourceLen is the byte
+ length of the source buffer. Upon entry, destLen is the total size of the
+ destination buffer, which must be at least 0.1% larger than sourceLen plus
+ 12 bytes. Upon exit, destLen is the actual size of the compressed buffer.
+
+ compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_BUF_ERROR if there was not enough room in the output buffer,
+ Z_STREAM_ERROR if the level parameter is invalid.
+*/
+int ZEXPORT compress2 (dest, destLen, source, sourceLen, level)
+ Bytef *dest;
+ uLongf *destLen;
+ const Bytef *source;
+ uLong sourceLen;
+ int level;
+{
+ z_stream stream;
+ int err;
+
+ stream.next_in = (z_const Bytef *)source;
+ stream.avail_in = (uInt)sourceLen;
+#ifdef MAXSEG_64K
+ /* Check for source > 64K on 16-bit machine: */
+ if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR;
+#endif
+ stream.next_out = dest;
+ stream.avail_out = (uInt)*destLen;
+ if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR;
+
+ stream.zalloc = (alloc_func)0;
+ stream.zfree = (free_func)0;
+ stream.opaque = (voidpf)0;
+
+ err = deflateInit(&stream, level);
+ if (err != Z_OK) return err;
+
+ err = deflate(&stream, Z_FINISH);
+ if (err != Z_STREAM_END) {
+ deflateEnd(&stream);
+ return err == Z_OK ? Z_BUF_ERROR : err;
+ }
+ *destLen = stream.total_out;
+
+ err = deflateEnd(&stream);
+ return err;
+}
+
+/* ===========================================================================
+ */
+int ZEXPORT compress (dest, destLen, source, sourceLen)
+ Bytef *dest;
+ uLongf *destLen;
+ const Bytef *source;
+ uLong sourceLen;
+{
+ return compress2(dest, destLen, source, sourceLen, Z_DEFAULT_COMPRESSION);
+}
+
+/* ===========================================================================
+ If the default memLevel or windowBits for deflateInit() is changed, then
+ this function needs to be updated.
+ */
+uLong ZEXPORT compressBound (sourceLen)
+ uLong sourceLen;
+{
+ return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) +
+ (sourceLen >> 25) + 13;
+}
--- /dev/null
+/* crc32.c -- compute the CRC-32 of a data stream
+ * Copyright (C) 1995-2006, 2010, 2011, 2012 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ *
+ * Thanks to Rodney Brown <rbrown64@csc.com.au> for his contribution of faster
+ * CRC methods: exclusive-oring 32 bits of data at a time, and pre-computing
+ * tables for updating the shift register in one step with three exclusive-ors
+ * instead of four steps with four exclusive-ors. This results in about a
+ * factor of two increase in speed on a Power PC G4 (PPC7455) using gcc -O3.
+ */
+
+/* @(#) $Id$ */
+
+/*
+ Note on the use of DYNAMIC_CRC_TABLE: there is no mutex or semaphore
+ protection on the static variables used to control the first-use generation
+ of the crc tables. Therefore, if you #define DYNAMIC_CRC_TABLE, you should
+ first call get_crc_table() to initialize the tables before allowing more than
+ one thread to use crc32().
+
+ DYNAMIC_CRC_TABLE and MAKECRCH can be #defined to write out crc32.h.
+ */
+
+#ifdef MAKECRCH
+# include <stdio.h>
+# ifndef DYNAMIC_CRC_TABLE
+# define DYNAMIC_CRC_TABLE
+# endif /* !DYNAMIC_CRC_TABLE */
+#endif /* MAKECRCH */
+
+#include "zutil.h" /* for STDC and FAR definitions */
+
+#define local static
+
+/* Definitions for doing the crc four data bytes at a time. */
+#if !defined(NOBYFOUR) && defined(Z_U4)
+# define BYFOUR
+#endif
+#ifdef BYFOUR
+ local unsigned long crc32_little OF((unsigned long,
+ const unsigned char FAR *, unsigned));
+ local unsigned long crc32_big OF((unsigned long,
+ const unsigned char FAR *, unsigned));
+# define TBLS 8
+#else
+# define TBLS 1
+#endif /* BYFOUR */
+
+/* Local functions for crc concatenation */
+local unsigned long gf2_matrix_times OF((unsigned long *mat,
+ unsigned long vec));
+local void gf2_matrix_square OF((unsigned long *square, unsigned long *mat));
+local uLong crc32_combine_ OF((uLong crc1, uLong crc2, z_off64_t len2));
+
+
+#ifdef DYNAMIC_CRC_TABLE
+
+local volatile int crc_table_empty = 1;
+local z_crc_t FAR crc_table[TBLS][256];
+local void make_crc_table OF((void));
+#ifdef MAKECRCH
+ local void write_table OF((FILE *, const z_crc_t FAR *));
+#endif /* MAKECRCH */
+/*
+ Generate tables for a byte-wise 32-bit CRC calculation on the polynomial:
+ x^32+x^26+x^23+x^22+x^16+x^12+x^11+x^10+x^8+x^7+x^5+x^4+x^2+x+1.
+
+ Polynomials over GF(2) are represented in binary, one bit per coefficient,
+ with the lowest powers in the most significant bit. Then adding polynomials
+ is just exclusive-or, and multiplying a polynomial by x is a right shift by
+ one. If we call the above polynomial p, and represent a byte as the
+ polynomial q, also with the lowest power in the most significant bit (so the
+ byte 0xb1 is the polynomial x^7+x^3+x+1), then the CRC is (q*x^32) mod p,
+ where a mod b means the remainder after dividing a by b.
+
+ This calculation is done using the shift-register method of multiplying and
+ taking the remainder. The register is initialized to zero, and for each
+ incoming bit, x^32 is added mod p to the register if the bit is a one (where
+ x^32 mod p is p+x^32 = x^26+...+1), and the register is multiplied mod p by
+ x (which is shifting right by one and adding x^32 mod p if the bit shifted
+ out is a one). We start with the highest power (least significant bit) of
+ q and repeat for all eight bits of q.
+
+ The first table is simply the CRC of all possible eight bit values. This is
+ all the information needed to generate CRCs on data a byte at a time for all
+ combinations of CRC register values and incoming bytes. The remaining tables
+ allow for word-at-a-time CRC calculation for both big-endian and little-
+ endian machines, where a word is four bytes.
+*/
+local void make_crc_table()
+{
+ z_crc_t c;
+ int n, k;
+ z_crc_t poly; /* polynomial exclusive-or pattern */
+ /* terms of polynomial defining this crc (except x^32): */
+ static volatile int first = 1; /* flag to limit concurrent making */
+ static const unsigned char p[] = {0,1,2,4,5,7,8,10,11,12,16,22,23,26};
+
+ /* See if another task is already doing this (not thread-safe, but better
+ than nothing -- significantly reduces duration of vulnerability in
+ case the advice about DYNAMIC_CRC_TABLE is ignored) */
+ if (first) {
+ first = 0;
+
+ /* make exclusive-or pattern from polynomial (0xedb88320UL) */
+ poly = 0;
+ for (n = 0; n < (int)(sizeof(p)/sizeof(unsigned char)); n++)
+ poly |= (z_crc_t)1 << (31 - p[n]);
+
+ /* generate a crc for every 8-bit value */
+ for (n = 0; n < 256; n++) {
+ c = (z_crc_t)n;
+ for (k = 0; k < 8; k++)
+ c = c & 1 ? poly ^ (c >> 1) : c >> 1;
+ crc_table[0][n] = c;
+ }
+
+#ifdef BYFOUR
+ /* generate crc for each value followed by one, two, and three zeros,
+ and then the byte reversal of those as well as the first table */
+ for (n = 0; n < 256; n++) {
+ c = crc_table[0][n];
+ crc_table[4][n] = ZSWAP32(c);
+ for (k = 1; k < 4; k++) {
+ c = crc_table[0][c & 0xff] ^ (c >> 8);
+ crc_table[k][n] = c;
+ crc_table[k + 4][n] = ZSWAP32(c);
+ }
+ }
+#endif /* BYFOUR */
+
+ crc_table_empty = 0;
+ }
+ else { /* not first */
+ /* wait for the other guy to finish (not efficient, but rare) */
+ while (crc_table_empty)
+ ;
+ }
+
+#ifdef MAKECRCH
+ /* write out CRC tables to crc32.h */
+ {
+ FILE *out;
+
+ out = fopen("crc32.h", "w");
+ if (out == NULL) return;
+ fprintf(out, "/* crc32.h -- tables for rapid CRC calculation\n");
+ fprintf(out, " * Generated automatically by crc32.c\n */\n\n");
+ fprintf(out, "local const z_crc_t FAR ");
+ fprintf(out, "crc_table[TBLS][256] =\n{\n {\n");
+ write_table(out, crc_table[0]);
+# ifdef BYFOUR
+ fprintf(out, "#ifdef BYFOUR\n");
+ for (k = 1; k < 8; k++) {
+ fprintf(out, " },\n {\n");
+ write_table(out, crc_table[k]);
+ }
+ fprintf(out, "#endif\n");
+# endif /* BYFOUR */
+ fprintf(out, " }\n};\n");
+ fclose(out);
+ }
+#endif /* MAKECRCH */
+}
+
+#ifdef MAKECRCH
+local void write_table(out, table)
+ FILE *out;
+ const z_crc_t FAR *table;
+{
+ int n;
+
+ for (n = 0; n < 256; n++)
+ fprintf(out, "%s0x%08lxUL%s", n % 5 ? "" : " ",
+ (unsigned long)(table[n]),
+ n == 255 ? "\n" : (n % 5 == 4 ? ",\n" : ", "));
+}
+#endif /* MAKECRCH */
+
+#else /* !DYNAMIC_CRC_TABLE */
+/* ========================================================================
+ * Tables of CRC-32s of all single-byte values, made by make_crc_table().
+ */
+#include "crc32.h"
+#endif /* DYNAMIC_CRC_TABLE */
+
+/* =========================================================================
+ * This function can be used by asm versions of crc32()
+ */
+const z_crc_t FAR * ZEXPORT get_crc_table()
+{
+#ifdef DYNAMIC_CRC_TABLE
+ if (crc_table_empty)
+ make_crc_table();
+#endif /* DYNAMIC_CRC_TABLE */
+ return (const z_crc_t FAR *)crc_table;
+}
+
+/* ========================================================================= */
+#define DO1 crc = crc_table[0][((int)crc ^ (*buf++)) & 0xff] ^ (crc >> 8)
+#define DO8 DO1; DO1; DO1; DO1; DO1; DO1; DO1; DO1
+
+/* ========================================================================= */
+unsigned long ZEXPORT crc32(crc, buf, len)
+ unsigned long crc;
+ const unsigned char FAR *buf;
+ uInt len;
+{
+ if (buf == Z_NULL) return 0UL;
+
+#ifdef DYNAMIC_CRC_TABLE
+ if (crc_table_empty)
+ make_crc_table();
+#endif /* DYNAMIC_CRC_TABLE */
+
+#ifdef BYFOUR
+ if (sizeof(void *) == sizeof(ptrdiff_t)) {
+ z_crc_t endian;
+
+ endian = 1;
+ if (*((unsigned char *)(&endian)))
+ return crc32_little(crc, buf, len);
+ else
+ return crc32_big(crc, buf, len);
+ }
+ /* Minor modifications follow that make clear to compilers that
+ * it is intended that some code is unreachable. */
+ else
+#endif /* BYFOUR */
+ {
+ crc = crc ^ 0xffffffffUL;
+ while (len >= 8) {
+ DO8;
+ len -= 8;
+ }
+ if (len) do {
+ DO1;
+ } while (--len);
+ return crc ^ 0xffffffffUL;
+ }
+}
+
+#ifdef BYFOUR
+
+/* ========================================================================= */
+#define DOLIT4 c ^= *buf4++; \
+ c = crc_table[3][c & 0xff] ^ crc_table[2][(c >> 8) & 0xff] ^ \
+ crc_table[1][(c >> 16) & 0xff] ^ crc_table[0][c >> 24]
+#define DOLIT32 DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4; DOLIT4
+
+/* ========================================================================= */
+local unsigned long crc32_little(crc, buf, len)
+ unsigned long crc;
+ const unsigned char FAR *buf;
+ unsigned len;
+{
+ register z_crc_t c;
+ register const z_crc_t FAR *buf4;
+
+ c = (z_crc_t)crc;
+ c = ~c;
+ while (len && ((ptrdiff_t)buf & 3)) {
+ c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
+ len--;
+ }
+
+ buf4 = (const z_crc_t FAR *)(const void FAR *)buf;
+ while (len >= 32) {
+ DOLIT32;
+ len -= 32;
+ }
+ while (len >= 4) {
+ DOLIT4;
+ len -= 4;
+ }
+ buf = (const unsigned char FAR *)buf4;
+
+ if (len) do {
+ c = crc_table[0][(c ^ *buf++) & 0xff] ^ (c >> 8);
+ } while (--len);
+ c = ~c;
+ return (unsigned long)c;
+}
+
+/* ========================================================================= */
+#define DOBIG4 c ^= *++buf4; \
+ c = crc_table[4][c & 0xff] ^ crc_table[5][(c >> 8) & 0xff] ^ \
+ crc_table[6][(c >> 16) & 0xff] ^ crc_table[7][c >> 24]
+#define DOBIG32 DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4; DOBIG4
+
+/* ========================================================================= */
+local unsigned long crc32_big(crc, buf, len)
+ unsigned long crc;
+ const unsigned char FAR *buf;
+ unsigned len;
+{
+ register z_crc_t c;
+ register const z_crc_t FAR *buf4;
+
+ c = ZSWAP32((z_crc_t)crc);
+ c = ~c;
+ while (len && ((ptrdiff_t)buf & 3)) {
+ c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
+ len--;
+ }
+
+ buf4 = (const z_crc_t FAR *)(const void FAR *)buf;
+ buf4--;
+ while (len >= 32) {
+ DOBIG32;
+ len -= 32;
+ }
+ while (len >= 4) {
+ DOBIG4;
+ len -= 4;
+ }
+ buf4++;
+ buf = (const unsigned char FAR *)buf4;
+
+ if (len) do {
+ c = crc_table[4][(c >> 24) ^ *buf++] ^ (c << 8);
+ } while (--len);
+ c = ~c;
+ return (unsigned long)(ZSWAP32(c));
+}
+
+#endif /* BYFOUR */
+
+#define GF2_DIM 32 /* dimension of GF(2) vectors (length of CRC) */
+
+/* ========================================================================= */
+local unsigned long gf2_matrix_times(mat, vec)
+ unsigned long *mat;
+ unsigned long vec;
+{
+ unsigned long sum;
+
+ sum = 0;
+ while (vec) {
+ if (vec & 1)
+ sum ^= *mat;
+ vec >>= 1;
+ mat++;
+ }
+ return sum;
+}
+
+/* ========================================================================= */
+local void gf2_matrix_square(square, mat)
+ unsigned long *square;
+ unsigned long *mat;
+{
+ int n;
+
+ for (n = 0; n < GF2_DIM; n++)
+ square[n] = gf2_matrix_times(mat, mat[n]);
+}
+
+/* ========================================================================= */
+local uLong crc32_combine_(crc1, crc2, len2)
+ uLong crc1;
+ uLong crc2;
+ z_off64_t len2;
+{
+ int n;
+ unsigned long row;
+ unsigned long even[GF2_DIM]; /* even-power-of-two zeros operator */
+ unsigned long odd[GF2_DIM]; /* odd-power-of-two zeros operator */
+
+ /* degenerate case (also disallow negative lengths) */
+ if (len2 <= 0)
+ return crc1;
+
+ /* put operator for one zero bit in odd */
+ odd[0] = 0xedb88320UL; /* CRC-32 polynomial */
+ row = 1;
+ for (n = 1; n < GF2_DIM; n++) {
+ odd[n] = row;
+ row <<= 1;
+ }
+
+ /* put operator for two zero bits in even */
+ gf2_matrix_square(even, odd);
+
+ /* put operator for four zero bits in odd */
+ gf2_matrix_square(odd, even);
+
+ /* apply len2 zeros to crc1 (first square will put the operator for one
+ zero byte, eight zero bits, in even) */
+ do {
+ /* apply zeros operator for this bit of len2 */
+ gf2_matrix_square(even, odd);
+ if (len2 & 1)
+ crc1 = gf2_matrix_times(even, crc1);
+ len2 >>= 1;
+
+ /* if no more bits set, then done */
+ if (len2 == 0)
+ break;
+
+ /* another iteration of the loop with odd and even swapped */
+ gf2_matrix_square(odd, even);
+ if (len2 & 1)
+ crc1 = gf2_matrix_times(odd, crc1);
+ len2 >>= 1;
+
+ /* if no more bits set, then done */
+ } while (len2 != 0);
+
+ /* return combined crc */
+ crc1 ^= crc2;
+ return crc1;
+}
+
+/* ========================================================================= */
+uLong ZEXPORT crc32_combine(crc1, crc2, len2)
+ uLong crc1;
+ uLong crc2;
+ z_off_t len2;
+{
+ return crc32_combine_(crc1, crc2, len2);
+}
+
+uLong ZEXPORT crc32_combine64(crc1, crc2, len2)
+ uLong crc1;
+ uLong crc2;
+ z_off64_t len2;
+{
+ return crc32_combine_(crc1, crc2, len2);
+}
--- /dev/null
+/* crc32.h -- tables for rapid CRC calculation
+ * Generated automatically by crc32.c
+ */
+
+local const z_crc_t FAR crc_table[TBLS][256] =
+{
+ {
+ 0x00000000UL, 0x77073096UL, 0xee0e612cUL, 0x990951baUL, 0x076dc419UL,
+ 0x706af48fUL, 0xe963a535UL, 0x9e6495a3UL, 0x0edb8832UL, 0x79dcb8a4UL,
+ 0xe0d5e91eUL, 0x97d2d988UL, 0x09b64c2bUL, 0x7eb17cbdUL, 0xe7b82d07UL,
+ 0x90bf1d91UL, 0x1db71064UL, 0x6ab020f2UL, 0xf3b97148UL, 0x84be41deUL,
+ 0x1adad47dUL, 0x6ddde4ebUL, 0xf4d4b551UL, 0x83d385c7UL, 0x136c9856UL,
+ 0x646ba8c0UL, 0xfd62f97aUL, 0x8a65c9ecUL, 0x14015c4fUL, 0x63066cd9UL,
+ 0xfa0f3d63UL, 0x8d080df5UL, 0x3b6e20c8UL, 0x4c69105eUL, 0xd56041e4UL,
+ 0xa2677172UL, 0x3c03e4d1UL, 0x4b04d447UL, 0xd20d85fdUL, 0xa50ab56bUL,
+ 0x35b5a8faUL, 0x42b2986cUL, 0xdbbbc9d6UL, 0xacbcf940UL, 0x32d86ce3UL,
+ 0x45df5c75UL, 0xdcd60dcfUL, 0xabd13d59UL, 0x26d930acUL, 0x51de003aUL,
+ 0xc8d75180UL, 0xbfd06116UL, 0x21b4f4b5UL, 0x56b3c423UL, 0xcfba9599UL,
+ 0xb8bda50fUL, 0x2802b89eUL, 0x5f058808UL, 0xc60cd9b2UL, 0xb10be924UL,
+ 0x2f6f7c87UL, 0x58684c11UL, 0xc1611dabUL, 0xb6662d3dUL, 0x76dc4190UL,
+ 0x01db7106UL, 0x98d220bcUL, 0xefd5102aUL, 0x71b18589UL, 0x06b6b51fUL,
+ 0x9fbfe4a5UL, 0xe8b8d433UL, 0x7807c9a2UL, 0x0f00f934UL, 0x9609a88eUL,
+ 0xe10e9818UL, 0x7f6a0dbbUL, 0x086d3d2dUL, 0x91646c97UL, 0xe6635c01UL,
+ 0x6b6b51f4UL, 0x1c6c6162UL, 0x856530d8UL, 0xf262004eUL, 0x6c0695edUL,
+ 0x1b01a57bUL, 0x8208f4c1UL, 0xf50fc457UL, 0x65b0d9c6UL, 0x12b7e950UL,
+ 0x8bbeb8eaUL, 0xfcb9887cUL, 0x62dd1ddfUL, 0x15da2d49UL, 0x8cd37cf3UL,
+ 0xfbd44c65UL, 0x4db26158UL, 0x3ab551ceUL, 0xa3bc0074UL, 0xd4bb30e2UL,
+ 0x4adfa541UL, 0x3dd895d7UL, 0xa4d1c46dUL, 0xd3d6f4fbUL, 0x4369e96aUL,
+ 0x346ed9fcUL, 0xad678846UL, 0xda60b8d0UL, 0x44042d73UL, 0x33031de5UL,
+ 0xaa0a4c5fUL, 0xdd0d7cc9UL, 0x5005713cUL, 0x270241aaUL, 0xbe0b1010UL,
+ 0xc90c2086UL, 0x5768b525UL, 0x206f85b3UL, 0xb966d409UL, 0xce61e49fUL,
+ 0x5edef90eUL, 0x29d9c998UL, 0xb0d09822UL, 0xc7d7a8b4UL, 0x59b33d17UL,
+ 0x2eb40d81UL, 0xb7bd5c3bUL, 0xc0ba6cadUL, 0xedb88320UL, 0x9abfb3b6UL,
+ 0x03b6e20cUL, 0x74b1d29aUL, 0xead54739UL, 0x9dd277afUL, 0x04db2615UL,
+ 0x73dc1683UL, 0xe3630b12UL, 0x94643b84UL, 0x0d6d6a3eUL, 0x7a6a5aa8UL,
+ 0xe40ecf0bUL, 0x9309ff9dUL, 0x0a00ae27UL, 0x7d079eb1UL, 0xf00f9344UL,
+ 0x8708a3d2UL, 0x1e01f268UL, 0x6906c2feUL, 0xf762575dUL, 0x806567cbUL,
+ 0x196c3671UL, 0x6e6b06e7UL, 0xfed41b76UL, 0x89d32be0UL, 0x10da7a5aUL,
+ 0x67dd4accUL, 0xf9b9df6fUL, 0x8ebeeff9UL, 0x17b7be43UL, 0x60b08ed5UL,
+ 0xd6d6a3e8UL, 0xa1d1937eUL, 0x38d8c2c4UL, 0x4fdff252UL, 0xd1bb67f1UL,
+ 0xa6bc5767UL, 0x3fb506ddUL, 0x48b2364bUL, 0xd80d2bdaUL, 0xaf0a1b4cUL,
+ 0x36034af6UL, 0x41047a60UL, 0xdf60efc3UL, 0xa867df55UL, 0x316e8eefUL,
+ 0x4669be79UL, 0xcb61b38cUL, 0xbc66831aUL, 0x256fd2a0UL, 0x5268e236UL,
+ 0xcc0c7795UL, 0xbb0b4703UL, 0x220216b9UL, 0x5505262fUL, 0xc5ba3bbeUL,
+ 0xb2bd0b28UL, 0x2bb45a92UL, 0x5cb36a04UL, 0xc2d7ffa7UL, 0xb5d0cf31UL,
+ 0x2cd99e8bUL, 0x5bdeae1dUL, 0x9b64c2b0UL, 0xec63f226UL, 0x756aa39cUL,
+ 0x026d930aUL, 0x9c0906a9UL, 0xeb0e363fUL, 0x72076785UL, 0x05005713UL,
+ 0x95bf4a82UL, 0xe2b87a14UL, 0x7bb12baeUL, 0x0cb61b38UL, 0x92d28e9bUL,
+ 0xe5d5be0dUL, 0x7cdcefb7UL, 0x0bdbdf21UL, 0x86d3d2d4UL, 0xf1d4e242UL,
+ 0x68ddb3f8UL, 0x1fda836eUL, 0x81be16cdUL, 0xf6b9265bUL, 0x6fb077e1UL,
+ 0x18b74777UL, 0x88085ae6UL, 0xff0f6a70UL, 0x66063bcaUL, 0x11010b5cUL,
+ 0x8f659effUL, 0xf862ae69UL, 0x616bffd3UL, 0x166ccf45UL, 0xa00ae278UL,
+ 0xd70dd2eeUL, 0x4e048354UL, 0x3903b3c2UL, 0xa7672661UL, 0xd06016f7UL,
+ 0x4969474dUL, 0x3e6e77dbUL, 0xaed16a4aUL, 0xd9d65adcUL, 0x40df0b66UL,
+ 0x37d83bf0UL, 0xa9bcae53UL, 0xdebb9ec5UL, 0x47b2cf7fUL, 0x30b5ffe9UL,
+ 0xbdbdf21cUL, 0xcabac28aUL, 0x53b39330UL, 0x24b4a3a6UL, 0xbad03605UL,
+ 0xcdd70693UL, 0x54de5729UL, 0x23d967bfUL, 0xb3667a2eUL, 0xc4614ab8UL,
+ 0x5d681b02UL, 0x2a6f2b94UL, 0xb40bbe37UL, 0xc30c8ea1UL, 0x5a05df1bUL,
+ 0x2d02ef8dUL
+#ifdef BYFOUR
+ },
+ {
+ 0x00000000UL, 0x191b3141UL, 0x32366282UL, 0x2b2d53c3UL, 0x646cc504UL,
+ 0x7d77f445UL, 0x565aa786UL, 0x4f4196c7UL, 0xc8d98a08UL, 0xd1c2bb49UL,
+ 0xfaefe88aUL, 0xe3f4d9cbUL, 0xacb54f0cUL, 0xb5ae7e4dUL, 0x9e832d8eUL,
+ 0x87981ccfUL, 0x4ac21251UL, 0x53d92310UL, 0x78f470d3UL, 0x61ef4192UL,
+ 0x2eaed755UL, 0x37b5e614UL, 0x1c98b5d7UL, 0x05838496UL, 0x821b9859UL,
+ 0x9b00a918UL, 0xb02dfadbUL, 0xa936cb9aUL, 0xe6775d5dUL, 0xff6c6c1cUL,
+ 0xd4413fdfUL, 0xcd5a0e9eUL, 0x958424a2UL, 0x8c9f15e3UL, 0xa7b24620UL,
+ 0xbea97761UL, 0xf1e8e1a6UL, 0xe8f3d0e7UL, 0xc3de8324UL, 0xdac5b265UL,
+ 0x5d5daeaaUL, 0x44469febUL, 0x6f6bcc28UL, 0x7670fd69UL, 0x39316baeUL,
+ 0x202a5aefUL, 0x0b07092cUL, 0x121c386dUL, 0xdf4636f3UL, 0xc65d07b2UL,
+ 0xed705471UL, 0xf46b6530UL, 0xbb2af3f7UL, 0xa231c2b6UL, 0x891c9175UL,
+ 0x9007a034UL, 0x179fbcfbUL, 0x0e848dbaUL, 0x25a9de79UL, 0x3cb2ef38UL,
+ 0x73f379ffUL, 0x6ae848beUL, 0x41c51b7dUL, 0x58de2a3cUL, 0xf0794f05UL,
+ 0xe9627e44UL, 0xc24f2d87UL, 0xdb541cc6UL, 0x94158a01UL, 0x8d0ebb40UL,
+ 0xa623e883UL, 0xbf38d9c2UL, 0x38a0c50dUL, 0x21bbf44cUL, 0x0a96a78fUL,
+ 0x138d96ceUL, 0x5ccc0009UL, 0x45d73148UL, 0x6efa628bUL, 0x77e153caUL,
+ 0xbabb5d54UL, 0xa3a06c15UL, 0x888d3fd6UL, 0x91960e97UL, 0xded79850UL,
+ 0xc7cca911UL, 0xece1fad2UL, 0xf5facb93UL, 0x7262d75cUL, 0x6b79e61dUL,
+ 0x4054b5deUL, 0x594f849fUL, 0x160e1258UL, 0x0f152319UL, 0x243870daUL,
+ 0x3d23419bUL, 0x65fd6ba7UL, 0x7ce65ae6UL, 0x57cb0925UL, 0x4ed03864UL,
+ 0x0191aea3UL, 0x188a9fe2UL, 0x33a7cc21UL, 0x2abcfd60UL, 0xad24e1afUL,
+ 0xb43fd0eeUL, 0x9f12832dUL, 0x8609b26cUL, 0xc94824abUL, 0xd05315eaUL,
+ 0xfb7e4629UL, 0xe2657768UL, 0x2f3f79f6UL, 0x362448b7UL, 0x1d091b74UL,
+ 0x04122a35UL, 0x4b53bcf2UL, 0x52488db3UL, 0x7965de70UL, 0x607eef31UL,
+ 0xe7e6f3feUL, 0xfefdc2bfUL, 0xd5d0917cUL, 0xcccba03dUL, 0x838a36faUL,
+ 0x9a9107bbUL, 0xb1bc5478UL, 0xa8a76539UL, 0x3b83984bUL, 0x2298a90aUL,
+ 0x09b5fac9UL, 0x10aecb88UL, 0x5fef5d4fUL, 0x46f46c0eUL, 0x6dd93fcdUL,
+ 0x74c20e8cUL, 0xf35a1243UL, 0xea412302UL, 0xc16c70c1UL, 0xd8774180UL,
+ 0x9736d747UL, 0x8e2de606UL, 0xa500b5c5UL, 0xbc1b8484UL, 0x71418a1aUL,
+ 0x685abb5bUL, 0x4377e898UL, 0x5a6cd9d9UL, 0x152d4f1eUL, 0x0c367e5fUL,
+ 0x271b2d9cUL, 0x3e001cddUL, 0xb9980012UL, 0xa0833153UL, 0x8bae6290UL,
+ 0x92b553d1UL, 0xddf4c516UL, 0xc4eff457UL, 0xefc2a794UL, 0xf6d996d5UL,
+ 0xae07bce9UL, 0xb71c8da8UL, 0x9c31de6bUL, 0x852aef2aUL, 0xca6b79edUL,
+ 0xd37048acUL, 0xf85d1b6fUL, 0xe1462a2eUL, 0x66de36e1UL, 0x7fc507a0UL,
+ 0x54e85463UL, 0x4df36522UL, 0x02b2f3e5UL, 0x1ba9c2a4UL, 0x30849167UL,
+ 0x299fa026UL, 0xe4c5aeb8UL, 0xfdde9ff9UL, 0xd6f3cc3aUL, 0xcfe8fd7bUL,
+ 0x80a96bbcUL, 0x99b25afdUL, 0xb29f093eUL, 0xab84387fUL, 0x2c1c24b0UL,
+ 0x350715f1UL, 0x1e2a4632UL, 0x07317773UL, 0x4870e1b4UL, 0x516bd0f5UL,
+ 0x7a468336UL, 0x635db277UL, 0xcbfad74eUL, 0xd2e1e60fUL, 0xf9ccb5ccUL,
+ 0xe0d7848dUL, 0xaf96124aUL, 0xb68d230bUL, 0x9da070c8UL, 0x84bb4189UL,
+ 0x03235d46UL, 0x1a386c07UL, 0x31153fc4UL, 0x280e0e85UL, 0x674f9842UL,
+ 0x7e54a903UL, 0x5579fac0UL, 0x4c62cb81UL, 0x8138c51fUL, 0x9823f45eUL,
+ 0xb30ea79dUL, 0xaa1596dcUL, 0xe554001bUL, 0xfc4f315aUL, 0xd7626299UL,
+ 0xce7953d8UL, 0x49e14f17UL, 0x50fa7e56UL, 0x7bd72d95UL, 0x62cc1cd4UL,
+ 0x2d8d8a13UL, 0x3496bb52UL, 0x1fbbe891UL, 0x06a0d9d0UL, 0x5e7ef3ecUL,
+ 0x4765c2adUL, 0x6c48916eUL, 0x7553a02fUL, 0x3a1236e8UL, 0x230907a9UL,
+ 0x0824546aUL, 0x113f652bUL, 0x96a779e4UL, 0x8fbc48a5UL, 0xa4911b66UL,
+ 0xbd8a2a27UL, 0xf2cbbce0UL, 0xebd08da1UL, 0xc0fdde62UL, 0xd9e6ef23UL,
+ 0x14bce1bdUL, 0x0da7d0fcUL, 0x268a833fUL, 0x3f91b27eUL, 0x70d024b9UL,
+ 0x69cb15f8UL, 0x42e6463bUL, 0x5bfd777aUL, 0xdc656bb5UL, 0xc57e5af4UL,
+ 0xee530937UL, 0xf7483876UL, 0xb809aeb1UL, 0xa1129ff0UL, 0x8a3fcc33UL,
+ 0x9324fd72UL
+ },
+ {
+ 0x00000000UL, 0x01c26a37UL, 0x0384d46eUL, 0x0246be59UL, 0x0709a8dcUL,
+ 0x06cbc2ebUL, 0x048d7cb2UL, 0x054f1685UL, 0x0e1351b8UL, 0x0fd13b8fUL,
+ 0x0d9785d6UL, 0x0c55efe1UL, 0x091af964UL, 0x08d89353UL, 0x0a9e2d0aUL,
+ 0x0b5c473dUL, 0x1c26a370UL, 0x1de4c947UL, 0x1fa2771eUL, 0x1e601d29UL,
+ 0x1b2f0bacUL, 0x1aed619bUL, 0x18abdfc2UL, 0x1969b5f5UL, 0x1235f2c8UL,
+ 0x13f798ffUL, 0x11b126a6UL, 0x10734c91UL, 0x153c5a14UL, 0x14fe3023UL,
+ 0x16b88e7aUL, 0x177ae44dUL, 0x384d46e0UL, 0x398f2cd7UL, 0x3bc9928eUL,
+ 0x3a0bf8b9UL, 0x3f44ee3cUL, 0x3e86840bUL, 0x3cc03a52UL, 0x3d025065UL,
+ 0x365e1758UL, 0x379c7d6fUL, 0x35dac336UL, 0x3418a901UL, 0x3157bf84UL,
+ 0x3095d5b3UL, 0x32d36beaUL, 0x331101ddUL, 0x246be590UL, 0x25a98fa7UL,
+ 0x27ef31feUL, 0x262d5bc9UL, 0x23624d4cUL, 0x22a0277bUL, 0x20e69922UL,
+ 0x2124f315UL, 0x2a78b428UL, 0x2bbade1fUL, 0x29fc6046UL, 0x283e0a71UL,
+ 0x2d711cf4UL, 0x2cb376c3UL, 0x2ef5c89aUL, 0x2f37a2adUL, 0x709a8dc0UL,
+ 0x7158e7f7UL, 0x731e59aeUL, 0x72dc3399UL, 0x7793251cUL, 0x76514f2bUL,
+ 0x7417f172UL, 0x75d59b45UL, 0x7e89dc78UL, 0x7f4bb64fUL, 0x7d0d0816UL,
+ 0x7ccf6221UL, 0x798074a4UL, 0x78421e93UL, 0x7a04a0caUL, 0x7bc6cafdUL,
+ 0x6cbc2eb0UL, 0x6d7e4487UL, 0x6f38fadeUL, 0x6efa90e9UL, 0x6bb5866cUL,
+ 0x6a77ec5bUL, 0x68315202UL, 0x69f33835UL, 0x62af7f08UL, 0x636d153fUL,
+ 0x612bab66UL, 0x60e9c151UL, 0x65a6d7d4UL, 0x6464bde3UL, 0x662203baUL,
+ 0x67e0698dUL, 0x48d7cb20UL, 0x4915a117UL, 0x4b531f4eUL, 0x4a917579UL,
+ 0x4fde63fcUL, 0x4e1c09cbUL, 0x4c5ab792UL, 0x4d98dda5UL, 0x46c49a98UL,
+ 0x4706f0afUL, 0x45404ef6UL, 0x448224c1UL, 0x41cd3244UL, 0x400f5873UL,
+ 0x4249e62aUL, 0x438b8c1dUL, 0x54f16850UL, 0x55330267UL, 0x5775bc3eUL,
+ 0x56b7d609UL, 0x53f8c08cUL, 0x523aaabbUL, 0x507c14e2UL, 0x51be7ed5UL,
+ 0x5ae239e8UL, 0x5b2053dfUL, 0x5966ed86UL, 0x58a487b1UL, 0x5deb9134UL,
+ 0x5c29fb03UL, 0x5e6f455aUL, 0x5fad2f6dUL, 0xe1351b80UL, 0xe0f771b7UL,
+ 0xe2b1cfeeUL, 0xe373a5d9UL, 0xe63cb35cUL, 0xe7fed96bUL, 0xe5b86732UL,
+ 0xe47a0d05UL, 0xef264a38UL, 0xeee4200fUL, 0xeca29e56UL, 0xed60f461UL,
+ 0xe82fe2e4UL, 0xe9ed88d3UL, 0xebab368aUL, 0xea695cbdUL, 0xfd13b8f0UL,
+ 0xfcd1d2c7UL, 0xfe976c9eUL, 0xff5506a9UL, 0xfa1a102cUL, 0xfbd87a1bUL,
+ 0xf99ec442UL, 0xf85cae75UL, 0xf300e948UL, 0xf2c2837fUL, 0xf0843d26UL,
+ 0xf1465711UL, 0xf4094194UL, 0xf5cb2ba3UL, 0xf78d95faUL, 0xf64fffcdUL,
+ 0xd9785d60UL, 0xd8ba3757UL, 0xdafc890eUL, 0xdb3ee339UL, 0xde71f5bcUL,
+ 0xdfb39f8bUL, 0xddf521d2UL, 0xdc374be5UL, 0xd76b0cd8UL, 0xd6a966efUL,
+ 0xd4efd8b6UL, 0xd52db281UL, 0xd062a404UL, 0xd1a0ce33UL, 0xd3e6706aUL,
+ 0xd2241a5dUL, 0xc55efe10UL, 0xc49c9427UL, 0xc6da2a7eUL, 0xc7184049UL,
+ 0xc25756ccUL, 0xc3953cfbUL, 0xc1d382a2UL, 0xc011e895UL, 0xcb4dafa8UL,
+ 0xca8fc59fUL, 0xc8c97bc6UL, 0xc90b11f1UL, 0xcc440774UL, 0xcd866d43UL,
+ 0xcfc0d31aUL, 0xce02b92dUL, 0x91af9640UL, 0x906dfc77UL, 0x922b422eUL,
+ 0x93e92819UL, 0x96a63e9cUL, 0x976454abUL, 0x9522eaf2UL, 0x94e080c5UL,
+ 0x9fbcc7f8UL, 0x9e7eadcfUL, 0x9c381396UL, 0x9dfa79a1UL, 0x98b56f24UL,
+ 0x99770513UL, 0x9b31bb4aUL, 0x9af3d17dUL, 0x8d893530UL, 0x8c4b5f07UL,
+ 0x8e0de15eUL, 0x8fcf8b69UL, 0x8a809decUL, 0x8b42f7dbUL, 0x89044982UL,
+ 0x88c623b5UL, 0x839a6488UL, 0x82580ebfUL, 0x801eb0e6UL, 0x81dcdad1UL,
+ 0x8493cc54UL, 0x8551a663UL, 0x8717183aUL, 0x86d5720dUL, 0xa9e2d0a0UL,
+ 0xa820ba97UL, 0xaa6604ceUL, 0xaba46ef9UL, 0xaeeb787cUL, 0xaf29124bUL,
+ 0xad6fac12UL, 0xacadc625UL, 0xa7f18118UL, 0xa633eb2fUL, 0xa4755576UL,
+ 0xa5b73f41UL, 0xa0f829c4UL, 0xa13a43f3UL, 0xa37cfdaaUL, 0xa2be979dUL,
+ 0xb5c473d0UL, 0xb40619e7UL, 0xb640a7beUL, 0xb782cd89UL, 0xb2cddb0cUL,
+ 0xb30fb13bUL, 0xb1490f62UL, 0xb08b6555UL, 0xbbd72268UL, 0xba15485fUL,
+ 0xb853f606UL, 0xb9919c31UL, 0xbcde8ab4UL, 0xbd1ce083UL, 0xbf5a5edaUL,
+ 0xbe9834edUL
+ },
+ {
+ 0x00000000UL, 0xb8bc6765UL, 0xaa09c88bUL, 0x12b5afeeUL, 0x8f629757UL,
+ 0x37def032UL, 0x256b5fdcUL, 0x9dd738b9UL, 0xc5b428efUL, 0x7d084f8aUL,
+ 0x6fbde064UL, 0xd7018701UL, 0x4ad6bfb8UL, 0xf26ad8ddUL, 0xe0df7733UL,
+ 0x58631056UL, 0x5019579fUL, 0xe8a530faUL, 0xfa109f14UL, 0x42acf871UL,
+ 0xdf7bc0c8UL, 0x67c7a7adUL, 0x75720843UL, 0xcdce6f26UL, 0x95ad7f70UL,
+ 0x2d111815UL, 0x3fa4b7fbUL, 0x8718d09eUL, 0x1acfe827UL, 0xa2738f42UL,
+ 0xb0c620acUL, 0x087a47c9UL, 0xa032af3eUL, 0x188ec85bUL, 0x0a3b67b5UL,
+ 0xb28700d0UL, 0x2f503869UL, 0x97ec5f0cUL, 0x8559f0e2UL, 0x3de59787UL,
+ 0x658687d1UL, 0xdd3ae0b4UL, 0xcf8f4f5aUL, 0x7733283fUL, 0xeae41086UL,
+ 0x525877e3UL, 0x40edd80dUL, 0xf851bf68UL, 0xf02bf8a1UL, 0x48979fc4UL,
+ 0x5a22302aUL, 0xe29e574fUL, 0x7f496ff6UL, 0xc7f50893UL, 0xd540a77dUL,
+ 0x6dfcc018UL, 0x359fd04eUL, 0x8d23b72bUL, 0x9f9618c5UL, 0x272a7fa0UL,
+ 0xbafd4719UL, 0x0241207cUL, 0x10f48f92UL, 0xa848e8f7UL, 0x9b14583dUL,
+ 0x23a83f58UL, 0x311d90b6UL, 0x89a1f7d3UL, 0x1476cf6aUL, 0xaccaa80fUL,
+ 0xbe7f07e1UL, 0x06c36084UL, 0x5ea070d2UL, 0xe61c17b7UL, 0xf4a9b859UL,
+ 0x4c15df3cUL, 0xd1c2e785UL, 0x697e80e0UL, 0x7bcb2f0eUL, 0xc377486bUL,
+ 0xcb0d0fa2UL, 0x73b168c7UL, 0x6104c729UL, 0xd9b8a04cUL, 0x446f98f5UL,
+ 0xfcd3ff90UL, 0xee66507eUL, 0x56da371bUL, 0x0eb9274dUL, 0xb6054028UL,
+ 0xa4b0efc6UL, 0x1c0c88a3UL, 0x81dbb01aUL, 0x3967d77fUL, 0x2bd27891UL,
+ 0x936e1ff4UL, 0x3b26f703UL, 0x839a9066UL, 0x912f3f88UL, 0x299358edUL,
+ 0xb4446054UL, 0x0cf80731UL, 0x1e4da8dfUL, 0xa6f1cfbaUL, 0xfe92dfecUL,
+ 0x462eb889UL, 0x549b1767UL, 0xec277002UL, 0x71f048bbUL, 0xc94c2fdeUL,
+ 0xdbf98030UL, 0x6345e755UL, 0x6b3fa09cUL, 0xd383c7f9UL, 0xc1366817UL,
+ 0x798a0f72UL, 0xe45d37cbUL, 0x5ce150aeUL, 0x4e54ff40UL, 0xf6e89825UL,
+ 0xae8b8873UL, 0x1637ef16UL, 0x048240f8UL, 0xbc3e279dUL, 0x21e91f24UL,
+ 0x99557841UL, 0x8be0d7afUL, 0x335cb0caUL, 0xed59b63bUL, 0x55e5d15eUL,
+ 0x47507eb0UL, 0xffec19d5UL, 0x623b216cUL, 0xda874609UL, 0xc832e9e7UL,
+ 0x708e8e82UL, 0x28ed9ed4UL, 0x9051f9b1UL, 0x82e4565fUL, 0x3a58313aUL,
+ 0xa78f0983UL, 0x1f336ee6UL, 0x0d86c108UL, 0xb53aa66dUL, 0xbd40e1a4UL,
+ 0x05fc86c1UL, 0x1749292fUL, 0xaff54e4aUL, 0x322276f3UL, 0x8a9e1196UL,
+ 0x982bbe78UL, 0x2097d91dUL, 0x78f4c94bUL, 0xc048ae2eUL, 0xd2fd01c0UL,
+ 0x6a4166a5UL, 0xf7965e1cUL, 0x4f2a3979UL, 0x5d9f9697UL, 0xe523f1f2UL,
+ 0x4d6b1905UL, 0xf5d77e60UL, 0xe762d18eUL, 0x5fdeb6ebUL, 0xc2098e52UL,
+ 0x7ab5e937UL, 0x680046d9UL, 0xd0bc21bcUL, 0x88df31eaUL, 0x3063568fUL,
+ 0x22d6f961UL, 0x9a6a9e04UL, 0x07bda6bdUL, 0xbf01c1d8UL, 0xadb46e36UL,
+ 0x15080953UL, 0x1d724e9aUL, 0xa5ce29ffUL, 0xb77b8611UL, 0x0fc7e174UL,
+ 0x9210d9cdUL, 0x2aacbea8UL, 0x38191146UL, 0x80a57623UL, 0xd8c66675UL,
+ 0x607a0110UL, 0x72cfaefeUL, 0xca73c99bUL, 0x57a4f122UL, 0xef189647UL,
+ 0xfdad39a9UL, 0x45115eccUL, 0x764dee06UL, 0xcef18963UL, 0xdc44268dUL,
+ 0x64f841e8UL, 0xf92f7951UL, 0x41931e34UL, 0x5326b1daUL, 0xeb9ad6bfUL,
+ 0xb3f9c6e9UL, 0x0b45a18cUL, 0x19f00e62UL, 0xa14c6907UL, 0x3c9b51beUL,
+ 0x842736dbUL, 0x96929935UL, 0x2e2efe50UL, 0x2654b999UL, 0x9ee8defcUL,
+ 0x8c5d7112UL, 0x34e11677UL, 0xa9362eceUL, 0x118a49abUL, 0x033fe645UL,
+ 0xbb838120UL, 0xe3e09176UL, 0x5b5cf613UL, 0x49e959fdUL, 0xf1553e98UL,
+ 0x6c820621UL, 0xd43e6144UL, 0xc68bceaaUL, 0x7e37a9cfUL, 0xd67f4138UL,
+ 0x6ec3265dUL, 0x7c7689b3UL, 0xc4caeed6UL, 0x591dd66fUL, 0xe1a1b10aUL,
+ 0xf3141ee4UL, 0x4ba87981UL, 0x13cb69d7UL, 0xab770eb2UL, 0xb9c2a15cUL,
+ 0x017ec639UL, 0x9ca9fe80UL, 0x241599e5UL, 0x36a0360bUL, 0x8e1c516eUL,
+ 0x866616a7UL, 0x3eda71c2UL, 0x2c6fde2cUL, 0x94d3b949UL, 0x090481f0UL,
+ 0xb1b8e695UL, 0xa30d497bUL, 0x1bb12e1eUL, 0x43d23e48UL, 0xfb6e592dUL,
+ 0xe9dbf6c3UL, 0x516791a6UL, 0xccb0a91fUL, 0x740cce7aUL, 0x66b96194UL,
+ 0xde0506f1UL
+ },
+ {
+ 0x00000000UL, 0x96300777UL, 0x2c610eeeUL, 0xba510999UL, 0x19c46d07UL,
+ 0x8ff46a70UL, 0x35a563e9UL, 0xa395649eUL, 0x3288db0eUL, 0xa4b8dc79UL,
+ 0x1ee9d5e0UL, 0x88d9d297UL, 0x2b4cb609UL, 0xbd7cb17eUL, 0x072db8e7UL,
+ 0x911dbf90UL, 0x6410b71dUL, 0xf220b06aUL, 0x4871b9f3UL, 0xde41be84UL,
+ 0x7dd4da1aUL, 0xebe4dd6dUL, 0x51b5d4f4UL, 0xc785d383UL, 0x56986c13UL,
+ 0xc0a86b64UL, 0x7af962fdUL, 0xecc9658aUL, 0x4f5c0114UL, 0xd96c0663UL,
+ 0x633d0ffaUL, 0xf50d088dUL, 0xc8206e3bUL, 0x5e10694cUL, 0xe44160d5UL,
+ 0x727167a2UL, 0xd1e4033cUL, 0x47d4044bUL, 0xfd850dd2UL, 0x6bb50aa5UL,
+ 0xfaa8b535UL, 0x6c98b242UL, 0xd6c9bbdbUL, 0x40f9bcacUL, 0xe36cd832UL,
+ 0x755cdf45UL, 0xcf0dd6dcUL, 0x593dd1abUL, 0xac30d926UL, 0x3a00de51UL,
+ 0x8051d7c8UL, 0x1661d0bfUL, 0xb5f4b421UL, 0x23c4b356UL, 0x9995bacfUL,
+ 0x0fa5bdb8UL, 0x9eb80228UL, 0x0888055fUL, 0xb2d90cc6UL, 0x24e90bb1UL,
+ 0x877c6f2fUL, 0x114c6858UL, 0xab1d61c1UL, 0x3d2d66b6UL, 0x9041dc76UL,
+ 0x0671db01UL, 0xbc20d298UL, 0x2a10d5efUL, 0x8985b171UL, 0x1fb5b606UL,
+ 0xa5e4bf9fUL, 0x33d4b8e8UL, 0xa2c90778UL, 0x34f9000fUL, 0x8ea80996UL,
+ 0x18980ee1UL, 0xbb0d6a7fUL, 0x2d3d6d08UL, 0x976c6491UL, 0x015c63e6UL,
+ 0xf4516b6bUL, 0x62616c1cUL, 0xd8306585UL, 0x4e0062f2UL, 0xed95066cUL,
+ 0x7ba5011bUL, 0xc1f40882UL, 0x57c40ff5UL, 0xc6d9b065UL, 0x50e9b712UL,
+ 0xeab8be8bUL, 0x7c88b9fcUL, 0xdf1ddd62UL, 0x492dda15UL, 0xf37cd38cUL,
+ 0x654cd4fbUL, 0x5861b24dUL, 0xce51b53aUL, 0x7400bca3UL, 0xe230bbd4UL,
+ 0x41a5df4aUL, 0xd795d83dUL, 0x6dc4d1a4UL, 0xfbf4d6d3UL, 0x6ae96943UL,
+ 0xfcd96e34UL, 0x468867adUL, 0xd0b860daUL, 0x732d0444UL, 0xe51d0333UL,
+ 0x5f4c0aaaUL, 0xc97c0dddUL, 0x3c710550UL, 0xaa410227UL, 0x10100bbeUL,
+ 0x86200cc9UL, 0x25b56857UL, 0xb3856f20UL, 0x09d466b9UL, 0x9fe461ceUL,
+ 0x0ef9de5eUL, 0x98c9d929UL, 0x2298d0b0UL, 0xb4a8d7c7UL, 0x173db359UL,
+ 0x810db42eUL, 0x3b5cbdb7UL, 0xad6cbac0UL, 0x2083b8edUL, 0xb6b3bf9aUL,
+ 0x0ce2b603UL, 0x9ad2b174UL, 0x3947d5eaUL, 0xaf77d29dUL, 0x1526db04UL,
+ 0x8316dc73UL, 0x120b63e3UL, 0x843b6494UL, 0x3e6a6d0dUL, 0xa85a6a7aUL,
+ 0x0bcf0ee4UL, 0x9dff0993UL, 0x27ae000aUL, 0xb19e077dUL, 0x44930ff0UL,
+ 0xd2a30887UL, 0x68f2011eUL, 0xfec20669UL, 0x5d5762f7UL, 0xcb676580UL,
+ 0x71366c19UL, 0xe7066b6eUL, 0x761bd4feUL, 0xe02bd389UL, 0x5a7ada10UL,
+ 0xcc4add67UL, 0x6fdfb9f9UL, 0xf9efbe8eUL, 0x43beb717UL, 0xd58eb060UL,
+ 0xe8a3d6d6UL, 0x7e93d1a1UL, 0xc4c2d838UL, 0x52f2df4fUL, 0xf167bbd1UL,
+ 0x6757bca6UL, 0xdd06b53fUL, 0x4b36b248UL, 0xda2b0dd8UL, 0x4c1b0aafUL,
+ 0xf64a0336UL, 0x607a0441UL, 0xc3ef60dfUL, 0x55df67a8UL, 0xef8e6e31UL,
+ 0x79be6946UL, 0x8cb361cbUL, 0x1a8366bcUL, 0xa0d26f25UL, 0x36e26852UL,
+ 0x95770cccUL, 0x03470bbbUL, 0xb9160222UL, 0x2f260555UL, 0xbe3bbac5UL,
+ 0x280bbdb2UL, 0x925ab42bUL, 0x046ab35cUL, 0xa7ffd7c2UL, 0x31cfd0b5UL,
+ 0x8b9ed92cUL, 0x1daede5bUL, 0xb0c2649bUL, 0x26f263ecUL, 0x9ca36a75UL,
+ 0x0a936d02UL, 0xa906099cUL, 0x3f360eebUL, 0x85670772UL, 0x13570005UL,
+ 0x824abf95UL, 0x147ab8e2UL, 0xae2bb17bUL, 0x381bb60cUL, 0x9b8ed292UL,
+ 0x0dbed5e5UL, 0xb7efdc7cUL, 0x21dfdb0bUL, 0xd4d2d386UL, 0x42e2d4f1UL,
+ 0xf8b3dd68UL, 0x6e83da1fUL, 0xcd16be81UL, 0x5b26b9f6UL, 0xe177b06fUL,
+ 0x7747b718UL, 0xe65a0888UL, 0x706a0fffUL, 0xca3b0666UL, 0x5c0b0111UL,
+ 0xff9e658fUL, 0x69ae62f8UL, 0xd3ff6b61UL, 0x45cf6c16UL, 0x78e20aa0UL,
+ 0xeed20dd7UL, 0x5483044eUL, 0xc2b30339UL, 0x612667a7UL, 0xf71660d0UL,
+ 0x4d476949UL, 0xdb776e3eUL, 0x4a6ad1aeUL, 0xdc5ad6d9UL, 0x660bdf40UL,
+ 0xf03bd837UL, 0x53aebca9UL, 0xc59ebbdeUL, 0x7fcfb247UL, 0xe9ffb530UL,
+ 0x1cf2bdbdUL, 0x8ac2bacaUL, 0x3093b353UL, 0xa6a3b424UL, 0x0536d0baUL,
+ 0x9306d7cdUL, 0x2957de54UL, 0xbf67d923UL, 0x2e7a66b3UL, 0xb84a61c4UL,
+ 0x021b685dUL, 0x942b6f2aUL, 0x37be0bb4UL, 0xa18e0cc3UL, 0x1bdf055aUL,
+ 0x8def022dUL
+ },
+ {
+ 0x00000000UL, 0x41311b19UL, 0x82623632UL, 0xc3532d2bUL, 0x04c56c64UL,
+ 0x45f4777dUL, 0x86a75a56UL, 0xc796414fUL, 0x088ad9c8UL, 0x49bbc2d1UL,
+ 0x8ae8effaUL, 0xcbd9f4e3UL, 0x0c4fb5acUL, 0x4d7eaeb5UL, 0x8e2d839eUL,
+ 0xcf1c9887UL, 0x5112c24aUL, 0x1023d953UL, 0xd370f478UL, 0x9241ef61UL,
+ 0x55d7ae2eUL, 0x14e6b537UL, 0xd7b5981cUL, 0x96848305UL, 0x59981b82UL,
+ 0x18a9009bUL, 0xdbfa2db0UL, 0x9acb36a9UL, 0x5d5d77e6UL, 0x1c6c6cffUL,
+ 0xdf3f41d4UL, 0x9e0e5acdUL, 0xa2248495UL, 0xe3159f8cUL, 0x2046b2a7UL,
+ 0x6177a9beUL, 0xa6e1e8f1UL, 0xe7d0f3e8UL, 0x2483dec3UL, 0x65b2c5daUL,
+ 0xaaae5d5dUL, 0xeb9f4644UL, 0x28cc6b6fUL, 0x69fd7076UL, 0xae6b3139UL,
+ 0xef5a2a20UL, 0x2c09070bUL, 0x6d381c12UL, 0xf33646dfUL, 0xb2075dc6UL,
+ 0x715470edUL, 0x30656bf4UL, 0xf7f32abbUL, 0xb6c231a2UL, 0x75911c89UL,
+ 0x34a00790UL, 0xfbbc9f17UL, 0xba8d840eUL, 0x79dea925UL, 0x38efb23cUL,
+ 0xff79f373UL, 0xbe48e86aUL, 0x7d1bc541UL, 0x3c2ade58UL, 0x054f79f0UL,
+ 0x447e62e9UL, 0x872d4fc2UL, 0xc61c54dbUL, 0x018a1594UL, 0x40bb0e8dUL,
+ 0x83e823a6UL, 0xc2d938bfUL, 0x0dc5a038UL, 0x4cf4bb21UL, 0x8fa7960aUL,
+ 0xce968d13UL, 0x0900cc5cUL, 0x4831d745UL, 0x8b62fa6eUL, 0xca53e177UL,
+ 0x545dbbbaUL, 0x156ca0a3UL, 0xd63f8d88UL, 0x970e9691UL, 0x5098d7deUL,
+ 0x11a9ccc7UL, 0xd2fae1ecUL, 0x93cbfaf5UL, 0x5cd76272UL, 0x1de6796bUL,
+ 0xdeb55440UL, 0x9f844f59UL, 0x58120e16UL, 0x1923150fUL, 0xda703824UL,
+ 0x9b41233dUL, 0xa76bfd65UL, 0xe65ae67cUL, 0x2509cb57UL, 0x6438d04eUL,
+ 0xa3ae9101UL, 0xe29f8a18UL, 0x21cca733UL, 0x60fdbc2aUL, 0xafe124adUL,
+ 0xeed03fb4UL, 0x2d83129fUL, 0x6cb20986UL, 0xab2448c9UL, 0xea1553d0UL,
+ 0x29467efbUL, 0x687765e2UL, 0xf6793f2fUL, 0xb7482436UL, 0x741b091dUL,
+ 0x352a1204UL, 0xf2bc534bUL, 0xb38d4852UL, 0x70de6579UL, 0x31ef7e60UL,
+ 0xfef3e6e7UL, 0xbfc2fdfeUL, 0x7c91d0d5UL, 0x3da0cbccUL, 0xfa368a83UL,
+ 0xbb07919aUL, 0x7854bcb1UL, 0x3965a7a8UL, 0x4b98833bUL, 0x0aa99822UL,
+ 0xc9fab509UL, 0x88cbae10UL, 0x4f5def5fUL, 0x0e6cf446UL, 0xcd3fd96dUL,
+ 0x8c0ec274UL, 0x43125af3UL, 0x022341eaUL, 0xc1706cc1UL, 0x804177d8UL,
+ 0x47d73697UL, 0x06e62d8eUL, 0xc5b500a5UL, 0x84841bbcUL, 0x1a8a4171UL,
+ 0x5bbb5a68UL, 0x98e87743UL, 0xd9d96c5aUL, 0x1e4f2d15UL, 0x5f7e360cUL,
+ 0x9c2d1b27UL, 0xdd1c003eUL, 0x120098b9UL, 0x533183a0UL, 0x9062ae8bUL,
+ 0xd153b592UL, 0x16c5f4ddUL, 0x57f4efc4UL, 0x94a7c2efUL, 0xd596d9f6UL,
+ 0xe9bc07aeUL, 0xa88d1cb7UL, 0x6bde319cUL, 0x2aef2a85UL, 0xed796bcaUL,
+ 0xac4870d3UL, 0x6f1b5df8UL, 0x2e2a46e1UL, 0xe136de66UL, 0xa007c57fUL,
+ 0x6354e854UL, 0x2265f34dUL, 0xe5f3b202UL, 0xa4c2a91bUL, 0x67918430UL,
+ 0x26a09f29UL, 0xb8aec5e4UL, 0xf99fdefdUL, 0x3accf3d6UL, 0x7bfde8cfUL,
+ 0xbc6ba980UL, 0xfd5ab299UL, 0x3e099fb2UL, 0x7f3884abUL, 0xb0241c2cUL,
+ 0xf1150735UL, 0x32462a1eUL, 0x73773107UL, 0xb4e17048UL, 0xf5d06b51UL,
+ 0x3683467aUL, 0x77b25d63UL, 0x4ed7facbUL, 0x0fe6e1d2UL, 0xccb5ccf9UL,
+ 0x8d84d7e0UL, 0x4a1296afUL, 0x0b238db6UL, 0xc870a09dUL, 0x8941bb84UL,
+ 0x465d2303UL, 0x076c381aUL, 0xc43f1531UL, 0x850e0e28UL, 0x42984f67UL,
+ 0x03a9547eUL, 0xc0fa7955UL, 0x81cb624cUL, 0x1fc53881UL, 0x5ef42398UL,
+ 0x9da70eb3UL, 0xdc9615aaUL, 0x1b0054e5UL, 0x5a314ffcUL, 0x996262d7UL,
+ 0xd85379ceUL, 0x174fe149UL, 0x567efa50UL, 0x952dd77bUL, 0xd41ccc62UL,
+ 0x138a8d2dUL, 0x52bb9634UL, 0x91e8bb1fUL, 0xd0d9a006UL, 0xecf37e5eUL,
+ 0xadc26547UL, 0x6e91486cUL, 0x2fa05375UL, 0xe836123aUL, 0xa9070923UL,
+ 0x6a542408UL, 0x2b653f11UL, 0xe479a796UL, 0xa548bc8fUL, 0x661b91a4UL,
+ 0x272a8abdUL, 0xe0bccbf2UL, 0xa18dd0ebUL, 0x62defdc0UL, 0x23efe6d9UL,
+ 0xbde1bc14UL, 0xfcd0a70dUL, 0x3f838a26UL, 0x7eb2913fUL, 0xb924d070UL,
+ 0xf815cb69UL, 0x3b46e642UL, 0x7a77fd5bUL, 0xb56b65dcUL, 0xf45a7ec5UL,
+ 0x370953eeUL, 0x763848f7UL, 0xb1ae09b8UL, 0xf09f12a1UL, 0x33cc3f8aUL,
+ 0x72fd2493UL
+ },
+ {
+ 0x00000000UL, 0x376ac201UL, 0x6ed48403UL, 0x59be4602UL, 0xdca80907UL,
+ 0xebc2cb06UL, 0xb27c8d04UL, 0x85164f05UL, 0xb851130eUL, 0x8f3bd10fUL,
+ 0xd685970dUL, 0xe1ef550cUL, 0x64f91a09UL, 0x5393d808UL, 0x0a2d9e0aUL,
+ 0x3d475c0bUL, 0x70a3261cUL, 0x47c9e41dUL, 0x1e77a21fUL, 0x291d601eUL,
+ 0xac0b2f1bUL, 0x9b61ed1aUL, 0xc2dfab18UL, 0xf5b56919UL, 0xc8f23512UL,
+ 0xff98f713UL, 0xa626b111UL, 0x914c7310UL, 0x145a3c15UL, 0x2330fe14UL,
+ 0x7a8eb816UL, 0x4de47a17UL, 0xe0464d38UL, 0xd72c8f39UL, 0x8e92c93bUL,
+ 0xb9f80b3aUL, 0x3cee443fUL, 0x0b84863eUL, 0x523ac03cUL, 0x6550023dUL,
+ 0x58175e36UL, 0x6f7d9c37UL, 0x36c3da35UL, 0x01a91834UL, 0x84bf5731UL,
+ 0xb3d59530UL, 0xea6bd332UL, 0xdd011133UL, 0x90e56b24UL, 0xa78fa925UL,
+ 0xfe31ef27UL, 0xc95b2d26UL, 0x4c4d6223UL, 0x7b27a022UL, 0x2299e620UL,
+ 0x15f32421UL, 0x28b4782aUL, 0x1fdeba2bUL, 0x4660fc29UL, 0x710a3e28UL,
+ 0xf41c712dUL, 0xc376b32cUL, 0x9ac8f52eUL, 0xada2372fUL, 0xc08d9a70UL,
+ 0xf7e75871UL, 0xae591e73UL, 0x9933dc72UL, 0x1c259377UL, 0x2b4f5176UL,
+ 0x72f11774UL, 0x459bd575UL, 0x78dc897eUL, 0x4fb64b7fUL, 0x16080d7dUL,
+ 0x2162cf7cUL, 0xa4748079UL, 0x931e4278UL, 0xcaa0047aUL, 0xfdcac67bUL,
+ 0xb02ebc6cUL, 0x87447e6dUL, 0xdefa386fUL, 0xe990fa6eUL, 0x6c86b56bUL,
+ 0x5bec776aUL, 0x02523168UL, 0x3538f369UL, 0x087faf62UL, 0x3f156d63UL,
+ 0x66ab2b61UL, 0x51c1e960UL, 0xd4d7a665UL, 0xe3bd6464UL, 0xba032266UL,
+ 0x8d69e067UL, 0x20cbd748UL, 0x17a11549UL, 0x4e1f534bUL, 0x7975914aUL,
+ 0xfc63de4fUL, 0xcb091c4eUL, 0x92b75a4cUL, 0xa5dd984dUL, 0x989ac446UL,
+ 0xaff00647UL, 0xf64e4045UL, 0xc1248244UL, 0x4432cd41UL, 0x73580f40UL,
+ 0x2ae64942UL, 0x1d8c8b43UL, 0x5068f154UL, 0x67023355UL, 0x3ebc7557UL,
+ 0x09d6b756UL, 0x8cc0f853UL, 0xbbaa3a52UL, 0xe2147c50UL, 0xd57ebe51UL,
+ 0xe839e25aUL, 0xdf53205bUL, 0x86ed6659UL, 0xb187a458UL, 0x3491eb5dUL,
+ 0x03fb295cUL, 0x5a456f5eUL, 0x6d2fad5fUL, 0x801b35e1UL, 0xb771f7e0UL,
+ 0xeecfb1e2UL, 0xd9a573e3UL, 0x5cb33ce6UL, 0x6bd9fee7UL, 0x3267b8e5UL,
+ 0x050d7ae4UL, 0x384a26efUL, 0x0f20e4eeUL, 0x569ea2ecUL, 0x61f460edUL,
+ 0xe4e22fe8UL, 0xd388ede9UL, 0x8a36abebUL, 0xbd5c69eaUL, 0xf0b813fdUL,
+ 0xc7d2d1fcUL, 0x9e6c97feUL, 0xa90655ffUL, 0x2c101afaUL, 0x1b7ad8fbUL,
+ 0x42c49ef9UL, 0x75ae5cf8UL, 0x48e900f3UL, 0x7f83c2f2UL, 0x263d84f0UL,
+ 0x115746f1UL, 0x944109f4UL, 0xa32bcbf5UL, 0xfa958df7UL, 0xcdff4ff6UL,
+ 0x605d78d9UL, 0x5737bad8UL, 0x0e89fcdaUL, 0x39e33edbUL, 0xbcf571deUL,
+ 0x8b9fb3dfUL, 0xd221f5ddUL, 0xe54b37dcUL, 0xd80c6bd7UL, 0xef66a9d6UL,
+ 0xb6d8efd4UL, 0x81b22dd5UL, 0x04a462d0UL, 0x33cea0d1UL, 0x6a70e6d3UL,
+ 0x5d1a24d2UL, 0x10fe5ec5UL, 0x27949cc4UL, 0x7e2adac6UL, 0x494018c7UL,
+ 0xcc5657c2UL, 0xfb3c95c3UL, 0xa282d3c1UL, 0x95e811c0UL, 0xa8af4dcbUL,
+ 0x9fc58fcaUL, 0xc67bc9c8UL, 0xf1110bc9UL, 0x740744ccUL, 0x436d86cdUL,
+ 0x1ad3c0cfUL, 0x2db902ceUL, 0x4096af91UL, 0x77fc6d90UL, 0x2e422b92UL,
+ 0x1928e993UL, 0x9c3ea696UL, 0xab546497UL, 0xf2ea2295UL, 0xc580e094UL,
+ 0xf8c7bc9fUL, 0xcfad7e9eUL, 0x9613389cUL, 0xa179fa9dUL, 0x246fb598UL,
+ 0x13057799UL, 0x4abb319bUL, 0x7dd1f39aUL, 0x3035898dUL, 0x075f4b8cUL,
+ 0x5ee10d8eUL, 0x698bcf8fUL, 0xec9d808aUL, 0xdbf7428bUL, 0x82490489UL,
+ 0xb523c688UL, 0x88649a83UL, 0xbf0e5882UL, 0xe6b01e80UL, 0xd1dadc81UL,
+ 0x54cc9384UL, 0x63a65185UL, 0x3a181787UL, 0x0d72d586UL, 0xa0d0e2a9UL,
+ 0x97ba20a8UL, 0xce0466aaUL, 0xf96ea4abUL, 0x7c78ebaeUL, 0x4b1229afUL,
+ 0x12ac6fadUL, 0x25c6adacUL, 0x1881f1a7UL, 0x2feb33a6UL, 0x765575a4UL,
+ 0x413fb7a5UL, 0xc429f8a0UL, 0xf3433aa1UL, 0xaafd7ca3UL, 0x9d97bea2UL,
+ 0xd073c4b5UL, 0xe71906b4UL, 0xbea740b6UL, 0x89cd82b7UL, 0x0cdbcdb2UL,
+ 0x3bb10fb3UL, 0x620f49b1UL, 0x55658bb0UL, 0x6822d7bbUL, 0x5f4815baUL,
+ 0x06f653b8UL, 0x319c91b9UL, 0xb48adebcUL, 0x83e01cbdUL, 0xda5e5abfUL,
+ 0xed3498beUL
+ },
+ {
+ 0x00000000UL, 0x6567bcb8UL, 0x8bc809aaUL, 0xeeafb512UL, 0x5797628fUL,
+ 0x32f0de37UL, 0xdc5f6b25UL, 0xb938d79dUL, 0xef28b4c5UL, 0x8a4f087dUL,
+ 0x64e0bd6fUL, 0x018701d7UL, 0xb8bfd64aUL, 0xddd86af2UL, 0x3377dfe0UL,
+ 0x56106358UL, 0x9f571950UL, 0xfa30a5e8UL, 0x149f10faUL, 0x71f8ac42UL,
+ 0xc8c07bdfUL, 0xada7c767UL, 0x43087275UL, 0x266fcecdUL, 0x707fad95UL,
+ 0x1518112dUL, 0xfbb7a43fUL, 0x9ed01887UL, 0x27e8cf1aUL, 0x428f73a2UL,
+ 0xac20c6b0UL, 0xc9477a08UL, 0x3eaf32a0UL, 0x5bc88e18UL, 0xb5673b0aUL,
+ 0xd00087b2UL, 0x6938502fUL, 0x0c5fec97UL, 0xe2f05985UL, 0x8797e53dUL,
+ 0xd1878665UL, 0xb4e03addUL, 0x5a4f8fcfUL, 0x3f283377UL, 0x8610e4eaUL,
+ 0xe3775852UL, 0x0dd8ed40UL, 0x68bf51f8UL, 0xa1f82bf0UL, 0xc49f9748UL,
+ 0x2a30225aUL, 0x4f579ee2UL, 0xf66f497fUL, 0x9308f5c7UL, 0x7da740d5UL,
+ 0x18c0fc6dUL, 0x4ed09f35UL, 0x2bb7238dUL, 0xc518969fUL, 0xa07f2a27UL,
+ 0x1947fdbaUL, 0x7c204102UL, 0x928ff410UL, 0xf7e848a8UL, 0x3d58149bUL,
+ 0x583fa823UL, 0xb6901d31UL, 0xd3f7a189UL, 0x6acf7614UL, 0x0fa8caacUL,
+ 0xe1077fbeUL, 0x8460c306UL, 0xd270a05eUL, 0xb7171ce6UL, 0x59b8a9f4UL,
+ 0x3cdf154cUL, 0x85e7c2d1UL, 0xe0807e69UL, 0x0e2fcb7bUL, 0x6b4877c3UL,
+ 0xa20f0dcbUL, 0xc768b173UL, 0x29c70461UL, 0x4ca0b8d9UL, 0xf5986f44UL,
+ 0x90ffd3fcUL, 0x7e5066eeUL, 0x1b37da56UL, 0x4d27b90eUL, 0x284005b6UL,
+ 0xc6efb0a4UL, 0xa3880c1cUL, 0x1ab0db81UL, 0x7fd76739UL, 0x9178d22bUL,
+ 0xf41f6e93UL, 0x03f7263bUL, 0x66909a83UL, 0x883f2f91UL, 0xed589329UL,
+ 0x546044b4UL, 0x3107f80cUL, 0xdfa84d1eUL, 0xbacff1a6UL, 0xecdf92feUL,
+ 0x89b82e46UL, 0x67179b54UL, 0x027027ecUL, 0xbb48f071UL, 0xde2f4cc9UL,
+ 0x3080f9dbUL, 0x55e74563UL, 0x9ca03f6bUL, 0xf9c783d3UL, 0x176836c1UL,
+ 0x720f8a79UL, 0xcb375de4UL, 0xae50e15cUL, 0x40ff544eUL, 0x2598e8f6UL,
+ 0x73888baeUL, 0x16ef3716UL, 0xf8408204UL, 0x9d273ebcUL, 0x241fe921UL,
+ 0x41785599UL, 0xafd7e08bUL, 0xcab05c33UL, 0x3bb659edUL, 0x5ed1e555UL,
+ 0xb07e5047UL, 0xd519ecffUL, 0x6c213b62UL, 0x094687daUL, 0xe7e932c8UL,
+ 0x828e8e70UL, 0xd49eed28UL, 0xb1f95190UL, 0x5f56e482UL, 0x3a31583aUL,
+ 0x83098fa7UL, 0xe66e331fUL, 0x08c1860dUL, 0x6da63ab5UL, 0xa4e140bdUL,
+ 0xc186fc05UL, 0x2f294917UL, 0x4a4ef5afUL, 0xf3762232UL, 0x96119e8aUL,
+ 0x78be2b98UL, 0x1dd99720UL, 0x4bc9f478UL, 0x2eae48c0UL, 0xc001fdd2UL,
+ 0xa566416aUL, 0x1c5e96f7UL, 0x79392a4fUL, 0x97969f5dUL, 0xf2f123e5UL,
+ 0x05196b4dUL, 0x607ed7f5UL, 0x8ed162e7UL, 0xebb6de5fUL, 0x528e09c2UL,
+ 0x37e9b57aUL, 0xd9460068UL, 0xbc21bcd0UL, 0xea31df88UL, 0x8f566330UL,
+ 0x61f9d622UL, 0x049e6a9aUL, 0xbda6bd07UL, 0xd8c101bfUL, 0x366eb4adUL,
+ 0x53090815UL, 0x9a4e721dUL, 0xff29cea5UL, 0x11867bb7UL, 0x74e1c70fUL,
+ 0xcdd91092UL, 0xa8beac2aUL, 0x46111938UL, 0x2376a580UL, 0x7566c6d8UL,
+ 0x10017a60UL, 0xfeaecf72UL, 0x9bc973caUL, 0x22f1a457UL, 0x479618efUL,
+ 0xa939adfdUL, 0xcc5e1145UL, 0x06ee4d76UL, 0x6389f1ceUL, 0x8d2644dcUL,
+ 0xe841f864UL, 0x51792ff9UL, 0x341e9341UL, 0xdab12653UL, 0xbfd69aebUL,
+ 0xe9c6f9b3UL, 0x8ca1450bUL, 0x620ef019UL, 0x07694ca1UL, 0xbe519b3cUL,
+ 0xdb362784UL, 0x35999296UL, 0x50fe2e2eUL, 0x99b95426UL, 0xfcdee89eUL,
+ 0x12715d8cUL, 0x7716e134UL, 0xce2e36a9UL, 0xab498a11UL, 0x45e63f03UL,
+ 0x208183bbUL, 0x7691e0e3UL, 0x13f65c5bUL, 0xfd59e949UL, 0x983e55f1UL,
+ 0x2106826cUL, 0x44613ed4UL, 0xaace8bc6UL, 0xcfa9377eUL, 0x38417fd6UL,
+ 0x5d26c36eUL, 0xb389767cUL, 0xd6eecac4UL, 0x6fd61d59UL, 0x0ab1a1e1UL,
+ 0xe41e14f3UL, 0x8179a84bUL, 0xd769cb13UL, 0xb20e77abUL, 0x5ca1c2b9UL,
+ 0x39c67e01UL, 0x80fea99cUL, 0xe5991524UL, 0x0b36a036UL, 0x6e511c8eUL,
+ 0xa7166686UL, 0xc271da3eUL, 0x2cde6f2cUL, 0x49b9d394UL, 0xf0810409UL,
+ 0x95e6b8b1UL, 0x7b490da3UL, 0x1e2eb11bUL, 0x483ed243UL, 0x2d596efbUL,
+ 0xc3f6dbe9UL, 0xa6916751UL, 0x1fa9b0ccUL, 0x7ace0c74UL, 0x9461b966UL,
+ 0xf10605deUL
+#endif
+ }
+};
--- /dev/null
+/* deflate.c -- compress data using the deflation algorithm
+ * Copyright (C) 1995-2013 Jean-loup Gailly and Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ * ALGORITHM
+ *
+ * The "deflation" process depends on being able to identify portions
+ * of the input text which are identical to earlier input (within a
+ * sliding window trailing behind the input currently being processed).
+ *
+ * The most straightforward technique turns out to be the fastest for
+ * most input files: try all possible matches and select the longest.
+ * The key feature of this algorithm is that insertions into the string
+ * dictionary are very simple and thus fast, and deletions are avoided
+ * completely. Insertions are performed at each input character, whereas
+ * string matches are performed only when the previous match ends. So it
+ * is preferable to spend more time in matches to allow very fast string
+ * insertions and avoid deletions. The matching algorithm for small
+ * strings is inspired from that of Rabin & Karp. A brute force approach
+ * is used to find longer strings when a small match has been found.
+ * A similar algorithm is used in comic (by Jan-Mark Wams) and freeze
+ * (by Leonid Broukhis).
+ * A previous version of this file used a more sophisticated algorithm
+ * (by Fiala and Greene) which is guaranteed to run in linear amortized
+ * time, but has a larger average cost, uses more memory and is patented.
+ * However the F&G algorithm may be faster for some highly redundant
+ * files if the parameter max_chain_length (described below) is too large.
+ *
+ * ACKNOWLEDGEMENTS
+ *
+ * The idea of lazy evaluation of matches is due to Jan-Mark Wams, and
+ * I found it in 'freeze' written by Leonid Broukhis.
+ * Thanks to many people for bug reports and testing.
+ *
+ * REFERENCES
+ *
+ * Deutsch, L.P.,"DEFLATE Compressed Data Format Specification".
+ * Available in http://tools.ietf.org/html/rfc1951
+ *
+ * A description of the Rabin and Karp algorithm is given in the book
+ * "Algorithms" by R. Sedgewick, Addison-Wesley, p252.
+ *
+ * Fiala,E.R., and Greene,D.H.
+ * Data Compression with Finite Windows, Comm.ACM, 32,4 (1989) 490-595
+ *
+ */
+
+/* @(#) $Id$ */
+
+#include "deflate.h"
+
+const char deflate_copyright[] =
+ " deflate 1.2.8 Copyright 1995-2013 Jean-loup Gailly and Mark Adler ";
+/*
+ If you use the zlib library in a product, an acknowledgment is welcome
+ in the documentation of your product. If for some reason you cannot
+ include such an acknowledgment, I would appreciate that you keep this
+ copyright string in the executable of your product.
+ */
+
+/* ===========================================================================
+ * Function prototypes.
+ */
+typedef enum {
+ need_more, /* block not completed, need more input or more output */
+ block_done, /* block flush performed */
+ finish_started, /* finish started, need only more output at next deflate */
+ finish_done /* finish done, accept no more input or output */
+} block_state;
+
+typedef block_state (*compress_func) OF((deflate_state *s, int flush));
+/* Compression function. Returns the block state after the call. */
+
+local void fill_window OF((deflate_state *s));
+local block_state deflate_stored OF((deflate_state *s, int flush));
+local block_state deflate_fast OF((deflate_state *s, int flush));
+#ifndef FASTEST
+local block_state deflate_slow OF((deflate_state *s, int flush));
+#endif
+local block_state deflate_rle OF((deflate_state *s, int flush));
+local block_state deflate_huff OF((deflate_state *s, int flush));
+local void lm_init OF((deflate_state *s));
+local void putShortMSB OF((deflate_state *s, uInt b));
+local void flush_pending OF((z_streamp strm));
+local int read_buf OF((z_streamp strm, Bytef *buf, unsigned size));
+#ifdef ASMV
+ void match_init OF((void)); /* asm code initialization */
+ uInt longest_match OF((deflate_state *s, IPos cur_match));
+#else
+local uInt longest_match OF((deflate_state *s, IPos cur_match));
+#endif
+
+#ifdef DEBUG
+local void check_match OF((deflate_state *s, IPos start, IPos match,
+ int length));
+#endif
+
+/* ===========================================================================
+ * Local data
+ */
+
+#define NIL 0
+/* Tail of hash chains */
+
+#ifndef TOO_FAR
+# define TOO_FAR 4096
+#endif
+/* Matches of length 3 are discarded if their distance exceeds TOO_FAR */
+
+/* Values for max_lazy_match, good_match and max_chain_length, depending on
+ * the desired pack level (0..9). The values given below have been tuned to
+ * exclude worst case performance for pathological files. Better values may be
+ * found for specific files.
+ */
+typedef struct config_s {
+ ush good_length; /* reduce lazy search above this match length */
+ ush max_lazy; /* do not perform lazy search above this match length */
+ ush nice_length; /* quit search above this match length */
+ ush max_chain;
+ compress_func func;
+} config;
+
+#ifdef FASTEST
+local const config configuration_table[2] = {
+/* good lazy nice chain */
+/* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */
+/* 1 */ {4, 4, 8, 4, deflate_fast}}; /* max speed, no lazy matches */
+#else
+local const config configuration_table[10] = {
+/* good lazy nice chain */
+/* 0 */ {0, 0, 0, 0, deflate_stored}, /* store only */
+/* 1 */ {4, 4, 8, 4, deflate_fast}, /* max speed, no lazy matches */
+/* 2 */ {4, 5, 16, 8, deflate_fast},
+/* 3 */ {4, 6, 32, 32, deflate_fast},
+
+/* 4 */ {4, 4, 16, 16, deflate_slow}, /* lazy matches */
+/* 5 */ {8, 16, 32, 32, deflate_slow},
+/* 6 */ {8, 16, 128, 128, deflate_slow},
+/* 7 */ {8, 32, 128, 256, deflate_slow},
+/* 8 */ {32, 128, 258, 1024, deflate_slow},
+/* 9 */ {32, 258, 258, 4096, deflate_slow}}; /* max compression */
+#endif
+
+/* Note: the deflate() code requires max_lazy >= MIN_MATCH and max_chain >= 4
+ * For deflate_fast() (levels <= 3) good is ignored and lazy has a different
+ * meaning.
+ */
+
+#define EQUAL 0
+/* result of memcmp for equal strings */
+
+#ifndef NO_DUMMY_DECL
+struct static_tree_desc_s {int dummy;}; /* for buggy compilers */
+#endif
+
+/* rank Z_BLOCK between Z_NO_FLUSH and Z_PARTIAL_FLUSH */
+#define RANK(f) (((f) << 1) - ((f) > 4 ? 9 : 0))
+
+/* ===========================================================================
+ * Update a hash value with the given input byte
+ * IN assertion: all calls to to UPDATE_HASH are made with consecutive
+ * input characters, so that a running hash key can be computed from the
+ * previous key instead of complete recalculation each time.
+ */
+#define UPDATE_HASH(s,h,c) (h = (((h)<<s->hash_shift) ^ (c)) & s->hash_mask)
+
+
+/* ===========================================================================
+ * Insert string str in the dictionary and set match_head to the previous head
+ * of the hash chain (the most recent string with same hash key). Return
+ * the previous length of the hash chain.
+ * If this file is compiled with -DFASTEST, the compression level is forced
+ * to 1, and no hash chains are maintained.
+ * IN assertion: all calls to to INSERT_STRING are made with consecutive
+ * input characters and the first MIN_MATCH bytes of str are valid
+ * (except for the last MIN_MATCH-1 bytes of the input file).
+ */
+#ifdef FASTEST
+#define INSERT_STRING(s, str, match_head) \
+ (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \
+ match_head = s->head[s->ins_h], \
+ s->head[s->ins_h] = (Pos)(str))
+#else
+#define INSERT_STRING(s, str, match_head) \
+ (UPDATE_HASH(s, s->ins_h, s->window[(str) + (MIN_MATCH-1)]), \
+ match_head = s->prev[(str) & s->w_mask] = s->head[s->ins_h], \
+ s->head[s->ins_h] = (Pos)(str))
+#endif
+
+/* ===========================================================================
+ * Initialize the hash table (avoiding 64K overflow for 16 bit systems).
+ * prev[] will be initialized on the fly.
+ */
+#define CLEAR_HASH(s) \
+ s->head[s->hash_size-1] = NIL; \
+ zmemzero((Bytef *)s->head, (unsigned)(s->hash_size-1)*sizeof(*s->head));
+
+/* ========================================================================= */
+int ZEXPORT deflateInit_(strm, level, version, stream_size)
+ z_streamp strm;
+ int level;
+ const char *version;
+ int stream_size;
+{
+ return deflateInit2_(strm, level, Z_DEFLATED, MAX_WBITS, DEF_MEM_LEVEL,
+ Z_DEFAULT_STRATEGY, version, stream_size);
+ /* To do: ignore strm->next_in if we use it as window */
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateInit2_(strm, level, method, windowBits, memLevel, strategy,
+ version, stream_size)
+ z_streamp strm;
+ int level;
+ int method;
+ int windowBits;
+ int memLevel;
+ int strategy;
+ const char *version;
+ int stream_size;
+{
+ deflate_state *s;
+ int wrap = 1;
+ static const char my_version[] = ZLIB_VERSION;
+
+ ushf *overlay;
+ /* We overlay pending_buf and d_buf+l_buf. This works since the average
+ * output size for (length,distance) codes is <= 24 bits.
+ */
+
+ if (version == Z_NULL || version[0] != my_version[0] ||
+ stream_size != sizeof(z_stream)) {
+ return Z_VERSION_ERROR;
+ }
+ if (strm == Z_NULL) return Z_STREAM_ERROR;
+
+ strm->msg = Z_NULL;
+ if (strm->zalloc == (alloc_func)0) {
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zalloc = zcalloc;
+ strm->opaque = (voidpf)0;
+#endif
+ }
+ if (strm->zfree == (free_func)0)
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zfree = zcfree;
+#endif
+
+#ifdef FASTEST
+ if (level != 0) level = 1;
+#else
+ if (level == Z_DEFAULT_COMPRESSION) level = 6;
+#endif
+
+ if (windowBits < 0) { /* suppress zlib wrapper */
+ wrap = 0;
+ windowBits = -windowBits;
+ }
+#ifdef GZIP
+ else if (windowBits > 15) {
+ wrap = 2; /* write gzip wrapper instead */
+ windowBits -= 16;
+ }
+#endif
+ if (memLevel < 1 || memLevel > MAX_MEM_LEVEL || method != Z_DEFLATED ||
+ windowBits < 8 || windowBits > 15 || level < 0 || level > 9 ||
+ strategy < 0 || strategy > Z_FIXED) {
+ return Z_STREAM_ERROR;
+ }
+ if (windowBits == 8) windowBits = 9; /* until 256-byte window bug fixed */
+ s = (deflate_state *) ZALLOC(strm, 1, sizeof(deflate_state));
+ if (s == Z_NULL) return Z_MEM_ERROR;
+ strm->state = (struct internal_state FAR *)s;
+ s->strm = strm;
+
+ s->wrap = wrap;
+ s->gzhead = Z_NULL;
+ s->w_bits = windowBits;
+ s->w_size = 1 << s->w_bits;
+ s->w_mask = s->w_size - 1;
+
+ s->hash_bits = memLevel + 7;
+ s->hash_size = 1 << s->hash_bits;
+ s->hash_mask = s->hash_size - 1;
+ s->hash_shift = ((s->hash_bits+MIN_MATCH-1)/MIN_MATCH);
+
+ s->window = (Bytef *) ZALLOC(strm, s->w_size, 2*sizeof(Byte));
+ s->prev = (Posf *) ZALLOC(strm, s->w_size, sizeof(Pos));
+ s->head = (Posf *) ZALLOC(strm, s->hash_size, sizeof(Pos));
+
+ s->high_water = 0; /* nothing written to s->window yet */
+
+ s->lit_bufsize = 1 << (memLevel + 6); /* 16K elements by default */
+
+ overlay = (ushf *) ZALLOC(strm, s->lit_bufsize, sizeof(ush)+2);
+ s->pending_buf = (uchf *) overlay;
+ s->pending_buf_size = (ulg)s->lit_bufsize * (sizeof(ush)+2L);
+
+ if (s->window == Z_NULL || s->prev == Z_NULL || s->head == Z_NULL ||
+ s->pending_buf == Z_NULL) {
+ s->status = FINISH_STATE;
+ strm->msg = ERR_MSG(Z_MEM_ERROR);
+ deflateEnd (strm);
+ return Z_MEM_ERROR;
+ }
+ s->d_buf = overlay + s->lit_bufsize/sizeof(ush);
+ s->l_buf = s->pending_buf + (1+sizeof(ush))*s->lit_bufsize;
+
+ s->level = level;
+ s->strategy = strategy;
+ s->method = (Byte)method;
+
+ return deflateReset(strm);
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateSetDictionary (strm, dictionary, dictLength)
+ z_streamp strm;
+ const Bytef *dictionary;
+ uInt dictLength;
+{
+ deflate_state *s;
+ uInt str, n;
+ int wrap;
+ unsigned avail;
+ z_const unsigned char *next;
+
+ if (strm == Z_NULL || strm->state == Z_NULL || dictionary == Z_NULL)
+ return Z_STREAM_ERROR;
+ s = strm->state;
+ wrap = s->wrap;
+ if (wrap == 2 || (wrap == 1 && s->status != INIT_STATE) || s->lookahead)
+ return Z_STREAM_ERROR;
+
+ /* when using zlib wrappers, compute Adler-32 for provided dictionary */
+ if (wrap == 1)
+ strm->adler = adler32(strm->adler, dictionary, dictLength);
+ s->wrap = 0; /* avoid computing Adler-32 in read_buf */
+
+ /* if dictionary would fill window, just replace the history */
+ if (dictLength >= s->w_size) {
+ if (wrap == 0) { /* already empty otherwise */
+ CLEAR_HASH(s);
+ s->strstart = 0;
+ s->block_start = 0L;
+ s->insert = 0;
+ }
+ dictionary += dictLength - s->w_size; /* use the tail */
+ dictLength = s->w_size;
+ }
+
+ /* insert dictionary into window and hash */
+ avail = strm->avail_in;
+ next = strm->next_in;
+ strm->avail_in = dictLength;
+ strm->next_in = (z_const Bytef *)dictionary;
+ fill_window(s);
+ while (s->lookahead >= MIN_MATCH) {
+ str = s->strstart;
+ n = s->lookahead - (MIN_MATCH-1);
+ do {
+ UPDATE_HASH(s, s->ins_h, s->window[str + MIN_MATCH-1]);
+#ifndef FASTEST
+ s->prev[str & s->w_mask] = s->head[s->ins_h];
+#endif
+ s->head[s->ins_h] = (Pos)str;
+ str++;
+ } while (--n);
+ s->strstart = str;
+ s->lookahead = MIN_MATCH-1;
+ fill_window(s);
+ }
+ s->strstart += s->lookahead;
+ s->block_start = (long)s->strstart;
+ s->insert = s->lookahead;
+ s->lookahead = 0;
+ s->match_length = s->prev_length = MIN_MATCH-1;
+ s->match_available = 0;
+ strm->next_in = next;
+ strm->avail_in = avail;
+ s->wrap = wrap;
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateResetKeep (strm)
+ z_streamp strm;
+{
+ deflate_state *s;
+
+ if (strm == Z_NULL || strm->state == Z_NULL ||
+ strm->zalloc == (alloc_func)0 || strm->zfree == (free_func)0) {
+ return Z_STREAM_ERROR;
+ }
+
+ strm->total_in = strm->total_out = 0;
+ strm->msg = Z_NULL; /* use zfree if we ever allocate msg dynamically */
+ strm->data_type = Z_UNKNOWN;
+
+ s = (deflate_state *)strm->state;
+ s->pending = 0;
+ s->pending_out = s->pending_buf;
+
+ if (s->wrap < 0) {
+ s->wrap = -s->wrap; /* was made negative by deflate(..., Z_FINISH); */
+ }
+ s->status = s->wrap ? INIT_STATE : BUSY_STATE;
+ strm->adler =
+#ifdef GZIP
+ s->wrap == 2 ? crc32(0L, Z_NULL, 0) :
+#endif
+ adler32(0L, Z_NULL, 0);
+ s->last_flush = Z_NO_FLUSH;
+
+ _tr_init(s);
+
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateReset (strm)
+ z_streamp strm;
+{
+ int ret;
+
+ ret = deflateResetKeep(strm);
+ if (ret == Z_OK)
+ lm_init(strm->state);
+ return ret;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateSetHeader (strm, head)
+ z_streamp strm;
+ gz_headerp head;
+{
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ if (strm->state->wrap != 2) return Z_STREAM_ERROR;
+ strm->state->gzhead = head;
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflatePending (strm, pending, bits)
+ unsigned *pending;
+ int *bits;
+ z_streamp strm;
+{
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ if (pending != Z_NULL)
+ *pending = strm->state->pending;
+ if (bits != Z_NULL)
+ *bits = strm->state->bi_valid;
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflatePrime (strm, bits, value)
+ z_streamp strm;
+ int bits;
+ int value;
+{
+ deflate_state *s;
+ int put;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ s = strm->state;
+ if ((Bytef *)(s->d_buf) < s->pending_out + ((Buf_size + 7) >> 3))
+ return Z_BUF_ERROR;
+ do {
+ put = Buf_size - s->bi_valid;
+ if (put > bits)
+ put = bits;
+ s->bi_buf |= (ush)((value & ((1 << put) - 1)) << s->bi_valid);
+ s->bi_valid += put;
+ _tr_flush_bits(s);
+ value >>= put;
+ bits -= put;
+ } while (bits);
+ return Z_OK;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateParams(strm, level, strategy)
+ z_streamp strm;
+ int level;
+ int strategy;
+{
+ deflate_state *s;
+ compress_func func;
+ int err = Z_OK;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ s = strm->state;
+
+#ifdef FASTEST
+ if (level != 0) level = 1;
+#else
+ if (level == Z_DEFAULT_COMPRESSION) level = 6;
+#endif
+ if (level < 0 || level > 9 || strategy < 0 || strategy > Z_FIXED) {
+ return Z_STREAM_ERROR;
+ }
+ func = configuration_table[s->level].func;
+
+ if ((strategy != s->strategy || func != configuration_table[level].func) &&
+ strm->total_in != 0) {
+ /* Flush the last buffer: */
+ err = deflate(strm, Z_BLOCK);
+ if (err == Z_BUF_ERROR && s->pending == 0)
+ err = Z_OK;
+ }
+ if (s->level != level) {
+ s->level = level;
+ s->max_lazy_match = configuration_table[level].max_lazy;
+ s->good_match = configuration_table[level].good_length;
+ s->nice_match = configuration_table[level].nice_length;
+ s->max_chain_length = configuration_table[level].max_chain;
+ }
+ s->strategy = strategy;
+ return err;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateTune(strm, good_length, max_lazy, nice_length, max_chain)
+ z_streamp strm;
+ int good_length;
+ int max_lazy;
+ int nice_length;
+ int max_chain;
+{
+ deflate_state *s;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ s = strm->state;
+ s->good_match = good_length;
+ s->max_lazy_match = max_lazy;
+ s->nice_match = nice_length;
+ s->max_chain_length = max_chain;
+ return Z_OK;
+}
+
+/* =========================================================================
+ * For the default windowBits of 15 and memLevel of 8, this function returns
+ * a close to exact, as well as small, upper bound on the compressed size.
+ * They are coded as constants here for a reason--if the #define's are
+ * changed, then this function needs to be changed as well. The return
+ * value for 15 and 8 only works for those exact settings.
+ *
+ * For any setting other than those defaults for windowBits and memLevel,
+ * the value returned is a conservative worst case for the maximum expansion
+ * resulting from using fixed blocks instead of stored blocks, which deflate
+ * can emit on compressed data for some combinations of the parameters.
+ *
+ * This function could be more sophisticated to provide closer upper bounds for
+ * every combination of windowBits and memLevel. But even the conservative
+ * upper bound of about 14% expansion does not seem onerous for output buffer
+ * allocation.
+ */
+uLong ZEXPORT deflateBound(strm, sourceLen)
+ z_streamp strm;
+ uLong sourceLen;
+{
+ deflate_state *s;
+ uLong complen, wraplen;
+ Bytef *str;
+
+ /* conservative upper bound for compressed data */
+ complen = sourceLen +
+ ((sourceLen + 7) >> 3) + ((sourceLen + 63) >> 6) + 5;
+
+ /* if can't get parameters, return conservative bound plus zlib wrapper */
+ if (strm == Z_NULL || strm->state == Z_NULL)
+ return complen + 6;
+
+ /* compute wrapper length */
+ s = strm->state;
+ switch (s->wrap) {
+ case 0: /* raw deflate */
+ wraplen = 0;
+ break;
+ case 1: /* zlib wrapper */
+ wraplen = 6 + (s->strstart ? 4 : 0);
+ break;
+ case 2: /* gzip wrapper */
+ wraplen = 18;
+ if (s->gzhead != Z_NULL) { /* user-supplied gzip header */
+ if (s->gzhead->extra != Z_NULL)
+ wraplen += 2 + s->gzhead->extra_len;
+ str = s->gzhead->name;
+ if (str != Z_NULL)
+ do {
+ wraplen++;
+ } while (*str++);
+ str = s->gzhead->comment;
+ if (str != Z_NULL)
+ do {
+ wraplen++;
+ } while (*str++);
+ if (s->gzhead->hcrc)
+ wraplen += 2;
+ }
+ break;
+ default: /* for compiler happiness */
+ wraplen = 6;
+ }
+
+ /* if not default parameters, return conservative bound */
+ if (s->w_bits != 15 || s->hash_bits != 8 + 7)
+ return complen + wraplen;
+
+ /* default settings: return tight bound for that case */
+ return sourceLen + (sourceLen >> 12) + (sourceLen >> 14) +
+ (sourceLen >> 25) + 13 - 6 + wraplen;
+}
+
+/* =========================================================================
+ * Put a short in the pending buffer. The 16-bit value is put in MSB order.
+ * IN assertion: the stream state is correct and there is enough room in
+ * pending_buf.
+ */
+local void putShortMSB (s, b)
+ deflate_state *s;
+ uInt b;
+{
+ put_byte(s, (Byte)(b >> 8));
+ put_byte(s, (Byte)(b & 0xff));
+}
+
+/* =========================================================================
+ * Flush as much pending output as possible. All deflate() output goes
+ * through this function so some applications may wish to modify it
+ * to avoid allocating a large strm->next_out buffer and copying into it.
+ * (See also read_buf()).
+ */
+local void flush_pending(strm)
+ z_streamp strm;
+{
+ unsigned len;
+ deflate_state *s = strm->state;
+
+ _tr_flush_bits(s);
+ len = s->pending;
+ if (len > strm->avail_out) len = strm->avail_out;
+ if (len == 0) return;
+
+ zmemcpy(strm->next_out, s->pending_out, len);
+ strm->next_out += len;
+ s->pending_out += len;
+ strm->total_out += len;
+ strm->avail_out -= len;
+ s->pending -= len;
+ if (s->pending == 0) {
+ s->pending_out = s->pending_buf;
+ }
+}
+
+/* ========================================================================= */
+int ZEXPORT deflate (strm, flush)
+ z_streamp strm;
+ int flush;
+{
+ int old_flush; /* value of flush param for previous deflate call */
+ deflate_state *s;
+
+ if (strm == Z_NULL || strm->state == Z_NULL ||
+ flush > Z_BLOCK || flush < 0) {
+ return Z_STREAM_ERROR;
+ }
+ s = strm->state;
+
+ if (strm->next_out == Z_NULL ||
+ (strm->next_in == Z_NULL && strm->avail_in != 0) ||
+ (s->status == FINISH_STATE && flush != Z_FINISH)) {
+ ERR_RETURN(strm, Z_STREAM_ERROR);
+ }
+ if (strm->avail_out == 0) ERR_RETURN(strm, Z_BUF_ERROR);
+
+ s->strm = strm; /* just in case */
+ old_flush = s->last_flush;
+ s->last_flush = flush;
+
+ /* Write the header */
+ if (s->status == INIT_STATE) {
+#ifdef GZIP
+ if (s->wrap == 2) {
+ strm->adler = crc32(0L, Z_NULL, 0);
+ put_byte(s, 31);
+ put_byte(s, 139);
+ put_byte(s, 8);
+ if (s->gzhead == Z_NULL) {
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, 0);
+ put_byte(s, s->level == 9 ? 2 :
+ (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ?
+ 4 : 0));
+ put_byte(s, OS_CODE);
+ s->status = BUSY_STATE;
+ }
+ else {
+ put_byte(s, (s->gzhead->text ? 1 : 0) +
+ (s->gzhead->hcrc ? 2 : 0) +
+ (s->gzhead->extra == Z_NULL ? 0 : 4) +
+ (s->gzhead->name == Z_NULL ? 0 : 8) +
+ (s->gzhead->comment == Z_NULL ? 0 : 16)
+ );
+ put_byte(s, (Byte)(s->gzhead->time & 0xff));
+ put_byte(s, (Byte)((s->gzhead->time >> 8) & 0xff));
+ put_byte(s, (Byte)((s->gzhead->time >> 16) & 0xff));
+ put_byte(s, (Byte)((s->gzhead->time >> 24) & 0xff));
+ put_byte(s, s->level == 9 ? 2 :
+ (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2 ?
+ 4 : 0));
+ put_byte(s, s->gzhead->os & 0xff);
+ if (s->gzhead->extra != Z_NULL) {
+ put_byte(s, s->gzhead->extra_len & 0xff);
+ put_byte(s, (s->gzhead->extra_len >> 8) & 0xff);
+ }
+ if (s->gzhead->hcrc)
+ strm->adler = crc32(strm->adler, s->pending_buf,
+ s->pending);
+ s->gzindex = 0;
+ s->status = EXTRA_STATE;
+ }
+ }
+ else
+#endif
+ {
+ uInt header = (Z_DEFLATED + ((s->w_bits-8)<<4)) << 8;
+ uInt level_flags;
+
+ if (s->strategy >= Z_HUFFMAN_ONLY || s->level < 2)
+ level_flags = 0;
+ else if (s->level < 6)
+ level_flags = 1;
+ else if (s->level == 6)
+ level_flags = 2;
+ else
+ level_flags = 3;
+ header |= (level_flags << 6);
+ if (s->strstart != 0) header |= PRESET_DICT;
+ header += 31 - (header % 31);
+
+ s->status = BUSY_STATE;
+ putShortMSB(s, header);
+
+ /* Save the adler32 of the preset dictionary: */
+ if (s->strstart != 0) {
+ putShortMSB(s, (uInt)(strm->adler >> 16));
+ putShortMSB(s, (uInt)(strm->adler & 0xffff));
+ }
+ strm->adler = adler32(0L, Z_NULL, 0);
+ }
+ }
+#ifdef GZIP
+ if (s->status == EXTRA_STATE) {
+ if (s->gzhead->extra != Z_NULL) {
+ uInt beg = s->pending; /* start of bytes to update crc */
+
+ while (s->gzindex < (s->gzhead->extra_len & 0xffff)) {
+ if (s->pending == s->pending_buf_size) {
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ flush_pending(strm);
+ beg = s->pending;
+ if (s->pending == s->pending_buf_size)
+ break;
+ }
+ put_byte(s, s->gzhead->extra[s->gzindex]);
+ s->gzindex++;
+ }
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ if (s->gzindex == s->gzhead->extra_len) {
+ s->gzindex = 0;
+ s->status = NAME_STATE;
+ }
+ }
+ else
+ s->status = NAME_STATE;
+ }
+ if (s->status == NAME_STATE) {
+ if (s->gzhead->name != Z_NULL) {
+ uInt beg = s->pending; /* start of bytes to update crc */
+ int val;
+
+ do {
+ if (s->pending == s->pending_buf_size) {
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ flush_pending(strm);
+ beg = s->pending;
+ if (s->pending == s->pending_buf_size) {
+ val = 1;
+ break;
+ }
+ }
+ val = s->gzhead->name[s->gzindex++];
+ put_byte(s, val);
+ } while (val != 0);
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ if (val == 0) {
+ s->gzindex = 0;
+ s->status = COMMENT_STATE;
+ }
+ }
+ else
+ s->status = COMMENT_STATE;
+ }
+ if (s->status == COMMENT_STATE) {
+ if (s->gzhead->comment != Z_NULL) {
+ uInt beg = s->pending; /* start of bytes to update crc */
+ int val;
+
+ do {
+ if (s->pending == s->pending_buf_size) {
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ flush_pending(strm);
+ beg = s->pending;
+ if (s->pending == s->pending_buf_size) {
+ val = 1;
+ break;
+ }
+ }
+ val = s->gzhead->comment[s->gzindex++];
+ put_byte(s, val);
+ } while (val != 0);
+ if (s->gzhead->hcrc && s->pending > beg)
+ strm->adler = crc32(strm->adler, s->pending_buf + beg,
+ s->pending - beg);
+ if (val == 0)
+ s->status = HCRC_STATE;
+ }
+ else
+ s->status = HCRC_STATE;
+ }
+ if (s->status == HCRC_STATE) {
+ if (s->gzhead->hcrc) {
+ if (s->pending + 2 > s->pending_buf_size)
+ flush_pending(strm);
+ if (s->pending + 2 <= s->pending_buf_size) {
+ put_byte(s, (Byte)(strm->adler & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 8) & 0xff));
+ strm->adler = crc32(0L, Z_NULL, 0);
+ s->status = BUSY_STATE;
+ }
+ }
+ else
+ s->status = BUSY_STATE;
+ }
+#endif
+
+ /* Flush as much pending output as possible */
+ if (s->pending != 0) {
+ flush_pending(strm);
+ if (strm->avail_out == 0) {
+ /* Since avail_out is 0, deflate will be called again with
+ * more output space, but possibly with both pending and
+ * avail_in equal to zero. There won't be anything to do,
+ * but this is not an error situation so make sure we
+ * return OK instead of BUF_ERROR at next call of deflate:
+ */
+ s->last_flush = -1;
+ return Z_OK;
+ }
+
+ /* Make sure there is something to do and avoid duplicate consecutive
+ * flushes. For repeated and useless calls with Z_FINISH, we keep
+ * returning Z_STREAM_END instead of Z_BUF_ERROR.
+ */
+ } else if (strm->avail_in == 0 && RANK(flush) <= RANK(old_flush) &&
+ flush != Z_FINISH) {
+ ERR_RETURN(strm, Z_BUF_ERROR);
+ }
+
+ /* User must not provide more input after the first FINISH: */
+ if (s->status == FINISH_STATE && strm->avail_in != 0) {
+ ERR_RETURN(strm, Z_BUF_ERROR);
+ }
+
+ /* Start a new block or continue the current one.
+ */
+ if (strm->avail_in != 0 || s->lookahead != 0 ||
+ (flush != Z_NO_FLUSH && s->status != FINISH_STATE)) {
+ block_state bstate;
+
+ bstate = s->strategy == Z_HUFFMAN_ONLY ? deflate_huff(s, flush) :
+ (s->strategy == Z_RLE ? deflate_rle(s, flush) :
+ (*(configuration_table[s->level].func))(s, flush));
+
+ if (bstate == finish_started || bstate == finish_done) {
+ s->status = FINISH_STATE;
+ }
+ if (bstate == need_more || bstate == finish_started) {
+ if (strm->avail_out == 0) {
+ s->last_flush = -1; /* avoid BUF_ERROR next call, see above */
+ }
+ return Z_OK;
+ /* If flush != Z_NO_FLUSH && avail_out == 0, the next call
+ * of deflate should use the same flush parameter to make sure
+ * that the flush is complete. So we don't have to output an
+ * empty block here, this will be done at next call. This also
+ * ensures that for a very small output buffer, we emit at most
+ * one empty block.
+ */
+ }
+ if (bstate == block_done) {
+ if (flush == Z_PARTIAL_FLUSH) {
+ _tr_align(s);
+ } else if (flush != Z_BLOCK) { /* FULL_FLUSH or SYNC_FLUSH */
+ _tr_stored_block(s, (char*)0, 0L, 0);
+ /* For a full flush, this empty block will be recognized
+ * as a special marker by inflate_sync().
+ */
+ if (flush == Z_FULL_FLUSH) {
+ CLEAR_HASH(s); /* forget history */
+ if (s->lookahead == 0) {
+ s->strstart = 0;
+ s->block_start = 0L;
+ s->insert = 0;
+ }
+ }
+ }
+ flush_pending(strm);
+ if (strm->avail_out == 0) {
+ s->last_flush = -1; /* avoid BUF_ERROR at next call, see above */
+ return Z_OK;
+ }
+ }
+ }
+ Assert(strm->avail_out > 0, "bug2");
+
+ if (flush != Z_FINISH) return Z_OK;
+ if (s->wrap <= 0) return Z_STREAM_END;
+
+ /* Write the trailer */
+#ifdef GZIP
+ if (s->wrap == 2) {
+ put_byte(s, (Byte)(strm->adler & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 8) & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 16) & 0xff));
+ put_byte(s, (Byte)((strm->adler >> 24) & 0xff));
+ put_byte(s, (Byte)(strm->total_in & 0xff));
+ put_byte(s, (Byte)((strm->total_in >> 8) & 0xff));
+ put_byte(s, (Byte)((strm->total_in >> 16) & 0xff));
+ put_byte(s, (Byte)((strm->total_in >> 24) & 0xff));
+ }
+ else
+#endif
+ {
+ putShortMSB(s, (uInt)(strm->adler >> 16));
+ putShortMSB(s, (uInt)(strm->adler & 0xffff));
+ }
+ flush_pending(strm);
+ /* If avail_out is zero, the application will call deflate again
+ * to flush the rest.
+ */
+ if (s->wrap > 0) s->wrap = -s->wrap; /* write the trailer only once! */
+ return s->pending != 0 ? Z_OK : Z_STREAM_END;
+}
+
+/* ========================================================================= */
+int ZEXPORT deflateEnd (strm)
+ z_streamp strm;
+{
+ int status;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+
+ status = strm->state->status;
+ if (status != INIT_STATE &&
+ status != EXTRA_STATE &&
+ status != NAME_STATE &&
+ status != COMMENT_STATE &&
+ status != HCRC_STATE &&
+ status != BUSY_STATE &&
+ status != FINISH_STATE) {
+ return Z_STREAM_ERROR;
+ }
+
+ /* Deallocate in reverse order of allocations: */
+ TRY_FREE(strm, strm->state->pending_buf);
+ TRY_FREE(strm, strm->state->head);
+ TRY_FREE(strm, strm->state->prev);
+ TRY_FREE(strm, strm->state->window);
+
+ ZFREE(strm, strm->state);
+ strm->state = Z_NULL;
+
+ return status == BUSY_STATE ? Z_DATA_ERROR : Z_OK;
+}
+
+/* =========================================================================
+ * Copy the source state to the destination state.
+ * To simplify the source, this is not supported for 16-bit MSDOS (which
+ * doesn't have enough memory anyway to duplicate compression states).
+ */
+int ZEXPORT deflateCopy (dest, source)
+ z_streamp dest;
+ z_streamp source;
+{
+#ifdef MAXSEG_64K
+ return Z_STREAM_ERROR;
+#else
+ deflate_state *ds;
+ deflate_state *ss;
+ ushf *overlay;
+
+
+ if (source == Z_NULL || dest == Z_NULL || source->state == Z_NULL) {
+ return Z_STREAM_ERROR;
+ }
+
+ ss = source->state;
+
+ zmemcpy((voidpf)dest, (voidpf)source, sizeof(z_stream));
+
+ ds = (deflate_state *) ZALLOC(dest, 1, sizeof(deflate_state));
+ if (ds == Z_NULL) return Z_MEM_ERROR;
+ dest->state = (struct internal_state FAR *) ds;
+ zmemcpy((voidpf)ds, (voidpf)ss, sizeof(deflate_state));
+ ds->strm = dest;
+
+ ds->window = (Bytef *) ZALLOC(dest, ds->w_size, 2*sizeof(Byte));
+ ds->prev = (Posf *) ZALLOC(dest, ds->w_size, sizeof(Pos));
+ ds->head = (Posf *) ZALLOC(dest, ds->hash_size, sizeof(Pos));
+ overlay = (ushf *) ZALLOC(dest, ds->lit_bufsize, sizeof(ush)+2);
+ ds->pending_buf = (uchf *) overlay;
+
+ if (ds->window == Z_NULL || ds->prev == Z_NULL || ds->head == Z_NULL ||
+ ds->pending_buf == Z_NULL) {
+ deflateEnd (dest);
+ return Z_MEM_ERROR;
+ }
+ /* following zmemcpy do not work for 16-bit MSDOS */
+ zmemcpy(ds->window, ss->window, ds->w_size * 2 * sizeof(Byte));
+ zmemcpy((voidpf)ds->prev, (voidpf)ss->prev, ds->w_size * sizeof(Pos));
+ zmemcpy((voidpf)ds->head, (voidpf)ss->head, ds->hash_size * sizeof(Pos));
+ zmemcpy(ds->pending_buf, ss->pending_buf, (uInt)ds->pending_buf_size);
+
+ ds->pending_out = ds->pending_buf + (ss->pending_out - ss->pending_buf);
+ ds->d_buf = overlay + ds->lit_bufsize/sizeof(ush);
+ ds->l_buf = ds->pending_buf + (1+sizeof(ush))*ds->lit_bufsize;
+
+ ds->l_desc.dyn_tree = ds->dyn_ltree;
+ ds->d_desc.dyn_tree = ds->dyn_dtree;
+ ds->bl_desc.dyn_tree = ds->bl_tree;
+
+ return Z_OK;
+#endif /* MAXSEG_64K */
+}
+
+/* ===========================================================================
+ * Read a new buffer from the current input stream, update the adler32
+ * and total number of bytes read. All deflate() input goes through
+ * this function so some applications may wish to modify it to avoid
+ * allocating a large strm->next_in buffer and copying from it.
+ * (See also flush_pending()).
+ */
+local int read_buf(strm, buf, size)
+ z_streamp strm;
+ Bytef *buf;
+ unsigned size;
+{
+ unsigned len = strm->avail_in;
+
+ if (len > size) len = size;
+ if (len == 0) return 0;
+
+ strm->avail_in -= len;
+
+ zmemcpy(buf, strm->next_in, len);
+ if (strm->state->wrap == 1) {
+ strm->adler = adler32(strm->adler, buf, len);
+ }
+#ifdef GZIP
+ else if (strm->state->wrap == 2) {
+ strm->adler = crc32(strm->adler, buf, len);
+ }
+#endif
+ strm->next_in += len;
+ strm->total_in += len;
+
+ return (int)len;
+}
+
+/* ===========================================================================
+ * Initialize the "longest match" routines for a new zlib stream
+ */
+local void lm_init (s)
+ deflate_state *s;
+{
+ s->window_size = (ulg)2L*s->w_size;
+
+ CLEAR_HASH(s);
+
+ /* Set the default configuration parameters:
+ */
+ s->max_lazy_match = configuration_table[s->level].max_lazy;
+ s->good_match = configuration_table[s->level].good_length;
+ s->nice_match = configuration_table[s->level].nice_length;
+ s->max_chain_length = configuration_table[s->level].max_chain;
+
+ s->strstart = 0;
+ s->block_start = 0L;
+ s->lookahead = 0;
+ s->insert = 0;
+ s->match_length = s->prev_length = MIN_MATCH-1;
+ s->match_available = 0;
+ s->ins_h = 0;
+#ifndef FASTEST
+#ifdef ASMV
+ match_init(); /* initialize the asm code */
+#endif
+#endif
+}
+
+#ifndef FASTEST
+/* ===========================================================================
+ * Set match_start to the longest match starting at the given string and
+ * return its length. Matches shorter or equal to prev_length are discarded,
+ * in which case the result is equal to prev_length and match_start is
+ * garbage.
+ * IN assertions: cur_match is the head of the hash chain for the current
+ * string (strstart) and its distance is <= MAX_DIST, and prev_length >= 1
+ * OUT assertion: the match length is not greater than s->lookahead.
+ */
+#ifndef ASMV
+/* For 80x86 and 680x0, an optimized version will be provided in match.asm or
+ * match.S. The code will be functionally equivalent.
+ */
+local uInt longest_match(s, cur_match)
+ deflate_state *s;
+ IPos cur_match; /* current match */
+{
+ unsigned chain_length = s->max_chain_length;/* max hash chain length */
+ register Bytef *scan = s->window + s->strstart; /* current string */
+ register Bytef *match; /* matched string */
+ register int len; /* length of current match */
+ int best_len = s->prev_length; /* best match length so far */
+ int nice_match = s->nice_match; /* stop if match long enough */
+ IPos limit = s->strstart > (IPos)MAX_DIST(s) ?
+ s->strstart - (IPos)MAX_DIST(s) : NIL;
+ /* Stop when cur_match becomes <= limit. To simplify the code,
+ * we prevent matches with the string of window index 0.
+ */
+ Posf *prev = s->prev;
+ uInt wmask = s->w_mask;
+
+#ifdef UNALIGNED_OK
+ /* Compare two bytes at a time. Note: this is not always beneficial.
+ * Try with and without -DUNALIGNED_OK to check.
+ */
+ register Bytef *strend = s->window + s->strstart + MAX_MATCH - 1;
+ register ush scan_start = *(ushf*)scan;
+ register ush scan_end = *(ushf*)(scan+best_len-1);
+#else
+ register Bytef *strend = s->window + s->strstart + MAX_MATCH;
+ register Byte scan_end1 = scan[best_len-1];
+ register Byte scan_end = scan[best_len];
+#endif
+
+ /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16.
+ * It is easy to get rid of this optimization if necessary.
+ */
+ Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever");
+
+ /* Do not waste too much time if we already have a good match: */
+ if (s->prev_length >= s->good_match) {
+ chain_length >>= 2;
+ }
+ /* Do not look for matches beyond the end of the input. This is necessary
+ * to make deflate deterministic.
+ */
+ if ((uInt)nice_match > s->lookahead) nice_match = s->lookahead;
+
+ Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead");
+
+ do {
+ Assert(cur_match < s->strstart, "no future");
+ match = s->window + cur_match;
+
+ /* Skip to next match if the match length cannot increase
+ * or if the match length is less than 2. Note that the checks below
+ * for insufficient lookahead only occur occasionally for performance
+ * reasons. Therefore uninitialized memory will be accessed, and
+ * conditional jumps will be made that depend on those values.
+ * However the length of the match is limited to the lookahead, so
+ * the output of deflate is not affected by the uninitialized values.
+ */
+#if (defined(UNALIGNED_OK) && MAX_MATCH == 258)
+ /* This code assumes sizeof(unsigned short) == 2. Do not use
+ * UNALIGNED_OK if your compiler uses a different size.
+ */
+ if (*(ushf*)(match+best_len-1) != scan_end ||
+ *(ushf*)match != scan_start) continue;
+
+ /* It is not necessary to compare scan[2] and match[2] since they are
+ * always equal when the other bytes match, given that the hash keys
+ * are equal and that HASH_BITS >= 8. Compare 2 bytes at a time at
+ * strstart+3, +5, ... up to strstart+257. We check for insufficient
+ * lookahead only every 4th comparison; the 128th check will be made
+ * at strstart+257. If MAX_MATCH-2 is not a multiple of 8, it is
+ * necessary to put more guard bytes at the end of the window, or
+ * to check more often for insufficient lookahead.
+ */
+ Assert(scan[2] == match[2], "scan[2]?");
+ scan++, match++;
+ do {
+ } while (*(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ *(ushf*)(scan+=2) == *(ushf*)(match+=2) &&
+ scan < strend);
+ /* The funny "do {}" generates better code on most compilers */
+
+ /* Here, scan <= window+strstart+257 */
+ Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
+ if (*scan == *match) scan++;
+
+ len = (MAX_MATCH - 1) - (int)(strend-scan);
+ scan = strend - (MAX_MATCH-1);
+
+#else /* UNALIGNED_OK */
+
+ if (match[best_len] != scan_end ||
+ match[best_len-1] != scan_end1 ||
+ *match != *scan ||
+ *++match != scan[1]) continue;
+
+ /* The check at best_len-1 can be removed because it will be made
+ * again later. (This heuristic is not always a win.)
+ * It is not necessary to compare scan[2] and match[2] since they
+ * are always equal when the other bytes match, given that
+ * the hash keys are equal and that HASH_BITS >= 8.
+ */
+ scan += 2, match++;
+ Assert(*scan == *match, "match[2]?");
+
+ /* We check for insufficient lookahead only every 8th comparison;
+ * the 256th check will be made at strstart+258.
+ */
+ do {
+ } while (*++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ scan < strend);
+
+ Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
+
+ len = MAX_MATCH - (int)(strend - scan);
+ scan = strend - MAX_MATCH;
+
+#endif /* UNALIGNED_OK */
+
+ if (len > best_len) {
+ s->match_start = cur_match;
+ best_len = len;
+ if (len >= nice_match) break;
+#ifdef UNALIGNED_OK
+ scan_end = *(ushf*)(scan+best_len-1);
+#else
+ scan_end1 = scan[best_len-1];
+ scan_end = scan[best_len];
+#endif
+ }
+ } while ((cur_match = prev[cur_match & wmask]) > limit
+ && --chain_length != 0);
+
+ if ((uInt)best_len <= s->lookahead) return (uInt)best_len;
+ return s->lookahead;
+}
+#endif /* ASMV */
+
+#else /* FASTEST */
+
+/* ---------------------------------------------------------------------------
+ * Optimized version for FASTEST only
+ */
+local uInt longest_match(s, cur_match)
+ deflate_state *s;
+ IPos cur_match; /* current match */
+{
+ register Bytef *scan = s->window + s->strstart; /* current string */
+ register Bytef *match; /* matched string */
+ register int len; /* length of current match */
+ register Bytef *strend = s->window + s->strstart + MAX_MATCH;
+
+ /* The code is optimized for HASH_BITS >= 8 and MAX_MATCH-2 multiple of 16.
+ * It is easy to get rid of this optimization if necessary.
+ */
+ Assert(s->hash_bits >= 8 && MAX_MATCH == 258, "Code too clever");
+
+ Assert((ulg)s->strstart <= s->window_size-MIN_LOOKAHEAD, "need lookahead");
+
+ Assert(cur_match < s->strstart, "no future");
+
+ match = s->window + cur_match;
+
+ /* Return failure if the match length is less than 2:
+ */
+ if (match[0] != scan[0] || match[1] != scan[1]) return MIN_MATCH-1;
+
+ /* The check at best_len-1 can be removed because it will be made
+ * again later. (This heuristic is not always a win.)
+ * It is not necessary to compare scan[2] and match[2] since they
+ * are always equal when the other bytes match, given that
+ * the hash keys are equal and that HASH_BITS >= 8.
+ */
+ scan += 2, match += 2;
+ Assert(*scan == *match, "match[2]?");
+
+ /* We check for insufficient lookahead only every 8th comparison;
+ * the 256th check will be made at strstart+258.
+ */
+ do {
+ } while (*++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ *++scan == *++match && *++scan == *++match &&
+ scan < strend);
+
+ Assert(scan <= s->window+(unsigned)(s->window_size-1), "wild scan");
+
+ len = MAX_MATCH - (int)(strend - scan);
+
+ if (len < MIN_MATCH) return MIN_MATCH - 1;
+
+ s->match_start = cur_match;
+ return (uInt)len <= s->lookahead ? (uInt)len : s->lookahead;
+}
+
+#endif /* FASTEST */
+
+#ifdef DEBUG
+/* ===========================================================================
+ * Check that the match at match_start is indeed a match.
+ */
+local void check_match(s, start, match, length)
+ deflate_state *s;
+ IPos start, match;
+ int length;
+{
+ /* check that the match is indeed a match */
+ if (zmemcmp(s->window + match,
+ s->window + start, length) != EQUAL) {
+ fprintf(stderr, " start %u, match %u, length %d\n",
+ start, match, length);
+ do {
+ fprintf(stderr, "%c%c", s->window[match++], s->window[start++]);
+ } while (--length != 0);
+ z_error("invalid match");
+ }
+ if (z_verbose > 1) {
+ fprintf(stderr,"\\[%d,%d]", start-match, length);
+ do { putc(s->window[start++], stderr); } while (--length != 0);
+ }
+}
+#else
+# define check_match(s, start, match, length)
+#endif /* DEBUG */
+
+/* ===========================================================================
+ * Fill the window when the lookahead becomes insufficient.
+ * Updates strstart and lookahead.
+ *
+ * IN assertion: lookahead < MIN_LOOKAHEAD
+ * OUT assertions: strstart <= window_size-MIN_LOOKAHEAD
+ * At least one byte has been read, or avail_in == 0; reads are
+ * performed for at least two bytes (required for the zip translate_eol
+ * option -- not supported here).
+ */
+local void fill_window(s)
+ deflate_state *s;
+{
+ register unsigned n, m;
+ register Posf *p;
+ unsigned more; /* Amount of free space at the end of the window. */
+ uInt wsize = s->w_size;
+
+ Assert(s->lookahead < MIN_LOOKAHEAD, "already enough lookahead");
+
+ do {
+ more = (unsigned)(s->window_size -(ulg)s->lookahead -(ulg)s->strstart);
+
+ /* Deal with !@#$% 64K limit: */
+ if (sizeof(int) <= 2) {
+ if (more == 0 && s->strstart == 0 && s->lookahead == 0) {
+ more = wsize;
+
+ } else if (more == (unsigned)(-1)) {
+ /* Very unlikely, but possible on 16 bit machine if
+ * strstart == 0 && lookahead == 1 (input done a byte at time)
+ */
+ more--;
+ }
+ }
+
+ /* If the window is almost full and there is insufficient lookahead,
+ * move the upper half to the lower one to make room in the upper half.
+ */
+ if (s->strstart >= wsize+MAX_DIST(s)) {
+
+ zmemcpy(s->window, s->window+wsize, (unsigned)wsize);
+ s->match_start -= wsize;
+ s->strstart -= wsize; /* we now have strstart >= MAX_DIST */
+ s->block_start -= (long) wsize;
+
+ /* Slide the hash table (could be avoided with 32 bit values
+ at the expense of memory usage). We slide even when level == 0
+ to keep the hash table consistent if we switch back to level > 0
+ later. (Using level 0 permanently is not an optimal usage of
+ zlib, so we don't care about this pathological case.)
+ */
+ n = s->hash_size;
+ p = &s->head[n];
+ do {
+ m = *--p;
+ *p = (Pos)(m >= wsize ? m-wsize : NIL);
+ } while (--n);
+
+ n = wsize;
+#ifndef FASTEST
+ p = &s->prev[n];
+ do {
+ m = *--p;
+ *p = (Pos)(m >= wsize ? m-wsize : NIL);
+ /* If n is not on any hash chain, prev[n] is garbage but
+ * its value will never be used.
+ */
+ } while (--n);
+#endif
+ more += wsize;
+ }
+ if (s->strm->avail_in == 0) break;
+
+ /* If there was no sliding:
+ * strstart <= WSIZE+MAX_DIST-1 && lookahead <= MIN_LOOKAHEAD - 1 &&
+ * more == window_size - lookahead - strstart
+ * => more >= window_size - (MIN_LOOKAHEAD-1 + WSIZE + MAX_DIST-1)
+ * => more >= window_size - 2*WSIZE + 2
+ * In the BIG_MEM or MMAP case (not yet supported),
+ * window_size == input_size + MIN_LOOKAHEAD &&
+ * strstart + s->lookahead <= input_size => more >= MIN_LOOKAHEAD.
+ * Otherwise, window_size == 2*WSIZE so more >= 2.
+ * If there was sliding, more >= WSIZE. So in all cases, more >= 2.
+ */
+ Assert(more >= 2, "more < 2");
+
+ n = read_buf(s->strm, s->window + s->strstart + s->lookahead, more);
+ s->lookahead += n;
+
+ /* Initialize the hash value now that we have some input: */
+ if (s->lookahead + s->insert >= MIN_MATCH) {
+ uInt str = s->strstart - s->insert;
+ s->ins_h = s->window[str];
+ UPDATE_HASH(s, s->ins_h, s->window[str + 1]);
+#if MIN_MATCH != 3
+ Call UPDATE_HASH() MIN_MATCH-3 more times
+#endif
+ while (s->insert) {
+ UPDATE_HASH(s, s->ins_h, s->window[str + MIN_MATCH-1]);
+#ifndef FASTEST
+ s->prev[str & s->w_mask] = s->head[s->ins_h];
+#endif
+ s->head[s->ins_h] = (Pos)str;
+ str++;
+ s->insert--;
+ if (s->lookahead + s->insert < MIN_MATCH)
+ break;
+ }
+ }
+ /* If the whole input has less than MIN_MATCH bytes, ins_h is garbage,
+ * but this is not important since only literal bytes will be emitted.
+ */
+
+ } while (s->lookahead < MIN_LOOKAHEAD && s->strm->avail_in != 0);
+
+ /* If the WIN_INIT bytes after the end of the current data have never been
+ * written, then zero those bytes in order to avoid memory check reports of
+ * the use of uninitialized (or uninitialised as Julian writes) bytes by
+ * the longest match routines. Update the high water mark for the next
+ * time through here. WIN_INIT is set to MAX_MATCH since the longest match
+ * routines allow scanning to strstart + MAX_MATCH, ignoring lookahead.
+ */
+ if (s->high_water < s->window_size) {
+ ulg curr = s->strstart + (ulg)(s->lookahead);
+ ulg init;
+
+ if (s->high_water < curr) {
+ /* Previous high water mark below current data -- zero WIN_INIT
+ * bytes or up to end of window, whichever is less.
+ */
+ init = s->window_size - curr;
+ if (init > WIN_INIT)
+ init = WIN_INIT;
+ zmemzero(s->window + curr, (unsigned)init);
+ s->high_water = curr + init;
+ }
+ else if (s->high_water < (ulg)curr + WIN_INIT) {
+ /* High water mark at or above current data, but below current data
+ * plus WIN_INIT -- zero out to current data plus WIN_INIT, or up
+ * to end of window, whichever is less.
+ */
+ init = (ulg)curr + WIN_INIT - s->high_water;
+ if (init > s->window_size - s->high_water)
+ init = s->window_size - s->high_water;
+ zmemzero(s->window + s->high_water, (unsigned)init);
+ s->high_water += init;
+ }
+ }
+
+ Assert((ulg)s->strstart <= s->window_size - MIN_LOOKAHEAD,
+ "not enough room for search");
+}
+
+/* ===========================================================================
+ * Flush the current block, with given end-of-file flag.
+ * IN assertion: strstart is set to the end of the current match.
+ */
+#define FLUSH_BLOCK_ONLY(s, last) { \
+ _tr_flush_block(s, (s->block_start >= 0L ? \
+ (charf *)&s->window[(unsigned)s->block_start] : \
+ (charf *)Z_NULL), \
+ (ulg)((long)s->strstart - s->block_start), \
+ (last)); \
+ s->block_start = s->strstart; \
+ flush_pending(s->strm); \
+ Tracev((stderr,"[FLUSH]")); \
+}
+
+/* Same but force premature exit if necessary. */
+#define FLUSH_BLOCK(s, last) { \
+ FLUSH_BLOCK_ONLY(s, last); \
+ if (s->strm->avail_out == 0) return (last) ? finish_started : need_more; \
+}
+
+/* ===========================================================================
+ * Copy without compression as much as possible from the input stream, return
+ * the current block state.
+ * This function does not insert new strings in the dictionary since
+ * uncompressible data is probably not useful. This function is used
+ * only for the level=0 compression option.
+ * NOTE: this function should be optimized to avoid extra copying from
+ * window to pending_buf.
+ */
+local block_state deflate_stored(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ /* Stored blocks are limited to 0xffff bytes, pending_buf is limited
+ * to pending_buf_size, and each stored block has a 5 byte header:
+ */
+ ulg max_block_size = 0xffff;
+ ulg max_start;
+
+ if (max_block_size > s->pending_buf_size - 5) {
+ max_block_size = s->pending_buf_size - 5;
+ }
+
+ /* Copy as much as possible from input to output: */
+ for (;;) {
+ /* Fill the window as much as possible: */
+ if (s->lookahead <= 1) {
+
+ Assert(s->strstart < s->w_size+MAX_DIST(s) ||
+ s->block_start >= (long)s->w_size, "slide too late");
+
+ fill_window(s);
+ if (s->lookahead == 0 && flush == Z_NO_FLUSH) return need_more;
+
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+ Assert(s->block_start >= 0L, "block gone");
+
+ s->strstart += s->lookahead;
+ s->lookahead = 0;
+
+ /* Emit a stored block if pending_buf will be full: */
+ max_start = s->block_start + max_block_size;
+ if (s->strstart == 0 || (ulg)s->strstart >= max_start) {
+ /* strstart == 0 is possible when wraparound on 16-bit machine */
+ s->lookahead = (uInt)(s->strstart - max_start);
+ s->strstart = (uInt)max_start;
+ FLUSH_BLOCK(s, 0);
+ }
+ /* Flush if we may have to slide, otherwise block_start may become
+ * negative and the data will be gone:
+ */
+ if (s->strstart - (uInt)s->block_start >= MAX_DIST(s)) {
+ FLUSH_BLOCK(s, 0);
+ }
+ }
+ s->insert = 0;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if ((long)s->strstart > s->block_start)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+
+/* ===========================================================================
+ * Compress as much as possible from the input stream, return the current
+ * block state.
+ * This function does not perform lazy evaluation of matches and inserts
+ * new strings in the dictionary only for unmatched strings or for short
+ * matches. It is used only for the fast compression options.
+ */
+local block_state deflate_fast(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ IPos hash_head; /* head of the hash chain */
+ int bflush; /* set if current block must be flushed */
+
+ for (;;) {
+ /* Make sure that we always have enough lookahead, except
+ * at the end of the input file. We need MAX_MATCH bytes
+ * for the next match, plus MIN_MATCH bytes to insert the
+ * string following the next match.
+ */
+ if (s->lookahead < MIN_LOOKAHEAD) {
+ fill_window(s);
+ if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) {
+ return need_more;
+ }
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+
+ /* Insert the string window[strstart .. strstart+2] in the
+ * dictionary, and set hash_head to the head of the hash chain:
+ */
+ hash_head = NIL;
+ if (s->lookahead >= MIN_MATCH) {
+ INSERT_STRING(s, s->strstart, hash_head);
+ }
+
+ /* Find the longest match, discarding those <= prev_length.
+ * At this point we have always match_length < MIN_MATCH
+ */
+ if (hash_head != NIL && s->strstart - hash_head <= MAX_DIST(s)) {
+ /* To simplify the code, we prevent matches with the string
+ * of window index 0 (in particular we have to avoid a match
+ * of the string with itself at the start of the input file).
+ */
+ s->match_length = longest_match (s, hash_head);
+ /* longest_match() sets match_start */
+ }
+ if (s->match_length >= MIN_MATCH) {
+ check_match(s, s->strstart, s->match_start, s->match_length);
+
+ _tr_tally_dist(s, s->strstart - s->match_start,
+ s->match_length - MIN_MATCH, bflush);
+
+ s->lookahead -= s->match_length;
+
+ /* Insert new strings in the hash table only if the match length
+ * is not too large. This saves time but degrades compression.
+ */
+#ifndef FASTEST
+ if (s->match_length <= s->max_insert_length &&
+ s->lookahead >= MIN_MATCH) {
+ s->match_length--; /* string at strstart already in table */
+ do {
+ s->strstart++;
+ INSERT_STRING(s, s->strstart, hash_head);
+ /* strstart never exceeds WSIZE-MAX_MATCH, so there are
+ * always MIN_MATCH bytes ahead.
+ */
+ } while (--s->match_length != 0);
+ s->strstart++;
+ } else
+#endif
+ {
+ s->strstart += s->match_length;
+ s->match_length = 0;
+ s->ins_h = s->window[s->strstart];
+ UPDATE_HASH(s, s->ins_h, s->window[s->strstart+1]);
+#if MIN_MATCH != 3
+ Call UPDATE_HASH() MIN_MATCH-3 more times
+#endif
+ /* If lookahead < MIN_MATCH, ins_h is garbage, but it does not
+ * matter since it will be recomputed at next deflate call.
+ */
+ }
+ } else {
+ /* No match, output a literal byte */
+ Tracevv((stderr,"%c", s->window[s->strstart]));
+ _tr_tally_lit (s, s->window[s->strstart], bflush);
+ s->lookahead--;
+ s->strstart++;
+ }
+ if (bflush) FLUSH_BLOCK(s, 0);
+ }
+ s->insert = s->strstart < MIN_MATCH-1 ? s->strstart : MIN_MATCH-1;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+
+#ifndef FASTEST
+/* ===========================================================================
+ * Same as above, but achieves better compression. We use a lazy
+ * evaluation for matches: a match is finally adopted only if there is
+ * no better match at the next window position.
+ */
+local block_state deflate_slow(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ IPos hash_head; /* head of hash chain */
+ int bflush; /* set if current block must be flushed */
+
+ /* Process the input block. */
+ for (;;) {
+ /* Make sure that we always have enough lookahead, except
+ * at the end of the input file. We need MAX_MATCH bytes
+ * for the next match, plus MIN_MATCH bytes to insert the
+ * string following the next match.
+ */
+ if (s->lookahead < MIN_LOOKAHEAD) {
+ fill_window(s);
+ if (s->lookahead < MIN_LOOKAHEAD && flush == Z_NO_FLUSH) {
+ return need_more;
+ }
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+
+ /* Insert the string window[strstart .. strstart+2] in the
+ * dictionary, and set hash_head to the head of the hash chain:
+ */
+ hash_head = NIL;
+ if (s->lookahead >= MIN_MATCH) {
+ INSERT_STRING(s, s->strstart, hash_head);
+ }
+
+ /* Find the longest match, discarding those <= prev_length.
+ */
+ s->prev_length = s->match_length, s->prev_match = s->match_start;
+ s->match_length = MIN_MATCH-1;
+
+ if (hash_head != NIL && s->prev_length < s->max_lazy_match &&
+ s->strstart - hash_head <= MAX_DIST(s)) {
+ /* To simplify the code, we prevent matches with the string
+ * of window index 0 (in particular we have to avoid a match
+ * of the string with itself at the start of the input file).
+ */
+ s->match_length = longest_match (s, hash_head);
+ /* longest_match() sets match_start */
+
+ if (s->match_length <= 5 && (s->strategy == Z_FILTERED
+#if TOO_FAR <= 32767
+ || (s->match_length == MIN_MATCH &&
+ s->strstart - s->match_start > TOO_FAR)
+#endif
+ )) {
+
+ /* If prev_match is also MIN_MATCH, match_start is garbage
+ * but we will ignore the current match anyway.
+ */
+ s->match_length = MIN_MATCH-1;
+ }
+ }
+ /* If there was a match at the previous step and the current
+ * match is not better, output the previous match:
+ */
+ if (s->prev_length >= MIN_MATCH && s->match_length <= s->prev_length) {
+ uInt max_insert = s->strstart + s->lookahead - MIN_MATCH;
+ /* Do not insert strings in hash table beyond this. */
+
+ check_match(s, s->strstart-1, s->prev_match, s->prev_length);
+
+ _tr_tally_dist(s, s->strstart -1 - s->prev_match,
+ s->prev_length - MIN_MATCH, bflush);
+
+ /* Insert in hash table all strings up to the end of the match.
+ * strstart-1 and strstart are already inserted. If there is not
+ * enough lookahead, the last two strings are not inserted in
+ * the hash table.
+ */
+ s->lookahead -= s->prev_length-1;
+ s->prev_length -= 2;
+ do {
+ if (++s->strstart <= max_insert) {
+ INSERT_STRING(s, s->strstart, hash_head);
+ }
+ } while (--s->prev_length != 0);
+ s->match_available = 0;
+ s->match_length = MIN_MATCH-1;
+ s->strstart++;
+
+ if (bflush) FLUSH_BLOCK(s, 0);
+
+ } else if (s->match_available) {
+ /* If there was no match at the previous position, output a
+ * single literal. If there was a match but the current match
+ * is longer, truncate the previous match to a single literal.
+ */
+ Tracevv((stderr,"%c", s->window[s->strstart-1]));
+ _tr_tally_lit(s, s->window[s->strstart-1], bflush);
+ if (bflush) {
+ FLUSH_BLOCK_ONLY(s, 0);
+ }
+ s->strstart++;
+ s->lookahead--;
+ if (s->strm->avail_out == 0) return need_more;
+ } else {
+ /* There is no previous match to compare with, wait for
+ * the next step to decide.
+ */
+ s->match_available = 1;
+ s->strstart++;
+ s->lookahead--;
+ }
+ }
+ Assert (flush != Z_NO_FLUSH, "no flush?");
+ if (s->match_available) {
+ Tracevv((stderr,"%c", s->window[s->strstart-1]));
+ _tr_tally_lit(s, s->window[s->strstart-1], bflush);
+ s->match_available = 0;
+ }
+ s->insert = s->strstart < MIN_MATCH-1 ? s->strstart : MIN_MATCH-1;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+#endif /* FASTEST */
+
+/* ===========================================================================
+ * For Z_RLE, simply look for runs of bytes, generate matches only of distance
+ * one. Do not maintain a hash table. (It will be regenerated if this run of
+ * deflate switches away from Z_RLE.)
+ */
+local block_state deflate_rle(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ int bflush; /* set if current block must be flushed */
+ uInt prev; /* byte at distance one to match */
+ Bytef *scan, *strend; /* scan goes up to strend for length of run */
+
+ for (;;) {
+ /* Make sure that we always have enough lookahead, except
+ * at the end of the input file. We need MAX_MATCH bytes
+ * for the longest run, plus one for the unrolled loop.
+ */
+ if (s->lookahead <= MAX_MATCH) {
+ fill_window(s);
+ if (s->lookahead <= MAX_MATCH && flush == Z_NO_FLUSH) {
+ return need_more;
+ }
+ if (s->lookahead == 0) break; /* flush the current block */
+ }
+
+ /* See how many times the previous byte repeats */
+ s->match_length = 0;
+ if (s->lookahead >= MIN_MATCH && s->strstart > 0) {
+ scan = s->window + s->strstart - 1;
+ prev = *scan;
+ if (prev == *++scan && prev == *++scan && prev == *++scan) {
+ strend = s->window + s->strstart + MAX_MATCH;
+ do {
+ } while (prev == *++scan && prev == *++scan &&
+ prev == *++scan && prev == *++scan &&
+ prev == *++scan && prev == *++scan &&
+ prev == *++scan && prev == *++scan &&
+ scan < strend);
+ s->match_length = MAX_MATCH - (int)(strend - scan);
+ if (s->match_length > s->lookahead)
+ s->match_length = s->lookahead;
+ }
+ Assert(scan <= s->window+(uInt)(s->window_size-1), "wild scan");
+ }
+
+ /* Emit match if have run of MIN_MATCH or longer, else emit literal */
+ if (s->match_length >= MIN_MATCH) {
+ check_match(s, s->strstart, s->strstart - 1, s->match_length);
+
+ _tr_tally_dist(s, 1, s->match_length - MIN_MATCH, bflush);
+
+ s->lookahead -= s->match_length;
+ s->strstart += s->match_length;
+ s->match_length = 0;
+ } else {
+ /* No match, output a literal byte */
+ Tracevv((stderr,"%c", s->window[s->strstart]));
+ _tr_tally_lit (s, s->window[s->strstart], bflush);
+ s->lookahead--;
+ s->strstart++;
+ }
+ if (bflush) FLUSH_BLOCK(s, 0);
+ }
+ s->insert = 0;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
+
+/* ===========================================================================
+ * For Z_HUFFMAN_ONLY, do not look for matches. Do not maintain a hash table.
+ * (It will be regenerated if this run of deflate switches away from Huffman.)
+ */
+local block_state deflate_huff(s, flush)
+ deflate_state *s;
+ int flush;
+{
+ int bflush; /* set if current block must be flushed */
+
+ for (;;) {
+ /* Make sure that we have a literal to write. */
+ if (s->lookahead == 0) {
+ fill_window(s);
+ if (s->lookahead == 0) {
+ if (flush == Z_NO_FLUSH)
+ return need_more;
+ break; /* flush the current block */
+ }
+ }
+
+ /* Output a literal byte */
+ s->match_length = 0;
+ Tracevv((stderr,"%c", s->window[s->strstart]));
+ _tr_tally_lit (s, s->window[s->strstart], bflush);
+ s->lookahead--;
+ s->strstart++;
+ if (bflush) FLUSH_BLOCK(s, 0);
+ }
+ s->insert = 0;
+ if (flush == Z_FINISH) {
+ FLUSH_BLOCK(s, 1);
+ return finish_done;
+ }
+ if (s->last_lit)
+ FLUSH_BLOCK(s, 0);
+ return block_done;
+}
--- /dev/null
+/* deflate.h -- internal compression state
+ * Copyright (C) 1995-2012 Jean-loup Gailly
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* @(#) $Id$ */
+
+#ifndef DEFLATE_H
+#define DEFLATE_H
+
+#include "zutil.h"
+
+/* define NO_GZIP when compiling if you want to disable gzip header and
+ trailer creation by deflate(). NO_GZIP would be used to avoid linking in
+ the crc code when it is not needed. For shared libraries, gzip encoding
+ should be left enabled. */
+#ifndef NO_GZIP
+# define GZIP
+#endif
+
+/* ===========================================================================
+ * Internal compression state.
+ */
+
+#define LENGTH_CODES 29
+/* number of length codes, not counting the special END_BLOCK code */
+
+#define LITERALS 256
+/* number of literal bytes 0..255 */
+
+#define L_CODES (LITERALS+1+LENGTH_CODES)
+/* number of Literal or Length codes, including the END_BLOCK code */
+
+#define D_CODES 30
+/* number of distance codes */
+
+#define BL_CODES 19
+/* number of codes used to transfer the bit lengths */
+
+#define HEAP_SIZE (2*L_CODES+1)
+/* maximum heap size */
+
+#define MAX_BITS 15
+/* All codes must not exceed MAX_BITS bits */
+
+#define Buf_size 16
+/* size of bit buffer in bi_buf */
+
+#define INIT_STATE 42
+#define EXTRA_STATE 69
+#define NAME_STATE 73
+#define COMMENT_STATE 91
+#define HCRC_STATE 103
+#define BUSY_STATE 113
+#define FINISH_STATE 666
+/* Stream status */
+
+
+/* Data structure describing a single value and its code string. */
+typedef struct ct_data_s {
+ union {
+ ush freq; /* frequency count */
+ ush code; /* bit string */
+ } fc;
+ union {
+ ush dad; /* father node in Huffman tree */
+ ush len; /* length of bit string */
+ } dl;
+} FAR ct_data;
+
+#define Freq fc.freq
+#define Code fc.code
+#define Dad dl.dad
+#define Len dl.len
+
+typedef struct static_tree_desc_s static_tree_desc;
+
+typedef struct tree_desc_s {
+ ct_data *dyn_tree; /* the dynamic tree */
+ int max_code; /* largest code with non zero frequency */
+ static_tree_desc *stat_desc; /* the corresponding static tree */
+} FAR tree_desc;
+
+typedef ush Pos;
+typedef Pos FAR Posf;
+typedef unsigned IPos;
+
+/* A Pos is an index in the character window. We use short instead of int to
+ * save space in the various tables. IPos is used only for parameter passing.
+ */
+
+typedef struct internal_state {
+ z_streamp strm; /* pointer back to this zlib stream */
+ int status; /* as the name implies */
+ Bytef *pending_buf; /* output still pending */
+ ulg pending_buf_size; /* size of pending_buf */
+ Bytef *pending_out; /* next pending byte to output to the stream */
+ uInt pending; /* nb of bytes in the pending buffer */
+ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
+ gz_headerp gzhead; /* gzip header information to write */
+ uInt gzindex; /* where in extra, name, or comment */
+ Byte method; /* can only be DEFLATED */
+ int last_flush; /* value of flush param for previous deflate call */
+
+ /* used by deflate.c: */
+
+ uInt w_size; /* LZ77 window size (32K by default) */
+ uInt w_bits; /* log2(w_size) (8..16) */
+ uInt w_mask; /* w_size - 1 */
+
+ Bytef *window;
+ /* Sliding window. Input bytes are read into the second half of the window,
+ * and move to the first half later to keep a dictionary of at least wSize
+ * bytes. With this organization, matches are limited to a distance of
+ * wSize-MAX_MATCH bytes, but this ensures that IO is always
+ * performed with a length multiple of the block size. Also, it limits
+ * the window size to 64K, which is quite useful on MSDOS.
+ * To do: use the user input buffer as sliding window.
+ */
+
+ ulg window_size;
+ /* Actual size of window: 2*wSize, except when the user input buffer
+ * is directly used as sliding window.
+ */
+
+ Posf *prev;
+ /* Link to older string with same hash index. To limit the size of this
+ * array to 64K, this link is maintained only for the last 32K strings.
+ * An index in this array is thus a window index modulo 32K.
+ */
+
+ Posf *head; /* Heads of the hash chains or NIL. */
+
+ uInt ins_h; /* hash index of string to be inserted */
+ uInt hash_size; /* number of elements in hash table */
+ uInt hash_bits; /* log2(hash_size) */
+ uInt hash_mask; /* hash_size-1 */
+
+ uInt hash_shift;
+ /* Number of bits by which ins_h must be shifted at each input
+ * step. It must be such that after MIN_MATCH steps, the oldest
+ * byte no longer takes part in the hash key, that is:
+ * hash_shift * MIN_MATCH >= hash_bits
+ */
+
+ long block_start;
+ /* Window position at the beginning of the current output block. Gets
+ * negative when the window is moved backwards.
+ */
+
+ uInt match_length; /* length of best match */
+ IPos prev_match; /* previous match */
+ int match_available; /* set if previous match exists */
+ uInt strstart; /* start of string to insert */
+ uInt match_start; /* start of matching string */
+ uInt lookahead; /* number of valid bytes ahead in window */
+
+ uInt prev_length;
+ /* Length of the best match at previous step. Matches not greater than this
+ * are discarded. This is used in the lazy match evaluation.
+ */
+
+ uInt max_chain_length;
+ /* To speed up deflation, hash chains are never searched beyond this
+ * length. A higher limit improves compression ratio but degrades the
+ * speed.
+ */
+
+ uInt max_lazy_match;
+ /* Attempt to find a better match only when the current match is strictly
+ * smaller than this value. This mechanism is used only for compression
+ * levels >= 4.
+ */
+# define max_insert_length max_lazy_match
+ /* Insert new strings in the hash table only if the match length is not
+ * greater than this length. This saves time but degrades compression.
+ * max_insert_length is used only for compression levels <= 3.
+ */
+
+ int level; /* compression level (1..9) */
+ int strategy; /* favor or force Huffman coding*/
+
+ uInt good_match;
+ /* Use a faster search when the previous match is longer than this */
+
+ int nice_match; /* Stop searching when current match exceeds this */
+
+ /* used by trees.c: */
+ /* Didn't use ct_data typedef below to suppress compiler warning */
+ struct ct_data_s dyn_ltree[HEAP_SIZE]; /* literal and length tree */
+ struct ct_data_s dyn_dtree[2*D_CODES+1]; /* distance tree */
+ struct ct_data_s bl_tree[2*BL_CODES+1]; /* Huffman tree for bit lengths */
+
+ struct tree_desc_s l_desc; /* desc. for literal tree */
+ struct tree_desc_s d_desc; /* desc. for distance tree */
+ struct tree_desc_s bl_desc; /* desc. for bit length tree */
+
+ ush bl_count[MAX_BITS+1];
+ /* number of codes at each bit length for an optimal tree */
+
+ int heap[2*L_CODES+1]; /* heap used to build the Huffman trees */
+ int heap_len; /* number of elements in the heap */
+ int heap_max; /* element of largest frequency */
+ /* The sons of heap[n] are heap[2*n] and heap[2*n+1]. heap[0] is not used.
+ * The same heap array is used to build all trees.
+ */
+
+ uch depth[2*L_CODES+1];
+ /* Depth of each subtree used as tie breaker for trees of equal frequency
+ */
+
+ uchf *l_buf; /* buffer for literals or lengths */
+
+ uInt lit_bufsize;
+ /* Size of match buffer for literals/lengths. There are 4 reasons for
+ * limiting lit_bufsize to 64K:
+ * - frequencies can be kept in 16 bit counters
+ * - if compression is not successful for the first block, all input
+ * data is still in the window so we can still emit a stored block even
+ * when input comes from standard input. (This can also be done for
+ * all blocks if lit_bufsize is not greater than 32K.)
+ * - if compression is not successful for a file smaller than 64K, we can
+ * even emit a stored file instead of a stored block (saving 5 bytes).
+ * This is applicable only for zip (not gzip or zlib).
+ * - creating new Huffman trees less frequently may not provide fast
+ * adaptation to changes in the input data statistics. (Take for
+ * example a binary file with poorly compressible code followed by
+ * a highly compressible string table.) Smaller buffer sizes give
+ * fast adaptation but have of course the overhead of transmitting
+ * trees more frequently.
+ * - I can't count above 4
+ */
+
+ uInt last_lit; /* running index in l_buf */
+
+ ushf *d_buf;
+ /* Buffer for distances. To simplify the code, d_buf and l_buf have
+ * the same number of elements. To use different lengths, an extra flag
+ * array would be necessary.
+ */
+
+ ulg opt_len; /* bit length of current block with optimal trees */
+ ulg static_len; /* bit length of current block with static trees */
+ uInt matches; /* number of string matches in current block */
+ uInt insert; /* bytes at end of window left to insert */
+
+#ifdef DEBUG
+ ulg compressed_len; /* total bit length of compressed file mod 2^32 */
+ ulg bits_sent; /* bit length of compressed data sent mod 2^32 */
+#endif
+
+ ush bi_buf;
+ /* Output buffer. bits are inserted starting at the bottom (least
+ * significant bits).
+ */
+ int bi_valid;
+ /* Number of valid bits in bi_buf. All bits above the last valid bit
+ * are always zero.
+ */
+
+ ulg high_water;
+ /* High water mark offset in window for initialized bytes -- bytes above
+ * this are set to zero in order to avoid memory check warnings when
+ * longest match routines access bytes past the input. This is then
+ * updated to the new high water mark.
+ */
+
+} FAR deflate_state;
+
+/* Output a byte on the stream.
+ * IN assertion: there is enough room in pending_buf.
+ */
+#define put_byte(s, c) {s->pending_buf[s->pending++] = (c);}
+
+
+#define MIN_LOOKAHEAD (MAX_MATCH+MIN_MATCH+1)
+/* Minimum amount of lookahead, except at the end of the input file.
+ * See deflate.c for comments about the MIN_MATCH+1.
+ */
+
+#define MAX_DIST(s) ((s)->w_size-MIN_LOOKAHEAD)
+/* In order to simplify the code, particularly on 16 bit machines, match
+ * distances are limited to MAX_DIST instead of WSIZE.
+ */
+
+#define WIN_INIT MAX_MATCH
+/* Number of bytes after end of data in window to initialize in order to avoid
+ memory checker errors from longest match routines */
+
+ /* in trees.c */
+void ZLIB_INTERNAL _tr_init OF((deflate_state *s));
+int ZLIB_INTERNAL _tr_tally OF((deflate_state *s, unsigned dist, unsigned lc));
+void ZLIB_INTERNAL _tr_flush_block OF((deflate_state *s, charf *buf,
+ ulg stored_len, int last));
+void ZLIB_INTERNAL _tr_flush_bits OF((deflate_state *s));
+void ZLIB_INTERNAL _tr_align OF((deflate_state *s));
+void ZLIB_INTERNAL _tr_stored_block OF((deflate_state *s, charf *buf,
+ ulg stored_len, int last));
+
+#define d_code(dist) \
+ ((dist) < 256 ? _dist_code[dist] : _dist_code[256+((dist)>>7)])
+/* Mapping from a distance to a distance code. dist is the distance - 1 and
+ * must not have side effects. _dist_code[256] and _dist_code[257] are never
+ * used.
+ */
+
+#ifndef DEBUG
+/* Inline versions of _tr_tally for speed: */
+
+#if defined(GEN_TREES_H) || !defined(STDC)
+ extern uch ZLIB_INTERNAL _length_code[];
+ extern uch ZLIB_INTERNAL _dist_code[];
+#else
+ extern const uch ZLIB_INTERNAL _length_code[];
+ extern const uch ZLIB_INTERNAL _dist_code[];
+#endif
+
+# define _tr_tally_lit(s, c, flush) \
+ { uch cc = (c); \
+ s->d_buf[s->last_lit] = 0; \
+ s->l_buf[s->last_lit++] = cc; \
+ s->dyn_ltree[cc].Freq++; \
+ flush = (s->last_lit == s->lit_bufsize-1); \
+ }
+# define _tr_tally_dist(s, distance, length, flush) \
+ { uch len = (length); \
+ ush dist = (distance); \
+ s->d_buf[s->last_lit] = dist; \
+ s->l_buf[s->last_lit++] = len; \
+ dist--; \
+ s->dyn_ltree[_length_code[len]+LITERALS+1].Freq++; \
+ s->dyn_dtree[d_code(dist)].Freq++; \
+ flush = (s->last_lit == s->lit_bufsize-1); \
+ }
+#else
+# define _tr_tally_lit(s, c, flush) flush = _tr_tally(s, 0, c)
+# define _tr_tally_dist(s, distance, length, flush) \
+ flush = _tr_tally(s, distance, length)
+#endif
+
+#endif /* DEFLATE_H */
--- /dev/null
+/* inffast.c -- fast decoding
+ * Copyright (C) 1995-2008, 2010, 2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "zutil.h"
+#include "inftrees.h"
+#include "inflate.h"
+#include "inffast.h"
+
+#ifndef ASMINF
+
+/* Allow machine dependent optimization for post-increment or pre-increment.
+ Based on testing to date,
+ Pre-increment preferred for:
+ - PowerPC G3 (Adler)
+ - MIPS R5000 (Randers-Pehrson)
+ Post-increment preferred for:
+ - none
+ No measurable difference:
+ - Pentium III (Anderson)
+ - M68060 (Nikl)
+ */
+#ifdef POSTINC
+# define OFF 0
+# define PUP(a) *(a)++
+#else
+# define OFF 1
+# define PUP(a) *++(a)
+#endif
+
+/*
+ Decode literal, length, and distance codes and write out the resulting
+ literal and match bytes until either not enough input or output is
+ available, an end-of-block is encountered, or a data error is encountered.
+ When large enough input and output buffers are supplied to inflate(), for
+ example, a 16K input buffer and a 64K output buffer, more than 95% of the
+ inflate execution time is spent in this routine.
+
+ Entry assumptions:
+
+ state->mode == LEN
+ strm->avail_in >= 6
+ strm->avail_out >= 258
+ start >= strm->avail_out
+ state->bits < 8
+
+ On return, state->mode is one of:
+
+ LEN -- ran out of enough output space or enough available input
+ TYPE -- reached end of block code, inflate() to interpret next block
+ BAD -- error in block data
+
+ Notes:
+
+ - The maximum input bits used by a length/distance pair is 15 bits for the
+ length code, 5 bits for the length extra, 15 bits for the distance code,
+ and 13 bits for the distance extra. This totals 48 bits, or six bytes.
+ Therefore if strm->avail_in >= 6, then there is enough input to avoid
+ checking for available input while decoding.
+
+ - The maximum bytes that a single length/distance pair can output is 258
+ bytes, which is the maximum length that can be coded. inflate_fast()
+ requires strm->avail_out >= 258 for each loop to avoid checking for
+ output space.
+ */
+void ZLIB_INTERNAL inflate_fast(strm, start)
+z_streamp strm;
+unsigned start; /* inflate()'s starting value for strm->avail_out */
+{
+ struct inflate_state FAR *state;
+ z_const unsigned char FAR *in; /* local strm->next_in */
+ z_const unsigned char FAR *last; /* have enough input while in < last */
+ unsigned char FAR *out; /* local strm->next_out */
+ unsigned char FAR *beg; /* inflate()'s initial strm->next_out */
+ unsigned char FAR *end; /* while out < end, enough space available */
+#ifdef INFLATE_STRICT
+ unsigned dmax; /* maximum distance from zlib header */
+#endif
+ unsigned wsize; /* window size or zero if not using window */
+ unsigned whave; /* valid bytes in the window */
+ unsigned wnext; /* window write index */
+ unsigned char FAR *window; /* allocated sliding window, if wsize != 0 */
+ unsigned long hold; /* local strm->hold */
+ unsigned bits; /* local strm->bits */
+ code const FAR *lcode; /* local strm->lencode */
+ code const FAR *dcode; /* local strm->distcode */
+ unsigned lmask; /* mask for first level of length codes */
+ unsigned dmask; /* mask for first level of distance codes */
+ code here; /* retrieved table entry */
+ unsigned op; /* code bits, operation, extra bits, or */
+ /* window position, window bytes to copy */
+ unsigned len; /* match length, unused bytes */
+ unsigned dist; /* match distance */
+ unsigned char FAR *from; /* where to copy match from */
+
+ /* copy state to local variables */
+ state = (struct inflate_state FAR *)strm->state;
+ in = strm->next_in - OFF;
+ last = in + (strm->avail_in - 5);
+ out = strm->next_out - OFF;
+ beg = out - (start - strm->avail_out);
+ end = out + (strm->avail_out - 257);
+#ifdef INFLATE_STRICT
+ dmax = state->dmax;
+#endif
+ wsize = state->wsize;
+ whave = state->whave;
+ wnext = state->wnext;
+ window = state->window;
+ hold = state->hold;
+ bits = state->bits;
+ lcode = state->lencode;
+ dcode = state->distcode;
+ lmask = (1U << state->lenbits) - 1;
+ dmask = (1U << state->distbits) - 1;
+
+ /* decode literals and length/distances until end-of-block or not enough
+ input data or output space */
+ do {
+ if (bits < 15) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ here = lcode[hold & lmask];
+ dolen:
+ op = (unsigned)(here.bits);
+ hold >>= op;
+ bits -= op;
+ op = (unsigned)(here.op);
+ if (op == 0) { /* literal */
+ Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+ "inflate: literal '%c'\n" :
+ "inflate: literal 0x%02x\n", here.val));
+ PUP(out) = (unsigned char)(here.val);
+ }
+ else if (op & 16) { /* length base */
+ len = (unsigned)(here.val);
+ op &= 15; /* number of extra bits */
+ if (op) {
+ if (bits < op) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ len += (unsigned)hold & ((1U << op) - 1);
+ hold >>= op;
+ bits -= op;
+ }
+ Tracevv((stderr, "inflate: length %u\n", len));
+ if (bits < 15) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ here = dcode[hold & dmask];
+ dodist:
+ op = (unsigned)(here.bits);
+ hold >>= op;
+ bits -= op;
+ op = (unsigned)(here.op);
+ if (op & 16) { /* distance base */
+ dist = (unsigned)(here.val);
+ op &= 15; /* number of extra bits */
+ if (bits < op) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ if (bits < op) {
+ hold += (unsigned long)(PUP(in)) << bits;
+ bits += 8;
+ }
+ }
+ dist += (unsigned)hold & ((1U << op) - 1);
+#ifdef INFLATE_STRICT
+ if (dist > dmax) {
+ strm->msg = (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#endif
+ hold >>= op;
+ bits -= op;
+ Tracevv((stderr, "inflate: distance %u\n", dist));
+ op = (unsigned)(out - beg); /* max distance in output */
+ if (dist > op) { /* see if copy from window */
+ op = dist - op; /* distance back in window */
+ if (op > whave) {
+ if (state->sane) {
+ strm->msg =
+ (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+ if (len <= op - whave) {
+ do {
+ PUP(out) = 0;
+ } while (--len);
+ continue;
+ }
+ len -= op - whave;
+ do {
+ PUP(out) = 0;
+ } while (--op > whave);
+ if (op == 0) {
+ from = out - dist;
+ do {
+ PUP(out) = PUP(from);
+ } while (--len);
+ continue;
+ }
+#endif
+ }
+ from = window - OFF;
+ if (wnext == 0) { /* very common case */
+ from += wsize - op;
+ if (op < len) { /* some from window */
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = out - dist; /* rest from output */
+ }
+ }
+ else if (wnext < op) { /* wrap around window */
+ from += wsize + wnext - op;
+ op -= wnext;
+ if (op < len) { /* some from end of window */
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = window - OFF;
+ if (wnext < len) { /* some from start of window */
+ op = wnext;
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = out - dist; /* rest from output */
+ }
+ }
+ }
+ else { /* contiguous in window */
+ from += wnext - op;
+ if (op < len) { /* some from window */
+ len -= op;
+ do {
+ PUP(out) = PUP(from);
+ } while (--op);
+ from = out - dist; /* rest from output */
+ }
+ }
+ while (len > 2) {
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ len -= 3;
+ }
+ if (len) {
+ PUP(out) = PUP(from);
+ if (len > 1)
+ PUP(out) = PUP(from);
+ }
+ }
+ else {
+ from = out - dist; /* copy direct from output */
+ do { /* minimum length is three */
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ PUP(out) = PUP(from);
+ len -= 3;
+ } while (len > 2);
+ if (len) {
+ PUP(out) = PUP(from);
+ if (len > 1)
+ PUP(out) = PUP(from);
+ }
+ }
+ }
+ else if ((op & 64) == 0) { /* 2nd level distance code */
+ here = dcode[here.val + (hold & ((1U << op) - 1))];
+ goto dodist;
+ }
+ else {
+ strm->msg = (char *)"invalid distance code";
+ state->mode = BAD;
+ break;
+ }
+ }
+ else if ((op & 64) == 0) { /* 2nd level length code */
+ here = lcode[here.val + (hold & ((1U << op) - 1))];
+ goto dolen;
+ }
+ else if (op & 32) { /* end-of-block */
+ Tracevv((stderr, "inflate: end of block\n"));
+ state->mode = TYPE;
+ break;
+ }
+ else {
+ strm->msg = (char *)"invalid literal/length code";
+ state->mode = BAD;
+ break;
+ }
+ } while (in < last && out < end);
+
+ /* return unused bytes (on entry, bits < 8, so in won't go too far back) */
+ len = bits >> 3;
+ in -= len;
+ bits -= len << 3;
+ hold &= (1U << bits) - 1;
+
+ /* update state and return */
+ strm->next_in = in + OFF;
+ strm->next_out = out + OFF;
+ strm->avail_in = (unsigned)(in < last ? 5 + (last - in) : 5 - (in - last));
+ strm->avail_out = (unsigned)(out < end ?
+ 257 + (end - out) : 257 - (out - end));
+ state->hold = hold;
+ state->bits = bits;
+ return;
+}
+
+/*
+ inflate_fast() speedups that turned out slower (on a PowerPC G3 750CXe):
+ - Using bit fields for code structure
+ - Different op definition to avoid & for extra bits (do & for table bits)
+ - Three separate decoding do-loops for direct, window, and wnext == 0
+ - Special case for distance > 1 copies to do overlapped load and store copy
+ - Explicit branch predictions (based on measured branch probabilities)
+ - Deferring match copy and interspersed it with decoding subsequent codes
+ - Swapping literal/length else
+ - Swapping window/direct else
+ - Larger unrolled copy loops (three is about right)
+ - Moving len -= 3 statement into middle of loop
+ */
+
+#endif /* !ASMINF */
--- /dev/null
+/* inffast.h -- header to use inffast.c
+ * Copyright (C) 1995-2003, 2010 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+void ZLIB_INTERNAL inflate_fast OF((z_streamp strm, unsigned start));
--- /dev/null
+ /* inffixed.h -- table for decoding fixed codes
+ * Generated automatically by makefixed().
+ */
+
+ /* WARNING: this file should *not* be used by applications.
+ It is part of the implementation of this library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+ static const code lenfix[512] = {
+ {96,7,0},{0,8,80},{0,8,16},{20,8,115},{18,7,31},{0,8,112},{0,8,48},
+ {0,9,192},{16,7,10},{0,8,96},{0,8,32},{0,9,160},{0,8,0},{0,8,128},
+ {0,8,64},{0,9,224},{16,7,6},{0,8,88},{0,8,24},{0,9,144},{19,7,59},
+ {0,8,120},{0,8,56},{0,9,208},{17,7,17},{0,8,104},{0,8,40},{0,9,176},
+ {0,8,8},{0,8,136},{0,8,72},{0,9,240},{16,7,4},{0,8,84},{0,8,20},
+ {21,8,227},{19,7,43},{0,8,116},{0,8,52},{0,9,200},{17,7,13},{0,8,100},
+ {0,8,36},{0,9,168},{0,8,4},{0,8,132},{0,8,68},{0,9,232},{16,7,8},
+ {0,8,92},{0,8,28},{0,9,152},{20,7,83},{0,8,124},{0,8,60},{0,9,216},
+ {18,7,23},{0,8,108},{0,8,44},{0,9,184},{0,8,12},{0,8,140},{0,8,76},
+ {0,9,248},{16,7,3},{0,8,82},{0,8,18},{21,8,163},{19,7,35},{0,8,114},
+ {0,8,50},{0,9,196},{17,7,11},{0,8,98},{0,8,34},{0,9,164},{0,8,2},
+ {0,8,130},{0,8,66},{0,9,228},{16,7,7},{0,8,90},{0,8,26},{0,9,148},
+ {20,7,67},{0,8,122},{0,8,58},{0,9,212},{18,7,19},{0,8,106},{0,8,42},
+ {0,9,180},{0,8,10},{0,8,138},{0,8,74},{0,9,244},{16,7,5},{0,8,86},
+ {0,8,22},{64,8,0},{19,7,51},{0,8,118},{0,8,54},{0,9,204},{17,7,15},
+ {0,8,102},{0,8,38},{0,9,172},{0,8,6},{0,8,134},{0,8,70},{0,9,236},
+ {16,7,9},{0,8,94},{0,8,30},{0,9,156},{20,7,99},{0,8,126},{0,8,62},
+ {0,9,220},{18,7,27},{0,8,110},{0,8,46},{0,9,188},{0,8,14},{0,8,142},
+ {0,8,78},{0,9,252},{96,7,0},{0,8,81},{0,8,17},{21,8,131},{18,7,31},
+ {0,8,113},{0,8,49},{0,9,194},{16,7,10},{0,8,97},{0,8,33},{0,9,162},
+ {0,8,1},{0,8,129},{0,8,65},{0,9,226},{16,7,6},{0,8,89},{0,8,25},
+ {0,9,146},{19,7,59},{0,8,121},{0,8,57},{0,9,210},{17,7,17},{0,8,105},
+ {0,8,41},{0,9,178},{0,8,9},{0,8,137},{0,8,73},{0,9,242},{16,7,4},
+ {0,8,85},{0,8,21},{16,8,258},{19,7,43},{0,8,117},{0,8,53},{0,9,202},
+ {17,7,13},{0,8,101},{0,8,37},{0,9,170},{0,8,5},{0,8,133},{0,8,69},
+ {0,9,234},{16,7,8},{0,8,93},{0,8,29},{0,9,154},{20,7,83},{0,8,125},
+ {0,8,61},{0,9,218},{18,7,23},{0,8,109},{0,8,45},{0,9,186},{0,8,13},
+ {0,8,141},{0,8,77},{0,9,250},{16,7,3},{0,8,83},{0,8,19},{21,8,195},
+ {19,7,35},{0,8,115},{0,8,51},{0,9,198},{17,7,11},{0,8,99},{0,8,35},
+ {0,9,166},{0,8,3},{0,8,131},{0,8,67},{0,9,230},{16,7,7},{0,8,91},
+ {0,8,27},{0,9,150},{20,7,67},{0,8,123},{0,8,59},{0,9,214},{18,7,19},
+ {0,8,107},{0,8,43},{0,9,182},{0,8,11},{0,8,139},{0,8,75},{0,9,246},
+ {16,7,5},{0,8,87},{0,8,23},{64,8,0},{19,7,51},{0,8,119},{0,8,55},
+ {0,9,206},{17,7,15},{0,8,103},{0,8,39},{0,9,174},{0,8,7},{0,8,135},
+ {0,8,71},{0,9,238},{16,7,9},{0,8,95},{0,8,31},{0,9,158},{20,7,99},
+ {0,8,127},{0,8,63},{0,9,222},{18,7,27},{0,8,111},{0,8,47},{0,9,190},
+ {0,8,15},{0,8,143},{0,8,79},{0,9,254},{96,7,0},{0,8,80},{0,8,16},
+ {20,8,115},{18,7,31},{0,8,112},{0,8,48},{0,9,193},{16,7,10},{0,8,96},
+ {0,8,32},{0,9,161},{0,8,0},{0,8,128},{0,8,64},{0,9,225},{16,7,6},
+ {0,8,88},{0,8,24},{0,9,145},{19,7,59},{0,8,120},{0,8,56},{0,9,209},
+ {17,7,17},{0,8,104},{0,8,40},{0,9,177},{0,8,8},{0,8,136},{0,8,72},
+ {0,9,241},{16,7,4},{0,8,84},{0,8,20},{21,8,227},{19,7,43},{0,8,116},
+ {0,8,52},{0,9,201},{17,7,13},{0,8,100},{0,8,36},{0,9,169},{0,8,4},
+ {0,8,132},{0,8,68},{0,9,233},{16,7,8},{0,8,92},{0,8,28},{0,9,153},
+ {20,7,83},{0,8,124},{0,8,60},{0,9,217},{18,7,23},{0,8,108},{0,8,44},
+ {0,9,185},{0,8,12},{0,8,140},{0,8,76},{0,9,249},{16,7,3},{0,8,82},
+ {0,8,18},{21,8,163},{19,7,35},{0,8,114},{0,8,50},{0,9,197},{17,7,11},
+ {0,8,98},{0,8,34},{0,9,165},{0,8,2},{0,8,130},{0,8,66},{0,9,229},
+ {16,7,7},{0,8,90},{0,8,26},{0,9,149},{20,7,67},{0,8,122},{0,8,58},
+ {0,9,213},{18,7,19},{0,8,106},{0,8,42},{0,9,181},{0,8,10},{0,8,138},
+ {0,8,74},{0,9,245},{16,7,5},{0,8,86},{0,8,22},{64,8,0},{19,7,51},
+ {0,8,118},{0,8,54},{0,9,205},{17,7,15},{0,8,102},{0,8,38},{0,9,173},
+ {0,8,6},{0,8,134},{0,8,70},{0,9,237},{16,7,9},{0,8,94},{0,8,30},
+ {0,9,157},{20,7,99},{0,8,126},{0,8,62},{0,9,221},{18,7,27},{0,8,110},
+ {0,8,46},{0,9,189},{0,8,14},{0,8,142},{0,8,78},{0,9,253},{96,7,0},
+ {0,8,81},{0,8,17},{21,8,131},{18,7,31},{0,8,113},{0,8,49},{0,9,195},
+ {16,7,10},{0,8,97},{0,8,33},{0,9,163},{0,8,1},{0,8,129},{0,8,65},
+ {0,9,227},{16,7,6},{0,8,89},{0,8,25},{0,9,147},{19,7,59},{0,8,121},
+ {0,8,57},{0,9,211},{17,7,17},{0,8,105},{0,8,41},{0,9,179},{0,8,9},
+ {0,8,137},{0,8,73},{0,9,243},{16,7,4},{0,8,85},{0,8,21},{16,8,258},
+ {19,7,43},{0,8,117},{0,8,53},{0,9,203},{17,7,13},{0,8,101},{0,8,37},
+ {0,9,171},{0,8,5},{0,8,133},{0,8,69},{0,9,235},{16,7,8},{0,8,93},
+ {0,8,29},{0,9,155},{20,7,83},{0,8,125},{0,8,61},{0,9,219},{18,7,23},
+ {0,8,109},{0,8,45},{0,9,187},{0,8,13},{0,8,141},{0,8,77},{0,9,251},
+ {16,7,3},{0,8,83},{0,8,19},{21,8,195},{19,7,35},{0,8,115},{0,8,51},
+ {0,9,199},{17,7,11},{0,8,99},{0,8,35},{0,9,167},{0,8,3},{0,8,131},
+ {0,8,67},{0,9,231},{16,7,7},{0,8,91},{0,8,27},{0,9,151},{20,7,67},
+ {0,8,123},{0,8,59},{0,9,215},{18,7,19},{0,8,107},{0,8,43},{0,9,183},
+ {0,8,11},{0,8,139},{0,8,75},{0,9,247},{16,7,5},{0,8,87},{0,8,23},
+ {64,8,0},{19,7,51},{0,8,119},{0,8,55},{0,9,207},{17,7,15},{0,8,103},
+ {0,8,39},{0,9,175},{0,8,7},{0,8,135},{0,8,71},{0,9,239},{16,7,9},
+ {0,8,95},{0,8,31},{0,9,159},{20,7,99},{0,8,127},{0,8,63},{0,9,223},
+ {18,7,27},{0,8,111},{0,8,47},{0,9,191},{0,8,15},{0,8,143},{0,8,79},
+ {0,9,255}
+ };
+
+ static const code distfix[32] = {
+ {16,5,1},{23,5,257},{19,5,17},{27,5,4097},{17,5,5},{25,5,1025},
+ {21,5,65},{29,5,16385},{16,5,3},{24,5,513},{20,5,33},{28,5,8193},
+ {18,5,9},{26,5,2049},{22,5,129},{64,5,0},{16,5,2},{23,5,385},
+ {19,5,25},{27,5,6145},{17,5,7},{25,5,1537},{21,5,97},{29,5,24577},
+ {16,5,4},{24,5,769},{20,5,49},{28,5,12289},{18,5,13},{26,5,3073},
+ {22,5,193},{64,5,0}
+ };
--- /dev/null
+/* inflate.c -- zlib decompression
+ * Copyright (C) 1995-2012 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ * Change history:
+ *
+ * 1.2.beta0 24 Nov 2002
+ * - First version -- complete rewrite of inflate to simplify code, avoid
+ * creation of window when not needed, minimize use of window when it is
+ * needed, make inffast.c even faster, implement gzip decoding, and to
+ * improve code readability and style over the previous zlib inflate code
+ *
+ * 1.2.beta1 25 Nov 2002
+ * - Use pointers for available input and output checking in inffast.c
+ * - Remove input and output counters in inffast.c
+ * - Change inffast.c entry and loop from avail_in >= 7 to >= 6
+ * - Remove unnecessary second byte pull from length extra in inffast.c
+ * - Unroll direct copy to three copies per loop in inffast.c
+ *
+ * 1.2.beta2 4 Dec 2002
+ * - Change external routine names to reduce potential conflicts
+ * - Correct filename to inffixed.h for fixed tables in inflate.c
+ * - Make hbuf[] unsigned char to match parameter type in inflate.c
+ * - Change strm->next_out[-state->offset] to *(strm->next_out - state->offset)
+ * to avoid negation problem on Alphas (64 bit) in inflate.c
+ *
+ * 1.2.beta3 22 Dec 2002
+ * - Add comments on state->bits assertion in inffast.c
+ * - Add comments on op field in inftrees.h
+ * - Fix bug in reuse of allocated window after inflateReset()
+ * - Remove bit fields--back to byte structure for speed
+ * - Remove distance extra == 0 check in inflate_fast()--only helps for lengths
+ * - Change post-increments to pre-increments in inflate_fast(), PPC biased?
+ * - Add compile time option, POSTINC, to use post-increments instead (Intel?)
+ * - Make MATCH copy in inflate() much faster for when inflate_fast() not used
+ * - Use local copies of stream next and avail values, as well as local bit
+ * buffer and bit count in inflate()--for speed when inflate_fast() not used
+ *
+ * 1.2.beta4 1 Jan 2003
+ * - Split ptr - 257 statements in inflate_table() to avoid compiler warnings
+ * - Move a comment on output buffer sizes from inffast.c to inflate.c
+ * - Add comments in inffast.c to introduce the inflate_fast() routine
+ * - Rearrange window copies in inflate_fast() for speed and simplification
+ * - Unroll last copy for window match in inflate_fast()
+ * - Use local copies of window variables in inflate_fast() for speed
+ * - Pull out common wnext == 0 case for speed in inflate_fast()
+ * - Make op and len in inflate_fast() unsigned for consistency
+ * - Add FAR to lcode and dcode declarations in inflate_fast()
+ * - Simplified bad distance check in inflate_fast()
+ * - Added inflateBackInit(), inflateBack(), and inflateBackEnd() in new
+ * source file infback.c to provide a call-back interface to inflate for
+ * programs like gzip and unzip -- uses window as output buffer to avoid
+ * window copying
+ *
+ * 1.2.beta5 1 Jan 2003
+ * - Improved inflateBack() interface to allow the caller to provide initial
+ * input in strm.
+ * - Fixed stored blocks bug in inflateBack()
+ *
+ * 1.2.beta6 4 Jan 2003
+ * - Added comments in inffast.c on effectiveness of POSTINC
+ * - Typecasting all around to reduce compiler warnings
+ * - Changed loops from while (1) or do {} while (1) to for (;;), again to
+ * make compilers happy
+ * - Changed type of window in inflateBackInit() to unsigned char *
+ *
+ * 1.2.beta7 27 Jan 2003
+ * - Changed many types to unsigned or unsigned short to avoid warnings
+ * - Added inflateCopy() function
+ *
+ * 1.2.0 9 Mar 2003
+ * - Changed inflateBack() interface to provide separate opaque descriptors
+ * for the in() and out() functions
+ * - Changed inflateBack() argument and in_func typedef to swap the length
+ * and buffer address return values for the input function
+ * - Check next_in and next_out for Z_NULL on entry to inflate()
+ *
+ * The history for versions after 1.2.0 are in ChangeLog in zlib distribution.
+ */
+
+#include "zutil.h"
+#include "inftrees.h"
+#include "inflate.h"
+#include "inffast.h"
+
+#ifdef MAKEFIXED
+# ifndef BUILDFIXED
+# define BUILDFIXED
+# endif
+#endif
+
+#if defined(__GNUC__) && __GNUC__>=7
+#pragma GCC diagnostic ignored "-Wimplicit-fallthrough"
+#endif
+
+/* function prototypes */
+local void fixedtables OF((struct inflate_state FAR *state));
+local int updatewindow OF((z_streamp strm, const unsigned char FAR *end,
+ unsigned copy));
+#ifdef BUILDFIXED
+ void makefixed OF((void));
+#endif
+local unsigned syncsearch OF((unsigned FAR *have, const unsigned char FAR *buf,
+ unsigned len));
+
+int ZEXPORT inflateResetKeep(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ strm->total_in = strm->total_out = state->total = 0;
+ strm->msg = Z_NULL;
+ if (state->wrap) /* to support ill-conceived Java test suite */
+ strm->adler = state->wrap & 1;
+ state->mode = HEAD;
+ state->last = 0;
+ state->havedict = 0;
+ state->dmax = 32768U;
+ state->head = Z_NULL;
+ state->hold = 0;
+ state->bits = 0;
+ state->lencode = state->distcode = state->next = state->codes;
+ state->sane = 1;
+ state->back = -1;
+ Tracev((stderr, "inflate: reset\n"));
+ return Z_OK;
+}
+
+int ZEXPORT inflateReset(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ state->wsize = 0;
+ state->whave = 0;
+ state->wnext = 0;
+ return inflateResetKeep(strm);
+}
+
+int ZEXPORT inflateReset2(strm, windowBits)
+z_streamp strm;
+int windowBits;
+{
+ int wrap;
+ struct inflate_state FAR *state;
+
+ /* get the state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+
+ /* extract wrap request from windowBits parameter */
+ if (windowBits < 0) {
+ wrap = 0;
+ windowBits = -windowBits;
+ }
+ else {
+ wrap = (windowBits >> 4) + 1;
+#ifdef GUNZIP
+ if (windowBits < 48)
+ windowBits &= 15;
+#endif
+ }
+
+ /* set number of window bits, free window if different */
+ if (windowBits && (windowBits < 8 || windowBits > 15))
+ return Z_STREAM_ERROR;
+ if (state->window != Z_NULL && state->wbits != (unsigned)windowBits) {
+ ZFREE(strm, state->window);
+ state->window = Z_NULL;
+ }
+
+ /* update state and reset the rest of it */
+ state->wrap = wrap;
+ state->wbits = (unsigned)windowBits;
+ return inflateReset(strm);
+}
+
+int ZEXPORT inflateInit2_(strm, windowBits, version, stream_size)
+z_streamp strm;
+int windowBits;
+const char *version;
+int stream_size;
+{
+ int ret;
+ struct inflate_state FAR *state;
+
+ if (version == Z_NULL || version[0] != ZLIB_VERSION[0] ||
+ stream_size != (int)(sizeof(z_stream)))
+ return Z_VERSION_ERROR;
+ if (strm == Z_NULL) return Z_STREAM_ERROR;
+ strm->msg = Z_NULL; /* in case we return an error */
+ if (strm->zalloc == (alloc_func)0) {
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zalloc = zcalloc;
+ strm->opaque = (voidpf)0;
+#endif
+ }
+ if (strm->zfree == (free_func)0)
+#ifdef Z_SOLO
+ return Z_STREAM_ERROR;
+#else
+ strm->zfree = zcfree;
+#endif
+ state = (struct inflate_state FAR *)
+ ZALLOC(strm, 1, sizeof(struct inflate_state));
+ if (state == Z_NULL) return Z_MEM_ERROR;
+ Tracev((stderr, "inflate: allocated\n"));
+ strm->state = (struct internal_state FAR *)state;
+ state->window = Z_NULL;
+ ret = inflateReset2(strm, windowBits);
+ if (ret != Z_OK) {
+ ZFREE(strm, state);
+ strm->state = Z_NULL;
+ }
+ return ret;
+}
+
+int ZEXPORT inflateInit_(strm, version, stream_size)
+z_streamp strm;
+const char *version;
+int stream_size;
+{
+ return inflateInit2_(strm, DEF_WBITS, version, stream_size);
+}
+
+int ZEXPORT inflatePrime(strm, bits, value)
+z_streamp strm;
+int bits;
+int value;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (bits < 0) {
+ state->hold = 0;
+ state->bits = 0;
+ return Z_OK;
+ }
+ if (bits > 16 || state->bits + bits > 32) return Z_STREAM_ERROR;
+ value &= (1L << bits) - 1;
+ state->hold += value << state->bits;
+ state->bits += bits;
+ return Z_OK;
+}
+
+/*
+ Return state with length and distance decoding tables and index sizes set to
+ fixed code decoding. Normally this returns fixed tables from inffixed.h.
+ If BUILDFIXED is defined, then instead this routine builds the tables the
+ first time it's called, and returns those tables the first time and
+ thereafter. This reduces the size of the code by about 2K bytes, in
+ exchange for a little execution time. However, BUILDFIXED should not be
+ used for threaded applications, since the rewriting of the tables and virgin
+ may not be thread-safe.
+ */
+local void fixedtables(state)
+struct inflate_state FAR *state;
+{
+#ifdef BUILDFIXED
+ static int virgin = 1;
+ static code *lenfix, *distfix;
+ static code fixed[544];
+
+ /* build fixed huffman tables if first call (may not be thread safe) */
+ if (virgin) {
+ unsigned sym, bits;
+ static code *next;
+
+ /* literal/length table */
+ sym = 0;
+ while (sym < 144) state->lens[sym++] = 8;
+ while (sym < 256) state->lens[sym++] = 9;
+ while (sym < 280) state->lens[sym++] = 7;
+ while (sym < 288) state->lens[sym++] = 8;
+ next = fixed;
+ lenfix = next;
+ bits = 9;
+ inflate_table(LENS, state->lens, 288, &(next), &(bits), state->work);
+
+ /* distance table */
+ sym = 0;
+ while (sym < 32) state->lens[sym++] = 5;
+ distfix = next;
+ bits = 5;
+ inflate_table(DISTS, state->lens, 32, &(next), &(bits), state->work);
+
+ /* do this just once */
+ virgin = 0;
+ }
+#else /* !BUILDFIXED */
+# include "inffixed.h"
+#endif /* BUILDFIXED */
+ state->lencode = lenfix;
+ state->lenbits = 9;
+ state->distcode = distfix;
+ state->distbits = 5;
+}
+
+#ifdef MAKEFIXED
+#include <stdio.h>
+
+/*
+ Write out the inffixed.h that is #include'd above. Defining MAKEFIXED also
+ defines BUILDFIXED, so the tables are built on the fly. makefixed() writes
+ those tables to stdout, which would be piped to inffixed.h. A small program
+ can simply call makefixed to do this:
+
+ void makefixed(void);
+
+ int main(void)
+ {
+ makefixed();
+ return 0;
+ }
+
+ Then that can be linked with zlib built with MAKEFIXED defined and run:
+
+ a.out > inffixed.h
+ */
+void makefixed()
+{
+ unsigned low, size;
+ struct inflate_state state;
+
+ fixedtables(&state);
+ puts(" /* inffixed.h -- table for decoding fixed codes");
+ puts(" * Generated automatically by makefixed().");
+ puts(" */");
+ puts("");
+ puts(" /* WARNING: this file should *not* be used by applications.");
+ puts(" It is part of the implementation of this library and is");
+ puts(" subject to change. Applications should only use zlib.h.");
+ puts(" */");
+ puts("");
+ size = 1U << 9;
+ printf(" static const code lenfix[%u] = {", size);
+ low = 0;
+ for (;;) {
+ if ((low % 7) == 0) printf("\n ");
+ printf("{%u,%u,%d}", (low & 127) == 99 ? 64 : state.lencode[low].op,
+ state.lencode[low].bits, state.lencode[low].val);
+ if (++low == size) break;
+ putchar(',');
+ }
+ puts("\n };");
+ size = 1U << 5;
+ printf("\n static const code distfix[%u] = {", size);
+ low = 0;
+ for (;;) {
+ if ((low % 6) == 0) printf("\n ");
+ printf("{%u,%u,%d}", state.distcode[low].op, state.distcode[low].bits,
+ state.distcode[low].val);
+ if (++low == size) break;
+ putchar(',');
+ }
+ puts("\n };");
+}
+#endif /* MAKEFIXED */
+
+/*
+ Update the window with the last wsize (normally 32K) bytes written before
+ returning. If window does not exist yet, create it. This is only called
+ when a window is already in use, or when output has been written during this
+ inflate call, but the end of the deflate stream has not been reached yet.
+ It is also called to create a window for dictionary data when a dictionary
+ is loaded.
+
+ Providing output buffers larger than 32K to inflate() should provide a speed
+ advantage, since only the last 32K of output is copied to the sliding window
+ upon return from inflate(), and since all distances after the first 32K of
+ output will fall in the output data, making match copies simpler and faster.
+ The advantage may be dependent on the size of the processor's data caches.
+ */
+local int updatewindow(strm, end, copy)
+z_streamp strm;
+const Bytef *end;
+unsigned copy;
+{
+ struct inflate_state FAR *state;
+ unsigned dist;
+
+ state = (struct inflate_state FAR *)strm->state;
+
+ /* if it hasn't been done already, allocate space for the window */
+ if (state->window == Z_NULL) {
+ state->window = (unsigned char FAR *)
+ ZALLOC(strm, 1U << state->wbits,
+ sizeof(unsigned char));
+ if (state->window == Z_NULL) return 1;
+ }
+
+ /* if window not in use yet, initialize */
+ if (state->wsize == 0) {
+ state->wsize = 1U << state->wbits;
+ state->wnext = 0;
+ state->whave = 0;
+ }
+
+ /* copy state->wsize or less output bytes into the circular window */
+ if (copy >= state->wsize) {
+ zmemcpy(state->window, end - state->wsize, state->wsize);
+ state->wnext = 0;
+ state->whave = state->wsize;
+ }
+ else {
+ dist = state->wsize - state->wnext;
+ if (dist > copy) dist = copy;
+ zmemcpy(state->window + state->wnext, end - copy, dist);
+ copy -= dist;
+ if (copy) {
+ zmemcpy(state->window, end - copy, copy);
+ state->wnext = copy;
+ state->whave = state->wsize;
+ }
+ else {
+ state->wnext += dist;
+ if (state->wnext == state->wsize) state->wnext = 0;
+ if (state->whave < state->wsize) state->whave += dist;
+ }
+ }
+ return 0;
+}
+
+/* Macros for inflate(): */
+
+/* check function to use adler32() for zlib or crc32() for gzip */
+#ifdef GUNZIP
+# define UPDATE(check, buf, len) \
+ (state->flags ? crc32(check, buf, len) : adler32(check, buf, len))
+#else
+# define UPDATE(check, buf, len) adler32(check, buf, len)
+#endif
+
+/* check macros for header crc */
+#ifdef GUNZIP
+# define CRC2(check, word) \
+ do { \
+ hbuf[0] = (unsigned char)(word); \
+ hbuf[1] = (unsigned char)((word) >> 8); \
+ check = crc32(check, hbuf, 2); \
+ } while (0)
+
+# define CRC4(check, word) \
+ do { \
+ hbuf[0] = (unsigned char)(word); \
+ hbuf[1] = (unsigned char)((word) >> 8); \
+ hbuf[2] = (unsigned char)((word) >> 16); \
+ hbuf[3] = (unsigned char)((word) >> 24); \
+ check = crc32(check, hbuf, 4); \
+ } while (0)
+#endif
+
+/* Load registers with state in inflate() for speed */
+#define LOAD() \
+ do { \
+ put = strm->next_out; \
+ left = strm->avail_out; \
+ next = strm->next_in; \
+ have = strm->avail_in; \
+ hold = state->hold; \
+ bits = state->bits; \
+ } while (0)
+
+/* Restore state from registers in inflate() */
+#define RESTORE() \
+ do { \
+ strm->next_out = put; \
+ strm->avail_out = left; \
+ strm->next_in = next; \
+ strm->avail_in = have; \
+ state->hold = hold; \
+ state->bits = bits; \
+ } while (0)
+
+/* Clear the input bit accumulator */
+#define INITBITS() \
+ do { \
+ hold = 0; \
+ bits = 0; \
+ } while (0)
+
+/* Get a byte of input into the bit accumulator, or return from inflate()
+ if there is no input available. */
+#define PULLBYTE() \
+ do { \
+ if (have == 0) goto inf_leave; \
+ have--; \
+ hold += (unsigned long)(*next++) << bits; \
+ bits += 8; \
+ } while (0)
+
+/* Assure that there are at least n bits in the bit accumulator. If there is
+ not enough available input to do that, then return from inflate(). */
+#define NEEDBITS(n) \
+ do { \
+ while (bits < (unsigned)(n)) \
+ PULLBYTE(); \
+ } while (0)
+
+/* Return the low n bits of the bit accumulator (n < 16) */
+#define BITS(n) \
+ ((unsigned)hold & ((1U << (n)) - 1))
+
+/* Remove n bits from the bit accumulator */
+#define DROPBITS(n) \
+ do { \
+ hold >>= (n); \
+ bits -= (unsigned)(n); \
+ } while (0)
+
+/* Remove zero to seven bits as needed to go to a byte boundary */
+#define BYTEBITS() \
+ do { \
+ hold >>= bits & 7; \
+ bits -= bits & 7; \
+ } while (0)
+
+/*
+ inflate() uses a state machine to process as much input data and generate as
+ much output data as possible before returning. The state machine is
+ structured roughly as follows:
+
+ for (;;) switch (state) {
+ ...
+ case STATEn:
+ if (not enough input data or output space to make progress)
+ return;
+ ... make progress ...
+ state = STATEm;
+ break;
+ ...
+ }
+
+ so when inflate() is called again, the same case is attempted again, and
+ if the appropriate resources are provided, the machine proceeds to the
+ next state. The NEEDBITS() macro is usually the way the state evaluates
+ whether it can proceed or should return. NEEDBITS() does the return if
+ the requested bits are not available. The typical use of the BITS macros
+ is:
+
+ NEEDBITS(n);
+ ... do something with BITS(n) ...
+ DROPBITS(n);
+
+ where NEEDBITS(n) either returns from inflate() if there isn't enough
+ input left to load n bits into the accumulator, or it continues. BITS(n)
+ gives the low n bits in the accumulator. When done, DROPBITS(n) drops
+ the low n bits off the accumulator. INITBITS() clears the accumulator
+ and sets the number of available bits to zero. BYTEBITS() discards just
+ enough bits to put the accumulator on a byte boundary. After BYTEBITS()
+ and a NEEDBITS(8), then BITS(8) would return the next byte in the stream.
+
+ NEEDBITS(n) uses PULLBYTE() to get an available byte of input, or to return
+ if there is no input available. The decoding of variable length codes uses
+ PULLBYTE() directly in order to pull just enough bytes to decode the next
+ code, and no more.
+
+ Some states loop until they get enough input, making sure that enough
+ state information is maintained to continue the loop where it left off
+ if NEEDBITS() returns in the loop. For example, want, need, and keep
+ would all have to actually be part of the saved state in case NEEDBITS()
+ returns:
+
+ case STATEw:
+ while (want < need) {
+ NEEDBITS(n);
+ keep[want++] = BITS(n);
+ DROPBITS(n);
+ }
+ state = STATEx;
+ case STATEx:
+
+ As shown above, if the next state is also the next case, then the break
+ is omitted.
+
+ A state may also return if there is not enough output space available to
+ complete that state. Those states are copying stored data, writing a
+ literal byte, and copying a matching string.
+
+ When returning, a "goto inf_leave" is used to update the total counters,
+ update the check value, and determine whether any progress has been made
+ during that inflate() call in order to return the proper return code.
+ Progress is defined as a change in either strm->avail_in or strm->avail_out.
+ When there is a window, goto inf_leave will update the window with the last
+ output written. If a goto inf_leave occurs in the middle of decompression
+ and there is no window currently, goto inf_leave will create one and copy
+ output to the window for the next call of inflate().
+
+ In this implementation, the flush parameter of inflate() only affects the
+ return code (per zlib.h). inflate() always writes as much as possible to
+ strm->next_out, given the space available and the provided input--the effect
+ documented in zlib.h of Z_SYNC_FLUSH. Furthermore, inflate() always defers
+ the allocation of and copying into a sliding window until necessary, which
+ provides the effect documented in zlib.h for Z_FINISH when the entire input
+ stream available. So the only thing the flush parameter actually does is:
+ when flush is set to Z_FINISH, inflate() cannot return Z_OK. Instead it
+ will return Z_BUF_ERROR if it has not reached the end of the stream.
+ */
+
+int ZEXPORT inflate(strm, flush)
+z_streamp strm;
+int flush;
+{
+ struct inflate_state FAR *state;
+ z_const unsigned char FAR *next; /* next input */
+ unsigned char FAR *put; /* next output */
+ unsigned have, left; /* available input and output */
+ unsigned long hold; /* bit buffer */
+ unsigned bits; /* bits in bit buffer */
+ unsigned in, out; /* save starting available input and output */
+ unsigned copy; /* number of stored or match bytes to copy */
+ unsigned char FAR *from; /* where to copy match bytes from */
+ code here; /* current decoding table entry */
+ code last; /* parent table entry */
+ unsigned len; /* length to copy for repeats, bits to drop */
+ int ret; /* return code */
+#ifdef GUNZIP
+ unsigned char hbuf[4]; /* buffer for gzip header crc calculation */
+#endif
+ static const unsigned short order[19] = /* permutation of code lengths */
+ {16, 17, 18, 0, 8, 7, 9, 6, 10, 5, 11, 4, 12, 3, 13, 2, 14, 1, 15};
+
+ if (strm == Z_NULL || strm->state == Z_NULL || strm->next_out == Z_NULL ||
+ (strm->next_in == Z_NULL && strm->avail_in != 0))
+ return Z_STREAM_ERROR;
+
+ state = (struct inflate_state FAR *)strm->state;
+ if (state->mode == TYPE) state->mode = TYPEDO; /* skip check */
+ LOAD();
+ in = have;
+ out = left;
+ ret = Z_OK;
+ for (;;)
+ switch (state->mode) {
+ case HEAD:
+ if (state->wrap == 0) {
+ state->mode = TYPEDO;
+ break;
+ }
+ NEEDBITS(16);
+#ifdef GUNZIP
+ if ((state->wrap & 2) && hold == 0x8b1f) { /* gzip header */
+ state->check = crc32(0L, Z_NULL, 0);
+ CRC2(state->check, hold);
+ INITBITS();
+ state->mode = FLAGS;
+ break;
+ }
+ state->flags = 0; /* expect zlib header */
+ if (state->head != Z_NULL)
+ state->head->done = -1;
+ if (!(state->wrap & 1) || /* check if zlib header allowed */
+#else
+ if (
+#endif
+ ((BITS(8) << 8) + (hold >> 8)) % 31) {
+ strm->msg = (char *)"incorrect header check";
+ state->mode = BAD;
+ break;
+ }
+ if (BITS(4) != Z_DEFLATED) {
+ strm->msg = (char *)"unknown compression method";
+ state->mode = BAD;
+ break;
+ }
+ DROPBITS(4);
+ len = BITS(4) + 8;
+ if (state->wbits == 0)
+ state->wbits = len;
+ else if (len > state->wbits) {
+ strm->msg = (char *)"invalid window size";
+ state->mode = BAD;
+ break;
+ }
+ state->dmax = 1U << len;
+ Tracev((stderr, "inflate: zlib header ok\n"));
+ strm->adler = state->check = adler32(0L, Z_NULL, 0);
+ state->mode = hold & 0x200 ? DICTID : TYPE;
+ INITBITS();
+ break;
+#ifdef GUNZIP
+ case FLAGS:
+ NEEDBITS(16);
+ state->flags = (int)(hold);
+ if ((state->flags & 0xff) != Z_DEFLATED) {
+ strm->msg = (char *)"unknown compression method";
+ state->mode = BAD;
+ break;
+ }
+ if (state->flags & 0xe000) {
+ strm->msg = (char *)"unknown header flags set";
+ state->mode = BAD;
+ break;
+ }
+ if (state->head != Z_NULL)
+ state->head->text = (int)((hold >> 8) & 1);
+ if (state->flags & 0x0200) CRC2(state->check, hold);
+ INITBITS();
+ state->mode = TIME;
+ case TIME:
+ NEEDBITS(32);
+ if (state->head != Z_NULL)
+ state->head->time = hold;
+ if (state->flags & 0x0200) CRC4(state->check, hold);
+ INITBITS();
+ state->mode = OS;
+ case OS:
+ NEEDBITS(16);
+ if (state->head != Z_NULL) {
+ state->head->xflags = (int)(hold & 0xff);
+ state->head->os = (int)(hold >> 8);
+ }
+ if (state->flags & 0x0200) CRC2(state->check, hold);
+ INITBITS();
+ state->mode = EXLEN;
+ case EXLEN:
+ if (state->flags & 0x0400) {
+ NEEDBITS(16);
+ state->length = (unsigned)(hold);
+ if (state->head != Z_NULL)
+ state->head->extra_len = (unsigned)hold;
+ if (state->flags & 0x0200) CRC2(state->check, hold);
+ INITBITS();
+ }
+ else if (state->head != Z_NULL)
+ state->head->extra = Z_NULL;
+ state->mode = EXTRA;
+ case EXTRA:
+ if (state->flags & 0x0400) {
+ copy = state->length;
+ if (copy > have) copy = have;
+ if (copy) {
+ if (state->head != Z_NULL &&
+ state->head->extra != Z_NULL) {
+ len = state->head->extra_len - state->length;
+ zmemcpy(state->head->extra + len, next,
+ len + copy > state->head->extra_max ?
+ state->head->extra_max - len : copy);
+ }
+ if (state->flags & 0x0200)
+ state->check = crc32(state->check, next, copy);
+ have -= copy;
+ next += copy;
+ state->length -= copy;
+ }
+ if (state->length) goto inf_leave;
+ }
+ state->length = 0;
+ state->mode = NAME;
+ case NAME:
+ if (state->flags & 0x0800) {
+ if (have == 0) goto inf_leave;
+ copy = 0;
+ do {
+ len = (unsigned)(next[copy++]);
+ if (state->head != Z_NULL &&
+ state->head->name != Z_NULL &&
+ state->length < state->head->name_max)
+ state->head->name[state->length++] = len;
+ } while (len && copy < have);
+ if (state->flags & 0x0200)
+ state->check = crc32(state->check, next, copy);
+ have -= copy;
+ next += copy;
+ if (len) goto inf_leave;
+ }
+ else if (state->head != Z_NULL)
+ state->head->name = Z_NULL;
+ state->length = 0;
+ state->mode = COMMENT;
+ case COMMENT:
+ if (state->flags & 0x1000) {
+ if (have == 0) goto inf_leave;
+ copy = 0;
+ do {
+ len = (unsigned)(next[copy++]);
+ if (state->head != Z_NULL &&
+ state->head->comment != Z_NULL &&
+ state->length < state->head->comm_max)
+ state->head->comment[state->length++] = len;
+ } while (len && copy < have);
+ if (state->flags & 0x0200)
+ state->check = crc32(state->check, next, copy);
+ have -= copy;
+ next += copy;
+ if (len) goto inf_leave;
+ }
+ else if (state->head != Z_NULL)
+ state->head->comment = Z_NULL;
+ state->mode = HCRC;
+ case HCRC:
+ if (state->flags & 0x0200) {
+ NEEDBITS(16);
+ if (hold != (state->check & 0xffff)) {
+ strm->msg = (char *)"header crc mismatch";
+ state->mode = BAD;
+ break;
+ }
+ INITBITS();
+ }
+ if (state->head != Z_NULL) {
+ state->head->hcrc = (int)((state->flags >> 9) & 1);
+ state->head->done = 1;
+ }
+ strm->adler = state->check = crc32(0L, Z_NULL, 0);
+ state->mode = TYPE;
+ break;
+#endif
+ case DICTID:
+ NEEDBITS(32);
+ strm->adler = state->check = ZSWAP32(hold);
+ INITBITS();
+ state->mode = DICT;
+ case DICT:
+ if (state->havedict == 0) {
+ RESTORE();
+ return Z_NEED_DICT;
+ }
+ strm->adler = state->check = adler32(0L, Z_NULL, 0);
+ state->mode = TYPE;
+ case TYPE:
+ if (flush == Z_BLOCK || flush == Z_TREES) goto inf_leave;
+ case TYPEDO:
+ if (state->last) {
+ BYTEBITS();
+ state->mode = CHECK;
+ break;
+ }
+ NEEDBITS(3);
+ state->last = BITS(1);
+ DROPBITS(1);
+ switch (BITS(2)) {
+ case 0: /* stored block */
+ Tracev((stderr, "inflate: stored block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = STORED;
+ break;
+ case 1: /* fixed block */
+ fixedtables(state);
+ Tracev((stderr, "inflate: fixed codes block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = LEN_; /* decode codes */
+ if (flush == Z_TREES) {
+ DROPBITS(2);
+ goto inf_leave;
+ }
+ break;
+ case 2: /* dynamic block */
+ Tracev((stderr, "inflate: dynamic codes block%s\n",
+ state->last ? " (last)" : ""));
+ state->mode = TABLE;
+ break;
+ case 3:
+ strm->msg = (char *)"invalid block type";
+ state->mode = BAD;
+ }
+ DROPBITS(2);
+ break;
+ case STORED:
+ BYTEBITS(); /* go to byte boundary */
+ NEEDBITS(32);
+ if ((hold & 0xffff) != ((hold >> 16) ^ 0xffff)) {
+ strm->msg = (char *)"invalid stored block lengths";
+ state->mode = BAD;
+ break;
+ }
+ state->length = (unsigned)hold & 0xffff;
+ Tracev((stderr, "inflate: stored length %u\n",
+ state->length));
+ INITBITS();
+ state->mode = COPY_;
+ if (flush == Z_TREES) goto inf_leave;
+ case COPY_:
+ state->mode = COPY;
+ case COPY:
+ copy = state->length;
+ if (copy) {
+ if (copy > have) copy = have;
+ if (copy > left) copy = left;
+ if (copy == 0) goto inf_leave;
+ zmemcpy(put, next, copy);
+ have -= copy;
+ next += copy;
+ left -= copy;
+ put += copy;
+ state->length -= copy;
+ break;
+ }
+ Tracev((stderr, "inflate: stored end\n"));
+ state->mode = TYPE;
+ break;
+ case TABLE:
+ NEEDBITS(14);
+ state->nlen = BITS(5) + 257;
+ DROPBITS(5);
+ state->ndist = BITS(5) + 1;
+ DROPBITS(5);
+ state->ncode = BITS(4) + 4;
+ DROPBITS(4);
+#ifndef PKZIP_BUG_WORKAROUND
+ if (state->nlen > 286 || state->ndist > 30) {
+ strm->msg = (char *)"too many length or distance symbols";
+ state->mode = BAD;
+ break;
+ }
+#endif
+ Tracev((stderr, "inflate: table sizes ok\n"));
+ state->have = 0;
+ state->mode = LENLENS;
+ case LENLENS:
+ while (state->have < state->ncode) {
+ NEEDBITS(3);
+ state->lens[order[state->have++]] = (unsigned short)BITS(3);
+ DROPBITS(3);
+ }
+ while (state->have < 19)
+ state->lens[order[state->have++]] = 0;
+ state->next = state->codes;
+ state->lencode = (const code FAR *)(state->next);
+ state->lenbits = 7;
+ ret = inflate_table(CODES, state->lens, 19, &(state->next),
+ &(state->lenbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid code lengths set";
+ state->mode = BAD;
+ break;
+ }
+ Tracev((stderr, "inflate: code lengths ok\n"));
+ state->have = 0;
+ state->mode = CODELENS;
+ case CODELENS:
+ while (state->have < state->nlen + state->ndist) {
+ for (;;) {
+ here = state->lencode[BITS(state->lenbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if (here.val < 16) {
+ DROPBITS(here.bits);
+ state->lens[state->have++] = here.val;
+ }
+ else {
+ if (here.val == 16) {
+ NEEDBITS(here.bits + 2);
+ DROPBITS(here.bits);
+ if (state->have == 0) {
+ strm->msg = (char *)"invalid bit length repeat";
+ state->mode = BAD;
+ break;
+ }
+ len = state->lens[state->have - 1];
+ copy = 3 + BITS(2);
+ DROPBITS(2);
+ }
+ else if (here.val == 17) {
+ NEEDBITS(here.bits + 3);
+ DROPBITS(here.bits);
+ len = 0;
+ copy = 3 + BITS(3);
+ DROPBITS(3);
+ }
+ else {
+ NEEDBITS(here.bits + 7);
+ DROPBITS(here.bits);
+ len = 0;
+ copy = 11 + BITS(7);
+ DROPBITS(7);
+ }
+ if (state->have + copy > state->nlen + state->ndist) {
+ strm->msg = (char *)"invalid bit length repeat";
+ state->mode = BAD;
+ break;
+ }
+ while (copy--)
+ state->lens[state->have++] = (unsigned short)len;
+ }
+ }
+
+ /* handle error breaks in while */
+ if (state->mode == BAD) break;
+
+ /* check for end-of-block code (better have one) */
+ if (state->lens[256] == 0) {
+ strm->msg = (char *)"invalid code -- missing end-of-block";
+ state->mode = BAD;
+ break;
+ }
+
+ /* build code tables -- note: do not change the lenbits or distbits
+ values here (9 and 6) without reading the comments in inftrees.h
+ concerning the ENOUGH constants, which depend on those values */
+ state->next = state->codes;
+ state->lencode = (const code FAR *)(state->next);
+ state->lenbits = 9;
+ ret = inflate_table(LENS, state->lens, state->nlen, &(state->next),
+ &(state->lenbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid literal/lengths set";
+ state->mode = BAD;
+ break;
+ }
+ state->distcode = (const code FAR *)(state->next);
+ state->distbits = 6;
+ ret = inflate_table(DISTS, state->lens + state->nlen, state->ndist,
+ &(state->next), &(state->distbits), state->work);
+ if (ret) {
+ strm->msg = (char *)"invalid distances set";
+ state->mode = BAD;
+ break;
+ }
+ Tracev((stderr, "inflate: codes ok\n"));
+ state->mode = LEN_;
+ if (flush == Z_TREES) goto inf_leave;
+ case LEN_:
+ state->mode = LEN;
+ case LEN:
+ if (have >= 6 && left >= 258) {
+ RESTORE();
+ inflate_fast(strm, out);
+ LOAD();
+ if (state->mode == TYPE)
+ state->back = -1;
+ break;
+ }
+ state->back = 0;
+ for (;;) {
+ here = state->lencode[BITS(state->lenbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if (here.op && (here.op & 0xf0) == 0) {
+ last = here;
+ for (;;) {
+ here = state->lencode[last.val +
+ (BITS(last.bits + last.op) >> last.bits)];
+ if ((unsigned)(last.bits + here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ DROPBITS(last.bits);
+ state->back += last.bits;
+ }
+ DROPBITS(here.bits);
+ state->back += here.bits;
+ state->length = (unsigned)here.val;
+ if ((int)(here.op) == 0) {
+ Tracevv((stderr, here.val >= 0x20 && here.val < 0x7f ?
+ "inflate: literal '%c'\n" :
+ "inflate: literal 0x%02x\n", here.val));
+ state->mode = LIT;
+ break;
+ }
+ if (here.op & 32) {
+ Tracevv((stderr, "inflate: end of block\n"));
+ state->back = -1;
+ state->mode = TYPE;
+ break;
+ }
+ if (here.op & 64) {
+ strm->msg = (char *)"invalid literal/length code";
+ state->mode = BAD;
+ break;
+ }
+ state->extra = (unsigned)(here.op) & 15;
+ state->mode = LENEXT;
+ case LENEXT:
+ if (state->extra) {
+ NEEDBITS(state->extra);
+ state->length += BITS(state->extra);
+ DROPBITS(state->extra);
+ state->back += state->extra;
+ }
+ Tracevv((stderr, "inflate: length %u\n", state->length));
+ state->was = state->length;
+ state->mode = DIST;
+ case DIST:
+ for (;;) {
+ here = state->distcode[BITS(state->distbits)];
+ if ((unsigned)(here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ if ((here.op & 0xf0) == 0) {
+ last = here;
+ for (;;) {
+ here = state->distcode[last.val +
+ (BITS(last.bits + last.op) >> last.bits)];
+ if ((unsigned)(last.bits + here.bits) <= bits) break;
+ PULLBYTE();
+ }
+ DROPBITS(last.bits);
+ state->back += last.bits;
+ }
+ DROPBITS(here.bits);
+ state->back += here.bits;
+ if (here.op & 64) {
+ strm->msg = (char *)"invalid distance code";
+ state->mode = BAD;
+ break;
+ }
+ state->offset = (unsigned)here.val;
+ state->extra = (unsigned)(here.op) & 15;
+ state->mode = DISTEXT;
+ case DISTEXT:
+ if (state->extra) {
+ NEEDBITS(state->extra);
+ state->offset += BITS(state->extra);
+ DROPBITS(state->extra);
+ state->back += state->extra;
+ }
+#ifdef INFLATE_STRICT
+ if (state->offset > state->dmax) {
+ strm->msg = (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#endif
+ Tracevv((stderr, "inflate: distance %u\n", state->offset));
+ state->mode = MATCH;
+ case MATCH:
+ if (left == 0) goto inf_leave;
+ copy = out - left;
+ if (state->offset > copy) { /* copy from window */
+ copy = state->offset - copy;
+ if (copy > state->whave) {
+ if (state->sane) {
+ strm->msg = (char *)"invalid distance too far back";
+ state->mode = BAD;
+ break;
+ }
+#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+ Trace((stderr, "inflate.c too far\n"));
+ copy -= state->whave;
+ if (copy > state->length) copy = state->length;
+ if (copy > left) copy = left;
+ left -= copy;
+ state->length -= copy;
+ do {
+ *put++ = 0;
+ } while (--copy);
+ if (state->length == 0) state->mode = LEN;
+ break;
+#endif
+ }
+ if (copy > state->wnext) {
+ copy -= state->wnext;
+ from = state->window + (state->wsize - copy);
+ }
+ else
+ from = state->window + (state->wnext - copy);
+ if (copy > state->length) copy = state->length;
+ }
+ else { /* copy from output */
+ from = put - state->offset;
+ copy = state->length;
+ }
+ if (copy > left) copy = left;
+ left -= copy;
+ state->length -= copy;
+ do {
+ *put++ = *from++;
+ } while (--copy);
+ if (state->length == 0) state->mode = LEN;
+ break;
+ case LIT:
+ if (left == 0) goto inf_leave;
+ *put++ = (unsigned char)(state->length);
+ left--;
+ state->mode = LEN;
+ break;
+ case CHECK:
+ if (state->wrap) {
+ NEEDBITS(32);
+ out -= left;
+ strm->total_out += out;
+ state->total += out;
+ if (out)
+ strm->adler = state->check =
+ UPDATE(state->check, put - out, out);
+ out = left;
+ if ((
+#ifdef GUNZIP
+ state->flags ? hold :
+#endif
+ ZSWAP32(hold)) != state->check) {
+ strm->msg = (char *)"incorrect data check";
+ state->mode = BAD;
+ break;
+ }
+ INITBITS();
+ Tracev((stderr, "inflate: check matches trailer\n"));
+ }
+#ifdef GUNZIP
+ state->mode = LENGTH;
+ case LENGTH:
+ if (state->wrap && state->flags) {
+ NEEDBITS(32);
+ if (hold != (state->total & 0xffffffffUL)) {
+ strm->msg = (char *)"incorrect length check";
+ state->mode = BAD;
+ break;
+ }
+ INITBITS();
+ Tracev((stderr, "inflate: length matches trailer\n"));
+ }
+#endif
+ state->mode = DONE;
+ case DONE:
+ ret = Z_STREAM_END;
+ goto inf_leave;
+ case BAD:
+ ret = Z_DATA_ERROR;
+ goto inf_leave;
+ case MEM:
+ return Z_MEM_ERROR;
+ case SYNC:
+ default:
+ return Z_STREAM_ERROR;
+ }
+
+ /*
+ Return from inflate(), updating the total counts and the check value.
+ If there was no progress during the inflate() call, return a buffer
+ error. Call updatewindow() to create and/or update the window state.
+ Note: a memory error from inflate() is non-recoverable.
+ */
+ inf_leave:
+ RESTORE();
+ if (state->wsize || (out != strm->avail_out && state->mode < BAD &&
+ (state->mode < CHECK || flush != Z_FINISH)))
+ if (updatewindow(strm, strm->next_out, out - strm->avail_out)) {
+ state->mode = MEM;
+ return Z_MEM_ERROR;
+ }
+ in -= strm->avail_in;
+ out -= strm->avail_out;
+ strm->total_in += in;
+ strm->total_out += out;
+ state->total += out;
+ if (state->wrap && out)
+ strm->adler = state->check =
+ UPDATE(state->check, strm->next_out - out, out);
+ strm->data_type = state->bits + (state->last ? 64 : 0) +
+ (state->mode == TYPE ? 128 : 0) +
+ (state->mode == LEN_ || state->mode == COPY_ ? 256 : 0);
+ if (((in == 0 && out == 0) || flush == Z_FINISH) && ret == Z_OK)
+ ret = Z_BUF_ERROR;
+ return ret;
+}
+
+int ZEXPORT inflateEnd(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+ if (strm == Z_NULL || strm->state == Z_NULL || strm->zfree == (free_func)0)
+ return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (state->window != Z_NULL) ZFREE(strm, state->window);
+ ZFREE(strm, strm->state);
+ strm->state = Z_NULL;
+ Tracev((stderr, "inflate: end\n"));
+ return Z_OK;
+}
+
+int ZEXPORT inflateGetDictionary(strm, dictionary, dictLength)
+z_streamp strm;
+Bytef *dictionary;
+uInt *dictLength;
+{
+ struct inflate_state FAR *state;
+
+ /* check state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+
+ /* copy dictionary */
+ if (state->whave && dictionary != Z_NULL) {
+ zmemcpy(dictionary, state->window + state->wnext,
+ state->whave - state->wnext);
+ zmemcpy(dictionary + state->whave - state->wnext,
+ state->window, state->wnext);
+ }
+ if (dictLength != Z_NULL)
+ *dictLength = state->whave;
+ return Z_OK;
+}
+
+int ZEXPORT inflateSetDictionary(strm, dictionary, dictLength)
+z_streamp strm;
+const Bytef *dictionary;
+uInt dictLength;
+{
+ struct inflate_state FAR *state;
+ unsigned long dictid;
+ int ret;
+
+ /* check state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (state->wrap != 0 && state->mode != DICT)
+ return Z_STREAM_ERROR;
+
+ /* check for correct dictionary identifier */
+ if (state->mode == DICT) {
+ dictid = adler32(0L, Z_NULL, 0);
+ dictid = adler32(dictid, dictionary, dictLength);
+ if (dictid != state->check)
+ return Z_DATA_ERROR;
+ }
+
+ /* copy dictionary to window using updatewindow(), which will amend the
+ existing dictionary if appropriate */
+ ret = updatewindow(strm, dictionary + dictLength, dictLength);
+ if (ret) {
+ state->mode = MEM;
+ return Z_MEM_ERROR;
+ }
+ state->havedict = 1;
+ Tracev((stderr, "inflate: dictionary set\n"));
+ return Z_OK;
+}
+
+int ZEXPORT inflateGetHeader(strm, head)
+z_streamp strm;
+gz_headerp head;
+{
+ struct inflate_state FAR *state;
+
+ /* check state */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if ((state->wrap & 2) == 0) return Z_STREAM_ERROR;
+
+ /* save header structure */
+ state->head = head;
+ head->done = 0;
+ return Z_OK;
+}
+
+/*
+ Search buf[0..len-1] for the pattern: 0, 0, 0xff, 0xff. Return when found
+ or when out of input. When called, *have is the number of pattern bytes
+ found in order so far, in 0..3. On return *have is updated to the new
+ state. If on return *have equals four, then the pattern was found and the
+ return value is how many bytes were read including the last byte of the
+ pattern. If *have is less than four, then the pattern has not been found
+ yet and the return value is len. In the latter case, syncsearch() can be
+ called again with more data and the *have state. *have is initialized to
+ zero for the first call.
+ */
+local unsigned syncsearch(have, buf, len)
+unsigned FAR *have;
+const unsigned char FAR *buf;
+unsigned len;
+{
+ unsigned got;
+ unsigned next;
+
+ got = *have;
+ next = 0;
+ while (next < len && got < 4) {
+ if ((int)(buf[next]) == (got < 2 ? 0 : 0xff))
+ got++;
+ else if (buf[next])
+ got = 0;
+ else
+ got = 4 - got;
+ next++;
+ }
+ *have = got;
+ return next;
+}
+
+int ZEXPORT inflateSync(strm)
+z_streamp strm;
+{
+ unsigned len; /* number of bytes to look at or looked at */
+ unsigned long in, out; /* temporary to save total_in and total_out */
+ unsigned char buf[4]; /* to restore bit buffer to byte string */
+ struct inflate_state FAR *state;
+
+ /* check parameters */
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ if (strm->avail_in == 0 && state->bits < 8) return Z_BUF_ERROR;
+
+ /* if first time, start search in bit buffer */
+ if (state->mode != SYNC) {
+ state->mode = SYNC;
+ state->hold <<= state->bits & 7;
+ state->bits -= state->bits & 7;
+ len = 0;
+ while (state->bits >= 8) {
+ buf[len++] = (unsigned char)(state->hold);
+ state->hold >>= 8;
+ state->bits -= 8;
+ }
+ state->have = 0;
+ syncsearch(&(state->have), buf, len);
+ }
+
+ /* search available input */
+ len = syncsearch(&(state->have), strm->next_in, strm->avail_in);
+ strm->avail_in -= len;
+ strm->next_in += len;
+ strm->total_in += len;
+
+ /* return no joy or set up to restart inflate() on a new block */
+ if (state->have != 4) return Z_DATA_ERROR;
+ in = strm->total_in; out = strm->total_out;
+ inflateReset(strm);
+ strm->total_in = in; strm->total_out = out;
+ state->mode = TYPE;
+ return Z_OK;
+}
+
+/*
+ Returns true if inflate is currently at the end of a block generated by
+ Z_SYNC_FLUSH or Z_FULL_FLUSH. This function is used by one PPP
+ implementation to provide an additional safety check. PPP uses
+ Z_SYNC_FLUSH but removes the length bytes of the resulting empty stored
+ block. When decompressing, PPP checks that at the end of input packet,
+ inflate is waiting for these length bytes.
+ */
+int ZEXPORT inflateSyncPoint(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ return state->mode == STORED && state->bits == 0;
+}
+
+int ZEXPORT inflateCopy(dest, source)
+z_streamp dest;
+z_streamp source;
+{
+ struct inflate_state FAR *state;
+ struct inflate_state FAR *copy;
+ unsigned char FAR *window;
+ unsigned wsize;
+
+ /* check input */
+ if (dest == Z_NULL || source == Z_NULL || source->state == Z_NULL ||
+ source->zalloc == (alloc_func)0 || source->zfree == (free_func)0)
+ return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)source->state;
+
+ /* allocate space */
+ copy = (struct inflate_state FAR *)
+ ZALLOC(source, 1, sizeof(struct inflate_state));
+ if (copy == Z_NULL) return Z_MEM_ERROR;
+ window = Z_NULL;
+ if (state->window != Z_NULL) {
+ window = (unsigned char FAR *)
+ ZALLOC(source, 1U << state->wbits, sizeof(unsigned char));
+ if (window == Z_NULL) {
+ ZFREE(source, copy);
+ return Z_MEM_ERROR;
+ }
+ }
+
+ /* copy state */
+ zmemcpy((voidpf)dest, (voidpf)source, sizeof(z_stream));
+ zmemcpy((voidpf)copy, (voidpf)state, sizeof(struct inflate_state));
+ if (state->lencode >= state->codes &&
+ state->lencode <= state->codes + ENOUGH - 1) {
+ copy->lencode = copy->codes + (state->lencode - state->codes);
+ copy->distcode = copy->codes + (state->distcode - state->codes);
+ }
+ copy->next = copy->codes + (state->next - state->codes);
+ if (window != Z_NULL) {
+ wsize = 1U << state->wbits;
+ zmemcpy(window, state->window, wsize);
+ }
+ copy->window = window;
+ dest->state = (struct internal_state FAR *)copy;
+ return Z_OK;
+}
+
+int ZEXPORT inflateUndermine(strm, subvert)
+z_streamp strm;
+int subvert;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return Z_STREAM_ERROR;
+ state = (struct inflate_state FAR *)strm->state;
+ state->sane = !subvert;
+#ifdef INFLATE_ALLOW_INVALID_DISTANCE_TOOFAR_ARRR
+ return Z_OK;
+#else
+ state->sane = 1;
+ return Z_DATA_ERROR;
+#endif
+}
+
+long ZEXPORT inflateMark(strm)
+z_streamp strm;
+{
+ struct inflate_state FAR *state;
+
+ if (strm == Z_NULL || strm->state == Z_NULL) return ~0xFFFFL; /* Original code returned -1L << 16, but that is undefined behaviour */
+ state = (struct inflate_state FAR *)strm->state;
+ return ((long)(state->back) << 16) +
+ (state->mode == COPY ? state->length :
+ (state->mode == MATCH ? state->was - state->length : 0));
+}
--- /dev/null
+/* inflate.h -- internal inflate state definition
+ * Copyright (C) 1995-2009 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* define NO_GZIP when compiling if you want to disable gzip header and
+ trailer decoding by inflate(). NO_GZIP would be used to avoid linking in
+ the crc code when it is not needed. For shared libraries, gzip decoding
+ should be left enabled. */
+#ifndef NO_GZIP
+# define GUNZIP
+#endif
+
+/* Possible inflate modes between inflate() calls */
+typedef enum {
+ HEAD, /* i: waiting for magic header */
+ FLAGS, /* i: waiting for method and flags (gzip) */
+ TIME, /* i: waiting for modification time (gzip) */
+ OS, /* i: waiting for extra flags and operating system (gzip) */
+ EXLEN, /* i: waiting for extra length (gzip) */
+ EXTRA, /* i: waiting for extra bytes (gzip) */
+ NAME, /* i: waiting for end of file name (gzip) */
+ COMMENT, /* i: waiting for end of comment (gzip) */
+ HCRC, /* i: waiting for header crc (gzip) */
+ DICTID, /* i: waiting for dictionary check value */
+ DICT, /* waiting for inflateSetDictionary() call */
+ TYPE, /* i: waiting for type bits, including last-flag bit */
+ TYPEDO, /* i: same, but skip check to exit inflate on new block */
+ STORED, /* i: waiting for stored size (length and complement) */
+ COPY_, /* i/o: same as COPY below, but only first time in */
+ COPY, /* i/o: waiting for input or output to copy stored block */
+ TABLE, /* i: waiting for dynamic block table lengths */
+ LENLENS, /* i: waiting for code length code lengths */
+ CODELENS, /* i: waiting for length/lit and distance code lengths */
+ LEN_, /* i: same as LEN below, but only first time in */
+ LEN, /* i: waiting for length/lit/eob code */
+ LENEXT, /* i: waiting for length extra bits */
+ DIST, /* i: waiting for distance code */
+ DISTEXT, /* i: waiting for distance extra bits */
+ MATCH, /* o: waiting for output space to copy string */
+ LIT, /* o: waiting for output space to write literal */
+ CHECK, /* i: waiting for 32-bit check value */
+ LENGTH, /* i: waiting for 32-bit length (gzip) */
+ DONE, /* finished check, done -- remain here until reset */
+ BAD, /* got a data error -- remain here until reset */
+ MEM, /* got an inflate() memory error -- remain here until reset */
+ SYNC /* looking for synchronization bytes to restart inflate() */
+} inflate_mode;
+
+/*
+ State transitions between above modes -
+
+ (most modes can go to BAD or MEM on error -- not shown for clarity)
+
+ Process header:
+ HEAD -> (gzip) or (zlib) or (raw)
+ (gzip) -> FLAGS -> TIME -> OS -> EXLEN -> EXTRA -> NAME -> COMMENT ->
+ HCRC -> TYPE
+ (zlib) -> DICTID or TYPE
+ DICTID -> DICT -> TYPE
+ (raw) -> TYPEDO
+ Read deflate blocks:
+ TYPE -> TYPEDO -> STORED or TABLE or LEN_ or CHECK
+ STORED -> COPY_ -> COPY -> TYPE
+ TABLE -> LENLENS -> CODELENS -> LEN_
+ LEN_ -> LEN
+ Read deflate codes in fixed or dynamic block:
+ LEN -> LENEXT or LIT or TYPE
+ LENEXT -> DIST -> DISTEXT -> MATCH -> LEN
+ LIT -> LEN
+ Process trailer:
+ CHECK -> LENGTH -> DONE
+ */
+
+/* state maintained between inflate() calls. Approximately 10K bytes. */
+struct inflate_state {
+ inflate_mode mode; /* current inflate mode */
+ int last; /* true if processing last block */
+ int wrap; /* bit 0 true for zlib, bit 1 true for gzip */
+ int havedict; /* true if dictionary provided */
+ int flags; /* gzip header method and flags (0 if zlib) */
+ unsigned dmax; /* zlib header max distance (INFLATE_STRICT) */
+ unsigned long check; /* protected copy of check value */
+ unsigned long total; /* protected copy of output count */
+ gz_headerp head; /* where to save gzip header information */
+ /* sliding window */
+ unsigned wbits; /* log base 2 of requested window size */
+ unsigned wsize; /* window size or zero if not using window */
+ unsigned whave; /* valid bytes in the window */
+ unsigned wnext; /* window write index */
+ unsigned char FAR *window; /* allocated sliding window, if needed */
+ /* bit accumulator */
+ unsigned long hold; /* input bit accumulator */
+ unsigned bits; /* number of bits in "in" */
+ /* for string and stored block copying */
+ unsigned length; /* literal or length of data to copy */
+ unsigned offset; /* distance back to copy string from */
+ /* for table and code decoding */
+ unsigned extra; /* extra bits needed */
+ /* fixed and dynamic code tables */
+ code const FAR *lencode; /* starting table for length/literal codes */
+ code const FAR *distcode; /* starting table for distance codes */
+ unsigned lenbits; /* index bits for lencode */
+ unsigned distbits; /* index bits for distcode */
+ /* dynamic table building */
+ unsigned ncode; /* number of code length code lengths */
+ unsigned nlen; /* number of length code lengths */
+ unsigned ndist; /* number of distance code lengths */
+ unsigned have; /* number of code lengths in lens[] */
+ code FAR *next; /* next available space in codes[] */
+ unsigned short lens[320]; /* temporary storage for code lengths */
+ unsigned short work[288]; /* work area for code table building */
+ code codes[ENOUGH]; /* space for code tables */
+ int sane; /* if false, allow invalid distance too far */
+ int back; /* bits back of last unprocessed length/lit */
+ unsigned was; /* initial length of match */
+};
--- /dev/null
+/* inftrees.c -- generate Huffman trees for efficient decoding
+ * Copyright (C) 1995-2013 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+#include "zutil.h"
+#include "inftrees.h"
+
+#define MAXBITS 15
+
+const char inflate_copyright[] =
+ " inflate 1.2.8 Copyright 1995-2013 Mark Adler ";
+/*
+ If you use the zlib library in a product, an acknowledgment is welcome
+ in the documentation of your product. If for some reason you cannot
+ include such an acknowledgment, I would appreciate that you keep this
+ copyright string in the executable of your product.
+ */
+
+/*
+ Build a set of tables to decode the provided canonical Huffman code.
+ The code lengths are lens[0..codes-1]. The result starts at *table,
+ whose indices are 0..2^bits-1. work is a writable array of at least
+ lens shorts, which is used as a work area. type is the type of code
+ to be generated, CODES, LENS, or DISTS. On return, zero is success,
+ -1 is an invalid code, and +1 means that ENOUGH isn't enough. table
+ on return points to the next available entry's address. bits is the
+ requested root table index bits, and on return it is the actual root
+ table index bits. It will differ if the request is greater than the
+ longest code or if it is less than the shortest code.
+ */
+int ZLIB_INTERNAL inflate_table(type, lens, codes, table, bits, work)
+codetype type;
+unsigned short FAR *lens;
+unsigned codes;
+code FAR * FAR *table;
+unsigned FAR *bits;
+unsigned short FAR *work;
+{
+ unsigned len; /* a code's length in bits */
+ unsigned sym; /* index of code symbols */
+ unsigned min, max; /* minimum and maximum code lengths */
+ unsigned root; /* number of index bits for root table */
+ unsigned curr; /* number of index bits for current table */
+ unsigned drop; /* code bits to drop for sub-table */
+ int left; /* number of prefix codes available */
+ unsigned used; /* code entries in table used */
+ unsigned huff; /* Huffman code */
+ unsigned incr; /* for incrementing code, index */
+ unsigned fill; /* index for replicating entries */
+ unsigned low; /* low bits for current root entry */
+ unsigned mask; /* mask for low root bits */
+ code here; /* table entry for duplication */
+ code FAR *next; /* next available space in table */
+ const unsigned short FAR *base; /* base value table to use */
+ const unsigned short FAR *extra; /* extra bits table to use */
+ int end; /* use base and extra for symbol > end */
+ unsigned short count[MAXBITS+1]; /* number of codes of each length */
+ unsigned short offs[MAXBITS+1]; /* offsets in table for each length */
+ static const unsigned short lbase[31] = { /* Length codes 257..285 base */
+ 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 15, 17, 19, 23, 27, 31,
+ 35, 43, 51, 59, 67, 83, 99, 115, 131, 163, 195, 227, 258, 0, 0};
+ static const unsigned short lext[31] = { /* Length codes 257..285 extra */
+ 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 18, 18, 18, 18,
+ 19, 19, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 16, 72, 78};
+ static const unsigned short dbase[32] = { /* Distance codes 0..29 base */
+ 1, 2, 3, 4, 5, 7, 9, 13, 17, 25, 33, 49, 65, 97, 129, 193,
+ 257, 385, 513, 769, 1025, 1537, 2049, 3073, 4097, 6145,
+ 8193, 12289, 16385, 24577, 0, 0};
+ static const unsigned short dext[32] = { /* Distance codes 0..29 extra */
+ 16, 16, 16, 16, 17, 17, 18, 18, 19, 19, 20, 20, 21, 21, 22, 22,
+ 23, 23, 24, 24, 25, 25, 26, 26, 27, 27,
+ 28, 28, 29, 29, 64, 64};
+
+ /*
+ Process a set of code lengths to create a canonical Huffman code. The
+ code lengths are lens[0..codes-1]. Each length corresponds to the
+ symbols 0..codes-1. The Huffman code is generated by first sorting the
+ symbols by length from short to long, and retaining the symbol order
+ for codes with equal lengths. Then the code starts with all zero bits
+ for the first code of the shortest length, and the codes are integer
+ increments for the same length, and zeros are appended as the length
+ increases. For the deflate format, these bits are stored backwards
+ from their more natural integer increment ordering, and so when the
+ decoding tables are built in the large loop below, the integer codes
+ are incremented backwards.
+
+ This routine assumes, but does not check, that all of the entries in
+ lens[] are in the range 0..MAXBITS. The caller must assure this.
+ 1..MAXBITS is interpreted as that code length. zero means that that
+ symbol does not occur in this code.
+
+ The codes are sorted by computing a count of codes for each length,
+ creating from that a table of starting indices for each length in the
+ sorted table, and then entering the symbols in order in the sorted
+ table. The sorted table is work[], with that space being provided by
+ the caller.
+
+ The length counts are used for other purposes as well, i.e. finding
+ the minimum and maximum length codes, determining if there are any
+ codes at all, checking for a valid set of lengths, and looking ahead
+ at length counts to determine sub-table sizes when building the
+ decoding tables.
+ */
+
+ /* accumulate lengths for codes (assumes lens[] all in 0..MAXBITS) */
+ for (len = 0; len <= MAXBITS; len++)
+ count[len] = 0;
+ for (sym = 0; sym < codes; sym++)
+ count[lens[sym]]++;
+
+ /* bound code lengths, force root to be within code lengths */
+ root = *bits;
+ for (max = MAXBITS; max >= 1; max--)
+ if (count[max] != 0) break;
+ if (root > max) root = max;
+ if (max == 0) { /* no symbols to code at all */
+ here.op = (unsigned char)64; /* invalid code marker */
+ here.bits = (unsigned char)1;
+ here.val = (unsigned short)0;
+ *(*table)++ = here; /* make a table to force an error */
+ *(*table)++ = here;
+ *bits = 1;
+ return 0; /* no symbols, but wait for decoding to report error */
+ }
+ for (min = 1; min < max; min++)
+ if (count[min] != 0) break;
+ if (root < min) root = min;
+
+ /* check for an over-subscribed or incomplete set of lengths */
+ left = 1;
+ for (len = 1; len <= MAXBITS; len++) {
+ left <<= 1;
+ left -= count[len];
+ if (left < 0) return -1; /* over-subscribed */
+ }
+ if (left > 0 && (type == CODES || max != 1))
+ return -1; /* incomplete set */
+
+ /* generate offsets into symbol table for each length for sorting */
+ offs[1] = 0;
+ for (len = 1; len < MAXBITS; len++)
+ offs[len + 1] = offs[len] + count[len];
+
+ /* sort symbols by length, by symbol order within each length */
+ for (sym = 0; sym < codes; sym++)
+ if (lens[sym] != 0) work[offs[lens[sym]]++] = (unsigned short)sym;
+
+ /*
+ Create and fill in decoding tables. In this loop, the table being
+ filled is at next and has curr index bits. The code being used is huff
+ with length len. That code is converted to an index by dropping drop
+ bits off of the bottom. For codes where len is less than drop + curr,
+ those top drop + curr - len bits are incremented through all values to
+ fill the table with replicated entries.
+
+ root is the number of index bits for the root table. When len exceeds
+ root, sub-tables are created pointed to by the root entry with an index
+ of the low root bits of huff. This is saved in low to check for when a
+ new sub-table should be started. drop is zero when the root table is
+ being filled, and drop is root when sub-tables are being filled.
+
+ When a new sub-table is needed, it is necessary to look ahead in the
+ code lengths to determine what size sub-table is needed. The length
+ counts are used for this, and so count[] is decremented as codes are
+ entered in the tables.
+
+ used keeps track of how many table entries have been allocated from the
+ provided *table space. It is checked for LENS and DIST tables against
+ the constants ENOUGH_LENS and ENOUGH_DISTS to guard against changes in
+ the initial root table size constants. See the comments in inftrees.h
+ for more information.
+
+ sym increments through all symbols, and the loop terminates when
+ all codes of length max, i.e. all codes, have been processed. This
+ routine permits incomplete codes, so another loop after this one fills
+ in the rest of the decoding tables with invalid code markers.
+ */
+
+ /* set up for code type */
+ switch (type) {
+ case CODES:
+ base = extra = work; /* dummy value--not used */
+ end = 19;
+ break;
+ case LENS:
+ base = lbase;
+ base -= 257;
+ extra = lext;
+ extra -= 257;
+ end = 256;
+ break;
+ default: /* DISTS */
+ base = dbase;
+ extra = dext;
+ end = -1;
+ }
+
+ /* initialize state for loop */
+ huff = 0; /* starting code */
+ sym = 0; /* starting code symbol */
+ len = min; /* starting code length */
+ next = *table; /* current table to fill in */
+ curr = root; /* current table index bits */
+ drop = 0; /* current bits to drop from code for index */
+ low = (unsigned)(-1); /* trigger new sub-table when len > root */
+ used = 1U << root; /* use root table entries */
+ mask = used - 1; /* mask for comparing low */
+
+ /* check available table space */
+ if ((type == LENS && used > ENOUGH_LENS) ||
+ (type == DISTS && used > ENOUGH_DISTS))
+ return 1;
+
+ /* process all codes and make table entries */
+ for (;;) {
+ /* create table entry */
+ here.bits = (unsigned char)(len - drop);
+ if ((int)(work[sym]) < end) {
+ here.op = (unsigned char)0;
+ here.val = work[sym];
+ }
+ else if ((int)(work[sym]) > end) {
+ here.op = (unsigned char)(extra[work[sym]]);
+ here.val = base[work[sym]];
+ }
+ else {
+ here.op = (unsigned char)(32 + 64); /* end of block */
+ here.val = 0;
+ }
+
+ /* replicate for those indices with low len bits equal to huff */
+ incr = 1U << (len - drop);
+ fill = 1U << curr;
+ min = fill; /* save offset to next table */
+ do {
+ fill -= incr;
+ next[(huff >> drop) + fill] = here;
+ } while (fill != 0);
+
+ /* backwards increment the len-bit code huff */
+ incr = 1U << (len - 1);
+ while (huff & incr)
+ incr >>= 1;
+ if (incr != 0) {
+ huff &= incr - 1;
+ huff += incr;
+ }
+ else
+ huff = 0;
+
+ /* go to next symbol, update count, len */
+ sym++;
+ if (--(count[len]) == 0) {
+ if (len == max) break;
+ len = lens[work[sym]];
+ }
+
+ /* create new sub-table if needed */
+ if (len > root && (huff & mask) != low) {
+ /* if first time, transition to sub-tables */
+ if (drop == 0)
+ drop = root;
+
+ /* increment past last table */
+ next += min; /* here min is 1 << curr */
+
+ /* determine length of next table */
+ curr = len - drop;
+ left = (int)(1 << curr);
+ while (curr + drop < max) {
+ left -= count[curr + drop];
+ if (left <= 0) break;
+ curr++;
+ left <<= 1;
+ }
+
+ /* check for enough space */
+ used += 1U << curr;
+ if ((type == LENS && used > ENOUGH_LENS) ||
+ (type == DISTS && used > ENOUGH_DISTS))
+ return 1;
+
+ /* point entry in root table to sub-table */
+ low = huff & mask;
+ (*table)[low].op = (unsigned char)curr;
+ (*table)[low].bits = (unsigned char)root;
+ (*table)[low].val = (unsigned short)(next - *table);
+ }
+ }
+
+ /* fill in remaining table entry if code is incomplete (guaranteed to have
+ at most one remaining entry, since if the code is incomplete, the
+ maximum code length that was allowed to get this far is one bit) */
+ if (huff != 0) {
+ here.op = (unsigned char)64; /* invalid code marker */
+ here.bits = (unsigned char)(len - drop);
+ here.val = (unsigned short)0;
+ next[huff] = here;
+ }
+
+ /* set return parameters */
+ *table += used;
+ *bits = root;
+ return 0;
+}
--- /dev/null
+/* inftrees.h -- header to use inftrees.c
+ * Copyright (C) 1995-2005, 2010 Mark Adler
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* Structure for decoding tables. Each entry provides either the
+ information needed to do the operation requested by the code that
+ indexed that table entry, or it provides a pointer to another
+ table that indexes more bits of the code. op indicates whether
+ the entry is a pointer to another table, a literal, a length or
+ distance, an end-of-block, or an invalid code. For a table
+ pointer, the low four bits of op is the number of index bits of
+ that table. For a length or distance, the low four bits of op
+ is the number of extra bits to get after the code. bits is
+ the number of bits in this code or part of the code to drop off
+ of the bit buffer. val is the actual byte to output in the case
+ of a literal, the base length or distance, or the offset from
+ the current table to the next table. Each entry is four bytes. */
+typedef struct {
+ unsigned char op; /* operation, extra bits, table bits */
+ unsigned char bits; /* bits in this part of the code */
+ unsigned short val; /* offset in table or code value */
+} code;
+
+/* op values as set by inflate_table():
+ 00000000 - literal
+ 0000tttt - table link, tttt != 0 is the number of table index bits
+ 0001eeee - length or distance, eeee is the number of extra bits
+ 01100000 - end of block
+ 01000000 - invalid code
+ */
+
+/* Maximum size of the dynamic table. The maximum number of code structures is
+ 1444, which is the sum of 852 for literal/length codes and 592 for distance
+ codes. These values were found by exhaustive searches using the program
+ examples/enough.c found in the zlib distribtution. The arguments to that
+ program are the number of symbols, the initial root table size, and the
+ maximum bit length of a code. "enough 286 9 15" for literal/length codes
+ returns returns 852, and "enough 30 6 15" for distance codes returns 592.
+ The initial root table size (9 or 6) is found in the fifth argument of the
+ inflate_table() calls in inflate.c and infback.c. If the root table size is
+ changed, then these maximum sizes would be need to be recalculated and
+ updated. */
+#define ENOUGH_LENS 852
+#define ENOUGH_DISTS 592
+#define ENOUGH (ENOUGH_LENS+ENOUGH_DISTS)
+
+/* Type of code to build for inflate_table() */
+typedef enum {
+ CODES,
+ LENS,
+ DISTS
+} codetype;
+
+int ZLIB_INTERNAL inflate_table OF((codetype type, unsigned short FAR *lens,
+ unsigned codes, code FAR * FAR *table,
+ unsigned FAR *bits, unsigned short FAR *work));
--- /dev/null
+/* trees.c -- output deflated data using Huffman coding
+ * Copyright (C) 1995-2012 Jean-loup Gailly
+ * detect_data_type() function provided freely by Cosmin Truta, 2006
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/*
+ * ALGORITHM
+ *
+ * The "deflation" process uses several Huffman trees. The more
+ * common source values are represented by shorter bit sequences.
+ *
+ * Each code tree is stored in a compressed form which is itself
+ * a Huffman encoding of the lengths of all the code strings (in
+ * ascending order by source values). The actual code strings are
+ * reconstructed from the lengths in the inflate process, as described
+ * in the deflate specification.
+ *
+ * REFERENCES
+ *
+ * Deutsch, L.P.,"'Deflate' Compressed Data Format Specification".
+ * Available in ftp.uu.net:/pub/archiving/zip/doc/deflate-1.1.doc
+ *
+ * Storer, James A.
+ * Data Compression: Methods and Theory, pp. 49-50.
+ * Computer Science Press, 1988. ISBN 0-7167-8156-5.
+ *
+ * Sedgewick, R.
+ * Algorithms, p290.
+ * Addison-Wesley, 1983. ISBN 0-201-06672-6.
+ */
+
+/* @(#) $Id$ */
+
+/* #define GEN_TREES_H */
+
+#include "deflate.h"
+
+#ifdef DEBUG
+# include <ctype.h>
+#endif
+
+/* ===========================================================================
+ * Constants
+ */
+
+#define MAX_BL_BITS 7
+/* Bit length codes must not exceed MAX_BL_BITS bits */
+
+#define END_BLOCK 256
+/* end of block literal code */
+
+#define REP_3_6 16
+/* repeat previous bit length 3-6 times (2 bits of repeat count) */
+
+#define REPZ_3_10 17
+/* repeat a zero length 3-10 times (3 bits of repeat count) */
+
+#define REPZ_11_138 18
+/* repeat a zero length 11-138 times (7 bits of repeat count) */
+
+local const int extra_lbits[LENGTH_CODES] /* extra bits for each length code */
+ = {0,0,0,0,0,0,0,0,1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,0};
+
+local const int extra_dbits[D_CODES] /* extra bits for each distance code */
+ = {0,0,0,0,1,1,2,2,3,3,4,4,5,5,6,6,7,7,8,8,9,9,10,10,11,11,12,12,13,13};
+
+local const int extra_blbits[BL_CODES]/* extra bits for each bit length code */
+ = {0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,3,7};
+
+local const uch bl_order[BL_CODES]
+ = {16,17,18,0,8,7,9,6,10,5,11,4,12,3,13,2,14,1,15};
+/* The lengths of the bit length codes are sent in order of decreasing
+ * probability, to avoid transmitting the lengths for unused bit length codes.
+ */
+
+/* ===========================================================================
+ * Local data. These are initialized only once.
+ */
+
+#define DIST_CODE_LEN 512 /* see definition of array dist_code below */
+
+#if defined(GEN_TREES_H) || !defined(STDC)
+/* non ANSI compilers may not accept trees.h */
+
+local ct_data static_ltree[L_CODES+2];
+/* The static literal tree. Since the bit lengths are imposed, there is no
+ * need for the L_CODES extra codes used during heap construction. However
+ * The codes 286 and 287 are needed to build a canonical tree (see _tr_init
+ * below).
+ */
+
+local ct_data static_dtree[D_CODES];
+/* The static distance tree. (Actually a trivial tree since all codes use
+ * 5 bits.)
+ */
+
+uch _dist_code[DIST_CODE_LEN];
+/* Distance codes. The first 256 values correspond to the distances
+ * 3 .. 258, the last 256 values correspond to the top 8 bits of
+ * the 15 bit distances.
+ */
+
+uch _length_code[MAX_MATCH-MIN_MATCH+1];
+/* length code for each normalized match length (0 == MIN_MATCH) */
+
+local int base_length[LENGTH_CODES];
+/* First normalized length for each code (0 = MIN_MATCH) */
+
+local int base_dist[D_CODES];
+/* First normalized distance for each code (0 = distance of 1) */
+
+#else
+# include "trees.h"
+#endif /* GEN_TREES_H */
+
+struct static_tree_desc_s {
+ const ct_data *static_tree; /* static tree or NULL */
+ const intf *extra_bits; /* extra bits for each code or NULL */
+ int extra_base; /* base index for extra_bits */
+ int elems; /* max number of elements in the tree */
+ int max_length; /* max bit length for the codes */
+};
+
+local static_tree_desc static_l_desc =
+{static_ltree, extra_lbits, LITERALS+1, L_CODES, MAX_BITS};
+
+local static_tree_desc static_d_desc =
+{static_dtree, extra_dbits, 0, D_CODES, MAX_BITS};
+
+local static_tree_desc static_bl_desc =
+{(const ct_data *)0, extra_blbits, 0, BL_CODES, MAX_BL_BITS};
+
+/* ===========================================================================
+ * Local (static) routines in this file.
+ */
+
+local void tr_static_init OF((void));
+local void init_block OF((deflate_state *s));
+local void pqdownheap OF((deflate_state *s, ct_data *tree, int k));
+local void gen_bitlen OF((deflate_state *s, tree_desc *desc));
+local void gen_codes OF((ct_data *tree, int max_code, ushf *bl_count));
+local void build_tree OF((deflate_state *s, tree_desc *desc));
+local void scan_tree OF((deflate_state *s, ct_data *tree, int max_code));
+local void send_tree OF((deflate_state *s, ct_data *tree, int max_code));
+local int build_bl_tree OF((deflate_state *s));
+local void send_all_trees OF((deflate_state *s, int lcodes, int dcodes,
+ int blcodes));
+local void compress_block OF((deflate_state *s, const ct_data *ltree,
+ const ct_data *dtree));
+local int detect_data_type OF((deflate_state *s));
+local unsigned bi_reverse OF((unsigned value, int length));
+local void bi_windup OF((deflate_state *s));
+local void bi_flush OF((deflate_state *s));
+local void copy_block OF((deflate_state *s, charf *buf, unsigned len,
+ int header));
+
+#ifdef GEN_TREES_H
+local void gen_trees_header OF((void));
+#endif
+
+#ifndef DEBUG
+# define send_code(s, c, tree) send_bits(s, tree[c].Code, tree[c].Len)
+ /* Send a code of the given tree. c and tree must not have side effects */
+
+#else /* DEBUG */
+# define send_code(s, c, tree) \
+ { if (z_verbose>2) fprintf(stderr,"\ncd %3d ",(c)); \
+ send_bits(s, tree[c].Code, tree[c].Len); }
+#endif
+
+/* ===========================================================================
+ * Output a short LSB first on the stream.
+ * IN assertion: there is enough room in pendingBuf.
+ */
+#define put_short(s, w) { \
+ put_byte(s, (uch)((w) & 0xff)); \
+ put_byte(s, (uch)((ush)(w) >> 8)); \
+}
+
+/* ===========================================================================
+ * Send a value on a given number of bits.
+ * IN assertion: length <= 16 and value fits in length bits.
+ */
+#ifdef DEBUG
+local void send_bits OF((deflate_state *s, int value, int length));
+
+local void send_bits(s, value, length)
+ deflate_state *s;
+ int value; /* value to send */
+ int length; /* number of bits */
+{
+ Tracevv((stderr," l %2d v %4x ", length, value));
+ Assert(length > 0 && length <= 15, "invalid length");
+ s->bits_sent += (ulg)length;
+
+ /* If not enough room in bi_buf, use (valid) bits from bi_buf and
+ * (16 - bi_valid) bits from value, leaving (width - (16-bi_valid))
+ * unused bits in value.
+ */
+ if (s->bi_valid > (int)Buf_size - length) {
+ s->bi_buf |= (ush)value << s->bi_valid;
+ put_short(s, s->bi_buf);
+ s->bi_buf = (ush)value >> (Buf_size - s->bi_valid);
+ s->bi_valid += length - Buf_size;
+ } else {
+ s->bi_buf |= (ush)value << s->bi_valid;
+ s->bi_valid += length;
+ }
+}
+#else /* !DEBUG */
+
+#define send_bits(s, value, length) \
+{ int len = length;\
+ if (s->bi_valid > (int)Buf_size - len) {\
+ int val = value;\
+ s->bi_buf |= (ush)val << s->bi_valid;\
+ put_short(s, s->bi_buf);\
+ s->bi_buf = (ush)val >> (Buf_size - s->bi_valid);\
+ s->bi_valid += len - Buf_size;\
+ } else {\
+ s->bi_buf |= (ush)(value) << s->bi_valid;\
+ s->bi_valid += len;\
+ }\
+}
+#endif /* DEBUG */
+
+
+/* the arguments must not have side effects */
+
+/* ===========================================================================
+ * Initialize the various 'constant' tables.
+ */
+local void tr_static_init()
+{
+#if defined(GEN_TREES_H) || !defined(STDC)
+ static int static_init_done = 0;
+ int n; /* iterates over tree elements */
+ int bits; /* bit counter */
+ int length; /* length value */
+ int code; /* code value */
+ int dist; /* distance index */
+ ush bl_count[MAX_BITS+1];
+ /* number of codes at each bit length for an optimal tree */
+
+ if (static_init_done) return;
+
+ /* For some embedded targets, global variables are not initialized: */
+#ifdef NO_INIT_GLOBAL_POINTERS
+ static_l_desc.static_tree = static_ltree;
+ static_l_desc.extra_bits = extra_lbits;
+ static_d_desc.static_tree = static_dtree;
+ static_d_desc.extra_bits = extra_dbits;
+ static_bl_desc.extra_bits = extra_blbits;
+#endif
+
+ /* Initialize the mapping length (0..255) -> length code (0..28) */
+ length = 0;
+ for (code = 0; code < LENGTH_CODES-1; code++) {
+ base_length[code] = length;
+ for (n = 0; n < (1<<extra_lbits[code]); n++) {
+ _length_code[length++] = (uch)code;
+ }
+ }
+ Assert (length == 256, "tr_static_init: length != 256");
+ /* Note that the length 255 (match length 258) can be represented
+ * in two different ways: code 284 + 5 bits or code 285, so we
+ * overwrite length_code[255] to use the best encoding:
+ */
+ _length_code[length-1] = (uch)code;
+
+ /* Initialize the mapping dist (0..32K) -> dist code (0..29) */
+ dist = 0;
+ for (code = 0 ; code < 16; code++) {
+ base_dist[code] = dist;
+ for (n = 0; n < (1<<extra_dbits[code]); n++) {
+ _dist_code[dist++] = (uch)code;
+ }
+ }
+ Assert (dist == 256, "tr_static_init: dist != 256");
+ dist >>= 7; /* from now on, all distances are divided by 128 */
+ for ( ; code < D_CODES; code++) {
+ base_dist[code] = dist << 7;
+ for (n = 0; n < (1<<(extra_dbits[code]-7)); n++) {
+ _dist_code[256 + dist++] = (uch)code;
+ }
+ }
+ Assert (dist == 256, "tr_static_init: 256+dist != 512");
+
+ /* Construct the codes of the static literal tree */
+ for (bits = 0; bits <= MAX_BITS; bits++) bl_count[bits] = 0;
+ n = 0;
+ while (n <= 143) static_ltree[n++].Len = 8, bl_count[8]++;
+ while (n <= 255) static_ltree[n++].Len = 9, bl_count[9]++;
+ while (n <= 279) static_ltree[n++].Len = 7, bl_count[7]++;
+ while (n <= 287) static_ltree[n++].Len = 8, bl_count[8]++;
+ /* Codes 286 and 287 do not exist, but we must include them in the
+ * tree construction to get a canonical Huffman tree (longest code
+ * all ones)
+ */
+ gen_codes((ct_data *)static_ltree, L_CODES+1, bl_count);
+
+ /* The static distance tree is trivial: */
+ for (n = 0; n < D_CODES; n++) {
+ static_dtree[n].Len = 5;
+ static_dtree[n].Code = bi_reverse((unsigned)n, 5);
+ }
+ static_init_done = 1;
+
+# ifdef GEN_TREES_H
+ gen_trees_header();
+# endif
+#endif /* defined(GEN_TREES_H) || !defined(STDC) */
+}
+
+/* ===========================================================================
+ * Genererate the file trees.h describing the static trees.
+ */
+#ifdef GEN_TREES_H
+# ifndef DEBUG
+# include <stdio.h>
+# endif
+
+# define SEPARATOR(i, last, width) \
+ ((i) == (last)? "\n};\n\n" : \
+ ((i) % (width) == (width)-1 ? ",\n" : ", "))
+
+void gen_trees_header()
+{
+ FILE *header = fopen("trees.h", "w");
+ int i;
+
+ Assert (header != NULL, "Can't open trees.h");
+ fprintf(header,
+ "/* header created automatically with -DGEN_TREES_H */\n\n");
+
+ fprintf(header, "local const ct_data static_ltree[L_CODES+2] = {\n");
+ for (i = 0; i < L_CODES+2; i++) {
+ fprintf(header, "{{%3u},{%3u}}%s", static_ltree[i].Code,
+ static_ltree[i].Len, SEPARATOR(i, L_CODES+1, 5));
+ }
+
+ fprintf(header, "local const ct_data static_dtree[D_CODES] = {\n");
+ for (i = 0; i < D_CODES; i++) {
+ fprintf(header, "{{%2u},{%2u}}%s", static_dtree[i].Code,
+ static_dtree[i].Len, SEPARATOR(i, D_CODES-1, 5));
+ }
+
+ fprintf(header, "const uch ZLIB_INTERNAL _dist_code[DIST_CODE_LEN] = {\n");
+ for (i = 0; i < DIST_CODE_LEN; i++) {
+ fprintf(header, "%2u%s", _dist_code[i],
+ SEPARATOR(i, DIST_CODE_LEN-1, 20));
+ }
+
+ fprintf(header,
+ "const uch ZLIB_INTERNAL _length_code[MAX_MATCH-MIN_MATCH+1]= {\n");
+ for (i = 0; i < MAX_MATCH-MIN_MATCH+1; i++) {
+ fprintf(header, "%2u%s", _length_code[i],
+ SEPARATOR(i, MAX_MATCH-MIN_MATCH, 20));
+ }
+
+ fprintf(header, "local const int base_length[LENGTH_CODES] = {\n");
+ for (i = 0; i < LENGTH_CODES; i++) {
+ fprintf(header, "%1u%s", base_length[i],
+ SEPARATOR(i, LENGTH_CODES-1, 20));
+ }
+
+ fprintf(header, "local const int base_dist[D_CODES] = {\n");
+ for (i = 0; i < D_CODES; i++) {
+ fprintf(header, "%5u%s", base_dist[i],
+ SEPARATOR(i, D_CODES-1, 10));
+ }
+
+ fclose(header);
+}
+#endif /* GEN_TREES_H */
+
+/* ===========================================================================
+ * Initialize the tree data structures for a new zlib stream.
+ */
+void ZLIB_INTERNAL _tr_init(s)
+ deflate_state *s;
+{
+ tr_static_init();
+
+ s->l_desc.dyn_tree = s->dyn_ltree;
+ s->l_desc.stat_desc = &static_l_desc;
+
+ s->d_desc.dyn_tree = s->dyn_dtree;
+ s->d_desc.stat_desc = &static_d_desc;
+
+ s->bl_desc.dyn_tree = s->bl_tree;
+ s->bl_desc.stat_desc = &static_bl_desc;
+
+ s->bi_buf = 0;
+ s->bi_valid = 0;
+#ifdef DEBUG
+ s->compressed_len = 0L;
+ s->bits_sent = 0L;
+#endif
+
+ /* Initialize the first block of the first file: */
+ init_block(s);
+}
+
+/* ===========================================================================
+ * Initialize a new block.
+ */
+local void init_block(s)
+ deflate_state *s;
+{
+ int n; /* iterates over tree elements */
+
+ /* Initialize the trees. */
+ for (n = 0; n < L_CODES; n++) s->dyn_ltree[n].Freq = 0;
+ for (n = 0; n < D_CODES; n++) s->dyn_dtree[n].Freq = 0;
+ for (n = 0; n < BL_CODES; n++) s->bl_tree[n].Freq = 0;
+
+ s->dyn_ltree[END_BLOCK].Freq = 1;
+ s->opt_len = s->static_len = 0L;
+ s->last_lit = s->matches = 0;
+}
+
+#define SMALLEST 1
+/* Index within the heap array of least frequent node in the Huffman tree */
+
+
+/* ===========================================================================
+ * Remove the smallest element from the heap and recreate the heap with
+ * one less element. Updates heap and heap_len.
+ */
+#define pqremove(s, tree, top) \
+{\
+ top = s->heap[SMALLEST]; \
+ s->heap[SMALLEST] = s->heap[s->heap_len--]; \
+ pqdownheap(s, tree, SMALLEST); \
+}
+
+/* ===========================================================================
+ * Compares to subtrees, using the tree depth as tie breaker when
+ * the subtrees have equal frequency. This minimizes the worst case length.
+ */
+#define smaller(tree, n, m, depth) \
+ (tree[n].Freq < tree[m].Freq || \
+ (tree[n].Freq == tree[m].Freq && depth[n] <= depth[m]))
+
+/* ===========================================================================
+ * Restore the heap property by moving down the tree starting at node k,
+ * exchanging a node with the smallest of its two sons if necessary, stopping
+ * when the heap property is re-established (each father smaller than its
+ * two sons).
+ */
+local void pqdownheap(s, tree, k)
+ deflate_state *s;
+ ct_data *tree; /* the tree to restore */
+ int k; /* node to move down */
+{
+ int v = s->heap[k];
+ int j = k << 1; /* left son of k */
+ while (j <= s->heap_len) {
+ /* Set j to the smallest of the two sons: */
+ if (j < s->heap_len &&
+ smaller(tree, s->heap[j+1], s->heap[j], s->depth)) {
+ j++;
+ }
+ /* Exit if v is smaller than both sons */
+ if (smaller(tree, v, s->heap[j], s->depth)) break;
+
+ /* Exchange v with the smallest son */
+ s->heap[k] = s->heap[j]; k = j;
+
+ /* And continue down the tree, setting j to the left son of k */
+ j <<= 1;
+ }
+ s->heap[k] = v;
+}
+
+/* ===========================================================================
+ * Compute the optimal bit lengths for a tree and update the total bit length
+ * for the current block.
+ * IN assertion: the fields freq and dad are set, heap[heap_max] and
+ * above are the tree nodes sorted by increasing frequency.
+ * OUT assertions: the field len is set to the optimal bit length, the
+ * array bl_count contains the frequencies for each bit length.
+ * The length opt_len is updated; static_len is also updated if stree is
+ * not null.
+ */
+local void gen_bitlen(s, desc)
+ deflate_state *s;
+ tree_desc *desc; /* the tree descriptor */
+{
+ ct_data *tree = desc->dyn_tree;
+ int max_code = desc->max_code;
+ const ct_data *stree = desc->stat_desc->static_tree;
+ const intf *extra = desc->stat_desc->extra_bits;
+ int base = desc->stat_desc->extra_base;
+ int max_length = desc->stat_desc->max_length;
+ int h; /* heap index */
+ int n, m; /* iterate over the tree elements */
+ int bits; /* bit length */
+ int xbits; /* extra bits */
+ ush f; /* frequency */
+ int overflow = 0; /* number of elements with bit length too large */
+
+ for (bits = 0; bits <= MAX_BITS; bits++) s->bl_count[bits] = 0;
+
+ /* In a first pass, compute the optimal bit lengths (which may
+ * overflow in the case of the bit length tree).
+ */
+ tree[s->heap[s->heap_max]].Len = 0; /* root of the heap */
+
+ for (h = s->heap_max+1; h < HEAP_SIZE; h++) {
+ n = s->heap[h];
+ bits = tree[tree[n].Dad].Len + 1;
+ if (bits > max_length) bits = max_length, overflow++;
+ tree[n].Len = (ush)bits;
+ /* We overwrite tree[n].Dad which is no longer needed */
+
+ if (n > max_code) continue; /* not a leaf node */
+
+ s->bl_count[bits]++;
+ xbits = 0;
+ if (n >= base) xbits = extra[n-base];
+ f = tree[n].Freq;
+ s->opt_len += (ulg)f * (bits + xbits);
+ if (stree) s->static_len += (ulg)f * (stree[n].Len + xbits);
+ }
+ if (overflow == 0) return;
+
+ Trace((stderr,"\nbit length overflow\n"));
+ /* This happens for example on obj2 and pic of the Calgary corpus */
+
+ /* Find the first bit length which could increase: */
+ do {
+ bits = max_length-1;
+ while (s->bl_count[bits] == 0) bits--;
+ s->bl_count[bits]--; /* move one leaf down the tree */
+ s->bl_count[bits+1] += 2; /* move one overflow item as its brother */
+ s->bl_count[max_length]--;
+ /* The brother of the overflow item also moves one step up,
+ * but this does not affect bl_count[max_length]
+ */
+ overflow -= 2;
+ } while (overflow > 0);
+
+ /* Now recompute all bit lengths, scanning in increasing frequency.
+ * h is still equal to HEAP_SIZE. (It is simpler to reconstruct all
+ * lengths instead of fixing only the wrong ones. This idea is taken
+ * from 'ar' written by Haruhiko Okumura.)
+ */
+ for (bits = max_length; bits != 0; bits--) {
+ n = s->bl_count[bits];
+ while (n != 0) {
+ m = s->heap[--h];
+ if (m > max_code) continue;
+ if ((unsigned) tree[m].Len != (unsigned) bits) {
+ Trace((stderr,"code %d bits %d->%d\n", m, tree[m].Len, bits));
+ s->opt_len += ((long)bits - (long)tree[m].Len)
+ *(long)tree[m].Freq;
+ tree[m].Len = (ush)bits;
+ }
+ n--;
+ }
+ }
+}
+
+/* ===========================================================================
+ * Generate the codes for a given tree and bit counts (which need not be
+ * optimal).
+ * IN assertion: the array bl_count contains the bit length statistics for
+ * the given tree and the field len is set for all tree elements.
+ * OUT assertion: the field code is set for all tree elements of non
+ * zero code length.
+ */
+local void gen_codes (tree, max_code, bl_count)
+ ct_data *tree; /* the tree to decorate */
+ int max_code; /* largest code with non zero frequency */
+ ushf *bl_count; /* number of codes at each bit length */
+{
+ ush next_code[MAX_BITS+1]; /* next code value for each bit length */
+ ush code = 0; /* running code value */
+ int bits; /* bit index */
+ int n; /* code index */
+
+ /* The distribution counts are first used to generate the code values
+ * without bit reversal.
+ */
+ for (bits = 1; bits <= MAX_BITS; bits++) {
+ next_code[bits] = code = (code + bl_count[bits-1]) << 1;
+ }
+ /* Check that the bit counts in bl_count are consistent. The last code
+ * must be all ones.
+ */
+ Assert (code + bl_count[MAX_BITS]-1 == (1<<MAX_BITS)-1,
+ "inconsistent bit counts");
+ Tracev((stderr,"\ngen_codes: max_code %d ", max_code));
+
+ for (n = 0; n <= max_code; n++) {
+ int len = tree[n].Len;
+ if (len == 0) continue;
+ /* Now reverse the bits */
+ tree[n].Code = bi_reverse(next_code[len]++, len);
+
+ Tracecv(tree != static_ltree, (stderr,"\nn %3d %c l %2d c %4x (%x) ",
+ n, (isgraph(n) ? n : ' '), len, tree[n].Code, next_code[len]-1));
+ }
+}
+
+/* ===========================================================================
+ * Construct one Huffman tree and assigns the code bit strings and lengths.
+ * Update the total bit length for the current block.
+ * IN assertion: the field freq is set for all tree elements.
+ * OUT assertions: the fields len and code are set to the optimal bit length
+ * and corresponding code. The length opt_len is updated; static_len is
+ * also updated if stree is not null. The field max_code is set.
+ */
+local void build_tree(s, desc)
+ deflate_state *s;
+ tree_desc *desc; /* the tree descriptor */
+{
+ ct_data *tree = desc->dyn_tree;
+ const ct_data *stree = desc->stat_desc->static_tree;
+ int elems = desc->stat_desc->elems;
+ int n, m; /* iterate over heap elements */
+ int max_code = -1; /* largest code with non zero frequency */
+ int node; /* new node being created */
+
+ /* Construct the initial heap, with least frequent element in
+ * heap[SMALLEST]. The sons of heap[n] are heap[2*n] and heap[2*n+1].
+ * heap[0] is not used.
+ */
+ s->heap_len = 0, s->heap_max = HEAP_SIZE;
+
+ for (n = 0; n < elems; n++) {
+ if (tree[n].Freq != 0) {
+ s->heap[++(s->heap_len)] = max_code = n;
+ s->depth[n] = 0;
+ } else {
+ tree[n].Len = 0;
+ }
+ }
+
+ /* The pkzip format requires that at least one distance code exists,
+ * and that at least one bit should be sent even if there is only one
+ * possible code. So to avoid special checks later on we force at least
+ * two codes of non zero frequency.
+ */
+ while (s->heap_len < 2) {
+ node = s->heap[++(s->heap_len)] = (max_code < 2 ? ++max_code : 0);
+ tree[node].Freq = 1;
+ s->depth[node] = 0;
+ s->opt_len--; if (stree) s->static_len -= stree[node].Len;
+ /* node is 0 or 1 so it does not have extra bits */
+ }
+ desc->max_code = max_code;
+
+ /* The elements heap[heap_len/2+1 .. heap_len] are leaves of the tree,
+ * establish sub-heaps of increasing lengths:
+ */
+ for (n = s->heap_len/2; n >= 1; n--) pqdownheap(s, tree, n);
+
+ /* Construct the Huffman tree by repeatedly combining the least two
+ * frequent nodes.
+ */
+ node = elems; /* next internal node of the tree */
+ do {
+ pqremove(s, tree, n); /* n = node of least frequency */
+ m = s->heap[SMALLEST]; /* m = node of next least frequency */
+
+ s->heap[--(s->heap_max)] = n; /* keep the nodes sorted by frequency */
+ s->heap[--(s->heap_max)] = m;
+
+ /* Create a new node father of n and m */
+ tree[node].Freq = tree[n].Freq + tree[m].Freq;
+ s->depth[node] = (uch)((s->depth[n] >= s->depth[m] ?
+ s->depth[n] : s->depth[m]) + 1);
+ tree[n].Dad = tree[m].Dad = (ush)node;
+#ifdef DUMP_BL_TREE
+ if (tree == s->bl_tree) {
+ fprintf(stderr,"\nnode %d(%d), sons %d(%d) %d(%d)",
+ node, tree[node].Freq, n, tree[n].Freq, m, tree[m].Freq);
+ }
+#endif
+ /* and insert the new node in the heap */
+ s->heap[SMALLEST] = node++;
+ pqdownheap(s, tree, SMALLEST);
+
+ } while (s->heap_len >= 2);
+
+ s->heap[--(s->heap_max)] = s->heap[SMALLEST];
+
+ /* At this point, the fields freq and dad are set. We can now
+ * generate the bit lengths.
+ */
+ gen_bitlen(s, (tree_desc *)desc);
+
+ /* The field len is now set, we can generate the bit codes */
+ gen_codes ((ct_data *)tree, max_code, s->bl_count);
+}
+
+/* ===========================================================================
+ * Scan a literal or distance tree to determine the frequencies of the codes
+ * in the bit length tree.
+ */
+local void scan_tree (s, tree, max_code)
+ deflate_state *s;
+ ct_data *tree; /* the tree to be scanned */
+ int max_code; /* and its largest code of non zero frequency */
+{
+ int n; /* iterates over all tree elements */
+ int prevlen = -1; /* last emitted length */
+ int curlen; /* length of current code */
+ int nextlen = tree[0].Len; /* length of next code */
+ int count = 0; /* repeat count of the current code */
+ int max_count = 7; /* max repeat count */
+ int min_count = 4; /* min repeat count */
+
+ if (nextlen == 0) max_count = 138, min_count = 3;
+ tree[max_code+1].Len = (ush)0xffff; /* guard */
+
+ for (n = 0; n <= max_code; n++) {
+ curlen = nextlen; nextlen = tree[n+1].Len;
+ if (++count < max_count && curlen == nextlen) {
+ continue;
+ } else if (count < min_count) {
+ s->bl_tree[curlen].Freq += count;
+ } else if (curlen != 0) {
+ if (curlen != prevlen) s->bl_tree[curlen].Freq++;
+ s->bl_tree[REP_3_6].Freq++;
+ } else if (count <= 10) {
+ s->bl_tree[REPZ_3_10].Freq++;
+ } else {
+ s->bl_tree[REPZ_11_138].Freq++;
+ }
+ count = 0; prevlen = curlen;
+ if (nextlen == 0) {
+ max_count = 138, min_count = 3;
+ } else if (curlen == nextlen) {
+ max_count = 6, min_count = 3;
+ } else {
+ max_count = 7, min_count = 4;
+ }
+ }
+}
+
+/* ===========================================================================
+ * Send a literal or distance tree in compressed form, using the codes in
+ * bl_tree.
+ */
+local void send_tree (s, tree, max_code)
+ deflate_state *s;
+ ct_data *tree; /* the tree to be scanned */
+ int max_code; /* and its largest code of non zero frequency */
+{
+ int n; /* iterates over all tree elements */
+ int prevlen = -1; /* last emitted length */
+ int curlen; /* length of current code */
+ int nextlen = tree[0].Len; /* length of next code */
+ int count = 0; /* repeat count of the current code */
+ int max_count = 7; /* max repeat count */
+ int min_count = 4; /* min repeat count */
+
+ /* tree[max_code+1].Len = -1; */ /* guard already set */
+ if (nextlen == 0) max_count = 138, min_count = 3;
+
+ for (n = 0; n <= max_code; n++) {
+ curlen = nextlen; nextlen = tree[n+1].Len;
+ if (++count < max_count && curlen == nextlen) {
+ continue;
+ } else if (count < min_count) {
+ do { send_code(s, curlen, s->bl_tree); } while (--count != 0);
+
+ } else if (curlen != 0) {
+ if (curlen != prevlen) {
+ send_code(s, curlen, s->bl_tree); count--;
+ }
+ Assert(count >= 3 && count <= 6, " 3_6?");
+ send_code(s, REP_3_6, s->bl_tree); send_bits(s, count-3, 2);
+
+ } else if (count <= 10) {
+ send_code(s, REPZ_3_10, s->bl_tree); send_bits(s, count-3, 3);
+
+ } else {
+ send_code(s, REPZ_11_138, s->bl_tree); send_bits(s, count-11, 7);
+ }
+ count = 0; prevlen = curlen;
+ if (nextlen == 0) {
+ max_count = 138, min_count = 3;
+ } else if (curlen == nextlen) {
+ max_count = 6, min_count = 3;
+ } else {
+ max_count = 7, min_count = 4;
+ }
+ }
+}
+
+/* ===========================================================================
+ * Construct the Huffman tree for the bit lengths and return the index in
+ * bl_order of the last bit length code to send.
+ */
+local int build_bl_tree(s)
+ deflate_state *s;
+{
+ int max_blindex; /* index of last bit length code of non zero freq */
+
+ /* Determine the bit length frequencies for literal and distance trees */
+ scan_tree(s, (ct_data *)s->dyn_ltree, s->l_desc.max_code);
+ scan_tree(s, (ct_data *)s->dyn_dtree, s->d_desc.max_code);
+
+ /* Build the bit length tree: */
+ build_tree(s, (tree_desc *)(&(s->bl_desc)));
+ /* opt_len now includes the length of the tree representations, except
+ * the lengths of the bit lengths codes and the 5+5+4 bits for the counts.
+ */
+
+ /* Determine the number of bit length codes to send. The pkzip format
+ * requires that at least 4 bit length codes be sent. (appnote.txt says
+ * 3 but the actual value used is 4.)
+ */
+ for (max_blindex = BL_CODES-1; max_blindex >= 3; max_blindex--) {
+ if (s->bl_tree[bl_order[max_blindex]].Len != 0) break;
+ }
+ /* Update opt_len to include the bit length tree and counts */
+ s->opt_len += 3*(max_blindex+1) + 5+5+4;
+ Tracev((stderr, "\ndyn trees: dyn %ld, stat %ld",
+ s->opt_len, s->static_len));
+
+ return max_blindex;
+}
+
+/* ===========================================================================
+ * Send the header for a block using dynamic Huffman trees: the counts, the
+ * lengths of the bit length codes, the literal tree and the distance tree.
+ * IN assertion: lcodes >= 257, dcodes >= 1, blcodes >= 4.
+ */
+local void send_all_trees(s, lcodes, dcodes, blcodes)
+ deflate_state *s;
+ int lcodes, dcodes, blcodes; /* number of codes for each tree */
+{
+ int rank; /* index in bl_order */
+
+ Assert (lcodes >= 257 && dcodes >= 1 && blcodes >= 4, "not enough codes");
+ Assert (lcodes <= L_CODES && dcodes <= D_CODES && blcodes <= BL_CODES,
+ "too many codes");
+ Tracev((stderr, "\nbl counts: "));
+ send_bits(s, lcodes-257, 5); /* not +255 as stated in appnote.txt */
+ send_bits(s, dcodes-1, 5);
+ send_bits(s, blcodes-4, 4); /* not -3 as stated in appnote.txt */
+ for (rank = 0; rank < blcodes; rank++) {
+ Tracev((stderr, "\nbl code %2d ", bl_order[rank]));
+ send_bits(s, s->bl_tree[bl_order[rank]].Len, 3);
+ }
+ Tracev((stderr, "\nbl tree: sent %ld", s->bits_sent));
+
+ send_tree(s, (ct_data *)s->dyn_ltree, lcodes-1); /* literal tree */
+ Tracev((stderr, "\nlit tree: sent %ld", s->bits_sent));
+
+ send_tree(s, (ct_data *)s->dyn_dtree, dcodes-1); /* distance tree */
+ Tracev((stderr, "\ndist tree: sent %ld", s->bits_sent));
+}
+
+/* ===========================================================================
+ * Send a stored block
+ */
+void ZLIB_INTERNAL _tr_stored_block(s, buf, stored_len, last)
+ deflate_state *s;
+ charf *buf; /* input block */
+ ulg stored_len; /* length of input block */
+ int last; /* one if this is the last block for a file */
+{
+ send_bits(s, (STORED_BLOCK<<1)+last, 3); /* send block type */
+#ifdef DEBUG
+ s->compressed_len = (s->compressed_len + 3 + 7) & (ulg)~7L;
+ s->compressed_len += (stored_len + 4) << 3;
+#endif
+ copy_block(s, buf, (unsigned)stored_len, 1); /* with header */
+}
+
+/* ===========================================================================
+ * Flush the bits in the bit buffer to pending output (leaves at most 7 bits)
+ */
+void ZLIB_INTERNAL _tr_flush_bits(s)
+ deflate_state *s;
+{
+ bi_flush(s);
+}
+
+/* ===========================================================================
+ * Send one empty static block to give enough lookahead for inflate.
+ * This takes 10 bits, of which 7 may remain in the bit buffer.
+ */
+void ZLIB_INTERNAL _tr_align(s)
+ deflate_state *s;
+{
+ send_bits(s, STATIC_TREES<<1, 3);
+ send_code(s, END_BLOCK, static_ltree);
+#ifdef DEBUG
+ s->compressed_len += 10L; /* 3 for block type, 7 for EOB */
+#endif
+ bi_flush(s);
+}
+
+/* ===========================================================================
+ * Determine the best encoding for the current block: dynamic trees, static
+ * trees or store, and output the encoded block to the zip file.
+ */
+void ZLIB_INTERNAL _tr_flush_block(s, buf, stored_len, last)
+ deflate_state *s;
+ charf *buf; /* input block, or NULL if too old */
+ ulg stored_len; /* length of input block */
+ int last; /* one if this is the last block for a file */
+{
+ ulg opt_lenb, static_lenb; /* opt_len and static_len in bytes */
+ int max_blindex = 0; /* index of last bit length code of non zero freq */
+
+ /* Build the Huffman trees unless a stored block is forced */
+ if (s->level > 0) {
+
+ /* Check if the file is binary or text */
+ if (s->strm->data_type == Z_UNKNOWN)
+ s->strm->data_type = detect_data_type(s);
+
+ /* Construct the literal and distance trees */
+ build_tree(s, (tree_desc *)(&(s->l_desc)));
+ Tracev((stderr, "\nlit data: dyn %ld, stat %ld", s->opt_len,
+ s->static_len));
+
+ build_tree(s, (tree_desc *)(&(s->d_desc)));
+ Tracev((stderr, "\ndist data: dyn %ld, stat %ld", s->opt_len,
+ s->static_len));
+ /* At this point, opt_len and static_len are the total bit lengths of
+ * the compressed block data, excluding the tree representations.
+ */
+
+ /* Build the bit length tree for the above two trees, and get the index
+ * in bl_order of the last bit length code to send.
+ */
+ max_blindex = build_bl_tree(s);
+
+ /* Determine the best encoding. Compute the block lengths in bytes. */
+ opt_lenb = (s->opt_len+3+7)>>3;
+ static_lenb = (s->static_len+3+7)>>3;
+
+ Tracev((stderr, "\nopt %lu(%lu) stat %lu(%lu) stored %lu lit %u ",
+ opt_lenb, s->opt_len, static_lenb, s->static_len, stored_len,
+ s->last_lit));
+
+ if (static_lenb <= opt_lenb) opt_lenb = static_lenb;
+
+ } else {
+ Assert(buf != (char*)0, "lost buf");
+ opt_lenb = static_lenb = stored_len + 5; /* force a stored block */
+ }
+
+#ifdef FORCE_STORED
+ if (buf != (char*)0) { /* force stored block */
+#else
+ if (stored_len+4 <= opt_lenb && buf != (char*)0) {
+ /* 4: two words for the lengths */
+#endif
+ /* The test buf != NULL is only necessary if LIT_BUFSIZE > WSIZE.
+ * Otherwise we can't have processed more than WSIZE input bytes since
+ * the last block flush, because compression would have been
+ * successful. If LIT_BUFSIZE <= WSIZE, it is never too late to
+ * transform a block into a stored block.
+ */
+ _tr_stored_block(s, buf, stored_len, last);
+
+#ifdef FORCE_STATIC
+ } else if (static_lenb >= 0) { /* force static trees */
+#else
+ } else if (s->strategy == Z_FIXED || static_lenb == opt_lenb) {
+#endif
+ send_bits(s, (STATIC_TREES<<1)+last, 3);
+ compress_block(s, (const ct_data *)static_ltree,
+ (const ct_data *)static_dtree);
+#ifdef DEBUG
+ s->compressed_len += 3 + s->static_len;
+#endif
+ } else {
+ send_bits(s, (DYN_TREES<<1)+last, 3);
+ send_all_trees(s, s->l_desc.max_code+1, s->d_desc.max_code+1,
+ max_blindex+1);
+ compress_block(s, (const ct_data *)s->dyn_ltree,
+ (const ct_data *)s->dyn_dtree);
+#ifdef DEBUG
+ s->compressed_len += 3 + s->opt_len;
+#endif
+ }
+ Assert (s->compressed_len == s->bits_sent, "bad compressed size");
+ /* The above check is made mod 2^32, for files larger than 512 MB
+ * and uLong implemented on 32 bits.
+ */
+ init_block(s);
+
+ if (last) {
+ bi_windup(s);
+#ifdef DEBUG
+ s->compressed_len += 7; /* align on byte boundary */
+#endif
+ }
+ Tracev((stderr,"\ncomprlen %lu(%lu) ", s->compressed_len>>3,
+ s->compressed_len-7*last));
+}
+
+/* ===========================================================================
+ * Save the match info and tally the frequency counts. Return true if
+ * the current block must be flushed.
+ */
+int ZLIB_INTERNAL _tr_tally (s, dist, lc)
+ deflate_state *s;
+ unsigned dist; /* distance of matched string */
+ unsigned lc; /* match length-MIN_MATCH or unmatched char (if dist==0) */
+{
+ s->d_buf[s->last_lit] = (ush)dist;
+ s->l_buf[s->last_lit++] = (uch)lc;
+ if (dist == 0) {
+ /* lc is the unmatched char */
+ s->dyn_ltree[lc].Freq++;
+ } else {
+ s->matches++;
+ /* Here, lc is the match length - MIN_MATCH */
+ dist--; /* dist = match distance - 1 */
+ Assert((ush)dist < (ush)MAX_DIST(s) &&
+ (ush)lc <= (ush)(MAX_MATCH-MIN_MATCH) &&
+ (ush)d_code(dist) < (ush)D_CODES, "_tr_tally: bad match");
+
+ s->dyn_ltree[_length_code[lc]+LITERALS+1].Freq++;
+ s->dyn_dtree[d_code(dist)].Freq++;
+ }
+
+#ifdef TRUNCATE_BLOCK
+ /* Try to guess if it is profitable to stop the current block here */
+ if ((s->last_lit & 0x1fff) == 0 && s->level > 2) {
+ /* Compute an upper bound for the compressed length */
+ ulg out_length = (ulg)s->last_lit*8L;
+ ulg in_length = (ulg)((long)s->strstart - s->block_start);
+ int dcode;
+ for (dcode = 0; dcode < D_CODES; dcode++) {
+ out_length += (ulg)s->dyn_dtree[dcode].Freq *
+ (5L+extra_dbits[dcode]);
+ }
+ out_length >>= 3;
+ Tracev((stderr,"\nlast_lit %u, in %ld, out ~%ld(%ld%%) ",
+ s->last_lit, in_length, out_length,
+ 100L - out_length*100L/in_length));
+ if (s->matches < s->last_lit/2 && out_length < in_length/2) return 1;
+ }
+#endif
+ return (s->last_lit == s->lit_bufsize-1);
+ /* We avoid equality with lit_bufsize because of wraparound at 64K
+ * on 16 bit machines and because stored blocks are restricted to
+ * 64K-1 bytes.
+ */
+}
+
+/* ===========================================================================
+ * Send the block data compressed using the given Huffman trees
+ */
+local void compress_block(s, ltree, dtree)
+ deflate_state *s;
+ const ct_data *ltree; /* literal tree */
+ const ct_data *dtree; /* distance tree */
+{
+ unsigned dist; /* distance of matched string */
+ int lc; /* match length or unmatched char (if dist == 0) */
+ unsigned lx = 0; /* running index in l_buf */
+ unsigned code; /* the code to send */
+ int extra; /* number of extra bits to send */
+
+ if (s->last_lit != 0) do {
+ dist = s->d_buf[lx];
+ lc = s->l_buf[lx++];
+ if (dist == 0) {
+ send_code(s, lc, ltree); /* send a literal byte */
+ Tracecv(isgraph(lc), (stderr," '%c' ", lc));
+ } else {
+ /* Here, lc is the match length - MIN_MATCH */
+ code = _length_code[lc];
+ send_code(s, code+LITERALS+1, ltree); /* send the length code */
+ extra = extra_lbits[code];
+ if (extra != 0) {
+ lc -= base_length[code];
+ send_bits(s, lc, extra); /* send the extra length bits */
+ }
+ dist--; /* dist is now the match distance - 1 */
+ code = d_code(dist);
+ Assert (code < D_CODES, "bad d_code");
+
+ send_code(s, code, dtree); /* send the distance code */
+ extra = extra_dbits[code];
+ if (extra != 0) {
+ dist -= base_dist[code];
+ send_bits(s, dist, extra); /* send the extra distance bits */
+ }
+ } /* literal or match pair ? */
+
+ /* Check that the overlay between pending_buf and d_buf+l_buf is ok: */
+ Assert((uInt)(s->pending) < s->lit_bufsize + 2*lx,
+ "pendingBuf overflow");
+
+ } while (lx < s->last_lit);
+
+ send_code(s, END_BLOCK, ltree);
+}
+
+/* ===========================================================================
+ * Check if the data type is TEXT or BINARY, using the following algorithm:
+ * - TEXT if the two conditions below are satisfied:
+ * a) There are no non-portable control characters belonging to the
+ * "black list" (0..6, 14..25, 28..31).
+ * b) There is at least one printable character belonging to the
+ * "white list" (9 {TAB}, 10 {LF}, 13 {CR}, 32..255).
+ * - BINARY otherwise.
+ * - The following partially-portable control characters form a
+ * "gray list" that is ignored in this detection algorithm:
+ * (7 {BEL}, 8 {BS}, 11 {VT}, 12 {FF}, 26 {SUB}, 27 {ESC}).
+ * IN assertion: the fields Freq of dyn_ltree are set.
+ */
+local int detect_data_type(s)
+ deflate_state *s;
+{
+ /* black_mask is the bit mask of black-listed bytes
+ * set bits 0..6, 14..25, and 28..31
+ * 0xf3ffc07f = binary 11110011111111111100000001111111
+ */
+ unsigned long black_mask = 0xf3ffc07fUL;
+ int n;
+
+ /* Check for non-textual ("black-listed") bytes. */
+ for (n = 0; n <= 31; n++, black_mask >>= 1)
+ if ((black_mask & 1) && (s->dyn_ltree[n].Freq != 0))
+ return Z_BINARY;
+
+ /* Check for textual ("white-listed") bytes. */
+ if (s->dyn_ltree[9].Freq != 0 || s->dyn_ltree[10].Freq != 0
+ || s->dyn_ltree[13].Freq != 0)
+ return Z_TEXT;
+ for (n = 32; n < LITERALS; n++)
+ if (s->dyn_ltree[n].Freq != 0)
+ return Z_TEXT;
+
+ /* There are no "black-listed" or "white-listed" bytes:
+ * this stream either is empty or has tolerated ("gray-listed") bytes only.
+ */
+ return Z_BINARY;
+}
+
+/* ===========================================================================
+ * Reverse the first len bits of a code, using straightforward code (a faster
+ * method would use a table)
+ * IN assertion: 1 <= len <= 15
+ */
+local unsigned bi_reverse(code, len)
+ unsigned code; /* the value to invert */
+ int len; /* its bit length */
+{
+ register unsigned res = 0;
+ do {
+ res |= code & 1;
+ code >>= 1, res <<= 1;
+ } while (--len > 0);
+ return res >> 1;
+}
+
+/* ===========================================================================
+ * Flush the bit buffer, keeping at most 7 bits in it.
+ */
+local void bi_flush(s)
+ deflate_state *s;
+{
+ if (s->bi_valid == 16) {
+ put_short(s, s->bi_buf);
+ s->bi_buf = 0;
+ s->bi_valid = 0;
+ } else if (s->bi_valid >= 8) {
+ put_byte(s, (Byte)s->bi_buf);
+ s->bi_buf >>= 8;
+ s->bi_valid -= 8;
+ }
+}
+
+/* ===========================================================================
+ * Flush the bit buffer and align the output on a byte boundary
+ */
+local void bi_windup(s)
+ deflate_state *s;
+{
+ if (s->bi_valid > 8) {
+ put_short(s, s->bi_buf);
+ } else if (s->bi_valid > 0) {
+ put_byte(s, (Byte)s->bi_buf);
+ }
+ s->bi_buf = 0;
+ s->bi_valid = 0;
+#ifdef DEBUG
+ s->bits_sent = (s->bits_sent+7) & ~7;
+#endif
+}
+
+/* ===========================================================================
+ * Copy a stored block, storing first the length and its
+ * one's complement if requested.
+ */
+local void copy_block(s, buf, len, header)
+ deflate_state *s;
+ charf *buf; /* the input data */
+ unsigned len; /* its length */
+ int header; /* true if block header must be written */
+{
+ bi_windup(s); /* align on byte boundary */
+
+ if (header) {
+ put_short(s, (ush)len);
+ put_short(s, (ush)~len);
+#ifdef DEBUG
+ s->bits_sent += 2*16;
+#endif
+ }
+#ifdef DEBUG
+ s->bits_sent += (ulg)len<<3;
+#endif
+ while (len--) {
+ put_byte(s, *buf++);
+ }
+}
--- /dev/null
+/* header created automatically with -DGEN_TREES_H */
+
+local const ct_data static_ltree[L_CODES+2] = {
+{{ 12},{ 8}}, {{140},{ 8}}, {{ 76},{ 8}}, {{204},{ 8}}, {{ 44},{ 8}},
+{{172},{ 8}}, {{108},{ 8}}, {{236},{ 8}}, {{ 28},{ 8}}, {{156},{ 8}},
+{{ 92},{ 8}}, {{220},{ 8}}, {{ 60},{ 8}}, {{188},{ 8}}, {{124},{ 8}},
+{{252},{ 8}}, {{ 2},{ 8}}, {{130},{ 8}}, {{ 66},{ 8}}, {{194},{ 8}},
+{{ 34},{ 8}}, {{162},{ 8}}, {{ 98},{ 8}}, {{226},{ 8}}, {{ 18},{ 8}},
+{{146},{ 8}}, {{ 82},{ 8}}, {{210},{ 8}}, {{ 50},{ 8}}, {{178},{ 8}},
+{{114},{ 8}}, {{242},{ 8}}, {{ 10},{ 8}}, {{138},{ 8}}, {{ 74},{ 8}},
+{{202},{ 8}}, {{ 42},{ 8}}, {{170},{ 8}}, {{106},{ 8}}, {{234},{ 8}},
+{{ 26},{ 8}}, {{154},{ 8}}, {{ 90},{ 8}}, {{218},{ 8}}, {{ 58},{ 8}},
+{{186},{ 8}}, {{122},{ 8}}, {{250},{ 8}}, {{ 6},{ 8}}, {{134},{ 8}},
+{{ 70},{ 8}}, {{198},{ 8}}, {{ 38},{ 8}}, {{166},{ 8}}, {{102},{ 8}},
+{{230},{ 8}}, {{ 22},{ 8}}, {{150},{ 8}}, {{ 86},{ 8}}, {{214},{ 8}},
+{{ 54},{ 8}}, {{182},{ 8}}, {{118},{ 8}}, {{246},{ 8}}, {{ 14},{ 8}},
+{{142},{ 8}}, {{ 78},{ 8}}, {{206},{ 8}}, {{ 46},{ 8}}, {{174},{ 8}},
+{{110},{ 8}}, {{238},{ 8}}, {{ 30},{ 8}}, {{158},{ 8}}, {{ 94},{ 8}},
+{{222},{ 8}}, {{ 62},{ 8}}, {{190},{ 8}}, {{126},{ 8}}, {{254},{ 8}},
+{{ 1},{ 8}}, {{129},{ 8}}, {{ 65},{ 8}}, {{193},{ 8}}, {{ 33},{ 8}},
+{{161},{ 8}}, {{ 97},{ 8}}, {{225},{ 8}}, {{ 17},{ 8}}, {{145},{ 8}},
+{{ 81},{ 8}}, {{209},{ 8}}, {{ 49},{ 8}}, {{177},{ 8}}, {{113},{ 8}},
+{{241},{ 8}}, {{ 9},{ 8}}, {{137},{ 8}}, {{ 73},{ 8}}, {{201},{ 8}},
+{{ 41},{ 8}}, {{169},{ 8}}, {{105},{ 8}}, {{233},{ 8}}, {{ 25},{ 8}},
+{{153},{ 8}}, {{ 89},{ 8}}, {{217},{ 8}}, {{ 57},{ 8}}, {{185},{ 8}},
+{{121},{ 8}}, {{249},{ 8}}, {{ 5},{ 8}}, {{133},{ 8}}, {{ 69},{ 8}},
+{{197},{ 8}}, {{ 37},{ 8}}, {{165},{ 8}}, {{101},{ 8}}, {{229},{ 8}},
+{{ 21},{ 8}}, {{149},{ 8}}, {{ 85},{ 8}}, {{213},{ 8}}, {{ 53},{ 8}},
+{{181},{ 8}}, {{117},{ 8}}, {{245},{ 8}}, {{ 13},{ 8}}, {{141},{ 8}},
+{{ 77},{ 8}}, {{205},{ 8}}, {{ 45},{ 8}}, {{173},{ 8}}, {{109},{ 8}},
+{{237},{ 8}}, {{ 29},{ 8}}, {{157},{ 8}}, {{ 93},{ 8}}, {{221},{ 8}},
+{{ 61},{ 8}}, {{189},{ 8}}, {{125},{ 8}}, {{253},{ 8}}, {{ 19},{ 9}},
+{{275},{ 9}}, {{147},{ 9}}, {{403},{ 9}}, {{ 83},{ 9}}, {{339},{ 9}},
+{{211},{ 9}}, {{467},{ 9}}, {{ 51},{ 9}}, {{307},{ 9}}, {{179},{ 9}},
+{{435},{ 9}}, {{115},{ 9}}, {{371},{ 9}}, {{243},{ 9}}, {{499},{ 9}},
+{{ 11},{ 9}}, {{267},{ 9}}, {{139},{ 9}}, {{395},{ 9}}, {{ 75},{ 9}},
+{{331},{ 9}}, {{203},{ 9}}, {{459},{ 9}}, {{ 43},{ 9}}, {{299},{ 9}},
+{{171},{ 9}}, {{427},{ 9}}, {{107},{ 9}}, {{363},{ 9}}, {{235},{ 9}},
+{{491},{ 9}}, {{ 27},{ 9}}, {{283},{ 9}}, {{155},{ 9}}, {{411},{ 9}},
+{{ 91},{ 9}}, {{347},{ 9}}, {{219},{ 9}}, {{475},{ 9}}, {{ 59},{ 9}},
+{{315},{ 9}}, {{187},{ 9}}, {{443},{ 9}}, {{123},{ 9}}, {{379},{ 9}},
+{{251},{ 9}}, {{507},{ 9}}, {{ 7},{ 9}}, {{263},{ 9}}, {{135},{ 9}},
+{{391},{ 9}}, {{ 71},{ 9}}, {{327},{ 9}}, {{199},{ 9}}, {{455},{ 9}},
+{{ 39},{ 9}}, {{295},{ 9}}, {{167},{ 9}}, {{423},{ 9}}, {{103},{ 9}},
+{{359},{ 9}}, {{231},{ 9}}, {{487},{ 9}}, {{ 23},{ 9}}, {{279},{ 9}},
+{{151},{ 9}}, {{407},{ 9}}, {{ 87},{ 9}}, {{343},{ 9}}, {{215},{ 9}},
+{{471},{ 9}}, {{ 55},{ 9}}, {{311},{ 9}}, {{183},{ 9}}, {{439},{ 9}},
+{{119},{ 9}}, {{375},{ 9}}, {{247},{ 9}}, {{503},{ 9}}, {{ 15},{ 9}},
+{{271},{ 9}}, {{143},{ 9}}, {{399},{ 9}}, {{ 79},{ 9}}, {{335},{ 9}},
+{{207},{ 9}}, {{463},{ 9}}, {{ 47},{ 9}}, {{303},{ 9}}, {{175},{ 9}},
+{{431},{ 9}}, {{111},{ 9}}, {{367},{ 9}}, {{239},{ 9}}, {{495},{ 9}},
+{{ 31},{ 9}}, {{287},{ 9}}, {{159},{ 9}}, {{415},{ 9}}, {{ 95},{ 9}},
+{{351},{ 9}}, {{223},{ 9}}, {{479},{ 9}}, {{ 63},{ 9}}, {{319},{ 9}},
+{{191},{ 9}}, {{447},{ 9}}, {{127},{ 9}}, {{383},{ 9}}, {{255},{ 9}},
+{{511},{ 9}}, {{ 0},{ 7}}, {{ 64},{ 7}}, {{ 32},{ 7}}, {{ 96},{ 7}},
+{{ 16},{ 7}}, {{ 80},{ 7}}, {{ 48},{ 7}}, {{112},{ 7}}, {{ 8},{ 7}},
+{{ 72},{ 7}}, {{ 40},{ 7}}, {{104},{ 7}}, {{ 24},{ 7}}, {{ 88},{ 7}},
+{{ 56},{ 7}}, {{120},{ 7}}, {{ 4},{ 7}}, {{ 68},{ 7}}, {{ 36},{ 7}},
+{{100},{ 7}}, {{ 20},{ 7}}, {{ 84},{ 7}}, {{ 52},{ 7}}, {{116},{ 7}},
+{{ 3},{ 8}}, {{131},{ 8}}, {{ 67},{ 8}}, {{195},{ 8}}, {{ 35},{ 8}},
+{{163},{ 8}}, {{ 99},{ 8}}, {{227},{ 8}}
+};
+
+local const ct_data static_dtree[D_CODES] = {
+{{ 0},{ 5}}, {{16},{ 5}}, {{ 8},{ 5}}, {{24},{ 5}}, {{ 4},{ 5}},
+{{20},{ 5}}, {{12},{ 5}}, {{28},{ 5}}, {{ 2},{ 5}}, {{18},{ 5}},
+{{10},{ 5}}, {{26},{ 5}}, {{ 6},{ 5}}, {{22},{ 5}}, {{14},{ 5}},
+{{30},{ 5}}, {{ 1},{ 5}}, {{17},{ 5}}, {{ 9},{ 5}}, {{25},{ 5}},
+{{ 5},{ 5}}, {{21},{ 5}}, {{13},{ 5}}, {{29},{ 5}}, {{ 3},{ 5}},
+{{19},{ 5}}, {{11},{ 5}}, {{27},{ 5}}, {{ 7},{ 5}}, {{23},{ 5}}
+};
+
+const uch ZLIB_INTERNAL _dist_code[DIST_CODE_LEN] = {
+ 0, 1, 2, 3, 4, 4, 5, 5, 6, 6, 6, 6, 7, 7, 7, 7, 8, 8, 8, 8,
+ 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10,
+10, 10, 10, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11,
+11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12,
+12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 13, 13, 13, 13,
+13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13,
+13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
+14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15,
+15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15,
+15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 0, 0, 16, 17,
+18, 18, 19, 19, 20, 20, 20, 20, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22,
+23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25,
+26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26,
+26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27,
+27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27,
+27, 27, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
+28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
+28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28,
+28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
+29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
+29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29,
+29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29
+};
+
+const uch ZLIB_INTERNAL _length_code[MAX_MATCH-MIN_MATCH+1]= {
+ 0, 1, 2, 3, 4, 5, 6, 7, 8, 8, 9, 9, 10, 10, 11, 11, 12, 12, 12, 12,
+13, 13, 13, 13, 14, 14, 14, 14, 15, 15, 15, 15, 16, 16, 16, 16, 16, 16, 16, 16,
+17, 17, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 19, 19, 19, 19,
+19, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 22, 22, 22, 22,
+22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23, 23, 23, 23, 23, 23, 23,
+23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24,
+25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25,
+25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26,
+26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26,
+26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27,
+27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 28
+};
+
+local const int base_length[LENGTH_CODES] = {
+0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 12, 14, 16, 20, 24, 28, 32, 40, 48, 56,
+64, 80, 96, 112, 128, 160, 192, 224, 0
+};
+
+local const int base_dist[D_CODES] = {
+ 0, 1, 2, 3, 4, 6, 8, 12, 16, 24,
+ 32, 48, 64, 96, 128, 192, 256, 384, 512, 768,
+ 1024, 1536, 2048, 3072, 4096, 6144, 8192, 12288, 16384, 24576
+};
+
--- /dev/null
+/* uncompr.c -- decompress a memory buffer
+ * Copyright (C) 1995-2003, 2010 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#define ZLIB_INTERNAL
+#include "zlib.h"
+
+/* ===========================================================================
+ Decompresses the source buffer into the destination buffer. sourceLen is
+ the byte length of the source buffer. Upon entry, destLen is the total
+ size of the destination buffer, which must be large enough to hold the
+ entire uncompressed data. (The size of the uncompressed data must have
+ been saved previously by the compressor and transmitted to the decompressor
+ by some mechanism outside the scope of this compression library.)
+ Upon exit, destLen is the actual size of the compressed buffer.
+
+ uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_BUF_ERROR if there was not enough room in the output
+ buffer, or Z_DATA_ERROR if the input data was corrupted.
+*/
+int ZEXPORT uncompress (dest, destLen, source, sourceLen)
+ Bytef *dest;
+ uLongf *destLen;
+ const Bytef *source;
+ uLong sourceLen;
+{
+ z_stream stream;
+ int err;
+
+ stream.next_in = (z_const Bytef *)source;
+ stream.avail_in = (uInt)sourceLen;
+ /* Check for source > 64K on 16-bit machine: */
+ if ((uLong)stream.avail_in != sourceLen) return Z_BUF_ERROR;
+
+ stream.next_out = dest;
+ stream.avail_out = (uInt)*destLen;
+ if ((uLong)stream.avail_out != *destLen) return Z_BUF_ERROR;
+
+ stream.zalloc = (alloc_func)0;
+ stream.zfree = (free_func)0;
+
+ err = inflateInit(&stream);
+ if (err != Z_OK) return err;
+
+ err = inflate(&stream, Z_FINISH);
+ if (err != Z_STREAM_END) {
+ inflateEnd(&stream);
+ if (err == Z_NEED_DICT || (err == Z_BUF_ERROR && stream.avail_in == 0))
+ return Z_DATA_ERROR;
+ return err;
+ }
+ *destLen = stream.total_out;
+
+ err = inflateEnd(&stream);
+ return err;
+}
--- /dev/null
+/* zconf.h -- configuration of the zlib compression library
+ * Copyright (C) 1995-2013 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#ifndef ZCONF_H
+#define ZCONF_H
+
+#if defined(__MSDOS__) && !defined(MSDOS)
+# define MSDOS
+#endif
+#if (defined(OS_2) || defined(__OS2__)) && !defined(OS2)
+# define OS2
+#endif
+#if defined(_WINDOWS) && !defined(WINDOWS)
+# define WINDOWS
+#endif
+#if defined(_WIN32) || defined(_WIN32_WCE) || defined(__WIN32__)
+# ifndef WIN32
+# define WIN32
+# endif
+#endif
+#if (defined(MSDOS) || defined(OS2) || defined(WINDOWS)) && !defined(WIN32)
+# if !defined(__GNUC__) && !defined(__FLAT__) && !defined(__386__)
+# ifndef SYS16BIT
+# define SYS16BIT
+# endif
+# endif
+#endif
+
+/*
+ * Compile with -DMAXSEG_64K if the alloc function cannot allocate more
+ * than 64k bytes at a time (needed on systems with 16-bit int).
+ */
+#ifdef SYS16BIT
+# define MAXSEG_64K
+#endif
+#ifdef MSDOS
+# define UNALIGNED_OK
+#endif
+
+#ifdef __STDC_VERSION__
+# ifndef STDC
+# define STDC
+# endif
+# if __STDC_VERSION__ >= 199901L
+# ifndef STDC99
+# define STDC99
+# endif
+# endif
+#endif
+#if !defined(STDC) && (defined(__STDC__) || defined(__cplusplus))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(__GNUC__) || defined(__BORLANDC__))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(MSDOS) || defined(WINDOWS) || defined(WIN32))
+# define STDC
+#endif
+#if !defined(STDC) && (defined(OS2) || defined(__HOS_AIX__))
+# define STDC
+#endif
+
+#if defined(__OS400__) && !defined(STDC) /* iSeries (formerly AS/400). */
+# define STDC
+#endif
+
+#ifndef STDC
+# ifndef const /* cannot use !defined(STDC) && !defined(const) on Mac */
+# define const /* note: need a more gentle solution here */
+# endif
+#endif
+
+#if defined(ZLIB_CONST) && !defined(z_const)
+# define z_const const
+#else
+# define z_const
+#endif
+
+/* Some Mac compilers merge all .h files incorrectly: */
+#if defined(__MWERKS__)||defined(applec)||defined(THINK_C)||defined(__SC__)
+# define NO_DUMMY_DECL
+#endif
+
+/* Maximum value for memLevel in deflateInit2 */
+#ifndef MAX_MEM_LEVEL
+# ifdef MAXSEG_64K
+# define MAX_MEM_LEVEL 8
+# else
+# define MAX_MEM_LEVEL 9
+# endif
+#endif
+
+/* Maximum value for windowBits in deflateInit2 and inflateInit2.
+ * WARNING: reducing MAX_WBITS makes minigzip unable to extract .gz files
+ * created by gzip. (Files created by minigzip can still be extracted by
+ * gzip.)
+ */
+#ifndef MAX_WBITS
+# define MAX_WBITS 15 /* 32K LZ77 window */
+#endif
+
+/* The memory requirements for deflate are (in bytes):
+ (1 << (windowBits+2)) + (1 << (memLevel+9))
+ that is: 128K for windowBits=15 + 128K for memLevel = 8 (default values)
+ plus a few kilobytes for small objects. For example, if you want to reduce
+ the default memory requirements from 256K to 128K, compile with
+ make CFLAGS="-O -DMAX_WBITS=14 -DMAX_MEM_LEVEL=7"
+ Of course this will generally degrade compression (there's no free lunch).
+
+ The memory requirements for inflate are (in bytes) 1 << windowBits
+ that is, 32K for windowBits=15 (default value) plus a few kilobytes
+ for small objects.
+*/
+
+ /* Type declarations */
+
+#ifndef OF /* function prototypes */
+# ifdef STDC
+# define OF(args) args
+# else
+# define OF(args) ()
+# endif
+#endif
+
+#ifndef Z_ARG /* function prototypes for stdarg */
+# if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# define Z_ARG(args) args
+# else
+# define Z_ARG(args) ()
+# endif
+#endif
+
+/* The following definitions for FAR are needed only for MSDOS mixed
+ * model programming (small or medium model with some far allocations).
+ * This was tested only with MSC; for other MSDOS compilers you may have
+ * to define NO_MEMCPY in zutil.h. If you don't need the mixed model,
+ * just define FAR to be empty.
+ */
+#ifdef SYS16BIT
+# if defined(M_I86SM) || defined(M_I86MM)
+ /* MSC small or medium model */
+# define SMALL_MEDIUM
+# ifdef _MSC_VER
+# define FAR _far
+# else
+# define FAR far
+# endif
+# endif
+# if (defined(__SMALL__) || defined(__MEDIUM__))
+ /* Turbo C small or medium model */
+# define SMALL_MEDIUM
+# ifdef __BORLANDC__
+# define FAR _far
+# else
+# define FAR far
+# endif
+# endif
+#endif
+
+#if defined(WINDOWS) || defined(WIN32)
+ /* If building or using zlib as a DLL, define ZLIB_DLL.
+ * This is not mandatory, but it offers a little performance increase.
+ */
+# ifdef ZLIB_DLL
+# if defined(WIN32) && (!defined(__BORLANDC__) || (__BORLANDC__ >= 0x500))
+# ifdef ZLIB_INTERNAL
+# define ZEXTERN extern __declspec(dllexport)
+# else
+# define ZEXTERN extern __declspec(dllimport)
+# endif
+# endif
+# endif /* ZLIB_DLL */
+ /* If building or using zlib with the WINAPI/WINAPIV calling convention,
+ * define ZLIB_WINAPI.
+ * Caution: the standard ZLIB1.DLL is NOT compiled using ZLIB_WINAPI.
+ */
+# ifdef ZLIB_WINAPI
+# ifdef FAR
+# undef FAR
+# endif
+# include <windows.h>
+ /* No need for _export, use ZLIB.DEF instead. */
+ /* For complete Windows compatibility, use WINAPI, not __stdcall. */
+# define ZEXPORT WINAPI
+# ifdef WIN32
+# define ZEXPORTVA WINAPIV
+# else
+# define ZEXPORTVA FAR CDECL
+# endif
+# endif
+#endif
+
+#if defined (__BEOS__)
+# ifdef ZLIB_DLL
+# ifdef ZLIB_INTERNAL
+# define ZEXPORT __declspec(dllexport)
+# define ZEXPORTVA __declspec(dllexport)
+# else
+# define ZEXPORT __declspec(dllimport)
+# define ZEXPORTVA __declspec(dllimport)
+# endif
+# endif
+#endif
+
+#ifndef ZEXTERN
+# define ZEXTERN extern
+#endif
+#ifndef ZEXPORT
+# define ZEXPORT
+#endif
+#ifndef ZEXPORTVA
+# define ZEXPORTVA
+#endif
+
+#ifndef FAR
+# define FAR
+#endif
+
+#if !defined(__MACTYPES__)
+typedef unsigned char Byte; /* 8 bits */
+#endif
+typedef unsigned int uInt; /* 16 bits or more */
+typedef unsigned long uLong; /* 32 bits or more */
+
+#ifdef SMALL_MEDIUM
+ /* Borland C/C++ and some old MSC versions ignore FAR inside typedef */
+# define Bytef Byte FAR
+#else
+ typedef Byte FAR Bytef;
+#endif
+typedef char FAR charf;
+typedef int FAR intf;
+typedef uInt FAR uIntf;
+typedef uLong FAR uLongf;
+
+#ifdef STDC
+ typedef void const *voidpc;
+ typedef void FAR *voidpf;
+ typedef void *voidp;
+#else
+ typedef Byte const *voidpc;
+ typedef Byte FAR *voidpf;
+ typedef Byte *voidp;
+#endif
+
+#if !defined(Z_U4) && !defined(Z_SOLO) && defined(STDC)
+# include <limits.h>
+# if (UINT_MAX == 0xffffffffUL)
+# define Z_U4 unsigned
+# elif (ULONG_MAX == 0xffffffffUL)
+# define Z_U4 unsigned long
+# elif (USHRT_MAX == 0xffffffffUL)
+# define Z_U4 unsigned short
+# endif
+#endif
+
+#ifdef Z_U4
+ typedef Z_U4 z_crc_t;
+#else
+ typedef unsigned long z_crc_t;
+#endif
+
+#ifdef HAVE_UNISTD_H /* may be set to #if 1 by ./configure */
+# define Z_HAVE_UNISTD_H
+#endif
+
+#ifdef HAVE_STDARG_H /* may be set to #if 1 by ./configure */
+# define Z_HAVE_STDARG_H
+#endif
+
+#ifdef STDC
+# ifndef Z_SOLO
+# include <sys/types.h> /* for off_t */
+# endif
+#endif
+
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# ifndef Z_SOLO
+# include <stdarg.h> /* for va_list */
+# endif
+#endif
+
+#ifdef _WIN32
+# ifndef Z_SOLO
+# include <stddef.h> /* for wchar_t */
+# endif
+#endif
+
+/* a little trick to accommodate both "#define _LARGEFILE64_SOURCE" and
+ * "#define _LARGEFILE64_SOURCE 1" as requesting 64-bit operations, (even
+ * though the former does not conform to the LFS document), but considering
+ * both "#undef _LARGEFILE64_SOURCE" and "#define _LARGEFILE64_SOURCE 0" as
+ * equivalently requesting no 64-bit operations
+ */
+#if defined(_LARGEFILE64_SOURCE) && -_LARGEFILE64_SOURCE - -1 == 1
+# undef _LARGEFILE64_SOURCE
+#endif
+
+#if defined(__WATCOMC__) && !defined(Z_HAVE_UNISTD_H)
+# define Z_HAVE_UNISTD_H
+#endif
+#ifndef Z_SOLO
+# if defined(Z_HAVE_UNISTD_H) || defined(_LARGEFILE64_SOURCE)
+# include <unistd.h> /* for SEEK_*, off_t, and _LFS64_LARGEFILE */
+# ifdef VMS
+# include <unixio.h> /* for off_t */
+# endif
+# ifndef z_off_t
+# define z_off_t off_t
+# endif
+# endif
+#endif
+
+#if defined(_LFS64_LARGEFILE) && _LFS64_LARGEFILE-0
+# define Z_LFS64
+#endif
+
+#if defined(_LARGEFILE64_SOURCE) && defined(Z_LFS64)
+# define Z_LARGE64
+#endif
+
+#if defined(_FILE_OFFSET_BITS) && _FILE_OFFSET_BITS-0 == 64 && defined(Z_LFS64)
+# define Z_WANT64
+#endif
+
+#if !defined(SEEK_SET) && !defined(Z_SOLO)
+# define SEEK_SET 0 /* Seek from beginning of file. */
+# define SEEK_CUR 1 /* Seek from current position. */
+# define SEEK_END 2 /* Set file pointer to EOF plus "offset" */
+#endif
+
+#ifndef z_off_t
+# define z_off_t long
+#endif
+
+#if !defined(_WIN32) && defined(Z_LARGE64)
+# define z_off64_t off64_t
+#else
+# if defined(_WIN32) && !defined(__GNUC__) && !defined(Z_SOLO)
+# define z_off64_t __int64
+# else
+# define z_off64_t z_off_t
+# endif
+#endif
+
+/* MVS linker does not support external names larger than 8 bytes */
+#if defined(__MVS__)
+ #pragma map(deflateInit_,"DEIN")
+ #pragma map(deflateInit2_,"DEIN2")
+ #pragma map(deflateEnd,"DEEND")
+ #pragma map(deflateBound,"DEBND")
+ #pragma map(inflateInit_,"ININ")
+ #pragma map(inflateInit2_,"ININ2")
+ #pragma map(inflateEnd,"INEND")
+ #pragma map(inflateSync,"INSY")
+ #pragma map(inflateSetDictionary,"INSEDI")
+ #pragma map(compressBound,"CMBND")
+ #pragma map(inflate_table,"INTABL")
+ #pragma map(inflate_fast,"INFA")
+ #pragma map(inflate_copyright,"INCOPY")
+#endif
+
+#endif /* ZCONF_H */
--- /dev/null
+/* zlib.h -- interface of the 'zlib' general purpose compression library
+ version 1.2.8, April 28th, 2013
+
+ Copyright (C) 1995-2013 Jean-loup Gailly and Mark Adler
+
+ This software is provided 'as-is', without any express or implied
+ warranty. In no event will the authors be held liable for any damages
+ arising from the use of this software.
+
+ Permission is granted to anyone to use this software for any purpose,
+ including commercial applications, and to alter it and redistribute it
+ freely, subject to the following restrictions:
+
+ 1. The origin of this software must not be misrepresented; you must not
+ claim that you wrote the original software. If you use this software
+ in a product, an acknowledgment in the product documentation would be
+ appreciated but is not required.
+ 2. Altered source versions must be plainly marked as such, and must not be
+ misrepresented as being the original software.
+ 3. This notice may not be removed or altered from any source distribution.
+
+ Jean-loup Gailly Mark Adler
+ jloup@gzip.org madler@alumni.caltech.edu
+
+
+ The data format used by the zlib library is described by RFCs (Request for
+ Comments) 1950 to 1952 in the files http://tools.ietf.org/html/rfc1950
+ (zlib format), rfc1951 (deflate format) and rfc1952 (gzip format).
+*/
+
+#ifndef ZLIB_H
+#define ZLIB_H
+
+#include "zconf.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+#define ZLIB_VERSION "1.2.8"
+#define ZLIB_VERNUM 0x1280
+#define ZLIB_VER_MAJOR 1
+#define ZLIB_VER_MINOR 2
+#define ZLIB_VER_REVISION 8
+#define ZLIB_VER_SUBREVISION 0
+
+/*
+ The 'zlib' compression library provides in-memory compression and
+ decompression functions, including integrity checks of the uncompressed data.
+ This version of the library supports only one compression method (deflation)
+ but other algorithms will be added later and will have the same stream
+ interface.
+
+ Compression can be done in a single step if the buffers are large enough,
+ or can be done by repeated calls of the compression function. In the latter
+ case, the application must provide more input and/or consume the output
+ (providing more output space) before each call.
+
+ The compressed data format used by default by the in-memory functions is
+ the zlib format, which is a zlib wrapper documented in RFC 1950, wrapped
+ around a deflate stream, which is itself documented in RFC 1951.
+
+ The library also supports reading and writing files in gzip (.gz) format
+ with an interface similar to that of stdio using the functions that start
+ with "gz". The gzip format is different from the zlib format. gzip is a
+ gzip wrapper, documented in RFC 1952, wrapped around a deflate stream.
+
+ This library can optionally read and write gzip streams in memory as well.
+
+ The zlib format was designed to be compact and fast for use in memory
+ and on communications channels. The gzip format was designed for single-
+ file compression on file systems, has a larger header than zlib to maintain
+ directory information, and uses a different, slower check method than zlib.
+
+ The library does not install any signal handler. The decoder checks
+ the consistency of the compressed data, so the library should never crash
+ even in case of corrupted input.
+*/
+
+typedef voidpf (*alloc_func) OF((voidpf opaque, uInt items, uInt size));
+typedef void (*free_func) OF((voidpf opaque, voidpf address));
+
+struct internal_state;
+
+typedef struct z_stream_s {
+ z_const Bytef *next_in; /* next input byte */
+ uInt avail_in; /* number of bytes available at next_in */
+ uLong total_in; /* total number of input bytes read so far */
+
+ Bytef *next_out; /* next output byte should be put there */
+ uInt avail_out; /* remaining free space at next_out */
+ uLong total_out; /* total number of bytes output so far */
+
+ z_const char *msg; /* last error message, NULL if no error */
+ struct internal_state FAR *state; /* not visible by applications */
+
+ alloc_func zalloc; /* used to allocate the internal state */
+ free_func zfree; /* used to free the internal state */
+ voidpf opaque; /* private data object passed to zalloc and zfree */
+
+ int data_type; /* best guess about the data type: binary or text */
+ uLong adler; /* adler32 value of the uncompressed data */
+ uLong reserved; /* reserved for future use */
+} z_stream;
+
+typedef z_stream FAR *z_streamp;
+
+/*
+ gzip header information passed to and from zlib routines. See RFC 1952
+ for more details on the meanings of these fields.
+*/
+typedef struct gz_header_s {
+ int text; /* true if compressed data believed to be text */
+ uLong time; /* modification time */
+ int xflags; /* extra flags (not used when writing a gzip file) */
+ int os; /* operating system */
+ Bytef *extra; /* pointer to extra field or Z_NULL if none */
+ uInt extra_len; /* extra field length (valid if extra != Z_NULL) */
+ uInt extra_max; /* space at extra (only when reading header) */
+ Bytef *name; /* pointer to zero-terminated file name or Z_NULL */
+ uInt name_max; /* space at name (only when reading header) */
+ Bytef *comment; /* pointer to zero-terminated comment or Z_NULL */
+ uInt comm_max; /* space at comment (only when reading header) */
+ int hcrc; /* true if there was or will be a header crc */
+ int done; /* true when done reading gzip header (not used
+ when writing a gzip file) */
+} gz_header;
+
+typedef gz_header FAR *gz_headerp;
+
+/*
+ The application must update next_in and avail_in when avail_in has dropped
+ to zero. It must update next_out and avail_out when avail_out has dropped
+ to zero. The application must initialize zalloc, zfree and opaque before
+ calling the init function. All other fields are set by the compression
+ library and must not be updated by the application.
+
+ The opaque value provided by the application will be passed as the first
+ parameter for calls of zalloc and zfree. This can be useful for custom
+ memory management. The compression library attaches no meaning to the
+ opaque value.
+
+ zalloc must return Z_NULL if there is not enough memory for the object.
+ If zlib is used in a multi-threaded application, zalloc and zfree must be
+ thread safe.
+
+ On 16-bit systems, the functions zalloc and zfree must be able to allocate
+ exactly 65536 bytes, but will not be required to allocate more than this if
+ the symbol MAXSEG_64K is defined (see zconf.h). WARNING: On MSDOS, pointers
+ returned by zalloc for objects of exactly 65536 bytes *must* have their
+ offset normalized to zero. The default allocation function provided by this
+ library ensures this (see zutil.c). To reduce memory requirements and avoid
+ any allocation of 64K objects, at the expense of compression ratio, compile
+ the library with -DMAX_WBITS=14 (see zconf.h).
+
+ The fields total_in and total_out can be used for statistics or progress
+ reports. After compression, total_in holds the total size of the
+ uncompressed data and may be saved for use in the decompressor (particularly
+ if the decompressor wants to decompress everything in a single step).
+*/
+
+ /* constants */
+
+#define Z_NO_FLUSH 0
+#define Z_PARTIAL_FLUSH 1
+#define Z_SYNC_FLUSH 2
+#define Z_FULL_FLUSH 3
+#define Z_FINISH 4
+#define Z_BLOCK 5
+#define Z_TREES 6
+/* Allowed flush values; see deflate() and inflate() below for details */
+
+#define Z_OK 0
+#define Z_STREAM_END 1
+#define Z_NEED_DICT 2
+#define Z_ERRNO (-1)
+#define Z_STREAM_ERROR (-2)
+#define Z_DATA_ERROR (-3)
+#define Z_MEM_ERROR (-4)
+#define Z_BUF_ERROR (-5)
+#define Z_VERSION_ERROR (-6)
+/* Return codes for the compression/decompression functions. Negative values
+ * are errors, positive values are used for special but normal events.
+ */
+
+#define Z_NO_COMPRESSION 0
+#define Z_BEST_SPEED 1
+#define Z_BEST_COMPRESSION 9
+#define Z_DEFAULT_COMPRESSION (-1)
+/* compression levels */
+
+#define Z_FILTERED 1
+#define Z_HUFFMAN_ONLY 2
+#define Z_RLE 3
+#define Z_FIXED 4
+#define Z_DEFAULT_STRATEGY 0
+/* compression strategy; see deflateInit2() below for details */
+
+#define Z_BINARY 0
+#define Z_TEXT 1
+#define Z_ASCII Z_TEXT /* for compatibility with 1.2.2 and earlier */
+#define Z_UNKNOWN 2
+/* Possible values of the data_type field (though see inflate()) */
+
+#define Z_DEFLATED 8
+/* The deflate compression method (the only one supported in this version) */
+
+#define Z_NULL 0 /* for initializing zalloc, zfree, opaque */
+
+#define zlib_version zlibVersion()
+/* for compatibility with versions < 1.0.2 */
+
+
+ /* basic functions */
+
+ZEXTERN const char * ZEXPORT zlibVersion OF((void));
+/* The application can compare zlibVersion and ZLIB_VERSION for consistency.
+ If the first character differs, the library code actually used is not
+ compatible with the zlib.h header file used by the application. This check
+ is automatically made by deflateInit and inflateInit.
+ */
+
+/*
+ZEXTERN int ZEXPORT deflateInit OF((z_streamp strm, int level));
+
+ Initializes the internal stream state for compression. The fields
+ zalloc, zfree and opaque must be initialized before by the caller. If
+ zalloc and zfree are set to Z_NULL, deflateInit updates them to use default
+ allocation functions.
+
+ The compression level must be Z_DEFAULT_COMPRESSION, or between 0 and 9:
+ 1 gives best speed, 9 gives best compression, 0 gives no compression at all
+ (the input data is simply copied a block at a time). Z_DEFAULT_COMPRESSION
+ requests a default compromise between speed and compression (currently
+ equivalent to level 6).
+
+ deflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_STREAM_ERROR if level is not a valid compression level, or
+ Z_VERSION_ERROR if the zlib library version (zlib_version) is incompatible
+ with the version assumed by the caller (ZLIB_VERSION). msg is set to null
+ if there is no error message. deflateInit does not perform any compression:
+ this will be done by deflate().
+*/
+
+
+ZEXTERN int ZEXPORT deflate OF((z_streamp strm, int flush));
+/*
+ deflate compresses as much data as possible, and stops when the input
+ buffer becomes empty or the output buffer becomes full. It may introduce
+ some output latency (reading input without producing any output) except when
+ forced to flush.
+
+ The detailed semantics are as follows. deflate performs one or both of the
+ following actions:
+
+ - Compress more input starting at next_in and update next_in and avail_in
+ accordingly. If not all input can be processed (because there is not
+ enough room in the output buffer), next_in and avail_in are updated and
+ processing will resume at this point for the next call of deflate().
+
+ - Provide more output starting at next_out and update next_out and avail_out
+ accordingly. This action is forced if the parameter flush is non zero.
+ Forcing flush frequently degrades the compression ratio, so this parameter
+ should be set only when necessary (in interactive applications). Some
+ output may be provided even if flush is not set.
+
+ Before the call of deflate(), the application should ensure that at least
+ one of the actions is possible, by providing more input and/or consuming more
+ output, and updating avail_in or avail_out accordingly; avail_out should
+ never be zero before the call. The application can consume the compressed
+ output when it wants, for example when the output buffer is full (avail_out
+ == 0), or after each call of deflate(). If deflate returns Z_OK and with
+ zero avail_out, it must be called again after making room in the output
+ buffer because there might be more output pending.
+
+ Normally the parameter flush is set to Z_NO_FLUSH, which allows deflate to
+ decide how much data to accumulate before producing output, in order to
+ maximize compression.
+
+ If the parameter flush is set to Z_SYNC_FLUSH, all pending output is
+ flushed to the output buffer and the output is aligned on a byte boundary, so
+ that the decompressor can get all input data available so far. (In
+ particular avail_in is zero after the call if enough output space has been
+ provided before the call.) Flushing may degrade compression for some
+ compression algorithms and so it should be used only when necessary. This
+ completes the current deflate block and follows it with an empty stored block
+ that is three bits plus filler bits to the next byte, followed by four bytes
+ (00 00 ff ff).
+
+ If flush is set to Z_PARTIAL_FLUSH, all pending output is flushed to the
+ output buffer, but the output is not aligned to a byte boundary. All of the
+ input data so far will be available to the decompressor, as for Z_SYNC_FLUSH.
+ This completes the current deflate block and follows it with an empty fixed
+ codes block that is 10 bits long. This assures that enough bytes are output
+ in order for the decompressor to finish the block before the empty fixed code
+ block.
+
+ If flush is set to Z_BLOCK, a deflate block is completed and emitted, as
+ for Z_SYNC_FLUSH, but the output is not aligned on a byte boundary, and up to
+ seven bits of the current block are held to be written as the next byte after
+ the next deflate block is completed. In this case, the decompressor may not
+ be provided enough bits at this point in order to complete decompression of
+ the data provided so far to the compressor. It may need to wait for the next
+ block to be emitted. This is for advanced applications that need to control
+ the emission of deflate blocks.
+
+ If flush is set to Z_FULL_FLUSH, all output is flushed as with
+ Z_SYNC_FLUSH, and the compression state is reset so that decompression can
+ restart from this point if previous compressed data has been damaged or if
+ random access is desired. Using Z_FULL_FLUSH too often can seriously degrade
+ compression.
+
+ If deflate returns with avail_out == 0, this function must be called again
+ with the same value of the flush parameter and more output space (updated
+ avail_out), until the flush is complete (deflate returns with non-zero
+ avail_out). In the case of a Z_FULL_FLUSH or Z_SYNC_FLUSH, make sure that
+ avail_out is greater than six to avoid repeated flush markers due to
+ avail_out == 0 on return.
+
+ If the parameter flush is set to Z_FINISH, pending input is processed,
+ pending output is flushed and deflate returns with Z_STREAM_END if there was
+ enough output space; if deflate returns with Z_OK, this function must be
+ called again with Z_FINISH and more output space (updated avail_out) but no
+ more input data, until it returns with Z_STREAM_END or an error. After
+ deflate has returned Z_STREAM_END, the only possible operations on the stream
+ are deflateReset or deflateEnd.
+
+ Z_FINISH can be used immediately after deflateInit if all the compression
+ is to be done in a single step. In this case, avail_out must be at least the
+ value returned by deflateBound (see below). Then deflate is guaranteed to
+ return Z_STREAM_END. If not enough output space is provided, deflate will
+ not return Z_STREAM_END, and it must be called again as described above.
+
+ deflate() sets strm->adler to the adler32 checksum of all input read
+ so far (that is, total_in bytes).
+
+ deflate() may update strm->data_type if it can make a good guess about
+ the input data type (Z_BINARY or Z_TEXT). In doubt, the data is considered
+ binary. This field is only for information purposes and does not affect the
+ compression algorithm in any manner.
+
+ deflate() returns Z_OK if some progress has been made (more input
+ processed or more output produced), Z_STREAM_END if all input has been
+ consumed and all output has been produced (only when flush is set to
+ Z_FINISH), Z_STREAM_ERROR if the stream state was inconsistent (for example
+ if next_in or next_out was Z_NULL), Z_BUF_ERROR if no progress is possible
+ (for example avail_in or avail_out was zero). Note that Z_BUF_ERROR is not
+ fatal, and deflate() can be called again with more input and more output
+ space to continue compressing.
+*/
+
+
+ZEXTERN int ZEXPORT deflateEnd OF((z_streamp strm));
+/*
+ All dynamically allocated data structures for this stream are freed.
+ This function discards any unprocessed input and does not flush any pending
+ output.
+
+ deflateEnd returns Z_OK if success, Z_STREAM_ERROR if the
+ stream state was inconsistent, Z_DATA_ERROR if the stream was freed
+ prematurely (some input or output was discarded). In the error case, msg
+ may be set but then points to a static string (which must not be
+ deallocated).
+*/
+
+
+/*
+ZEXTERN int ZEXPORT inflateInit OF((z_streamp strm));
+
+ Initializes the internal stream state for decompression. The fields
+ next_in, avail_in, zalloc, zfree and opaque must be initialized before by
+ the caller. If next_in is not Z_NULL and avail_in is large enough (the
+ exact value depends on the compression method), inflateInit determines the
+ compression method from the zlib header and allocates all data structures
+ accordingly; otherwise the allocation will be deferred to the first call of
+ inflate. If zalloc and zfree are set to Z_NULL, inflateInit updates them to
+ use default allocation functions.
+
+ inflateInit returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
+ version assumed by the caller, or Z_STREAM_ERROR if the parameters are
+ invalid, such as a null pointer to the structure. msg is set to null if
+ there is no error message. inflateInit does not perform any decompression
+ apart from possibly reading the zlib header if present: actual decompression
+ will be done by inflate(). (So next_in and avail_in may be modified, but
+ next_out and avail_out are unused and unchanged.) The current implementation
+ of inflateInit() does not process any header information -- that is deferred
+ until inflate() is called.
+*/
+
+
+ZEXTERN int ZEXPORT inflate OF((z_streamp strm, int flush));
+/*
+ inflate decompresses as much data as possible, and stops when the input
+ buffer becomes empty or the output buffer becomes full. It may introduce
+ some output latency (reading input without producing any output) except when
+ forced to flush.
+
+ The detailed semantics are as follows. inflate performs one or both of the
+ following actions:
+
+ - Decompress more input starting at next_in and update next_in and avail_in
+ accordingly. If not all input can be processed (because there is not
+ enough room in the output buffer), next_in is updated and processing will
+ resume at this point for the next call of inflate().
+
+ - Provide more output starting at next_out and update next_out and avail_out
+ accordingly. inflate() provides as much output as possible, until there is
+ no more input data or no more space in the output buffer (see below about
+ the flush parameter).
+
+ Before the call of inflate(), the application should ensure that at least
+ one of the actions is possible, by providing more input and/or consuming more
+ output, and updating the next_* and avail_* values accordingly. The
+ application can consume the uncompressed output when it wants, for example
+ when the output buffer is full (avail_out == 0), or after each call of
+ inflate(). If inflate returns Z_OK and with zero avail_out, it must be
+ called again after making room in the output buffer because there might be
+ more output pending.
+
+ The flush parameter of inflate() can be Z_NO_FLUSH, Z_SYNC_FLUSH, Z_FINISH,
+ Z_BLOCK, or Z_TREES. Z_SYNC_FLUSH requests that inflate() flush as much
+ output as possible to the output buffer. Z_BLOCK requests that inflate()
+ stop if and when it gets to the next deflate block boundary. When decoding
+ the zlib or gzip format, this will cause inflate() to return immediately
+ after the header and before the first block. When doing a raw inflate,
+ inflate() will go ahead and process the first block, and will return when it
+ gets to the end of that block, or when it runs out of data.
+
+ The Z_BLOCK option assists in appending to or combining deflate streams.
+ Also to assist in this, on return inflate() will set strm->data_type to the
+ number of unused bits in the last byte taken from strm->next_in, plus 64 if
+ inflate() is currently decoding the last block in the deflate stream, plus
+ 128 if inflate() returned immediately after decoding an end-of-block code or
+ decoding the complete header up to just before the first byte of the deflate
+ stream. The end-of-block will not be indicated until all of the uncompressed
+ data from that block has been written to strm->next_out. The number of
+ unused bits may in general be greater than seven, except when bit 7 of
+ data_type is set, in which case the number of unused bits will be less than
+ eight. data_type is set as noted here every time inflate() returns for all
+ flush options, and so can be used to determine the amount of currently
+ consumed input in bits.
+
+ The Z_TREES option behaves as Z_BLOCK does, but it also returns when the
+ end of each deflate block header is reached, before any actual data in that
+ block is decoded. This allows the caller to determine the length of the
+ deflate block header for later use in random access within a deflate block.
+ 256 is added to the value of strm->data_type when inflate() returns
+ immediately after reaching the end of the deflate block header.
+
+ inflate() should normally be called until it returns Z_STREAM_END or an
+ error. However if all decompression is to be performed in a single step (a
+ single call of inflate), the parameter flush should be set to Z_FINISH. In
+ this case all pending input is processed and all pending output is flushed;
+ avail_out must be large enough to hold all of the uncompressed data for the
+ operation to complete. (The size of the uncompressed data may have been
+ saved by the compressor for this purpose.) The use of Z_FINISH is not
+ required to perform an inflation in one step. However it may be used to
+ inform inflate that a faster approach can be used for the single inflate()
+ call. Z_FINISH also informs inflate to not maintain a sliding window if the
+ stream completes, which reduces inflate's memory footprint. If the stream
+ does not complete, either because not all of the stream is provided or not
+ enough output space is provided, then a sliding window will be allocated and
+ inflate() can be called again to continue the operation as if Z_NO_FLUSH had
+ been used.
+
+ In this implementation, inflate() always flushes as much output as
+ possible to the output buffer, and always uses the faster approach on the
+ first call. So the effects of the flush parameter in this implementation are
+ on the return value of inflate() as noted below, when inflate() returns early
+ when Z_BLOCK or Z_TREES is used, and when inflate() avoids the allocation of
+ memory for a sliding window when Z_FINISH is used.
+
+ If a preset dictionary is needed after this call (see inflateSetDictionary
+ below), inflate sets strm->adler to the Adler-32 checksum of the dictionary
+ chosen by the compressor and returns Z_NEED_DICT; otherwise it sets
+ strm->adler to the Adler-32 checksum of all output produced so far (that is,
+ total_out bytes) and returns Z_OK, Z_STREAM_END or an error code as described
+ below. At the end of the stream, inflate() checks that its computed adler32
+ checksum is equal to that saved by the compressor and returns Z_STREAM_END
+ only if the checksum is correct.
+
+ inflate() can decompress and check either zlib-wrapped or gzip-wrapped
+ deflate data. The header type is detected automatically, if requested when
+ initializing with inflateInit2(). Any information contained in the gzip
+ header is not retained, so applications that need that information should
+ instead use raw inflate, see inflateInit2() below, or inflateBack() and
+ perform their own processing of the gzip header and trailer. When processing
+ gzip-wrapped deflate data, strm->adler32 is set to the CRC-32 of the output
+ producted so far. The CRC-32 is checked against the gzip trailer.
+
+ inflate() returns Z_OK if some progress has been made (more input processed
+ or more output produced), Z_STREAM_END if the end of the compressed data has
+ been reached and all uncompressed output has been produced, Z_NEED_DICT if a
+ preset dictionary is needed at this point, Z_DATA_ERROR if the input data was
+ corrupted (input stream not conforming to the zlib format or incorrect check
+ value), Z_STREAM_ERROR if the stream structure was inconsistent (for example
+ next_in or next_out was Z_NULL), Z_MEM_ERROR if there was not enough memory,
+ Z_BUF_ERROR if no progress is possible or if there was not enough room in the
+ output buffer when Z_FINISH is used. Note that Z_BUF_ERROR is not fatal, and
+ inflate() can be called again with more input and more output space to
+ continue decompressing. If Z_DATA_ERROR is returned, the application may
+ then call inflateSync() to look for a good compression block if a partial
+ recovery of the data is desired.
+*/
+
+
+ZEXTERN int ZEXPORT inflateEnd OF((z_streamp strm));
+/*
+ All dynamically allocated data structures for this stream are freed.
+ This function discards any unprocessed input and does not flush any pending
+ output.
+
+ inflateEnd returns Z_OK if success, Z_STREAM_ERROR if the stream state
+ was inconsistent. In the error case, msg may be set but then points to a
+ static string (which must not be deallocated).
+*/
+
+
+ /* Advanced functions */
+
+/*
+ The following functions are needed only in some special applications.
+*/
+
+/*
+ZEXTERN int ZEXPORT deflateInit2 OF((z_streamp strm,
+ int level,
+ int method,
+ int windowBits,
+ int memLevel,
+ int strategy));
+
+ This is another version of deflateInit with more compression options. The
+ fields next_in, zalloc, zfree and opaque must be initialized before by the
+ caller.
+
+ The method parameter is the compression method. It must be Z_DEFLATED in
+ this version of the library.
+
+ The windowBits parameter is the base two logarithm of the window size
+ (the size of the history buffer). It should be in the range 8..15 for this
+ version of the library. Larger values of this parameter result in better
+ compression at the expense of memory usage. The default value is 15 if
+ deflateInit is used instead.
+
+ windowBits can also be -8..-15 for raw deflate. In this case, -windowBits
+ determines the window size. deflate() will then generate raw deflate data
+ with no zlib header or trailer, and will not compute an adler32 check value.
+
+ windowBits can also be greater than 15 for optional gzip encoding. Add
+ 16 to windowBits to write a simple gzip header and trailer around the
+ compressed data instead of a zlib wrapper. The gzip header will have no
+ file name, no extra data, no comment, no modification time (set to zero), no
+ header crc, and the operating system will be set to 255 (unknown). If a
+ gzip stream is being written, strm->adler is a crc32 instead of an adler32.
+
+ The memLevel parameter specifies how much memory should be allocated
+ for the internal compression state. memLevel=1 uses minimum memory but is
+ slow and reduces compression ratio; memLevel=9 uses maximum memory for
+ optimal speed. The default value is 8. See zconf.h for total memory usage
+ as a function of windowBits and memLevel.
+
+ The strategy parameter is used to tune the compression algorithm. Use the
+ value Z_DEFAULT_STRATEGY for normal data, Z_FILTERED for data produced by a
+ filter (or predictor), Z_HUFFMAN_ONLY to force Huffman encoding only (no
+ string match), or Z_RLE to limit match distances to one (run-length
+ encoding). Filtered data consists mostly of small values with a somewhat
+ random distribution. In this case, the compression algorithm is tuned to
+ compress them better. The effect of Z_FILTERED is to force more Huffman
+ coding and less string matching; it is somewhat intermediate between
+ Z_DEFAULT_STRATEGY and Z_HUFFMAN_ONLY. Z_RLE is designed to be almost as
+ fast as Z_HUFFMAN_ONLY, but give better compression for PNG image data. The
+ strategy parameter only affects the compression ratio but not the
+ correctness of the compressed output even if it is not set appropriately.
+ Z_FIXED prevents the use of dynamic Huffman codes, allowing for a simpler
+ decoder for special applications.
+
+ deflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_STREAM_ERROR if any parameter is invalid (such as an invalid
+ method), or Z_VERSION_ERROR if the zlib library version (zlib_version) is
+ incompatible with the version assumed by the caller (ZLIB_VERSION). msg is
+ set to null if there is no error message. deflateInit2 does not perform any
+ compression: this will be done by deflate().
+*/
+
+ZEXTERN int ZEXPORT deflateSetDictionary OF((z_streamp strm,
+ const Bytef *dictionary,
+ uInt dictLength));
+/*
+ Initializes the compression dictionary from the given byte sequence
+ without producing any compressed output. When using the zlib format, this
+ function must be called immediately after deflateInit, deflateInit2 or
+ deflateReset, and before any call of deflate. When doing raw deflate, this
+ function must be called either before any call of deflate, or immediately
+ after the completion of a deflate block, i.e. after all input has been
+ consumed and all output has been delivered when using any of the flush
+ options Z_BLOCK, Z_PARTIAL_FLUSH, Z_SYNC_FLUSH, or Z_FULL_FLUSH. The
+ compressor and decompressor must use exactly the same dictionary (see
+ inflateSetDictionary).
+
+ The dictionary should consist of strings (byte sequences) that are likely
+ to be encountered later in the data to be compressed, with the most commonly
+ used strings preferably put towards the end of the dictionary. Using a
+ dictionary is most useful when the data to be compressed is short and can be
+ predicted with good accuracy; the data can then be compressed better than
+ with the default empty dictionary.
+
+ Depending on the size of the compression data structures selected by
+ deflateInit or deflateInit2, a part of the dictionary may in effect be
+ discarded, for example if the dictionary is larger than the window size
+ provided in deflateInit or deflateInit2. Thus the strings most likely to be
+ useful should be put at the end of the dictionary, not at the front. In
+ addition, the current implementation of deflate will use at most the window
+ size minus 262 bytes of the provided dictionary.
+
+ Upon return of this function, strm->adler is set to the adler32 value
+ of the dictionary; the decompressor may later use this value to determine
+ which dictionary has been used by the compressor. (The adler32 value
+ applies to the whole dictionary even if only a subset of the dictionary is
+ actually used by the compressor.) If a raw deflate was requested, then the
+ adler32 value is not computed and strm->adler is not set.
+
+ deflateSetDictionary returns Z_OK if success, or Z_STREAM_ERROR if a
+ parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is
+ inconsistent (for example if deflate has already been called for this stream
+ or if not at a block boundary for raw deflate). deflateSetDictionary does
+ not perform any compression: this will be done by deflate().
+*/
+
+ZEXTERN int ZEXPORT deflateCopy OF((z_streamp dest,
+ z_streamp source));
+/*
+ Sets the destination stream as a complete copy of the source stream.
+
+ This function can be useful when several compression strategies will be
+ tried, for example when there are several ways of pre-processing the input
+ data with a filter. The streams that will be discarded should then be freed
+ by calling deflateEnd. Note that deflateCopy duplicates the internal
+ compression state which can be quite large, so this strategy is slow and can
+ consume lots of memory.
+
+ deflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
+ (such as zalloc being Z_NULL). msg is left unchanged in both source and
+ destination.
+*/
+
+ZEXTERN int ZEXPORT deflateReset OF((z_streamp strm));
+/*
+ This function is equivalent to deflateEnd followed by deflateInit,
+ but does not free and reallocate all the internal compression state. The
+ stream will keep the same compression level and any other attributes that
+ may have been set by deflateInit2.
+
+ deflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent (such as zalloc or state being Z_NULL).
+*/
+
+ZEXTERN int ZEXPORT deflateParams OF((z_streamp strm,
+ int level,
+ int strategy));
+/*
+ Dynamically update the compression level and compression strategy. The
+ interpretation of level and strategy is as in deflateInit2. This can be
+ used to switch between compression and straight copy of the input data, or
+ to switch to a different kind of input data requiring a different strategy.
+ If the compression level is changed, the input available so far is
+ compressed with the old level (and may be flushed); the new level will take
+ effect only at the next call of deflate().
+
+ Before the call of deflateParams, the stream state must be set as for
+ a call of deflate(), since the currently available input may have to be
+ compressed and flushed. In particular, strm->avail_out must be non-zero.
+
+ deflateParams returns Z_OK if success, Z_STREAM_ERROR if the source
+ stream state was inconsistent or if a parameter was invalid, Z_BUF_ERROR if
+ strm->avail_out was zero.
+*/
+
+ZEXTERN int ZEXPORT deflateTune OF((z_streamp strm,
+ int good_length,
+ int max_lazy,
+ int nice_length,
+ int max_chain));
+/*
+ Fine tune deflate's internal compression parameters. This should only be
+ used by someone who understands the algorithm used by zlib's deflate for
+ searching for the best matching string, and even then only by the most
+ fanatic optimizer trying to squeeze out the last compressed bit for their
+ specific input data. Read the deflate.c source code for the meaning of the
+ max_lazy, good_length, nice_length, and max_chain parameters.
+
+ deflateTune() can be called after deflateInit() or deflateInit2(), and
+ returns Z_OK on success, or Z_STREAM_ERROR for an invalid deflate stream.
+ */
+
+ZEXTERN uLong ZEXPORT deflateBound OF((z_streamp strm,
+ uLong sourceLen));
+/*
+ deflateBound() returns an upper bound on the compressed size after
+ deflation of sourceLen bytes. It must be called after deflateInit() or
+ deflateInit2(), and after deflateSetHeader(), if used. This would be used
+ to allocate an output buffer for deflation in a single pass, and so would be
+ called before deflate(). If that first deflate() call is provided the
+ sourceLen input bytes, an output buffer allocated to the size returned by
+ deflateBound(), and the flush value Z_FINISH, then deflate() is guaranteed
+ to return Z_STREAM_END. Note that it is possible for the compressed size to
+ be larger than the value returned by deflateBound() if flush options other
+ than Z_FINISH or Z_NO_FLUSH are used.
+*/
+
+ZEXTERN int ZEXPORT deflatePending OF((z_streamp strm,
+ unsigned *pending,
+ int *bits));
+/*
+ deflatePending() returns the number of bytes and bits of output that have
+ been generated, but not yet provided in the available output. The bytes not
+ provided would be due to the available output space having being consumed.
+ The number of bits of output not provided are between 0 and 7, where they
+ await more bits to join them in order to fill out a full byte. If pending
+ or bits are Z_NULL, then those values are not set.
+
+ deflatePending returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+ */
+
+ZEXTERN int ZEXPORT deflatePrime OF((z_streamp strm,
+ int bits,
+ int value));
+/*
+ deflatePrime() inserts bits in the deflate output stream. The intent
+ is that this function is used to start off the deflate output with the bits
+ leftover from a previous deflate stream when appending to it. As such, this
+ function can only be used for raw deflate, and must be used before the first
+ deflate() call after a deflateInit2() or deflateReset(). bits must be less
+ than or equal to 16, and that many of the least significant bits of value
+ will be inserted in the output.
+
+ deflatePrime returns Z_OK if success, Z_BUF_ERROR if there was not enough
+ room in the internal buffer to insert the bits, or Z_STREAM_ERROR if the
+ source stream state was inconsistent.
+*/
+
+ZEXTERN int ZEXPORT deflateSetHeader OF((z_streamp strm,
+ gz_headerp head));
+/*
+ deflateSetHeader() provides gzip header information for when a gzip
+ stream is requested by deflateInit2(). deflateSetHeader() may be called
+ after deflateInit2() or deflateReset() and before the first call of
+ deflate(). The text, time, os, extra field, name, and comment information
+ in the provided gz_header structure are written to the gzip header (xflag is
+ ignored -- the extra flags are set according to the compression level). The
+ caller must assure that, if not Z_NULL, name and comment are terminated with
+ a zero byte, and that if extra is not Z_NULL, that extra_len bytes are
+ available there. If hcrc is true, a gzip header crc is included. Note that
+ the current versions of the command-line version of gzip (up through version
+ 1.3.x) do not support header crc's, and will report that it is a "multi-part
+ gzip file" and give up.
+
+ If deflateSetHeader is not used, the default gzip header has text false,
+ the time set to zero, and os set to 255, with no extra, name, or comment
+ fields. The gzip header is returned to the default state by deflateReset().
+
+ deflateSetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+*/
+
+/*
+ZEXTERN int ZEXPORT inflateInit2 OF((z_streamp strm,
+ int windowBits));
+
+ This is another version of inflateInit with an extra parameter. The
+ fields next_in, avail_in, zalloc, zfree and opaque must be initialized
+ before by the caller.
+
+ The windowBits parameter is the base two logarithm of the maximum window
+ size (the size of the history buffer). It should be in the range 8..15 for
+ this version of the library. The default value is 15 if inflateInit is used
+ instead. windowBits must be greater than or equal to the windowBits value
+ provided to deflateInit2() while compressing, or it must be equal to 15 if
+ deflateInit2() was not used. If a compressed stream with a larger window
+ size is given as input, inflate() will return with the error code
+ Z_DATA_ERROR instead of trying to allocate a larger window.
+
+ windowBits can also be zero to request that inflate use the window size in
+ the zlib header of the compressed stream.
+
+ windowBits can also be -8..-15 for raw inflate. In this case, -windowBits
+ determines the window size. inflate() will then process raw deflate data,
+ not looking for a zlib or gzip header, not generating a check value, and not
+ looking for any check values for comparison at the end of the stream. This
+ is for use with other formats that use the deflate compressed data format
+ such as zip. Those formats provide their own check values. If a custom
+ format is developed using the raw deflate format for compressed data, it is
+ recommended that a check value such as an adler32 or a crc32 be applied to
+ the uncompressed data as is done in the zlib, gzip, and zip formats. For
+ most applications, the zlib format should be used as is. Note that comments
+ above on the use in deflateInit2() applies to the magnitude of windowBits.
+
+ windowBits can also be greater than 15 for optional gzip decoding. Add
+ 32 to windowBits to enable zlib and gzip decoding with automatic header
+ detection, or add 16 to decode only the gzip format (the zlib format will
+ return a Z_DATA_ERROR). If a gzip stream is being decoded, strm->adler is a
+ crc32 instead of an adler32.
+
+ inflateInit2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_VERSION_ERROR if the zlib library version is incompatible with the
+ version assumed by the caller, or Z_STREAM_ERROR if the parameters are
+ invalid, such as a null pointer to the structure. msg is set to null if
+ there is no error message. inflateInit2 does not perform any decompression
+ apart from possibly reading the zlib header if present: actual decompression
+ will be done by inflate(). (So next_in and avail_in may be modified, but
+ next_out and avail_out are unused and unchanged.) The current implementation
+ of inflateInit2() does not process any header information -- that is
+ deferred until inflate() is called.
+*/
+
+ZEXTERN int ZEXPORT inflateSetDictionary OF((z_streamp strm,
+ const Bytef *dictionary,
+ uInt dictLength));
+/*
+ Initializes the decompression dictionary from the given uncompressed byte
+ sequence. This function must be called immediately after a call of inflate,
+ if that call returned Z_NEED_DICT. The dictionary chosen by the compressor
+ can be determined from the adler32 value returned by that call of inflate.
+ The compressor and decompressor must use exactly the same dictionary (see
+ deflateSetDictionary). For raw inflate, this function can be called at any
+ time to set the dictionary. If the provided dictionary is smaller than the
+ window and there is already data in the window, then the provided dictionary
+ will amend what's there. The application must insure that the dictionary
+ that was used for compression is provided.
+
+ inflateSetDictionary returns Z_OK if success, Z_STREAM_ERROR if a
+ parameter is invalid (e.g. dictionary being Z_NULL) or the stream state is
+ inconsistent, Z_DATA_ERROR if the given dictionary doesn't match the
+ expected one (incorrect adler32 value). inflateSetDictionary does not
+ perform any decompression: this will be done by subsequent calls of
+ inflate().
+*/
+
+ZEXTERN int ZEXPORT inflateGetDictionary OF((z_streamp strm,
+ Bytef *dictionary,
+ uInt *dictLength));
+/*
+ Returns the sliding dictionary being maintained by inflate. dictLength is
+ set to the number of bytes in the dictionary, and that many bytes are copied
+ to dictionary. dictionary must have enough space, where 32768 bytes is
+ always enough. If inflateGetDictionary() is called with dictionary equal to
+ Z_NULL, then only the dictionary length is returned, and nothing is copied.
+ Similary, if dictLength is Z_NULL, then it is not set.
+
+ inflateGetDictionary returns Z_OK on success, or Z_STREAM_ERROR if the
+ stream state is inconsistent.
+*/
+
+ZEXTERN int ZEXPORT inflateSync OF((z_streamp strm));
+/*
+ Skips invalid compressed data until a possible full flush point (see above
+ for the description of deflate with Z_FULL_FLUSH) can be found, or until all
+ available input is skipped. No output is provided.
+
+ inflateSync searches for a 00 00 FF FF pattern in the compressed data.
+ All full flush points have this pattern, but not all occurrences of this
+ pattern are full flush points.
+
+ inflateSync returns Z_OK if a possible full flush point has been found,
+ Z_BUF_ERROR if no more input was provided, Z_DATA_ERROR if no flush point
+ has been found, or Z_STREAM_ERROR if the stream structure was inconsistent.
+ In the success case, the application may save the current current value of
+ total_in which indicates where valid compressed data was found. In the
+ error case, the application may repeatedly call inflateSync, providing more
+ input each time, until success or end of the input data.
+*/
+
+ZEXTERN int ZEXPORT inflateCopy OF((z_streamp dest,
+ z_streamp source));
+/*
+ Sets the destination stream as a complete copy of the source stream.
+
+ This function can be useful when randomly accessing a large stream. The
+ first pass through the stream can periodically record the inflate state,
+ allowing restarting inflate at those points when randomly accessing the
+ stream.
+
+ inflateCopy returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_STREAM_ERROR if the source stream state was inconsistent
+ (such as zalloc being Z_NULL). msg is left unchanged in both source and
+ destination.
+*/
+
+ZEXTERN int ZEXPORT inflateReset OF((z_streamp strm));
+/*
+ This function is equivalent to inflateEnd followed by inflateInit,
+ but does not free and reallocate all the internal decompression state. The
+ stream will keep attributes that may have been set by inflateInit2.
+
+ inflateReset returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent (such as zalloc or state being Z_NULL).
+*/
+
+ZEXTERN int ZEXPORT inflateReset2 OF((z_streamp strm,
+ int windowBits));
+/*
+ This function is the same as inflateReset, but it also permits changing
+ the wrap and window size requests. The windowBits parameter is interpreted
+ the same as it is for inflateInit2.
+
+ inflateReset2 returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent (such as zalloc or state being Z_NULL), or if
+ the windowBits parameter is invalid.
+*/
+
+ZEXTERN int ZEXPORT inflatePrime OF((z_streamp strm,
+ int bits,
+ int value));
+/*
+ This function inserts bits in the inflate input stream. The intent is
+ that this function is used to start inflating at a bit position in the
+ middle of a byte. The provided bits will be used before any bytes are used
+ from next_in. This function should only be used with raw inflate, and
+ should be used before the first inflate() call after inflateInit2() or
+ inflateReset(). bits must be less than or equal to 16, and that many of the
+ least significant bits of value will be inserted in the input.
+
+ If bits is negative, then the input stream bit buffer is emptied. Then
+ inflatePrime() can be called again to put bits in the buffer. This is used
+ to clear out bits leftover after feeding inflate a block description prior
+ to feeding inflate codes.
+
+ inflatePrime returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+*/
+
+ZEXTERN long ZEXPORT inflateMark OF((z_streamp strm));
+/*
+ This function returns two values, one in the lower 16 bits of the return
+ value, and the other in the remaining upper bits, obtained by shifting the
+ return value down 16 bits. If the upper value is -1 and the lower value is
+ zero, then inflate() is currently decoding information outside of a block.
+ If the upper value is -1 and the lower value is non-zero, then inflate is in
+ the middle of a stored block, with the lower value equaling the number of
+ bytes from the input remaining to copy. If the upper value is not -1, then
+ it is the number of bits back from the current bit position in the input of
+ the code (literal or length/distance pair) currently being processed. In
+ that case the lower value is the number of bytes already emitted for that
+ code.
+
+ A code is being processed if inflate is waiting for more input to complete
+ decoding of the code, or if it has completed decoding but is waiting for
+ more output space to write the literal or match data.
+
+ inflateMark() is used to mark locations in the input data for random
+ access, which may be at bit positions, and to note those cases where the
+ output of a code may span boundaries of random access blocks. The current
+ location in the input stream can be determined from avail_in and data_type
+ as noted in the description for the Z_BLOCK flush parameter for inflate.
+
+ inflateMark returns the value noted above or -1 << 16 if the provided
+ source stream state was inconsistent.
+*/
+
+ZEXTERN int ZEXPORT inflateGetHeader OF((z_streamp strm,
+ gz_headerp head));
+/*
+ inflateGetHeader() requests that gzip header information be stored in the
+ provided gz_header structure. inflateGetHeader() may be called after
+ inflateInit2() or inflateReset(), and before the first call of inflate().
+ As inflate() processes the gzip stream, head->done is zero until the header
+ is completed, at which time head->done is set to one. If a zlib stream is
+ being decoded, then head->done is set to -1 to indicate that there will be
+ no gzip header information forthcoming. Note that Z_BLOCK or Z_TREES can be
+ used to force inflate() to return immediately after header processing is
+ complete and before any actual data is decompressed.
+
+ The text, time, xflags, and os fields are filled in with the gzip header
+ contents. hcrc is set to true if there is a header CRC. (The header CRC
+ was valid if done is set to one.) If extra is not Z_NULL, then extra_max
+ contains the maximum number of bytes to write to extra. Once done is true,
+ extra_len contains the actual extra field length, and extra contains the
+ extra field, or that field truncated if extra_max is less than extra_len.
+ If name is not Z_NULL, then up to name_max characters are written there,
+ terminated with a zero unless the length is greater than name_max. If
+ comment is not Z_NULL, then up to comm_max characters are written there,
+ terminated with a zero unless the length is greater than comm_max. When any
+ of extra, name, or comment are not Z_NULL and the respective field is not
+ present in the header, then that field is set to Z_NULL to signal its
+ absence. This allows the use of deflateSetHeader() with the returned
+ structure to duplicate the header. However if those fields are set to
+ allocated memory, then the application will need to save those pointers
+ elsewhere so that they can be eventually freed.
+
+ If inflateGetHeader is not used, then the header information is simply
+ discarded. The header is always checked for validity, including the header
+ CRC if present. inflateReset() will reset the process to discard the header
+ information. The application would need to call inflateGetHeader() again to
+ retrieve the header from the next gzip stream.
+
+ inflateGetHeader returns Z_OK if success, or Z_STREAM_ERROR if the source
+ stream state was inconsistent.
+*/
+
+/*
+ZEXTERN int ZEXPORT inflateBackInit OF((z_streamp strm, int windowBits,
+ unsigned char FAR *window));
+
+ Initialize the internal stream state for decompression using inflateBack()
+ calls. The fields zalloc, zfree and opaque in strm must be initialized
+ before the call. If zalloc and zfree are Z_NULL, then the default library-
+ derived memory allocation routines are used. windowBits is the base two
+ logarithm of the window size, in the range 8..15. window is a caller
+ supplied buffer of that size. Except for special applications where it is
+ assured that deflate was used with small window sizes, windowBits must be 15
+ and a 32K byte window must be supplied to be able to decompress general
+ deflate streams.
+
+ See inflateBack() for the usage of these routines.
+
+ inflateBackInit will return Z_OK on success, Z_STREAM_ERROR if any of
+ the parameters are invalid, Z_MEM_ERROR if the internal state could not be
+ allocated, or Z_VERSION_ERROR if the version of the library does not match
+ the version of the header file.
+*/
+
+typedef unsigned (*in_func) OF((void FAR *,
+ z_const unsigned char FAR * FAR *));
+typedef int (*out_func) OF((void FAR *, unsigned char FAR *, unsigned));
+
+ZEXTERN int ZEXPORT inflateBack OF((z_streamp strm,
+ in_func in, void FAR *in_desc,
+ out_func out, void FAR *out_desc));
+/*
+ inflateBack() does a raw inflate with a single call using a call-back
+ interface for input and output. This is potentially more efficient than
+ inflate() for file i/o applications, in that it avoids copying between the
+ output and the sliding window by simply making the window itself the output
+ buffer. inflate() can be faster on modern CPUs when used with large
+ buffers. inflateBack() trusts the application to not change the output
+ buffer passed by the output function, at least until inflateBack() returns.
+
+ inflateBackInit() must be called first to allocate the internal state
+ and to initialize the state with the user-provided window buffer.
+ inflateBack() may then be used multiple times to inflate a complete, raw
+ deflate stream with each call. inflateBackEnd() is then called to free the
+ allocated state.
+
+ A raw deflate stream is one with no zlib or gzip header or trailer.
+ This routine would normally be used in a utility that reads zip or gzip
+ files and writes out uncompressed files. The utility would decode the
+ header and process the trailer on its own, hence this routine expects only
+ the raw deflate stream to decompress. This is different from the normal
+ behavior of inflate(), which expects either a zlib or gzip header and
+ trailer around the deflate stream.
+
+ inflateBack() uses two subroutines supplied by the caller that are then
+ called by inflateBack() for input and output. inflateBack() calls those
+ routines until it reads a complete deflate stream and writes out all of the
+ uncompressed data, or until it encounters an error. The function's
+ parameters and return types are defined above in the in_func and out_func
+ typedefs. inflateBack() will call in(in_desc, &buf) which should return the
+ number of bytes of provided input, and a pointer to that input in buf. If
+ there is no input available, in() must return zero--buf is ignored in that
+ case--and inflateBack() will return a buffer error. inflateBack() will call
+ out(out_desc, buf, len) to write the uncompressed data buf[0..len-1]. out()
+ should return zero on success, or non-zero on failure. If out() returns
+ non-zero, inflateBack() will return with an error. Neither in() nor out()
+ are permitted to change the contents of the window provided to
+ inflateBackInit(), which is also the buffer that out() uses to write from.
+ The length written by out() will be at most the window size. Any non-zero
+ amount of input may be provided by in().
+
+ For convenience, inflateBack() can be provided input on the first call by
+ setting strm->next_in and strm->avail_in. If that input is exhausted, then
+ in() will be called. Therefore strm->next_in must be initialized before
+ calling inflateBack(). If strm->next_in is Z_NULL, then in() will be called
+ immediately for input. If strm->next_in is not Z_NULL, then strm->avail_in
+ must also be initialized, and then if strm->avail_in is not zero, input will
+ initially be taken from strm->next_in[0 .. strm->avail_in - 1].
+
+ The in_desc and out_desc parameters of inflateBack() is passed as the
+ first parameter of in() and out() respectively when they are called. These
+ descriptors can be optionally used to pass any information that the caller-
+ supplied in() and out() functions need to do their job.
+
+ On return, inflateBack() will set strm->next_in and strm->avail_in to
+ pass back any unused input that was provided by the last in() call. The
+ return values of inflateBack() can be Z_STREAM_END on success, Z_BUF_ERROR
+ if in() or out() returned an error, Z_DATA_ERROR if there was a format error
+ in the deflate stream (in which case strm->msg is set to indicate the nature
+ of the error), or Z_STREAM_ERROR if the stream was not properly initialized.
+ In the case of Z_BUF_ERROR, an input or output error can be distinguished
+ using strm->next_in which will be Z_NULL only if in() returned an error. If
+ strm->next_in is not Z_NULL, then the Z_BUF_ERROR was due to out() returning
+ non-zero. (in() will always be called before out(), so strm->next_in is
+ assured to be defined if out() returns non-zero.) Note that inflateBack()
+ cannot return Z_OK.
+*/
+
+ZEXTERN int ZEXPORT inflateBackEnd OF((z_streamp strm));
+/*
+ All memory allocated by inflateBackInit() is freed.
+
+ inflateBackEnd() returns Z_OK on success, or Z_STREAM_ERROR if the stream
+ state was inconsistent.
+*/
+
+/* Declaration not used by TNG is not available */
+/*ZEXTERN uLong ZEXPORT zlibCompileFlags OF((void));*/
+/* Return flags indicating compile-time options.
+
+ Type sizes, two bits each, 00 = 16 bits, 01 = 32, 10 = 64, 11 = other:
+ 1.0: size of uInt
+ 3.2: size of uLong
+ 5.4: size of voidpf (pointer)
+ 7.6: size of z_off_t
+
+ Compiler, assembler, and debug options:
+ 8: DEBUG
+ 9: ASMV or ASMINF -- use ASM code
+ 10: ZLIB_WINAPI -- exported functions use the WINAPI calling convention
+ 11: 0 (reserved)
+
+ One-time table building (smaller code, but not thread-safe if true):
+ 12: BUILDFIXED -- build static block decoding tables when needed
+ 13: DYNAMIC_CRC_TABLE -- build CRC calculation tables when needed
+ 14,15: 0 (reserved)
+
+ Library content (indicates missing functionality):
+ 16: NO_GZCOMPRESS -- gz* functions cannot compress (to avoid linking
+ deflate code when not needed)
+ 17: NO_GZIP -- deflate can't write gzip streams, and inflate can't detect
+ and decode gzip streams (to avoid linking crc code)
+ 18-19: 0 (reserved)
+
+ Operation variations (changes in library functionality):
+ 20: PKZIP_BUG_WORKAROUND -- slightly more permissive inflate
+ 21: FASTEST -- deflate algorithm with only one, lowest compression level
+ 22,23: 0 (reserved)
+
+ The sprintf variant used by gzprintf (zero is best):
+ 24: 0 = vs*, 1 = s* -- 1 means limited to 20 arguments after the format
+ 25: 0 = *nprintf, 1 = *printf -- 1 means gzprintf() not secure!
+ 26: 0 = returns value, 1 = void -- 1 means inferred string length returned
+
+ Remainder:
+ 27-31: 0 (reserved)
+ */
+
+#ifndef Z_SOLO
+
+ /* utility functions */
+
+/*
+ The following utility functions are implemented on top of the basic
+ stream-oriented functions. To simplify the interface, some default options
+ are assumed (compression level and memory usage, standard memory allocation
+ functions). The source code of these utility functions can be modified if
+ you need special options.
+*/
+
+ZEXTERN int ZEXPORT compress OF((Bytef *dest, uLongf *destLen,
+ const Bytef *source, uLong sourceLen));
+/*
+ Compresses the source buffer into the destination buffer. sourceLen is
+ the byte length of the source buffer. Upon entry, destLen is the total size
+ of the destination buffer, which must be at least the value returned by
+ compressBound(sourceLen). Upon exit, destLen is the actual size of the
+ compressed buffer.
+
+ compress returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_BUF_ERROR if there was not enough room in the output
+ buffer.
+*/
+
+ZEXTERN int ZEXPORT compress2 OF((Bytef *dest, uLongf *destLen,
+ const Bytef *source, uLong sourceLen,
+ int level));
+/*
+ Compresses the source buffer into the destination buffer. The level
+ parameter has the same meaning as in deflateInit. sourceLen is the byte
+ length of the source buffer. Upon entry, destLen is the total size of the
+ destination buffer, which must be at least the value returned by
+ compressBound(sourceLen). Upon exit, destLen is the actual size of the
+ compressed buffer.
+
+ compress2 returns Z_OK if success, Z_MEM_ERROR if there was not enough
+ memory, Z_BUF_ERROR if there was not enough room in the output buffer,
+ Z_STREAM_ERROR if the level parameter is invalid.
+*/
+
+ZEXTERN uLong ZEXPORT compressBound OF((uLong sourceLen));
+/*
+ compressBound() returns an upper bound on the compressed size after
+ compress() or compress2() on sourceLen bytes. It would be used before a
+ compress() or compress2() call to allocate the destination buffer.
+*/
+
+ZEXTERN int ZEXPORT uncompress OF((Bytef *dest, uLongf *destLen,
+ const Bytef *source, uLong sourceLen));
+/*
+ Decompresses the source buffer into the destination buffer. sourceLen is
+ the byte length of the source buffer. Upon entry, destLen is the total size
+ of the destination buffer, which must be large enough to hold the entire
+ uncompressed data. (The size of the uncompressed data must have been saved
+ previously by the compressor and transmitted to the decompressor by some
+ mechanism outside the scope of this compression library.) Upon exit, destLen
+ is the actual size of the uncompressed buffer.
+
+ uncompress returns Z_OK if success, Z_MEM_ERROR if there was not
+ enough memory, Z_BUF_ERROR if there was not enough room in the output
+ buffer, or Z_DATA_ERROR if the input data was corrupted or incomplete. In
+ the case where there is not enough room, uncompress() will fill the output
+ buffer with the uncompressed data up to that point.
+*/
+
+ /* gzip file access functions */
+
+/*
+ This library supports reading and writing files in gzip (.gz) format with
+ an interface similar to that of stdio, using the functions that start with
+ "gz". The gzip format is different from the zlib format. gzip is a gzip
+ wrapper, documented in RFC 1952, wrapped around a deflate stream.
+*/
+
+typedef struct gzFile_s *gzFile; /* semi-opaque gzip file descriptor */
+
+/*
+ZEXTERN gzFile ZEXPORT gzopen OF((const char *path, const char *mode));
+
+ Opens a gzip (.gz) file for reading or writing. The mode parameter is as
+ in fopen ("rb" or "wb") but can also include a compression level ("wb9") or
+ a strategy: 'f' for filtered data as in "wb6f", 'h' for Huffman-only
+ compression as in "wb1h", 'R' for run-length encoding as in "wb1R", or 'F'
+ for fixed code compression as in "wb9F". (See the description of
+ deflateInit2 for more information about the strategy parameter.) 'T' will
+ request transparent writing or appending with no compression and not using
+ the gzip format.
+
+ "a" can be used instead of "w" to request that the gzip stream that will
+ be written be appended to the file. "+" will result in an error, since
+ reading and writing to the same gzip file is not supported. The addition of
+ "x" when writing will create the file exclusively, which fails if the file
+ already exists. On systems that support it, the addition of "e" when
+ reading or writing will set the flag to close the file on an execve() call.
+
+ These functions, as well as gzip, will read and decode a sequence of gzip
+ streams in a file. The append function of gzopen() can be used to create
+ such a file. (Also see gzflush() for another way to do this.) When
+ appending, gzopen does not test whether the file begins with a gzip stream,
+ nor does it look for the end of the gzip streams to begin appending. gzopen
+ will simply append a gzip stream to the existing file.
+
+ gzopen can be used to read a file which is not in gzip format; in this
+ case gzread will directly read from the file without decompression. When
+ reading, this will be detected automatically by looking for the magic two-
+ byte gzip header.
+
+ gzopen returns NULL if the file could not be opened, if there was
+ insufficient memory to allocate the gzFile state, or if an invalid mode was
+ specified (an 'r', 'w', or 'a' was not provided, or '+' was provided).
+ errno can be checked to determine if the reason gzopen failed was that the
+ file could not be opened.
+*/
+
+ZEXTERN gzFile ZEXPORT gzdopen OF((int fd, const char *mode));
+/*
+ gzdopen associates a gzFile with the file descriptor fd. File descriptors
+ are obtained from calls like open, dup, creat, pipe or fileno (if the file
+ has been previously opened with fopen). The mode parameter is as in gzopen.
+
+ The next call of gzclose on the returned gzFile will also close the file
+ descriptor fd, just like fclose(fdopen(fd, mode)) closes the file descriptor
+ fd. If you want to keep fd open, use fd = dup(fd_keep); gz = gzdopen(fd,
+ mode);. The duplicated descriptor should be saved to avoid a leak, since
+ gzdopen does not close fd if it fails. If you are using fileno() to get the
+ file descriptor from a FILE *, then you will have to use dup() to avoid
+ double-close()ing the file descriptor. Both gzclose() and fclose() will
+ close the associated file descriptor, so they need to have different file
+ descriptors.
+
+ gzdopen returns NULL if there was insufficient memory to allocate the
+ gzFile state, if an invalid mode was specified (an 'r', 'w', or 'a' was not
+ provided, or '+' was provided), or if fd is -1. The file descriptor is not
+ used until the next gz* read, write, seek, or close operation, so gzdopen
+ will not detect if fd is invalid (unless fd is -1).
+*/
+
+ZEXTERN int ZEXPORT gzbuffer OF((gzFile file, unsigned size));
+/*
+ Set the internal buffer size used by this library's functions. The
+ default buffer size is 8192 bytes. This function must be called after
+ gzopen() or gzdopen(), and before any other calls that read or write the
+ file. The buffer memory allocation is always deferred to the first read or
+ write. Two buffers are allocated, either both of the specified size when
+ writing, or one of the specified size and the other twice that size when
+ reading. A larger buffer size of, for example, 64K or 128K bytes will
+ noticeably increase the speed of decompression (reading).
+
+ The new buffer size also affects the maximum length for gzprintf().
+
+ gzbuffer() returns 0 on success, or -1 on failure, such as being called
+ too late.
+*/
+
+ZEXTERN int ZEXPORT gzsetparams OF((gzFile file, int level, int strategy));
+/*
+ Dynamically update the compression level or strategy. See the description
+ of deflateInit2 for the meaning of these parameters.
+
+ gzsetparams returns Z_OK if success, or Z_STREAM_ERROR if the file was not
+ opened for writing.
+*/
+
+ZEXTERN int ZEXPORT gzread OF((gzFile file, voidp buf, unsigned len));
+/*
+ Reads the given number of uncompressed bytes from the compressed file. If
+ the input file is not in gzip format, gzread copies the given number of
+ bytes into the buffer directly from the file.
+
+ After reaching the end of a gzip stream in the input, gzread will continue
+ to read, looking for another gzip stream. Any number of gzip streams may be
+ concatenated in the input file, and will all be decompressed by gzread().
+ If something other than a gzip stream is encountered after a gzip stream,
+ that remaining trailing garbage is ignored (and no error is returned).
+
+ gzread can be used to read a gzip file that is being concurrently written.
+ Upon reaching the end of the input, gzread will return with the available
+ data. If the error code returned by gzerror is Z_OK or Z_BUF_ERROR, then
+ gzclearerr can be used to clear the end of file indicator in order to permit
+ gzread to be tried again. Z_OK indicates that a gzip stream was completed
+ on the last gzread. Z_BUF_ERROR indicates that the input file ended in the
+ middle of a gzip stream. Note that gzread does not return -1 in the event
+ of an incomplete gzip stream. This error is deferred until gzclose(), which
+ will return Z_BUF_ERROR if the last gzread ended in the middle of a gzip
+ stream. Alternatively, gzerror can be used before gzclose to detect this
+ case.
+
+ gzread returns the number of uncompressed bytes actually read, less than
+ len for end of file, or -1 for error.
+*/
+
+ZEXTERN int ZEXPORT gzwrite OF((gzFile file,
+ voidpc buf, unsigned len));
+/*
+ Writes the given number of uncompressed bytes into the compressed file.
+ gzwrite returns the number of uncompressed bytes written or 0 in case of
+ error.
+*/
+
+ZEXTERN int ZEXPORTVA gzprintf Z_ARG((gzFile file, const char *format, ...));
+/*
+ Converts, formats, and writes the arguments to the compressed file under
+ control of the format string, as in fprintf. gzprintf returns the number of
+ uncompressed bytes actually written, or 0 in case of error. The number of
+ uncompressed bytes written is limited to 8191, or one less than the buffer
+ size given to gzbuffer(). The caller should assure that this limit is not
+ exceeded. If it is exceeded, then gzprintf() will return an error (0) with
+ nothing written. In this case, there may also be a buffer overflow with
+ unpredictable consequences, which is possible only if zlib was compiled with
+ the insecure functions sprintf() or vsprintf() because the secure snprintf()
+ or vsnprintf() functions were not available. This can be determined using
+ zlibCompileFlags().
+*/
+
+ZEXTERN int ZEXPORT gzputs OF((gzFile file, const char *s));
+/*
+ Writes the given null-terminated string to the compressed file, excluding
+ the terminating null character.
+
+ gzputs returns the number of characters written, or -1 in case of error.
+*/
+
+ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
+/*
+ Reads bytes from the compressed file until len-1 characters are read, or a
+ newline character is read and transferred to buf, or an end-of-file
+ condition is encountered. If any characters are read or if len == 1, the
+ string is terminated with a null character. If no characters are read due
+ to an end-of-file or len < 1, then the buffer is left untouched.
+
+ gzgets returns buf which is a null-terminated string, or it returns NULL
+ for end-of-file or in case of error. If there was an error, the contents at
+ buf are indeterminate.
+*/
+
+ZEXTERN int ZEXPORT gzputc OF((gzFile file, int c));
+/*
+ Writes c, converted to an unsigned char, into the compressed file. gzputc
+ returns the value that was written, or -1 in case of error.
+*/
+
+ZEXTERN int ZEXPORT gzgetc OF((gzFile file));
+/*
+ Reads one byte from the compressed file. gzgetc returns this byte or -1
+ in case of end of file or error. This is implemented as a macro for speed.
+ As such, it does not do all of the checking the other functions do. I.e.
+ it does not check to see if file is NULL, nor whether the structure file
+ points to has been clobbered or not.
+*/
+
+ZEXTERN int ZEXPORT gzungetc OF((int c, gzFile file));
+/*
+ Push one character back onto the stream to be read as the first character
+ on the next read. At least one character of push-back is allowed.
+ gzungetc() returns the character pushed, or -1 on failure. gzungetc() will
+ fail if c is -1, and may fail if a character has been pushed but not read
+ yet. If gzungetc is used immediately after gzopen or gzdopen, at least the
+ output buffer size of pushed characters is allowed. (See gzbuffer above.)
+ The pushed character will be discarded if the stream is repositioned with
+ gzseek() or gzrewind().
+*/
+
+ZEXTERN int ZEXPORT gzflush OF((gzFile file, int flush));
+/*
+ Flushes all pending output into the compressed file. The parameter flush
+ is as in the deflate() function. The return value is the zlib error number
+ (see function gzerror below). gzflush is only permitted when writing.
+
+ If the flush parameter is Z_FINISH, the remaining data is written and the
+ gzip stream is completed in the output. If gzwrite() is called again, a new
+ gzip stream will be started in the output. gzread() is able to read such
+ concatented gzip streams.
+
+ gzflush should be called only when strictly necessary because it will
+ degrade compression if called too often.
+*/
+
+/*
+ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile file,
+ z_off_t offset, int whence));
+
+ Sets the starting position for the next gzread or gzwrite on the given
+ compressed file. The offset represents a number of bytes in the
+ uncompressed data stream. The whence parameter is defined as in lseek(2);
+ the value SEEK_END is not supported.
+
+ If the file is opened for reading, this function is emulated but can be
+ extremely slow. If the file is opened for writing, only forward seeks are
+ supported; gzseek then compresses a sequence of zeroes up to the new
+ starting position.
+
+ gzseek returns the resulting offset location as measured in bytes from
+ the beginning of the uncompressed stream, or -1 in case of error, in
+ particular if the file is opened for writing and the new starting position
+ would be before the current position.
+*/
+
+ZEXTERN int ZEXPORT gzrewind OF((gzFile file));
+/*
+ Rewinds the given file. This function is supported only for reading.
+
+ gzrewind(file) is equivalent to (int)gzseek(file, 0L, SEEK_SET)
+*/
+
+/*
+ZEXTERN z_off_t ZEXPORT gztell OF((gzFile file));
+
+ Returns the starting position for the next gzread or gzwrite on the given
+ compressed file. This position represents a number of bytes in the
+ uncompressed data stream, and is zero when starting, even if appending or
+ reading a gzip stream from the middle of a file using gzdopen().
+
+ gztell(file) is equivalent to gzseek(file, 0L, SEEK_CUR)
+*/
+
+/*
+ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile file));
+
+ Returns the current offset in the file being read or written. This offset
+ includes the count of bytes that precede the gzip stream, for example when
+ appending or when using gzdopen() for reading. When reading, the offset
+ does not include as yet unused buffered input. This information can be used
+ for a progress indicator. On error, gzoffset() returns -1.
+*/
+
+ZEXTERN int ZEXPORT gzeof OF((gzFile file));
+/*
+ Returns true (1) if the end-of-file indicator has been set while reading,
+ false (0) otherwise. Note that the end-of-file indicator is set only if the
+ read tried to go past the end of the input, but came up short. Therefore,
+ just like feof(), gzeof() may return false even if there is no more data to
+ read, in the event that the last read request was for the exact number of
+ bytes remaining in the input file. This will happen if the input file size
+ is an exact multiple of the buffer size.
+
+ If gzeof() returns true, then the read functions will return no more data,
+ unless the end-of-file indicator is reset by gzclearerr() and the input file
+ has grown since the previous end of file was detected.
+*/
+
+ZEXTERN int ZEXPORT gzdirect OF((gzFile file));
+/*
+ Returns true (1) if file is being copied directly while reading, or false
+ (0) if file is a gzip stream being decompressed.
+
+ If the input file is empty, gzdirect() will return true, since the input
+ does not contain a gzip stream.
+
+ If gzdirect() is used immediately after gzopen() or gzdopen() it will
+ cause buffers to be allocated to allow reading the file to determine if it
+ is a gzip file. Therefore if gzbuffer() is used, it should be called before
+ gzdirect().
+
+ When writing, gzdirect() returns true (1) if transparent writing was
+ requested ("wT" for the gzopen() mode), or false (0) otherwise. (Note:
+ gzdirect() is not needed when writing. Transparent writing must be
+ explicitly requested, so the application already knows the answer. When
+ linking statically, using gzdirect() will include all of the zlib code for
+ gzip file reading and decompression, which may not be desired.)
+*/
+
+ZEXTERN int ZEXPORT gzclose OF((gzFile file));
+/*
+ Flushes all pending output if necessary, closes the compressed file and
+ deallocates the (de)compression state. Note that once file is closed, you
+ cannot call gzerror with file, since its structures have been deallocated.
+ gzclose must not be called more than once on the same file, just as free
+ must not be called more than once on the same allocation.
+
+ gzclose will return Z_STREAM_ERROR if file is not valid, Z_ERRNO on a
+ file operation error, Z_MEM_ERROR if out of memory, Z_BUF_ERROR if the
+ last read ended in the middle of a gzip stream, or Z_OK on success.
+*/
+
+ZEXTERN int ZEXPORT gzclose_r OF((gzFile file));
+ZEXTERN int ZEXPORT gzclose_w OF((gzFile file));
+/*
+ Same as gzclose(), but gzclose_r() is only for use when reading, and
+ gzclose_w() is only for use when writing or appending. The advantage to
+ using these instead of gzclose() is that they avoid linking in zlib
+ compression or decompression code that is not used when only reading or only
+ writing respectively. If gzclose() is used, then both compression and
+ decompression code will be included the application when linking to a static
+ zlib library.
+*/
+
+ZEXTERN const char * ZEXPORT gzerror OF((gzFile file, int *errnum));
+/*
+ Returns the error message for the last error which occurred on the given
+ compressed file. errnum is set to zlib error number. If an error occurred
+ in the file system and not in the compression library, errnum is set to
+ Z_ERRNO and the application may consult errno to get the exact error code.
+
+ The application must not modify the returned string. Future calls to
+ this function may invalidate the previously returned string. If file is
+ closed, then the string previously returned by gzerror will no longer be
+ available.
+
+ gzerror() should be used to distinguish errors from end-of-file for those
+ functions above that do not distinguish those cases in their return values.
+*/
+
+ZEXTERN void ZEXPORT gzclearerr OF((gzFile file));
+/*
+ Clears the error and end-of-file flags for file. This is analogous to the
+ clearerr() function in stdio. This is useful for continuing to read a gzip
+ file that is being written concurrently.
+*/
+
+#endif /* !Z_SOLO */
+
+ /* checksum functions */
+
+/*
+ These functions are not related to compression but are exported
+ anyway because they might be useful in applications using the compression
+ library.
+*/
+
+ZEXTERN uLong ZEXPORT adler32 OF((uLong adler, const Bytef *buf, uInt len));
+/*
+ Update a running Adler-32 checksum with the bytes buf[0..len-1] and
+ return the updated checksum. If buf is Z_NULL, this function returns the
+ required initial value for the checksum.
+
+ An Adler-32 checksum is almost as reliable as a CRC32 but can be computed
+ much faster.
+
+ Usage example:
+
+ uLong adler = adler32(0L, Z_NULL, 0);
+
+ while (read_buffer(buffer, length) != EOF) {
+ adler = adler32(adler, buffer, length);
+ }
+ if (adler != original_adler) error();
+*/
+
+/*
+ZEXTERN uLong ZEXPORT adler32_combine OF((uLong adler1, uLong adler2,
+ z_off_t len2));
+
+ Combine two Adler-32 checksums into one. For two sequences of bytes, seq1
+ and seq2 with lengths len1 and len2, Adler-32 checksums were calculated for
+ each, adler1 and adler2. adler32_combine() returns the Adler-32 checksum of
+ seq1 and seq2 concatenated, requiring only adler1, adler2, and len2. Note
+ that the z_off_t type (like off_t) is a signed integer. If len2 is
+ negative, the result has no meaning or utility.
+*/
+
+ZEXTERN uLong ZEXPORT crc32 OF((uLong crc, const Bytef *buf, uInt len));
+/*
+ Update a running CRC-32 with the bytes buf[0..len-1] and return the
+ updated CRC-32. If buf is Z_NULL, this function returns the required
+ initial value for the crc. Pre- and post-conditioning (one's complement) is
+ performed within this function so it shouldn't be done by the application.
+
+ Usage example:
+
+ uLong crc = crc32(0L, Z_NULL, 0);
+
+ while (read_buffer(buffer, length) != EOF) {
+ crc = crc32(crc, buffer, length);
+ }
+ if (crc != original_crc) error();
+*/
+
+/*
+ZEXTERN uLong ZEXPORT crc32_combine OF((uLong crc1, uLong crc2, z_off_t len2));
+
+ Combine two CRC-32 check values into one. For two sequences of bytes,
+ seq1 and seq2 with lengths len1 and len2, CRC-32 check values were
+ calculated for each, crc1 and crc2. crc32_combine() returns the CRC-32
+ check value of seq1 and seq2 concatenated, requiring only crc1, crc2, and
+ len2.
+*/
+
+
+ /* various hacks, don't look :) */
+
+/* deflateInit and inflateInit are macros to allow checking the zlib version
+ * and the compiler's view of z_stream:
+ */
+ZEXTERN int ZEXPORT deflateInit_ OF((z_streamp strm, int level,
+ const char *version, int stream_size));
+ZEXTERN int ZEXPORT inflateInit_ OF((z_streamp strm,
+ const char *version, int stream_size));
+ZEXTERN int ZEXPORT deflateInit2_ OF((z_streamp strm, int level, int method,
+ int windowBits, int memLevel,
+ int strategy, const char *version,
+ int stream_size));
+ZEXTERN int ZEXPORT inflateInit2_ OF((z_streamp strm, int windowBits,
+ const char *version, int stream_size));
+ZEXTERN int ZEXPORT inflateBackInit_ OF((z_streamp strm, int windowBits,
+ unsigned char FAR *window,
+ const char *version,
+ int stream_size));
+#define deflateInit(strm, level) \
+ deflateInit_((strm), (level), ZLIB_VERSION, (int)sizeof(z_stream))
+#define inflateInit(strm) \
+ inflateInit_((strm), ZLIB_VERSION, (int)sizeof(z_stream))
+#define deflateInit2(strm, level, method, windowBits, memLevel, strategy) \
+ deflateInit2_((strm),(level),(method),(windowBits),(memLevel),\
+ (strategy), ZLIB_VERSION, (int)sizeof(z_stream))
+#define inflateInit2(strm, windowBits) \
+ inflateInit2_((strm), (windowBits), ZLIB_VERSION, \
+ (int)sizeof(z_stream))
+#define inflateBackInit(strm, windowBits, window) \
+ inflateBackInit_((strm), (windowBits), (window), \
+ ZLIB_VERSION, (int)sizeof(z_stream))
+
+#ifndef Z_SOLO
+
+/* gzgetc() macro and its supporting function and exposed data structure. Note
+ * that the real internal state is much larger than the exposed structure.
+ * This abbreviated structure exposes just enough for the gzgetc() macro. The
+ * user should not mess with these exposed elements, since their names or
+ * behavior could change in the future, perhaps even capriciously. They can
+ * only be used by the gzgetc() macro. You have been warned.
+ */
+struct gzFile_s {
+ unsigned have;
+ unsigned char *next;
+ z_off64_t pos;
+};
+ZEXTERN int ZEXPORT gzgetc_ OF((gzFile file)); /* backward compatibility */
+#ifdef Z_PREFIX_SET
+# undef z_gzgetc
+# define z_gzgetc(g) \
+ ((g)->have ? ((g)->have--, (g)->pos++, *((g)->next)++) : gzgetc(g))
+#else
+# define gzgetc(g) \
+ ((g)->have ? ((g)->have--, (g)->pos++, *((g)->next)++) : gzgetc(g))
+#endif
+
+/* provide 64-bit offset functions if _LARGEFILE64_SOURCE defined, and/or
+ * change the regular functions to 64 bits if _FILE_OFFSET_BITS is 64 (if
+ * both are true, the application gets the *64 functions, and the regular
+ * functions are changed to 64 bits) -- in case these are set on systems
+ * without large file support, _LFS64_LARGEFILE must also be true
+ */
+#ifdef Z_LARGE64
+ ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
+ ZEXTERN z_off64_t ZEXPORT gzseek64 OF((gzFile, z_off64_t, int));
+ ZEXTERN z_off64_t ZEXPORT gztell64 OF((gzFile));
+ ZEXTERN z_off64_t ZEXPORT gzoffset64 OF((gzFile));
+ ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off64_t));
+ ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off64_t));
+#endif
+
+#if !defined(ZLIB_INTERNAL) && defined(Z_WANT64)
+# ifdef Z_PREFIX_SET
+# define z_gzopen z_gzopen64
+# define z_gzseek z_gzseek64
+# define z_gztell z_gztell64
+# define z_gzoffset z_gzoffset64
+# define z_adler32_combine z_adler32_combine64
+# define z_crc32_combine z_crc32_combine64
+# else
+# define gzopen gzopen64
+# define gzseek gzseek64
+# define gztell gztell64
+# define gzoffset gzoffset64
+# define adler32_combine adler32_combine64
+# define crc32_combine crc32_combine64
+# endif
+# ifndef Z_LARGE64
+ ZEXTERN gzFile ZEXPORT gzopen64 OF((const char *, const char *));
+ ZEXTERN z_off_t ZEXPORT gzseek64 OF((gzFile, z_off_t, int));
+ ZEXTERN z_off_t ZEXPORT gztell64 OF((gzFile));
+ ZEXTERN z_off_t ZEXPORT gzoffset64 OF((gzFile));
+ ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t));
+# endif
+#else
+ ZEXTERN gzFile ZEXPORT gzopen OF((const char *, const char *));
+ ZEXTERN z_off_t ZEXPORT gzseek OF((gzFile, z_off_t, int));
+ ZEXTERN z_off_t ZEXPORT gztell OF((gzFile));
+ ZEXTERN z_off_t ZEXPORT gzoffset OF((gzFile));
+ ZEXTERN uLong ZEXPORT adler32_combine OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine OF((uLong, uLong, z_off_t));
+#endif
+
+#else /* Z_SOLO */
+
+ ZEXTERN uLong ZEXPORT adler32_combine OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine OF((uLong, uLong, z_off_t));
+
+#endif /* !Z_SOLO */
+
+/* hack for buggy compilers */
+#if !defined(ZUTIL_H) && !defined(NO_DUMMY_DECL)
+ struct internal_state {int dummy;};
+#endif
+
+/* undocumented functions */
+ZEXTERN const char * ZEXPORT zError OF((int));
+ZEXTERN int ZEXPORT inflateSyncPoint OF((z_streamp));
+ZEXTERN const z_crc_t FAR * ZEXPORT get_crc_table OF((void));
+ZEXTERN int ZEXPORT inflateUndermine OF((z_streamp, int));
+ZEXTERN int ZEXPORT inflateResetKeep OF((z_streamp));
+ZEXTERN int ZEXPORT deflateResetKeep OF((z_streamp));
+#if defined(_WIN32) && !defined(Z_SOLO)
+ZEXTERN gzFile ZEXPORT gzopen_w OF((const wchar_t *path,
+ const char *mode));
+#endif
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# ifndef Z_SOLO
+ZEXTERN int ZEXPORTVA gzvprintf Z_ARG((gzFile file,
+ const char *format,
+ va_list va));
+# endif
+#endif
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* ZLIB_H */
--- /dev/null
+/* zutil.c -- target dependent utility functions for the compression library
+ * Copyright (C) 1995-2005, 2010, 2011, 2012 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* @(#) $Id$ */
+
+#include "zutil.h"
+
+#ifndef NO_DUMMY_DECL
+struct internal_state {int dummy;}; /* for buggy compilers */
+#endif
+
+z_const char * const z_errmsg[10] = {
+"need dictionary", /* Z_NEED_DICT 2 */
+"stream end", /* Z_STREAM_END 1 */
+"", /* Z_OK 0 */
+"file error", /* Z_ERRNO (-1) */
+"stream error", /* Z_STREAM_ERROR (-2) */
+"data error", /* Z_DATA_ERROR (-3) */
+"insufficient memory", /* Z_MEM_ERROR (-4) */
+"buffer error", /* Z_BUF_ERROR (-5) */
+"incompatible version",/* Z_VERSION_ERROR (-6) */
+""};
+
+
+const char * ZEXPORT zlibVersion()
+{
+ return ZLIB_VERSION;
+}
+
+/* This function is not used by TNG
+uLong ZEXPORT zlibCompileFlags()
+{
+ uLong flags;
+
+ flags = 0;
+ switch ((int)(sizeof(uInt))) {
+ case 2: break;
+ case 4: flags += 1; break;
+ case 8: flags += 2; break;
+ default: flags += 3;
+ }
+ switch ((int)(sizeof(uLong))) {
+ case 2: break;
+ case 4: flags += 1 << 2; break;
+ case 8: flags += 2 << 2; break;
+ default: flags += 3 << 2;
+ }
+ switch ((int)(sizeof(voidpf))) {
+ case 2: break;
+ case 4: flags += 1 << 4; break;
+ case 8: flags += 2 << 4; break;
+ default: flags += 3 << 4;
+ }
+ switch ((int)(sizeof(z_off_t))) {
+ case 2: break;
+ case 4: flags += 1 << 6; break;
+ case 8: flags += 2 << 6; break;
+ default: flags += 3 << 6;
+ }
+#ifdef DEBUG
+ flags += 1 << 8;
+#endif
+#if defined(ASMV) || defined(ASMINF)
+ flags += 1 << 9;
+#endif
+#ifdef ZLIB_WINAPI
+ flags += 1 << 10;
+#endif
+#ifdef BUILDFIXED
+ flags += 1 << 12;
+#endif
+#ifdef DYNAMIC_CRC_TABLE
+ flags += 1 << 13;
+#endif
+#ifdef NO_GZCOMPRESS
+ flags += 1L << 16;
+#endif
+#ifdef NO_GZIP
+ flags += 1L << 17;
+#endif
+#ifdef PKZIP_BUG_WORKAROUND
+ flags += 1L << 20;
+#endif
+#ifdef FASTEST
+ flags += 1L << 21;
+#endif
+#if defined(STDC) || defined(Z_HAVE_STDARG_H)
+# ifdef NO_vsnprintf
+ flags += 1L << 25;
+# ifdef HAS_vsprintf_void
+ flags += 1L << 26;
+# endif
+# else
+# ifdef HAS_vsnprintf_void
+ flags += 1L << 26;
+# endif
+# endif
+#else
+ flags += 1L << 24;
+# ifdef NO_snprintf
+ flags += 1L << 25;
+# ifdef HAS_sprintf_void
+ flags += 1L << 26;
+# endif
+# else
+# ifdef HAS_snprintf_void
+ flags += 1L << 26;
+# endif
+# endif
+#endif
+ return flags;
+}
+*/
+
+#ifdef DEBUG
+
+# ifndef verbose
+# define verbose 0
+# endif
+int ZLIB_INTERNAL z_verbose = verbose;
+
+void ZLIB_INTERNAL z_error (m)
+ char *m;
+{
+ fprintf(stderr, "%s\n", m);
+ exit(1);
+}
+#endif
+
+/* exported to allow conversion of error code to string for compress() and
+ * uncompress()
+ */
+const char * ZEXPORT zError(err)
+ int err;
+{
+ return ERR_MSG(err);
+}
+
+#if defined(_WIN32_WCE)
+ /* The Microsoft C Run-Time Library for Windows CE doesn't have
+ * errno. We define it as a global variable to simplify porting.
+ * Its value is always 0 and should not be used.
+ */
+ int errno = 0;
+#endif
+
+#ifndef HAVE_MEMCPY
+
+void ZLIB_INTERNAL zmemcpy(dest, source, len)
+ Bytef* dest;
+ const Bytef* source;
+ uInt len;
+{
+ if (len == 0) return;
+ do {
+ *dest++ = *source++; /* ??? to be unrolled */
+ } while (--len != 0);
+}
+
+int ZLIB_INTERNAL zmemcmp(s1, s2, len)
+ const Bytef* s1;
+ const Bytef* s2;
+ uInt len;
+{
+ uInt j;
+
+ for (j = 0; j < len; j++) {
+ if (s1[j] != s2[j]) return 2*(s1[j] > s2[j])-1;
+ }
+ return 0;
+}
+
+void ZLIB_INTERNAL zmemzero(dest, len)
+ Bytef* dest;
+ uInt len;
+{
+ if (len == 0) return;
+ do {
+ *dest++ = 0; /* ??? to be unrolled */
+ } while (--len != 0);
+}
+#endif
+
+#ifndef Z_SOLO
+
+#ifdef SYS16BIT
+
+#ifdef __TURBOC__
+/* Turbo C in 16-bit mode */
+
+# define MY_ZCALLOC
+
+/* Turbo C malloc() does not allow dynamic allocation of 64K bytes
+ * and farmalloc(64K) returns a pointer with an offset of 8, so we
+ * must fix the pointer. Warning: the pointer must be put back to its
+ * original form in order to free it, use zcfree().
+ */
+
+#define MAX_PTR 10
+/* 10*64K = 640K */
+
+local int next_ptr = 0;
+
+typedef struct ptr_table_s {
+ voidpf org_ptr;
+ voidpf new_ptr;
+} ptr_table;
+
+local ptr_table table[MAX_PTR];
+/* This table is used to remember the original form of pointers
+ * to large buffers (64K). Such pointers are normalized with a zero offset.
+ * Since MSDOS is not a preemptive multitasking OS, this table is not
+ * protected from concurrent access. This hack doesn't work anyway on
+ * a protected system like OS/2. Use Microsoft C instead.
+ */
+
+voidpf ZLIB_INTERNAL zcalloc (voidpf opaque, unsigned items, unsigned size)
+{
+ voidpf buf = opaque; /* just to make some compilers happy */
+ ulg bsize = (ulg)items*size;
+
+ /* If we allocate less than 65520 bytes, we assume that farmalloc
+ * will return a usable pointer which doesn't have to be normalized.
+ */
+ if (bsize < 65520L) {
+ buf = farmalloc(bsize);
+ if (*(ush*)&buf != 0) return buf;
+ } else {
+ buf = farmalloc(bsize + 16L);
+ }
+ if (buf == NULL || next_ptr >= MAX_PTR) return NULL;
+ table[next_ptr].org_ptr = buf;
+
+ /* Normalize the pointer to seg:0 */
+ *((ush*)&buf+1) += ((ush)((uch*)buf-0) + 15) >> 4;
+ *(ush*)&buf = 0;
+ table[next_ptr++].new_ptr = buf;
+ return buf;
+}
+
+void ZLIB_INTERNAL zcfree (voidpf opaque, voidpf ptr)
+{
+ int n;
+ if (*(ush*)&ptr != 0) { /* object < 64K */
+ farfree(ptr);
+ return;
+ }
+ /* Find the original pointer */
+ for (n = 0; n < next_ptr; n++) {
+ if (ptr != table[n].new_ptr) continue;
+
+ farfree(table[n].org_ptr);
+ while (++n < next_ptr) {
+ table[n-1] = table[n];
+ }
+ next_ptr--;
+ return;
+ }
+ ptr = opaque; /* just to make some compilers happy */
+ Assert(0, "zcfree: ptr not found");
+}
+
+#endif /* __TURBOC__ */
+
+
+#ifdef M_I86
+/* Microsoft C in 16-bit mode */
+
+# define MY_ZCALLOC
+
+#if (!defined(_MSC_VER) || (_MSC_VER <= 600))
+# define _halloc halloc
+# define _hfree hfree
+#endif
+
+voidpf ZLIB_INTERNAL zcalloc (voidpf opaque, uInt items, uInt size)
+{
+ if (opaque) opaque = 0; /* to make compiler happy */
+ return _halloc((long)items, size);
+}
+
+void ZLIB_INTERNAL zcfree (voidpf opaque, voidpf ptr)
+{
+ if (opaque) opaque = 0; /* to make compiler happy */
+ _hfree(ptr);
+}
+
+#endif /* M_I86 */
+
+#endif /* SYS16BIT */
+
+
+#ifndef MY_ZCALLOC /* Any system without a special alloc function */
+
+#ifndef STDC
+extern voidp malloc OF((uInt size));
+extern voidp calloc OF((uInt items, uInt size));
+extern void free OF((voidpf ptr));
+#endif
+
+voidpf ZLIB_INTERNAL zcalloc (opaque, items, size)
+ voidpf opaque;
+ unsigned items;
+ unsigned size;
+{
+ if (opaque) items += size - size; /* make compiler happy */
+ return sizeof(uInt) > 2 ? (voidpf)malloc(items * size) :
+ (voidpf)calloc(items, size);
+}
+
+void ZLIB_INTERNAL zcfree (opaque, ptr)
+ voidpf opaque;
+ voidpf ptr;
+{
+ free(ptr);
+ if (opaque) return; /* make compiler happy */
+}
+
+#endif /* MY_ZCALLOC */
+
+#endif /* !Z_SOLO */
--- /dev/null
+/* zutil.h -- internal interface and configuration of the compression library
+ * Copyright (C) 1995-2013 Jean-loup Gailly.
+ * For conditions of distribution and use, see copyright notice in zlib.h
+ */
+
+/* WARNING: this file should *not* be used by applications. It is
+ part of the implementation of the compression library and is
+ subject to change. Applications should only use zlib.h.
+ */
+
+/* @(#) $Id$ */
+
+#ifndef ZUTIL_H
+#define ZUTIL_H
+
+#ifdef HAVE_HIDDEN
+# define ZLIB_INTERNAL __attribute__((visibility ("hidden")))
+#else
+# define ZLIB_INTERNAL
+#endif
+
+#include "zlib.h"
+
+#if defined(STDC) && !defined(Z_SOLO)
+# if !(defined(_WIN32_WCE) && defined(_MSC_VER))
+# include <stddef.h>
+# endif
+# include <string.h>
+# include <stdlib.h>
+#endif
+
+#ifdef Z_SOLO
+ typedef long ptrdiff_t; /* guess -- will be caught if guess is wrong */
+#endif
+
+#ifndef local
+# define local static
+#endif
+/* compile with -Dlocal if your debugger can't find static symbols */
+
+typedef unsigned char uch;
+typedef uch FAR uchf;
+typedef unsigned short ush;
+typedef ush FAR ushf;
+typedef unsigned long ulg;
+
+extern z_const char * const z_errmsg[10]; /* indexed by 2-zlib_error */
+/* (size given to avoid silly warnings with Visual C++) */
+
+#define ERR_MSG(err) z_errmsg[Z_NEED_DICT-(err)]
+
+#define ERR_RETURN(strm,err) \
+ return (strm->msg = ERR_MSG(err), (err))
+/* To be used only when the state is known to be valid */
+
+ /* common constants */
+
+#ifndef DEF_WBITS
+# define DEF_WBITS MAX_WBITS
+#endif
+/* default windowBits for decompression. MAX_WBITS is for compression only */
+
+#if MAX_MEM_LEVEL >= 8
+# define DEF_MEM_LEVEL 8
+#else
+# define DEF_MEM_LEVEL MAX_MEM_LEVEL
+#endif
+/* default memLevel */
+
+#define STORED_BLOCK 0
+#define STATIC_TREES 1
+#define DYN_TREES 2
+/* The three kinds of block type */
+
+#define MIN_MATCH 3
+#define MAX_MATCH 258
+/* The minimum and maximum match lengths */
+
+#define PRESET_DICT 0x20 /* preset dictionary flag in zlib header */
+
+ /* target dependencies */
+
+#if defined(MSDOS) || (defined(WINDOWS) && !defined(WIN32))
+# define OS_CODE 0x00
+# ifndef Z_SOLO
+# if defined(__TURBOC__) || defined(__BORLANDC__)
+# if (__STDC__ == 1) && (defined(__LARGE__) || defined(__COMPACT__))
+ /* Allow compilation with ANSI keywords only enabled */
+ void _Cdecl farfree( void *block );
+ void *_Cdecl farmalloc( unsigned long nbytes );
+# else
+# include <alloc.h>
+# endif
+# else /* MSC or DJGPP */
+# include <malloc.h>
+# endif
+# endif
+#endif
+
+#ifdef AMIGA
+# define OS_CODE 0x01
+#endif
+
+#if defined(VAXC) || defined(VMS)
+# define OS_CODE 0x02
+# define F_OPEN(name, mode) \
+ fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512")
+#endif
+
+#if defined(ATARI) || defined(atarist)
+# define OS_CODE 0x05
+#endif
+
+#ifdef OS2
+# define OS_CODE 0x06
+# if defined(M_I86) && !defined(Z_SOLO)
+# include <malloc.h>
+# endif
+#endif
+
+#if defined(MACOS) || defined(TARGET_OS_MAC)
+# define OS_CODE 0x07
+# ifndef Z_SOLO
+# if defined(__MWERKS__) && __dest_os != __be_os && __dest_os != __win32_os
+# include <unix.h> /* for fdopen */
+# else
+# ifndef fdopen
+# define fdopen(fd,mode) NULL /* No fdopen() */
+# endif
+# endif
+# endif
+#endif
+
+#ifdef TOPS20
+# define OS_CODE 0x0a
+#endif
+
+#ifdef WIN32
+# ifndef __CYGWIN__ /* Cygwin is Unix, not Win32 */
+# define OS_CODE 0x0b
+# endif
+#endif
+
+#ifdef __50SERIES /* Prime/PRIMOS */
+# define OS_CODE 0x0f
+#endif
+
+#if defined(_BEOS_) || defined(RISCOS)
+# define fdopen(fd,mode) NULL /* No fdopen() */
+#endif
+
+#if (defined(_MSC_VER) && (_MSC_VER > 600)) && !defined __INTERIX
+# if defined(_WIN32_WCE)
+# define fdopen(fd,mode) NULL /* No fdopen() */
+# ifndef _PTRDIFF_T_DEFINED
+ typedef int ptrdiff_t;
+# define _PTRDIFF_T_DEFINED
+# endif
+# else
+# define fdopen(fd,type) _fdopen(fd,type)
+# endif
+#endif
+
+#if defined(__BORLANDC__) && !defined(MSDOS)
+ #pragma warn -8004
+ #pragma warn -8008
+ #pragma warn -8066
+#endif
+
+/* provide prototypes for these when building zlib without LFS */
+#if !defined(_WIN32) && \
+ (!defined(_LARGEFILE64_SOURCE) || _LFS64_LARGEFILE-0 == 0)
+ ZEXTERN uLong ZEXPORT adler32_combine64 OF((uLong, uLong, z_off_t));
+ ZEXTERN uLong ZEXPORT crc32_combine64 OF((uLong, uLong, z_off_t));
+#endif
+
+ /* common defaults */
+
+#ifndef OS_CODE
+# define OS_CODE 0x03 /* assume Unix */
+#endif
+
+#ifndef F_OPEN
+# define F_OPEN(name, mode) fopen((name), (mode))
+#endif
+
+ /* functions */
+
+#if defined(pyr) || defined(Z_SOLO)
+# define NO_MEMCPY
+#endif
+#if defined(SMALL_MEDIUM) && !defined(_MSC_VER) && !defined(__SC__)
+ /* Use our own functions for small and medium model with MSC <= 5.0.
+ * You may have to use the same strategy for Borland C (untested).
+ * The __SC__ check is for Symantec.
+ */
+# define NO_MEMCPY
+#endif
+#if defined(STDC) && !defined(HAVE_MEMCPY) && !defined(NO_MEMCPY)
+# define HAVE_MEMCPY
+#endif
+#ifdef HAVE_MEMCPY
+# ifdef SMALL_MEDIUM /* MSDOS small or medium model */
+# define zmemcpy _fmemcpy
+# define zmemcmp _fmemcmp
+# define zmemzero(dest, len) _fmemset(dest, 0, len)
+# else
+# define zmemcpy memcpy
+# define zmemcmp memcmp
+# define zmemzero(dest, len) memset(dest, 0, len)
+# endif
+#else
+ void ZLIB_INTERNAL zmemcpy OF((Bytef* dest, const Bytef* source, uInt len));
+ int ZLIB_INTERNAL zmemcmp OF((const Bytef* s1, const Bytef* s2, uInt len));
+ void ZLIB_INTERNAL zmemzero OF((Bytef* dest, uInt len));
+#endif
+
+/* Diagnostic functions */
+#ifdef DEBUG
+# include <stdio.h>
+ extern int ZLIB_INTERNAL z_verbose;
+ extern void ZLIB_INTERNAL z_error OF((char *m));
+# define Assert(cond,msg) {if(!(cond)) z_error(msg);}
+# define Trace(x) {if (z_verbose>=0) fprintf x ;}
+# define Tracev(x) {if (z_verbose>0) fprintf x ;}
+# define Tracevv(x) {if (z_verbose>1) fprintf x ;}
+# define Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;}
+# define Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;}
+#else
+# define Assert(cond,msg)
+# define Trace(x)
+# define Tracev(x)
+# define Tracevv(x)
+# define Tracec(c,x)
+# define Tracecv(c,x)
+#endif
+
+#ifndef Z_SOLO
+ voidpf ZLIB_INTERNAL zcalloc OF((voidpf opaque, unsigned items,
+ unsigned size));
+ void ZLIB_INTERNAL zcfree OF((voidpf opaque, voidpf ptr));
+#endif
+
+#define ZALLOC(strm, items, size) \
+ (*((strm)->zalloc))((strm)->opaque, (items), (size))
+#define ZFREE(strm, addr) (*((strm)->zfree))((strm)->opaque, (voidpf)(addr))
+#define TRY_FREE(s, p) {if (p) ZFREE(s, p);}
+
+/* Reverse the bytes in a 32-bit value */
+#define ZSWAP32(q) ((((q) >> 24) & 0xff) + (((q) >> 8) & 0xff00) + \
+ (((q) & 0xff00) << 8) + (((q) & 0xff) << 24))
+
+#endif /* ZUTIL_H */
/* This code is part of the tng binary trajectory format.
*
* Written by Magnus Lundborg
- * Copyright (c) 2012-2014, The GROMACS development team.
+ * Copyright (c) 2012-2017, The GROMACS development team.
* Check out http://www.gromacs.org for more information.
*
*
* See git log for full revision history.
*
* Revisions
+ *
+ * v. 1.8 - Added GROMACS energy block IDs.
+ * - Rewritten build system for the main library.
+ * - Added block ID for atom (or generic particle) mass.
+ * - Fixed bugs, such as:
+ * - Do not switch endianness when reading and writing TNG compressed data.
+ * - Update pointers to residues in the chain when writing multiple chains in one molecule.
+ * - Update frame set pointers when appending to file.
*
* v. 1.7 - Fifth stable release of the API
*
#define TNG_TRAJ_ANISOTROPIC_B_FACTORS 0x0000000010000007LL
#define TNG_TRAJ_OCCUPANCY 0x0000000010000008LL
#define TNG_TRAJ_GENERAL_COMMENTS 0x0000000010000009LL
+#define TNG_TRAJ_MASSES 0x0000000010000010LL
/** @} */
#define TNG_GMX_ENERGY_TEMPERATURE 0x1000000010000011LL
#define TNG_GMX_ENERGY_PRESSURE 0x1000000010000012LL
#define TNG_GMX_ENERGY_CONSTR_RMSD 0x1000000010000013LL
-#define TNG_GMX_ENERGY_BOX_X 0x1000000010000014LL
-#define TNG_GMX_ENERGY_BOX_Y 0x1000000010000015LL
-#define TNG_GMX_ENERGY_BOX_Z 0x1000000010000016LL
-#define TNG_GMX_ENERGY_VOLUME 0x1000000010000017LL
-#define TNG_GMX_ENERGY_DENSITY 0x1000000010000018LL
-#define TNG_GMX_ENERGY_PV 0x1000000010000019LL
-#define TNG_GMX_ENERGY_ENTHALPY 0x1000000010000020LL
-#define TNG_GMX_ENERGY_VIR_XX 0x1000000010000021LL
-#define TNG_GMX_ENERGY_VIR_XY 0x1000000010000022LL
-#define TNG_GMX_ENERGY_VIR_XZ 0x1000000010000023LL
-#define TNG_GMX_ENERGY_VIR_YX 0x1000000010000024LL
-#define TNG_GMX_ENERGY_VIR_YY 0x1000000010000025LL
-#define TNG_GMX_ENERGY_VIR_YZ 0x1000000010000026LL
-#define TNG_GMX_ENERGY_VIR_ZX 0x1000000010000027LL
-#define TNG_GMX_ENERGY_VIR_ZY 0x1000000010000028LL
-#define TNG_GMX_ENERGY_VIR_ZZ 0x1000000010000029LL
-#define TNG_GMX_ENERGY_PRES_XX 0x1000000010000030LL
-#define TNG_GMX_ENERGY_PRES_XY 0x1000000010000031LL
-#define TNG_GMX_ENERGY_PRES_XZ 0x1000000010000032LL
-#define TNG_GMX_ENERGY_PRES_YX 0x1000000010000033LL
-#define TNG_GMX_ENERGY_PRES_YY 0x1000000010000034LL
-#define TNG_GMX_ENERGY_PRES_YZ 0x1000000010000035LL
-#define TNG_GMX_ENERGY_PRES_ZX 0x1000000010000036LL
-#define TNG_GMX_ENERGY_PRES_ZY 0x1000000010000037LL
-#define TNG_GMX_ENERGY_PRES_ZZ 0x1000000010000038LL
-#define TNG_GMX_ENERGY_SURFXSURFTEN 0x1000000010000039LL
-#define TNG_GMX_ENERGY_T_SYSTEM 0x1000000010000040LL
-#define TNG_GMX_ENERGY_LAMB_SYSTEM 0x1000000010000041LL
-#define TNG_GMX_SELECTION_GROUP_NAMES 0x1000000010000042LL
-#define TNG_GMX_ATOM_SELECTION_GROUP 0x1000000010000043LL
+#define TNG_GMX_ENERGY_CONSTR2_RMSD 0x1000000010000014LL
+#define TNG_GMX_ENERGY_BOX_X 0x1000000010000015LL
+#define TNG_GMX_ENERGY_BOX_Y 0x1000000010000016LL
+#define TNG_GMX_ENERGY_BOX_Z 0x1000000010000017LL
+#define TNG_GMX_ENERGY_BOXXX 0x1000000010000018LL
+#define TNG_GMX_ENERGY_BOXYY 0x1000000010000019LL
+#define TNG_GMX_ENERGY_BOXZZ 0x1000000010000020LL
+#define TNG_GMX_ENERGY_BOXYX 0x1000000010000021LL
+#define TNG_GMX_ENERGY_BOXZX 0x1000000010000022LL
+#define TNG_GMX_ENERGY_BOXZY 0x1000000010000023LL
+#define TNG_GMX_ENERGY_BOXVELXX 0x1000000010000024LL
+#define TNG_GMX_ENERGY_BOXVELYY 0x1000000010000025LL
+#define TNG_GMX_ENERGY_BOXVELZZ 0x1000000010000026LL
+#define TNG_GMX_ENERGY_BOXVELYX 0x1000000010000027LL
+#define TNG_GMX_ENERGY_BOXVELZX 0x1000000010000028LL
+#define TNG_GMX_ENERGY_BOXVELZY 0x1000000010000029LL
+#define TNG_GMX_ENERGY_VOLUME 0x1000000010000030LL
+#define TNG_GMX_ENERGY_DENSITY 0x1000000010000031LL
+#define TNG_GMX_ENERGY_PV 0x1000000010000032LL
+#define TNG_GMX_ENERGY_ENTHALPY 0x1000000010000033LL
+#define TNG_GMX_ENERGY_VIR_XX 0x1000000010000034LL
+#define TNG_GMX_ENERGY_VIR_XY 0x1000000010000035LL
+#define TNG_GMX_ENERGY_VIR_XZ 0x1000000010000036LL
+#define TNG_GMX_ENERGY_VIR_YX 0x1000000010000037LL
+#define TNG_GMX_ENERGY_VIR_YY 0x1000000010000038LL
+#define TNG_GMX_ENERGY_VIR_YZ 0x1000000010000039LL
+#define TNG_GMX_ENERGY_VIR_ZX 0x1000000010000040LL
+#define TNG_GMX_ENERGY_VIR_ZY 0x1000000010000041LL
+#define TNG_GMX_ENERGY_VIR_ZZ 0x1000000010000042LL
+#define TNG_GMX_ENERGY_SHAKEVIR_XX 0x1000000010000043LL
+#define TNG_GMX_ENERGY_SHAKEVIR_XY 0x1000000010000044LL
+#define TNG_GMX_ENERGY_SHAKEVIR_XZ 0x1000000010000045LL
+#define TNG_GMX_ENERGY_SHAKEVIR_YX 0x1000000010000046LL
+#define TNG_GMX_ENERGY_SHAKEVIR_YY 0x1000000010000047LL
+#define TNG_GMX_ENERGY_SHAKEVIR_YZ 0x1000000010000048LL
+#define TNG_GMX_ENERGY_SHAKEVIR_ZX 0x1000000010000049LL
+#define TNG_GMX_ENERGY_SHAKEVIR_ZY 0x1000000010000050LL
+#define TNG_GMX_ENERGY_SHAKEVIR_ZZ 0x1000000010000051LL
+#define TNG_GMX_ENERGY_FORCEVIR_XX 0x1000000010000052LL
+#define TNG_GMX_ENERGY_FORCEVIR_XY 0x1000000010000053LL
+#define TNG_GMX_ENERGY_FORCEVIR_XZ 0x1000000010000054LL
+#define TNG_GMX_ENERGY_FORCEVIR_YX 0x1000000010000055LL
+#define TNG_GMX_ENERGY_FORCEVIR_YY 0x1000000010000056LL
+#define TNG_GMX_ENERGY_FORCEVIR_YZ 0x1000000010000057LL
+#define TNG_GMX_ENERGY_FORCEVIR_ZX 0x1000000010000058LL
+#define TNG_GMX_ENERGY_FORCEVIR_ZY 0x1000000010000059LL
+#define TNG_GMX_ENERGY_FORCEVIR_ZZ 0x1000000010000060LL
+#define TNG_GMX_ENERGY_PRES_XX 0x1000000010000061LL
+#define TNG_GMX_ENERGY_PRES_XY 0x1000000010000062LL
+#define TNG_GMX_ENERGY_PRES_XZ 0x1000000010000063LL
+#define TNG_GMX_ENERGY_PRES_YX 0x1000000010000064LL
+#define TNG_GMX_ENERGY_PRES_YY 0x1000000010000065LL
+#define TNG_GMX_ENERGY_PRES_YZ 0x1000000010000066LL
+#define TNG_GMX_ENERGY_PRES_ZX 0x1000000010000067LL
+#define TNG_GMX_ENERGY_PRES_ZY 0x1000000010000068LL
+#define TNG_GMX_ENERGY_PRES_ZZ 0x1000000010000069LL
+#define TNG_GMX_ENERGY_SURFXSURFTEN 0x1000000010000070LL
+#define TNG_GMX_ENERGY_MUX 0x1000000010000071LL
+#define TNG_GMX_ENERGY_MUY 0x1000000010000072LL
+#define TNG_GMX_ENERGY_MUZ 0x1000000010000073LL
+#define TNG_GMX_ENERGY_VCOS 0x1000000010000074LL
+#define TNG_GMX_ENERGY_VISC 0x1000000010000075LL
+#define TNG_GMX_ENERGY_BAROSTAT 0x1000000010000076LL
+#define TNG_GMX_ENERGY_T_SYSTEM 0x1000000010000077LL
+#define TNG_GMX_ENERGY_LAMB_SYSTEM 0x1000000010000078LL
+#define TNG_GMX_SELECTION_GROUP_NAMES 0x1000000010000079LL
+#define TNG_GMX_ATOM_SELECTION_GROUP 0x1000000010000080LL
/** @} */
/** Flag to specify if a data block contains data related to particles or not.*/
* opened.
* @param block_id is the id number of the particle data block to read.
* @param values is a pointer to a 1-dimensional array (memory unallocated), which
- * will be filled with data. The length of the array will be (n_frames * n_values_per_frame).
+ * will be filled with data. The length of the array will be
+ * (n_frames_with_data (see stride_length) * n_values_per_frame).
* Since **values is allocated in this function it is the callers
* responsibility to free the memory.
* @param n_frames is set to the number of particles in the returned data. This is
* If hash_mode == TNG_USE_HASH the md5 hash in the file will be
* compared to the md5 hash of the read contents to ensure valid data.
* @param values is a pointer to a 1-dimensional array (memory unallocated), which
- * will be filled with data. The length of the array will be (n_frames * n_values_per_frame).
+ * will be filled with data. The length of the array will be
+ * (n_frames_with_data (see stride_length) * n_values_per_frame).
* Since **values is allocated in this function it is the callers
* responsibility to free the memory.
* @param stride_length is set to the stride length (writing interval) of
* @param block_id is the id number of the particle data block to read.
* @param values is a pointer to a 1-dimensional array (memory unallocated), which
* will be filled with data. The length of the array will be
- * (n_frames * n_particles * n_values_per_frame).
+ * (n_frames_with_data (see stride_length) * n_particles * n_values_per_frame).
* Since **values is allocated in this function it is the callers
* responsibility to free the memory.
* @param n_frames is set to the number of frames in the returned data. This is
* compared to the md5 hash of the read contents to ensure valid data.
* @param values is a pointer to a 1-dimensional array (memory unallocated), which
* will be filled with data. The length of the array will be
- * (n_frames * n_particles * n_values_per_frame).
+ * (n_frames_with_data (see stride_length) * n_particles * n_values_per_frame).
* Since **values is allocated in this function it is the callers
* responsibility to free the memory.
* @param stride_length is set to the stride length (writing interval) of
* @param tng_data is the trajectory to read from.
* @param block_id is the ID number of the block containing the data of interest.
* @param values will be set to point at a 1-dimensional array containing the
- * requested data. The variable may point at already allocated memory or be a
- * NULL pointer. The memory must be freed afterwards.
+ * requested data. The variable may point at already allocated memory (which will
+ * be reallocated with realloc()), or be a
+ * NULL pointer. The calling code must free the memory afterwards.
* @param data_type will be pointing to a character indicating the size of the
* data of the returned values, e.g. TNG_INT_DATA, TNG_FLOAT_DATA or TNG_DOUBLE_DATA.
* @param retrieved_frame_number will be pointing at the frame number of the
* @param data_block_ids_in_next_frame is set to an array (of length
* n_data_blocks_in_next_frame) that lists the data block IDs with data for
* next_frame. It must be pointing at NULL or previously allocated memory.
- * Memory for the array is allocated by this function.
+ * Memory for the array is reallocated by this function using realloc().
* The memory must be freed by the client afterwards or
* there will be a memory leak.
* @pre \code tng_data != 0 \endcode The trajectory container (tng_data)
# - Config file for the TNG_IO package
-# It defines the following variables
-# TNG_IO_INCLUDE_DIRS - include directories for TNG_IO
-# TNG_IO_LIBRARIES - libraries to link against
-# TNG_IO_DEFINITIONS - definitions used when compiling
-# Compute paths
-get_filename_component(TNG_IO_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH)
-set(TNG_IO_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@")
-set(TNG_IO_DEFINITIONS "@TNG_COMPILE_DEFS@")
+include(${CMAKE_CURRENT_LIST_DIR}/tng_io.cmake)
-set(TNG_IO_LIBRARIES tng_io)
+get_target_property(_libs tng_io::tng_io INTERFACE_LINK_LIBRARIES)
+if (_libs MATCHES "ZLIB::")
+ include(CMakeFindDependencyMacro)
+ find_dependency(ZLIB)
+endif()
+unset(_libs)
+# Provide information in variables as well for backwards compatibility
+set(TNG_IO_LIBRARIES tng_io::tng_io)
+get_target_property(TNG_IO_INCLUDE_DIRS tng_io::tng_io INTERFACE_INCLUDE_DIRECTORIES)
+get_target_property(TNG_IO_DEFINITIONS tng_io::tng_io INTERFACE_COMPILE_DEFINITIONS)
/* This code is part of the tng binary trajectory format.
*
* Written by Magnus Lundborg
- * Copyright (c) 2012-2015, The GROMACS development team.
+ * Copyright (c) 2012-2017, The GROMACS development team.
* Check out http://www.gromacs.org for more information.
*
*
#include <string.h>
#include <time.h>
#include <math.h>
-#ifdef USE_ZLIB
#include <zlib.h>
-#endif
#include "tng/md5.h"
#include "compression/tng_compress.h"
FILE *output_file;
/** Function to swap 32 bit values to and from the endianness of the
* input file */
- tng_function_status (*input_endianness_swap_func_32)(const tng_trajectory_t, int32_t *);
+ tng_function_status (*input_endianness_swap_func_32)(const tng_trajectory_t, uint32_t *);
/** Function to swap 64 bit values to and from the endianness of the
* input file */
- tng_function_status (*input_endianness_swap_func_64)(const tng_trajectory_t, int64_t *);
+ tng_function_status (*input_endianness_swap_func_64)(const tng_trajectory_t, uint64_t *);
/** Function to swap 32 bit values to and from the endianness of the
* input file */
- tng_function_status (*output_endianness_swap_func_32)(const tng_trajectory_t, int32_t *);
+ tng_function_status (*output_endianness_swap_func_32)(const tng_trajectory_t, uint32_t *);
/** Function to swap 64 bit values to and from the endianness of the
* input file */
- tng_function_status (*output_endianness_swap_func_64)(const tng_trajectory_t, int64_t *);
+ tng_function_status (*output_endianness_swap_func_64)(const tng_trajectory_t, uint64_t *);
/** The endianness of 32 bit values of the current computer */
char endianness_32;
/** The endianness of 64 bit values of the current computer */
* byte order is not recognised.
*/
static tng_function_status tng_swap_byte_order_big_endian_32
- (const tng_trajectory_t tng_data, int32_t *v)
+ (const tng_trajectory_t tng_data, uint32_t *v)
{
switch(tng_data->endianness_32)
{
* byte order is not recognised.
*/
static tng_function_status tng_swap_byte_order_big_endian_64
- (const tng_trajectory_t tng_data, int64_t *v)
+ (const tng_trajectory_t tng_data, uint64_t *v)
{
switch(tng_data->endianness_64)
{
* byte order is not recognised.
*/
static tng_function_status tng_swap_byte_order_little_endian_32
- (const tng_trajectory_t tng_data, int32_t *v)
+ (const tng_trajectory_t tng_data, uint32_t *v)
{
switch(tng_data->endianness_32)
{
* byte order is not recognised.
*/
static tng_function_status tng_swap_byte_order_little_endian_64
- (const tng_trajectory_t tng_data, int64_t *v)
+ (const tng_trajectory_t tng_data, uint64_t *v)
{
switch(tng_data->endianness_64)
{
}
} while ((temp[count-1] != '\0') && (count < TNG_MAX_STR_LEN));
- temp_alloc = realloc(*str, count);
+ temp_alloc = (char *)realloc(*str, count);
if(!temp_alloc)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n", count,
- __FILE__, line_nr);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, line_nr);
free(*str);
*str = 0;
return TNG_FAILURE;
{
case 8:
if(tng_data->input_endianness_swap_func_64 &&
- tng_data->input_endianness_swap_func_64(tng_data, dest) != TNG_SUCCESS)
+ tng_data->input_endianness_swap_func_64(tng_data, (uint64_t *)dest) != TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
__FILE__, line_nr);
break;
case 4:
if(tng_data->input_endianness_swap_func_32 &&
- tng_data->input_endianness_swap_func_32(tng_data, dest) != TNG_SUCCESS)
+ tng_data->input_endianness_swap_func_32(tng_data, (uint32_t *)dest) != TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
__FILE__, line_nr);
md5_state_t *md5_state,
const int line_nr)
{
- int32_t temp_i32;
- int64_t temp_i64;
+ uint32_t temp_i32;
+ uint64_t temp_i64;
switch(len)
{
case 8:
- temp_i64 = *((int64_t *)src);
+ temp_i64 = *((uint64_t *)src);
if(tng_data->output_endianness_swap_func_64 &&
tng_data->output_endianness_swap_func_64(tng_data, &temp_i64) != TNG_SUCCESS)
{
}
break;
case 4:
- temp_i32 = *((int32_t *)src);
+ temp_i32 = *((uint32_t *)src);
if(tng_data->output_endianness_swap_func_32 &&
tng_data->output_endianness_swap_func_32(tng_data, &temp_i32) != TNG_SUCCESS)
{
curr_file_pos = ftello(tng_data->input_file);
if(curr_file_pos < start_pos + block->block_contents_size)
{
- temp_data = malloc(start_pos + block->block_contents_size - curr_file_pos);
+ temp_data = (char *)malloc(start_pos + block->block_contents_size - curr_file_pos);
if(!temp_data)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- start_pos + block->block_contents_size - curr_file_pos, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
if(fread(temp_data, start_pos + block->block_contents_size - curr_file_pos,
{
tng_gen_block_t block;
- *block_p = malloc(sizeof(struct tng_gen_block));
+ *block_p = (struct tng_gen_block *)malloc(sizeof(struct tng_gen_block));
if(!*block_p)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_gen_block), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(tng_data->input_endianness_swap_func_64 &&
- tng_data->input_endianness_swap_func_64(tng_data, &block->header_contents_size) != TNG_SUCCESS)
+ tng_data->input_endianness_swap_func_64(tng_data, (uint64_t *)&block->header_contents_size) != TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
__FILE__, __LINE__);
free(block->block_contents);
}
- block->block_contents = malloc(block->block_contents_size);
+ block->block_contents = (char *)malloc(block->block_contents_size);
if(!block->block_contents)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- block->block_contents_size, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
return(TNG_CRITICAL);
}
{
tng_gen_block_t block;
FILE *temp = tng_data->input_file;
- int64_t output_file_pos, pos, contents_start_pos;
+ uint64_t output_file_pos, pos, contents_start_pos;
if(tng_output_file_init(tng_data) != TNG_SUCCESS)
{
tng_gen_block_t block;
tng_trajectory_frame_set_t frame_set;
FILE *temp = tng_data->input_file;
- int64_t pos, output_file_pos, contents_start_pos;
+ uint64_t pos, output_file_pos, contents_start_pos;
if(tng_output_file_init(tng_data) != TNG_SUCCESS)
{
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", pos,
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n", pos,
__FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_FAILURE);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n", *pos,
__FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_FAILURE);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", *pos,
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n", *pos,
__FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
fseeko(tng_data->input_file, block_start_pos, SEEK_SET);
- contents = malloc(block_len);
+ contents = (char *)malloc(block_len);
if(!contents)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- block_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
tng_data->current_trajectory_frame_set_output_file_pos = new_pos;
+ if(tng_data->input_file == tng_data->output_file)
+ {
+ tng_data->current_trajectory_frame_set_input_file_pos = new_pos;
+ }
tng_frame_set_pointers_update(tng_data, hash_mode);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
curr_frame_set_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_FAILURE);
* termination */
if(!block->name)
{
- block->name = malloc(1);
+ block->name = (char *)malloc(1);
if(!block->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
* termination */
if(!tng_data->first_program_name)
{
- tng_data->first_program_name = malloc(1);
+ tng_data->first_program_name = (char *)malloc(1);
if(!tng_data->first_program_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->last_program_name)
{
- tng_data->last_program_name = malloc(1);
+ tng_data->last_program_name = (char *)malloc(1);
if(!tng_data->last_program_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->first_user_name)
{
- tng_data->first_user_name = malloc(1);
+ tng_data->first_user_name = (char *)malloc(1);
if(!tng_data->first_user_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->last_user_name)
{
- tng_data->last_user_name = malloc(1);
+ tng_data->last_user_name = (char *)malloc(1);
if(!tng_data->last_user_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->first_computer_name)
{
- tng_data->first_computer_name = malloc(1);
+ tng_data->first_computer_name = (char *)malloc(1);
if(!tng_data->first_computer_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->last_computer_name)
{
- tng_data->last_computer_name = malloc(1);
+ tng_data->last_computer_name = (char *)malloc(1);
if(!tng_data->last_computer_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->first_pgp_signature)
{
- tng_data->first_pgp_signature = malloc(1);
+ tng_data->first_pgp_signature = (char *)malloc(1);
if(!tng_data->first_pgp_signature)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->last_pgp_signature)
{
- tng_data->last_pgp_signature = malloc(1);
+ tng_data->last_pgp_signature = (char *)malloc(1);
if(!tng_data->last_pgp_signature)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
if(!tng_data->forcefield_name)
{
- tng_data->forcefield_name = malloc(1);
+ tng_data->forcefield_name = (char *)malloc(1);
if(!tng_data->forcefield_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
name_len = strlen("GENERAL INFO");
- block->name = malloc(name_len + 1);
+ block->name = (char *)malloc(name_len + 1);
if(!block->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%u bytes). %s: %d\n",
- (unsigned int)(name_len+1), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
}
molecule = &tng_data->molecules[i];
if(!molecule->name)
{
- molecule->name = malloc(1);
+ molecule->name = (char *)malloc(1);
if(!molecule->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
if(!chain->name)
{
- chain->name = malloc(1);
+ chain->name = (char *)malloc(1);
if(!chain->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
if(!residue->name)
{
- residue->name = malloc(1);
+ residue->name = (char *)malloc(1);
if(!residue->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
*len += sizeof(atom->id);
if(!atom->name)
{
- atom->name = malloc(1);
+ atom->name = (char *)malloc(1);
if(!atom->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
if(!atom->atom_type)
{
- atom->atom_type = malloc(1);
+ atom->atom_type = (char *)malloc(1);
if(!atom->atom_type)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (1 byte). %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
return(TNG_CRITICAL);
}
tng_data->n_particles = 0;
- tng_data->molecules = malloc(tng_data->n_molecules *
- sizeof(struct tng_molecule));
+ tng_data->molecules = (struct tng_molecule *)malloc(tng_data->n_molecules *
+ sizeof(struct tng_molecule));
if(!tng_data->molecules)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- tng_data->n_molecules * sizeof(struct tng_molecule),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
return(TNG_CRITICAL);
}
{
free(tng_data->molecule_cnt_list);
}
- tng_data->molecule_cnt_list = malloc(sizeof(int64_t) *
- tng_data->n_molecules);
+ tng_data->molecule_cnt_list = (int64_t *)malloc(sizeof(int64_t) *
+ tng_data->n_molecules);
if(!tng_data->molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- tng_data->n_molecules * sizeof(struct tng_molecule),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
return(TNG_CRITICAL);
}
-/* fprintf(stderr, "TNG library: Read id: %"PRId64" offset: %d\n", molecule->id, offset);*/
+/* fprintf(stderr, "TNG library: Read id: %" PRId64 " offset: %d\n", molecule->id, offset);*/
tng_freadstr(tng_data, &molecule->name, hash_mode, &md5_state, __LINE__);
if(tng_file_input_numerical(tng_data, &molecule->quaternary_str,
if(molecule->n_chains > 0)
{
- molecule->chains = malloc(molecule->n_chains *
- sizeof(struct tng_chain));
+ molecule->chains = (struct tng_chain *)malloc(molecule->n_chains *
+ sizeof(struct tng_chain));
if(!molecule->chains)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- molecule->n_chains * sizeof(struct tng_chain),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
if(molecule->n_residues > 0)
{
- molecule->residues = malloc(molecule->n_residues *
- sizeof(struct tng_residue));
+ molecule->residues = (struct tng_residue *)malloc(molecule->n_residues *
+ sizeof(struct tng_residue));
if(!molecule->residues)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- molecule->n_residues * sizeof(struct tng_residue),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
if(molecule->chains)
{
free(molecule->chains);
residue = 0;
}
- molecule->atoms = malloc(molecule->n_atoms *
- sizeof(struct tng_atom));
+ molecule->atoms = (struct tng_atom *)malloc(molecule->n_atoms *
+ sizeof(struct tng_atom));
if(!molecule->atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- molecule->n_atoms * sizeof(struct tng_atom),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
if(molecule->chains)
{
free(molecule->chains);
if(molecule->n_bonds > 0)
{
- tng_data->molecules[i].bonds = malloc(molecule->n_bonds *
- sizeof(struct tng_bond));
+ tng_data->molecules[i].bonds = (struct tng_bond *)malloc(molecule->n_bonds *
+ sizeof(struct tng_bond));
if(!molecule->bonds)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- molecule->n_bonds * sizeof(struct tng_bond),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
if(molecule->chains)
{
free(molecule->chains);
name_len = (unsigned int)strlen("MOLECULES");
- block->name = malloc(name_len + 1);
+ block->name = (char *)malloc(name_len + 1);
if(!block->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- name_len+1, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n", __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
}
if(!frame_set->molecule_cnt_list)
{
frame_set->molecule_cnt_list =
- malloc(sizeof(int64_t) * tng_data->n_molecules);
+ (int64_t *)malloc(sizeof(int64_t) * tng_data->n_molecules);
if(!frame_set->molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * tng_data->n_molecules,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
{
if(strncmp(block->md5_hash, hash, TNG_MD5_HASH_LEN) != 0)
{
- fprintf(stderr, "TNG library: Frame set block contents corrupt (first frame %"PRId64"). Hashes do not match. "
+ fprintf(stderr, "TNG library: Frame set block contents corrupt (first frame %" PRId64 "). Hashes do not match. "
"%s: %d\n", frame_set->first_frame, __FILE__, __LINE__);
}
}
if(!block->name || strlen(block->name) < name_len)
{
- temp_name = realloc(block->name, name_len + 1);
+ temp_name = (char *)realloc(block->name, name_len + 1);
if(!temp_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%u bytes). %s: %d\n",
- name_len+1, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(block->name);
block->name = 0;
return(TNG_CRITICAL);
* size or if the contents can be read. */
frame_set->n_mapping_blocks++;
- mappings = realloc(frame_set->mappings,
- sizeof(struct tng_particle_mapping) *
- frame_set->n_mapping_blocks);
+ mappings = (tng_particle_mapping_t)realloc(frame_set->mappings,
+ sizeof(struct tng_particle_mapping) *
+ frame_set->n_mapping_blocks);
if(!mappings)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- block->block_contents_size, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(frame_set->mappings);
frame_set->mappings = 0;
return(TNG_CRITICAL);
return(TNG_CRITICAL);
}
- mapping->real_particle_numbers = malloc(mapping->n_particles *
- sizeof(int64_t));
+ mapping->real_particle_numbers = (int64_t *)malloc(mapping->n_particles *
+ sizeof(int64_t));
if(!mapping->real_particle_numbers)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- mapping->n_particles * sizeof(int64_t), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
if(!block->name || strlen(block->name) < name_len)
{
- temp_name = realloc(block->name, name_len + 1);
+ temp_name = (char *)realloc(block->name, name_len + 1);
if(!temp_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%u bytes). %s: %d\n",
- name_len+1, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(block->name);
block->name = 0;
return(TNG_CRITICAL);
if(block_type_flag == TNG_TRAJECTORY_BLOCK)
{
frame_set->n_particle_data_blocks++;
- data = realloc(frame_set->tr_particle_data,
- sizeof(struct tng_data) *
- frame_set->n_particle_data_blocks);
+ data = (tng_data_t)realloc(frame_set->tr_particle_data,
+ sizeof(struct tng_data) *
+ frame_set->n_particle_data_blocks);
if(!data)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_data) *
- frame_set->n_particle_data_blocks,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(frame_set->tr_particle_data);
frame_set->tr_particle_data = 0;
return(TNG_CRITICAL);
else
{
tng_data->n_particle_data_blocks++;
- data = realloc(tng_data->non_tr_particle_data,
- sizeof(struct tng_data) *
- tng_data->n_particle_data_blocks);
+ data = (tng_data_t)realloc(tng_data->non_tr_particle_data,
+ sizeof(struct tng_data) *
+ tng_data->n_particle_data_blocks);
if(!data)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_data) *
- tng_data->n_particle_data_blocks,
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
free(tng_data->non_tr_particle_data);
tng_data->non_tr_particle_data = 0;
if(n_frames == 1 && tng_data->frame_set_n_frames > 1)
{
nalgo = tng_compress_nalgo();
- alt_algo = malloc(nalgo * sizeof *tng_data->compress_algo_pos);
+ alt_algo = (int *)malloc(nalgo * sizeof *tng_data->compress_algo_pos);
/* If we have already determined the initial coding and
* initial coding parameter do not determine them again. */
if(!tng_data->compress_algo_pos)
{
nalgo = tng_compress_nalgo();
- tng_data->compress_algo_pos=malloc(nalgo *
- sizeof *tng_data->compress_algo_pos);
+ tng_data->compress_algo_pos = (int *)malloc(nalgo *
+ sizeof *tng_data->compress_algo_pos);
tng_data->compress_algo_pos[0] = alt_algo[0];
tng_data->compress_algo_pos[1] = alt_algo[1];
tng_data->compress_algo_pos[2] = -1;
if(!tng_data->compress_algo_pos)
{
nalgo = tng_compress_nalgo();
- tng_data->compress_algo_pos=malloc(nalgo *
- sizeof *tng_data->compress_algo_pos);
+ tng_data->compress_algo_pos = (int *)malloc(nalgo *
+ sizeof *tng_data->compress_algo_pos);
tng_data->compress_algo_pos[0] = -1;
tng_data->compress_algo_pos[1] = -1;
tng_data->compress_algo_pos[2] = -1;
if(n_frames == 1 && tng_data->frame_set_n_frames > 1)
{
nalgo = tng_compress_nalgo();
- alt_algo=malloc(nalgo * sizeof *tng_data->compress_algo_vel);
+ alt_algo = (int *)malloc(nalgo * sizeof *tng_data->compress_algo_vel);
/* If we have already determined the initial coding and
* initial coding parameter do not determine them again. */
if(!tng_data->compress_algo_vel)
{
nalgo = tng_compress_nalgo();
- tng_data->compress_algo_vel=malloc(nalgo *
- sizeof *tng_data->compress_algo_vel);
+ tng_data->compress_algo_vel = (int *)malloc(nalgo *
+ sizeof *tng_data->compress_algo_vel);
tng_data->compress_algo_vel[0] = alt_algo[0];
tng_data->compress_algo_vel[1] = alt_algo[1];
tng_data->compress_algo_vel[2] = -1;
if(!tng_data->compress_algo_vel)
{
nalgo = tng_compress_nalgo();
- tng_data->compress_algo_vel=malloc(nalgo *
- sizeof *tng_data->compress_algo_vel);
+ tng_data->compress_algo_vel = (int *)malloc(nalgo *
+ sizeof *tng_data->compress_algo_vel);
tng_data->compress_algo_vel[0] = -1;
tng_data->compress_algo_vel[1] = -1;
tng_data->compress_algo_vel[2] = -1;
if(type == TNG_FLOAT_DATA)
{
- f_dest = malloc(uncompressed_len);
+ f_dest = (float *)malloc(uncompressed_len);
if(!f_dest)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- uncompressed_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
result = tng_compress_uncompress_float(*data, f_dest);
}
else
{
- d_dest = malloc(uncompressed_len);
+ d_dest = (double *)malloc(uncompressed_len);
if(!d_dest)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- uncompressed_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
result = tng_compress_uncompress(*data, d_dest);
return(TNG_SUCCESS);
}
-#ifdef USE_ZLIB
static tng_function_status tng_gzip_compress(const tng_trajectory_t tng_data,
char **data, const int64_t len,
int64_t *new_len)
(void)tng_data;
max_len = compressBound(len);
- dest = malloc(max_len);
+ dest = (Bytef *)malloc(max_len);
if(!dest)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%lu bytes). %s: %d\n",
- max_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
(void)tng_data;
uLongf new_len = uncompressed_len;
- dest = malloc(uncompressed_len);
+ dest = (Bytef *)malloc(uncompressed_len);
if(!dest)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- uncompressed_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
return(TNG_SUCCESS);
}
-#endif
/**
* @brief Allocate memory for storing particle data.
if(data->datatype == TNG_CHAR_DATA)
{
- data->strings = malloc(sizeof(char ***) * frame_alloc);
+ data->strings = (char ****)malloc(sizeof(char ***) * frame_alloc);
for(i = 0; i < frame_alloc; i++)
{
- data->strings[i] = malloc(sizeof(char **) *
+ data->strings[i] = (char ***)malloc(sizeof(char **) *
n_particles);
if(!data->strings[i])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(union data_values *) * n_particles,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
for(j = 0; j < n_particles; j++)
{
- data->strings[i][j] = malloc(sizeof(char *) *
+ data->strings[i][j] = (char **)malloc(sizeof(char *) *
n_values_per_frame);
if(!data->strings[i][j])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(union data_values) * n_values_per_frame,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
for(k = 0; k < n_values_per_frame; k++)
size = sizeof(double);
}
- values = realloc(data->values,
- size * frame_alloc *
- n_particles * n_values_per_frame);
+ values = (void ***)realloc(data->values,
+ size * frame_alloc *
+ n_particles * n_values_per_frame);
if(!values)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- size * frame_alloc *
- n_particles * n_values_per_frame,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(data->values);
data->values = 0;
return(TNG_CRITICAL);
if(block_type_flag == TNG_TRAJECTORY_BLOCK)
{
frame_set->n_data_blocks++;
- data = realloc(frame_set->tr_data, sizeof(struct tng_data) *
- frame_set->n_data_blocks);
+ data = (tng_data_t)realloc(frame_set->tr_data, sizeof(struct tng_data) *
+ frame_set->n_data_blocks);
if(!data)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_data) * frame_set->n_data_blocks,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(frame_set->tr_data);
frame_set->tr_data = 0;
return(TNG_CRITICAL);
else
{
tng_data->n_data_blocks++;
- data = realloc(tng_data->non_tr_data, sizeof(struct tng_data) *
- tng_data->n_data_blocks);
+ data = (tng_data_t)realloc(tng_data->non_tr_data, sizeof(struct tng_data) *
+ tng_data->n_data_blocks);
if(!data)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_data) * tng_data->n_data_blocks,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->non_tr_data);
tng_data->non_tr_data = 0;
return(TNG_CRITICAL);
if(data->datatype == TNG_CHAR_DATA)
{
- data->strings = malloc(sizeof(char ***));
- data->strings[0] = malloc(sizeof(char **) * frame_alloc);
+ data->strings = (char ****)malloc(sizeof(char ***));
+ data->strings[0] = (char ***)malloc(sizeof(char **) * frame_alloc);
for(i = 0; i < frame_alloc; i++)
{
- data->strings[0][i] = malloc(sizeof(char *) * n_values_per_frame);
+ data->strings[0][i] = (char **)malloc(sizeof(char *) * n_values_per_frame);
if(!data->strings[0][i])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- n_values_per_frame,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
for(j = 0; j < n_values_per_frame; j++)
size = sizeof(double);
}
- values = realloc(data->values,
- size * frame_alloc *
- n_values_per_frame);
+ values = (void **)realloc(data->values,
+ size * frame_alloc *
+ n_values_per_frame);
if(!values)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- size * frame_alloc *
- n_values_per_frame,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(data->values);
data->values = 0;
return(TNG_CRITICAL);
/* fprintf(stderr, "TNG library: %s\n", block->name);*/
- /* This must be caught early to avoid creating a data block if not necessary. */
-#ifndef USE_ZLIB
- if(codec_id == TNG_GZIP_COMPRESSION)
- {
- fprintf(stderr, "TNG library: Cannot uncompress data block. %s: %d\n", __FILE__,
- __LINE__);
- return(TNG_FAILURE);
- }
-#endif
-
switch(datatype)
{
case TNG_CHAR_DATA:
data->block_id = block->id;
- data->block_name = malloc(strlen(block->name) + 1);
+ data->block_name = (char *)malloc(strlen(block->name) + 1);
if(!data->block_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n",
- (unsigned int)strlen(block->name)+1, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
strcpy(data->block_name, block->name);
n_frames_div = (n_frames % stride_length) ? n_frames / stride_length + 1 : n_frames / stride_length;
- contents = malloc(block_data_len);
+ contents = (char *)malloc(block_data_len);
if(!contents)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- block_data_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
fprintf(stderr, "TNG library: XTC compression not implemented yet.\n");
break;
case TNG_TNG_COMPRESSION:
-/* fprintf(stderr, "TNG library: Before TNG uncompression: %"PRId64"\n", block->block_contents_size);*/
+/* fprintf(stderr, "TNG library: Before TNG uncompression: %" PRId64 "\n", block->block_contents_size);*/
if(tng_uncompress(tng_data, block, datatype,
&contents, full_data_len) != TNG_SUCCESS)
{
free(contents);
return(TNG_CRITICAL);
}
-/* fprintf(stderr, "TNG library: After TNG uncompression: %"PRId64"\n", block->block_contents_size);*/
+/* fprintf(stderr, "TNG library: After TNG uncompression: %" PRId64 "\n", block->block_contents_size);*/
break;
-#ifdef USE_ZLIB
case TNG_GZIP_COMPRESSION:
- /* fprintf(stderr, "TNG library: Before compression: %"PRId64"\n", block->block_contents_size); */
+ /* fprintf(stderr, "TNG library: Before compression: %" PRId64 "\n", block->block_contents_size); */
if(tng_gzip_uncompress(tng_data, &contents,
block_data_len, full_data_len) != TNG_SUCCESS)
{
free(contents);
return(TNG_CRITICAL);
}
- /* fprintf(stderr, "TNG library: After compression: %"PRId64"\n", block->block_contents_size); */
+ /* fprintf(stderr, "TNG library: After compression: %" PRId64 "\n", block->block_contents_size); */
break;
-#endif
}
}
else
{
free(second_dim_values[k]);
}
- second_dim_values[k] = malloc(len);
+ second_dim_values[k] = (char *)malloc(len);
if(!second_dim_values[k])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(contents);
return(TNG_CRITICAL);
}
{
free(data->strings[0][i][j]);
}
- data->strings[0][i][j] = malloc(len);
+ data->strings[0][i][j] = (char *)malloc(len);
if(!data->strings[0][i][j])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(contents);
return(TNG_CRITICAL);
}
for(i = 0; i < full_data_len; i+=size)
{
if(tng_data->input_endianness_swap_func_32(tng_data,
- (int32_t *)((char *)data->values + i))
+ (uint32_t *)((char *)data->values + i))
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
for(i = 0; i < full_data_len; i+=size)
{
if(tng_data->input_endianness_swap_func_64(tng_data,
- (int64_t *)((char *)data->values + i))
+ (uint64_t *)((char *)data->values + i))
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
if(!block->name || strlen(block->name) < len)
{
- temp_name = realloc(block->name, len);
+ temp_name = (char *)realloc(block->name, len);
if(!temp_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n", len+1,
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
free(block->name);
block->name = 0;
}
}
}
+ else
+ {
+ /* This just appeases gcc-7 -Wmaybe-uninitialized.
+ * FIXME: It would be better to refactor so that
+ * TNG_PARTICLE_DEPENDENT triggers two distinct code paths.
+ */
+ num_first_particle = -1;
+ n_particles = -1;
+ }
if(data->dependency & TNG_PARTICLE_DEPENDENT)
{
{
full_data_len = size * frame_step * data->n_values_per_frame;
}
- contents = malloc(full_data_len);
+ contents = (char *)malloc(full_data_len);
if(!contents)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- full_data_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
for(i = 0; i < full_data_len; i+=size)
{
if(tng_data->output_endianness_swap_func_32(tng_data,
- (int32_t *)(contents + i))
+ (uint32_t *)(contents + i))
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
if(fabs(multiplier - 1.0) > 0.00001 ||
tng_data->output_endianness_swap_func_32)
{
- for(i = 0; full_data_len; i+=size)
+ for(i = 0; i < full_data_len; i+=size)
{
*(float *)(contents + i) *= (float)multiplier;
if(tng_data->output_endianness_swap_func_32 &&
tng_data->output_endianness_swap_func_32(tng_data,
- (int32_t *)(contents + i))
+ (uint32_t *)(contents + i))
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
for(i = 0; i < full_data_len; i+=size)
{
if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)(contents + i))
+ (uint64_t *)(contents + i))
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
for(i = 0; i < full_data_len; i+=size)
{
if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)(contents + i))
+ (uint64_t *)(contents + i))
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
*(double *)(contents + i) *= multiplier;
if(tng_data->output_endianness_swap_func_64 &&
tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *)(contents + i))
+ (uint64_t *)(contents + i))
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
return(stat);
}
break;
-#ifdef USE_ZLIB
case TNG_GZIP_COMPRESSION:
- /* fprintf(stderr, "TNG library: Before compression: %"PRId64"\n", block->block_contents_size); */
+ /* fprintf(stderr, "TNG library: Before compression: %" PRId64 "\n", block->block_contents_size); */
stat = tng_gzip_compress(tng_data,
&contents,
full_data_len,
}
data->codec_id = TNG_UNCOMPRESSED;
}
- /* fprintf(stderr, "TNG library: After compression: %"PRId64"\n", block->block_contents_size); */
+ /* fprintf(stderr, "TNG library: After compression: %" PRId64 "\n", block->block_contents_size); */
break;
-#endif
}
if(block_data_len != full_data_len)
{
// {
// if(tng_block_header_read(tng_data, block) != TNG_SUCCESS)
// {
-// fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", pos,
+// fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n", pos,
// __FILE__, __LINE__);
// tng_data->input_file = temp;
// tng_block_destroy(&block);
// }
// if(!block->name)
// {
-// block->name = malloc(len);
+// block->name = (char *)malloc(len);
// if(!block->name)
// {
-// fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n", len,
+// fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
// __FILE__, __LINE__);
// return(TNG_CRITICAL);
// }
}
if(!atom->name)
{
- atom->name = malloc(len);
+ atom->name = (char *)malloc(len);
if(!atom->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!atom->atom_type)
{
- atom->atom_type = malloc(len);
+ atom->atom_type = (char *)malloc(len);
if(!atom->atom_type)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer.");
- new_molecules = realloc(tng_data->molecules,
- sizeof(struct tng_molecule) *
- (tng_data->n_molecules + 1));
+ new_molecules = (tng_molecule_t)realloc(tng_data->molecules,
+ sizeof(struct tng_molecule) *
+ (tng_data->n_molecules + 1));
if(!new_molecules)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->molecules);
tng_data->molecules = 0;
return(TNG_CRITICAL);
}
- new_molecule_cnt_list = realloc(tng_data->molecule_cnt_list,
- sizeof(int64_t) *
- (tng_data->n_molecules + 1));
+ new_molecule_cnt_list = (int64_t *)realloc(tng_data->molecule_cnt_list,
+ sizeof(int64_t) *
+ (tng_data->n_molecules + 1));
if(!new_molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * (tng_data->n_molecules + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->molecule_cnt_list);
tng_data->molecule_cnt_list = 0;
free(new_molecules);
id = 1;
}
- new_molecules = realloc(tng_data->molecules,
- sizeof(struct tng_molecule) *
- (tng_data->n_molecules + 1));
+ new_molecules = (tng_molecule_t)realloc(tng_data->molecules,
+ sizeof(struct tng_molecule) *
+ (tng_data->n_molecules + 1));
if(!new_molecules)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_molecule) * (tng_data->n_molecules + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->molecules);
tng_data->molecules = 0;
return(TNG_CRITICAL);
}
- new_molecule_cnt_list = realloc(tng_data->molecule_cnt_list,
- sizeof(int64_t) *
- (tng_data->n_molecules + 1));
+ new_molecule_cnt_list = (int64_t *)realloc(tng_data->molecule_cnt_list,
+ sizeof(int64_t) *
+ (tng_data->n_molecules + 1));
if(!new_molecule_cnt_list)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * (tng_data->n_molecules + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->molecule_cnt_list);
tng_data->molecule_cnt_list = 0;
free(new_molecules);
}
if(!molecule->name)
{
- molecule->name = malloc(len);
+ molecule->name = (char *)malloc(len);
if(!molecule->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
tng_data_dest->n_molecules = 0;
tng_data_dest->n_particles = 0;
- molecule_temp = realloc(tng_data_dest->molecules,
- sizeof(struct tng_molecule) * tng_data_src->n_molecules);
+ molecule_temp = (tng_molecule_t)realloc(tng_data_dest->molecules,
+ sizeof(struct tng_molecule) * tng_data_src->n_molecules);
if(!molecule_temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_molecule) * tng_data_src->n_molecules,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data_dest->molecules);
tng_data_dest->molecules = 0;
return(TNG_CRITICAL);
}
- list_temp = realloc(tng_data_dest->molecule_cnt_list,
- sizeof(int64_t) * tng_data_src->n_molecules);
+ list_temp = (int64_t *)realloc(tng_data_dest->molecule_cnt_list,
+ sizeof(int64_t) * tng_data_src->n_molecules);
if(!list_temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * tng_data_src->n_molecules,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data_dest->molecule_cnt_list);
tng_data_dest->molecule_cnt_list = 0;
free(molecule_temp);
molecule_temp->n_bonds = molecule->n_bonds;
if(molecule->n_bonds > 0)
{
- bond_temp = realloc(molecule_temp->bonds, sizeof(struct tng_bond) *
- molecule->n_bonds);
+ bond_temp = (tng_bond_t)realloc(molecule_temp->bonds, sizeof(struct tng_bond) *
+ molecule->n_bonds);
if(!bond_temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_bond) * molecule->n_bonds,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(molecule_temp->bonds);
molecule_temp->n_bonds = 0;
return(TNG_CRITICAL);
TNG_ASSERT(tng_data, "TNG library: Trajectory container not properly setup.");
TNG_ASSERT(name, "TNG library: name must not be a NULL pointer.");
- new_chains = realloc(molecule->chains,
- sizeof(struct tng_chain) *
- (molecule->n_chains + 1));
+ new_chains = (tng_chain_t)realloc(molecule->chains,
+ sizeof(struct tng_chain) *
+ (molecule->n_chains + 1));
if(!new_chains)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_chain) * (molecule->n_chains + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(molecule->chains);
molecule->chains = 0;
return(TNG_CRITICAL);
tng_bond_t new_bonds;
(void)tng_data;
- new_bonds = realloc(molecule->bonds,
- sizeof(struct tng_bond) *
- (molecule->n_bonds + 1));
+ new_bonds = (tng_bond_t)realloc(molecule->bonds,
+ sizeof(struct tng_bond) *
+ (molecule->n_bonds + 1));
if(!new_bonds)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_bond) * (molecule->n_bonds + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
*bond = 0;
free(molecule->bonds);
molecule->bonds = 0;
}
if(!chain->name)
{
- chain->name = malloc(len);
+ chain->name = (char *)malloc(len);
if(!chain->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
curr_index = -1;
}
- new_residues = realloc(molecule->residues,
- sizeof(struct tng_residue) *
- (molecule->n_residues + 1));
+ new_residues = (tng_residue_t)realloc(molecule->residues,
+ sizeof(struct tng_residue) *
+ (molecule->n_residues + 1));
if(!new_residues)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_residue) * (molecule->n_residues + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(molecule->residues);
molecule->residues = 0;
return(TNG_CRITICAL);
}
if(!residue->name)
{
- residue->name = malloc(len);
+ residue->name = (char *)malloc(len);
if(!residue->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
residue->atoms_offset = molecule->n_atoms;
}
- new_atoms = realloc(molecule->atoms,
- sizeof(struct tng_atom) *
- (molecule->n_atoms + 1));
+ new_atoms = (tng_atom_t)realloc(molecule->atoms,
+ sizeof(struct tng_atom) *
+ (molecule->n_atoms + 1));
if(!new_atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_atom) * (molecule->n_atoms + 1),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(molecule->atoms);
molecule->atoms = 0;
return(TNG_CRITICAL);
tng_function_status DECLSPECDLLEXPORT tng_molecule_alloc(const tng_trajectory_t tng_data,
tng_molecule_t *molecule_p)
{
- *molecule_p = malloc(sizeof(struct tng_molecule));
+ *molecule_p = (tng_molecule_t)malloc(sizeof(struct tng_molecule));
if(!*molecule_p)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_molecule), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
return(TNG_SUCCESS);
}
- *from_atoms = malloc(sizeof(int64_t) * (*n_bonds));
+ *from_atoms = (int64_t *)malloc(sizeof(int64_t) * (*n_bonds));
if(!*from_atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
- *to_atoms = malloc(sizeof(int64_t) * (*n_bonds));
+ *to_atoms = (int64_t *)malloc(sizeof(int64_t) * (*n_bonds));
if(!*to_atoms)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * (*n_bonds), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*from_atoms);
*from_atoms = 0;
return(TNG_CRITICAL);
frame_set->n_mapping_blocks++;
- mapping = realloc(frame_set->mappings, sizeof(struct tng_particle_mapping) *
- frame_set->n_mapping_blocks);
+ mapping = (tng_particle_mapping_t)realloc(frame_set->mappings, sizeof(struct tng_particle_mapping) *
+ frame_set->n_mapping_blocks);
if(!mapping)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(struct tng_particle_mapping)*frame_set->n_mapping_blocks,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(frame_set->mappings);
frame_set->mappings = 0;
return(TNG_CRITICAL);
frame_set->mappings[frame_set->n_mapping_blocks - 1].num_first_particle = num_first_particle;
frame_set->mappings[frame_set->n_mapping_blocks - 1].n_particles = n_particles;
- frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers = malloc(sizeof(int64_t) * n_particles);
+ frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers = (int64_t *)malloc(sizeof(int64_t) * n_particles);
if(!frame_set->mappings[frame_set->n_mapping_blocks - 1].real_particle_numbers)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * n_particles, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
tng_trajectory_frame_set_t frame_set;
tng_trajectory_t tng_data;
- *tng_data_p = malloc(sizeof(struct tng_trajectory));
+ *tng_data_p = (tng_trajectory_t)malloc(sizeof(struct tng_trajectory));
if(!*tng_data_p)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_trajectory), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
TNG_ASSERT(src != 0, "TNG library: Source trajectory must not be NULL.");
- *dest_p = malloc(sizeof(struct tng_trajectory));
+ *dest_p = (tng_trajectory_t)malloc(sizeof(struct tng_trajectory));
if(!*dest_p)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIuPTR" bytes). %s: %d\n",
- sizeof(struct tng_trajectory), __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
if(src->input_file_path)
{
- dest->input_file_path = malloc(strlen(src->input_file_path) + 1);
+ dest->input_file_path = (char *)malloc(strlen(src->input_file_path) + 1);
if(!dest->input_file_path)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n",
- (unsigned int)strlen(src->input_file_path) + 1, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
strcpy(dest->input_file_path, src->input_file_path);
dest->input_file = 0;
if(src->output_file_path)
{
- dest->output_file_path = malloc(strlen(src->output_file_path) + 1);
+ dest->output_file_path = (char *)malloc(strlen(src->output_file_path) + 1);
if(!dest->output_file_path)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n",
- (unsigned int)strlen(src->output_file_path) + 1, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
strcpy(dest->output_file_path, src->output_file_path);
}
len = tng_min_size(strlen(file_name) + 1, TNG_MAX_STR_LEN);
- temp = realloc(tng_data->input_file_path, len);
+ temp = (char *)realloc(tng_data->input_file_path, len);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->input_file_path);
tng_data->input_file_path = 0;
return(TNG_CRITICAL);
}
len = tng_min_size(strlen(file_name) + 1, TNG_MAX_STR_LEN);
- temp = realloc(tng_data->output_file_path, len);
+ temp = (char *)realloc(tng_data->output_file_path, len);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->output_file_path);
tng_data->output_file_path = 0;
return(TNG_CRITICAL);
}
len = tng_min_size(strlen(file_name) + 1, TNG_MAX_STR_LEN);
- temp = realloc(tng_data->output_file_path, len);
+ temp = (char *)realloc(tng_data->output_file_path, len);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(tng_data->output_file_path);
tng_data->output_file_path = 0;
return(TNG_CRITICAL);
}
if(!tng_data->first_program_name)
{
- tng_data->first_program_name = malloc(len);
+ tng_data->first_program_name = (char *)malloc(len);
if(!tng_data->first_program_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->last_program_name)
{
- tng_data->last_program_name = malloc(len);
+ tng_data->last_program_name = (char *)malloc(len);
if(!tng_data->last_program_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->first_user_name)
{
- tng_data->first_user_name = malloc(len);
+ tng_data->first_user_name = (char *)malloc(len);
if(!tng_data->first_user_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->last_user_name)
{
- tng_data->last_user_name = malloc(len);
+ tng_data->last_user_name = (char *)malloc(len);
if(!tng_data->last_user_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->first_computer_name)
{
- tng_data->first_computer_name = malloc(len);
+ tng_data->first_computer_name = (char *)malloc(len);
if(!tng_data->first_computer_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->last_computer_name)
{
- tng_data->last_computer_name = malloc(len);
+ tng_data->last_computer_name = (char *)malloc(len);
if(!tng_data->last_computer_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->first_pgp_signature)
{
- tng_data->first_pgp_signature = malloc(len);
+ tng_data->first_pgp_signature = (char *)malloc(len);
if(!tng_data->first_pgp_signature)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->last_pgp_signature)
{
- tng_data->last_pgp_signature = malloc(len);
+ tng_data->last_pgp_signature = (char *)malloc(len);
if(!tng_data->last_pgp_signature)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
}
if(!tng_data->forcefield_name)
{
- tng_data->forcefield_name = malloc(len);
+ tng_data->forcefield_name = (char *)malloc(len);
if(!tng_data->forcefield_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n", len,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
}
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", last_file_pos,
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n", last_file_pos,
__FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_FAILURE);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n", file_pos,
__FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n", file_pos,
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n", file_pos,
__FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
}
tng_block_init(&block);
- block->name = malloc(TNG_MAX_STR_LEN);
+ block->name = (char *)malloc(TNG_MAX_STR_LEN);
if(!block->name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- TNG_MAX_STR_LEN, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
}
if(tot_len > orig_len)
{
tng_migrate_data_in_file(tng_data, orig_len+1, tot_len - orig_len, hash_mode);
+ tng_data->last_trajectory_frame_set_input_file_pos = tng_data->last_trajectory_frame_set_output_file_pos;
}
stat = tng_reread_frame_set_at_file_pos(tng_data, tng_data->last_trajectory_frame_set_input_file_pos);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET ||
block->id == -1)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
}
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(stat);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
}
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(stat);
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
return(TNG_CRITICAL);
if(tng_data->input_endianness_swap_func_64)
{
if(tng_data->input_endianness_swap_func_64(tng_data,
- &frame_set->medium_stride_prev_frame_set_file_pos)
+ (uint64_t *)&frame_set->medium_stride_prev_frame_set_file_pos)
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
if(tng_data->input_endianness_swap_func_64)
{
if(tng_data->input_endianness_swap_func_64(tng_data,
- &frame_set->long_stride_prev_frame_set_file_pos)
+ (uint64_t *)&frame_set->long_stride_prev_frame_set_file_pos)
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL || block->id != TNG_TRAJECTORY_FRAME_SET)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
return(TNG_CRITICAL);
}
char ***first_dim_values, **second_dim_values;
tng_trajectory_frame_set_t frame_set;
tng_data_t data;
- char *new_data_c=new_data;
+ char *new_data_c = (char *)new_data;
tng_function_status stat;
frame_set = &tng_data->current_trajectory_frame_set;
}
data->block_id = id;
- data->block_name = malloc(strlen(block_name) + 1);
+ data->block_name = (char *)malloc(strlen(block_name) + 1);
if(!data->block_name)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%ud bytes). %s: %d\n",
- (unsigned int)strlen(block_name)+1, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
strncpy(data->block_name, block_name, strlen(block_name) + 1);
{
free(second_dim_values[k]);
}
- second_dim_values[k] = malloc(len);
+ second_dim_values[k] = (char *)malloc(len);
if(!second_dim_values[k])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
strncpy(second_dim_values[k],
{
free(second_dim_values[j]);
}
- second_dim_values[j] = malloc(len);
+ second_dim_values[j] = (char *)malloc(len);
if(!second_dim_values[j])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%d bytes). %s: %d\n",
- len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
strncpy(second_dim_values[j],
stat = tng_block_header_read(tng_data, block);
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
tng_data->input_file = temp;
}
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
tng_data->input_file = temp;
}
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
tng_block_destroy(&block);
tng_data->input_file = temp;
data.datatype == TNG_DOUBLE_DATA) &&
tng_data->output_endianness_swap_func_64)
{
- copy = malloc(write_n_particles * n_values_per_frame * size);
+ copy = (char *)malloc(write_n_particles * n_values_per_frame * size);
memcpy(copy, values, write_n_particles * n_values_per_frame * size);
for(i = 0; i < write_n_particles * n_values_per_frame; i++)
{
if(tng_data->output_endianness_swap_func_64(tng_data,
- (int64_t *) copy+i)
+ (uint64_t *) copy+i)
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
else if(data.datatype == TNG_FLOAT_DATA &&
tng_data->output_endianness_swap_func_32)
{
- copy = malloc(write_n_particles * n_values_per_frame * size);
+ copy = (char *)malloc(write_n_particles * n_values_per_frame * size);
memcpy(copy, values, write_n_particles * n_values_per_frame * size);
for(i = 0; i < write_n_particles * n_values_per_frame; i++)
{
if(tng_data->output_endianness_swap_func_32(tng_data,
- (int32_t *) copy+i)
+ (uint32_t *) copy+i)
!= TNG_SUCCESS)
{
fprintf(stderr, "TNG library: Cannot swap byte order. %s: %d\n",
return(stat);
}
}
- *values = malloc(sizeof(union data_values *) * n_frames);
+ *values = (union data_values **)malloc(sizeof(union data_values *) * n_frames);
if(!*values)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(union data_values **) * n_frames,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
for(i = 0; i < n_frames; i++)
{
- (*values)[i] = malloc(sizeof(union data_values) *
+ (*values)[i] = (union data_values *)malloc(sizeof(union data_values) *
n_values_per_frame);
if(!(*values)[i])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(union data_values) * n_values_per_frame,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(values);
values = 0;
return(TNG_CRITICAL);
return(stat);
}
}
- *values = malloc(sizeof(union data_values **) * n_frames);
+ *values = (union data_values ***)malloc(sizeof(union data_values **) * n_frames);
if(!*values)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(union data_values **) * n_frames,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
return(TNG_CRITICAL);
}
for(i = 0; i < n_frames; i++)
{
- (*values)[i] = malloc(sizeof(union data_values *) *
+ (*values)[i] = (union data_values **)malloc(sizeof(union data_values *) *
n_particles);
if(!(*values)[i])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(union data_values *) * n_particles,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*values);
*values = 0;
return(TNG_CRITICAL);
}
for(j = 0; j < n_particles; j++)
{
- (*values)[i][j] = malloc(sizeof(union data_values) *
+ (*values)[i][j] = (union data_values *)malloc(sizeof(union data_values) *
n_values_per_frame);
if(!(*values)[i][j])
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(union data_values *) * n_particles,
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
tng_particle_data_values_free(tng_data, *values, n_frames,
n_particles, n_values_per_frame,
type);
tng_block_destroy(&block);
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
return(stat);
}
for(k = 0; k < *n_values_per_frame; k++)
{
len = strlen(data->strings[i][j][k]) + 1;
- (*values)[i][mapping][k].c = malloc(len);
+ (*values)[i][mapping][k].c = (char *)malloc(len);
strncpy((*values)[i][mapping][k].c,
data->strings[i][j][k], len);
}
for(j = 0; j < *n_values_per_frame; j++)
{
len = strlen(data->strings[0][i][j]) + 1;
- (*values)[0][i][j].c = malloc(len);
+ (*values)[0][i][j].c = (char *)malloc(len);
strncpy((*values)[0][i][j].c, data->strings[0][i][j], len);
}
}
tng_block_destroy(&block);
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
return(stat);
}
full_data_len *= (*n_particles);
}
- temp = realloc(*values, full_data_len);
+ temp = (char *)realloc(*values, full_data_len);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- full_data_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*values);
*values = 0;
return(TNG_CRITICAL);
tng_block_destroy(&block);
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
return(stat);
}
if(block_index < 0)
{
- fprintf(stderr, "TNG library: Could not find particle data block with id %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Could not find particle data block with id %" PRId64 ". %s: %d\n",
block_id, __FILE__, __LINE__);
return(TNG_FAILURE);
}
for(k = 0; k < *n_values_per_frame; k++)
{
len = strlen(data->strings[current_frame_pos][j][k]) + 1;
- (*values)[i][mapping][k].c = malloc(len);
+ (*values)[i][mapping][k].c = (char *)malloc(len);
strncpy((*values)[i][mapping][k].c, data->strings[current_frame_pos][j][k], len);
}
}
for(j = 0; j < *n_values_per_frame; j++)
{
len = strlen(data->strings[0][current_frame_pos][j]) + 1;
- (*values)[0][i][j].c = malloc(len);
+ (*values)[0][i][j].c = (char *)malloc(len);
strncpy((*values)[0][i][j].c, data->strings[0][current_frame_pos][j], len);
}
}
tng_block_destroy(&block);
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
return(stat);
}
full_data_len *= (*n_particles);
}
- temp = realloc(*values, full_data_len);
+ temp = (char *)realloc(*values, full_data_len);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- full_data_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*values);
*values = 0;
return(TNG_CRITICAL);
tng_output_append_file_set(*tng_data_p, filename);
fseeko((*tng_data_p)->output_file, 0, SEEK_END);
+
+ (*tng_data_p)->output_endianness_swap_func_32 = (*tng_data_p)->input_endianness_swap_func_32;
+ (*tng_data_p)->output_endianness_swap_func_64 = (*tng_data_p)->input_endianness_swap_func_64;
}
return(stat);
stat = tng_frame_set_of_frame_find(tng_data, frame_nr);
if(stat != TNG_SUCCESS)
{
- fprintf(stderr, "TNG library: Cannot find frame nr %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot find frame nr %" PRId64 ". %s: %d\n",
frame_nr, __FILE__, __LINE__);
return(stat);
}
*n_particles = mol->n_atoms;
- *names = malloc(sizeof(char *) * *n_particles);
- *types = malloc(sizeof(char *) * *n_particles);
- *res_names = malloc(sizeof(char *) * *n_particles);
- *chain_names = malloc(sizeof(char *) * *n_particles);
- *res_ids = malloc(sizeof(int64_t) * *n_particles);
- *chain_ids = malloc(sizeof(int64_t) * *n_particles);
+ *names = (char **)malloc(sizeof(char *) * *n_particles);
+ *types = (char **)malloc(sizeof(char *) * *n_particles);
+ *res_names = (char **)malloc(sizeof(char *) * *n_particles);
+ *chain_names = (char **)malloc(sizeof(char *) * *n_particles);
+ *res_ids = (int64_t *)malloc(sizeof(int64_t) * *n_particles);
+ *chain_ids = (int64_t *)malloc(sizeof(int64_t) * *n_particles);
for(i = 0; i < *n_particles; i++)
{
atom = &mol->atoms[i];
res = atom->residue;
chain = res->chain;
- (*names)[i] = malloc(strlen(atom->name));
+ (*names)[i] = (char *)malloc(strlen(atom->name));
strcpy(*names[i], atom->name);
- (*types)[i] = malloc(strlen(atom->atom_type));
+ (*types)[i] = (char *)malloc(strlen(atom->atom_type));
strcpy(*types[i], atom->atom_type);
- (*res_names)[i] = malloc(strlen(res->name));
+ (*res_names)[i] = (char *)malloc(strlen(res->name));
strcpy(*res_names[i], res->name);
- (*chain_names)[i] = malloc(strlen(chain->name));
+ (*chain_names)[i] = (char *)malloc(strlen(chain->name));
strcpy(*chain_names[i], chain->name);
(*res_ids)[i] = res->id;
(*chain_ids)[i] = chain->id;
&n_values_per_frame,
&type);
+ if(stat == TNG_SUCCESS && type != TNG_FLOAT_DATA)
+ {
+ return(TNG_FAILURE);
+ }
+
return(stat);
}
&n_values_per_frame,
&type);
+ if(stat == TNG_SUCCESS && type != TNG_FLOAT_DATA)
+ {
+ return(TNG_FAILURE);
+ }
+
return(stat);
}
&n_values_per_frame,
&type);
+ if(stat == TNG_SUCCESS && type != TNG_FLOAT_DATA)
+ {
+ return(TNG_FAILURE);
+ }
+
return(stat);
}
&n_values_per_frame,
&type);
+ if(stat == TNG_SUCCESS && type != TNG_FLOAT_DATA)
+ {
+ return(TNG_FAILURE);
+ }
+
return(stat);
}
full_data_len = size * n_particles * data->n_values_per_frame;
-// fprintf(stderr, "TNG library: TEMP: i = %"PRId64", full_data_len = %"PRId64", size = %d, n_particles = %"PRId64", n_values_per_frame = %"PRId64"\n",
+// fprintf(stderr, "TNG library: TEMP: i = %" PRId64 ", full_data_len = %" PRId64 ", size = %d, n_particles = %" PRId64 ", n_values_per_frame = %" PRId64 "\n",
// i, full_data_len, size, n_particles, data->n_values_per_frame);
- temp = realloc(*values, full_data_len);
+ temp = (char *)realloc(*values, full_data_len);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- full_data_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*values);
*values = 0;
return(TNG_CRITICAL);
full_data_len = size * data->n_values_per_frame;
- temp = realloc(*values, full_data_len);
+ temp = (char *)realloc(*values, full_data_len);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRId64" bytes). %s: %d\n",
- full_data_len, __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*values);
*values = 0;
return(TNG_CRITICAL);
if(i <= 0)
{
- fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot set writing frequency to %" PRId64 ". %s: %d\n",
i, __FILE__, __LINE__);
return(TNG_FAILURE);
}
if(i <= 0)
{
- fprintf(stderr, "TNG library: Cannot set writing frequency to %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot set writing frequency to %" PRId64 ". %s: %d\n",
i, __FILE__, __LINE__);
return(TNG_FAILURE);
}
{
TNG_ASSERT(requested_data_block_ids, "TNG library: If the number of requested data blocks is > 0 then the array of data block IDs must not be NULL.");
size = sizeof(int64_t) * n_requested_data_block_ids;
- temp = realloc(*data_block_ids_in_next_frame, size);
+ temp = (int64_t *)realloc(*data_block_ids_in_next_frame, size);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * (*n_data_blocks_in_next_frame),
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
__FILE__, __LINE__);
free(*data_block_ids_in_next_frame);
*data_block_ids_in_next_frame = 0;
tng_block_destroy(&block);
if(stat == TNG_CRITICAL)
{
- fprintf(stderr, "TNG library: Cannot read block header at pos %"PRId64". %s: %d\n",
+ fprintf(stderr, "TNG library: Cannot read block header at pos %" PRId64 ". %s: %d\n",
file_pos, __FILE__, __LINE__);
return(stat);
}
if(n_requested_data_block_ids <= 0)
{
size = sizeof(int64_t) * (*n_data_blocks_in_next_frame);
- temp = realloc(*data_block_ids_in_next_frame, size);
+ temp = (int64_t *)realloc(*data_block_ids_in_next_frame, size);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * (*n_data_blocks_in_next_frame),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*data_block_ids_in_next_frame);
*data_block_ids_in_next_frame = 0;
return(TNG_CRITICAL);
if(n_requested_data_block_ids <= 0)
{
size = sizeof(int64_t) * (*n_data_blocks_in_next_frame);
- temp = realloc(*data_block_ids_in_next_frame, size);
+ temp = (int64_t *)realloc(*data_block_ids_in_next_frame, size);
if(!temp)
{
- fprintf(stderr, "TNG library: Cannot allocate memory (%"PRIu64" bytes). %s: %d\n",
- sizeof(int64_t) * (*n_data_blocks_in_next_frame),
- __FILE__, __LINE__);
+ fprintf(stderr, "TNG library: Cannot allocate memory. %s: %d\n",
+ __FILE__, __LINE__);
free(*data_block_ids_in_next_frame);
*data_block_ids_in_next_frame = 0;
return(TNG_CRITICAL);
* modify it under the terms of the Revised BSD License.
*/
-#include "../../include/tng_io.h"
+#include "tng/tng_io.h"
/* The following is for calling the library from fortran */
add_subdirectory(compression)
endif()
-link_directories(${TNG_IO_BINARY_DIR}/src/lib)
-
add_definitions(-DTNG_EXAMPLE_FILES_DIR="${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/tests/example_files/") # Directory where to find input test files and save output files.
if(TNG_BUILD_TEST)
if(${CMAKE_Fortran_COMPILER_WORKS})
get_filename_component (Fortran_COMPILER_NAME ${CMAKE_Fortran_COMPILER} NAME)
if (Fortran_COMPILER_NAME STREQUAL "gfortran")
- set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer ${OpenMP_C_FLAGS} -std=legacy")
+ set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -fcray-pointer ${OpenMP_C_FLAGS} -std=legacy -cpp -ffixed-line-length-none")
endif()
if(OPENMP_FOUND)
add_executable(md_openmp_f md_openmp.f)
c
c The program uses Open MP directives to allow parallel computation.
c
-c The velocity Verlet time integration scheme is used.
+c The velocity Verlet time integration scheme is used.
c
c The particles interact with a central pair potential.
c
c
c Licensing:
c
-c This code is distributed under the GNU LGPL license.
+c This code is distributed under the GNU LGPL license.
c
c Modified:
c
write ( *, '(a)' ) ' '
write ( *, '(a)' ) ' A molecular dynamics program.'
write ( *, '(a)' ) ' '
- write ( *, '(a,i8)' )
+ write ( *, '(a,i8)' )
& ' NP, the number of particles in the simulation is ', np
- write ( *, '(a,i8)' )
+ write ( *, '(a,i8)' )
& ' STEP_NUM, the number of time steps, is ', step_num
- write ( *, '(a,g14.6)' )
+ write ( *, '(a,g14.6)' )
& ' DT, the size of each time step, is ', dt
write ( *, '(a)' ) ' '
- write ( *, '(a,i8)' )
+ write ( *, '(a,i8)' )
& ' The number of processors = ', omp_get_num_procs ( )
- write ( *, '(a,i8)' )
+ write ( *, '(a,i8)' )
& ' The number of threads = ', omp_get_max_threads ( )
- write ( *, '(a)' ) ' '
+ write ( *, '(a)' ) ' '
write ( *, '(a)' ) ' Initializing trajectory storage.'
call tng_trajectory_init(traj_p)
c
c N.B. The TNG output file should be modified according to needs
-c
- call tng_output_file_set(traj, TNG_EXAMPLE_FILES_DIR "tng_md_out_f77.tng")
+c
+ call tng_output_file_set(traj, TNG_EXAMPLE_FILES_DIR"tng_md_out_f77.tng")
write ( *, '(a)' ) ' Creating molecules in trajectory.'
tng_n_particles = np
c
c Add the box shape data block
-c
+c
call tng_data_block_add(traj, TNG_TRAJ_BOX_SHAPE, "BOX SHAPE",
& TNG_DOUBLE_DATA, TNG_NON_TRAJECTORY_BLOCK, int(1, 8),
& int(9, 8), int(1, 8), TNG_UNCOMPRESSED, box_shape)
c
c Write the file headers
-c
+c
call tng_file_headers_write(traj, TNG_USE_HASH)
-
+
c
c Set initial positions, velocities, and accelerations.
-c
- write ( *, '(a)' )
+c
+ write ( *, '(a)' )
& ' Initializing positions, velocities, and accelerations.'
seed = 123456789
call initialize ( np, nd, box, seed, pos, vel, acc )
write ( *, '(a)' ) ' '
write ( *, '(a)' ) ' Computing initial forces and energies.'
- call compute ( np, nd, pos, vel, mass, force, potential,
+ call compute ( np, nd, pos, vel, mass, force, potential,
& kinetic )
e0 = potential + kinetic
c Saving frequency
c
step_save = 5
-
+
step_print = 0
step_print_index = 0
step_print_num = 10
& ' steps particle positions, velocities and forces are'
write ( *, '(a)' ) ' saved to a TNG trajectory file.'
write ( *, '(a)' )
- write ( *, '(a)' )
+ write ( *, '(a)' )
& ' At each step, we report the potential and kinetic energies.'
- write ( *, '(a)' )
+ write ( *, '(a)' )
& ' The sum of these energies should be a constant.'
- write ( *, '(a)' )
+ write ( *, '(a)' )
& ' As an accuracy check, we also print the relative error'
write ( *, '(a)' ) ' in the total energy.'
write ( *, '(a)' ) ' '
- write ( *, '(a)' )
+ write ( *, '(a)' )
& ' Step Potential Kinetic (P+K-E0)/E0'
- write ( *, '(a)' )
+ write ( *, '(a)' )
& ' Energy P Energy K ' //
& 'Relative Energy Error'
write ( *, '(a)' ) ' '
step = 0
- write ( *, '(2x,i8,2x,g14.6,2x,g14.6,2x,g14.6)' )
+ write ( *, '(2x,i8,2x,g14.6,2x,g14.6,2x,g14.6)' )
& step, potential, kinetic, ( potential + kinetic - e0 ) / e0
step_print_index = step_print_index + 1
step_print = ( step_print_index * step_num ) / step_print_num
-c
-c Create a frame set for writing data
+c
+c Create a frame set for writing data
c
call tng_num_frames_per_frame_set_get(traj,
& n_frames_per_frame_set)
& "POSITIONS", TNG_DOUBLE_DATA, TNG_TRAJECTORY_BLOCK,
& n_frames_per_frame_set, int(3, 8), int(1, 8), int(0, 8),
& tng_n_particles, TNG_UNCOMPRESSED, %VAL(int(0, 8)))
-
+
call tng_particle_data_block_add(traj, TNG_TRAJ_VELOCITIES,
& "VELOCITIES", TNG_DOUBLE_DATA, TNG_TRAJECTORY_BLOCK,
& n_frames_per_frame_set, int(3, 8), int(1, 8), int(0, 8),
& tng_n_particles, TNG_UNCOMPRESSED, %VAL(int(0, 8)))
-
+
call tng_particle_data_block_add(traj, TNG_TRAJ_FORCES,
& "FORCES", TNG_DOUBLE_DATA, TNG_TRAJECTORY_BLOCK,
& n_frames_per_frame_set, int(3, 8), int(1, 8), int(0, 8),
c
c The potential energy data block is saved sparsely.
-c
+c
call tng_data_block_add(traj, int(10101, 8),
& "POTENTIAL ENERGY", TNG_DOUBLE_DATA, TNG_TRAJECTORY_BLOCK,
& n_frames_per_frame_set, int(1, 8), sparse_save,
& TNG_UNCOMPRESSED, %VAL(int(0, 8)))
-
+
c
c Write the frame set to disk
c
call tng_frame_set_write(traj, TNG_USE_HASH)
-
+
wtime = omp_get_wtime ( )
do step = 1, step_num
- call compute ( np, nd, pos, vel, mass, force, potential,
+ call compute ( np, nd, pos, vel, mass, force, potential,
& kinetic )
if ( step .eq. step_print ) then
- write ( *, '(2x,i8,2x,g14.6,2x,g14.6,2x,g14.6)' )
+ write ( *, '(2x,i8,2x,g14.6,2x,g14.6,2x,g14.6)' )
& step, potential, kinetic, ( potential + kinetic - e0 ) / e0
step_print_index = step_print_index + 1
& TNG_TRAJ_FORCES, int(0, 8), tng_n_particles, force,
& TNG_USE_HASH)
frames_saved_cnt = frames_saved_cnt + 1
-
+
if (mod(step, step_save * sparse_save) .EQ. 0) then
call tng_frame_data_write(traj, frames_saved_cnt,
& int(10101, 8), potential, TNG_USE_HASH)
end if
-
+
end if
call update ( np, nd, pos, vel, force, acc, mass, dt )
wtime = omp_get_wtime ( ) - wtime
write ( *, '(a)' ) ' '
- write ( *, '(a)' )
+ write ( *, '(a)' )
& ' Elapsed time for main computation:'
write ( *, '(2x,g14.6,a)' ) wtime, ' seconds'
c
c
c Licensing:
c
-c This code is distributed under the GNU LGPL license.
+c This code is distributed under the GNU LGPL license.
c
c Modified:
c
pot = 0.0D+00
kin = 0.0D+00
-c$omp parallel
-c$omp& shared ( f, nd, np, pos, vel )
-c$omp& private ( d, d2, i, j, k, rij )
+c$omp parallel
+c$omp& shared ( f, nd, np, pos, vel )
+c$omp& private ( d, d2, i, j, k, rij )
c$omp do reduction ( + : pot, kin )
do i = 1, np
c$omp end parallel
kin = kin * 0.5D+00 * mass
-
+
return
end
subroutine dist ( nd, r1, r2, dr, d )
c
c Licensing:
c
-c This code is distributed under the GNU LGPL license.
+c This code is distributed under the GNU LGPL license.
c
c Modified:
c
c
c Licensing:
c
-c This code is distributed under the GNU LGPL license.
+c This code is distributed under the GNU LGPL license.
c
c Modified:
c
end do
end do
-c$omp parallel
+c$omp parallel
c$omp& shared ( acc, box, nd, np, pos, vel )
c$omp& private ( i, j )
c
c Licensing:
c
-c This code is distributed under the GNU LGPL license.
+c This code is distributed under the GNU LGPL license.
c
c Modified:
c
c
c Licensing:
c
-c This code is distributed under the GNU LGPL license.
+c This code is distributed under the GNU LGPL license.
c
c Modified:
c
save month
data month /
- & 'January ', 'February ', 'March ', 'April ',
- & 'May ', 'June ', 'July ', 'August ',
+ & 'January ', 'February ', 'March ', 'April ',
+ & 'May ', 'June ', 'July ', 'August ',
& 'September', 'October ', 'November ', 'December ' /
call date_and_time ( date, time )
end if
end if
- write ( *,
- & '(i2,1x,a,1x,i4,2x,i2,a1,i2.2,a1,i2.2,a1,i3.3,1x,a)' )
+ write ( *,
+ & '(i2,1x,a,1x,i4,2x,i2,a1,i2.2,a1,i2.2,a1,i3.3,1x,a)' )
& d, month(m), y, h, ':', n, ':', s, '.', mm, ampm
return
c
c Licensing:
c
-c This code is distributed under the GNU LGPL license.
+c This code is distributed under the GNU LGPL license.
c
c Modified:
c
rmass = 1.0D+00 / mass
-c$omp parallel
+c$omp parallel
c$omp& shared ( acc, dt, f, nd, np, pos, rmass, vel )
c$omp& private ( i, j )
do j = 1, np
do i = 1, nd
- pos(i,j) = pos(i,j)
+ pos(i,j) = pos(i,j)
& + vel(i,j) * dt + 0.5D+00 * acc(i,j) * dt * dt
- vel(i,j) = vel(i,j)
+ vel(i,j) = vel(i,j)
& + 0.5D+00 * dt * ( f(i,j) * rmass + acc(i,j) )
acc(i,j) = f(i,j) * rmass
const char hash_mode)
{
int i, j, k, nr, cnt, dependency;
- float *data, *molpos, *charges;
- int64_t mapping[300], n_particles, n_frames_per_frame_set, tot_n_mols;
+ float *data, *molpos, *charges, *masses;
+ int64_t mapping[300], n_particles;
+ int64_t read_n_frames, read_stride_length, read_n_particles, read_n_values_per_frame;
+ int64_t n_frames_per_frame_set, tot_n_mols;
int64_t codec_id;
int64_t dist_exp = -9, temp_int, temp_int2;
// int64_t frame_nr;
double box_shape[9], temp_double;
char atom_type[16], annotation[128];
char temp_str[TNG_MAX_STR_LEN];
+ char read_data_type;
tng_trajectory_frame_set_t frame_set;
tng_function_status stat = TNG_SUCCESS;
exit(1);
}
- /* Set partial charges (treat the water as TIP3P. */
+ /* Set partial charges (treat the water as TIP3P). */
tng_num_particles_get(*traj, &n_particles);
charges = malloc(sizeof(float) * n_particles);
for(i = 0; i < n_particles; i++)
{
break;
}
- if(atom_type[0] == 'O')
+ /* We only have water in the system. If the atom is oxygen set its
+ * partial charge to -0.834, if it's a hydrogen set its partial charge to
+ * 0.417. */
+ switch(atom_type[0])
{
- charges[i] = -0.834;
- }
- else if(atom_type[0] == 'H')
- {
- charges[i] = 0.417;
+ case 'O':
+ charges[i] = -0.834;
+ break;
+ case 'H':
+ charges[i] = 0.417;
+ break;
+ default:
+ printf("Failed setting partial charges. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
}
}
if(stat == TNG_CRITICAL)
1, 1, 1, 0, n_particles,
TNG_UNCOMPRESSED, charges);
free(charges);
+ charges = 0;
if(stat != TNG_SUCCESS)
{
printf("Failed adding partial charges. %s: %d\n",
return(TNG_CRITICAL);
}
+ /* Set atom masses. */
+ masses = malloc(sizeof(float) * n_particles);
+ for(i = 0; i < n_particles; i++)
+ {
+ stat = tng_atom_type_of_particle_nr_get(*traj, i, atom_type,
+ sizeof(atom_type));
+ if(stat == TNG_CRITICAL)
+ {
+ break;
+ }
+ /* We only have water in the system. If the atom is oxygen set its
+ * mass to 16.00000, if it's a hydrogen set its mass to
+ * 1.00800. */
+ switch(atom_type[0])
+ {
+ case 'O':
+ masses[i] = 16.00000;
+ break;
+ case 'H':
+ masses[i] = 1.00800;
+ break;
+ default:
+ printf("Failed setting atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+ }
+ if(stat == TNG_CRITICAL)
+ {
+ free(masses);
+ printf("Failed setting atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
+
+ stat = tng_particle_data_block_add(*traj, TNG_TRAJ_MASSES, "ATOM MASSES",
+ TNG_FLOAT_DATA, TNG_NON_TRAJECTORY_BLOCK,
+ 1, 1, 1, 0, n_particles,
+ TNG_GZIP_COMPRESSION, masses);
+ free(masses);
+ masses = 0;
+ if(stat != TNG_SUCCESS)
+ {
+ printf("Failed adding atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_CRITICAL);
+ }
/* Generate a custom annotation data block */
strcpy(annotation, "This trajectory was generated from tng_io_testing. "
return(stat);
}
+ stat = tng_particle_data_vector_get(*traj, TNG_TRAJ_MASSES, (void **)&masses, &read_n_frames,
+ &read_stride_length, &read_n_particles,
+ &read_n_values_per_frame, &read_data_type);
+ if(stat != TNG_SUCCESS)
+ {
+ free(masses);
+ return(stat);
+ }
+ if(read_n_particles != n_particles)
+ {
+ printf("Number of particles does not match when reading atom masses. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_FAILURE);
+ }
+
+ /* Above we have written only water molecules (in the order oxygen, hydrogen, hydrogen ...).
+ * Test that the first and second as well as the very last atoms (oxygen, hydrogen and hydrogen)
+ * have the correct atom masses. */
+ if(fabs(masses[0] - 16.00000) > 0.0001 || fabs(masses[1] - 1.00800) > 0.0001 ||
+ fabs(masses[read_n_particles-1] - 1.00800) > 0.0001)
+ {
+ printf("Atom masses do not match when reading written file. %s: %d\n",
+ __FILE__, __LINE__);
+ return(TNG_FAILURE);
+ }
+ free(masses);
+
i = 0;
while(stat == TNG_SUCCESS)
{
__FILE__, __LINE__);
return(TNG_FAILURE);
}
-
stat = tng_util_trajectory_close(&traj);
if(stat != TNG_SUCCESS)
{
int main()
{
- tng_trajectory_t traj;
+ tng_trajectory_t traj = 0;
char time_str[TNG_MAX_DATE_STR_LEN];
char version_str[TNG_MAX_STR_LEN];
char hash_mode = TNG_USE_HASH;
--- /dev/null
+# Test project to test building with libtng_io
+#
+# Combinations to test for full coverage:
+# TEST_ZLIB=ON (22 combinations)
+# ZLIB_LIBRARY=shared/static
+# TEST_BUNDLING=ON (4 combinations)
+# BUILD_SHARED_LIBS=ON/OFF
+# TEST_EXECUTABLE=ON/OFF
+# TEST_BUNDLING=OFF (7 combinations)
+# TEST_EXECUTABLE=ON
+# TNG_IO_DIR=sh.sh/st.sh/st.st
+# TEST_EXECUTABLE=OFF
+# BUILD_SHARED_LIBS=ON
+# TNG_IO_DIR=sh.sh/st.sh/st.st
+# BUILD_SHARED_LIBS=OFF
+# TNG_IO_DIR=sh.sh
+# TEST_ZLIB=OFF (27 combinations)
+# TEST_BUNDLING=ON (12 combinations)
+# ZLIB_LIBRARY=shared/static/none
+# BUILD_SHARED_LIBS=ON/OFF
+# TEST_EXECUTABLE=ON/OFF
+# TEST_BUNDLING=OFF (15 combinations)
+# TEST_EXECUTABLE=ON
+# TNG_IO_DIR=sh.sh/sh.st/sh.int/st.sh/st.st/st.int
+# TEST_EXECUTABLE=OFF
+# BUILD_SHARED_LIBS=ON
+# TNG_IO_DIR=sh.sh/sh.st/sh.int/st.sh/st.st/st.int
+# BUILD_SHARED_LIBS=OFF
+# TNG_IO_DIR=sh.sh/sh.st/sh.int
+#
+# Combinations that cannot work:
+# TEST_ZLIB=ON, tng built with internal zlib
+# TEST_ZLIB=ON, tng built with BUILD_SHARED_LIBS=ON + static zlib
+# BUILD_SHARED_LIBS=ON, tng built as static (unless compiled with PIC)
+
+cmake_minimum_required(VERSION 3.1)
+
+project(tng_io_test)
+
+option(BUILD_SHARED_LIBS "Test building a shared library" ON)
+option(TEST_EXECUTABLE "Test building an executable instead of a library" OFF)
+option(TEST_BUNDLING "Test bundling tng" OFF)
+option(TEST_ZLIB "Test with zlib in using code" OFF)
+option(TEST_BUNDLED_ZLIB "Test bundling zlib with tng" OFF)
+if (NOT TEST_BUNDLING)
+ set(TEST_BUNDLED_ZLIB OFF)
+endif()
+
+if (TEST_ZLIB OR NOT TEST_BUNDLED_ZLIB)
+ find_package(ZLIB REQUIRED)
+endif()
+
+if (TEST_BUNDLING)
+ include(../../../BuildTNG.cmake)
+ if (TEST_BUNDLED_ZLIB)
+ message(STATUS "Bundling tng_io with internal ZLIB")
+ add_tng_io_library(tng_io OBJECT OWN_ZLIB)
+ else()
+ message(STATUS "Bundling tng_io with external ZLIB")
+ add_tng_io_library(tng_io OBJECT)
+ endif()
+ add_library(tng_io::tng_io ALIAS tng_io)
+else()
+ message(STATUS "Using external tng_io")
+ find_package(TNG_IO REQUIRED)
+endif()
+
+set(SOURCES use_tng.c)
+if (TEST_ZLIB)
+ message(STATUS "Using zlib in test application")
+ list(APPEND SOURCES use_zlib.c)
+else()
+ message(STATUS "Not using zlib in test application")
+ list(APPEND SOURCES dummy_zlib.c)
+endif()
+
+if (TEST_EXECUTABLE)
+ message(STATUS "Building an executable linked against tng_io")
+ add_executable(test_target main.c ${SOURCES})
+else()
+ message(STATUS "Building a library linked against tng_io")
+ add_library(test_target ${SOURCES})
+ install(TARGETS test_target EXPORT test DESTINATION lib)
+ install(EXPORT test DESTINATION lib/cmake/test)
+ add_executable(test_exe main.c)
+ target_link_libraries(test_exe PRIVATE test_target)
+endif()
+
+if (TEST_BUNDLING)
+ target_link_libraries(test_target PRIVATE $<BUILD_INTERFACE:tng_io::tng_io>)
+else()
+ target_link_libraries(test_target PRIVATE tng_io::tng_io)
+endif()
+if (TEST_ZLIB)
+ target_link_libraries(test_target PRIVATE ZLIB::ZLIB)
+endif()
--- /dev/null
+void test_zlib(void)
+{
+}
--- /dev/null
+extern void test_tng(void);
+extern void test_zlib(void);
+
+int main(int argc, char *argv[])
+{
+ test_tng();
+ test_zlib();
+ return 0;
+}
--- /dev/null
+#include "tng/tng_io.h"
+
+void test_tng(void)
+{
+ tng_trajectory_t data;
+ char buf[256];
+ tng_version(data, buf, 256);
+}
--- /dev/null
+#include "zlib.h"
+
+void test_zlib(void)
+{
+ zlibVersion();
+}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
add_subdirectory(gmxlib)
add_subdirectory(mdlib)
+add_subdirectory(applied-forces)
add_subdirectory(listed-forces)
add_subdirectory(commandline)
add_subdirectory(domdec)
add_subdirectory(analysisdata)
add_subdirectory(selection)
add_subdirectory(trajectoryanalysis)
+ add_subdirectory(energyanalysis)
add_subdirectory(tools)
endif()
tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
-if(GMX_USE_TNG)
- list(APPEND LIBGROMACS_SOURCES ${TNG_SOURCES})
- if (NOT GMX_EXTERNAL_TNG)
- tng_set_source_properties(WITH_ZLIB ${HAVE_ZLIB})
- endif()
-endif()
-
get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES_TO_LINK LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER)
include_directories(${LMFIT_INCLUDE_DIR_ORDER} SYSTEM "${LMFIT_INCLUDE_DIRECTORY}")
list(APPEND LIBGROMACS_SOURCES ${LMFIT_SOURCES})
set(GENERATED_VERSION_FILE utility/baseversion-gen.c)
gmx_configure_version_file(
utility/baseversion-gen.c.cmakein ${GENERATED_VERSION_FILE}
- REMOTE_HASH SOURCE_FILE)
+ REMOTE_HASH)
list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
if (GMX_USE_CUDA)
+ # Work around FindCUDA that prevents using target_link_libraries()
+ # with keywords otherwise...
+ set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
else()
add_library(libgromacs ${LIBGROMACS_SOURCES})
# we do it in the compilation command (after testing that the compiler
# supports the suppressions).
include(CheckCXXCompilerFlag)
-check_cxx_compiler_flag(-Wno-unused-parameter HAS_NO_UNUSED_PARAMETER)
-if (HAS_NO_UNUSED_PARAMETER)
- set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter")
+check_cxx_compiler_flag(-Wno-unused HAS_NO_UNUSED)
+if (HAS_NO_UNUSED)
+ set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter -Wno-unused-function")
endif()
set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
+gmx_setup_tng_for_libgromacs()
+
target_link_libraries(libgromacs
+ PRIVATE
${EXTRAE_LIBRARIES}
${GMX_EXTRA_LIBRARIES}
- ${TNG_IO_LIBRARIES}
+ ${GMX_COMMON_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
- ${XML_LIBRARIES}
${LMFIT_LIBRARIES_TO_LINK}
${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES}
- ${GMX_STDLIB_LIBRARIES})
+ ${GMX_STDLIB_LIBRARIES}
+ PUBLIC
+ ${GMX_PUBLIC_LIBRARIES}
+ )
set_target_properties(libgromacs PROPERTIES
OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
SOVERSION ${LIBRARY_SOVERSION_MAJOR}
install(FILES ${OPENCL_KERNELS} DESTINATION
${OCL_INSTALL_DIR} COMPONENT libraries)
endif()
+
+if (BUILD_TESTING)
+ add_subdirectory(compat/tests)
+endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
public:
//! Creates a handle associated with the given data object.
explicit AnalysisDataHandleImpl(AnalysisData *data)
- : data_(*data), currentFrame_(NULL)
+ : data_(*data), currentFrame_(nullptr)
{
}
*/
AnalysisDataHandle::AnalysisDataHandle()
- : impl_(NULL)
+ : impl_(nullptr)
{
}
void
AnalysisDataHandle::startFrame(int index, real x, real dx)
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
- GMX_RELEASE_ASSERT(impl_->currentFrame_ == NULL,
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ == nullptr,
"startFrame() called twice without calling finishFrame()");
impl_->currentFrame_ =
&impl_->data_.impl_->storage_.startFrame(index, x, dx);
void
AnalysisDataHandle::selectDataSet(int index)
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
- GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != nullptr,
"selectDataSet() called without calling startFrame()");
impl_->currentFrame_->selectDataSet(index);
}
void
AnalysisDataHandle::setPoint(int column, real value, bool bPresent)
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
- GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != nullptr,
"setPoint() called without calling startFrame()");
impl_->currentFrame_->setValue(column, value, bPresent);
}
void
AnalysisDataHandle::setPoint(int column, real value, real error, bool bPresent)
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
- GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != nullptr,
"setPoint() called without calling startFrame()");
impl_->currentFrame_->setValue(column, value, error, bPresent);
}
void
-AnalysisDataHandle::setPoints(int firstColumn, int count, const real *values)
+AnalysisDataHandle::setPoints(int firstColumn, int count, const real *values,
+ bool bPresent)
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
- GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != nullptr,
"setPoints() called without calling startFrame()");
for (int i = 0; i < count; ++i)
{
- impl_->currentFrame_->setValue(firstColumn + i, values[i]);
+ impl_->currentFrame_->setValue(firstColumn + i, values[i], bPresent);
}
}
void
AnalysisDataHandle::finishPointSet()
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
GMX_RELEASE_ASSERT(impl_->data_.isMultipoint(),
"finishPointSet() called for non-multipoint data");
- GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != nullptr,
"finishPointSet() called without calling startFrame()");
impl_->currentFrame_->finishPointSet();
}
void
AnalysisDataHandle::finishFrame()
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
- GMX_RELEASE_ASSERT(impl_->currentFrame_ != NULL,
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_->currentFrame_ != nullptr,
"finishFrame() called without calling startFrame()");
AnalysisDataStorageFrame *frame = impl_->currentFrame_;
- impl_->currentFrame_ = NULL;
+ impl_->currentFrame_ = nullptr;
frame->finishFrame();
}
void
AnalysisDataHandle::finishData()
{
- GMX_RELEASE_ASSERT(impl_ != NULL, "Invalid data handle used");
+ GMX_RELEASE_ASSERT(impl_ != nullptr, "Invalid data handle used");
// Deletes the implementation pointer.
impl_->data_.finishData(*this);
- impl_ = NULL;
+ impl_ = nullptr;
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
AnalysisDataHandle();
//! Returns whether this data handle is valid.
- bool isValid() const { return impl_ != NULL; }
+ bool isValid() const { return impl_ != nullptr; }
/*! \brief
* Start data for a new frame.
* \param[in] firstColumn Zero-based column index.
* \param[in] count Number of columns to set.
* \param[in] values Value array of \p column items.
+ * \param[in] bPresent Present flag to set for the column.
*
- * Equivalent to calling setPoint(firstColumn + i, values[i]) for
+ * Equivalent to calling setPoint(firstColumn + i, values[i], bPresent) for
* i from 0 to count.
*
* Does not throw.
*/
- void setPoints(int firstColumn, int count, const real *values);
+ void setPoints(int firstColumn, int count, const real *values, bool bPresent = true);
/*! \brief
* Finish data for the current point set.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
impl_->bAllowMissing_ = false;
}
- impl_->modules_.push_back(Impl::ModuleInfo(module));
+ impl_->modules_.emplace_back(module);
}
void
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
: source_(*data), firstColumn_(firstColumn), columnSpan_(columnSpan),
bParallel_(false)
{
- GMX_RELEASE_ASSERT(data != NULL, "Source data must not be NULL");
+ GMX_RELEASE_ASSERT(data != nullptr, "Source data must not be NULL");
GMX_RELEASE_ASSERT(firstColumn >= 0 && columnSpan > 0, "Invalid proxy column");
setMultipoint(source_.isMultipoint());
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
AnalysisDataStorageImpl::AnalysisDataStorageImpl()
- : data_(NULL), modules_(NULL),
+ : data_(nullptr), modules_(nullptr),
storageLimit_(0), pendingLimit_(1),
firstFrameLocation_(0), firstUnnotifiedIndex_(0), nextIndex_(0)
{
int index)
: storageImpl_(*storageImpl), header_(index, 0.0, 0.0), status_(eMissing)
{
- GMX_RELEASE_ASSERT(storageImpl->data_ != NULL,
+ GMX_RELEASE_ASSERT(storageImpl->data_ != nullptr,
"Storage frame constructed before data started");
// With non-multipoint data, the point set structure is static,
// so initialize it only once here.
for (int i = 0; i < baseData().dataSetCount(); ++i)
{
int columnCount = baseData().columnCount(i);
- pointSets_.push_back(
- AnalysisDataPointSetInfo(offset, columnCount, i, 0));
+ pointSets_.emplace_back(offset, columnCount, i, 0);
offset += columnCount;
}
}
}
else if (storageImpl().needStorage())
{
- pointSets_.push_back(
- AnalysisDataPointSetInfo(values_.size(), valueCount,
- dataSetIndex, firstColumn));
+ pointSets_.emplace_back(values_.size(), valueCount,
+ dataSetIndex, firstColumn);
std::copy(begin, end, std::back_inserter(values_));
}
}
AnalysisDataStorageFrame::AnalysisDataStorageFrame(
const AbstractAnalysisData &data)
- : data_(NULL), currentDataSet_(0), currentOffset_(0),
+ : data_(nullptr), currentDataSet_(0), currentOffset_(0),
columnCount_(data.columnCount(0)), bPointSetInProgress_(false)
{
int totalColumnCount = 0;
void
AnalysisDataStorageFrame::selectDataSet(int index)
{
- GMX_RELEASE_ASSERT(data_ != NULL, "Invalid frame accessed");
+ GMX_RELEASE_ASSERT(data_ != nullptr, "Invalid frame accessed");
const AbstractAnalysisData &baseData = data_->baseData();
GMX_RELEASE_ASSERT(index >= 0 && index < baseData.dataSetCount(),
"Out of range data set index");
void
AnalysisDataStorageFrame::finishPointSet()
{
- GMX_RELEASE_ASSERT(data_ != NULL, "Invalid frame accessed");
+ GMX_RELEASE_ASSERT(data_ != nullptr, "Invalid frame accessed");
GMX_RELEASE_ASSERT(data_->baseData().isMultipoint(),
"Should not be called for non-multipoint data");
if (bPointSetInProgress_)
void
AnalysisDataStorageFrame::finishFrame()
{
- GMX_RELEASE_ASSERT(data_ != NULL, "Invalid frame accessed");
+ GMX_RELEASE_ASSERT(data_ != nullptr, "Invalid frame accessed");
data_->storageImpl().finishFrame(data_->frameIndex());
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
AnalysisDataDisplacementModule::Impl::Impl()
: nmax(0), tmax(0.0), ndim(3),
bFirst(true), t0(0.0), dt(0.0), t(0.0), ci(0),
- max_store(-1), nstored(0), oldval(NULL),
- histm(NULL)
+ max_store(-1), nstored(0), oldval(nullptr),
+ histm(nullptr)
{
}
AnalysisDataDisplacementModule::setMSDHistogram(
AnalysisDataBinAverageModulePointer histm)
{
- GMX_RELEASE_ASSERT(_impl->histm == NULL, "Can only set MSD histogram once");
+ GMX_RELEASE_ASSERT(_impl->histm == nullptr, "Can only set MSD histogram once");
_impl->histm = histm.get();
addModule(histm);
}
i += _impl->max_store;
}
_impl->currValues_.clear();
- _impl->currValues_.push_back(AnalysisDataValue(step * _impl->dt));
+ _impl->currValues_.emplace_back(step * _impl->dt);
int k = 1;
for (int j = 0; j < _impl->nmax; j += _impl->ndim, ++k)
{
- _impl->oldval[i + j + d];
dist2 += displ * displ;
}
- _impl->currValues_.push_back(AnalysisDataValue(dist2));
+ _impl->currValues_.emplace_back(dist2);
}
moduleManager().notifyPointsAdd(AnalysisDataPointSetRef(header, _impl->currValues_));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
impl_->lifetimeHistograms_.reserve(data->dataSetCount());
for (int i = 0; i < data->dataSetCount(); ++i)
{
- impl_->currentLifetimes_.push_back(std::vector<int>(data->columnCount(i), 0));
- impl_->lifetimeHistograms_.push_back(std::deque<int>());
+ impl_->currentLifetimes_.emplace_back(data->columnCount(i), 0);
+ impl_->lifetimeHistograms_.emplace_back();
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/unique_cptr.h"
namespace
{
*/
AnalysisDataPlotSettings::AnalysisDataPlotSettings()
- : selections_(NULL), timeUnit_(TimeUnit_Default), plotFormat_(1)
+ : selections_(nullptr), timeUnit_(TimeUnit_Default), plotFormat_(1)
{
}
};
AbstractPlotModule::Impl::Impl(const AnalysisDataPlotSettings &settings)
- : settings_(settings), fp_(NULL), bPlain_(false), bOmitX_(false),
+ : settings_(settings), fp_(nullptr), bPlain_(false), bOmitX_(false),
bErrorsAsSeparateColumn_(false), xscale_(1.0)
{
strcpy(xformat_, "%11.3f");
void
AbstractPlotModule::Impl::closeFile()
{
- if (fp_ != NULL)
+ if (fp_ != nullptr)
{
if (bPlain_)
{
{
xvgrclose(fp_);
}
- fp_ = NULL;
+ fp_ = nullptr;
}
}
void
AbstractPlotModule::appendLegend(const char *setname)
{
- impl_->legend_.push_back(setname);
+ impl_->legend_.emplace_back(setname);
}
GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
&& width <= 99 && precision <= 99,
"Invalid width or precision");
- GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
+ GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != nullptr,
"Invalid format specifier");
sprintf(impl_->xformat_, "%%%d.%d%c", width, precision, format);
}
GMX_RELEASE_ASSERT(width >= 0 && precision >= 0
&& width <= 99 && precision <= 99,
"Invalid width or precision");
- GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != NULL,
+ GMX_RELEASE_ASSERT(strchr("eEfFgG", format) != nullptr,
"Invalid format specifier");
sprintf(impl_->yformat_, " %%%d.%d%c", width, precision, format);
}
= (impl_->settings_.plotFormat() > 0
? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
: exvgNONE);
- gmx_output_env_t *oenv;
+ gmx_output_env_t *oenv;
output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
- scoped_cptr<gmx_output_env_t, output_env_done> oenvGuard(oenv);
+ const unique_cptr<gmx_output_env_t, output_env_done> oenvGuard(oenv);
impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
oenv);
const SelectionCollection *selections
= impl_->settings_.selectionCollection();
- if (selections != NULL && output_env_get_xvg_format(oenv) != exvgNONE)
+ if (selections != nullptr && output_env_get_xvg_format(oenv) != exvgNONE)
{
selections->printXvgrInfo(impl_->fp_);
}
bool
AbstractPlotModule::isFileOpen() const
{
- return impl_->fp_ != NULL;
+ return impl_->fp_ != nullptr;
}
{
for (int d = 0; d < DIM; ++d)
{
- if (bWrite_[i])
+ if (bWrite_[d])
{
writeValue(points.values()[i + d]);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
//! Appends a value to this point set.
- void addValue(real y) { values_.push_back(Value(y)); }
+ void addValue(real y) { values_.emplace_back(y); }
//! Appends a value with an error estimate to this point set.
void addValueWithError(real y, real error)
{
- values_.push_back(Value(y, error));
+ values_.emplace_back(y, error);
}
private:
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void checkReferenceDataPoint(TestReferenceChecker *checker,
const AnalysisDataValue &value)
{
- TestReferenceChecker compound(checker->checkCompound("DataValue", NULL));
+ TestReferenceChecker compound(checker->checkCompound("DataValue", nullptr));
compound.checkReal(value.value(), "Value");
if (compound.checkPresent(value.hasError(), "Error"))
{
} // namespace
MockAnalysisDataModule::Impl::Impl(int flags)
- : source_(NULL), flags_(flags), frameIndex_(0)
+ : source_(nullptr), flags_(flags), frameIndex_(0)
{
}
if (frameChecker_)
{
TestReferenceChecker checker(
- frameChecker_.checkCompound("DataValues", NULL));
+ frameChecker_.checkCompound("DataValues", nullptr));
checker.checkInteger(points.columnCount(), "Count");
if (checker.checkPresent(source_->dataSetCount() > 1, "DataSet"))
{
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_libgromacs_sources(
+ electricfield.cpp
+ )
+
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares data structure and utilities for electric fields
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_applied_forces
+ */
+#include "gmxpre.h"
+
+#include "electricfield.h"
+
+#include <cmath>
+
+#include <string>
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/iforceprovider.h"
+#include "gromacs/mdtypes/imdmodule.h"
+#include "gromacs/mdtypes/imdoutputprovider.h"
+#include "gromacs/mdtypes/imdpoptionprovider.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/ioptionscontainerwithsections.h"
+#include "gromacs/options/optionsection.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/keyvaluetreetransform.h"
+#include "gromacs/utility/pleasecite.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+/*! \internal
+ * \brief Declaration of storage unit for fields
+ */
+class ElectricFieldData
+{
+ public:
+ ElectricFieldData() : a_(0), omega_(0), t0_(0), sigma_(0)
+ {
+ }
+
+ /*! \brief
+ * Adds an option section to specify parameters for this field component.
+ */
+ void initMdpOptions(IOptionsContainerWithSections *options, const char *sectionName)
+ {
+ auto section = options->addSection(OptionSection(sectionName));
+ section.addOption(RealOption("E0").store(&a_));
+ section.addOption(RealOption("omega").store(&omega_));
+ section.addOption(RealOption("t0").store(&t0_));
+ section.addOption(RealOption("sigma").store(&sigma_));
+ }
+ /*! \brief
+ * Creates mdp parameters for this field component.
+ */
+ void buildMdpOutput(KeyValueTreeObjectBuilder *builder, const std::string &name) const
+ {
+ builder->addUniformArray<real>("E-" + name, {1, a_, -1});
+ builder->addUniformArray<real>("E-" + name + "t", {omega_, t0_, sigma_});
+ }
+
+ /*! \brief Evaluates this field component at given time.
+ *
+ * \param[in] t The time to evualate at
+ * \return The electric field
+ */
+ real evaluate(real t) const
+ {
+ if (sigma_ > 0)
+ {
+ return a_ * (std::cos(omega_*(t-t0_))
+ * std::exp(-square(t-t0_)/(2.0*square(sigma_))));
+ }
+ else
+ {
+ return a_ * std::cos(omega_*t);
+ }
+ }
+
+ /*! \brief Initiate the field values
+ *
+ * \param[in] a Amplitude
+ * \param[in] omega Frequency
+ * \param[in] t0 Peak of the pulse
+ * \param[in] sigma Width of the pulse
+ */
+ void setField(real a, real omega, real t0, real sigma)
+ {
+ a_ = a;
+ omega_ = omega;
+ t0_ = t0;
+ sigma_ = sigma;
+ }
+
+ //! Return the amplitude
+ real a() const { return a_; }
+ //! Return the frequency
+ real omega() const { return omega_; }
+ //! Return the time for the peak of the pulse
+ real t0() const { return t0_; }
+ //! Return the width of the pulse (0 means inifinite)
+ real sigma() const { return sigma_; }
+
+ private:
+ //! Coeffient (V / nm)
+ real a_;
+ //! Frequency (1/ps)
+ real omega_;
+ //! Central time point (ps) for pulse
+ real t0_;
+ //! Width of pulse (ps, if zero there is no pulse)
+ real sigma_;
+};
+
+/*! \internal
+ * \brief Describe time dependent electric field
+ *
+ * Class that implements a force to be evaluated in mdrun.
+ * The electric field can be pulsed and oscillating, simply
+ * oscillating, or static, in each of X,Y,Z directions.
+ */
+class ElectricField final : public IMDModule,
+ public IMdpOptionProvider, public IMDOutputProvider,
+ public IForceProvider
+{
+ public:
+ ElectricField() : fpField_(nullptr) {}
+
+ // From IMDModule
+ IMdpOptionProvider *mdpOptionProvider() override { return this; }
+ IMDOutputProvider *outputProvider() override { return this; }
+ void initForceProviders(ForceProviders *forceProviders) override
+ {
+ if (isActive())
+ {
+ forceProviders->addForceProviderWithoutVirialContribution(this);
+ }
+ }
+
+ // From IMdpOptionProvider
+ void initMdpTransform(IKeyValueTreeTransformRules *transform) override;
+ void initMdpOptions(IOptionsContainerWithSections *options) override;
+ void buildMdpOutput(KeyValueTreeObjectBuilder *builder) const override;
+
+ // From IMDOutputProvider
+ void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
+ bool bAppendFiles, const gmx_output_env_t *oenv) override;
+ void finishOutput() override;
+
+ // From IForceProvider
+ //! \copydoc IForceProvider::calculateForces()
+ void calculateForces(const t_commrec *cr,
+ const t_mdatoms *mdatoms,
+ const matrix box,
+ double t,
+ const rvec *x,
+ ArrayRef<RVec> force) override;
+
+ private:
+ //! Return whether or not to apply a field
+ bool isActive() const;
+
+ /*! \brief Return the field strength
+ *
+ * \param[in] dim The spatial direction
+ * \param[in] t The time (ps)
+ * \return The field strength in V/nm units
+ */
+ real field(int dim, real t) const;
+
+ /*! \brief Return amplitude of field
+ *
+ * \param[in] dim Direction of the field (XX, YY, ZZ)
+ * \return Amplitude of the field
+ */
+ real a(int dim) const { return efield_[dim].a(); }
+ /*! \brief Return frequency of field (1/ps)
+ *
+ * \param[in] dim Direction of the field (XX, YY, ZZ)
+ * \return Frequency of the field
+ */
+ real omega(int dim) const { return efield_[dim].omega(); }
+ /*! \brief Return time of pulse peak
+ *
+ * \param[in] dim Direction of the field (XX, YY, ZZ)
+ * \return Time of pulse peak
+ */
+ real t0(int dim) const { return efield_[dim].t0(); }
+ /*! \brief Return width of the pulse
+ *
+ * \param[in] dim Direction of the field (XX, YY, ZZ)
+ * \return Width of the pulse
+ */
+ real sigma(int dim) const { return efield_[dim].sigma(); }
+
+ /*! \brief Print the field components to a file
+ *
+ * \param[in] t The time
+ * Will throw and exit with fatal error if file is not open.
+ */
+ void printComponents(double t) const;
+
+ //! The field strength in each dimension
+ ElectricFieldData efield_[DIM];
+ //! File pointer for electric field
+ FILE *fpField_;
+};
+
+//! Converts static parameters from mdp format to E0.
+real convertStaticParameters(const std::string &value)
+{
+ // TODO: Better context for the exceptions here (possibly
+ // also convert them to warning_errors or such).
+ const std::vector<std::string> sx = splitString(value);
+ if (sx.empty())
+ {
+ return 0.0;
+ }
+ const int n = fromString<int>(sx[0]);
+ if (n <= 0)
+ {
+ return 0.0;
+ }
+ if (n != 1)
+ {
+ GMX_THROW(InvalidInputError("Only one electric field term supported for each dimension"));
+ }
+ if (sx.size() != 3)
+ {
+ GMX_THROW(InvalidInputError("Expected exactly one electric field amplitude value"));
+ }
+ return fromString<real>(sx[1]);
+}
+
+//! Converts dynamic parameters from mdp format to (omega, t0, sigma).
+void convertDynamicParameters(gmx::KeyValueTreeObjectBuilder *builder,
+ const std::string &value)
+{
+ const std::vector<std::string> sxt = splitString(value);
+ if (sxt.empty())
+ {
+ return;
+ }
+ const int n = fromString<int>(sxt[0]);
+ switch (n)
+ {
+ case 1:
+ if (sxt.size() != 3)
+ {
+ GMX_THROW(InvalidInputError("Please specify 1 omega 0 for non-pulsed fields"));
+ }
+ builder->addValue<real>("omega", fromString<real>(sxt[1]));
+ break;
+ case 3:
+ if (sxt.size() != 7)
+ {
+ GMX_THROW(InvalidInputError("Please specify 1 omega 0 t0 0 sigma 0 for pulsed fields"));
+ }
+ builder->addValue<real>("omega", fromString<real>(sxt[1]));
+ builder->addValue<real>("t0", fromString<real>(sxt[3]));
+ builder->addValue<real>("sigma", fromString<real>(sxt[5]));
+ break;
+ default:
+ GMX_THROW(InvalidInputError("Incomprehensible input for electric field"));
+ }
+}
+
+void ElectricField::initMdpTransform(IKeyValueTreeTransformRules *rules)
+{
+ rules->addRule().from<std::string>("/E-x").to<real>("/electric-field/x/E0")
+ .transformWith(&convertStaticParameters);
+ rules->addRule().from<std::string>("/E-xt").toObject("/electric-field/x")
+ .transformWith(&convertDynamicParameters);
+ rules->addRule().from<std::string>("/E-y").to<real>("/electric-field/y/E0")
+ .transformWith(&convertStaticParameters);
+ rules->addRule().from<std::string>("/E-yt").toObject("/electric-field/y")
+ .transformWith(&convertDynamicParameters);
+ rules->addRule().from<std::string>("/E-z").to<real>("/electric-field/z/E0")
+ .transformWith(&convertStaticParameters);
+ rules->addRule().from<std::string>("/E-zt").toObject("/electric-field/z")
+ .transformWith(&convertDynamicParameters);
+}
+
+void ElectricField::initMdpOptions(IOptionsContainerWithSections *options)
+{
+ auto section = options->addSection(OptionSection("electric-field"));
+ efield_[XX].initMdpOptions(§ion, "x");
+ efield_[YY].initMdpOptions(§ion, "y");
+ efield_[ZZ].initMdpOptions(§ion, "z");
+}
+
+void ElectricField::buildMdpOutput(KeyValueTreeObjectBuilder *builder) const
+{
+ const char *const comment[] = {
+ "; Electric fields",
+ "; Format for E-x, etc. is: number of cosines (int; only 1 is supported),",
+ "; amplitude (real; V/nm), and phase (real; value is meaningless",
+ "; for a cosine of frequency 0.",
+ "; Format for E-xt, etc. is: omega (1/ps), time for the pulse peak (ps),",
+ "; and sigma (ps) width of the pulse. Sigma = 0 removes the pulse,",
+ "; leaving the field to be a cosine function."
+ };
+ builder->addValue<std::string>("comment-electric-field", joinStrings(comment, "\n"));
+ efield_[XX].buildMdpOutput(builder, "x");
+ efield_[YY].buildMdpOutput(builder, "y");
+ efield_[ZZ].buildMdpOutput(builder, "z");
+}
+
+void ElectricField::initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
+ bool bAppendFiles, const gmx_output_env_t *oenv)
+{
+ if (isActive())
+ {
+ please_cite(fplog, "Caleman2008a");
+
+ // Optional outpuf file showing the field, see manual.
+ if (opt2bSet("-field", nfile, fnm))
+ {
+ if (bAppendFiles)
+ {
+ fpField_ = gmx_fio_fopen(opt2fn("-field", nfile, fnm), "a+");
+ }
+ else
+ {
+ fpField_ = xvgropen(opt2fn("-field", nfile, fnm),
+ "Applied electric field", "Time (ps)",
+ "E (V/nm)", oenv);
+ }
+ }
+ }
+}
+
+void ElectricField::finishOutput()
+{
+ if (fpField_ != nullptr)
+ {
+ // This is opened sometimes with xvgropen, sometimes with
+ // gmx_fio_fopen, so we use the least common denominator for closing.
+ gmx_fio_fclose(fpField_);
+ fpField_ = nullptr;
+ }
+}
+
+real ElectricField::field(int dim, real t) const
+{
+ return efield_[dim].evaluate(t);
+}
+
+bool ElectricField::isActive() const
+{
+ return (efield_[XX].a() != 0 ||
+ efield_[YY].a() != 0 ||
+ efield_[ZZ].a() != 0);
+}
+
+void ElectricField::printComponents(double t) const
+{
+ fprintf(fpField_, "%10g %10g %10g %10g\n", t,
+ field(XX, t), field(YY, t), field(ZZ, t));
+}
+
+void ElectricField::calculateForces(const t_commrec *cr,
+ const t_mdatoms *mdatoms,
+ const matrix /* box */,
+ double t,
+ const rvec * /* x */,
+ ArrayRef<RVec> force)
+{
+ if (isActive())
+ {
+ rvec *f = as_rvec_array(force.data());
+
+ for (int m = 0; (m < DIM); m++)
+ {
+ real Ext = FIELDFAC*field(m, t);
+
+ if (Ext != 0)
+ {
+ // TODO: Check parallellism
+ for (int i = 0; i < mdatoms->homenr; ++i)
+ {
+ // NOTE: Not correct with perturbed charges
+ f[i][m] += mdatoms->chargeA[i]*Ext;
+ }
+ }
+ }
+ if (MASTER(cr) && fpField_ != nullptr)
+ {
+ printComponents(t);
+ }
+ }
+}
+
+} // namespace
+
+std::unique_ptr<IMDModule> createElectricFieldModule()
+{
+ return std::unique_ptr<IMDModule>(new ElectricField());
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_APPLIED_FORCES_ELECTRICFIELD_H
+#define GMX_APPLIED_FORCES_ELECTRICFIELD_H
+
+#include <memory>
+
+namespace gmx
+{
+
+class IMDModule;
+
+/*! \brief
+ * Creates a module for an external electric field.
+ *
+ * The returned class describes the time dependent electric field that can
+ * be applied to all charges in a simulation. The field is described
+ * by the following:
+ * E(t) = A cos(omega*(t-t0))*exp(-sqr(t-t0)/(2.0*sqr(sigma)));
+ * If sigma = 0 there is no pulse and we have instead
+ * E(t) = A cos(omega*t)
+ *
+ * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
+ *
+ * WARNING:
+ * There can be problems with the virial.
+ * Since the field is not self-consistent this is unavoidable.
+ * For neutral molecules the virial is correct within this approximation.
+ * For neutral systems with many charged molecules the error is small.
+ * But for systems with a net charge or a few charged molecules
+ * the error can be significant when the field is high.
+ * Solution: implement a self-consistent electric field into PME.
+ */
+std::unique_ptr<IMDModule> createElectricFieldModule();
+
+} // namespace gmx
+
+#endif
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2015,2016, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(AppliedForcesUnitTest applied-forces-test
+ electricfield.cpp
+ )
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "angle" trajectory analysis module.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_applied_forces
+ */
+#include "gmxpre.h"
+
+#include "gromacs/applied-forces/electricfield.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/iforceprovider.h"
+#include "gromacs/mdtypes/imdmodule.h"
+#include "gromacs/mdtypes/imdpoptionprovider.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/options/options.h"
+#include "gromacs/options/treesupport.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/keyvaluetreetransform.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringcompare.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/testasserts.h"
+
+namespace
+{
+
+/********************************************************************
+ * ElectricFieldTest
+ */
+
+class ElectricFieldTest : public ::testing::Test
+{
+ public:
+ void test(int dim,
+ real E0,
+ real omega,
+ real t0,
+ real sigma,
+ real expectedValue)
+ {
+ gmx::test::FloatingPointTolerance tolerance(
+ gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
+ auto module(gmx::createElectricFieldModule());
+
+ // Prepare MDP inputs
+ const char *dimXYZ[3] = { "x", "y", "z" };
+ GMX_RELEASE_ASSERT(dim >= 0 && dim < DIM, "Dimension should be 0, 1 or 2");
+
+ gmx::KeyValueTreeBuilder mdpValues;
+ mdpValues.rootObject().addValue(gmx::formatString("E%s", dimXYZ[dim]),
+ gmx::formatString("1 %g 0", E0));
+ mdpValues.rootObject().addValue(gmx::formatString("E%s-t", dimXYZ[dim]),
+ gmx::formatString("3 %g 0 %g 0 %g 0", omega, t0, sigma));
+
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
+ module->mdpOptionProvider()->initMdpTransform(transform.rules());
+ auto result = transform.transform(mdpValues.build(), nullptr);
+ gmx::Options moduleOptions;
+ module->mdpOptionProvider()->initMdpOptions(&moduleOptions);
+ gmx::assignOptionsFromKeyValueTree(&moduleOptions, result.object(), nullptr);
+
+ ForceProviders forceProviders;
+ module->initForceProviders(&forceProviders);
+
+ t_mdatoms md;
+ PaddedRVecVector f = { { 0, 0, 0 } };
+ md.homenr = 1;
+ snew(md.chargeA, md.homenr);
+ md.chargeA[0] = 1;
+
+ t_commrec *cr = init_commrec();
+ forceProviders.calculateForces(cr, &md, nullptr, 0, nullptr,
+ gmx::EmptyArrayRef(), f);
+ done_commrec(cr);
+
+ EXPECT_REAL_EQ_TOL(f[0][dim], expectedValue, tolerance);
+ sfree(md.chargeA);
+ }
+};
+
+TEST_F(ElectricFieldTest, Static)
+{
+ test(0, 1, 0, 0, 0, 96.4853363);
+}
+
+TEST_F(ElectricFieldTest, Oscillating)
+{
+ test(0, 1, 5, 0.2, 0, 96.4853363);
+}
+
+TEST_F(ElectricFieldTest, Pulsed)
+{
+ test(0, 1, 5, 0.5, 1, -68.215782);
+}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \ingroup module_commandline
*/
-const CommandLineHelpContext *g_globalContext = NULL;
+const CommandLineHelpContext *g_globalContext = nullptr;
} // namespace
Impl(TextWriter *writer, HelpOutputFormat format,
const HelpLinks *links)
: writerContext_(writer, format, links), moduleDisplayName_("gmx"),
- completionWriter_(NULL), bHidden_(false)
+ completionWriter_(nullptr), bHidden_(false)
{
}
//! Creates an implementation class from a low-level context.
explicit Impl(const HelpWriterContext &writerContext)
: writerContext_(writerContext),
- completionWriter_(NULL), bHidden_(false)
+ completionWriter_(nullptr), bHidden_(false)
{
}
CommandLineHelpContext::CommandLineHelpContext(
ShellCompletionWriter *writer)
- : impl_(new Impl(&writer->outputWriter(), eHelpOutputFormat_Other, NULL))
+ : impl_(new Impl(&writer->outputWriter(), eHelpOutputFormat_Other, nullptr))
{
impl_->completionWriter_ = writer;
}
bool CommandLineHelpContext::isCompletionExport() const
{
- return impl_->completionWriter_ != NULL;
+ return impl_->completionWriter_ != nullptr;
}
ShellCompletionWriter &CommandLineHelpContext::shellCompletionWriter() const
GlobalCommandLineHelpContext::GlobalCommandLineHelpContext(
const CommandLineHelpContext &context)
{
- GMX_RELEASE_ASSERT(g_globalContext == NULL,
+ GMX_RELEASE_ASSERT(g_globalContext == nullptr,
"Global context set more than once");
g_globalContext = &context;
}
GlobalCommandLineHelpContext::~GlobalCommandLineHelpContext()
{
- g_globalContext = NULL;
+ g_globalContext = nullptr;
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (bExported)
{
- exportedTopics_.push_back(topic->name());
+ exportedTopics_.emplace_back(topic->name());
}
addSubTopic(std::move(topic));
}
++topicName)
{
const IHelpTopic *topic = findSubTopic(topicName->c_str());
- GMX_RELEASE_ASSERT(topic != NULL, "Exported help topic no longer found");
+ GMX_RELEASE_ASSERT(topic != nullptr, "Exported help topic no longer found");
exporter->exportTopic(*topic);
}
// For now, the title is only set for the export to make it not appear in
CommandLineHelpContext
RootHelpTopic::createContext(const HelpWriterContext &context) const
{
- if (helpModule_.context_ != NULL)
+ if (helpModule_.context_ != nullptr)
{
return CommandLineHelpContext(*helpModule_.context_);
}
virtual bool hasSubTopics() const { return false; }
virtual const IHelpTopic *findSubTopic(const char * /*name*/) const
{
- return NULL;
+ return nullptr;
}
virtual void writeHelp(const HelpWriterContext &context) const;
for (module = modules.begin(); module != modules.end(); ++module)
{
int nameLength = static_cast<int>(module->first.length());
- if (module->second->shortDescription() != NULL
+ if (module->second->shortDescription() != nullptr
&& nameLength > maxNameLength)
{
maxNameLength = nameLength;
"Available commands:");
TextWriter &file = context.outputFile();
TextTableFormatter formatter;
- formatter.addColumn(NULL, maxNameLength + 1, false);
- formatter.addColumn(NULL, 72 - maxNameLength, true);
+ formatter.addColumn(nullptr, maxNameLength + 1, false);
+ formatter.addColumn(nullptr, 72 - maxNameLength, true);
formatter.setFirstColumnIndent(4);
for (module = modules.begin(); module != modules.end(); ++module)
{
const char *name = module->first.c_str();
const char *description = module->second->shortDescription();
- if (description != NULL)
+ if (description != nullptr)
{
formatter.clear();
formatter.addColumnLine(0, name);
}
virtual const char *name() const { return module_.name(); }
- virtual const char *title() const { return NULL; }
+ virtual const char *title() const { return nullptr; }
virtual bool hasSubTopics() const { return false; }
virtual const IHelpTopic *findSubTopic(const char * /*name*/) const
{
- return NULL;
+ return nullptr;
}
virtual void writeHelp(const HelpWriterContext &context) const;
module != helpModule.modules_.end();
++module)
{
- if (module->second->shortDescription() != NULL)
+ if (module->second->shortDescription() != nullptr)
{
std::string linkName("[gmx-" + module->first + "]");
const char *name = module->first.c_str();
{
TextReader linksFile("links.dat");
std::string line;
- while (linksFile.readLineTrimmed(&line))
+ linksFile.setTrimTrailingWhiteSpace(true);
+ while (linksFile.readLine(&line))
{
links_.addLink("[REF]." + line + "[ref]",
formatString(":ref:`.%s <%s>`", line.c_str(), line.c_str()),
const std::string & /*tag*/,
const std::string & /*displayName*/)
{
- modules_.push_back(module.name());
+ modules_.emplace_back(module.name());
{
CommandLineHelpContext context(&bashWriter_);
// We use the display name to pass the name of the module to the
const CommandLineModuleGroupList &groups)
: rootTopic_(*this), programContext_(programContext),
binaryName_(binaryName), modules_(modules), groups_(groups),
- context_(NULL), moduleOverride_(NULL), bHidden_(false),
+ context_(nullptr), moduleOverride_(nullptr), bHidden_(false),
outputRedirector_(&defaultFileOutputRedirector())
{
}
CommandLineModuleMap::const_iterator module;
for (module = modules_.begin(); module != modules_.end(); ++module)
{
- if (module->second->shortDescription() != NULL)
+ if (module->second->shortDescription() != nullptr)
{
const char *const moduleName = module->first.c_str();
std::string tag(formatString("%s-%s", program, moduleName));
const char *const exportFormats[] = { "rst", "completion" };
std::string exportFormat;
- Options options(NULL, NULL);
+ Options options;
options.addOption(StringOption("export").store(&exportFormat)
.enumValue(exportFormats));
CommandLineParser(&options).parse(&argc, argv);
CommandLineHelpContext context(&writer, eHelpOutputFormat_Console, &links,
impl_->binaryName_);
context.setShowHidden(impl_->bHidden_);
- if (impl_->moduleOverride_ != NULL)
+ if (impl_->moduleOverride_ != nullptr)
{
context.setModuleDisplayName(impl_->programContext_.displayName());
impl_->moduleOverride_->writeHelp(context);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Does not throw.
*/
OptionsFilter()
- : formatter_(NULL), filterType_(eSelectOtherOptions),
+ : formatter_(nullptr), filterType_(eSelectOtherOptions),
bShowHidden_(false)
{
}
IOptionsFormatter *formatter,
const Options &options);
- virtual void visitSubSection(const Options §ion);
+ virtual void visitSection(const OptionSectionInfo §ion);
virtual void visitOption(const OptionInfo &option);
private:
{
formatter_ = formatter;
filterType_ = type;
- visitSubSection(options);
+ visitSection(options.rootSection());
}
-void OptionsFilter::visitSubSection(const Options §ion)
+void OptionsFilter::visitSection(const OptionSectionInfo §ion)
{
OptionsIterator iterator(section);
- iterator.acceptSubSections(this);
+ iterator.acceptSections(this);
iterator.acceptOptions(this);
}
return;
}
const FileNameOptionInfo *const fileOption = option.toType<FileNameOptionInfo>();
- if (fileOption != NULL && fileOption->isInputFile())
+ if (fileOption != nullptr && fileOption->isInputFile())
{
if (filterType_ == eSelectInputFileOptions)
{
}
return;
}
- if (fileOption != NULL && fileOption->isInputOutputFile())
+ if (fileOption != nullptr && fileOption->isInputOutputFile())
{
if (filterType_ == eSelectInputOutputFileOptions)
{
}
return;
}
- if (fileOption != NULL && fileOption->isOutputFile())
+ if (fileOption != nullptr && fileOption->isOutputFile())
{
if (filterType_ == eSelectOutputFileOptions)
{
}
//! Formats the default option value as a string.
-std::string
-defaultOptionValue(const OptionInfo &option)
+std::string defaultOptionValue(const OptionInfo &option)
{
- if (option.valueCount() == 0
- || (option.valueCount() == 1 && option.formatValue(0).empty()))
- {
- return option.formatDefaultValueIfSet();
- }
- else
- {
- std::string result;
- for (int i = 0; i < option.valueCount(); ++i)
- {
- if (i != 0)
- {
- result.append(" ");
- }
- result.append(option.formatValue(i));
- }
- return result;
- }
+ return joinStrings(option.defaultValuesAsStrings(), " ");
}
//! Formats the flags for a file option as a string.
const FloatOptionInfo *floatOption = option.toType<FloatOptionInfo>();
const DoubleOptionInfo *doubleOption = option.toType<DoubleOptionInfo>();
- if ((floatOption != NULL && floatOption->isTime())
- || (doubleOption != NULL && doubleOption->isTime()))
+ if ((floatOption != nullptr && floatOption->isTime())
+ || (doubleOption != nullptr && doubleOption->isTime()))
{
// TODO: It could be nicer to have this in basicoptions.cpp.
description = replaceAll(description, "%t", common.timeUnit);
private:
void writeSectionStartIfNecessary()
{
- if (title_ != NULL)
+ if (title_ != nullptr)
{
context_.writeTitle(title_);
- title_ = NULL;
+ title_ = nullptr;
}
if (!bDidOutput_)
{
- if (header_ != NULL)
+ if (header_ != nullptr)
{
context_.paragraphBreak();
context_.writeTextBlock(header_);
const CommonFormatterData &common,
const char *title)
: context_(context), common_(common),
- title_(title), header_(NULL), bDidOutput_(false)
+ title_(title), header_(nullptr), bDidOutput_(false)
{
}
std::string defaultValue(defaultOptionValue(option));
std::string info;
const FileNameOptionInfo *fileOption = option.toType<FileNameOptionInfo>();
- if (fileOption != NULL)
+ if (fileOption != nullptr)
{
const bool bAbbrev = (context_.outputFormat() == eHelpOutputFormat_Console);
info = fileOptionFlagsAsString(*fileOption, bAbbrev);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void finalizeForCommandLine()
{
gmx::finalize();
- setLibraryFileFinder(NULL);
+ setLibraryFileFinder(nullptr);
g_libFileFinder.reset();
- setProgramContext(NULL);
+ setProgramContext(nullptr);
g_commandLineContext.reset();
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int argc = 1;
// TODO: The constness should not be cast away.
argv[0] = const_cast<char *>(name);
- argv[1] = NULL;
+ argv[1] = nullptr;
GlobalCommandLineHelpContext global(context);
mainFunction(argc, argv);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
CommandLineCommonOptionsHolder::CommandLineCommonOptionsHolder()
- : options_(NULL, NULL), bHelp_(false), bHidden_(false),
+ : bHelp_(false), bHidden_(false),
bQuiet_(false), bVersion_(false), bCopyright_(true),
niceLevel_(19), bNiceSet_(false), bBackup_(true), bFpexcept_(false),
debugLevel_(0)
CommandLineModuleManager::Impl::Impl(const char *binaryName,
CommandLineProgramContext *programContext)
: programContext_(*programContext),
- binaryName_(binaryName != NULL ? binaryName : ""),
- helpModule_(NULL), singleModule_(NULL),
+ binaryName_(binaryName != nullptr ? binaryName : ""),
+ helpModule_(nullptr), singleModule_(nullptr),
bQuiet_(false)
{
GMX_RELEASE_ASSERT(binaryName_.find('-') == std::string::npos,
void CommandLineModuleManager::Impl::ensureHelpModuleExists()
{
- if (helpModule_ == NULL)
+ if (helpModule_ == nullptr)
{
helpModule_ = new CommandLineHelpModule(programContext_, binaryName_,
modules_, moduleGroups_);
// TODO: It would be nice to propagate at least the -quiet option to
// the modules so that they can also be quiet in response to this.
- if (module == NULL)
+ if (module == nullptr)
{
// If not in single-module mode, process options to the wrapper binary.
// TODO: Ideally, this could be done by CommandLineParser.
// which path is taken: (*argv)[0] is the module name.
}
}
- if (module != NULL)
+ if (module != nullptr)
{
- if (singleModule_ == NULL)
+ if (singleModule_ == nullptr)
{
programContext_.setDisplayName(binaryName_ + " " + module->name());
}
}
if (!optionsHolder->finishOptions())
{
- return NULL;
+ return nullptr;
}
// If no module specified and no other action, show the help.
// Also explicitly specifying -h for the wrapper binary goes here.
- if (module == NULL || optionsHolder->shouldShowHelp())
+ if (module == nullptr || optionsHolder->shouldShowHelp())
{
ensureHelpModuleExists();
- if (module != NULL)
+ if (module != nullptr)
{
helpModule_->setModuleOverride(*module);
}
optionsHolder.binaryInfoSettings());
fprintf(out, "\n");
}
- if (module == NULL)
+ if (module == nullptr)
{
return 0;
}
CommandLineProgramContext &programContext = gmx::initForCommandLine(&argc, &argv);
try
{
- CommandLineModuleManager manager(NULL, &programContext);
+ CommandLineModuleManager manager(nullptr, &programContext);
manager.setSingleModule(module);
int rc = manager.run(argc, argv);
gmx::finalizeForCommandLine();
CommandLineModuleMap::const_iterator moduleIter = allModules_.find(name);
GMX_RELEASE_ASSERT(moduleIter != allModules_.end(),
"Non-existent module added to a group");
- if (description == NULL)
+ if (description == nullptr)
{
description = moduleIter->second->shortDescription();
- GMX_RELEASE_ASSERT(description != NULL,
+ GMX_RELEASE_ASSERT(description != nullptr,
"Module without a description added to a group");
}
std::string tag(formatString("%s-%s", binaryName_, name));
void CommandLineModuleGroup::addModule(const char *name)
{
- impl_->addModule(name, NULL);
+ impl_->addModule(name, nullptr);
}
void CommandLineModuleGroup::addModuleWithDescription(const char *name,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (!module_)
{
- GMX_RELEASE_ASSERT(factory_ != NULL, "Neither factory nor module provided");
+ GMX_RELEASE_ASSERT(factory_ != nullptr, "Neither factory nor module provided");
module_ = factory_();
}
module_->init(settings);
ICommandLineOptionsModule *module = module_.get();
if (!module)
{
- GMX_RELEASE_ASSERT(factory_ != NULL, "Neither factory nor module provided");
+ GMX_RELEASE_ASSERT(factory_ != nullptr, "Neither factory nor module provided");
moduleGuard = factory_();
module = moduleGuard.get();
}
- Options options(name(), shortDescription());
+ Options options;
OptionsBehaviorCollection behaviors(&options);
CommandLineOptionsModuleSettings settings(&behaviors);
module->initOptions(&options, &settings);
void CommandLineOptionsModule::parseOptions(int argc, char *argv[])
{
FileNameOptionManager fileoptManager;
- Options options(name_, description_);
+ Options options;
options.addManager(&fileoptManager);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// Lone '-' or '--' is not an option.
if (arg[0] != '-' || arg[1] == '\0' || (arg[1] == '-' && arg[2] == '\0'))
{
- return NULL;
+ return nullptr;
}
// Something starting with '--' is always an option.
if (arg[1] == '-')
GMX_IGNORE_RETURN_VALUE(std::strtod(arg, &endptr));
if (*endptr == '\0')
{
- return NULL;
+ return nullptr;
}
return arg + 1;
}
impl_->assigner_.start();
int newi = 1;
- for (int i = 1; i != *argc; ++i)
+ for (int i = 1; i < *argc; ++i)
{
const char *const arg = argv[i];
const char *const optionName = impl_->toOptionName(arg);
- if (optionName != NULL)
+ if (optionName != nullptr)
{
if (bInOption)
{
if (impl_->bSkipUnknown_)
{
*argc = newi;
- argv[newi] = NULL;
+ argv[newi] = nullptr;
}
// Finish the last option.
if (bInOption)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
std::string quoteIfNecessary(const char *str)
{
- const bool bSpaces = (std::strchr(str, ' ') != NULL);
+ const bool bSpaces = (std::strchr(str, ' ') != nullptr);
if (bSpaces)
{
return formatString("'%s'", str);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
- return NULL;
+ return nullptr;
}
const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
fprintf(stderr, "No option %s\n", opt);
- return NULL;
+ return nullptr;
}
int opt2fns(char **fns[], const char *opt, int nfile, const t_filenm fnm[])
}
fprintf(stderr, "ftp2fn: No filetype %s\n", ftp2ext_with_dot(ftp));
- return NULL;
+ return nullptr;
}
int ftp2fns(char **fns[], int ftp, int nfile, const t_filenm fnm[])
{
if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
{
- return NULL;
+ return nullptr;
}
else
{
}
}
fprintf(stderr, "No option %s\n", opt);
- return NULL;
+ return nullptr;
}
const char *ftp2fn_null(int ftp, int nfile, const t_filenm fnm[])
{
if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
{
- return NULL;
+ return nullptr;
}
else
{
}
}
fprintf(stderr, "ftp2fn: No filetype %s\n", ftp2ext_with_dot(ftp));
- return NULL;
+ return nullptr;
}
gmx_bool is_optional(const t_filenm *fnm)
}
else
{
- ret[i].opt = NULL;
+ ret[i].opt = nullptr;
}
if (tfn[i].fn)
}
else
{
- ret[i].fn = NULL;
+ ret[i].fn = nullptr;
}
if (tfn[i].nfiles > 0)
sfree(fnm[i].fns[j]);
}
sfree(fnm[i].fns);
- fnm[i].fns = NULL;
+ fnm[i].fns = nullptr;
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/filetypes.h"
#include "gromacs/utility/basedefinitions.h"
-struct t_commrec;
//! \addtogroup module_commandline
//! \{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_fatal(FARGS, "No string option %s in pargs", option);
- return NULL;
+ return nullptr;
}
-gmx_bool opt2parg_bSet(const char *option, int nparg, t_pargs pa[])
+gmx_bool opt2parg_bSet(const char *option, int nparg, const t_pargs *pa)
{
int i;
gmx_fatal(FARGS, "No such option %s in pargs", option);
- return NULL;
+ return nullptr;
}
/********************************************************************
int getDefaultXvgFormat(gmx::ConstArrayRef<const char *> xvgFormats)
{
const char *const select = getenv("GMX_VIEW_XVG");
- if (select != NULL)
+ if (select != nullptr)
{
ConstArrayRef<const char *>::const_iterator i =
std::find(xvgFormats.begin(), xvgFormats.end(), std::string(select));
if (i != xvgFormats.end())
{
- return i - xvgFormats.begin();
+ return std::distance(xvgFormats.begin(), i);
}
else
{
struct FileNameData
{
//! Creates a conversion helper for a given `t_filenm` struct.
- explicit FileNameData(t_filenm *fnm) : fnm(fnm), optionInfo(NULL)
+ explicit FileNameData(t_filenm *fnm) : fnm(fnm), optionInfo(nullptr)
{
}
{
//! Creates a conversion helper for a given `t_pargs` struct.
explicit ProgramArgData(t_pargs *pa)
- : pa(pa), optionInfo(NULL), enumIndex(0), boolValue(false)
+ : pa(pa), optionInfo(nullptr), enumIndex(0), boolValue(false)
{
}
void OptionsAdapter::filenmToOptions(Options *options, t_filenm *fnm)
{
- if (fnm->opt == NULL)
+ if (fnm->opt == nullptr)
{
// Existing code may use opt2fn() instead of ftp2fn() for
// options that use the default option name, so we need to
const char *const name = &fnm->opt[1];
const char * defName = fnm->fn;
int defType = -1;
- if (defName == NULL)
+ if (defName == nullptr)
{
defName = ftp2defnm(fnm->ftp);
}
GMX_RELEASE_ASSERT(defType != efNR,
"File name option specifies an invalid extension");
}
- fileNameOptions_.push_back(FileNameData(fnm));
+ fileNameOptions_.emplace_back(fnm);
FileNameData &data = fileNameOptions_.back();
data.optionInfo = options->addOption(
FileNameOption(name).storeVector(&data.values)
const bool bHidden = startsWith(pa->desc, "HIDDEN");
const char *const name = &pa->option[1];
const char *const desc = (bHidden ? &pa->desc[6] : pa->desc);
- programArgs_.push_back(ProgramArgData(pa));
+ programArgs_.emplace_back(pa);
ProgramArgData &data = programArgs_.back();
switch (pa->type)
{
return;
case etSTR:
{
- const char *const defValue = (*pa->u.c != NULL ? *pa->u.c : "");
+ const char *const defValue = (*pa->u.c != nullptr ? *pa->u.c : "");
data.optionInfo = options->addOption(
StringOption(name).store(&data.stringValue)
.defaultValue(defValue)
return;
case etENUM:
{
- const int defaultIndex = (pa->u.c[0] != NULL ? nenum(pa->u.c) - 1 : 0);
+ const int defaultIndex = (pa->u.c[0] != nullptr ? nenum(pa->u.c) - 1 : 0);
data.optionInfo = options->addOption(
EnumIntOption(name).store(&data.enumIndex)
.defaultValue(defaultIndex)
/* This array should match the order of the enum in oenv.h */
const char *const xvg_formats[] = { "xmgrace", "xmgr", "none" };
- // Handle the flags argument, which is a bit field
- // The FF macro returns whether or not the bit is set
-#define FF(arg) ((Flags & arg) == arg)
+ // Lambda function to test the (local) Flags parameter against a bit mask.
+ auto isFlagSet = [Flags](unsigned long bits) {
+ return (Flags & bits) == bits;
+ };
try
{
bool bView = false;
int xvgFormat = 0;
gmx::OptionsAdapter adapter(*argc, argv);
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
gmx::OptionsBehaviorCollection behaviors(&options);
gmx::FileNameOptionManager fileOptManager;
fileOptManager.disableInputOptionChecking(
- FF(PCA_NOT_READ_NODE) || FF(PCA_DISABLE_INPUT_FILE_CHECKING));
+ isFlagSet(PCA_NOT_READ_NODE) || isFlagSet(PCA_DISABLE_INPUT_FILE_CHECKING));
options.addManager(&fileOptManager);
- if (FF(PCA_CAN_SET_DEFFNM))
+ if (isFlagSet(PCA_CAN_SET_DEFFNM))
{
fileOptManager.addDefaultFileNameOption(&options, "deffnm");
}
- if (FF(PCA_CAN_BEGIN))
+ if (isFlagSet(PCA_CAN_BEGIN))
{
options.addOption(
gmx::DoubleOption("b")
.store(&tbegin).storeIsSet(&bBeginTimeSet).timeValue()
.description("First frame (%t) to read from trajectory"));
}
- if (FF(PCA_CAN_END))
+ if (isFlagSet(PCA_CAN_END))
{
options.addOption(
gmx::DoubleOption("e")
.store(&tend).storeIsSet(&bEndTimeSet).timeValue()
.description("Last frame (%t) to read from trajectory"));
}
- if (FF(PCA_CAN_DT))
+ if (isFlagSet(PCA_CAN_DT))
{
options.addOption(
gmx::DoubleOption("dt")
.description("Only use frame when t MOD dt = first time (%t)"));
}
gmx::TimeUnit timeUnit = gmx::TimeUnit_Default;
- if (FF(PCA_TIME_UNIT))
+ if (isFlagSet(PCA_TIME_UNIT))
{
std::shared_ptr<gmx::TimeUnitBehavior> timeUnitBehavior(
new gmx::TimeUnitBehavior());
timeUnitBehavior->addTimeUnitOption(&options, "tu");
behaviors.addBehavior(timeUnitBehavior);
}
- if (FF(PCA_CAN_VIEW))
+ if (isFlagSet(PCA_CAN_VIEW))
{
options.addOption(
gmx::BooleanOption("w").store(&bView)
const gmx::CommandLineHelpContext *context =
gmx::GlobalCommandLineHelpContext::get();
- if (context != NULL)
+ if (context != nullptr)
{
GMX_RELEASE_ASSERT(gmx_node_rank() == 0,
"Help output should be handled higher up and "
}
/* Now parse all the command-line options */
- gmx::CommandLineParser(&options).skipUnknown(FF(PCA_NOEXIT_ON_ARGS))
+ gmx::CommandLineParser(&options).skipUnknown(isFlagSet(PCA_NOEXIT_ON_ARGS))
.parse(argc, argv);
behaviors.optionsFinishing();
options.finish();
setTimeValue(TDELTA, tdelta);
}
- adapter.copyValues(!FF(PCA_NOT_READ_NODE));
+ adapter.copyValues(!isFlagSet(PCA_NOT_READ_NODE));
return TRUE;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-#undef FF
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-struct t_commrec;
struct gmx_output_env_t;
#ifdef __cplusplus
*
* \p option must specify a valid argument in \p pa.
*/
-gmx_bool opt2parg_bSet(const char *option, int nparg, t_pargs pa[]);
+gmx_bool opt2parg_bSet(const char *option, int nparg, const t_pargs *pa);
/** Add option -w to view output files (must be implemented in program). */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/filetypes.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/options.h"
#include "gromacs/options/optionsvisitor.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
public:
const std::string &optionList() const { return optionList_; }
- virtual void visitSubSection(const Options §ion)
+ virtual void visitSection(const OptionSectionInfo §ion)
{
OptionsIterator iterator(section);
- iterator.acceptSubSections(this);
+ iterator.acceptSections(this);
iterator.acceptOptions(this);
}
virtual void visitOption(const OptionInfo &option)
optionList_.append("-");
const BooleanOptionInfo *booleanOption
= option.toType<BooleanOptionInfo>();
- if (booleanOption != NULL && booleanOption->defaultValue())
+ if (booleanOption != nullptr && booleanOption->defaultValue())
{
optionList_.append("no");
}
public:
explicit OptionCompletionWriter(TextWriter *out) : out_(*out) {}
- virtual void visitSubSection(const Options §ion)
+ virtual void visitSection(const OptionSectionInfo §ion)
{
OptionsIterator iterator(section);
- iterator.acceptSubSections(this);
+ iterator.acceptSections(this);
iterator.acceptOptions(this);
}
virtual void visitOption(const OptionInfo &option);
return;
}
const FileNameOptionInfo *fileOption = option.toType<FileNameOptionInfo>();
- if (fileOption != NULL)
+ if (fileOption != nullptr)
{
if (fileOption->isDirectoryOption())
{
return;
}
const StringOptionInfo *stringOption = option.toType<StringOptionInfo>();
- if (stringOption != NULL && stringOption->isEnumerated())
+ if (stringOption != nullptr && stringOption->isEnumerated())
{
std::string completion("compgen -S ' ' -W $'");
completion.append(joinStrings(stringOption->allowedValues(), "\\n"));
out.writeLine("COMPREPLY=()");
OptionsListWriter listWriter;
- listWriter.visitSubSection(options);
+ listWriter.visitSection(options.rootSection());
out.writeLine(formatString("if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -S ' ' -W $'%s' -- $c)); return 0; fi", listWriter.optionList().c_str()));
out.writeLine("case \"$p\" in");
OptionCompletionWriter optionWriter(&out);
- optionWriter.visitSubSection(options);
+ optionWriter.visitSection(options.rootSection());
out.writeLine("esac }");
}
impl_->file_->writeLine("if (( i == COMP_CWORD )); then");
impl_->file_->writeLine("c=${COMP_WORDS[COMP_CWORD]}");
OptionsListWriter lister;
- lister.visitSubSection(options);
+ lister.visitSection(options.rootSection());
std::string completions(lister.optionList());
for (ModuleNameList::const_iterator i = modules.begin();
i != modules.end(); ++i)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
cmdlineprogramcontext.cpp
pargs.cpp
$<TARGET_OBJECTS:onlinehelp-test-shared>)
-
-if (CMAKE_CXX_COMPILER_ID MATCHES "XL")
- # This suppression stops a very verbose cascade of messages about the
- # mocks, which is probably a compiler issue.
- # 1540-2924 (W) Cannot pass an argument of non-POD class type "const gmx::CommandLineHelpContext" through ellipsis.
- set_property(SOURCE cmdlinehelpmodule.cpp cmdlinemodulemanager.cpp cmdlinemodulemanagertest.cpp
- PROPERTY COMPILE_FLAGS "-qsuppress=1540-2924")
-endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::StringOutputStream stream;
gmx::TextWriter streamWriter(&stream);
gmx::CommandLineHelpContext context(&streamWriter, gmx::eHelpOutputFormat_Console,
- NULL, "test");
+ nullptr, "test");
context.setShowHidden(bHidden_);
writer->writeHelp(context);
stream.close();
{
using namespace gmx;
- Options options("test", "Short Description");
+ Options options;
options.addOption(BooleanOption("bool").description("Boolean option")
.defaultValue(true));
options.addOption(BooleanOption("hidden").description("Hidden option")
{
using namespace gmx;
- Options options("test", "Short Description");
+ Options options;
bool bValue = true;
options.addOption(BooleanOption("bool").description("Boolean option")
.store(iavalue).valueCount(2));
std::vector<std::string> svalues;
- svalues.push_back("foo");
+ svalues.emplace_back("foo");
options.addOption(StringOption("str").description("String option")
.storeVector(&svalues).multiValue());
using gmx::eftGenericData;
using gmx::eftTrajectory;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
options.addOption(FileNameOption("f")
.description("File name option with a long value")
.filetype(eftTrajectory).inputFile().required()
using gmx::DoubleOption;
using gmx::StringOption;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
options.addOption(BooleanOption("longboolean")
.description("Boolean option with a long name")
.defaultValue(true));
options.addOption(DoubleOption("dvec").description("Double vector option")
.vector().store(dblvec));
std::vector<std::string> values;
- values.push_back("A very long string value that overflows even the description column");
- values.push_back("Another very long string value that overflows even the description column");
+ values.emplace_back("A very long string value that overflows even the description column");
+ values.emplace_back("Another very long string value that overflows even the description column");
options.addOption(StringOption("string")
.description("String option with very long values (may "
"be less relevant with selections having "
using gmx::SelectionFileOption;
using gmx::SelectionOption;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
gmx::SelectionCollection selections;
gmx::SelectionOptionManager manager(&selections);
options.addManager(&manager);
{
using gmx::IntegerOption;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
gmx::IOptionsContainer &group1 = options.addGroup();
gmx::IOptionsContainer &group2 = options.addGroup();
group2.addOption(IntegerOption("sub2").description("Option in group 2"));
};
using gmx::IntegerOption;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
options.addOption(IntegerOption("int").description("Integer option")
.defaultValue(2));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
CommandLine args(cmdline);
initManager(args, "g_module");
- MockModule mod(NULL, NULL);
+ MockModule mod(nullptr, nullptr);
manager().setSingleModule(&mod);
using ::testing::_;
EXPECT_CALL(mod, writeHelp(_));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
CommandLineParserTest::CommandLineParserTest()
- : options_(NULL, NULL), parser_(&options_),
- flag_(false), ivalue1p_(0), ivalue12_(0)
+ : parser_(&options_), flag_(false), ivalue1p_(0), ivalue12_(0)
{
using gmx::BooleanOption;
using gmx::IntegerOption;
EXPECT_STREQ("-opt2", args.arg(2));
EXPECT_STREQ("value", args.arg(3));
EXPECT_STREQ("-opt3", args.arg(4));
- EXPECT_TRUE(args.arg(5) == NULL);
+ EXPECT_TRUE(args.arg(5) == nullptr);
EXPECT_TRUE(flag_);
ASSERT_EQ(1U, ivalues_.size());
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void testBinaryPathSearch(const char *argv0)
{
- ASSERT_TRUE(env_.get() != NULL);
+ ASSERT_TRUE(env_.get() != nullptr);
gmx::CommandLineProgramContext info(1, &argv0, move(env_));
EXPECT_EQ(expectedExecutable_, info.fullBinaryPath());
}
TEST_F(CommandLineProgramContextTest, FindsBinaryFromCurrentDirectory)
{
env_->workingDirectory_ = Path::join(env_->getWorkingDirectory(), "bin");
- env_->path_.push_back("");
+ env_->path_.emplace_back("");
testBinaryPathSearch("test-exe");
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
ParseCommonArgsTest()
- : oenv_(NULL), fileCount_(0)
+ : oenv_(nullptr), fileCount_(0)
{
}
virtual ~ParseCommonArgsTest()
bool bOk = parse_common_args(&args_.argc(), args_.argv(), flags,
fnm.size(), fnm.data(),
pa.size(), pa.data(),
- 0, NULL, 0, NULL, &oenv_);
+ 0, nullptr, 0, nullptr, &oenv_);
EXPECT_TRUE(bOk);
}
void parseFromArray(gmx::ConstArrayRef<const char *> cmdline,
{
std::string filename(tempFiles_.getTemporaryFilePath(extension));
gmx::TextWriter::writeFileFromString(filename, "Dummy file");
- if (name != NULL)
+ if (name != nullptr)
{
args_.append(name);
switch (type)
TEST_F(ParseCommonArgsTest, ParsesEnumArgs)
{
- const char *value1[] = {NULL, "none", "on", "off", NULL };
- const char *value2[] = {NULL, "def", "value", "value_other", NULL };
- const char *value3[] = {NULL, "default", "value", NULL };
+ const char *value1[] = {nullptr, "none", "on", "off", nullptr };
+ const char *value2[] = {nullptr, "def", "value", "value_other", nullptr };
+ const char *value3[] = {nullptr, "default", "value", nullptr };
t_pargs pa[] = {
{ "-s1", FALSE, etENUM, {value1}, "Description" },
{ "-s2", FALSE, etENUM, {value2}, "Description" },
EXPECT_STREQ("test.xvg", opt2fn_null("-o2", nfile(), fnm));
char **files;
EXPECT_EQ(2, opt2fns(&files, "-om", nfile(), fnm));
- EXPECT_TRUE(files != NULL);
- if (files != NULL)
+ EXPECT_TRUE(files != nullptr);
+ if (files != nullptr)
{
EXPECT_STREQ("test1.xvg", files[0]);
EXPECT_STREQ("test2.xvg", files[1]);
TEST_F(ParseCommonArgsTest, ParsesFileArgsWithDefaults)
{
t_filenm fnm[] = {
- { efTPS, NULL, NULL, ffWRITE },
- { efTRX, "-f2", NULL, ffOPTWR },
+ { efTPS, nullptr, nullptr, ffWRITE },
+ { efTRX, "-f2", nullptr, ffOPTWR },
{ efTRX, "-f3", "trj3", ffWRITE },
{ efXVG, "-o", "out", ffWRITE },
{ efXVG, "-om", "outm", ffWRMULT }
parseFromArray(cmdline, 0, fnm, gmx::EmptyArrayRef());
EXPECT_STREQ("topol.tpr", ftp2fn(efTPS, nfile(), fnm));
EXPECT_STREQ("traj.xtc", opt2fn("-f2", nfile(), fnm));
- EXPECT_NULL(opt2fn_null("-f2", nfile(), fnm));
+ EXPECT_EQ(nullptr, opt2fn_null("-f2", nfile(), fnm));
EXPECT_STREQ("trj3.xtc", opt2fn("-f3", nfile(), fnm));
EXPECT_STREQ("out.xvg", opt2fn("-o", nfile(), fnm));
EXPECT_STREQ("outm.xvg", opt2fn("-om", nfile(), fnm));
TEST_F(ParseCommonArgsTest, ParsesFileArgsWithDefaultFileName)
{
t_filenm fnm[] = {
- { efTPS, "-s", NULL, ffWRITE },
- { efTRX, "-f2", NULL, ffWRITE },
+ { efTPS, "-s", nullptr, ffWRITE },
+ { efTRX, "-f2", nullptr, ffWRITE },
{ efTRX, "-f3", "trj3", ffWRITE },
{ efXVG, "-o", "out", ffWRITE },
{ efXVG, "-om", "outm", ffWRMULT }
TEST_F(ParseCommonArgsTest, HandlesNonExistentInputFiles)
{
t_filenm fnm[] = {
- { efTPS, "-s", NULL, ffREAD },
+ { efTPS, "-s", nullptr, ffREAD },
{ efTRX, "-f", "trj", ffREAD },
{ efTRX, "-f2", "trj2", ffREAD },
{ efTRX, "-f3", "trj3", ffREAD },
TEST_F(ParseCommonArgsTest, HandlesNonExistentOptionalInputFiles)
{
t_filenm fnm[] = {
- { efTPS, "-s", NULL, ffOPTRD },
+ { efTPS, "-s", nullptr, ffOPTRD },
{ efTRX, "-f", "trj", ffOPTRD }
};
const char *const cmdline[] = {
TEST_F(ParseCommonArgsTest, HandlesCompressedFiles)
{
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efGRO, "-g", NULL, ffREAD }
+ { efTRX, "-f", nullptr, ffREAD },
+ { efGRO, "-g", nullptr, ffREAD }
};
args_.append("test");
std::string expectedF = addFileArg("-f", ".pdb.gz", efFull);
TEST_F(ParseCommonArgsTest, AcceptsUnknownTrajectoryExtension)
{
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD }
+ { efTRX, "-f", nullptr, ffREAD }
};
args_.append("test");
std::string expected = addFileArg("-f", ".foo", efFull);
TEST_F(ParseCommonArgsTest, CompletesExtensionFromExistingFile)
{
t_filenm fnm[] = {
- { efTRX, "-f1", NULL, ffREAD },
- { efTRX, "-f2", NULL, ffREAD },
- { efTRX, "-f3", NULL, ffREAD },
- { efTRX, "-f4", NULL, ffREAD }
+ { efTRX, "-f1", nullptr, ffREAD },
+ { efTRX, "-f2", nullptr, ffREAD },
+ { efTRX, "-f3", nullptr, ffREAD },
+ { efTRX, "-f4", nullptr, ffREAD }
};
args_.append("test");
std::string expected1 = addFileArg("-f1", "1.xtc", efNoExtension);
TEST_F(ParseCommonArgsTest, CompletesExtensionFromExistingFileWithDefaultFileName)
{
t_filenm fnm[] = {
- { efTRX, "-f1", NULL, ffREAD },
+ { efTRX, "-f1", nullptr, ffREAD },
{ efSTO, "-f2", "foo", ffREAD },
- { efTRX, "-f3", NULL, ffREAD },
- { efSTX, "-f4", NULL, ffREAD }
+ { efTRX, "-f3", nullptr, ffREAD },
+ { efSTX, "-f4", nullptr, ffREAD }
};
args_.append("test");
std::string expected1 = addFileArg("-f1", "1.trr", efNoExtension);
std::string expected2 = addFileArg("-f2", ".pdb", efEmptyValue);
std::string expected3 = addFileArg("-f3", ".trr", efEmptyValue);
- std::string expected4 = addFileArg(NULL, ".pdb", efEmptyValue);
+ std::string expected4 = addFileArg(nullptr, ".pdb", efEmptyValue);
std::string deffnm = gmx::Path::stripExtension(expected3);
args_.append("-deffnm");
args_.append(deffnm);
TEST_F(ParseCommonArgsTest, HandlesNonReadNode)
{
t_filenm fnm[] = {
- { efTPS, "-s", NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
- { efTRX, "-f2", NULL, ffREAD }
+ { efTPS, "-s", nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTRX, "-f2", nullptr, ffREAD }
};
const char *const cmdline[] = {
"test", "-f", "-f2", "other"
};
parseFromArray(cmdline, PCA_NOT_READ_NODE, fnm, gmx::EmptyArrayRef());
- EXPECT_NULL(fnm[0].fns);
- EXPECT_NULL(fnm[1].fns);
- EXPECT_NULL(fnm[2].fns);
+ EXPECT_EQ(nullptr, fnm[0].fns);
+ EXPECT_EQ(nullptr, fnm[1].fns);
+ EXPECT_EQ(nullptr, fnm[2].fns);
done_filenms(nfile(), fnm);
}
TEST_F(ParseCommonArgsTest, HandlesNonReadNodeWithDefaultFileName)
{
t_filenm fnm[] = {
- { efTPS, "-s", NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
- { efTRX, "-f2", NULL, ffREAD }
+ { efTPS, "-s", nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTRX, "-f2", nullptr, ffREAD }
};
const char *const cmdline[] = {
"test", "-deffnm", "def", "-f", "-f2", "other"
};
parseFromArray(cmdline, PCA_CAN_SET_DEFFNM | PCA_NOT_READ_NODE, fnm, gmx::EmptyArrayRef());
- EXPECT_NULL(fnm[0].fns);
- EXPECT_NULL(fnm[1].fns);
- EXPECT_NULL(fnm[2].fns);
+ EXPECT_EQ(nullptr, fnm[0].fns);
+ EXPECT_EQ(nullptr, fnm[1].fns);
+ EXPECT_EQ(nullptr, fnm[2].fns);
done_filenms(nfile(), fnm);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
#define NVIEW asize(can_view_ftp)
static const char* view_program[] = {
- NULL,
- "ghostview", "display", NULL, "xterm -e rasmol"
+ nullptr,
+ "ghostview", "display", nullptr, "xterm -e rasmol"
};
static int can_view(int ftp)
if (output_env_get_view(oenv) && fn)
{
- if (getenv("DISPLAY") == NULL)
+ if (getenv("DISPLAY") == nullptr)
{
fprintf(stderr, "Can not view %s, no DISPLAY environment variable.\n", fn);
}
if (can_view(fnm[i].ftp) && is_output(&(fnm[i])) &&
( !is_optional(&(fnm[i])) || is_set(&(fnm[i])) ) )
{
- do_view(oenv, fnm[i].fns[0], NULL);
+ do_view(oenv, fnm[i].fns[0], nullptr);
}
}
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_COMPAT_MAKE_UNIQUE_H
+#define GMX_COMPAT_MAKE_UNIQUE_H
+/*! \libinternal
+ * \file
+ * \brief Provides template gmx::compat::make_unique
+ *
+ * The implementation of gmx::compat::make_unique is copied with little
+ * modification from C++ standardization doc N3656
+ * at http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2013/n3656.htm
+ * though additional wrapping has been added for use in \Gromacs.
+ *
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ * \ingroup group_compatibility
+ */
+/*! \addtogroup group_compatibility
+ * ### gmx::compat::make_unique
+ *
+ * Provide a trivially adapted implementation of the C++ standard library `make_unique` function template.
+ * When All supported \Gromacs build platforms provide `std::make_unique`, this should be removed.
+ *
+ */
+#include <cstddef>
+
+#include <memory>
+#include <type_traits>
+#include <utility>
+
+namespace gmx
+{
+namespace compat
+{
+
+///\cond
+
+// All gmx::compat code should use std::unique_ptr
+using ::std::unique_ptr;
+
+template<class T> struct Unique_if {
+ typedef unique_ptr<T> Single_object;
+};
+
+template<class T> struct Unique_if<T[]> {
+ typedef unique_ptr<T[]> Unknown_bound;
+};
+
+template<class T, size_t N> struct Unique_if<T[N]> {
+ typedef void Known_bound;
+};
+
+template<class T, class ... Args>
+typename Unique_if<T>::Single_object
+make_unique(Args && ... args)
+{
+ return unique_ptr<T>(new T(::std::forward<Args>(args) ...));
+}
+
+template<class T>
+typename Unique_if<T>::Unknown_bound
+make_unique(size_t n)
+{
+ typedef typename ::std::remove_extent<T>::type U;
+ return unique_ptr<T>(new U[n]());
+}
+
+template<class T, class ... Args>
+typename Unique_if<T>::Known_bound
+make_unique(Args && ...) = delete;
+
+///\endcond
+
+} // namespace gmx::compat
+} // namespace gmx
+
+#endif // header guard
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+if (GMX_BUILD_UNITTESTS)
+ gmx_add_unit_test(CompatibilityHelpersTests compat-test
+ make_unique.cpp
+ )
+endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Tests for gmx::compat::make_unique
+ *
+ * \author M. Eric Irrgang <ericirrgang@gmail.com>
+ * \ingroup group_compatibility
+ */
+#include "gmxpre.h"
+
+#include "gromacs/compat/make_unique.h"
+
+#include <gtest/gtest.h>
+
+namespace gmx
+{
+
+namespace
+{
+
+struct dummy
+{
+ char foo;
+ char bar;
+ dummy() :
+ foo {0},
+ bar {0}
+ {};
+ dummy(const char a, const char b) :
+ foo {a},
+ bar {b}
+ {};
+};
+
+TEST(CompatibilityHelper, MakeUniqueCompiles)
+{
+ // Check template parameters
+ auto ptr = gmx::compat::make_unique<dummy>();
+ ASSERT_NE(ptr, nullptr);
+ ASSERT_NE(ptr.get(), nullptr);
+ constexpr bool is_dummy = std::is_same < decltype(ptr), std::unique_ptr < dummy>>::value;
+ ASSERT_TRUE(is_dummy);
+
+ // Check template and function parameters
+ ptr = gmx::compat::make_unique<dummy>('a', 'b');
+ ASSERT_EQ(ptr->foo, 'a');
+}
+
+
+} // anonymous namespace
+} // namespace gmx
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/futil.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/strconvert.h"
/*! \brief Shortcut macro to select modes. */
#define MODE(x) ((mode & (x)) == (x))
};
/*! \brief Routine to compute ACF using FFT. */
-static void low_do_four_core(int nfour, int nframes, real c1[], real cfour[],
+static void low_do_four_core(int nframes, real c1[], real cfour[],
int nCos)
{
int i = 0;
-
+ std::vector<std::vector<real> > data;
+ data.resize(1);
+ data[0].resize(nframes, 0);
switch (nCos)
{
case enNorm:
for (i = 0; (i < nframes); i++)
{
- cfour[i] = c1[i];
+ data[0][i] = c1[i];
}
break;
case enCos:
for (i = 0; (i < nframes); i++)
{
- cfour[i] = cos(c1[i]);
+ data[0][i] = cos(c1[i]);
}
break;
case enSin:
for (i = 0; (i < nframes); i++)
{
- cfour[i] = sin(c1[i]);
+ data[0][i] = sin(c1[i]);
}
break;
default:
gmx_fatal(FARGS, "nCos = %d, %s %d", nCos, __FILE__, __LINE__);
}
- many_auto_correl(1, nframes, nfour, &cfour);
+ many_auto_correl(&data);
+ for (i = 0; (i < nframes); i++)
+ {
+ cfour[i] = data[0][i];
+ }
}
/*! \brief Routine to comput ACF without FFT. */
}
/*! \brief Routine to normalize ACF, dividing by corr[0]. */
-void normalize_acf(int nout, real corr[])
+static void normalize_acf(int nout, real corr[])
{
int j;
double c0;
}
/*! \brief Routine that averages ACFs. */
-void average_acf(gmx_bool bVerbose, int n, int nitem, real **c1)
+static void average_acf(gmx_bool bVerbose, int n, int nitem, real **c1)
{
real c0;
int i, j;
}
/*! \brief Normalize ACFs. */
-void norm_and_scale_vectors(int nframes, real c1[], real scale)
+static void norm_and_scale_vectors(int nframes, real c1[], real scale)
{
int j, m;
real *rij;
}
/*! \brief High level ACF routine. */
-void do_four_core(unsigned long mode, int nfour, int nf2, int nframes,
- real c1[], real csum[], real ctmp[])
+static void do_four_core(unsigned long mode, int nframes,
+ real c1[], real csum[], real ctmp[])
{
real *cfour;
char buf[32];
real fac;
int j, m, m1;
- snew(cfour, nfour);
+ snew(cfour, nframes);
if (MODE(eacNormal))
{
/********************************************
* N O R M A L
********************************************/
- low_do_four_core(nfour, nf2, c1, csum, enNorm);
+ low_do_four_core(nframes, c1, csum, enNorm);
}
else if (MODE(eacCos))
{
/* Copy the data to temp array. Since we need it twice
* we can't overwrite original.
*/
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
ctmp[j] = c1[j];
}
/* Cosine term of AC function */
- low_do_four_core(nfour, nf2, ctmp, cfour, enCos);
- for (j = 0; (j < nf2); j++)
+ low_do_four_core(nframes, ctmp, cfour, enCos);
+ for (j = 0; (j < nframes); j++)
{
c1[j] = cfour[j];
}
/* Sine term of AC function */
- low_do_four_core(nfour, nf2, ctmp, cfour, enSin);
- for (j = 0; (j < nf2); j++)
+ low_do_four_core(nframes, ctmp, cfour, enSin);
+ for (j = 0; (j < nframes); j++)
{
c1[j] += cfour[j];
csum[j] = c1[j];
/* Because of normalization the number of -0.5 to subtract
* depends on the number of data points!
*/
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
- csum[j] = -0.5*(nf2-j);
+ csum[j] = -0.5*(nframes-j);
}
/***** DIAGONAL ELEMENTS ************/
for (m = 0; (m < DIM); m++)
{
/* Copy the vector data in a linear array */
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
ctmp[j] = gmx::square(c1[DIM*j+m]);
}
if (debug)
{
sprintf(buf, "c1diag%d.xvg", m);
- dump_tmp(buf, nf2, ctmp);
+ dump_tmp(buf, nframes, ctmp);
}
- low_do_four_core(nfour, nf2, ctmp, cfour, enNorm);
+ low_do_four_core(nframes, ctmp, cfour, enNorm);
if (debug)
{
sprintf(buf, "c1dfout%d.xvg", m);
- dump_tmp(buf, nf2, cfour);
+ dump_tmp(buf, nframes, cfour);
}
fac = 1.5;
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
csum[j] += fac*(cfour[j]);
}
{
/* Copy the vector data in a linear array */
m1 = (m+1) % DIM;
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
ctmp[j] = c1[DIM*j+m]*c1[DIM*j+m1];
}
if (debug)
{
sprintf(buf, "c1off%d.xvg", m);
- dump_tmp(buf, nf2, ctmp);
+ dump_tmp(buf, nframes, ctmp);
}
- low_do_four_core(nfour, nf2, ctmp, cfour, enNorm);
+ low_do_four_core(nframes, ctmp, cfour, enNorm);
if (debug)
{
sprintf(buf, "c1ofout%d.xvg", m);
- dump_tmp(buf, nf2, cfour);
+ dump_tmp(buf, nframes, cfour);
}
fac = 3.0;
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
csum[j] += fac*cfour[j];
}
* First for XX, then for YY, then for ZZ
* After that we sum them and normalise
*/
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
csum[j] = 0.0;
}
for (m = 0; (m < DIM); m++)
{
/* Copy the vector data in a linear array */
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
ctmp[j] = c1[DIM*j+m];
}
- low_do_four_core(nfour, nf2, ctmp, cfour, enNorm);
- for (j = 0; (j < nf2); j++)
+ low_do_four_core(nframes, ctmp, cfour, enNorm);
+ for (j = 0; (j < nframes); j++)
{
csum[j] += cfour[j];
}
}
sfree(cfour);
- for (j = 0; (j < nf2); j++)
+ for (j = 0; (j < nframes); j++)
{
c1[j] = csum[j]/(real)(nframes-j);
}
gmx_bool bVerbose, real tbeginfit, real tendfit,
int eFitFn)
{
- FILE *fp, *gp = NULL;
- int i, nfour;
+ FILE *fp, *gp = nullptr;
+ int i;
real *csum;
real *ctmp, *fit;
real sum, Ct2av, Ctav;
gmx::boolToString(bNormalize));
printf("mode = %lu, dt = %g, nrestart = %d\n", mode, dt, nrestart);
}
- if (bFour)
- {
- /* For FTT corr., we need to pad the data with at least nframes zeros */
- nfour = 2;
- while (2*nframes > nfour)
- {
- nfour *= 2;
- }
- if (debug)
- {
- fprintf(debug, "Using FFT to calculate %s, #points for FFT = %d\n",
- title, nfour);
- }
-
- /* Allocate temp arrays */
- snew(csum, nfour);
- snew(ctmp, nfour);
- }
- else
- {
- nfour = 0; /* To keep the compiler happy */
- snew(csum, nframes);
- snew(ctmp, nframes);
- }
+ /* Allocate temp arrays */
+ snew(csum, nframes);
+ snew(ctmp, nframes);
/* Loop over items (e.g. molecules or dihedrals)
* In this loop the actual correlation functions are computed, but without
if (bFour)
{
- do_four_core(mode, nfour, nframes, nframes, c1[i], csum, ctmp);
+ do_four_core(mode, nframes, c1[i], csum, ctmp);
}
else
{
}
else
{
- fit = NULL;
- fp = NULL;
+ fit = nullptr;
+ fp = nullptr;
}
if (bAver)
{
if (eFitFn != effnNONE)
{
- fit_acf(nout, eFitFn, oenv, fn != NULL, tbeginfit, tendfit, dt, c1[0], fit);
+ fit_acf(nout, eFitFn, oenv, fn != nullptr, tbeginfit, tendfit, dt, c1[0], fit);
sum = print_and_integrate(fp, nout, dt, c1[0], fit, 1);
}
else
{
- sum = print_and_integrate(fp, nout, dt, c1[0], NULL, 1);
+ sum = print_and_integrate(fp, nout, dt, c1[0], nullptr, 1);
}
if (bVerbose)
{
}
if (eFitFn != effnNONE)
{
- fit_acf(nout, eFitFn, oenv, fn != NULL, tbeginfit, tendfit, dt, c1[i], fit);
+ fit_acf(nout, eFitFn, oenv, fn != nullptr, tbeginfit, tendfit, dt, c1[i], fit);
sum = print_and_integrate(fp, nout, dt, c1[i], fit, 1);
}
else
{
- sum = print_and_integrate(fp, nout, dt, c1[i], NULL, 1);
+ sum = print_and_integrate(fp, nout, dt, c1[i], nullptr, 1);
if (debug)
{
fprintf(debug,
}
/*! \brief Legend for selecting Legendre polynomials. */
-static const char *Leg[] = { NULL, "0", "1", "2", "3", NULL };
+static const char *Leg[] = { nullptr, "0", "1", "2", "3", nullptr };
t_pargs *add_acf_pargs(int *npargs, t_pargs *pa)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the array).
*/
const char *s_ffn[effnNR+2] = {
- NULL, "none", "exp", "aexp", "exp_exp",
+ nullptr, "none", "exp", "aexp", "exp_exp",
"exp5", "exp7", "exp9",
- NULL, NULL, NULL, NULL, NULL
+ nullptr, nullptr, nullptr, nullptr, nullptr
};
/*! \brief Long description for each fitting function type */
}
else
{
- return NULL;
+ return nullptr;
}
}
{
x[j] = ttt;
y[j] = c1[i];
- if (NULL == sig)
+ if (nullptr == sig)
{
// No weighting if all values are divided by 1.
dy[j] = 1;
}
}
/* Generate debug output */
- if (NULL != fn_fitted)
+ if (nullptr != fn_fitted)
{
fp = xvgropen(fn_fitted, "Data + Fit", "Time (ps)",
"Data (t)", oenv);
tendfit = ncorr*dt;
}
nf_int = std::min(ncorr, (int)(tendfit/dt));
- sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
+ sum = print_and_integrate(debug, nf_int, dt, c1, nullptr, 1);
if (bPrint)
{
}
nf_int = std::min(ncorr, (int)((tStart+1e-4)/dt));
- sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
- tail_corr = do_lmfit(ncorr, c1, sig, dt, NULL, tStart, tendfit, oenv,
- bDebugMode(), fitfn, fitparm, 0, NULL);
+ sum = print_and_integrate(debug, nf_int, dt, c1, nullptr, 1);
+ tail_corr = do_lmfit(ncorr, c1, sig, dt, nullptr, tStart, tendfit, oenv,
+ bDebugMode(), fitfn, fitparm, 0, nullptr);
sumtot = sum+tail_corr;
if (fit && ((jmax == 1) || (j == 1)))
{
#include "manyautocorrelation.h"
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <cmath>
-
#include <algorithm>
#include "gromacs/fft/fft.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxomp.h"
-#include "gromacs/utility/smalloc.h"
-int many_auto_correl(int nfunc, int ndata, int nfft, real **c)
+int many_auto_correl(std::vector<std::vector<real> > *c)
{
+ size_t nfunc = (*c).size();
+ if (nfunc == 0)
+ {
+ GMX_THROW(gmx::InconsistentInputError("Empty array of vectors supplied"));
+ }
+ size_t ndata = (*c)[0].size();
+ if (ndata == 0)
+ {
+ GMX_THROW(gmx::InconsistentInputError("Empty vector supplied"));
+ }
+#ifndef NDEBUG
+ for (size_t i = 1; i < nfunc; i++)
+ {
+ if ((*c)[i].size() != ndata)
+ {
+ char buf[256];
+ snprintf(buf, sizeof(buf), "Vectors of different lengths supplied (%d %d)",
+ static_cast<int>((*c)[i].size()),
+ static_cast<int>(ndata));
+ GMX_THROW(gmx::InconsistentInputError(buf));
+ }
+ }
+#endif
+ // Add buffer size to the arrays.
+ size_t nfft = (3*ndata/2) + 1;
+ // Pad arrays with zeros
+ for (auto &i : *c)
+ {
+ i.resize(nfft, 0);
+ }
#pragma omp parallel
{
try
{
- typedef real complex[2];
- int i, j;
- gmx_fft_t fft1;
- complex *in, *out;
- int i0, i1;
- int nthreads, thread_id;
+ gmx_fft_t fft1;
+ std::vector<real> in, out;
- nthreads = gmx_omp_get_max_threads();
- thread_id = gmx_omp_get_thread_num();
- if ((0 == thread_id))
- {
- // fprintf(stderr, "There are %d threads for correlation functions\n", nthreads);
- }
- i0 = thread_id*nfunc/nthreads;
- i1 = std::min(nfunc, (thread_id+1)*nfunc/nthreads);
+ int nthreads = gmx_omp_get_max_threads();
+ int thread_id = gmx_omp_get_thread_num();
+ int i0 = (thread_id*nfunc)/nthreads;
+ int i1 = std::min(nfunc, ((thread_id+1)*nfunc)/nthreads);
gmx_fft_init_1d(&fft1, nfft, GMX_FFT_FLAG_CONSERVATIVE);
/* Allocate temporary arrays */
- snew(in, nfft);
- snew(out, nfft);
- for (i = i0; (i < i1); i++)
+ in.resize(2*nfft, 0);
+ out.resize(2*nfft, 0);
+ for (int i = i0; (i < i1); i++)
{
- for (j = 0; j < ndata; j++)
- {
- in[j][0] = c[i][j];
- in[j][1] = 0;
- }
- for (; (j < nfft); j++)
+ for (size_t j = 0; j < ndata; j++)
{
- in[j][0] = in[j][1] = 0;
+ in[2*j+0] = (*c)[i][j];
+ in[2*j+1] = 0;
}
-
- gmx_fft_1d(fft1, GMX_FFT_BACKWARD, (void *)in, (void *)out);
- for (j = 0; j < nfft; j++)
+ gmx_fft_1d(fft1, GMX_FFT_BACKWARD, (void *)in.data(), (void *)out.data());
+ for (size_t j = 0; j < nfft; j++)
{
- in[j][0] = (out[j][0]*out[j][0] + out[j][1]*out[j][1])/nfft;
- in[j][1] = 0;
+ in[2*j+0] = (out[2*j+0]*out[2*j+0] + out[2*j+1]*out[2*j+1])/nfft;
+ in[2*j+1] = 0;
}
- for (; (j < nfft); j++)
+ gmx_fft_1d(fft1, GMX_FFT_FORWARD, (void *)in.data(), (void *)out.data());
+ for (size_t j = 0; (j < nfft); j++)
{
- in[j][0] = in[j][1] = 0;
- }
-
- gmx_fft_1d(fft1, GMX_FFT_FORWARD, (void *)in, (void *)out);
- for (j = 0; (j < nfft); j++)
- {
- c[i][j] = out[j][0];
+ (*c)[i][j] = out[2*j+0];
}
}
/* Free the memory */
gmx_fft_destroy(fft1);
- sfree(in);
- sfree(out);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
- // gmx_fft_cleanup();
+ for (auto &i : *c)
+ {
+ i.resize(ndata);
+ }
+
return 0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MANYAUTOCORRELATION_H
#define GMX_MANYAUTOCORRELATION_H
+#include <vector>
+
#include "gromacs/fft/fft.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
/*! \brief
* Perform many autocorrelation calculations.
*
* This routine performs many autocorrelation function calculations using FFTs.
- * The GROMACS FFT library wrapper is employed. On return the c[] arrays contain
+ * The GROMACS FFT library wrapper is employed. On return the c vector contain
* a symmetric function that is useful for further FFT:ing, for instance in order to
* compute spectra.
*
+ * The vectors c[i] should all have the same length, but this is not checked for.
+ *
+ * The c arrays will be extend and filled with zero beyond ndata before
+ * computing the correlation.
+ *
* The functions uses OpenMP parallellization.
*
- * \param[in] nfunc Number of data functions to autocorrelate
- * \param[in] ndata Number of valid data points in the data
- * \param[in] nfft Length of the data arrays, this should at least be 50% larger than ndata. The c arrays will filled with zero beyond ndata before computing the correlation.
- * \param[inout] c Data array of size nfunc x nfft, will also be used for output
+ * \param[inout] c Data array
* \return fft error code, or zero if everything went fine (see fft/fft.h)
+ * \throws gmx::InconsistentInputError if the input is inconsistent.
*/
-int many_auto_correl(int nfunc, int ndata, int nfft, real **c);
-
-#ifdef __cplusplus
-}
-#endif
+int many_auto_correl(std::vector<std::vector<real> > *c);
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014, by the GROMACS development team, led by
+# Copyright (c) 2014,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test(CorrelationsTest correlations-test
autocorr.cpp
+ manyautocorrelation.cpp
correlationdataset.cpp
expfit.cpp)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::string fileName = "testCOS3.xvg";
data_ = CorrelationDataSetPointer(new CorrelationDataSet(fileName));
nrFrames_ = data_->getNrLines();
- tempArgs_ = add_acf_pargs(&n, NULL);
+ tempArgs_ = add_acf_pargs(&n, nullptr);
}
static void TearDownTestCase()
{
sfree(tempArgs_);
- tempArgs_ = NULL;
+ tempArgs_ = nullptr;
gmx_fft_cleanup();
}
}
}
real *ptr = result.data();
- low_do_autocorr(0, 0, 0, nrFrames_, 1,
+ low_do_autocorr(nullptr, nullptr, nullptr, nrFrames_, 1,
get_acfnout(), &ptr, data_->getDt(), mode,
nrRestart, bAverage, bNormalize,
bVerbose, data_->getStartTime(), data_->getEndTime(),
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (int i = 0; i < nrColumns_; i++)
{
sfree(tempValues_[i]);
- tempValues_[i] = NULL;
+ tempValues_[i] = nullptr;
}
sfree(tempValues_);
- tempValues_ = NULL;
+ tempValues_ = nullptr;
}
real CorrelationDataSet::getValue(int set, int time) const
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// Static initiation, only run once every test.
static void SetUpTestCase()
{
- double ** tempValues = NULL;
+ double ** tempValues = nullptr;
std::vector<std::string> fileName;
fileName.push_back(test::TestFileManager::getInputFilePath("testINVEXP.xvg"));
fileName.push_back(test::TestFileManager::getInputFilePath("testPRES.xvg"));
for (int j = 0; j < nrColumns; j++)
{
sfree(tempValues[j]);
- tempValues[j] = NULL;
+ tempValues[j] = nullptr;
}
sfree(tempValues);
- tempValues = NULL;
+ tempValues = nullptr;
}
}
output_env_init_default(&oenv);
do_lmfit(data_[testType].nrLines_,
&(data_[testType].y_[0]),
- NULL,
+ nullptr,
data_[testType].dt_,
&(data_[testType].x_[0]),
data_[testType].startTime_,
data_[testType].endTime_,
- oenv, false, type, result, 0, NULL);
+ oenv, false, type, result, 0, nullptr);
output_env_done(oenv);
checker_.setDefaultTolerance(test::relativeToleranceAsFloatingPoint(1, tolerance));
checker_.checkSequenceArray(nfitparm, result, "result");
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements low level test of manyautocorrelation routines
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_correlationfunctions
+ */
+#include "gmxpre.h"
+
+#include "gromacs/correlationfunctions/manyautocorrelation.h"
+
+#include <cmath>
+
+#include <memory>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/exceptions.h"
+
+#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
+
+namespace gmx
+{
+namespace
+{
+
+class ManyAutocorrelationTest : public ::testing::Test
+{
+};
+
+TEST_F (ManyAutocorrelationTest, Empty)
+{
+ std::vector<std::vector<real> > c;
+ EXPECT_THROW_GMX(many_auto_correl(&c), gmx::InconsistentInputError);
+}
+
+#ifndef NDEBUG
+TEST_F (ManyAutocorrelationTest, DifferentLength)
+{
+ std::vector<std::vector<real> > c;
+ c.resize(3);
+ c[0].resize(10);
+ c[1].resize(10);
+ c[2].resize(8);
+ EXPECT_THROW_GMX(many_auto_correl(&c), gmx::InconsistentInputError);
+}
+#endif
+
+}
+
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "dlbtiming.h"
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/utility/gmxassert.h"
+
+#include "domdec_internal.h"
+
+/*! \brief Struct for timing the region for dynamic load balancing */
+struct BalanceRegion
+{
+ /*! \brief Constructor */
+ BalanceRegion() :
+ isOpen(false),
+ isOpenOnCpu(false),
+ isOpenOnGpu(false),
+ cyclesOpenCpu(0),
+ cyclesLastCpu(0)
+ {
+ }
+
+ bool isOpen; /**< Are we in an open balancing region? */
+ bool isOpenOnCpu; /**< Is the, currently open, region still open on the CPU side? */
+ bool isOpenOnGpu; /**< Is the, currently open, region open on the GPU side? */
+ gmx_cycles_t cyclesOpenCpu; /**< Cycle count when opening the CPU region */
+ gmx_cycles_t cyclesLastCpu; /**< Cycle count at the last call to \p ddCloseBalanceRegionCpu() */
+};
+
+BalanceRegion *ddBalanceRegionAllocate()
+{
+ return new BalanceRegion;
+}
+
+/*! \brief Returns the pointer to the balance region.
+ *
+ * This should be replaced by a properly managed BalanceRegion class,
+ * but that requires a lot of refactoring in domdec.cpp.
+ */
+static BalanceRegion *getBalanceRegion(const gmx_domdec_t *dd)
+{
+ GMX_ASSERT(dd != nullptr && dd->comm != nullptr, "Balance regions should only be used with DD");
+ BalanceRegion *region = dd->comm->balanceRegion;
+ GMX_ASSERT(region != nullptr, "Balance region should be initialized before use");
+ return region;
+}
+
+void ddOpenBalanceRegionCpu(const gmx_domdec_t *dd,
+ DdAllowBalanceRegionReopen gmx_unused allowReopen)
+{
+ BalanceRegion *reg = getBalanceRegion(dd);
+ if (dd->comm->bRecordLoad)
+ {
+ GMX_ASSERT(allowReopen == DdAllowBalanceRegionReopen::yes || !reg->isOpen, "Should not open an already opened region");
+
+ reg->cyclesOpenCpu = gmx_cycles_read();
+ reg->isOpen = true;
+ reg->isOpenOnCpu = true;
+ reg->isOpenOnGpu = false;
+ }
+}
+
+void ddOpenBalanceRegionGpu(const gmx_domdec_t *dd)
+{
+ BalanceRegion *reg = getBalanceRegion(dd);
+ if (reg->isOpen)
+ {
+ GMX_ASSERT(!reg->isOpenOnGpu, "Can not re-open a GPU balance region");
+ reg->isOpenOnGpu = true;
+ }
+}
+
+void ddReopenBalanceRegionCpu(const gmx_domdec_t *dd)
+{
+ BalanceRegion *reg = getBalanceRegion(dd);
+ /* If the GPU is busy, don't reopen as we are overlapping with work */
+ if (reg->isOpen && !reg->isOpenOnGpu)
+ {
+ reg->cyclesOpenCpu = gmx_cycles_read();
+ }
+}
+
+void ddCloseBalanceRegionCpu(const gmx_domdec_t *dd)
+{
+ BalanceRegion *reg = getBalanceRegion(dd);
+ if (reg->isOpen && reg->isOpenOnCpu)
+ {
+ GMX_ASSERT(reg->isOpenOnCpu, "Can only close an open region");
+ gmx_cycles_t cycles = gmx_cycles_read();
+ reg->isOpenOnCpu = false;
+
+ if (reg->isOpenOnGpu)
+ {
+ /* Store the cycles for estimating the GPU/CPU overlap time */
+ reg->cyclesLastCpu = cycles;
+ }
+ else
+ {
+ /* We can close the region */
+ float cyclesCpu = cycles - reg->cyclesOpenCpu;
+ dd_cycles_add(dd, cyclesCpu, ddCyclF);
+ reg->isOpen = false;
+ }
+ }
+}
+
+void ddCloseBalanceRegionGpu(const gmx_domdec_t *dd,
+ float waitGpuCyclesInCpuRegion,
+ DdBalanceRegionWaitedForGpu waitedForGpu)
+{
+ BalanceRegion *reg = getBalanceRegion(dd);
+ if (reg->isOpen)
+ {
+ GMX_ASSERT(reg->isOpenOnGpu, "Can not close a non-open GPU balance region");
+ GMX_ASSERT(!reg->isOpenOnCpu, "The GPU region should be closed after closing the CPU region");
+
+ float waitGpuCyclesEstimate = gmx_cycles_read() - reg->cyclesLastCpu;
+ if (waitedForGpu == DdBalanceRegionWaitedForGpu::no)
+ {
+ /* The actual time could be anywhere between 0 and
+ * waitCyclesEstimate. Using half is the best we can do.
+ */
+ const float unknownWaitEstimateFactor = 0.5f;
+ waitGpuCyclesEstimate *= unknownWaitEstimateFactor;
+ }
+
+ float cyclesCpu = reg->cyclesLastCpu - reg->cyclesOpenCpu;
+ dd_cycles_add(dd, cyclesCpu + waitGpuCyclesEstimate, ddCyclF);
+
+ /* Register the total GPU wait time, to redistribute with GPU sharing */
+ dd_cycles_add(dd, waitGpuCyclesInCpuRegion + waitGpuCyclesEstimate, ddCyclWaitGPU);
+
+ /* Close the region */
+ reg->isOpenOnGpu = false;
+ reg->isOpen = false;
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ *
+ * \brief This file declares functions for timing the load imbalance due to domain decomposition.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \inlibraryapi
+ * \ingroup module_domdec
+ */
+
+#ifndef GMX_DOMDEC_DLBTIMING_H
+#define GMX_DOMDEC_DLBTIMING_H
+
+struct BalanceRegion;
+struct gmx_domdec_t;
+
+/*! \brief Tells if we should open the balancing region */
+enum class DdOpenBalanceRegionBeforeForceComputation
+{
+ no, //!< Do not open a balancing region
+ yes //!< Open the balancing region before update or after pair-search
+};
+
+/*! \brief Tells if we should close the balancing region after the force computation has completed */
+enum class DdCloseBalanceRegionAfterForceComputation
+{
+ no, //!< Do not close a balancing region
+ yes //!< Close the balancing region after computation completed
+};
+
+/*! \brief Tells if we should open the balancing region */
+enum class DdAllowBalanceRegionReopen
+{
+ no, //!< Do not allow opening an already open region
+ yes //!< Allow opening an already open region
+};
+
+/*! \brief Tells if we had to wait for a GPU to finish computation */
+enum class DdBalanceRegionWaitedForGpu
+{
+ no, //!< The GPU finished computation before the CPU needed the result
+ yes //!< We had to wait for the GPU to finish computation
+};
+
+/*! \brief Returns a pointer to a constructed \p BalanceRegion struct
+ *
+ * Should be replaced by a proper constructor once BalanceRegion is a proper
+ * class (requires restructering in domdec.cpp).
+ */
+BalanceRegion *ddBalanceRegionAllocate();
+
+/*! \brief Open the load balance timing region on the CPU
+ *
+ * Opens the balancing region for timing how much time it takes to perform
+ * the (balancable part of) the MD step. This should be called right after
+ * the last communication during the previous step to maximize the region.
+ * In practice this means right after the force communication finished
+ * or just before neighbor search at search steps.
+ * It is assumed that computation done in the region either scales along
+ * with the domain size or takes constant time.
+ *
+ * \param[in,out] dd The domain decomposition struct
+ * \param[in] allowReopen Allows calling with a potentially already opened region
+ */
+void ddOpenBalanceRegionCpu(const gmx_domdec_t *dd,
+ DdAllowBalanceRegionReopen allowReopen);
+
+/*! \brief Open the load balance timing region for the CPU
+ *
+ * This can only be called within a region that is open on the CPU side.
+ */
+void ddOpenBalanceRegionGpu(const gmx_domdec_t *dd);
+
+/*! \brief Re-open the, already opened, load balance timing region
+ *
+ * This function should be called after every MPI communication that occurs
+ * in the main MD loop.
+ * Note that the current setup assumes that all MPI communication acts like
+ * a global barrier. But if some ranks don't participate in communication
+ * or if some ranks communicate faster with neighbors than others,
+ * the obtained timings might not accurately reflect the computation time.
+ *
+ * \param[in,out] dd The domain decomposition struct
+ */
+void ddReopenBalanceRegionCpu(const gmx_domdec_t *dd);
+
+/*! \brief Close the load balance timing region on the CPU side
+ *
+ * \param[in,out] dd The domain decomposition struct
+ */
+void ddCloseBalanceRegionCpu(const gmx_domdec_t *dd);
+
+/*! \brief Close the load balance timing region on the GPU side
+ *
+ * This should be called after the CPU receives the last (local) results
+ * from the GPU. The wait time for these results is estimated, depending
+ * on the \p waitedForGpu parameter.
+ * If called on an already closed region, this call does nothing.
+ *
+ * \param[in,out] dd The domain decomposition struct
+ * \param[in] waitCyclesGpuInCpuRegion The time we waited for the GPU earlier, overlapping completely with the open CPU region
+ * \param[in] waitedForGpu Tells if we waited for the GPU to finish now
+ */
+void ddCloseBalanceRegionGpu(const gmx_domdec_t *dd,
+ float waitCyclesGpuInCpuRegion,
+ DdBalanceRegionWaitedForGpu waitedForGpu);
+
+#endif
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_grid.h"
#include "gromacs/mdlib/nsgrid.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/qsort_threadsafe.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
#include "domdec_constraints.h"
#include "domdec_internal.h"
{
int atnr;
- if (dd == NULL)
+ if (dd == nullptr)
{
atnr = i + 1;
}
return &dd->comm->cgs_gl;
}
-static bool dlbIsOn(const gmx_domdec_comm_t *comm)
+/*! \brief Returns true if the DLB state indicates that the balancer is on. */
+static bool isDlbOn(const gmx_domdec_comm_t *comm)
{
return (comm->dlbState == edlbsOnCanTurnOff ||
- comm->dlbState == edlbsOnForever);
+ comm->dlbState == edlbsOnUser);
+}
+/*! \brief Returns true if the DLB state indicates that the balancer is off/disabled.
+ */
+static bool isDlbDisabled(const gmx_domdec_comm_t *comm)
+{
+ return (comm->dlbState == edlbsOffUser ||
+ comm->dlbState == edlbsOffForever);
}
static void vec_rvec_init(vec_rvec_t *v)
{
v->nalloc = 0;
- v->v = NULL;
+ v->v = nullptr;
}
static void vec_rvec_check_alloc(vec_rvec_t *v, int n)
if (state->ddp_count != dd->ddp_count)
{
- gmx_incons("The state does not the domain decomposition state");
+ gmx_incons("The MD state does not match the domain decomposition state");
}
- state->ncg_gl = dd->ncg_home;
- if (state->ncg_gl > state->cg_gl_nalloc)
- {
- state->cg_gl_nalloc = over_alloc_dd(state->ncg_gl);
- srenew(state->cg_gl, state->cg_gl_nalloc);
- }
- for (i = 0; i < state->ncg_gl; i++)
+ state->cg_gl.resize(dd->ncg_home);
+ for (i = 0; i < dd->ncg_home; i++)
{
state->cg_gl[i] = dd->index_gl[i];
}
dim = dd->dim[d];
shift0[dim] = zones->izone[izone].shift0[dim];
shift1[dim] = zones->izone[izone].shift1[dim];
- if (dd->comm->tric_dir[dim] || (dlbIsOn(dd->comm) && d > 0))
+ if (dd->comm->tric_dir[dim] || (isDlbOn(dd->comm) && d > 0))
{
/* A conservative approach, this can be optimized */
shift0[dim] -= 1;
}
}
+int dd_natoms_mdatoms(const gmx_domdec_t *dd)
+{
+ /* We currently set mdatoms entries for all atoms:
+ * local + non-local + communicated for vsite + constraints
+ */
+
+ return dd->comm->nat[ddnatNR - 1];
+}
+
int dd_natoms_vsite(const gmx_domdec_t *dd)
{
return dd->comm->nat[ddnatVSITE];
consider PBC in the treatment of fshift */
bShiftForcesNeedPbc = (dd->ci[dd->dim[d]] == 0);
bScrew = (bShiftForcesNeedPbc && dd->bScrewPBC && dd->dim[d] == XX);
- if (fshift == NULL && !bScrew)
+ if (fshift == nullptr && !bScrew)
{
bShiftForcesNeedPbc = FALSE;
}
static void dd_collect_cg(gmx_domdec_t *dd,
t_state *state_local)
{
- gmx_domdec_master_t *ma = NULL;
- int buf2[2], *ibuf, i, ncg_home = 0, *cg = NULL, nat_home = 0;
+ gmx_domdec_master_t *ma = nullptr;
+ int buf2[2], *ibuf, i, ncg_home = 0, *cg = nullptr, nat_home = 0;
if (state_local->ddp_count == dd->comm->master_cg_ddp_count)
{
cgs_gl = &dd->comm->cgs_gl;
- ncg_home = state_local->ncg_gl;
- cg = state_local->cg_gl;
+ ncg_home = state_local->cg_gl.size();
+ cg = state_local->cg_gl.data();
nat_home = 0;
for (i = 0; i < ncg_home; i++)
{
}
else
{
- ibuf = NULL;
+ ibuf = nullptr;
}
/* Collect the charge group and atom counts on the master */
dd_gather(dd, 2*sizeof(int), buf2, ibuf);
/* Collect the charge group indices on the master */
dd_gatherv(dd,
ncg_home*sizeof(int), cg,
- DDMASTER(dd) ? ma->ibuf : NULL,
- DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
- DDMASTER(dd) ? ma->cg : NULL);
+ DDMASTER(dd) ? ma->ibuf : nullptr,
+ DDMASTER(dd) ? ma->ibuf+dd->nnodes : nullptr,
+ DDMASTER(dd) ? ma->cg : nullptr);
dd->comm->master_cg_ddp_count = state_local->ddp_count;
}
static void dd_collect_vec_sendrecv(gmx_domdec_t *dd,
- rvec *lv, rvec *v)
+ const rvec *lv, rvec *v)
{
gmx_domdec_master_t *ma;
int n, i, c, a, nalloc = 0;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
t_block *cgs_gl;
ma = dd->ma;
if (!DDMASTER(dd))
{
#if GMX_MPI
- MPI_Send(lv, dd->nat_home*sizeof(rvec), MPI_BYTE, DDMASTERRANK(dd),
- dd->rank, dd->mpi_comm_all);
+ MPI_Send(const_cast<void *>(static_cast<const void *>(lv)), dd->nat_home*sizeof(rvec), MPI_BYTE,
+ DDMASTERRANK(dd), dd->rank, dd->mpi_comm_all);
#endif
}
else
}
static void dd_collect_vec_gatherv(gmx_domdec_t *dd,
- rvec *lv, rvec *v)
+ const rvec *lv, rvec *v)
{
gmx_domdec_master_t *ma;
- int *rcounts = NULL, *disps = NULL;
+ int *rcounts = nullptr, *disps = nullptr;
int n, i, c, a;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
t_block *cgs_gl;
ma = dd->ma;
}
}
-void dd_collect_vec(gmx_domdec_t *dd,
- t_state *state_local, rvec *lv, rvec *v)
+void dd_collect_vec(gmx_domdec_t *dd,
+ t_state *state_local,
+ const PaddedRVecVector *localVector,
+ rvec *v)
{
dd_collect_cg(dd, state_local);
+ const rvec *lv = as_rvec_array(localVector->data());
+
if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
{
dd_collect_vec_sendrecv(dd, lv, v);
}
}
+void dd_collect_vec(gmx_domdec_t *dd,
+ t_state *state_local,
+ const PaddedRVecVector *localVector,
+ PaddedRVecVector *vector)
+{
+ dd_collect_vec(dd, state_local, localVector, as_rvec_array(vector->data()));
+}
+
void dd_collect_state(gmx_domdec_t *dd,
t_state *state_local, t_state *state)
{
- int est, i, j, nh;
-
- nh = state->nhchainlength;
+ int nh = state->nhchainlength;
if (DDMASTER(dd))
{
- for (i = 0; i < efptNR; i++)
+ for (int i = 0; i < efptNR; i++)
{
state->lambda[i] = state_local->lambda[i];
}
copy_mat(state_local->fvir_prev, state->fvir_prev);
copy_mat(state_local->pres_prev, state->pres_prev);
- for (i = 0; i < state_local->ngtc; i++)
+ for (int i = 0; i < state_local->ngtc; i++)
{
- for (j = 0; j < nh; j++)
+ for (int j = 0; j < nh; j++)
{
state->nosehoover_xi[i*nh+j] = state_local->nosehoover_xi[i*nh+j];
state->nosehoover_vxi[i*nh+j] = state_local->nosehoover_vxi[i*nh+j];
}
state->therm_integral[i] = state_local->therm_integral[i];
}
- for (i = 0; i < state_local->nnhpres; i++)
+ for (int i = 0; i < state_local->nnhpres; i++)
{
- for (j = 0; j < nh; j++)
+ for (int j = 0; j < nh; j++)
{
state->nhpres_xi[i*nh+j] = state_local->nhpres_xi[i*nh+j];
state->nhpres_vxi[i*nh+j] = state_local->nhpres_vxi[i*nh+j];
}
}
+ state->baros_integral = state_local->baros_integral;
}
- for (est = 0; est < estNR; est++)
+ if (state_local->flags & (1 << estX))
{
- if (EST_DISTR(est) && (state_local->flags & (1<<est)))
- {
- switch (est)
- {
- case estX:
- dd_collect_vec(dd, state_local, state_local->x, state->x);
- break;
- case estV:
- dd_collect_vec(dd, state_local, state_local->v, state->v);
- break;
- case est_SDX_NOTSUPPORTED:
- break;
- case estCGP:
- dd_collect_vec(dd, state_local, state_local->cg_p, state->cg_p);
- break;
- case estDISRE_INITF:
- case estDISRE_RM3TAV:
- case estORIRE_INITF:
- case estORIRE_DTAV:
- break;
- default:
- gmx_incons("Unknown state entry encountered in dd_collect_state");
- }
- }
+ dd_collect_vec(dd, state_local, &state_local->x, &state->x);
+ }
+ if (state_local->flags & (1 << estV))
+ {
+ dd_collect_vec(dd, state_local, &state_local->v, &state->v);
+ }
+ if (state_local->flags & (1 << estCGP))
+ {
+ dd_collect_vec(dd, state_local, &state_local->cg_p, &state->cg_p);
}
}
-static void dd_realloc_state(t_state *state, rvec **f, int nalloc)
+static void dd_resize_state(t_state *state, PaddedRVecVector *f, int natoms)
{
- int est;
-
if (debug)
{
- fprintf(debug, "Reallocating state: currently %d, required %d, allocating %d\n", state->nalloc, nalloc, over_alloc_dd(nalloc));
+ fprintf(debug, "Resizing state: currently %d, required %d\n", state->natoms, natoms);
}
- state->nalloc = over_alloc_dd(nalloc);
-
- for (est = 0; est < estNR; est++)
- {
- if (EST_DISTR(est) && (state->flags & (1<<est)))
- {
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries.
- */
- switch (est)
- {
- case estX:
- srenew(state->x, state->nalloc + 1);
- break;
- case estV:
- srenew(state->v, state->nalloc + 1);
- break;
- case est_SDX_NOTSUPPORTED:
- break;
- case estCGP:
- srenew(state->cg_p, state->nalloc + 1);
- break;
- case estDISRE_INITF:
- case estDISRE_RM3TAV:
- case estORIRE_INITF:
- case estORIRE_DTAV:
- /* No reallocation required */
- break;
- default:
- gmx_incons("Unknown state entry encountered in dd_realloc_state");
- }
- }
- }
+ state_change_natoms(state, natoms);
- if (f != NULL)
+ if (f != nullptr)
{
- srenew(*f, state->nalloc);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ f->resize(natoms + 1);
}
}
-static void dd_check_alloc_ncg(t_forcerec *fr, t_state *state, rvec **f,
- int nalloc)
+static void dd_check_alloc_ncg(t_forcerec *fr,
+ t_state *state,
+ PaddedRVecVector *f,
+ int numChargeGroups)
{
- if (nalloc > fr->cg_nalloc)
+ if (numChargeGroups > fr->cg_nalloc)
{
if (debug)
{
- fprintf(debug, "Reallocating forcerec: currently %d, required %d, allocating %d\n", fr->cg_nalloc, nalloc, over_alloc_dd(nalloc));
+ fprintf(debug, "Reallocating forcerec: currently %d, required %d, allocating %d\n", fr->cg_nalloc, numChargeGroups, over_alloc_dd(numChargeGroups));
}
- fr->cg_nalloc = over_alloc_dd(nalloc);
+ fr->cg_nalloc = over_alloc_dd(numChargeGroups);
srenew(fr->cginfo, fr->cg_nalloc);
if (fr->cutoff_scheme == ecutsGROUP)
{
srenew(fr->cg_cm, fr->cg_nalloc);
}
}
- if (fr->cutoff_scheme == ecutsVERLET && nalloc > state->nalloc)
+ if (fr->cutoff_scheme == ecutsVERLET)
{
/* We don't use charge groups, we use x in state to set up
* the atom communication.
*/
- dd_realloc_state(state, f, nalloc);
+ dd_resize_state(state, f, numChargeGroups);
}
}
{
gmx_domdec_master_t *ma;
int n, i, c, a, nalloc = 0;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
if (DDMASTER(dd))
{
rvec *v, rvec *lv)
{
gmx_domdec_master_t *ma;
- int *scounts = NULL, *disps = NULL;
+ int *scounts = nullptr, *disps = nullptr;
int n, i, c, a;
- rvec *buf = NULL;
+ rvec *buf = nullptr;
if (DDMASTER(dd))
{
static void dd_distribute_dfhist(gmx_domdec_t *dd, df_history_t *dfhist)
{
- int i;
+ if (dfhist == nullptr)
+ {
+ return;
+ }
+
dd_bcast(dd, sizeof(int), &dfhist->bEquil);
dd_bcast(dd, sizeof(int), &dfhist->nlambda);
dd_bcast(dd, sizeof(real), &dfhist->wl_delta);
dd_bcast(dd, sizeof(real)*nlam, dfhist->sum_minvar);
dd_bcast(dd, sizeof(real)*nlam, dfhist->sum_variance);
- for (i = 0; i < nlam; i++)
+ for (int i = 0; i < nlam; i++)
{
dd_bcast(dd, sizeof(real)*nlam, dfhist->accum_p[i]);
dd_bcast(dd, sizeof(real)*nlam, dfhist->accum_m[i]);
static void dd_distribute_state(gmx_domdec_t *dd, t_block *cgs,
t_state *state, t_state *state_local,
- rvec **f)
+ PaddedRVecVector *f)
{
- int i, j, nh;
-
- nh = state->nhchainlength;
+ int nh = state->nhchainlength;
if (DDMASTER(dd))
{
- for (i = 0; i < efptNR; i++)
+ for (int i = 0; i < efptNR; i++)
{
state_local->lambda[i] = state->lambda[i];
}
copy_mat(state->boxv, state_local->boxv);
copy_mat(state->svir_prev, state_local->svir_prev);
copy_mat(state->fvir_prev, state_local->fvir_prev);
- copy_df_history(&state_local->dfhist, &state->dfhist);
- for (i = 0; i < state_local->ngtc; i++)
+ if (state->dfhist != nullptr)
{
- for (j = 0; j < nh; j++)
+ copy_df_history(state_local->dfhist, state->dfhist);
+ }
+ for (int i = 0; i < state_local->ngtc; i++)
+ {
+ for (int j = 0; j < nh; j++)
{
state_local->nosehoover_xi[i*nh+j] = state->nosehoover_xi[i*nh+j];
state_local->nosehoover_vxi[i*nh+j] = state->nosehoover_vxi[i*nh+j];
}
state_local->therm_integral[i] = state->therm_integral[i];
}
- for (i = 0; i < state_local->nnhpres; i++)
+ for (int i = 0; i < state_local->nnhpres; i++)
{
- for (j = 0; j < nh; j++)
+ for (int j = 0; j < nh; j++)
{
state_local->nhpres_xi[i*nh+j] = state->nhpres_xi[i*nh+j];
state_local->nhpres_vxi[i*nh+j] = state->nhpres_vxi[i*nh+j];
}
}
+ state_local->baros_integral = state->baros_integral;
}
- dd_bcast(dd, ((efptNR)*sizeof(real)), state_local->lambda);
+ dd_bcast(dd, ((efptNR)*sizeof(real)), state_local->lambda.data());
dd_bcast(dd, sizeof(int), &state_local->fep_state);
dd_bcast(dd, sizeof(real), &state_local->veta);
dd_bcast(dd, sizeof(real), &state_local->vol0);
dd_bcast(dd, sizeof(state_local->boxv), state_local->boxv);
dd_bcast(dd, sizeof(state_local->svir_prev), state_local->svir_prev);
dd_bcast(dd, sizeof(state_local->fvir_prev), state_local->fvir_prev);
- dd_bcast(dd, ((state_local->ngtc*nh)*sizeof(double)), state_local->nosehoover_xi);
- dd_bcast(dd, ((state_local->ngtc*nh)*sizeof(double)), state_local->nosehoover_vxi);
- dd_bcast(dd, state_local->ngtc*sizeof(double), state_local->therm_integral);
- dd_bcast(dd, ((state_local->nnhpres*nh)*sizeof(double)), state_local->nhpres_xi);
- dd_bcast(dd, ((state_local->nnhpres*nh)*sizeof(double)), state_local->nhpres_vxi);
+ dd_bcast(dd, ((state_local->ngtc*nh)*sizeof(double)), state_local->nosehoover_xi.data());
+ dd_bcast(dd, ((state_local->ngtc*nh)*sizeof(double)), state_local->nosehoover_vxi.data());
+ dd_bcast(dd, state_local->ngtc*sizeof(double), state_local->therm_integral.data());
+ dd_bcast(dd, ((state_local->nnhpres*nh)*sizeof(double)), state_local->nhpres_xi.data());
+ dd_bcast(dd, ((state_local->nnhpres*nh)*sizeof(double)), state_local->nhpres_vxi.data());
/* communicate df_history -- required for restarting from checkpoint */
- dd_distribute_dfhist(dd, &state_local->dfhist);
+ dd_distribute_dfhist(dd, state_local->dfhist);
+
+ dd_resize_state(state_local, f, dd->nat_home);
- if (dd->nat_home > state_local->nalloc)
+ if (state_local->flags & (1 << estX))
{
- dd_realloc_state(state_local, f, dd->nat_home);
+ dd_distribute_vec(dd, cgs, as_rvec_array(state->x.data()), as_rvec_array(state_local->x.data()));
}
- for (i = 0; i < estNR; i++)
+ if (state_local->flags & (1 << estV))
{
- if (EST_DISTR(i) && (state_local->flags & (1<<i)))
- {
- switch (i)
- {
- case estX:
- dd_distribute_vec(dd, cgs, state->x, state_local->x);
- break;
- case estV:
- dd_distribute_vec(dd, cgs, state->v, state_local->v);
- break;
- case est_SDX_NOTSUPPORTED:
- break;
- case estCGP:
- dd_distribute_vec(dd, cgs, state->cg_p, state_local->cg_p);
- break;
- case estDISRE_INITF:
- case estDISRE_RM3TAV:
- case estORIRE_INITF:
- case estORIRE_DTAV:
- /* Not implemented yet */
- break;
- default:
- gmx_incons("Unknown state entry encountered in dd_distribute_state");
- }
- }
+ dd_distribute_vec(dd, cgs, as_rvec_array(state->v.data()), as_rvec_array(state_local->v.data()));
+ }
+ if (state_local->flags & (1 << estCGP))
+ {
+ dd_distribute_vec(dd, cgs, as_rvec_array(state->cg_p.data()), as_rvec_array(state_local->cg_p.data()));
}
}
static void write_dd_grid_pdb(const char *fn, gmx_int64_t step,
gmx_domdec_t *dd, matrix box, gmx_ddbox_t *ddbox)
{
- rvec grid_s[2], *grid_r = NULL, cx, r;
+ rvec grid_s[2], *grid_r = nullptr, cx, r;
char fname[STRLEN], buf[22];
FILE *out;
int a, i, d, z, y, x;
snew(grid_r, 2*dd->nnodes);
}
- dd_gather(dd, 2*sizeof(rvec), grid_s, DDMASTER(dd) ? grid_r : NULL);
+ dd_gather(dd, 2*sizeof(rvec), grid_s, DDMASTER(dd) ? grid_r : nullptr);
if (DDMASTER(dd))
{
char fname[STRLEN], buf[22];
FILE *out;
int i, ii, resnr, c;
- char *atomname, *resname;
+ const char *atomname, *resname;
real b;
gmx_domdec_t *dd;
fprintf(out, "TITLE %s\n", title);
gmx_write_pdb_box(out, dd->bScrewPBC ? epbcSCREW : epbcXYZ, box);
+ int molb = 0;
for (i = 0; i < natoms; i++)
{
ii = dd->gatindex[i];
- gmx_mtop_atominfo_global(mtop, ii, &atomname, &resnr, &resname);
+ mtopGetAtomAndResidueName(mtop, ii, &molb, &atomname, &resnr, &resname, nullptr);
if (i < dd->comm->nat[ddnatZONE])
{
c = 0;
/* This assumes DD cells with identical x coordinates
* are numbered sequentially.
*/
- if (dd->comm->pmenodes == NULL)
+ if (dd->comm->pmenodes == nullptr)
{
if (sim_nodeid < dd->nnodes)
{
void get_pme_nnodes(const gmx_domdec_t *dd,
int *npmenodes_x, int *npmenodes_y)
{
- if (dd != NULL)
+ if (dd != nullptr)
{
*npmenodes_x = dd->comm->npmenodes_x;
*npmenodes_y = dd->comm->npmenodes_y;
}
static void rebuild_cgindex(gmx_domdec_t *dd,
- const int *gcgs_index, t_state *state)
+ const int *gcgs_index, const t_state *state)
{
- int nat, i, *ind, *dd_cg_gl, *cgindex, cg_gl;
+ int * gmx_restrict dd_cg_gl = dd->index_gl;
+ int * gmx_restrict cgindex = dd->cgindex;
+ int nat = 0;
- ind = state->cg_gl;
- dd_cg_gl = dd->index_gl;
- cgindex = dd->cgindex;
- nat = 0;
+ /* Copy back the global charge group indices from state
+ * and rebuild the local charge group to atom index.
+ */
cgindex[0] = nat;
- for (i = 0; i < state->ncg_gl; i++)
+ for (unsigned int i = 0; i < state->cg_gl.size(); i++)
{
cgindex[i] = nat;
- cg_gl = ind[i];
+ int cg_gl = state->cg_gl[i];
dd_cg_gl[i] = cg_gl;
nat += gcgs_index[cg_gl+1] - gcgs_index[cg_gl];
}
- cgindex[i] = nat;
+ cgindex[state->cg_gl.size()] = nat;
- dd->ncg_home = state->ncg_gl;
+ dd->ncg_home = state->cg_gl.size();
dd->nat_home = nat;
set_zones_ncg_home(dd);
int *cginfo;
int cg;
- if (fr != NULL)
+ if (fr != nullptr)
{
cginfo_mb = fr->cginfo_mb;
cginfo = fr->cginfo;
}
}
- if (bLocalCG != NULL)
+ if (bLocalCG != nullptr)
{
for (cg = cg0; cg < cg1; cg++)
{
int i, ngl, nerr;
nerr = 0;
- if (bLocalCG == NULL)
+ if (bLocalCG == nullptr)
{
return nerr;
}
{
cellsize_min[d] = ddbox->box_size[d]*ddbox->skew_fac[d];
npulse[d] = 1;
- if (dd->nc[d] == 1 || comm->slb_frac[d] == NULL)
+ if (dd->nc[d] == 1 || comm->slb_frac[d] == nullptr)
{
/* Uniform grid */
cell_dx = ddbox->box_size[d]/dd->nc[d];
}
}
- if (!dlbIsOn(comm))
+ if (!isDlbOn(comm))
{
copy_rvec(cellsize_min, comm->cellsize_min);
}
for (d = 0; d < comm->npmedecompdim; d++)
{
set_pme_maxshift(dd, &comm->ddpme[d],
- comm->slb_frac[dd->dim[d]] == NULL, ddbox,
+ comm->slb_frac[dd->dim[d]] == nullptr, ddbox,
comm->ddpme[d].slb_dim_f);
}
}
srenew(cd->ind, np);
for (i = cd->np_nalloc; i < np; i++)
{
- cd->ind[i].index = NULL;
+ cd->ind[i].index = nullptr;
cd->ind[i].nalloc = 0;
}
cd->np_nalloc = np;
copy_rvec(comm->cell_x0, comm->old_cell_x0);
copy_rvec(comm->cell_x1, comm->old_cell_x1);
- if (dlbIsOn(comm))
+ if (isDlbOn(comm))
{
if (DDMASTER(dd))
{
/* Without PBC we don't have restrictions on the outer cells */
if (!(dim >= ddbox->npbcdim &&
(dd->ci[dim] == 0 || dd->ci[dim] == dd->nc[dim] - 1)) &&
- dlbIsOn(comm) &&
+ isDlbOn(comm) &&
(comm->cell_x1[dim] - comm->cell_x0[dim])*ddbox->skew_fac[dim] <
comm->cellsize_min[dim])
{
}
}
- if ((dlbIsOn(dd->comm) && dd->ndim > 1) || ddbox->nboundeddim < DIM)
+ if ((isDlbOn(dd->comm) && dd->ndim > 1) || ddbox->nboundeddim < DIM)
{
/* Communicate the boundaries and update cell_ns_x0/1 */
dd_move_cellx(dd, ddbox, cell_ns_x0, cell_ns_x1);
- if (dlbIsOn(dd->comm) && dd->ndim > 1)
+ if (isDlbOn(dd->comm) && dd->ndim > 1)
{
check_grid_jump(step, dd, dd->comm->cutoff, ddbox, TRUE);
}
gmx_domdec_t *dd)
{
gmx_domdec_master_t *ma;
- int **tmp_ind = NULL, *tmp_nalloc = NULL;
+ int **tmp_ind = nullptr, *tmp_nalloc = nullptr;
int i, icg, j, k, k0, k1, d;
matrix tcm;
rvec cg_cm;
t_block *cgs, matrix box, gmx_ddbox_t *ddbox,
rvec pos[])
{
- gmx_domdec_master_t *ma = NULL;
+ gmx_domdec_master_t *ma = nullptr;
ivec npulse;
int i, cg_gl;
int *ibuf, buf2[2] = { 0, 0 };
}
else
{
- ibuf = NULL;
+ ibuf = nullptr;
}
dd_scatter(dd, 2*sizeof(int), ibuf, buf2);
}
dd_scatterv(dd,
- bMaster ? ma->ibuf : NULL,
- bMaster ? ma->ibuf+dd->nnodes : NULL,
- bMaster ? ma->cg : NULL,
+ bMaster ? ma->ibuf : nullptr,
+ bMaster ? ma->ibuf+dd->nnodes : nullptr,
+ bMaster ? ma->cg : nullptr,
dd->ncg_home*sizeof(int), dd->index_gl);
/* Determine the home charge group sizes */
static void rotate_state_atom(t_state *state, int a)
{
- int est;
-
- for (est = 0; est < estNR; est++)
+ if (state->flags & (1 << estX))
{
- if (EST_DISTR(est) && (state->flags & (1<<est)))
- {
- switch (est)
- {
- case estX:
- /* Rotate the complete state; for a rectangular box only */
- state->x[a][YY] = state->box[YY][YY] - state->x[a][YY];
- state->x[a][ZZ] = state->box[ZZ][ZZ] - state->x[a][ZZ];
- break;
- case estV:
- state->v[a][YY] = -state->v[a][YY];
- state->v[a][ZZ] = -state->v[a][ZZ];
- break;
- case est_SDX_NOTSUPPORTED:
- break;
- case estCGP:
- state->cg_p[a][YY] = -state->cg_p[a][YY];
- state->cg_p[a][ZZ] = -state->cg_p[a][ZZ];
- break;
- case estDISRE_INITF:
- case estDISRE_RM3TAV:
- case estORIRE_INITF:
- case estORIRE_DTAV:
- /* These are distances, so not affected by rotation */
- break;
- default:
- gmx_incons("Unknown state entry encountered in rotate_state_atom");
- }
- }
+ /* Rotate the complete state; for a rectangular box only */
+ state->x[a][YY] = state->box[YY][YY] - state->x[a][YY];
+ state->x[a][ZZ] = state->box[ZZ][ZZ] - state->x[a][ZZ];
+ }
+ if (state->flags & (1 << estV))
+ {
+ state->v[a][YY] = -state->v[a][YY];
+ state->v[a][ZZ] = -state->v[a][ZZ];
+ }
+ if (state->flags & (1 << estCGP))
+ {
+ state->cg_p[a][YY] = -state->cg_p[a][YY];
+ state->cg_p[a][ZZ] = -state->cg_p[a][ZZ];
}
}
if (pos_d >= limit1[d])
{
cg_move_error(fplog, dd, step, cg, d, 1,
- cg_cm != state->x, limitd[d],
+ cg_cm != as_rvec_array(state->x.data()), limitd[d],
cg_cm[cg], cm_new, pos_d);
}
dev[d] = 1;
if (pos_d < limit0[d])
{
cg_move_error(fplog, dd, step, cg, d, -1,
- cg_cm != state->x, limitd[d],
+ cg_cm != as_rvec_array(state->x.data()), limitd[d],
cg_cm[cg], cm_new, pos_d);
}
dev[d] = -1;
static void dd_redistribute_cg(FILE *fplog, gmx_int64_t step,
gmx_domdec_t *dd, ivec tric_dir,
- t_state *state, rvec **f,
+ t_state *state, PaddedRVecVector *f,
t_forcerec *fr,
gmx_bool bCompact,
t_nrnb *nrnb,
{
int *move;
int npbcdim;
- int ncg[DIM*2], nat[DIM*2];
- int c, i, cg, k, d, dim, dim2, dir, d2, d3;
+ int ncg[DIM*2] = { 0 }, nat[DIM*2] = { 0 };
+ int i, cg, k, d, dim, dim2, dir, d2, d3;
int mc, cdd, nrcg, ncg_recv, nvs, nvr, nvec, vec;
int sbuf[2], rbuf[2];
int home_pos_cg, home_pos_at, buf_pos;
int flag;
- gmx_bool bV = FALSE, bCGP = FALSE;
real pos_d;
matrix tcm;
- rvec *cg_cm = NULL, cell_x0, cell_x1, limitd, limit0, limit1;
+ rvec *cg_cm = nullptr, cell_x0, cell_x1, limitd, limit0, limit1;
int *cgindex;
cginfo_mb_t *cginfo_mb;
gmx_domdec_comm_t *comm;
cg_cm = fr->cg_cm;
}
- for (i = 0; i < estNR; i++)
- {
- if (EST_DISTR(i))
- {
- switch (i)
- {
- case estX: /* Always present */ break;
- case estV: bV = (state->flags & (1<<i)); break;
- case est_SDX_NOTSUPPORTED: break;
- case estCGP: bCGP = (state->flags & (1<<i)); break;
- case estLD_RNG:
- case estLD_RNGI:
- case estDISRE_INITF:
- case estDISRE_RM3TAV:
- case estORIRE_INITF:
- case estORIRE_DTAV:
- /* No processing required */
- break;
- default:
- gmx_incons("Unknown state entry encountered in dd_redistribute_cg");
- }
- }
- }
+ // Positions are always present, so there's nothing to flag
+ bool bV = state->flags & (1<<estV);
+ bool bCGP = state->flags & (1<<estCGP);
if (dd->ncg_tot > comm->nalloc_int)
{
}
move = comm->buf_int;
- /* Clear the count */
- for (c = 0; c < dd->ndim*2; c++)
- {
- ncg[c] = 0;
- nat[c] = 0;
- }
-
npbcdim = dd->npbcdim;
for (d = 0; (d < DIM); d++)
cgindex,
( thread *dd->ncg_home)/nthread,
((thread+1)*dd->ncg_home)/nthread,
- fr->cutoff_scheme == ecutsGROUP ? cg_cm : state->x,
+ fr->cutoff_scheme == ecutsGROUP ? cg_cm : as_rvec_array(state->x.data()),
move);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
*/
home_pos_cg =
compact_and_copy_vec_cg(dd->ncg_home, move, cgindex,
- nvec, state->x, comm, FALSE);
+ nvec, as_rvec_array(state->x.data()), comm, FALSE);
if (bCompact)
{
home_pos_cg -= *ncg_moved;
vec = 0;
home_pos_at =
compact_and_copy_vec_at(dd->ncg_home, move, cgindex,
- nvec, vec++, state->x, comm, bCompact);
+ nvec, vec++, as_rvec_array(state->x.data()),
+ comm, bCompact);
if (bV)
{
compact_and_copy_vec_at(dd->ncg_home, move, cgindex,
- nvec, vec++, state->v, comm, bCompact);
+ nvec, vec++, as_rvec_array(state->v.data()),
+ comm, bCompact);
}
if (bCGP)
{
compact_and_copy_vec_at(dd->ncg_home, move, cgindex,
- nvec, vec++, state->cg_p, comm, bCompact);
+ nvec, vec++, as_rvec_array(state->cg_p.data()),
+ comm, bCompact);
}
if (bCompact)
nvr += i;
}
+ dd_check_alloc_ncg(fr, state, f, home_pos_cg + ncg_recv);
+ if (fr->cutoff_scheme == ecutsGROUP)
+ {
+ /* Here we resize to more than necessary and shrink later */
+ dd_resize_state(state, f, home_pos_at + ncg_recv*MAX_CGCGSIZE);
+ }
+
/* Process the received charge groups */
buf_pos = 0;
for (cg = 0; cg < ncg_recv; cg++)
/* Check which direction this cg should go */
for (d2 = d+1; (d2 < dd->ndim && mc == -1); d2++)
{
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
/* The cell boundaries for dimension d2 are not equal
* for each cell row of the lower dimension(s),
dd->index_gl[home_pos_cg] = comm->buf_int[cg*DD_CGIBS];
dd->cgindex[home_pos_cg+1] = dd->cgindex[home_pos_cg] + nrcg;
/* Copy the state from the buffer */
- dd_check_alloc_ncg(fr, state, f, home_pos_cg+1);
if (fr->cutoff_scheme == ecutsGROUP)
{
cg_cm = fr->cg_cm;
comm->bLocalCG[dd->index_gl[home_pos_cg]] = TRUE;
}
- if (home_pos_at+nrcg > state->nalloc)
- {
- dd_realloc_state(state, f, home_pos_at+nrcg);
- }
for (i = 0; i < nrcg; i++)
{
copy_rvec(comm->vbuf.v[buf_pos++],
dd->ncg_home = home_pos_cg;
dd->nat_home = home_pos_at;
+ if (fr->cutoff_scheme == ecutsGROUP && !bCompact)
+ {
+ /* We overallocated before, we need to set the right size here */
+ dd_resize_state(state, f, dd->nat_home);
+ }
+
if (debug)
{
fprintf(debug,
}
}
-void dd_cycles_add(gmx_domdec_t *dd, float cycles, int ddCycl)
+void dd_cycles_add(const gmx_domdec_t *dd, float cycles, int ddCycl)
{
/* Note that the cycles value can be incorrect, either 0 or some
* extremely large value, when our thread migrated to another core
* for the normal loops and again half it for water loops.
*/
name = nrnb_str(i);
- if (strstr(name, "W3") != NULL || strstr(name, "W4") != NULL)
+ if (strstr(name, "W3") != nullptr || strstr(name, "W4") != nullptr)
{
sum += nrnb->n[i]*0.25*cost_nrnb(i);
}
for (i = eNR_NBKERNEL_FREE_ENERGY; i <= eNR_NB14; i++)
{
name = nrnb_str(i);
- if (strstr(name, "W3") != NULL || strstr(name, "W4") != NULL)
+ if (strstr(name, "W3") != nullptr || strstr(name, "W4") != nullptr)
{
sum += nrnb->n[i]*cost_nrnb(i);
}
{
gmx_domdec_comm_t *comm;
domdec_load_t *load;
- domdec_root_t *root = NULL;
+ domdec_root_t *root = nullptr;
int d, dim, i, pos;
float cell_frac = 0, sbuf[DD_NLOAD_MAX];
gmx_bool bSepPME;
(dd->ci[dd->dim[d+1]] == 0 && dd->ci[dd->dim[dd->ndim-1]] == 0))
{
load = &comm->load[d];
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
cell_frac = comm->cell_f1[d] - comm->cell_f0[d];
}
{
sbuf[pos++] = dd_force_load(comm);
sbuf[pos++] = sbuf[0];
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
sbuf[pos++] = sbuf[0];
sbuf[pos++] = cell_frac;
{
sbuf[pos++] = comm->load[d+1].sum;
sbuf[pos++] = comm->load[d+1].max;
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
sbuf[pos++] = comm->load[d+1].sum_m;
sbuf[pos++] = comm->load[d+1].cvol_min*cell_frac;
if (dd->ci[dim] == dd->master_ci[dim])
{
/* We are the root, process this row */
- if (dlbIsOn(comm))
+ if (isDlbOn(comm))
{
root = comm->root[d];
}
load->sum += load->load[pos++];
load->max = std::max(load->max, load->load[pos]);
pos++;
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
if (root->bLimited)
{
pos++;
}
}
- if (dlbIsOn(comm) && root->bLimited)
+ if (isDlbOn(comm) && root->bLimited)
{
load->sum_m *= dd->nc[dim];
load->flags |= (1<<d);
comm->load_step += comm->cycl[ddCyclStep];
comm->load_sum += comm->load[0].sum;
comm->load_max += comm->load[0].max;
- if (dlbIsOn(comm))
+ if (isDlbOn(comm))
{
for (d = 0; d < dd->ndim; d++)
{
}
}
+static float dd_force_load_fraction(gmx_domdec_t *dd)
+{
+ /* Return the relative performance loss on the total run time
+ * due to the force calculation load imbalance.
+ */
+ if (dd->comm->nload > 0 && dd->comm->load_step > 0)
+ {
+ return dd->comm->load_sum/(dd->comm->load_step*dd->nnodes);
+ }
+ else
+ {
+ return 0;
+ }
+}
+
static float dd_force_imb_perf_loss(gmx_domdec_t *dd)
{
/* Return the relative performance loss on the total run time
static void print_dd_load_av(FILE *fplog, gmx_domdec_t *dd)
{
- char buf[STRLEN];
- int npp, npme, nnodes, d, limp;
- float imbal, pme_f_ratio, lossf = 0, lossp = 0;
- gmx_bool bLim;
- gmx_domdec_comm_t *comm;
+ gmx_domdec_comm_t *comm = dd->comm;
- comm = dd->comm;
- if (DDMASTER(dd) && comm->nload > 0)
- {
- npp = dd->nnodes;
- npme = (dd->pme_nodeid >= 0) ? comm->npmenodes : 0;
- nnodes = npp + npme;
- if (dd->nnodes > 1 && comm->load_sum > 0)
- {
- imbal = comm->load_max*npp/comm->load_sum - 1;
- lossf = dd_force_imb_perf_loss(dd);
- sprintf(buf, " Average load imbalance: %.1f %%\n", imbal*100);
- fprintf(fplog, "%s", buf);
- fprintf(stderr, "\n");
- fprintf(stderr, "%s", buf);
- sprintf(buf, " Part of the total run time spent waiting due to load imbalance: %.1f %%\n", lossf*100);
- fprintf(fplog, "%s", buf);
- fprintf(stderr, "%s", buf);
- }
- bLim = FALSE;
- if (dlbIsOn(comm))
- {
- sprintf(buf, " Steps where the load balancing was limited by -rdd, -rcon and/or -dds:");
- for (d = 0; d < dd->ndim; d++)
- {
- limp = (200*comm->load_lim[d]+1)/(2*comm->nload);
- sprintf(buf+strlen(buf), " %c %d %%", dim2char(dd->dim[d]), limp);
- if (limp >= 50)
- {
- bLim = TRUE;
- }
- }
- sprintf(buf+strlen(buf), "\n");
- fprintf(fplog, "%s", buf);
- fprintf(stderr, "%s", buf);
+ /* Only the master rank prints loads and only if we measured loads */
+ if (!DDMASTER(dd) || comm->nload == 0)
+ {
+ return;
+ }
+
+ char buf[STRLEN];
+ int numPpRanks = dd->nnodes;
+ int numPmeRanks = (dd->pme_nodeid >= 0) ? comm->npmenodes : 0;
+ int numRanks = numPpRanks + numPmeRanks;
+ float lossFraction = 0;
+
+ /* Print the average load imbalance and performance loss */
+ if (dd->nnodes > 1 && comm->load_sum > 0)
+ {
+ float imbalance = comm->load_max*numPpRanks/comm->load_sum - 1;
+ lossFraction = dd_force_imb_perf_loss(dd);
+
+ std::string msg = "\n Dynamic load balancing report:\n";
+ std::string dlbStateStr = "";
+
+ switch (dd->comm->dlbState)
+ {
+ case edlbsOffUser:
+ dlbStateStr = "DLB was off during the run per user request.";
+ break;
+ case edlbsOffForever:
+ /* Currectly this can happen due to performance loss observed, cell size
+ * limitations or incompatibility with other settings observed during
+ * determineInitialDlbState(). */
+ dlbStateStr = "DLB got disabled because it was unsuitable to use.";
+ break;
+ case edlbsOffCanTurnOn:
+ dlbStateStr = "DLB was off during the run due to low measured imbalance.";
+ break;
+ case edlbsOffTemporarilyLocked:
+ dlbStateStr = "DLB was locked at the end of the run due to unfinished PP-PME balancing.";
+ break;
+ case edlbsOnCanTurnOff:
+ dlbStateStr = "DLB was turned on during the run due to measured imbalance.";
+ break;
+ case edlbsOnUser:
+ dlbStateStr = "DLB was permanently on during the run per user request.";
+ break;
+ default:
+ GMX_ASSERT(false, "Undocumented DLB state");
}
- if (npme > 0 && comm->load_mdf > 0 && comm->load_step > 0)
+
+ msg += " " + dlbStateStr + "\n";
+ msg += gmx::formatString(" Average load imbalance: %.1f%%.\n", imbalance*100);
+ msg += gmx::formatString(" The balanceable part of the MD step is %d%%, load imbalance is computed from this.\n",
+ static_cast<int>(dd_force_load_fraction(dd)*100 + 0.5));
+ msg += gmx::formatString(" Part of the total run time spent waiting due to load imbalance: %.1f%%.\n",
+ lossFraction*100);
+ fprintf(fplog, "%s", msg.c_str());
+ fprintf(stderr, "%s", msg.c_str());
+ }
+
+ /* Print during what percentage of steps the load balancing was limited */
+ bool dlbWasLimited = false;
+ if (isDlbOn(comm))
+ {
+ sprintf(buf, " Steps where the load balancing was limited by -rdd, -rcon and/or -dds:");
+ for (int d = 0; d < dd->ndim; d++)
{
- pme_f_ratio = comm->load_pme/comm->load_mdf;
- lossp = (comm->load_pme - comm->load_mdf)/comm->load_step;
- if (lossp <= 0)
+ int limitPercentage = (200*comm->load_lim[d] + 1)/(2*comm->nload);
+ sprintf(buf+strlen(buf), " %c %d %%",
+ dim2char(dd->dim[d]), limitPercentage);
+ if (limitPercentage >= 50)
{
- lossp *= (float)npme/(float)nnodes;
+ dlbWasLimited = true;
}
- else
- {
- lossp *= (float)npp/(float)nnodes;
- }
- sprintf(buf, " Average PME mesh/force load: %5.3f\n", pme_f_ratio);
- fprintf(fplog, "%s", buf);
- fprintf(stderr, "%s", buf);
- sprintf(buf, " Part of the total run time spent waiting due to PP/PME imbalance: %.1f %%\n", fabs(lossp)*100);
- fprintf(fplog, "%s", buf);
- fprintf(stderr, "%s", buf);
}
- fprintf(fplog, "\n");
- fprintf(stderr, "\n");
+ sprintf(buf + strlen(buf), "\n");
+ fprintf(fplog, "%s", buf);
+ fprintf(stderr, "%s", buf);
+ }
- if (lossf >= DD_PERF_LOSS_WARN)
+ /* Print the performance loss due to separate PME - PP rank imbalance */
+ float lossFractionPme = 0;
+ if (numPmeRanks > 0 && comm->load_mdf > 0 && comm->load_step > 0)
+ {
+ float pmeForceRatio = comm->load_pme/comm->load_mdf;
+ lossFractionPme = (comm->load_pme - comm->load_mdf)/comm->load_step;
+ if (lossFractionPme <= 0)
{
- sprintf(buf,
- "NOTE: %.1f %% of the available CPU time was lost due to load imbalance\n"
- " in the domain decomposition.\n", lossf*100);
- if (!dlbIsOn(comm))
- {
- sprintf(buf+strlen(buf), " You might want to use dynamic load balancing (option -dlb.)\n");
- }
- else if (bLim)
- {
- sprintf(buf+strlen(buf), " You might want to decrease the cell size limit (options -rdd, -rcon and/or -dds).\n");
- }
- fprintf(fplog, "%s\n", buf);
- fprintf(stderr, "%s\n", buf);
+ lossFractionPme *= numPmeRanks/static_cast<float>(numRanks);
+ }
+ else
+ {
+ lossFractionPme *= numPpRanks/static_cast<float>(numRanks);
+ }
+ sprintf(buf, " Average PME mesh/force load: %5.3f\n", pmeForceRatio);
+ fprintf(fplog, "%s", buf);
+ fprintf(stderr, "%s", buf);
+ sprintf(buf, " Part of the total run time spent waiting due to PP/PME imbalance: %.1f %%\n", fabs(lossFractionPme)*100);
+ fprintf(fplog, "%s", buf);
+ fprintf(stderr, "%s", buf);
+ }
+ fprintf(fplog, "\n");
+ fprintf(stderr, "\n");
+
+ if (lossFraction >= DD_PERF_LOSS_WARN)
+ {
+ sprintf(buf,
+ "NOTE: %.1f %% of the available CPU time was lost due to load imbalance\n"
+ " in the domain decomposition.\n", lossFraction*100);
+ if (!isDlbOn(comm))
+ {
+ sprintf(buf+strlen(buf), " You might want to use dynamic load balancing (option -dlb.)\n");
}
- if (npme > 0 && fabs(lossp) >= DD_PERF_LOSS_WARN)
+ else if (dlbWasLimited)
{
- sprintf(buf,
- "NOTE: %.1f %% performance was lost because the PME ranks\n"
- " had %s work to do than the PP ranks.\n"
- " You might want to %s the number of PME ranks\n"
- " or %s the cut-off and the grid spacing.\n",
- fabs(lossp*100),
- (lossp < 0) ? "less" : "more",
- (lossp < 0) ? "decrease" : "increase",
- (lossp < 0) ? "decrease" : "increase");
- fprintf(fplog, "%s\n", buf);
- fprintf(stderr, "%s\n", buf);
+ sprintf(buf+strlen(buf), " You might want to decrease the cell size limit (options -rdd, -rcon and/or -dds).\n");
}
+ fprintf(fplog, "%s\n", buf);
+ fprintf(stderr, "%s\n", buf);
+ }
+ if (numPmeRanks > 0 && fabs(lossFractionPme) >= DD_PERF_LOSS_WARN)
+ {
+ sprintf(buf,
+ "NOTE: %.1f %% performance was lost because the PME ranks\n"
+ " had %s work to do than the PP ranks.\n"
+ " You might want to %s the number of PME ranks\n"
+ " or %s the cut-off and the grid spacing.\n",
+ fabs(lossFractionPme*100),
+ (lossFractionPme < 0) ? "less" : "more",
+ (lossFractionPme < 0) ? "decrease" : "increase",
+ (lossFractionPme < 0) ? "decrease" : "increase");
+ fprintf(fplog, "%s\n", buf);
+ fprintf(stderr, "%s\n", buf);
}
}
fprintf(fplog, "\n");
}
fprintf(fplog, "DD step %s", gmx_step_str(step, buf));
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
fprintf(fplog, " vol min/aver %5.3f%c",
dd_vol_min(dd), flags ? '!' : ' ');
static void dd_print_load_verbose(gmx_domdec_t *dd)
{
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
fprintf(stderr, "vol %4.2f%c ",
dd_vol_min(dd), dd_load_flags(dd) ? '!' : ' ');
if (bPartOfGroup)
{
dd->comm->mpi_comm_load[dim_ind] = c_row;
- if (dd->comm->dlbState != edlbsOffForever)
+ if (!isDlbDisabled(dd->comm))
{
if (dd->ci[dim] == dd->master_ci[dim])
{
}
#endif
-void dd_setup_dlb_resource_sharing(t_commrec gmx_unused *cr,
- const gmx_hw_info_t gmx_unused *hwinfo,
- const gmx_hw_opt_t gmx_unused *hw_opt)
+void dd_setup_dlb_resource_sharing(t_commrec *cr,
+ int gpu_id)
{
#if GMX_MPI
int physicalnode_id_hash;
- int gpu_id;
gmx_domdec_t *dd;
MPI_Comm mpi_comm_pp_physicalnode;
- if (!(cr->duty & DUTY_PP) || hw_opt->gpu_opt.n_dev_use == 0)
+ if (!(cr->duty & DUTY_PP) || gpu_id < 0)
{
- /* Only PP nodes (currently) use GPUs.
- * If we don't have GPUs, there are no resources to share.
+ /* Only ranks with short-ranged tasks (currently) use GPUs.
+ * If we don't have GPUs assigned, there are no resources to share.
*/
return;
}
physicalnode_id_hash = gmx_physicalnode_id_hash();
- gpu_id = get_gpu_device_id(&hwinfo->gpu_info, &hw_opt->gpu_opt, cr->rank_pp_intranode);
-
dd = cr->dd;
if (debug)
{
MPI_Comm_free(&dd->comm->mpi_comm_gpu_shared);
}
+#else
+ GMX_UNUSED_VALUE(cr);
+ GMX_UNUSED_VALUE(gpu_id);
#endif
}
}
}
- if (dd->comm->dlbState != edlbsOffForever)
+ if (!isDlbDisabled(dd->comm))
{
snew(dd->comm->root, dd->ndim);
}
if (dd->nnodes <= GMX_DD_NNODES_SENDRECV)
{
- ma->vbuf = NULL;
+ ma->vbuf = nullptr;
}
else
{
}
static void split_communicator(FILE *fplog, t_commrec *cr, gmx_domdec_t *dd,
- int gmx_unused dd_rank_order,
+ DdRankOrder gmx_unused rankOrder,
int gmx_unused reorder)
{
gmx_domdec_comm_t *comm;
}
else
{
- switch (dd_rank_order)
+ switch (rankOrder)
{
- case ddrankorderPP_PME:
+ case DdRankOrder::pp_pme:
if (fplog)
{
fprintf(fplog, "Order of the ranks: PP first, PME last\n");
}
break;
- case ddrankorderINTERLEAVE:
+ case DdRankOrder::interleave:
/* Interleave the PP-only and PME-only ranks */
if (fplog)
{
}
comm->pmenodes = dd_interleaved_pme_ranks(dd);
break;
- case ddrankorderCARTESIAN:
+ case DdRankOrder::cartesian:
break;
default:
- gmx_fatal(FARGS, "Unknown dd_rank_order=%d", dd_rank_order);
+ gmx_fatal(FARGS, "Invalid ddRankOrder=%d", static_cast<int>(rankOrder));
}
if (dd_simnode2pmenode(dd, cr, cr->sim_nodeid) == -1)
/*! \brief Generates the MPI communicators for domain decomposition */
static void make_dd_communicators(FILE *fplog, t_commrec *cr,
- gmx_domdec_t *dd, int dd_rank_order)
+ gmx_domdec_t *dd, DdRankOrder ddRankOrder)
{
gmx_domdec_comm_t *comm;
int CartReorder;
copy_ivec(dd->nc, comm->ntot);
- comm->bCartesianPP = (dd_rank_order == ddrankorderCARTESIAN);
+ comm->bCartesianPP = (ddRankOrder == DdRankOrder::cartesian);
comm->bCartesianPP_PME = FALSE;
/* Reorder the nodes by default. This might change the MPI ranks.
* Real reordering is only supported on very few architectures,
* Blue Gene is one of them.
*/
- CartReorder = (getenv("GMX_NO_CART_REORDER") == NULL);
+ CartReorder = (getenv("GMX_NO_CART_REORDER") == nullptr);
if (cr->npmenodes > 0)
{
/* Split the communicator into a PP and PME part */
- split_communicator(fplog, cr, dd, dd_rank_order, CartReorder);
+ split_communicator(fplog, cr, dd, ddRankOrder, CartReorder);
if (comm->bCartesianPP_PME)
{
/* We (possibly) reordered the nodes in split_communicator,
int i, n;
double dbl;
- slb_frac = NULL;
- if (nc > 1 && size_string != NULL)
+ slb_frac = nullptr;
+ if (nc > 1 && size_string != nullptr)
{
if (fplog)
{
return r;
}
-static int check_dlb_support(FILE *fplog, t_commrec *cr,
- const char *dlb_opt, gmx_bool bRecordLoad,
- unsigned long Flags, const t_inputrec *ir)
+/*! \brief Depending on the DLB initial value return the DLB switched off state or issue an error.
+ */
+static int forceDlbOffOrBail(int cmdlineDlbState,
+ const std::string &reasonStr,
+ t_commrec *cr,
+ FILE *fplog)
{
- int dlbState = -1;
- char buf[STRLEN];
+ std::string dlbNotSupportedErr = "Dynamic load balancing requested, but ";
+ std::string dlbDisableNote = "NOTE: disabling dynamic load balancing as ";
+
+ if (cmdlineDlbState == edlbsOnUser)
+ {
+ gmx_fatal(FARGS, (dlbNotSupportedErr + reasonStr).c_str());
+ }
+ else if (cmdlineDlbState == edlbsOffCanTurnOn)
+ {
+ dd_warning(cr, fplog, (dlbDisableNote + reasonStr + "\n").c_str());
+ }
+ return edlbsOffForever;
+}
+
+/*! \brief Return the dynamic load balancer's initial state based on initial conditions and user inputs.
+ *
+ * This function parses the parameters of "-dlb" command line option setting
+ * corresponding state values. Then it checks the consistency of the determined
+ * state with other run parameters and settings. As a result, the initial state
+ * may be altered or an error may be thrown if incompatibility of options is detected.
+ *
+ * \param [in] fplog Pointer to mdrun log file.
+ * \param [in] cr Pointer to MPI communication object.
+ * \param [in] dlbOption Enum value for the DLB option.
+ * \param [in] bRecordLoad True if the load balancer is recording load information.
+ * \param [in] mdrunOptions Options for mdrun.
+ * \param [in] ir Pointer mdrun to input parameters.
+ * \returns DLB initial/startup state.
+ */
+static int determineInitialDlbState(FILE *fplog, t_commrec *cr,
+ DlbOption dlbOption, gmx_bool bRecordLoad,
+ const MdrunOptions &mdrunOptions,
+ const t_inputrec *ir)
+{
+ int dlbState = edlbsOffCanTurnOn;
- switch (dlb_opt[0])
+ switch (dlbOption)
{
- case 'a': dlbState = edlbsOffCanTurnOn; break;
- case 'n': dlbState = edlbsOffForever; break;
- case 'y': dlbState = edlbsOnForever; break;
- default: gmx_incons("Unknown dlb_opt");
+ case DlbOption::turnOnWhenUseful: dlbState = edlbsOffCanTurnOn; break;
+ case DlbOption::no: dlbState = edlbsOffUser; break;
+ case DlbOption::yes: dlbState = edlbsOnUser; break;
+ default: gmx_incons("Invalid dlbOption enum value");
}
- if (Flags & MD_RERUN)
+ /* Reruns don't support DLB: bail or override auto mode */
+ if (mdrunOptions.rerun)
{
- return edlbsOffForever;
+ std::string reasonStr = "it is not supported in reruns.";
+ return forceDlbOffOrBail(dlbState, reasonStr, cr, fplog);
}
+ /* Unsupported integrators */
if (!EI_DYNAMICS(ir->eI))
{
- if (dlbState == edlbsOnForever)
- {
- sprintf(buf, "NOTE: dynamic load balancing is only supported with dynamics, not with integrator '%s'\n", EI(ir->eI));
- dd_warning(cr, fplog, buf);
- }
-
- return edlbsOffForever;
+ auto reasonStr = gmx::formatString("it is only supported with dynamics, not with integrator '%s'.", EI(ir->eI));
+ return forceDlbOffOrBail(dlbState, reasonStr, cr, fplog);
}
+ /* Without cycle counters we can't time work to balance on */
if (!bRecordLoad)
{
- dd_warning(cr, fplog, "NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use dynamic load balancing.\n");
- return edlbsOffForever;
+ std::string reasonStr = "cycle counters unsupported or not enabled in the operating system kernel.";
+ return forceDlbOffOrBail(dlbState, reasonStr, cr, fplog);
}
- if (Flags & MD_REPRODUCIBLE)
+ if (mdrunOptions.reproducible)
{
+ std::string reasonStr = "you started a reproducible run.";
switch (dlbState)
{
+ case edlbsOffUser:
+ break;
case edlbsOffForever:
+ GMX_RELEASE_ASSERT(false, "edlbsOffForever is not a valid initial state");
break;
case edlbsOffCanTurnOn:
+ return forceDlbOffOrBail(dlbState, reasonStr, cr, fplog);
+ break;
case edlbsOnCanTurnOff:
- dd_warning(cr, fplog, "NOTE: reproducibility requested, will not use dynamic load balancing\n");
- dlbState = edlbsOffForever;
+ GMX_RELEASE_ASSERT(false, "edlbsOffCanTurnOff is not a valid initial state");
break;
- case edlbsOnForever:
- dd_warning(cr, fplog, "WARNING: reproducibility requested with dynamic load balancing, the simulation will NOT be binary reproducible\n");
+ case edlbsOnUser:
+ return forceDlbOffOrBail(dlbState, reasonStr + " In load balanced runs binary reproducibility cannot be ensured.", cr, fplog);
break;
default:
gmx_fatal(FARGS, "Death horror: undefined case (%d) for load balancing choice", dlbState);
int dim;
dd->ndim = 0;
- if (getenv("GMX_DD_ORDER_ZYX") != NULL)
+ if (getenv("GMX_DD_ORDER_ZYX") != nullptr)
{
/* Decomposition order z,y,x */
if (fplog)
}
comm->nalloc_int = 0;
- comm->buf_int = NULL;
+ comm->buf_int = nullptr;
vec_rvec_init(&comm->vbuf);
comm->load_mdf = 0;
comm->load_pme = 0;
+ /* This should be replaced by a unique pointer */
+ comm->balanceRegion = ddBalanceRegionAllocate();
+
return comm;
}
/*! \brief Set the cell size and interaction limits, as well as the DD grid */
static void set_dd_limits_and_grid(FILE *fplog, t_commrec *cr, gmx_domdec_t *dd,
- unsigned long Flags,
- ivec nc, int nPmeRanks,
- real comm_distance_min, real rconstr,
- const char *dlb_opt, real dlb_scale,
- const char *sizex, const char *sizey, const char *sizez,
+ const DomdecOptions &options,
+ const MdrunOptions &mdrunOptions,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
matrix box, const rvec *x,
dd->bScrewPBC = (ir->ePBC == epbcSCREW);
dd->pme_recv_f_alloc = 0;
- dd->pme_recv_f_buf = NULL;
+ dd->pme_recv_f_buf = nullptr;
/* Initialize to GPU share count to 0, might change later */
comm->nrank_gpu_shared = 0;
- comm->dlbState = check_dlb_support(fplog, cr, dlb_opt, comm->bRecordLoad, Flags, ir);
+ comm->dlbState = determineInitialDlbState(fplog, cr, options.dlbOption, comm->bRecordLoad, mdrunOptions, ir);
dd_dlb_set_should_check_whether_to_turn_dlb_on(dd, TRUE);
/* To consider turning DLB on after 2*nstlist steps we need to check
* at partitioning count 3. Thus we need to increase the first count by 2.
if (comm->bInterCGBondeds)
{
- if (comm_distance_min > 0)
+ if (options.minimumCommunicationRange > 0)
{
- comm->cutoff_mbody = comm_distance_min;
- if (Flags & MD_DDBONDCOMM)
+ comm->cutoff_mbody = options.minimumCommunicationRange;
+ if (options.useBondedCommunication)
{
comm->bBondComm = (comm->cutoff_mbody > comm->cutoff);
}
if (MASTER(cr))
{
dd_bonded_cg_distance(fplog, mtop, ir, x, box,
- Flags & MD_DDBONDCHECK, &r_2b, &r_mb);
+ options.checkBondedInteractions,
+ &r_2b, &r_mb);
}
gmx_bcast(sizeof(r_2b), &r_2b, cr);
gmx_bcast(sizeof(r_mb), &r_mb, cr);
/* We use an initial margin of 10% for the minimum cell size,
* except when we are just below the non-bonded cut-off.
*/
- if (Flags & MD_DDBONDCOMM)
+ if (options.useBondedCommunication)
{
if (std::max(r_2b, r_mb) > comm->cutoff)
{
comm->cellsize_limit = std::max(comm->cellsize_limit, r_bonded_limit);
}
- if (dd->bInterCGcons && rconstr <= 0)
+ real rconstr = 0;
+ if (dd->bInterCGcons && options.constraintCommunicationRange <= 0)
{
/* There is a cell size limit due to the constraints (P-LINCS) */
rconstr = constr_r_max(fplog, mtop, ir);
}
}
}
- else if (rconstr > 0 && fplog)
+ else if (options.constraintCommunicationRange > 0 && fplog)
{
/* Here we do not check for dd->bInterCGcons,
* because one can also set a cell size limit for virtual sites only
*/
fprintf(fplog,
"User supplied maximum distance required for P-LINCS: %.3f nm\n",
- rconstr);
+ options.constraintCommunicationRange);
+ rconstr = options.constraintCommunicationRange;
}
comm->cellsize_limit = std::max(comm->cellsize_limit, rconstr);
comm->cgs_gl = gmx_mtop_global_cgs(mtop);
- if (nc[XX] > 0)
+ if (options.numCells[XX] > 0)
{
- copy_ivec(nc, dd->nc);
+ copy_ivec(options.numCells, dd->nc);
set_dd_dim(fplog, dd);
set_ddbox_cr(cr, &dd->nc, ir, box, &comm->cgs_gl, x, ddbox);
- if (nPmeRanks >= 0)
+ if (options.numPmeRanks >= 0)
{
- cr->npmenodes = nPmeRanks;
+ cr->npmenodes = options.numPmeRanks;
}
else
{
}
else
{
- set_ddbox_cr(cr, NULL, ir, box, &comm->cgs_gl, x, ddbox);
+ set_ddbox_cr(cr, nullptr, ir, box, &comm->cgs_gl, x, ddbox);
/* We need to choose the optimal DD grid and possibly PME nodes */
real limit =
dd_choose_grid(fplog, cr, dd, ir, mtop, box, ddbox,
- nPmeRanks,
- comm->dlbState != edlbsOffForever, dlb_scale,
+ options.numPmeRanks,
+ !isDlbDisabled(comm),
+ options.dlbScaling,
comm->cellsize_limit, comm->cutoff,
comm->bInterCGBondeds);
gmx_bool bC = (dd->bInterCGcons && rconstr > r_bonded_limit);
sprintf(buf, "Change the number of ranks or mdrun option %s%s%s",
!bC ? "-rdd" : "-rcon",
- comm->dlbState != edlbsOffForever ? " or -dds" : "",
+ comm->dlbState != edlbsOffUser ? " or -dds" : "",
bC ? " or your LINCS settings" : "");
gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
*/
if (dd->ndim >= 2 && dd->dim[0] == XX && dd->dim[1] == YY &&
comm->npmenodes > dd->nc[XX] && comm->npmenodes % dd->nc[XX] == 0 &&
- getenv("GMX_PMEONEDD") == NULL)
+ getenv("GMX_PMEONEDD") == nullptr)
{
comm->npmedecompdim = 2;
comm->npmenodes_x = dd->nc[XX];
*npme_y = comm->npmenodes_y;
snew(comm->slb_frac, DIM);
- if (comm->dlbState == edlbsOffForever)
+ if (isDlbDisabled(comm))
{
- comm->slb_frac[XX] = get_slb_frac(fplog, "x", dd->nc[XX], sizex);
- comm->slb_frac[YY] = get_slb_frac(fplog, "y", dd->nc[YY], sizey);
- comm->slb_frac[ZZ] = get_slb_frac(fplog, "z", dd->nc[ZZ], sizez);
+ comm->slb_frac[XX] = get_slb_frac(fplog, "x", dd->nc[XX], options.cellSizeX);
+ comm->slb_frac[YY] = get_slb_frac(fplog, "y", dd->nc[YY], options.cellSizeY);
+ comm->slb_frac[ZZ] = get_slb_frac(fplog, "z", dd->nc[ZZ], options.cellSizeZ);
}
if (comm->bInterCGBondeds && comm->cutoff_mbody == 0)
{
- if (comm->bBondComm || comm->dlbState != edlbsOffForever)
+ if (comm->bBondComm || !isDlbDisabled(comm))
{
/* Set the bonded communication distance to halfway
* the minimum and the maximum,
*/
real acs = average_cellsize_min(dd, ddbox);
comm->cutoff_mbody = 0.5*(r_bonded + acs);
- if (comm->dlbState != edlbsOffForever)
+ if (!isDlbDisabled(comm))
{
/* Check if this does not limit the scaling */
- comm->cutoff_mbody = std::min(comm->cutoff_mbody, dlb_scale*acs);
+ comm->cutoff_mbody = std::min(comm->cutoff_mbody,
+ options.dlbScaling*acs);
}
if (!comm->bBondComm)
{
cellsize_min = std::min(cellsize_min, comm->cellsize_min[dd->dim[d]]);
}
+ /* Turn off DLB if we're too close to the cell size limit. */
if (cellsize_min < comm->cellsize_limit*1.05)
{
- char buf[STRLEN];
- sprintf(buf, "step %" GMX_PRId64 " Measured %.1f %% performance loss due to load imbalance, but the minimum cell size is smaller than 1.05 times the cell size limit. Will no longer try dynamic load balancing.\n", step, dd_force_imb_perf_loss(dd)*100);
- dd_warning(cr, fplog, buf);
+ auto str = gmx::formatString("step %" GMX_PRId64 " Measured %.1f %% performance loss due to load imbalance, "
+ "but the minimum cell size is smaller than 1.05 times the cell size limit."
+ "Will no longer try dynamic load balancing.\n", step, dd_force_imb_perf_loss(dd)*100);
+ dd_warning(cr, fplog, str.c_str());
- /* Change DLB from "auto" to "no". */
comm->dlbState = edlbsOffForever;
-
return;
}
else
{
/* Only communicate atoms based on cut-off */
- comm->cglink = NULL;
- comm->bLocalCG = NULL;
+ comm->cglink = nullptr;
+ comm->bLocalCG = nullptr;
}
}
real limit, shrink;
char buf[64];
- if (fplog == NULL)
+ if (fplog == nullptr)
{
return;
}
std::max(comm->cutoff, comm->cutoff_mbody));
fprintf(fplog, "%40s %-7s %6.3f nm\n",
"multi-body bonded interactions", "(-rdd)",
- (comm->bBondComm || dlbIsOn(dd->comm)) ? comm->cutoff_mbody : std::min(comm->cutoff, limit));
+ (comm->bBondComm || isDlbOn(dd->comm)) ? comm->cutoff_mbody : std::min(comm->cutoff, limit));
}
if (bInterCGVsites)
{
{
comm->cutoff_mbody = std::min(comm->cutoff, comm->cellsize_limit);
}
- if (dlbIsOn(comm))
+ if (isDlbOn(comm))
{
set_dlb_limits(dd);
}
{
fprintf(debug, "The DD cut-off is %f\n", comm->cutoff);
}
- if (comm->dlbState != edlbsOffForever)
+ if (!isDlbDisabled(comm))
{
set_cell_limits_dlb(dd, dlb_scale, ir, ddbox);
}
- print_dd_settings(fplog, dd, mtop, ir, dlbIsOn(comm), dlb_scale, ddbox);
+ print_dd_settings(fplog, dd, mtop, ir, isDlbOn(comm), dlb_scale, ddbox);
if (comm->dlbState == edlbsOffCanTurnOn)
{
if (fplog)
}
}
+DomdecOptions::DomdecOptions() :
+ checkBondedInteractions(TRUE),
+ useBondedCommunication(TRUE),
+ numPmeRanks(-1),
+ rankOrder(DdRankOrder::pp_pme),
+ minimumCommunicationRange(0),
+ constraintCommunicationRange(0),
+ dlbOption(DlbOption::turnOnWhenUseful),
+ dlbScaling(0.8),
+ cellSizeX(nullptr),
+ cellSizeY(nullptr),
+ cellSizeZ(nullptr)
+{
+ clear_ivec(numCells);
+}
+
gmx_domdec_t *init_domain_decomposition(FILE *fplog, t_commrec *cr,
- unsigned long Flags,
- ivec nc, int nPmeRanks,
- int dd_rank_order,
- real comm_distance_min, real rconstr,
- const char *dlb_opt, real dlb_scale,
- const char *sizex, const char *sizey, const char *sizez,
+ const DomdecOptions &options,
+ const MdrunOptions &mdrunOptions,
const gmx_mtop_t *mtop,
const t_inputrec *ir,
matrix box, rvec *x,
set_dd_envvar_options(fplog, dd, cr->nodeid);
- set_dd_limits_and_grid(fplog, cr, dd, Flags,
- nc, nPmeRanks,
- comm_distance_min, rconstr,
- dlb_opt, dlb_scale,
- sizex, sizey, sizez,
+ set_dd_limits_and_grid(fplog, cr, dd, options, mdrunOptions,
mtop, ir,
box, x,
ddbox,
npme_x, npme_y);
- make_dd_communicators(fplog, cr, dd, dd_rank_order);
+ make_dd_communicators(fplog, cr, dd, options.rankOrder);
if (cr->duty & DUTY_PP)
{
- set_ddgrid_parameters(fplog, dd, dlb_scale, mtop, ir, ddbox);
+ set_ddgrid_parameters(fplog, dd, options.dlbScaling, mtop, ir, ddbox);
setup_neighbor_relations(dd);
}
dd = cr->dd;
set_ddbox(dd, FALSE, cr, ir, state->box,
- TRUE, &dd->comm->cgs_gl, state->x, &ddbox);
+ TRUE, &dd->comm->cgs_gl, as_rvec_array(state->x.data()), &ddbox);
LocallyLimited = 0;
np = 1 + (int)(cutoff_req*inv_cell_size*ddbox.skew_fac[dim]);
- if (dd->comm->dlbState != edlbsOffForever && dim < ddbox.npbcdim &&
- dd->comm->cd[d].np_dlb > 0)
+ if (!isDlbDisabled(dd->comm) && (dim < ddbox.npbcdim) && (dd->comm->cd[d].np_dlb > 0))
{
if (np > dd->comm->cd[d].np_dlb)
{
}
}
- if (dd->comm->dlbState != edlbsOffForever)
+ if (!isDlbDisabled(dd->comm))
{
/* If DLB is not active yet, we don't need to check the grid jumps.
* Actually we shouldn't, because then the grid jump data is not set.
*/
- if (dlbIsOn(dd->comm) &&
+ if (isDlbOn(dd->comm) &&
check_grid_jump(0, dd, cutoff_req, &ddbox, FALSE))
{
LocallyLimited = 1;
gmx_bool dd_dlb_is_on(const gmx_domdec_t *dd)
{
- return dlbIsOn(dd->comm);
+ return isDlbOn(dd->comm);
}
gmx_bool dd_dlb_is_locked(const gmx_domdec_t *dd)
c->c[1][0] = comm->cell_x0[dim1];
/* All rows can see this row */
c->c[1][1] = comm->cell_x0[dim1];
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
c->c[1][1] = std::max(comm->cell_x0[dim1], comm->zone_d1[1].mch0);
if (bDistMB)
{
c->c[2][j] = comm->cell_x0[dim2];
}
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
/* Use the maximum of the i-cells that see a j-cell */
for (i = 0; i < zones->nizone; i++)
*/
c->cr1[0] = comm->cell_x1[dim1];
c->cr1[3] = comm->cell_x1[dim1];
- if (dlbIsOn(dd->comm))
+ if (isDlbOn(dd->comm))
{
c->cr1[0] = std::max(comm->cell_x1[dim1], comm->zone_d1[1].mch1);
if (bDistMB)
static void setup_dd_communication(gmx_domdec_t *dd,
matrix box, gmx_ddbox_t *ddbox,
- t_forcerec *fr, t_state *state, rvec **f)
+ t_forcerec *fr,
+ t_state *state, PaddedRVecVector *f)
{
int dim_ind, dim, dim0, dim1, dim2, dimd, p, nat_tot;
int nzone, nzone_send, zone, zonei, cg0, cg1;
real r_comm2, r_bcomm2;
dd_corners_t corners;
ivec tric_dist;
- rvec *cg_cm, *normal, *v_d, *v_0 = NULL, *v_1 = NULL, *recv_vr;
+ rvec *cg_cm, *normal, *v_d, *v_0 = nullptr, *v_1 = nullptr, *recv_vr;
real skew_fac2_d, skew_fac_01;
rvec sf2_round;
int nsend, nat;
cg_cm = fr->cg_cm;
break;
case ecutsVERLET:
- cg_cm = state->x;
+ cg_cm = as_rvec_array(state->x.data());
break;
default:
gmx_incons("unimplemented");
- cg_cm = NULL;
+ cg_cm = nullptr;
}
for (dim_ind = 0; dim_ind < dd->ndim; dim_ind++)
bBondComm = comm->bBondComm;
/* Do we need to determine extra distances for multi-body bondeds? */
- bDistMB = (comm->bInterCGMultiBody && dlbIsOn(dd->comm) && dd->ndim > 1);
+ bDistMB = (comm->bInterCGMultiBody && isDlbOn(dd->comm) && dd->ndim > 1);
/* Do we need to determine extra distances for only two-body bondeds? */
bDist2B = (bBondComm && !bDistMB);
}
else
{
- cg_cm = state->x;
+ cg_cm = as_rvec_array(state->x.data());
}
/* Communicate cg_cm */
if (cd->bInPlace)
* So we pass NULL for the forcerec.
*/
dd_set_cginfo(dd->index_gl, dd->ncg_home, dd->ncg_tot,
- NULL, comm->bLocalCG);
+ nullptr, comm->bLocalCG);
}
if (debug)
zones = &comm->zones;
/* Do we need to determine extra distances for multi-body bondeds? */
- bDistMB = (comm->bInterCGMultiBody && dlbIsOn(dd->comm) && dd->ndim > 1);
+ bDistMB = (comm->bInterCGMultiBody && isDlbOn(dd->comm) && dd->ndim > 1);
for (z = zone_start; z < zone_end; z++)
{
/* With a staggered grid we have different sizes
* for non-shifted dimensions.
*/
- if (dlbIsOn(dd->comm) && zones->shift[z][dim] == 0)
+ if (isDlbOn(dd->comm) && zones->shift[z][dim] == 0)
{
if (d == 1)
{
if (zones->shift[z][dim] > 0)
{
dim = dd->dim[d];
- if (!dlbIsOn(dd->comm) || d == 0)
+ if (!isDlbOn(dd->comm) || d == 0)
{
zones->size[z].x0[dim] = comm->cell_x1[dim];
zones->size[z].x1[dim] = comm->cell_x1[dim] + rcs;
{
int a, atot, cg, cg0, cg1, i;
- if (cgindex == NULL)
+ if (cgindex == nullptr)
{
/* Avoid the useless loop of the atoms within a cg */
order_vec_cg(ncg, sort, v, buf);
}
else
{
- cgindex = NULL;
+ cgindex = nullptr;
}
/* Remove the charge groups which are no longer at home here */
}
/* Reorder the state */
- for (i = 0; i < estNR; i++)
+ if (state->flags & (1 << estX))
{
- if (EST_DISTR(i) && (state->flags & (1<<i)))
- {
- switch (i)
- {
- case estX:
- order_vec_atom(dd->ncg_home, cgindex, cgsort, state->x, vbuf);
- break;
- case estV:
- order_vec_atom(dd->ncg_home, cgindex, cgsort, state->v, vbuf);
- break;
- case est_SDX_NOTSUPPORTED:
- break;
- case estCGP:
- order_vec_atom(dd->ncg_home, cgindex, cgsort, state->cg_p, vbuf);
- break;
- case estLD_RNG:
- case estLD_RNGI:
- case estDISRE_INITF:
- case estDISRE_RM3TAV:
- case estORIRE_INITF:
- case estORIRE_DTAV:
- /* No ordering required */
- break;
- default:
- gmx_incons("Unknown state entry encountered in dd_sort_state");
- break;
- }
- }
+ order_vec_atom(dd->ncg_home, cgindex, cgsort, as_rvec_array(state->x.data()), vbuf);
}
+ if (state->flags & (1 << estV))
+ {
+ order_vec_atom(dd->ncg_home, cgindex, cgsort, as_rvec_array(state->v.data()), vbuf);
+ }
+ if (state->flags & (1 << estCGP))
+ {
+ order_vec_atom(dd->ncg_home, cgindex, cgsort, as_rvec_array(state->cg_p.data()), vbuf);
+ }
+
if (fr->cutoff_scheme == ecutsGROUP)
{
/* Reorder cgcm */
comm->load_pme = 0;
}
-void print_dd_statistics(t_commrec *cr, t_inputrec *ir, FILE *fplog)
+void print_dd_statistics(t_commrec *cr, const t_inputrec *ir, FILE *fplog)
{
gmx_domdec_comm_t *comm;
int ddnat;
gmx_sumd(ddnatNR-ddnatZONE, comm->sum_nat, cr);
- if (fplog == NULL)
+ if (fplog == nullptr)
{
return;
}
const gmx_mtop_t *top_global,
const t_inputrec *ir,
t_state *state_local,
- rvec **f,
+ PaddedRVecVector *f,
t_mdatoms *mdatoms,
gmx_localtop_t *top_local,
t_forcerec *fr,
bNStGlobalComm = (step % nstglobalcomm == 0);
- if (!dlbIsOn(comm))
+ if (!isDlbOn(comm))
{
bDoDLB = FALSE;
}
}
comm->n_load_collect++;
- if (dlbIsOn(comm))
+ if (isDlbOn(comm))
{
if (DDMASTER(dd))
{
ncgindex_set = 0;
set_ddbox(dd, bMasterState, cr, ir, state_global->box,
- TRUE, cgs_gl, state_global->x, &ddbox);
+ TRUE, cgs_gl, as_rvec_array(state_global->x.data()), &ddbox);
get_cg_distribution(fplog, dd, cgs_gl,
- state_global->box, &ddbox, state_global->x);
+ state_global->box, &ddbox, as_rvec_array(state_global->x.data()));
dd_distribute_state(dd, cgs_gl,
state_global, state_local, f);
if (fr->cutoff_scheme == ecutsGROUP)
{
calc_cgcm(fplog, 0, dd->ncg_home,
- &top_local->cgs, state_local->x, fr->cg_cm);
+ &top_local->cgs, as_rvec_array(state_local->x.data()), fr->cg_cm);
}
inc_nrnb(nrnb, eNR_CGCM, dd->nat_home);
{
/* Redetermine the cg COMs */
calc_cgcm(fplog, 0, dd->ncg_home,
- &top_local->cgs, state_local->x, fr->cg_cm);
+ &top_local->cgs, as_rvec_array(state_local->x.data()), fr->cg_cm);
}
inc_nrnb(nrnb, eNR_CGCM, dd->nat_home);
dd_set_cginfo(dd->index_gl, 0, dd->ncg_home, fr, comm->bLocalCG);
set_ddbox(dd, bMasterState, cr, ir, state_local->box,
- TRUE, &top_local->cgs, state_local->x, &ddbox);
+ TRUE, &top_local->cgs, as_rvec_array(state_local->x.data()), &ddbox);
- bRedist = dlbIsOn(comm);
+ bRedist = isDlbOn(comm);
}
else
{
copy_rvec(comm->box_size, ddbox.box_size);
}
set_ddbox(dd, bMasterState, cr, ir, state_local->box,
- bNStGlobalComm, &top_local->cgs, state_local->x, &ddbox);
+ bNStGlobalComm, &top_local->cgs, as_rvec_array(state_local->x.data()), &ddbox);
bBoxChanged = TRUE;
bRedist = TRUE;
0, dd->ncg_home,
comm->zones.dens_zone0,
fr->cginfo,
- state_local->x,
- ncg_moved, bRedist ? comm->moved : NULL,
+ as_rvec_array(state_local->x.data()),
+ ncg_moved, bRedist ? comm->moved : nullptr,
fr->nbv->grp[eintLocal].kernel_type,
fr->nbv->grp[eintLocal].nbat);
}
dd_sort_state(dd, fr->cg_cm, fr, state_local,
bResortAll ? -1 : ncg_home_old);
+
+ /* After sorting and compacting we set the correct size */
+ dd_resize_state(state_local, f, dd->nat_home);
+
/* Rebuild all the indices */
ga2la_clear(dd->ga2la);
ncgindex_set = 0;
/*
write_dd_pdb("dd_home",step,"dump",top_global,cr,
- -1,state_local->x,state_local->box);
+ -1,as_rvec_array(state_local->x.data()),state_local->box);
*/
wallcycle_sub_start(wcycle, ewcsDD_MAKETOP);
dd_make_local_top(dd, &comm->zones, dd->npbcdim, state_local->box,
comm->cellsize_min, np,
fr,
- fr->cutoff_scheme == ecutsGROUP ? fr->cg_cm : state_local->x,
+ fr->cutoff_scheme == ecutsGROUP ? fr->cg_cm : as_rvec_array(state_local->x.data()),
vsite, top_global, top_local);
wallcycle_sub_stop(wcycle, ewcsDD_MAKETOP);
* or constraint communication.
*/
state_local->natoms = comm->nat[ddnatNR-1];
- if (state_local->natoms > state_local->nalloc)
- {
- dd_realloc_state(state_local, f, state_local->natoms);
- }
+
+ dd_resize_state(state_local, f, state_local->natoms);
if (fr->bF_NoVirSum)
{
forcerec_set_ranges(fr, dd->ncg_home, dd->ncg_tot,
dd->nat_tot, comm->nat[ddnatCON], nat_f_novirsum);
- /* We make the all mdatoms up to nat_tot_con.
- * We could save some work by only setting invmass
- * between nat_tot and nat_tot_con.
- */
- /* This call also sets the new number of home particles to dd->nat_home */
- atoms2md(top_global, ir,
- comm->nat[ddnatCON], dd->gatindex, dd->nat_home, mdatoms);
-
- /* Now we have the charges we can sort the FE interactions */
- dd_sort_local_top(dd, mdatoms, top_local);
-
- if (vsite != NULL)
- {
- /* Now we have updated mdatoms, we can do the last vsite bookkeeping */
- split_vsites_over_threads(top_local->idef.il, top_local->idef.iparams,
- mdatoms, FALSE, vsite);
- }
+ /* Update atom data for mdatoms and several algorithms */
+ mdAlgorithmsSetupAtomData(cr, ir, top_global, top_local, fr,
+ nullptr, mdatoms, vsite, nullptr);
if (ir->implicit_solvent)
{
make_local_gb(cr, fr->born, ir->gb_algorithm);
}
- setup_bonded_threading(fr, &top_local->idef);
-
if (!(cr->duty & DUTY_PME))
{
/* Send the charges and/or c6/sigmas to our PME only node */
* the last vsite construction, we need to communicate the constructing
* atom coordinates again (for spreading the forces this MD step).
*/
- dd_move_x_vsites(dd, state_local->box, state_local->x);
+ dd_move_x_vsites(dd, state_local->box, as_rvec_array(state_local->x.data()));
wallcycle_sub_stop(wcycle, ewcsDD_TOPOTHER);
if (comm->nstDDDump > 0 && step % comm->nstDDDump == 0)
{
- dd_move_x(dd, state_local->box, state_local->x);
+ dd_move_x(dd, state_local->box, as_rvec_array(state_local->x.data()));
write_dd_pdb("dd_dump", step, "dump", top_global, cr,
- -1, state_local->x, state_local->box);
+ -1, as_rvec_array(state_local->x.data()), state_local->box);
}
/* Store the partitioning step */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2005,2006,2007,2008,2009,2010,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2005,2006,2007,2008,2009,2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/hardware/hw_info.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/mdtypes/state.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/idef.h"
struct gmx_domdec_t;
struct gmx_ddbox_t;
struct gmx_domdec_zones_t;
+struct MdrunOptions;
struct t_commrec;
struct t_inputrec;
-
-#ifdef __cplusplus
-extern "C" {
-#endif
+class t_state;
/*! \brief Returns the global topology atom number belonging to local atom index i.
*
void dd_get_ns_ranges(const gmx_domdec_t *dd, int icg,
int *jcg0, int *jcg1, ivec shift0, ivec shift1);
+/*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
+int dd_natoms_mdatoms(const gmx_domdec_t *dd);
+
/*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
int dd_natoms_vsite(const gmx_domdec_t *dd);
/*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
int dd_pme_maxshift_y(const gmx_domdec_t *dd);
+/*! \brief The options for the domain decomposition MPI task ordering. */
+enum class DdRankOrder
+{
+ select, //!< First value (needed to cope with command-line parsing)
+ interleave, //!< Interleave the PP and PME ranks
+ pp_pme, //!< First all PP ranks, all PME rank at the end
+ cartesian, //!< Use Cartesian communicators for PP, PME and PP-PME
+ nr //!< The number of options
+};
+
+/*! \brief The options for the dynamic load balancing. */
+enum class DlbOption
+{
+ select, //!< First value (needed to cope with command-line parsing)
+ turnOnWhenUseful, //!< Turn on DLB when we think it would improve performance
+ no, //!< Never turn on DLB
+ yes, //!< Turn on DLB from the start and keep it on
+ nr //!< The number of options
+};
+
+/*! \libinternal \brief Structure containing all (command line) options for the domain decomposition */
+struct DomdecOptions
+{
+ /*! \brief Constructor */
+ DomdecOptions();
+
+ //! If true, check that all bonded interactions have been assigned to exactly one domain/rank.
+ gmx_bool checkBondedInteractions;
+ //! If true, don't communicate all atoms between the non-bonded cut-off and the larger bonded cut-off, but only those that have non-local bonded interactions. This significantly reduces the communication volume.
+ gmx_bool useBondedCommunication;
+ //! The domain decomposition grid cell count, 0 means let domdec choose based on the number of ranks.
+ ivec numCells;
+ //! The number of separate PME ranks requested, -1 = auto.
+ int numPmeRanks;
+ //! Ordering of the PP and PME ranks, values from enum above.
+ DdRankOrder rankOrder;
+ //! The minimum communication range, used for extended the communication range for bonded interactions (nm).
+ real minimumCommunicationRange;
+ //! Communication range for atom involved in constraints (P-LINCS) (nm).
+ real constraintCommunicationRange;
+ //! Dynamic load balancing option, values from enum above.
+ DlbOption dlbOption;
+ /*! \brief Fraction in (0,1) by whose reciprocal the initial
+ * DD cell size will be increased in order to provide a margin
+ * in which dynamic load balancing can act, while preserving
+ * the minimum cell size. */
+ real dlbScaling;
+ //! String containing a vector of the relative sizes in the x direction of the corresponding DD cells.
+ const char *cellSizeX;
+ //! String containing a vector of the relative sizes in the y direction of the corresponding DD cells.
+ const char *cellSizeY;
+ //! String containing a vector of the relative sizes in the z direction of the corresponding DD cells.
+ const char *cellSizeZ;
+};
+
/*! \brief Initialized the domain decomposition, chooses the DD grid and PME ranks, return the DD struct */
-gmx_domdec_t *init_domain_decomposition(FILE *fplog,
- t_commrec *cr,
- unsigned long Flags,
- ivec nc,
- int nPmeRanks,
- int dd_node_order,
- real comm_distance_min,
- real rconstr,
- const char *dlb_opt,
- real dlb_scale,
- const char *sizex,
- const char *sizey,
- const char *sizez,
- const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- matrix box,
- rvec *x,
- gmx_ddbox_t *ddbox,
- int *npme_x,
- int *npme_y);
+gmx_domdec_t *init_domain_decomposition(FILE *fplog,
+ t_commrec *cr,
+ const DomdecOptions &options,
+ const MdrunOptions &mdrunOptions,
+ const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ matrix box,
+ rvec *x,
+ gmx_ddbox_t *ddbox,
+ int *npme_x,
+ int *npme_y);
/*! \brief Initialize data structures for bonded interactions */
void dd_init_bondeds(FILE *fplog,
/*! \brief Clear a lock such that with DLB=auto DLB may get turned on later */
void dd_dlb_unlock(struct gmx_domdec_t *dd);
-/*! \brief Set up communication for averaging GPU wait times over ranks
+/*! \brief Set up communication for averaging GPU wait times over domains
*
* When domains (PP MPI ranks) share a GPU, the individual GPU wait times
* are meaningless, as it depends on the order in which tasks on the same
* GPU finish. Therefore there wait times need to be averaged over the ranks
* sharing the same GPU. This function sets up the communication for that.
*/
-void dd_setup_dlb_resource_sharing(struct t_commrec *cr,
- const gmx_hw_info_t *hwinfo,
- const gmx_hw_opt_t *hw_opt);
+void dd_setup_dlb_resource_sharing(t_commrec *cr,
+ int gpu_id);
/*! \brief Collects local rvec arrays \p lv to \p v on the master rank */
void dd_collect_vec(struct gmx_domdec_t *dd,
- t_state *state_local, rvec *lv, rvec *v);
+ t_state *state_local, const PaddedRVecVector *lv, rvec *v);
+
+/*! \brief Collects local rvec arrays \p lv to \p v on the master rank */
+void dd_collect_vec(struct gmx_domdec_t *dd,
+ t_state *state_local, const PaddedRVecVector *lv, PaddedRVecVector *v);
/*! \brief Collects the local state \p state_local to \p state on the master rank */
void dd_collect_state(struct gmx_domdec_t *dd,
};
/*! \brief Add the wallcycle count to the DD counter */
-void dd_cycles_add(struct gmx_domdec_t *dd, float cycles, int ddCycl);
+void dd_cycles_add(const gmx_domdec_t *dd, float cycles, int ddCycl);
/*! \brief Start the force flop count */
void dd_force_flop_start(struct gmx_domdec_t *dd, t_nrnb *nrnb);
const gmx_mtop_t *top_global,
const t_inputrec *ir,
t_state *state_local,
- rvec **f,
+ PaddedRVecVector *f,
t_mdatoms *mdatoms,
gmx_localtop_t *top_local,
t_forcerec *fr,
gmx_vsite_t *vsite,
- gmx_constr_t constr,
+ struct gmx_constr *constr,
t_nrnb *nrnb,
gmx_wallcycle_t wcycle,
gmx_bool bVerbose);
void reset_dd_statistics_counters(struct gmx_domdec_t *dd);
/*! \brief Print statistics for domain decomposition communication */
-void print_dd_statistics(struct t_commrec *cr, t_inputrec *ir, FILE *fplog);
+void print_dd_statistics(struct t_commrec *cr, const t_inputrec *ir, FILE *fplog);
/* In domdec_con.c */
const t_block *cgs, const rvec *x,
gmx_ddbox_t *ddbox);
-#ifdef __cplusplus
-}
-#endif
-
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
- if (cr_sum != NULL)
+ if (cr_sum != nullptr)
{
for (d = 0; d < DIM; d++)
{
if (box[j][d] != 0)
{
ddbox->tric_dir[d] = 1;
- if (dd_nc != NULL && (*dd_nc)[j] > 1 && (*dd_nc)[d] == 1)
+ if (dd_nc != nullptr && (*dd_nc)[j] > 1 && (*dd_nc)[d] == 1)
{
gmx_fatal(FARGS, "Domain decomposition has not been implemented for box vectors that have non-zero components in directions that do not use domain decomposition: ncells = %d %d %d, box vector[%d] = %f %f %f",
(*dd_nc)[XX], (*dd_nc)[YY], (*dd_nc)[ZZ],
{
low_set_ddbox(ir, &dd->nc, box, bCalcUnboundedSize,
bMasterState ? cgs->nr : dd->ncg_home, cgs, x,
- bMasterState ? NULL : cr_sum,
+ bMasterState ? nullptr : cr_sum,
ddbox);
}
{
if (MASTER(cr))
{
- low_set_ddbox(ir, dd_nc, box, TRUE, cgs->nr, cgs, x, NULL, ddbox);
+ low_set_ddbox(ir, dd_nc, box, TRUE, cgs->nr, cgs, x, nullptr, ddbox);
}
gmx_bcast(sizeof(gmx_ddbox_t), ddbox, cr);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
+#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "domdec_specatomcomm.h"
+#include "domdec_vsite.h"
#include "hash.h"
/*! \brief Struct used during constraint setup with domain decomposition */
if (dd->constraint_comm)
{
dd_move_x_specat(dd, dd->constraint_comm, box, x0, x1, bX1IsCoord);
+
+ ddReopenBalanceRegionCpu(dd);
}
}
}
else
{
- return NULL;
+ return nullptr;
}
}
t_ilist *ils_local,
ind_req_t *ireq)
{
- gmx_ga2la_t *ga2la;
- gmx_mtop_atomlookup_t alook;
- int settle;
- int nral, sa;
- int cg, a, a_gl, a_glsa, a_gls[3], a_locs[3];
- int mb, molnr, a_mol, offset;
- const gmx_molblock_t *molb;
- const t_iatom *ia1;
- gmx_bool a_home[3];
- int nlocal;
- gmx_bool bAssign;
-
- ga2la = dd->ga2la;
-
- alook = gmx_mtop_atomlookup_settle_init(mtop);
+ gmx_ga2la_t *ga2la = dd->ga2la;
+ int nral = NRAL(F_SETTLE);
- nral = NRAL(F_SETTLE);
-
- for (cg = cg_start; cg < cg_end; cg++)
+ int mb = 0;
+ for (int cg = cg_start; cg < cg_end; cg++)
{
if (GET_CGINFO_SETTLE(cginfo[cg]))
{
- for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
+ for (int a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
{
- a_gl = dd->gatindex[a];
-
- gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
- molb = &mtop->molblock[mb];
+ int a_gl = dd->gatindex[a];
+ int a_mol;
+ mtopGetMolblockIndex(mtop, a_gl, &mb, nullptr, &a_mol);
- settle = at2settle_mt[molb->type][a_mol];
+ const gmx_molblock_t *molb = &mtop->molblock[mb];
+ int settle = at2settle_mt[molb->type][a_mol];
if (settle >= 0)
{
- offset = a_gl - a_mol;
+ int offset = a_gl - a_mol;
- ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
+ t_iatom *ia1 = mtop->moltype[molb->type].ilist[F_SETTLE].iatoms;
- bAssign = FALSE;
- nlocal = 0;
- for (sa = 0; sa < nral; sa++)
+ int a_gls[3], a_locs[3];
+ gmx_bool bAssign = FALSE;
+ int nlocal = 0;
+ for (int sa = 0; sa < nral; sa++)
{
- a_glsa = offset + ia1[settle*(1+nral)+1+sa];
+ int a_glsa = offset + ia1[settle*(1+nral)+1+sa];
a_gls[sa] = a_glsa;
- a_home[sa] = ga2la_get_home(ga2la, a_glsa, &a_locs[sa]);
- if (a_home[sa])
+ if (ga2la_get_home(ga2la, a_glsa, &a_locs[sa]))
{
if (nlocal == 0 && a_gl == a_glsa)
{
ils_local->iatoms[ils_local->nr++] = ia1[settle*4];
- for (sa = 0; sa < nral; sa++)
+ for (int sa = 0; sa < nral; sa++)
{
if (ga2la_get_home(ga2la, a_gls[sa], &a_locs[sa]))
{
}
}
}
-
- gmx_mtop_atomlookup_destroy(alook);
}
/*! \brief Looks up constraint for the local atoms */
ind_req_t *ireq)
{
const t_blocka *at2con;
- gmx_ga2la_t *ga2la;
- gmx_mtop_atomlookup_t alook;
int ncon1;
- gmx_molblock_t *molb;
t_iatom *ia1, *ia2, *iap;
- int nhome, cg, a, a_gl, a_mol, a_loc, b_lo, offset, mb, molnr, b_mol, i, con, con_offset;
- gmx_domdec_constraints_t *dc;
- gmx_domdec_specat_comm_t *dcc;
+ int a_loc, b_lo, offset, b_mol, i, con, con_offset;
- dc = dd->constraints;
- dcc = dd->constraint_comm;
+ gmx_domdec_constraints_t *dc = dd->constraints;
+ gmx_domdec_specat_comm_t *dcc = dd->constraint_comm;
- ga2la = dd->ga2la;
+ gmx_ga2la_t *ga2la = dd->ga2la;
- alook = gmx_mtop_atomlookup_init(mtop);
-
- nhome = 0;
- for (cg = 0; cg < dd->ncg_home; cg++)
+ int mb = 0;
+ int nhome = 0;
+ for (int cg = 0; cg < dd->ncg_home; cg++)
{
if (GET_CGINFO_CONSTR(cginfo[cg]))
{
- for (a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
+ for (int a = dd->cgindex[cg]; a < dd->cgindex[cg+1]; a++)
{
- a_gl = dd->gatindex[a];
+ int a_gl = dd->gatindex[a];
+ int molnr, a_mol;
+ mtopGetMolblockIndex(mtop, a_gl, &mb, &molnr, &a_mol);
- gmx_mtop_atomnr_to_molblock_ind(alook, a_gl, &mb, &molnr, &a_mol);
- molb = &mtop->molblock[mb];
+ const gmx_molblock_t *molb = &mtop->molblock[mb];
ncon1 = mtop->moltype[molb->type].ilist[F_CONSTR].nr/NRAL(F_SETTLE);
}
}
- gmx_mtop_atomlookup_destroy(alook);
-
if (debug)
{
fprintf(debug,
else
{
// Currently unreachable
- at2con_mt = NULL;
- ireq = NULL;
+ at2con_mt = nullptr;
+ ireq = nullptr;
}
if (dd->bInterCGsettles)
else
{
/* Settle works inside charge groups, we assigned them already */
- at2settle_mt = NULL;
+ at2settle_mt = nullptr;
}
- if (at2settle_mt == NULL)
+ if (at2settle_mt == nullptr)
{
atoms_to_constraints(dd, mtop, cginfo, at2con_mt, nrec,
ilc_local, ireq);
/* Do the constraints, if present, on the first thread.
* Do the settles on all other threads.
*/
- t0_set = ((at2con_mt != NULL && dc->nthread > 1) ? 1 : 0);
+ t0_set = ((at2con_mt != nullptr && dc->nthread > 1) ? 1 : 0);
#pragma omp parallel for num_threads(dc->nthread) schedule(static)
for (thread = 0; thread < dc->nthread; thread++)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/timing/cyclecounter.h"
#include "gromacs/topology/block.h"
/*! \cond INTERNAL */
+struct BalanceRegion;
+
typedef struct
{
/* The numbers of charge groups to send and receive for each cell
ddnatHOME, ddnatZONE, ddnatVSITE, ddnatCON, ddnatNR
};
-/*! \brief Enum of dynamic load balancing states */
-enum {
- edlbsOffForever, /**< DLB is off and will never be turned on */
- edlbsOffCanTurnOn, /**< DLB is off and will turn on on imbalance */
- edlbsOffTemporarilyLocked, /**< DLB is off and temporarily can't turn on */
- edlbsOnCanTurnOff, /**< DLB is on and can turn off when slow */
- edlbsOnForever, /**< DLB is on and will stay on forever, because the user chose this */
- edlbsNR /**< The number of DLB states */
-};
-
-/* Allowed DLB state transitions in automatic mode:
+/*! \brief Enum of dynamic load balancing states
+ *
+ * Allowed DLB states and transitions
+ * - intialization at startup:
+ * -> edlbsOffUser ("-dlb no")
+ * -> edlbsOnUser ("-dlb yes")
+ * -> edlbsOffCanTurnOn ("-dlb auto")
+ *
+ * - in automatic mode (i.e. initial state edlbsOffCanTurnOn):
* edlbsOffCanTurnOn -> edlbsOnCanTurnOff
* edlbsOffCanTurnOn -> edlbsOffForever
* edlbsOffCanTurnOn -> edlbsOffTemporarilyLocked
* edlbsOffTemporarilyLocked -> edlbsOffCanTurnOn
* edlbsOnCanTurnOff -> edlbsOffCanTurnOn
*/
+enum {
+ edlbsOffUser, /**< DLB is permanently off per user request */
+ edlbsOffForever, /**< DLB is off due to a runtime condition (not supported or causes performance loss) and will never be turned on */
+ edlbsOffCanTurnOn, /**< DLB is off and will turn on on imbalance */
+ edlbsOffTemporarilyLocked, /**< DLB is off and temporarily can't turn on */
+ edlbsOnCanTurnOff, /**< DLB is on and can turn off when slow */
+ edlbsOnUser, /**< DLB is permanently on per user request */
+ edlbsNR /**< The number of DLB states */
+};
/*! \brief The PME domain decomposition for one dimension */
typedef struct
MPI_Comm mpi_comm_gpu_shared; /**< The MPI load communicator for ranks sharing a GPU */
#endif
- /** Maximum DLB scaling per load balancing step in percent */
- int dlb_scale_lim;
+ /* Information for managing the dynamic load balancing */
+ int dlb_scale_lim; /**< Maximum DLB scaling per load balancing step in percent */
+
+ BalanceRegion *balanceRegion; /**< Struct for timing the force load balancing region */
- /* Cycle counters */
+ /* Cycle counters over nstlist steps */
float cycl[ddCyclNr]; /**< Total cycles counted */
int cycl_n[ddCyclNr]; /**< The number of cycle recordings */
float cycl_max[ddCyclNr]; /**< The maximum cycle count */
#endif
}
-/* IBM's BlueGene(/L) MPI_Bcast dereferences the data pointer
- * even when 0 == nbytes, so we protect calls to it on BlueGene.
- * Fortunately dd_bcast() and dd_bcastc() are only
- * called during DD setup and partition.
- */
-
void dd_bcast(gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *data)
{
#if GMX_MPI
if (dd->nnodes > 1)
{
-#ifdef GMX_BLUEGENE
- if (nbytes > 0)
- {
-#endif
MPI_Bcast(data, nbytes, MPI_BYTE,
DDMASTERRANK(dd), dd->mpi_comm_all);
-#ifdef GMX_BLUEGENE
- }
-#endif
}
#endif
}
#if GMX_MPI
if (dd->nnodes > 1)
{
-#ifdef GMX_BLUEGENE
- if (nbytes > 0)
- {
-#endif
MPI_Bcast(dest, nbytes, MPI_BYTE,
DDMASTERRANK(dd), dd->mpi_comm_all);
-#ifdef GMX_BLUEGENE
- }
-#endif
}
#endif
}
-void dd_scatter(gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *src, void *dest)
+void dd_scatter(gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void *dest)
{
#if GMX_MPI
if (dd->nnodes > 1)
{
- MPI_Scatter(src, nbytes, MPI_BYTE,
+ /* Some MPI implementions don't specify const */
+ MPI_Scatter(const_cast<void *>(src), nbytes, MPI_BYTE,
dest, nbytes, MPI_BYTE,
DDMASTERRANK(dd), dd->mpi_comm_all);
}
}
}
-void dd_gather(gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, void gmx_unused *src, void gmx_unused *dest)
+void dd_gather(gmx_domdec_t gmx_unused *dd, int gmx_unused nbytes, const void gmx_unused *src, void gmx_unused *dest)
{
#if GMX_MPI
- MPI_Gather(src, nbytes, MPI_BYTE,
+ /* Some MPI implementions don't specify const */
+ MPI_Gather(const_cast<void *>(src), nbytes, MPI_BYTE,
dest, nbytes, MPI_BYTE,
DDMASTERRANK(dd), dd->mpi_comm_all);
#endif
}
void dd_scatterv(gmx_domdec_t gmx_unused *dd,
- int gmx_unused *scounts, int gmx_unused *disps, void *sbuf,
+ int gmx_unused *scounts, int gmx_unused *disps, const void *sbuf,
int rcount, void *rbuf)
{
#if GMX_MPI
/* MPI does not allow NULL pointers */
rbuf = &dum;
}
- MPI_Scatterv(sbuf, scounts, disps, MPI_BYTE,
+ /* Some MPI implementions don't specify const */
+ MPI_Scatterv(const_cast<void *>(sbuf), scounts, disps, MPI_BYTE,
rbuf, rcount, MPI_BYTE,
DDMASTERRANK(dd), dd->mpi_comm_all);
}
}
void dd_gatherv(gmx_domdec_t gmx_unused *dd,
- int gmx_unused scount, void gmx_unused *sbuf,
+ int gmx_unused scount, const void gmx_unused *sbuf,
int gmx_unused *rcounts, int gmx_unused *disps, void gmx_unused *rbuf)
{
#if GMX_MPI
/* MPI does not allow NULL pointers */
sbuf = &dum;
}
- MPI_Gatherv(sbuf, scount, MPI_BYTE,
+ /* Some MPI implementions don't specify const */
+ MPI_Gatherv(const_cast<void *>(sbuf), scount, MPI_BYTE,
rbuf, rcounts, disps, MPI_BYTE,
DDMASTERRANK(dd), dd->mpi_comm_all);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2012,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief Scatters \p nbytes from \p src on \p DDMASTERRANK to all PP ranks, received in \p dest */
void
-dd_scatter(struct gmx_domdec_t *dd, int nbytes, void *src, void *dest);
+dd_scatter(struct gmx_domdec_t *dd, int nbytes, const void *src, void *dest);
/*! \brief Gathers \p nbytes from \p src on all PP ranks, received in \p dest on \p DDMASTERRANK */
void
-dd_gather(struct gmx_domdec_t *dd, int nbytes, void *src, void *dest);
+dd_gather(struct gmx_domdec_t *dd, int nbytes, const void *src, void *dest);
/*! \brief Scatters \p scounts bytes from \p src on \p DDMASTERRANK to all PP ranks, receiving \p rcount bytes in \p dest.
*
* If rcount==0, rbuf is allowed to be NULL */
void
dd_scatterv(struct gmx_domdec_t *dd,
- int *scounts, int *disps, void *sbuf,
+ int *scounts, int *disps, const void *sbuf,
int rcount, void *rbuf);
/*! \brief Gathers \p rcount bytes from \p src on all PP ranks, received in \p scounts bytes in \p dest on \p DDMASTERRANK.
* If scount==0, sbuf is allowed to be NULL */
void
dd_gatherv(struct gmx_domdec_t *dd,
- int scount, void *sbuf,
+ int scount, const void *sbuf,
int *rcounts, int *disps, void *rbuf);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
}
}
+ if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
+ {
+ /* Check the PME grid restrictions.
+ * Currently these can only be invalid here with too few grid lines
+ * along the x dimension per rank doing PME.
+ */
+ int npme_x = (npme_tot > 1 ? npme[XX] : nc[XX]);
+
+ /* Currently we don't have the OpenMP thread count available here.
+ * But with threads we have only tighter restrictions and it's
+ * probably better anyhow to avoid settings where we need to reduce
+ * grid lines over multiple ranks, as the thread check will do.
+ */
+ bool useThreads = true;
+ bool errorsAreFatal = false;
+ if (!gmx_pme_check_restrictions(ir->pme_order, ir->nkx, ir->nky, ir->nkz,
+ npme_x, useThreads, errorsAreFatal))
+ {
+ return -1;
+ }
+ }
+
/* When two dimensions are (nearly) equal, use more cells
* for the smallest index, so the decomposition does not
* depend sensitively on the rounding of the box elements.
* we can save some time (e.g. 3D DD with pbc=xyz).
* Here we ignore SIMD bondeds as they always do (fast) PBC.
*/
- count_bonded_distances(mtop, ir, &pbcdxr, NULL);
+ count_bonded_distances(mtop, ir, &pbcdxr, nullptr);
pbcdxr /= (double)mtop->natoms;
}
else
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
spas = &spac->spas[d][dir];
/* Sum the buffer into the required forces */
- if (!bPBC || (!bScrew && fshift == NULL))
+ if (!bPBC || (!bScrew && fshift == nullptr))
{
for (i = 0; i < spas->nsend; i++)
{
rvec shift = {0, 0, 0};
nvec = 1;
- if (x1 != NULL)
+ if (x1 != nullptr)
{
nvec++;
}
#include <stdlib.h>
#include <string.h>
+#include <cassert>
+
#include <algorithm>
#include <string>
print_missing_interactions_atoms(fplog, cr, top_global, &top_local->idef);
write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr,
- -1, state_local->x, state_local->box);
+ -1, as_rvec_array(state_local->x.data()), state_local->box);
std::string errorMessage;
}
}
-/*! \brief Run the reverse ilist generation and store it when \p bAssign = TRUE */
+/*! \brief Run the reverse ilist generation and store it in r_il when \p bAssign = TRUE */
static int low_make_reverse_ilist(const t_ilist *il_mt, const t_atom *atom,
const int * const * vsite_pbc,
int *count,
a = ia[1+link];
if (bAssign)
{
+ assert(r_il); //with bAssign not allowed to be null
+ assert(r_index);
r_il[r_index[a]+count[a]] =
(ftype == F_CONSTRNC ? F_CONSTR : ftype);
r_il[r_index[a]+count[a]+1] = ia[0];
snew(count, nat_mt);
low_make_reverse_ilist(ilist, atoms->atom, vsite_pbc,
count,
- bConstr, bSettle, bBCheck, NULL, NULL,
+ bConstr, bSettle, bBCheck, nullptr, nullptr,
bLinkToAllAtoms, FALSE);
snew(ril_mt->index, nat_mt+1);
/* Make the atom to interaction list for this molecule type */
nint_mt[mt] =
make_reverse_ilist(molt->ilist, &molt->atoms,
- vsite_pbc_molt ? vsite_pbc_molt[mt] : NULL,
+ vsite_pbc_molt ? vsite_pbc_molt[mt] : nullptr,
rt->bConstr, rt->bSettle, rt->bBCheck, FALSE,
&rt->ril_mt[mt]);
{
t_atoms atoms_global;
- rt->ril_intermol.index = NULL;
- rt->ril_intermol.il = NULL;
+ rt->ril_intermol.index = nullptr;
+ rt->ril_intermol.il = nullptr;
atoms_global.nr = mtop->natoms;
- atoms_global.atom = NULL; /* Only used with virtual sites */
+ atoms_global.atom = nullptr; /* Only used with virtual sites */
*nint +=
make_reverse_ilist(mtop->intermolecular_ilist, &atoms_global,
- NULL,
+ nullptr,
rt->bConstr, rt->bSettle, rt->bBCheck, FALSE,
&rt->ril_intermol);
}
rt->nthread = gmx_omp_nthreads_get(emntDomdec);
snew(rt->th_work, rt->nthread);
- if (vsite_pbc_molt != NULL)
+ if (vsite_pbc_molt != nullptr)
{
for (thread = 0; thread < rt->nthread; thread++)
{
*/
dd->reverse_top = make_reverse_top(mtop, ir->efep != efepNO,
- vsite ? vsite->vsite_pbc_molt : NULL,
+ vsite ? vsite->vsite_pbc_molt : nullptr,
!dd->bInterCGcons, !dd->bInterCGsettles,
bBCheck, &dd->nbonded_global);
int nral1 = 0, ftv = 0;
vpbc = ((interaction_function[ftype].flags & IF_VSITE) &&
- vsite->vsite_pbc_loc != NULL);
+ vsite->vsite_pbc_loc != nullptr);
if (vpbc)
{
nral1 = 1 + NRAL(ftype);
}
else
{
- vsite_pbc = NULL;
- vsite_pbc_nalloc = NULL;
+ vsite_pbc = nullptr;
+ vsite_pbc_nalloc = nullptr;
}
rt->th_work[thread].nbonded =
real rc = -1;
ivec rcheck;
int d, nexcl;
- t_pbc pbc, *pbc_null = NULL;
+ t_pbc pbc, *pbc_null = nullptr;
if (debug)
{
}
else
{
- pbc_null = NULL;
+ pbc_null = nullptr;
}
}
}
for (i = 0; i < F_NRE; i++)
{
- top->idef.il[i].iatoms = NULL;
+ top->idef.il[i].iatoms = nullptr;
top->idef.il[i].nalloc = 0;
}
top->idef.ilsort = ilsortUNKNOWN;
buf[1] = state_global->ngtc;
buf[2] = state_global->nnhpres;
buf[3] = state_global->nhchainlength;
- buf[4] = state_global->dfhist.nlambda;
+ buf[4] = state_global->dfhist ? state_global->dfhist->nlambda : 0;
}
dd_bcast(dd, NITEM_DD_INIT_LOCAL_STATE*sizeof(int), buf);
- init_state(state_local, 0, buf[1], buf[2], buf[3], buf[4]);
+ init_gtc_state(state_local, buf[1], buf[2], buf[3]);
+ init_dfhist_state(state_local, buf[4]);
state_local->flags = buf[0];
}
t_atoms atoms;
atoms.nr = mtop->natoms;
- atoms.atom = NULL;
+ atoms.atom = nullptr;
make_reverse_ilist(mtop->intermolecular_ilist, &atoms,
- NULL, FALSE, FALSE, FALSE, TRUE, &ril_intermol);
+ nullptr, FALSE, FALSE, FALSE, TRUE, &ril_intermol);
}
snew(link, 1);
snew(link->index, ncg_mtop(mtop)+1);
link->nalloc_a = 0;
- link->a = NULL;
+ link->a = nullptr;
link->index[0] = 0;
cg_offset = 0;
* The constraints are discarded here.
*/
make_reverse_ilist(molt->ilist, &molt->atoms,
- NULL, FALSE, FALSE, FALSE, TRUE, &ril);
+ nullptr, FALSE, FALSE, FALSE, TRUE, &ril);
cgi_mb = &cginfo_mb[mb];
if (ePBC != epbcNONE)
{
- mk_mshift(NULL, graph, ePBC, box, x);
+ mk_mshift(nullptr, graph, ePBC, box, x);
shift_x(graph, box, x, xs);
/* By doing an extra mk_mshift the molecules that are broken
* will be made whole again. Such are the healing powers
* of GROMACS.
*/
- mk_mshift(NULL, graph, ePBC, box, xs);
+ mk_mshift(nullptr, graph, ePBC, box, xs);
}
else
{
if (vsite)
{
- construct_vsites(vsite, xs, 0.0, NULL,
+ construct_vsites(vsite, xs, 0.0, nullptr,
ffparams->iparams, molt->ilist,
- epbcNONE, TRUE, NULL, NULL);
+ epbcNONE, TRUE, nullptr, nullptr);
}
- calc_cgcm(NULL, 0, molt->cgs.nr, &molt->cgs, xs, cg_cm);
+ calc_cgcm(nullptr, 0, molt->cgs.nr, &molt->cgs, xs, cg_cm);
}
//! Returns whether \p molt has a virtual site
bExclRequired = inputrecExclForces(ir);
- vsite = init_vsite(mtop, NULL, TRUE);
+ vsite = init_vsite(mtop, nullptr, TRUE);
*r_2b = 0;
*r_mb = 0;
{
if (ir->ePBC != epbcNONE)
{
- mk_graph_ilist(NULL, molt->ilist, 0, molt->atoms.nr, FALSE, FALSE,
+ mk_graph_ilist(nullptr, molt->ilist, 0, molt->atoms.nr, FALSE, FALSE,
&graph);
}
for (mol = 0; mol < molb->nmol; mol++)
{
get_cgcm_mol(molt, &mtop->ffparams, ir->ePBC, &graph, box,
- have_vsite_molt(molt) ? vsite : NULL,
+ have_vsite_molt(molt) ? vsite : nullptr,
x+at_offset, xs, cg_cm);
bonded_distance_t bd_mol_2b = { 0, -1, -1, -1 };
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2006,2007,2008,2009,2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
{
if (dd->vsite_comm)
{
- dd_move_x_specat(dd, dd->vsite_comm, box, x, NULL, FALSE);
+ dd_move_x_specat(dd, dd->vsite_comm, box, x, nullptr, FALSE);
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] natoms_local An estimate of the number of home+communicated atoms
* \return a pointer to an initialized gmx_ga2la_t struct
*/
-static gmx_ga2la_t *ga2la_init(int natoms_total, int natoms_local)
+static inline gmx_ga2la_t *ga2la_init(int natoms_total, int natoms_local)
{
gmx_ga2la_t *ga2la;
* \param[in] a_loc The local atom index
* \param[in] cell The cell index
*/
-static void ga2la_set(gmx_ga2la_t *ga2la, int a_gl, int a_loc, int cell)
+static inline void ga2la_set(gmx_ga2la_t *ga2la, int a_gl, int a_loc, int cell)
{
int ind, ind_prev, i;
* \param[in,out] ga2la The global to local atom struct
* \param[in] a_gl The global atom index
*/
-static void ga2la_del(gmx_ga2la_t *ga2la, int a_gl)
+static inline void ga2la_del(gmx_ga2la_t *ga2la, int a_gl)
{
int ind, ind_prev;
* \param[in] a_gl The global atom index
* \param[in] a_loc The new local atom index
*/
-static void ga2la_change_la(gmx_ga2la_t *ga2la, int a_gl, int a_loc)
+static inline void ga2la_change_la(gmx_ga2la_t *ga2la, int a_gl, int a_loc)
{
int ind;
* \param[out] cell If the return value is TRUE, the zone or for atoms more than one cell away zone+nzone
* \return if the global atom a_gl available locally
*/
-static gmx_bool ga2la_get(const gmx_ga2la_t *ga2la, int a_gl, int *a_loc, int *cell)
+static inline gmx_bool ga2la_get(const gmx_ga2la_t *ga2la, int a_gl, int *a_loc, int *cell)
{
int ind;
* \param[out] a_loc If the return value is TRUE, the local atom index
* \return if the global atom a_gl is a home atom
*/
-static gmx_bool ga2la_get_home(const gmx_ga2la_t *ga2la, int a_gl, int *a_loc)
+static inline gmx_bool ga2la_get_home(const gmx_ga2la_t *ga2la, int a_gl, int *a_loc)
{
int ind;
* \param[in] a_gl The global atom index
* \return if the global atom a_gl is a home atom
*/
-static gmx_bool ga2la_is_home(const gmx_ga2la_t *ga2la, int a_gl)
+static inline gmx_bool ga2la_is_home(const gmx_ga2la_t *ga2la, int a_gl)
{
int ind;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
hash->nalloc = over_alloc_dd(hash->mod);
srenew(hash->hash, hash->nalloc);
- if (debug != NULL)
+ if (debug != nullptr)
{
fprintf(debug, "Hash table mod %d nalloc %d\n", hash->mod, hash->nalloc);
}
* With the current number of keys check if the table size is still
* good, if not optimize it with the current number of keys.
*/
-static void gmx_hash_clear_and_optimize(gmx_hash_t *hash)
+static inline void gmx_hash_clear_and_optimize(gmx_hash_t *hash)
{
/* Resize the hash table when the occupation is < 1/4 or > 2/3 */
if (hash->nkey > 0 &&
(4*hash->nkey < hash->mod || 3*hash->nkey > 2*hash->mod))
{
- if (debug != NULL)
+ if (debug != nullptr)
{
fprintf(debug, "Hash table size %d #key %d: resizing\n",
hash->mod, hash->nkey);
}
//! Initialize hash table.
-static gmx_hash_t *gmx_hash_init(int nkey_used_estimate)
+static inline gmx_hash_t *gmx_hash_init(int nkey_used_estimate)
{
gmx_hash_t *hash;
snew(hash, 1);
- hash->hash = NULL;
+ hash->hash = nullptr;
gmx_hash_realloc(hash, nkey_used_estimate);
}
//! Delete the hash entry for key.
-static void gmx_hash_del(gmx_hash_t *hash, int key)
+static inline void gmx_hash_del(gmx_hash_t *hash, int key)
{
int ind, ind_prev;
}
//! Change the value for present hash entry for key.
-static void gmx_hash_change_value(gmx_hash_t *hash, int key, int value)
+static inline void gmx_hash_change_value(gmx_hash_t *hash, int key, int value)
{
int ind;
}
//! Change the hash value if already set, otherwise set the hash value.
-static void gmx_hash_change_or_set(gmx_hash_t *hash, int key, int value)
+static inline void gmx_hash_change_or_set(gmx_hash_t *hash, int key, int value)
{
int ind;
}
//! Returns if the key is present, if the key is present *value is set.
-static gmx_bool gmx_hash_get(const gmx_hash_t *hash, int key, int *value)
+static inline gmx_bool gmx_hash_get(const gmx_hash_t *hash, int key, int *value)
{
int ind;
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+if (BUILD_TESTING)
+ add_subdirectory(tests)
+endif()
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(EnergyAnalysisUnitTests energyanalysis-test
+ legacyenergy.cpp
+)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx energy
+ *
+ * \todo These will be superseded by tests of the energyanalysis
+ * modules.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ */
+
+#include "gmxpre.h"
+
+#include <cstring>
+
+#include <string>
+
+#include "gromacs/gmxana/gmx_ana.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/stdiohelper.h"
+#include "testutils/testasserts.h"
+#include "testutils/textblockmatchers.h"
+#include "testutils/xvgtest.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+class DhdlTest : public CommandLineTestBase
+{
+ public:
+ void runTest()
+ {
+ auto &cmdline = commandLine();
+ cmdline.append("energy");
+
+ setInputFile("-s", "dhdl.tpr");
+ setInputFile("-f", "dhdl.edr");
+ setOutputFile("-odh", "dhdl.xvg", XvgMatch());
+
+ ASSERT_EQ(0, gmx_energy(cmdline.argc(), cmdline.argv()));
+
+ checkOutputFiles();
+ }
+};
+
+TEST_F(DhdlTest, ExtractDhdl)
+{
+ runTest();
+}
+
+class OriresTest : public CommandLineTestBase
+{
+ public:
+ void runTest(const char *stringForStdin)
+ {
+ auto &cmdline = commandLine();
+ cmdline.append("energy");
+
+ setInputFile("-s", "orires.tpr");
+ setInputFile("-f", "orires.edr");
+ test::XvgMatch xvg;
+ test::XvgMatch &toler = xvg.tolerance(gmx::test::relativeToleranceAsFloatingPoint(1, 1e-4));
+
+ setOutputFile("-oten", ".xvg", toler);
+ setOutputFile("-ora", ".xvg", toler);
+ setOutputFile("-ort", ".xvg", toler);
+ setOutputFile("-oda", ".xvg", toler);
+ setOutputFile("-odr", ".xvg", toler);
+
+ StdioTestHelper stdioHelper(&fileManager());
+ stdioHelper.redirectStringToStdin(stringForStdin);
+ ASSERT_EQ(0, gmx_energy(cmdline.argc(), cmdline.argv()));
+
+ checkOutputFiles();
+ }
+};
+
+TEST_F(OriresTest, ExtractOrires)
+{
+ runTest("Orient.-Rest.\nOri.-R.-RMSD\n0\n-1\n");
+}
+
+class EnergyTest : public CommandLineTestBase
+{
+ public:
+ void runTest(const char *stringForStdin)
+ {
+ auto &cmdline = commandLine();
+ cmdline.append("energy");
+
+ setInputFile("-f", "ener.edr");
+ setOutputFile("-o", "energy.xvg", XvgMatch());
+
+ StdioTestHelper stdioHelper(&fileManager());
+ stdioHelper.redirectStringToStdin(stringForStdin);
+ ASSERT_EQ(0, gmx_energy(cmdline.argc(), cmdline.argv()));
+
+ checkOutputFiles();
+ }
+};
+
+TEST_F(EnergyTest, ExtractEnergy)
+{
+ runTest("Potential\nKinetic-En.\nTotal-Energy\n");
+}
+
+TEST_F(EnergyTest, ExtractEnergyByNumber)
+{
+ runTest("4 6 9");
+}
+
+TEST_F(EnergyTest, ExtractEnergyMixed)
+{
+ runTest("Pressu\n7\nbox-z\nvol\n");
+}
+
+class ViscosityTest : public CommandLineTestBase
+{
+ public:
+ void runTest()
+ {
+ auto &cmdline = commandLine();
+ setInputFile("-f", "ener.edr");
+ setOutputFile("-vis", "visco.xvg", NoTextMatch());
+ setOutputFile("-o", "energy.xvg", NoTextMatch());
+
+ /* -vis can write a lot of non-conditional output files,
+ so we use temporary paths to clean up files that are
+ not the ones being tested in this test */
+ if (!cmdline.contains("-evisco"))
+ {
+ setOutputFile("-evisco", "evisco.xvg", NoTextMatch());
+ }
+ if (!cmdline.contains("-eviscoi"))
+ {
+ setOutputFile("-eviscoi", "eviscoi.xvg", NoTextMatch());
+ }
+ if (!cmdline.contains("-corr"))
+ {
+ setOutputFile("-corr", "corr.xvg", NoTextMatch());
+ }
+
+ ASSERT_EQ(0, gmx_energy(cmdline.argc(), cmdline.argv()));
+
+ checkOutputFiles();
+ }
+};
+
+TEST_F(ViscosityTest, EinsteinViscosity)
+{
+ auto tolerance = relativeToleranceAsFloatingPoint(1e-4, 1e-5);
+ setOutputFile("-evisco", "evisco.xvg", XvgMatch().tolerance(tolerance));
+ runTest();
+}
+
+TEST_F(ViscosityTest, EinsteinViscosityIntegral)
+{
+ auto tolerance = relativeToleranceAsFloatingPoint(1e-4, 1e-5);
+ setOutputFile("-eviscoi", "eviscoi.xvg", XvgMatch().tolerance(tolerance));
+ runTest();
+}
+
+} // namespace
+} // namespace test
+} // namespace gmx
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-odh">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "dH/d\xl\f{} and \xD\f{}H"
+xaxis label "Time (ps)"
+yaxis label "dH/d\xl\f{} and \xD\f{}H (kJ/mol [\xl\f{}]\S-1\N)"
+TYPE xy
+subtitle "T = 300 (K) \xl\f{} state 0: (mass-lambda, coul-lambda, vdw-lambda, bonded-lambda, restraint-lambda) = (0.0000, 0.0000, 0.0000, 0.0000, 0.0000)"
+s0 legend "Total Energy (kJ/mol)"
+s1 legend "dH/d\xl\f{} mass-lambda = 0.0000"
+s2 legend "dH/d\xl\f{} coul-lambda = 0.0000"
+s3 legend "dH/d\xl\f{} vdw-lambda = 0.0000"
+s4 legend "dH/d\xl\f{} bonded-lambda = 0.0000"
+s5 legend "dH/d\xl\f{} restraint-lambda = 0.0000"
+s6 legend "\xD\f{}H \xl\f{} to (0.0000, 0.0000, 0.0000, 0.0000, 0.0000)"
+s7 legend "\xD\f{}H \xl\f{} to (0.0000, 0.0000, 0.0500, 0.0000, 0.0000)"
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">9</Int>
+ <Real>0.0000</Real>
+ <Real>18390.227</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-196.12737</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-13.036427</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">9</Int>
+ <Real>0.0100</Real>
+ <Real>21152.699</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-35.961620</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-2.2861712</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">9</Int>
+ <Real>0.0200</Real>
+ <Real>21066.111</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>1.7135231</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.017940877</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">9</Int>
+ <Real>0.0300</Real>
+ <Real>19459.748</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>7.3273606</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.29574844</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">9</Int>
+ <Real>0.0400</Real>
+ <Real>19005.387</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>6.0574341</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.22905751</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">9</Int>
+ <Real>0.0500</Real>
+ <Real>18289.822</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>5.3447599</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.19143827</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">9</Int>
+ <Real>0.0600</Real>
+ <Real>17736.605</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-11.790483</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.82747537</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">9</Int>
+ <Real>0.0700</Real>
+ <Real>17300.516</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-54.836746</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-3.6717050</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">9</Int>
+ <Real>0.0800</Real>
+ <Real>16784.359</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-34.148647</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-2.3589497</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">9</Int>
+ <Real>0.0900</Real>
+ <Real>16278.450</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-9.2076368</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.69482511</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">9</Int>
+ <Real>0.1000</Real>
+ <Real>15822.979</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.9046206</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.25472176</Real>
+ </Sequence>
+ <Sequence Name="Row11">
+ <Int Name="Length">9</Int>
+ <Real>0.1100</Real>
+ <Real>15291.021</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-14.417473</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.99669981</Real>
+ </Sequence>
+ <Sequence Name="Row12">
+ <Int Name="Length">9</Int>
+ <Real>0.1200</Real>
+ <Real>14932.876</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-5.5879068</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.46490976</Real>
+ </Sequence>
+ <Sequence Name="Row13">
+ <Int Name="Length">9</Int>
+ <Real>0.1300</Real>
+ <Real>14519.196</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-24.104668</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.6748879</Real>
+ </Sequence>
+ <Sequence Name="Row14">
+ <Int Name="Length">9</Int>
+ <Real>0.1400</Real>
+ <Real>14052.404</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>4.2050481</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.10811933</Real>
+ </Sequence>
+ <Sequence Name="Row15">
+ <Int Name="Length">9</Int>
+ <Real>0.1500</Real>
+ <Real>13574.979</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.654684</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.59728938</Real>
+ </Sequence>
+ <Sequence Name="Row16">
+ <Int Name="Length">9</Int>
+ <Real>0.1600</Real>
+ <Real>13158.244</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>9.8413372</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.43559965</Real>
+ </Sequence>
+ <Sequence Name="Row17">
+ <Int Name="Length">9</Int>
+ <Real>0.1700</Real>
+ <Real>12742.010</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>8.8647861</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.37434009</Real>
+ </Sequence>
+ <Sequence Name="Row18">
+ <Int Name="Length">9</Int>
+ <Real>0.1800</Real>
+ <Real>12412.632</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-12.401940</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.94610727</Real>
+ </Sequence>
+ <Sequence Name="Row19">
+ <Int Name="Length">9</Int>
+ <Real>0.1900</Real>
+ <Real>12025.834</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-15.554813</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.0771699</Real>
+ </Sequence>
+ <Sequence Name="Row20">
+ <Int Name="Length">9</Int>
+ <Real>0.2000</Real>
+ <Real>11668.844</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-13.853206</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.94716883</Real>
+ </Sequence>
+ <Sequence Name="Row21">
+ <Int Name="Length">9</Int>
+ <Real>0.2100</Real>
+ <Real>11284.039</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-20.998755</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.4247464</Real>
+ </Sequence>
+ <Sequence Name="Row22">
+ <Int Name="Length">9</Int>
+ <Real>0.2200</Real>
+ <Real>10911.894</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-14.923985</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.0453514</Real>
+ </Sequence>
+ <Sequence Name="Row23">
+ <Int Name="Length">9</Int>
+ <Real>0.2300</Real>
+ <Real>10566.955</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-19.922283</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.4520115</Real>
+ </Sequence>
+ <Sequence Name="Row24">
+ <Int Name="Length">9</Int>
+ <Real>0.2400</Real>
+ <Real>10231.230</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>4.7994976</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.14404032</Real>
+ </Sequence>
+ <Sequence Name="Row25">
+ <Int Name="Length">9</Int>
+ <Real>0.2500</Real>
+ <Real>9968.4209</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>9.7707586</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.43524343</Real>
+ </Sequence>
+ <Sequence Name="Row26">
+ <Int Name="Length">9</Int>
+ <Real>0.2600</Real>
+ <Real>9683.9785</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>5.5255494</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.18996415</Real>
+ </Sequence>
+ <Sequence Name="Row27">
+ <Int Name="Length">9</Int>
+ <Real>0.2700</Real>
+ <Real>9378.0811</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>1.7950813</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.017419390</Real>
+ </Sequence>
+ <Sequence Name="Row28">
+ <Int Name="Length">9</Int>
+ <Real>0.2800</Real>
+ <Real>9007.4697</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-12.662108</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.87385261</Real>
+ </Sequence>
+ <Sequence Name="Row29">
+ <Int Name="Length">9</Int>
+ <Real>0.2900</Real>
+ <Real>8753.9697</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.3624085</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.18725003</Real>
+ </Sequence>
+ <Sequence Name="Row30">
+ <Int Name="Length">9</Int>
+ <Real>0.3000</Real>
+ <Real>8465.7949</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>1.3957028</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.027882095</Real>
+ </Sequence>
+ <Sequence Name="Row31">
+ <Int Name="Length">9</Int>
+ <Real>0.3100</Real>
+ <Real>8127.0200</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>3.6105075</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.086347379</Real>
+ </Sequence>
+ <Sequence Name="Row32">
+ <Int Name="Length">9</Int>
+ <Real>0.3200</Real>
+ <Real>7764.1157</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>11.106931</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.52358508</Real>
+ </Sequence>
+ <Sequence Name="Row33">
+ <Int Name="Length">9</Int>
+ <Real>0.3300</Real>
+ <Real>7480.6064</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.847497</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.62090510</Real>
+ </Sequence>
+ <Sequence Name="Row34">
+ <Int Name="Length">9</Int>
+ <Real>0.3400</Real>
+ <Real>7215.4707</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.040525</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.57890755</Real>
+ </Sequence>
+ <Sequence Name="Row35">
+ <Int Name="Length">9</Int>
+ <Real>0.3500</Real>
+ <Real>6892.3647</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>13.036567</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.63370013</Real>
+ </Sequence>
+ <Sequence Name="Row36">
+ <Int Name="Length">9</Int>
+ <Real>0.3600</Real>
+ <Real>6565.7085</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>10.898385</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.50941873</Real>
+ </Sequence>
+ <Sequence Name="Row37">
+ <Int Name="Length">9</Int>
+ <Real>0.3700</Real>
+ <Real>6260.1587</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.076806</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.57912481</Real>
+ </Sequence>
+ <Sequence Name="Row38">
+ <Int Name="Length">9</Int>
+ <Real>0.3800</Real>
+ <Real>6047.1582</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>14.722479</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.73049068</Real>
+ </Sequence>
+ <Sequence Name="Row39">
+ <Int Name="Length">9</Int>
+ <Real>0.3900</Real>
+ <Real>5769.3306</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>15.253819</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.76127720</Real>
+ </Sequence>
+ <Sequence Name="Row40">
+ <Int Name="Length">9</Int>
+ <Real>0.4000</Real>
+ <Real>5491.2158</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>15.621739</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.78124112</Real>
+ </Sequence>
+ <Sequence Name="Row41">
+ <Int Name="Length">9</Int>
+ <Real>0.4100</Real>
+ <Real>5239.2842</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>15.019732</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.74851453</Real>
+ </Sequence>
+ <Sequence Name="Row42">
+ <Int Name="Length">9</Int>
+ <Real>0.4200</Real>
+ <Real>4955.2236</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.970184</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.63469940</Real>
+ </Sequence>
+ <Sequence Name="Row43">
+ <Int Name="Length">9</Int>
+ <Real>0.4300</Real>
+ <Real>4695.3511</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>7.2544327</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.31172675</Real>
+ </Sequence>
+ <Sequence Name="Row44">
+ <Int Name="Length">9</Int>
+ <Real>0.4400</Real>
+ <Real>4476.2344</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.5105438</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.018204786</Real>
+ </Sequence>
+ <Sequence Name="Row45">
+ <Int Name="Length">9</Int>
+ <Real>0.4500</Real>
+ <Real>4234.5391</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.1897080</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.021179220</Real>
+ </Sequence>
+ <Sequence Name="Row46">
+ <Int Name="Length">9</Int>
+ <Real>0.4600</Real>
+ <Real>3972.7383</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.5433095</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.036578804</Real>
+ </Sequence>
+ <Sequence Name="Row47">
+ <Int Name="Length">9</Int>
+ <Real>0.4700</Real>
+ <Real>3675.9219</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>4.9355130</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.18048137</Real>
+ </Sequence>
+ <Sequence Name="Row48">
+ <Int Name="Length">9</Int>
+ <Real>0.4800</Real>
+ <Real>3402.2808</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>4.8340473</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.17349699</Real>
+ </Sequence>
+ <Sequence Name="Row49">
+ <Int Name="Length">9</Int>
+ <Real>0.4900</Real>
+ <Real>3210.3071</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>8.0225458</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.34982723</Real>
+ </Sequence>
+ <Sequence Name="Row50">
+ <Int Name="Length">9</Int>
+ <Real>0.5000</Real>
+ <Real>2963.7800</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>11.747848</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.56046647</Real>
+ </Sequence>
+ <Sequence Name="Row51">
+ <Int Name="Length">9</Int>
+ <Real>0.5100</Real>
+ <Real>2837.0615</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>1.7925872</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.018638892</Real>
+ </Sequence>
+ <Sequence Name="Row52">
+ <Int Name="Length">9</Int>
+ <Real>0.5200</Real>
+ <Real>2599.4478</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-10.107281</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.77151293</Real>
+ </Sequence>
+ <Sequence Name="Row53">
+ <Int Name="Length">9</Int>
+ <Real>0.5300</Real>
+ <Real>2392.7219</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-3.8234668</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.39228624</Real>
+ </Sequence>
+ <Sequence Name="Row54">
+ <Int Name="Length">9</Int>
+ <Real>0.5400</Real>
+ <Real>2141.3977</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>4.9235377</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.16121981</Real>
+ </Sequence>
+ <Sequence Name="Row55">
+ <Int Name="Length">9</Int>
+ <Real>0.5500</Real>
+ <Real>1894.3961</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>5.7242775</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.20739347</Real>
+ </Sequence>
+ <Sequence Name="Row56">
+ <Int Name="Length">9</Int>
+ <Real>0.5600</Real>
+ <Real>1650.1195</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>3.1604090</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.065963924</Real>
+ </Sequence>
+ <Sequence Name="Row57">
+ <Int Name="Length">9</Int>
+ <Real>0.5700</Real>
+ <Real>1442.5604</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-21.118731</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.3982593</Real>
+ </Sequence>
+ <Sequence Name="Row58">
+ <Int Name="Length">9</Int>
+ <Real>0.5800</Real>
+ <Real>1154.2802</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-11.551435</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.80686474</Real>
+ </Sequence>
+ <Sequence Name="Row59">
+ <Int Name="Length">9</Int>
+ <Real>0.5900</Real>
+ <Real>977.92596</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-19.052465</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-1.2597023</Real>
+ </Sequence>
+ <Sequence Name="Row60">
+ <Int Name="Length">9</Int>
+ <Real>0.6000</Real>
+ <Real>739.69891</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.54290044</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.15558498</Real>
+ </Sequence>
+ <Sequence Name="Row61">
+ <Int Name="Length">9</Int>
+ <Real>0.6100</Real>
+ <Real>502.32535</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.3928659</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.021699622</Real>
+ </Sequence>
+ <Sequence Name="Row62">
+ <Int Name="Length">9</Int>
+ <Real>0.6200</Real>
+ <Real>332.78494</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>3.9483552</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.10301653</Real>
+ </Sequence>
+ <Sequence Name="Row63">
+ <Int Name="Length">9</Int>
+ <Real>0.6300</Real>
+ <Real>117.40592</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.4123704</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.020102538</Real>
+ </Sequence>
+ <Sequence Name="Row64">
+ <Int Name="Length">9</Int>
+ <Real>0.6400</Real>
+ <Real>-35.941978</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-4.7306657</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.39635584</Real>
+ </Sequence>
+ <Sequence Name="Row65">
+ <Int Name="Length">9</Int>
+ <Real>0.6500</Real>
+ <Real>-246.84441</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-2.7428317</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.26893592</Real>
+ </Sequence>
+ <Sequence Name="Row66">
+ <Int Name="Length">9</Int>
+ <Real>0.6600</Real>
+ <Real>-401.82376</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-5.7742028</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.45050329</Real>
+ </Sequence>
+ <Sequence Name="Row67">
+ <Int Name="Length">9</Int>
+ <Real>0.6700</Real>
+ <Real>-515.35016</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-7.4531288</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.57305795</Real>
+ </Sequence>
+ <Sequence Name="Row68">
+ <Int Name="Length">9</Int>
+ <Real>0.6800</Real>
+ <Real>-706.58044</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>1.6042513</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.023598678</Real>
+ </Sequence>
+ <Sequence Name="Row69">
+ <Int Name="Length">9</Int>
+ <Real>0.6900</Real>
+ <Real>-890.52930</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>5.2660694</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.17871600</Real>
+ </Sequence>
+ <Sequence Name="Row70">
+ <Int Name="Length">9</Int>
+ <Real>0.7000</Real>
+ <Real>-1076.5763</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>4.0205736</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.085871026</Real>
+ </Sequence>
+ <Sequence Name="Row71">
+ <Int Name="Length">9</Int>
+ <Real>0.7100</Real>
+ <Real>-1205.3600</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>10.127654</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.45515704</Real>
+ </Sequence>
+ <Sequence Name="Row72">
+ <Int Name="Length">9</Int>
+ <Real>0.7200</Real>
+ <Real>-1401.7433</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>10.694732</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.49325097</Real>
+ </Sequence>
+ <Sequence Name="Row73">
+ <Int Name="Length">9</Int>
+ <Real>0.7300</Real>
+ <Real>-1511.8746</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>13.002579</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.62048405</Real>
+ </Sequence>
+ <Sequence Name="Row74">
+ <Int Name="Length">9</Int>
+ <Real>0.7400</Real>
+ <Real>-1686.1857</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.355764</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.58085251</Real>
+ </Sequence>
+ <Sequence Name="Row75">
+ <Int Name="Length">9</Int>
+ <Real>0.7500</Real>
+ <Real>-1870.8121</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>11.427918</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.52940631</Real>
+ </Sequence>
+ <Sequence Name="Row76">
+ <Int Name="Length">9</Int>
+ <Real>0.7600</Real>
+ <Real>-2049.8137</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>13.941729</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.67407155</Real>
+ </Sequence>
+ <Sequence Name="Row77">
+ <Int Name="Length">9</Int>
+ <Real>0.7700</Real>
+ <Real>-2238.1753</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>13.486353</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.64925963</Real>
+ </Sequence>
+ <Sequence Name="Row78">
+ <Int Name="Length">9</Int>
+ <Real>0.7800</Real>
+ <Real>-2392.8804</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.826356</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.61224586</Real>
+ </Sequence>
+ <Sequence Name="Row79">
+ <Int Name="Length">9</Int>
+ <Real>0.7900</Real>
+ <Real>-2588.4917</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>8.2970324</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.34881678</Real>
+ </Sequence>
+ <Sequence Name="Row80">
+ <Int Name="Length">9</Int>
+ <Real>0.8000</Real>
+ <Real>-2757.0720</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>11.945762</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.56193101</Real>
+ </Sequence>
+ <Sequence Name="Row81">
+ <Int Name="Length">9</Int>
+ <Real>0.8100</Real>
+ <Real>-2903.7708</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>5.3924117</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.18367814</Real>
+ </Sequence>
+ <Sequence Name="Row82">
+ <Int Name="Length">9</Int>
+ <Real>0.8200</Real>
+ <Real>-3047.7859</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>11.101733</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.51431257</Real>
+ </Sequence>
+ <Sequence Name="Row83">
+ <Int Name="Length">9</Int>
+ <Real>0.8300</Real>
+ <Real>-3161.5854</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>9.6307545</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.42988670</Real>
+ </Sequence>
+ <Sequence Name="Row84">
+ <Int Name="Length">9</Int>
+ <Real>0.8400</Real>
+ <Real>-3379.0830</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>12.023994</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.56784922</Real>
+ </Sequence>
+ <Sequence Name="Row85">
+ <Int Name="Length">9</Int>
+ <Real>0.8500</Real>
+ <Real>-3558.4021</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>11.185745</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.52070016</Real>
+ </Sequence>
+ <Sequence Name="Row86">
+ <Int Name="Length">9</Int>
+ <Real>0.8600</Real>
+ <Real>-3652.6042</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.8762925</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.010642702</Real>
+ </Sequence>
+ <Sequence Name="Row87">
+ <Int Name="Length">9</Int>
+ <Real>0.8700</Real>
+ <Real>-3829.2700</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>3.7260182</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.071571045</Real>
+ </Sequence>
+ <Sequence Name="Row88">
+ <Int Name="Length">9</Int>
+ <Real>0.8800</Real>
+ <Real>-3955.3086</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>6.0863285</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.22653362</Real>
+ </Sequence>
+ <Sequence Name="Row89">
+ <Int Name="Length">9</Int>
+ <Real>0.8900</Real>
+ <Real>-4086.2063</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>3.3721447</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.083420321</Real>
+ </Sequence>
+ <Sequence Name="Row90">
+ <Int Name="Length">9</Int>
+ <Real>0.9000</Real>
+ <Real>-4189.3530</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>3.2029264</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.073568165</Real>
+ </Sequence>
+ <Sequence Name="Row91">
+ <Int Name="Length">9</Int>
+ <Real>0.9100</Real>
+ <Real>-4346.2114</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.5930278</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.038073756</Real>
+ </Sequence>
+ <Sequence Name="Row92">
+ <Int Name="Length">9</Int>
+ <Real>0.9200</Real>
+ <Real>-4513.3115</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>5.4292865</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.20921849</Real>
+ </Sequence>
+ <Sequence Name="Row93">
+ <Int Name="Length">9</Int>
+ <Real>0.9300</Real>
+ <Real>-4716.2129</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.2852771</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.030672517</Real>
+ </Sequence>
+ <Sequence Name="Row94">
+ <Int Name="Length">9</Int>
+ <Real>0.9400</Real>
+ <Real>-4813.1924</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-7.1204696</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.53045851</Real>
+ </Sequence>
+ <Sequence Name="Row95">
+ <Int Name="Length">9</Int>
+ <Real>0.9500</Real>
+ <Real>-4961.3779</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.63605487</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.14009029</Real>
+ </Sequence>
+ <Sequence Name="Row96">
+ <Int Name="Length">9</Int>
+ <Real>0.9600</Real>
+ <Real>-5113.8364</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>1.3637644</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.024320509</Real>
+ </Sequence>
+ <Sequence Name="Row97">
+ <Int Name="Length">9</Int>
+ <Real>0.9700</Real>
+ <Real>-5263.4927</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.24821608</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>-0.11575874</Real>
+ </Sequence>
+ <Sequence Name="Row98">
+ <Int Name="Length">9</Int>
+ <Real>0.9800</Real>
+ <Real>-5368.6714</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.0372019</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0095707709</Real>
+ </Sequence>
+ <Sequence Name="Row99">
+ <Int Name="Length">9</Int>
+ <Real>0.9900</Real>
+ <Real>-5487.4829</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>4.7544155</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.15978737</Real>
+ </Sequence>
+ <Sequence Name="Row100">
+ <Int Name="Length">9</Int>
+ <Real>1.0000</Real>
+ <Real>-5616.9009</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>2.7037058</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.0000000</Real>
+ <Real>0.044261467</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "GROMACS Energies"
+xaxis label "Time (ps)"
+yaxis label "(kJ/mol)"
+TYPE xy
+s0 legend "Potential"
+s1 legend "Kinetic En."
+s2 legend "Total Energy"
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">4</Int>
+ <Real>0.000000</Real>
+ <Real>-32102.556641</Real>
+ <Real>6147.870117</Real>
+ <Real>-25954.687500</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">4</Int>
+ <Real>0.200000</Real>
+ <Real>-34450.820312</Real>
+ <Real>5885.405273</Real>
+ <Real>-28565.414062</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">4</Int>
+ <Real>0.400000</Real>
+ <Real>-33708.703125</Real>
+ <Real>6146.063477</Real>
+ <Real>-27562.640625</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">4</Int>
+ <Real>0.600000</Real>
+ <Real>-33897.753906</Real>
+ <Real>6079.209473</Real>
+ <Real>-27818.544922</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">4</Int>
+ <Real>0.800000</Real>
+ <Real>-33992.132812</Real>
+ <Real>6242.735352</Real>
+ <Real>-27749.398438</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">4</Int>
+ <Real>1.000000</Real>
+ <Real>-34110.496094</Real>
+ <Real>6005.650391</Real>
+ <Real>-28104.845703</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">4</Int>
+ <Real>1.200000</Real>
+ <Real>-34426.128906</Real>
+ <Real>6251.612305</Real>
+ <Real>-28174.515625</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">4</Int>
+ <Real>1.400000</Real>
+ <Real>-33967.996094</Real>
+ <Real>6241.403809</Real>
+ <Real>-27726.591797</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">4</Int>
+ <Real>1.600000</Real>
+ <Real>-34323.785156</Real>
+ <Real>6419.104492</Real>
+ <Real>-27904.679688</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">4</Int>
+ <Real>1.800000</Real>
+ <Real>-34305.316406</Real>
+ <Real>6256.709473</Real>
+ <Real>-28048.607422</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">4</Int>
+ <Real>2.000000</Real>
+ <Real>-34260.628906</Real>
+ <Real>6094.508301</Real>
+ <Real>-28166.121094</Real>
+ </Sequence>
+ <Sequence Name="Row11">
+ <Int Name="Length">4</Int>
+ <Real>2.200000</Real>
+ <Real>-34596.117188</Real>
+ <Real>6014.866699</Real>
+ <Real>-28581.250000</Real>
+ </Sequence>
+ <Sequence Name="Row12">
+ <Int Name="Length">4</Int>
+ <Real>2.400000</Real>
+ <Real>-34348.128906</Real>
+ <Real>6177.041016</Real>
+ <Real>-28171.087891</Real>
+ </Sequence>
+ <Sequence Name="Row13">
+ <Int Name="Length">4</Int>
+ <Real>2.600000</Real>
+ <Real>-33940.769531</Real>
+ <Real>5990.643066</Real>
+ <Real>-27950.126953</Real>
+ </Sequence>
+ <Sequence Name="Row14">
+ <Int Name="Length">4</Int>
+ <Real>2.800000</Real>
+ <Real>-34303.445312</Real>
+ <Real>6077.416992</Real>
+ <Real>-28226.027344</Real>
+ </Sequence>
+ <Sequence Name="Row15">
+ <Int Name="Length">4</Int>
+ <Real>3.000000</Real>
+ <Real>-34235.710938</Real>
+ <Real>6137.697754</Real>
+ <Real>-28098.013672</Real>
+ </Sequence>
+ <Sequence Name="Row16">
+ <Int Name="Length">4</Int>
+ <Real>3.200000</Real>
+ <Real>-34002.332031</Real>
+ <Real>6238.207031</Real>
+ <Real>-27764.125000</Real>
+ </Sequence>
+ <Sequence Name="Row17">
+ <Int Name="Length">4</Int>
+ <Real>3.400000</Real>
+ <Real>-34057.250000</Real>
+ <Real>6159.159180</Real>
+ <Real>-27898.089844</Real>
+ </Sequence>
+ <Sequence Name="Row18">
+ <Int Name="Length">4</Int>
+ <Real>3.600000</Real>
+ <Real>-34600.128906</Real>
+ <Real>6063.009766</Real>
+ <Real>-28537.119141</Real>
+ </Sequence>
+ <Sequence Name="Row19">
+ <Int Name="Length">4</Int>
+ <Real>3.800000</Real>
+ <Real>-34239.929688</Real>
+ <Real>6266.519043</Real>
+ <Real>-27973.410156</Real>
+ </Sequence>
+ <Sequence Name="Row20">
+ <Int Name="Length">4</Int>
+ <Real>4.000000</Real>
+ <Real>-34098.769531</Real>
+ <Real>6216.680176</Real>
+ <Real>-27882.089844</Real>
+ </Sequence>
+ <Sequence Name="Row21">
+ <Int Name="Length">4</Int>
+ <Real>4.200000</Real>
+ <Real>-34068.769531</Real>
+ <Real>6327.523926</Real>
+ <Real>-27741.246094</Real>
+ </Sequence>
+ <Sequence Name="Row22">
+ <Int Name="Length">4</Int>
+ <Real>4.400000</Real>
+ <Real>-33888.636719</Real>
+ <Real>6213.844727</Real>
+ <Real>-27674.792969</Real>
+ </Sequence>
+ <Sequence Name="Row23">
+ <Int Name="Length">4</Int>
+ <Real>4.600000</Real>
+ <Real>-33936.765625</Real>
+ <Real>6261.648438</Real>
+ <Real>-27675.117188</Real>
+ </Sequence>
+ <Sequence Name="Row24">
+ <Int Name="Length">4</Int>
+ <Real>4.800000</Real>
+ <Real>-33911.062500</Real>
+ <Real>6168.812500</Real>
+ <Real>-27742.250000</Real>
+ </Sequence>
+ <Sequence Name="Row25">
+ <Int Name="Length">4</Int>
+ <Real>5.000000</Real>
+ <Real>-33947.417969</Real>
+ <Real>6095.376953</Real>
+ <Real>-27852.041016</Real>
+ </Sequence>
+ <Sequence Name="Row26">
+ <Int Name="Length">4</Int>
+ <Real>5.200000</Real>
+ <Real>-34157.207031</Real>
+ <Real>5930.162109</Real>
+ <Real>-28227.044922</Real>
+ </Sequence>
+ <Sequence Name="Row27">
+ <Int Name="Length">4</Int>
+ <Real>5.400000</Real>
+ <Real>-33914.910156</Real>
+ <Real>6003.146973</Real>
+ <Real>-27911.763672</Real>
+ </Sequence>
+ <Sequence Name="Row28">
+ <Int Name="Length">4</Int>
+ <Real>5.600000</Real>
+ <Real>-33877.945312</Real>
+ <Real>6124.571777</Real>
+ <Real>-27753.373047</Real>
+ </Sequence>
+ <Sequence Name="Row29">
+ <Int Name="Length">4</Int>
+ <Real>5.800000</Real>
+ <Real>-34020.351562</Real>
+ <Real>6162.232910</Real>
+ <Real>-27858.119141</Real>
+ </Sequence>
+ <Sequence Name="Row30">
+ <Int Name="Length">4</Int>
+ <Real>6.000000</Real>
+ <Real>-34128.800781</Real>
+ <Real>6059.147461</Real>
+ <Real>-28069.652344</Real>
+ </Sequence>
+ <Sequence Name="Row31">
+ <Int Name="Length">4</Int>
+ <Real>6.200000</Real>
+ <Real>-34273.890625</Real>
+ <Real>6066.780273</Real>
+ <Real>-28207.109375</Real>
+ </Sequence>
+ <Sequence Name="Row32">
+ <Int Name="Length">4</Int>
+ <Real>6.400000</Real>
+ <Real>-33896.531250</Real>
+ <Real>6135.265137</Real>
+ <Real>-27761.265625</Real>
+ </Sequence>
+ <Sequence Name="Row33">
+ <Int Name="Length">4</Int>
+ <Real>6.600000</Real>
+ <Real>-34351.207031</Real>
+ <Real>6222.209961</Real>
+ <Real>-28128.996094</Real>
+ </Sequence>
+ <Sequence Name="Row34">
+ <Int Name="Length">4</Int>
+ <Real>6.800000</Real>
+ <Real>-34294.121094</Real>
+ <Real>6135.084961</Real>
+ <Real>-28159.035156</Real>
+ </Sequence>
+ <Sequence Name="Row35">
+ <Int Name="Length">4</Int>
+ <Real>7.000000</Real>
+ <Real>-34033.593750</Real>
+ <Real>6281.751953</Real>
+ <Real>-27751.841797</Real>
+ </Sequence>
+ <Sequence Name="Row36">
+ <Int Name="Length">4</Int>
+ <Real>7.200000</Real>
+ <Real>-33949.714844</Real>
+ <Real>6196.525391</Real>
+ <Real>-27753.189453</Real>
+ </Sequence>
+ <Sequence Name="Row37">
+ <Int Name="Length">4</Int>
+ <Real>7.400000</Real>
+ <Real>-33534.386719</Real>
+ <Real>5933.003418</Real>
+ <Real>-27601.382812</Real>
+ </Sequence>
+ <Sequence Name="Row38">
+ <Int Name="Length">4</Int>
+ <Real>7.600000</Real>
+ <Real>-34207.582031</Real>
+ <Real>6100.635742</Real>
+ <Real>-28106.945312</Real>
+ </Sequence>
+ <Sequence Name="Row39">
+ <Int Name="Length">4</Int>
+ <Real>7.800000</Real>
+ <Real>-34221.773438</Real>
+ <Real>6173.767090</Real>
+ <Real>-28048.005859</Real>
+ </Sequence>
+ <Sequence Name="Row40">
+ <Int Name="Length">4</Int>
+ <Real>8.000000</Real>
+ <Real>-34048.535156</Real>
+ <Real>6069.120117</Real>
+ <Real>-27979.414062</Real>
+ </Sequence>
+ <Sequence Name="Row41">
+ <Int Name="Length">4</Int>
+ <Real>8.200000</Real>
+ <Real>-34067.558594</Real>
+ <Real>6030.937988</Real>
+ <Real>-28036.621094</Real>
+ </Sequence>
+ <Sequence Name="Row42">
+ <Int Name="Length">4</Int>
+ <Real>8.400000</Real>
+ <Real>-34414.148438</Real>
+ <Real>6250.905273</Real>
+ <Real>-28163.242188</Real>
+ </Sequence>
+ <Sequence Name="Row43">
+ <Int Name="Length">4</Int>
+ <Real>8.600000</Real>
+ <Real>-33985.910156</Real>
+ <Real>6157.070312</Real>
+ <Real>-27828.839844</Real>
+ </Sequence>
+ <Sequence Name="Row44">
+ <Int Name="Length">4</Int>
+ <Real>8.800000</Real>
+ <Real>-33963.457031</Real>
+ <Real>6056.696289</Real>
+ <Real>-27906.761719</Real>
+ </Sequence>
+ <Sequence Name="Row45">
+ <Int Name="Length">4</Int>
+ <Real>9.000000</Real>
+ <Real>-34317.792969</Real>
+ <Real>6261.636230</Real>
+ <Real>-28056.156250</Real>
+ </Sequence>
+ <Sequence Name="Row46">
+ <Int Name="Length">4</Int>
+ <Real>9.200000</Real>
+ <Real>-34095.843750</Real>
+ <Real>6217.412109</Real>
+ <Real>-27878.431641</Real>
+ </Sequence>
+ <Sequence Name="Row47">
+ <Int Name="Length">4</Int>
+ <Real>9.400000</Real>
+ <Real>-34211.437500</Real>
+ <Real>6132.755371</Real>
+ <Real>-28078.681641</Real>
+ </Sequence>
+ <Sequence Name="Row48">
+ <Int Name="Length">4</Int>
+ <Real>9.600000</Real>
+ <Real>-34119.976562</Real>
+ <Real>6159.531250</Real>
+ <Real>-27960.445312</Real>
+ </Sequence>
+ <Sequence Name="Row49">
+ <Int Name="Length">4</Int>
+ <Real>9.800000</Real>
+ <Real>-34448.562500</Real>
+ <Real>6217.981934</Real>
+ <Real>-28230.580078</Real>
+ </Sequence>
+ <Sequence Name="Row50">
+ <Int Name="Length">4</Int>
+ <Real>10.000000</Real>
+ <Real>-33944.414062</Real>
+ <Real>6107.636719</Real>
+ <Real>-27836.777344</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "GROMACS Energies"
+xaxis label "Time (ps)"
+yaxis label "(kJ/mol), (bar)"
+TYPE xy
+s0 legend "Coul. recip."
+s1 legend "Kinetic En."
+s2 legend "Pres. DC"
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">4</Int>
+ <Real>0.000000</Real>
+ <Real>412.675140</Real>
+ <Real>6147.870117</Real>
+ <Real>-277.241913</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">4</Int>
+ <Real>0.200000</Real>
+ <Real>286.838928</Real>
+ <Real>5885.405273</Real>
+ <Real>-305.226624</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">4</Int>
+ <Real>0.400000</Real>
+ <Real>318.294525</Real>
+ <Real>6146.063477</Real>
+ <Real>-276.163300</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">4</Int>
+ <Real>0.600000</Real>
+ <Real>316.279175</Real>
+ <Real>6079.209473</Real>
+ <Real>-271.288391</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">4</Int>
+ <Real>0.800000</Real>
+ <Real>303.799255</Real>
+ <Real>6242.735352</Real>
+ <Real>-274.734497</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">4</Int>
+ <Real>1.000000</Real>
+ <Real>299.513519</Real>
+ <Real>6005.650391</Real>
+ <Real>-278.492157</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">4</Int>
+ <Real>1.200000</Real>
+ <Real>293.994965</Real>
+ <Real>6251.612305</Real>
+ <Real>-283.624084</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">4</Int>
+ <Real>1.400000</Real>
+ <Real>292.305603</Real>
+ <Real>6241.403809</Real>
+ <Real>-271.350677</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">4</Int>
+ <Real>1.600000</Real>
+ <Real>295.773956</Real>
+ <Real>6419.104492</Real>
+ <Real>-282.657257</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">4</Int>
+ <Real>1.800000</Real>
+ <Real>277.526611</Real>
+ <Real>6256.709473</Real>
+ <Real>-278.745453</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">4</Int>
+ <Real>2.000000</Real>
+ <Real>298.229156</Real>
+ <Real>6094.508301</Real>
+ <Real>-271.631927</Real>
+ </Sequence>
+ <Sequence Name="Row11">
+ <Int Name="Length">4</Int>
+ <Real>2.200000</Real>
+ <Real>304.681488</Real>
+ <Real>6014.866699</Real>
+ <Real>-276.008667</Real>
+ </Sequence>
+ <Sequence Name="Row12">
+ <Int Name="Length">4</Int>
+ <Real>2.400000</Real>
+ <Real>305.796234</Real>
+ <Real>6177.041016</Real>
+ <Real>-272.094727</Real>
+ </Sequence>
+ <Sequence Name="Row13">
+ <Int Name="Length">4</Int>
+ <Real>2.600000</Real>
+ <Real>306.506500</Real>
+ <Real>5990.643066</Real>
+ <Real>-260.638428</Real>
+ </Sequence>
+ <Sequence Name="Row14">
+ <Int Name="Length">4</Int>
+ <Real>2.800000</Real>
+ <Real>333.718231</Real>
+ <Real>6077.416992</Real>
+ <Real>-257.015717</Real>
+ </Sequence>
+ <Sequence Name="Row15">
+ <Int Name="Length">4</Int>
+ <Real>3.000000</Real>
+ <Real>309.297546</Real>
+ <Real>6137.697754</Real>
+ <Real>-263.238159</Real>
+ </Sequence>
+ <Sequence Name="Row16">
+ <Int Name="Length">4</Int>
+ <Real>3.200000</Real>
+ <Real>293.729523</Real>
+ <Real>6238.207031</Real>
+ <Real>-266.992706</Real>
+ </Sequence>
+ <Sequence Name="Row17">
+ <Int Name="Length">4</Int>
+ <Real>3.400000</Real>
+ <Real>293.085510</Real>
+ <Real>6159.159180</Real>
+ <Real>-262.892700</Real>
+ </Sequence>
+ <Sequence Name="Row18">
+ <Int Name="Length">4</Int>
+ <Real>3.600000</Real>
+ <Real>261.200470</Real>
+ <Real>6063.009766</Real>
+ <Real>-264.705597</Real>
+ </Sequence>
+ <Sequence Name="Row19">
+ <Int Name="Length">4</Int>
+ <Real>3.800000</Real>
+ <Real>316.416992</Real>
+ <Real>6266.519043</Real>
+ <Real>-262.703918</Real>
+ </Sequence>
+ <Sequence Name="Row20">
+ <Int Name="Length">4</Int>
+ <Real>4.000000</Real>
+ <Real>306.888702</Real>
+ <Real>6216.680176</Real>
+ <Real>-266.768372</Real>
+ </Sequence>
+ <Sequence Name="Row21">
+ <Int Name="Length">4</Int>
+ <Real>4.200000</Real>
+ <Real>288.428619</Real>
+ <Real>6327.523926</Real>
+ <Real>-269.623749</Real>
+ </Sequence>
+ <Sequence Name="Row22">
+ <Int Name="Length">4</Int>
+ <Real>4.400000</Real>
+ <Real>316.909424</Real>
+ <Real>6213.844727</Real>
+ <Real>-272.557800</Real>
+ </Sequence>
+ <Sequence Name="Row23">
+ <Int Name="Length">4</Int>
+ <Real>4.600000</Real>
+ <Real>315.392242</Real>
+ <Real>6261.648438</Real>
+ <Real>-269.936920</Real>
+ </Sequence>
+ <Sequence Name="Row24">
+ <Int Name="Length">4</Int>
+ <Real>4.800000</Real>
+ <Real>306.055420</Real>
+ <Real>6168.812500</Real>
+ <Real>-262.402161</Real>
+ </Sequence>
+ <Sequence Name="Row25">
+ <Int Name="Length">4</Int>
+ <Real>5.000000</Real>
+ <Real>294.990906</Real>
+ <Real>6095.376953</Real>
+ <Real>-258.683838</Real>
+ </Sequence>
+ <Sequence Name="Row26">
+ <Int Name="Length">4</Int>
+ <Real>5.200000</Real>
+ <Real>289.555115</Real>
+ <Real>5930.162109</Real>
+ <Real>-259.584320</Real>
+ </Sequence>
+ <Sequence Name="Row27">
+ <Int Name="Length">4</Int>
+ <Real>5.400000</Real>
+ <Real>307.466949</Real>
+ <Real>6003.146973</Real>
+ <Real>-266.808014</Real>
+ </Sequence>
+ <Sequence Name="Row28">
+ <Int Name="Length">4</Int>
+ <Real>5.600000</Real>
+ <Real>299.525543</Real>
+ <Real>6124.571777</Real>
+ <Real>-271.693329</Real>
+ </Sequence>
+ <Sequence Name="Row29">
+ <Int Name="Length">4</Int>
+ <Real>5.800000</Real>
+ <Real>303.685181</Real>
+ <Real>6162.232910</Real>
+ <Real>-265.650055</Real>
+ </Sequence>
+ <Sequence Name="Row30">
+ <Int Name="Length">4</Int>
+ <Real>6.000000</Real>
+ <Real>302.508575</Real>
+ <Real>6059.147461</Real>
+ <Real>-262.166931</Real>
+ </Sequence>
+ <Sequence Name="Row31">
+ <Int Name="Length">4</Int>
+ <Real>6.200000</Real>
+ <Real>305.190033</Real>
+ <Real>6066.780273</Real>
+ <Real>-268.883850</Real>
+ </Sequence>
+ <Sequence Name="Row32">
+ <Int Name="Length">4</Int>
+ <Real>6.400000</Real>
+ <Real>316.891418</Real>
+ <Real>6135.265137</Real>
+ <Real>-264.964966</Real>
+ </Sequence>
+ <Sequence Name="Row33">
+ <Int Name="Length">4</Int>
+ <Real>6.600000</Real>
+ <Real>305.526703</Real>
+ <Real>6222.209961</Real>
+ <Real>-263.851654</Real>
+ </Sequence>
+ <Sequence Name="Row34">
+ <Int Name="Length">4</Int>
+ <Real>6.800000</Real>
+ <Real>306.182434</Real>
+ <Real>6135.084961</Real>
+ <Real>-261.104309</Real>
+ </Sequence>
+ <Sequence Name="Row35">
+ <Int Name="Length">4</Int>
+ <Real>7.000000</Real>
+ <Real>313.867401</Real>
+ <Real>6281.751953</Real>
+ <Real>-263.505280</Real>
+ </Sequence>
+ <Sequence Name="Row36">
+ <Int Name="Length">4</Int>
+ <Real>7.200000</Real>
+ <Real>327.160248</Real>
+ <Real>6196.525391</Real>
+ <Real>-260.642639</Real>
+ </Sequence>
+ <Sequence Name="Row37">
+ <Int Name="Length">4</Int>
+ <Real>7.400000</Real>
+ <Real>330.673920</Real>
+ <Real>5933.003418</Real>
+ <Real>-255.867264</Real>
+ </Sequence>
+ <Sequence Name="Row38">
+ <Int Name="Length">4</Int>
+ <Real>7.600000</Real>
+ <Real>299.878540</Real>
+ <Real>6100.635742</Real>
+ <Real>-263.021698</Real>
+ </Sequence>
+ <Sequence Name="Row39">
+ <Int Name="Length">4</Int>
+ <Real>7.800000</Real>
+ <Real>298.238159</Real>
+ <Real>6173.767090</Real>
+ <Real>-263.497375</Real>
+ </Sequence>
+ <Sequence Name="Row40">
+ <Int Name="Length">4</Int>
+ <Real>8.000000</Real>
+ <Real>346.477814</Real>
+ <Real>6069.120117</Real>
+ <Real>-252.196213</Real>
+ </Sequence>
+ <Sequence Name="Row41">
+ <Int Name="Length">4</Int>
+ <Real>8.200000</Real>
+ <Real>314.671814</Real>
+ <Real>6030.937988</Real>
+ <Real>-262.904236</Real>
+ </Sequence>
+ <Sequence Name="Row42">
+ <Int Name="Length">4</Int>
+ <Real>8.400000</Real>
+ <Real>306.445038</Real>
+ <Real>6250.905273</Real>
+ <Real>-275.029877</Real>
+ </Sequence>
+ <Sequence Name="Row43">
+ <Int Name="Length">4</Int>
+ <Real>8.600000</Real>
+ <Real>337.485474</Real>
+ <Real>6157.070312</Real>
+ <Real>-268.037445</Real>
+ </Sequence>
+ <Sequence Name="Row44">
+ <Int Name="Length">4</Int>
+ <Real>8.800000</Real>
+ <Real>313.903717</Real>
+ <Real>6056.696289</Real>
+ <Real>-263.511719</Real>
+ </Sequence>
+ <Sequence Name="Row45">
+ <Int Name="Length">4</Int>
+ <Real>9.000000</Real>
+ <Real>286.324554</Real>
+ <Real>6261.636230</Real>
+ <Real>-268.191803</Real>
+ </Sequence>
+ <Sequence Name="Row46">
+ <Int Name="Length">4</Int>
+ <Real>9.200000</Real>
+ <Real>296.164307</Real>
+ <Real>6217.412109</Real>
+ <Real>-265.517853</Real>
+ </Sequence>
+ <Sequence Name="Row47">
+ <Int Name="Length">4</Int>
+ <Real>9.400000</Real>
+ <Real>278.793793</Real>
+ <Real>6132.755371</Real>
+ <Real>-278.546753</Real>
+ </Sequence>
+ <Sequence Name="Row48">
+ <Int Name="Length">4</Int>
+ <Real>9.600000</Real>
+ <Real>322.638519</Real>
+ <Real>6159.531250</Real>
+ <Real>-273.344574</Real>
+ </Sequence>
+ <Sequence Name="Row49">
+ <Int Name="Length">4</Int>
+ <Real>9.800000</Real>
+ <Real>294.918335</Real>
+ <Real>6217.981934</Real>
+ <Real>-271.223114</Real>
+ </Sequence>
+ <Sequence Name="Row50">
+ <Int Name="Length">4</Int>
+ <Real>10.000000</Real>
+ <Real>323.157379</Real>
+ <Real>6107.636719</Real>
+ <Real>-266.596802</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-o">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "GROMACS Energies"
+xaxis label "Time (ps)"
+yaxis label "(kJ/mol), (bar), (nm), (nm^3)"
+TYPE xy
+s0 legend "Total Energy"
+s1 legend "Pressure"
+s2 legend "Box-Z"
+s3 legend "Volume"
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">5</Int>
+ <Real>0.000000</Real>
+ <Real>-25954.687500</Real>
+ <Real>-4113.184082</Real>
+ <Real>2.908700</Real>
+ <Real>24.609161</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">5</Int>
+ <Real>0.200000</Real>
+ <Real>-28565.414062</Real>
+ <Real>2182.145752</Real>
+ <Real>2.862453</Real>
+ <Real>23.453901</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">5</Int>
+ <Real>0.400000</Real>
+ <Real>-27562.640625</Real>
+ <Real>-1272.206055</Real>
+ <Real>2.910590</Real>
+ <Real>24.657173</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">5</Int>
+ <Real>0.600000</Real>
+ <Real>-27818.544922</Real>
+ <Real>52.116547</Real>
+ <Real>2.919243</Real>
+ <Real>24.877728</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">5</Int>
+ <Real>0.800000</Real>
+ <Real>-27749.398438</Real>
+ <Real>21.307526</Real>
+ <Real>2.913108</Real>
+ <Real>24.721209</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">5</Int>
+ <Real>1.000000</Real>
+ <Real>-28104.845703</Real>
+ <Real>-255.442398</Real>
+ <Real>2.906520</Real>
+ <Real>24.553862</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">5</Int>
+ <Real>1.200000</Real>
+ <Real>-28174.515625</Real>
+ <Real>563.564453</Real>
+ <Real>2.897688</Real>
+ <Real>24.330708</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">5</Int>
+ <Real>1.400000</Real>
+ <Real>-27726.591797</Real>
+ <Real>-1227.515869</Real>
+ <Real>2.919131</Real>
+ <Real>24.874872</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">5</Int>
+ <Real>1.600000</Real>
+ <Real>-27904.679688</Real>
+ <Real>915.864136</Real>
+ <Real>2.899337</Real>
+ <Real>24.372284</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">5</Int>
+ <Real>1.800000</Real>
+ <Real>-28048.607422</Real>
+ <Real>-279.529633</Real>
+ <Real>2.906079</Real>
+ <Real>24.542704</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">5</Int>
+ <Real>2.000000</Real>
+ <Real>-28166.121094</Real>
+ <Real>-458.908936</Real>
+ <Real>2.918627</Real>
+ <Real>24.861990</Real>
+ </Sequence>
+ <Sequence Name="Row11">
+ <Int Name="Length">5</Int>
+ <Real>2.200000</Real>
+ <Real>-28581.250000</Real>
+ <Real>-189.055450</Real>
+ <Real>2.910862</Real>
+ <Real>24.664082</Real>
+ </Sequence>
+ <Sequence Name="Row12">
+ <Int Name="Length">5</Int>
+ <Real>2.400000</Real>
+ <Real>-28171.087891</Real>
+ <Real>371.100586</Real>
+ <Real>2.917799</Real>
+ <Real>24.840837</Real>
+ </Sequence>
+ <Sequence Name="Row13">
+ <Int Name="Length">5</Int>
+ <Real>2.600000</Real>
+ <Real>-27950.126953</Real>
+ <Real>445.505615</Real>
+ <Real>2.938793</Real>
+ <Real>25.380903</Real>
+ </Sequence>
+ <Sequence Name="Row14">
+ <Int Name="Length">5</Int>
+ <Real>2.800000</Real>
+ <Real>-28226.027344</Real>
+ <Real>-383.208984</Real>
+ <Real>2.945657</Real>
+ <Real>25.559153</Real>
+ </Sequence>
+ <Sequence Name="Row15">
+ <Int Name="Length">5</Int>
+ <Real>3.000000</Real>
+ <Real>-28098.013672</Real>
+ <Real>-739.696289</Real>
+ <Real>2.933936</Real>
+ <Real>25.255260</Real>
+ </Sequence>
+ <Sequence Name="Row16">
+ <Int Name="Length">5</Int>
+ <Real>3.200000</Real>
+ <Real>-27764.125000</Real>
+ <Real>556.054443</Real>
+ <Real>2.927019</Real>
+ <Real>25.077057</Real>
+ </Sequence>
+ <Sequence Name="Row17">
+ <Int Name="Length">5</Int>
+ <Real>3.400000</Real>
+ <Real>-27898.089844</Real>
+ <Real>-191.586060</Real>
+ <Real>2.934578</Real>
+ <Real>25.271851</Real>
+ </Sequence>
+ <Sequence Name="Row18">
+ <Int Name="Length">5</Int>
+ <Real>3.600000</Real>
+ <Real>-28537.119141</Real>
+ <Real>-64.853195</Real>
+ <Real>2.931219</Real>
+ <Real>25.185162</Real>
+ </Sequence>
+ <Sequence Name="Row19">
+ <Int Name="Length">5</Int>
+ <Real>3.800000</Real>
+ <Real>-27973.410156</Real>
+ <Real>-586.303345</Real>
+ <Real>2.934929</Real>
+ <Real>25.280926</Real>
+ </Sequence>
+ <Sequence Name="Row20">
+ <Int Name="Length">5</Int>
+ <Real>4.000000</Real>
+ <Real>-27882.089844</Real>
+ <Real>-361.731506</Real>
+ <Real>2.927429</Real>
+ <Real>25.087599</Real>
+ </Sequence>
+ <Sequence Name="Row21">
+ <Int Name="Length">5</Int>
+ <Real>4.200000</Real>
+ <Real>-27741.246094</Real>
+ <Real>259.893829</Real>
+ <Real>2.922239</Real>
+ <Real>24.954405</Real>
+ </Sequence>
+ <Sequence Name="Row22">
+ <Int Name="Length">5</Int>
+ <Real>4.400000</Real>
+ <Real>-27674.792969</Real>
+ <Real>520.501953</Real>
+ <Real>2.916972</Real>
+ <Real>24.819725</Real>
+ </Sequence>
+ <Sequence Name="Row23">
+ <Int Name="Length">5</Int>
+ <Real>4.600000</Real>
+ <Real>-27675.117188</Real>
+ <Real>268.957916</Real>
+ <Real>2.921674</Real>
+ <Real>24.939926</Real>
+ </Sequence>
+ <Sequence Name="Row24">
+ <Int Name="Length">5</Int>
+ <Real>4.800000</Real>
+ <Real>-27742.250000</Real>
+ <Real>-204.915268</Real>
+ <Real>2.935492</Real>
+ <Real>25.295462</Real>
+ </Sequence>
+ <Sequence Name="Row25">
+ <Int Name="Length">5</Int>
+ <Real>5.000000</Real>
+ <Real>-27852.041016</Real>
+ <Real>5.506622</Real>
+ <Real>2.942482</Real>
+ <Real>25.476610</Real>
+ </Sequence>
+ <Sequence Name="Row26">
+ <Int Name="Length">5</Int>
+ <Real>5.200000</Real>
+ <Real>-28227.044922</Real>
+ <Real>-274.371277</Real>
+ <Real>2.940779</Real>
+ <Real>25.432384</Real>
+ </Sequence>
+ <Sequence Name="Row27">
+ <Int Name="Length">5</Int>
+ <Real>5.400000</Real>
+ <Real>-27911.763672</Real>
+ <Real>592.697144</Real>
+ <Real>2.927356</Real>
+ <Real>25.085735</Real>
+ </Sequence>
+ <Sequence Name="Row28">
+ <Int Name="Length">5</Int>
+ <Real>5.600000</Real>
+ <Real>-27753.373047</Real>
+ <Real>683.389648</Real>
+ <Real>2.918517</Real>
+ <Real>24.859180</Real>
+ </Sequence>
+ <Sequence Name="Row29">
+ <Int Name="Length">5</Int>
+ <Real>5.800000</Real>
+ <Real>-27858.119141</Real>
+ <Real>-500.987946</Real>
+ <Real>2.929479</Real>
+ <Real>25.140350</Real>
+ </Sequence>
+ <Sequence Name="Row30">
+ <Int Name="Length">5</Int>
+ <Real>6.000000</Real>
+ <Real>-28069.652344</Real>
+ <Real>-272.158386</Real>
+ <Real>2.935930</Real>
+ <Real>25.306805</Real>
+ </Sequence>
+ <Sequence Name="Row31">
+ <Int Name="Length">5</Int>
+ <Real>6.200000</Real>
+ <Real>-28207.109375</Real>
+ <Real>682.146118</Real>
+ <Real>2.923578</Real>
+ <Real>24.988716</Real>
+ </Sequence>
+ <Sequence Name="Row32">
+ <Int Name="Length">5</Int>
+ <Real>6.400000</Real>
+ <Real>-27761.265625</Real>
+ <Real>-251.639786</Real>
+ <Real>2.930740</Real>
+ <Real>25.172831</Real>
+ </Sequence>
+ <Sequence Name="Row33">
+ <Int Name="Length">5</Int>
+ <Real>6.600000</Real>
+ <Real>-28128.996094</Real>
+ <Real>136.933014</Real>
+ <Real>2.932798</Real>
+ <Real>25.225883</Real>
+ </Sequence>
+ <Sequence Name="Row34">
+ <Int Name="Length">5</Int>
+ <Real>6.800000</Real>
+ <Real>-28159.035156</Real>
+ <Real>-172.420929</Real>
+ <Real>2.937919</Real>
+ <Real>25.358250</Real>
+ </Sequence>
+ <Sequence Name="Row35">
+ <Int Name="Length">5</Int>
+ <Real>7.000000</Real>
+ <Real>-27751.841797</Real>
+ <Real>187.738708</Real>
+ <Real>2.933440</Real>
+ <Real>25.242456</Real>
+ </Sequence>
+ <Sequence Name="Row36">
+ <Int Name="Length">5</Int>
+ <Real>7.200000</Real>
+ <Real>-27753.189453</Real>
+ <Real>181.039490</Real>
+ <Real>2.938785</Real>
+ <Real>25.380699</Real>
+ </Sequence>
+ <Sequence Name="Row37">
+ <Int Name="Length">5</Int>
+ <Real>7.400000</Real>
+ <Real>-27601.382812</Real>
+ <Real>-59.191101</Real>
+ <Real>2.947856</Real>
+ <Real>25.616447</Real>
+ </Sequence>
+ <Sequence Name="Row38">
+ <Int Name="Length">5</Int>
+ <Real>7.600000</Real>
+ <Real>-28106.945312</Real>
+ <Real>234.138947</Real>
+ <Real>2.934338</Real>
+ <Real>25.265654</Real>
+ </Sequence>
+ <Sequence Name="Row39">
+ <Int Name="Length">5</Int>
+ <Real>7.800000</Real>
+ <Real>-28048.005859</Real>
+ <Real>352.149719</Real>
+ <Real>2.933455</Real>
+ <Real>25.242838</Real>
+ </Sequence>
+ <Sequence Name="Row40">
+ <Int Name="Length">5</Int>
+ <Real>8.000000</Real>
+ <Real>-27979.414062</Real>
+ <Real>-506.414001</Real>
+ <Real>2.954965</Real>
+ <Real>25.802214</Real>
+ </Sequence>
+ <Sequence Name="Row41">
+ <Int Name="Length">5</Int>
+ <Real>8.200000</Real>
+ <Real>-28036.621094</Real>
+ <Real>-413.985809</Real>
+ <Real>2.934557</Real>
+ <Real>25.271296</Real>
+ </Sequence>
+ <Sequence Name="Row42">
+ <Int Name="Length">5</Int>
+ <Real>8.400000</Real>
+ <Real>-28163.242188</Real>
+ <Real>449.511932</Real>
+ <Real>2.912586</Real>
+ <Real>24.707930</Real>
+ </Sequence>
+ <Sequence Name="Row43">
+ <Int Name="Length">5</Int>
+ <Real>8.600000</Real>
+ <Real>-27828.839844</Real>
+ <Real>421.591461</Real>
+ <Real>2.925114</Real>
+ <Real>25.028139</Real>
+ </Sequence>
+ <Sequence Name="Row44">
+ <Int Name="Length">5</Int>
+ <Real>8.800000</Real>
+ <Real>-27906.761719</Real>
+ <Real>-277.707733</Real>
+ <Real>2.933428</Real>
+ <Real>25.242149</Real>
+ </Sequence>
+ <Sequence Name="Row45">
+ <Int Name="Length">5</Int>
+ <Real>9.000000</Real>
+ <Real>-28056.156250</Real>
+ <Real>-76.575607</Real>
+ <Real>2.924834</Real>
+ <Real>25.020935</Real>
+ </Sequence>
+ <Sequence Name="Row46">
+ <Int Name="Length">5</Int>
+ <Real>9.200000</Real>
+ <Real>-27878.431641</Real>
+ <Real>-443.641296</Real>
+ <Real>2.929722</Real>
+ <Real>25.146606</Real>
+ </Sequence>
+ <Sequence Name="Row47">
+ <Int Name="Length">5</Int>
+ <Real>9.400000</Real>
+ <Real>-28078.681641</Real>
+ <Real>727.809448</Real>
+ <Real>2.906425</Real>
+ <Real>24.551456</Real>
+ </Sequence>
+ <Sequence Name="Row48">
+ <Int Name="Length">5</Int>
+ <Real>9.600000</Real>
+ <Real>-27960.445312</Real>
+ <Real>-348.396515</Real>
+ <Real>2.915571</Real>
+ <Real>24.783981</Real>
+ </Sequence>
+ <Sequence Name="Row49">
+ <Int Name="Length">5</Int>
+ <Real>9.800000</Real>
+ <Real>-28230.580078</Real>
+ <Real>260.881683</Real>
+ <Real>2.919360</Real>
+ <Real>24.880718</Real>
+ </Sequence>
+ <Sequence Name="Row50">
+ <Int Name="Length">5</Int>
+ <Real>10.000000</Real>
+ <Real>-27836.777344</Real>
+ <Real>-291.007599</Real>
+ <Real>2.927743</Real>
+ <Real>25.095673</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-oten">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Order tensor"
+xaxis label "Time (ps)"
+yaxis label ""
+TYPE xy
+s0 legend "eig1"
+s1 legend "eig2"
+s2 legend "eig3"
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">4</Int>
+ <Real>0.000000</Real>
+ <Real>0.000874024</Real>
+ <Real>-0.000514914</Real>
+ <Real>-0.00035911</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">4</Int>
+ <Real>0.002000</Real>
+ <Real>0.000957853</Real>
+ <Real>-0.000568174</Real>
+ <Real>-0.00038968</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">4</Int>
+ <Real>0.004000</Real>
+ <Real>0.0010501</Real>
+ <Real>-0.000591766</Real>
+ <Real>-0.000458333</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">4</Int>
+ <Real>0.006000</Real>
+ <Real>0.00109263</Real>
+ <Real>-0.000597102</Real>
+ <Real>-0.000495525</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">4</Int>
+ <Real>0.008000</Real>
+ <Real>0.00110458</Real>
+ <Real>-0.000597999</Real>
+ <Real>-0.000506579</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">4</Int>
+ <Real>0.010000</Real>
+ <Real>0.00110374</Real>
+ <Real>-0.000602079</Real>
+ <Real>-0.000501658</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">4</Int>
+ <Real>0.012000</Real>
+ <Real>0.00109991</Real>
+ <Real>-0.000609947</Real>
+ <Real>-0.00048996</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">4</Int>
+ <Real>0.014000</Real>
+ <Real>0.00109939</Real>
+ <Real>-0.000620441</Real>
+ <Real>-0.000478945</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">4</Int>
+ <Real>0.016000</Real>
+ <Real>0.00110964</Real>
+ <Real>-0.00063242</Real>
+ <Real>-0.000477215</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">4</Int>
+ <Real>0.018000</Real>
+ <Real>0.00114132</Real>
+ <Real>-0.000644279</Real>
+ <Real>-0.000497043</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">4</Int>
+ <Real>0.020000</Real>
+ <Real>0.00120594</Real>
+ <Real>-0.000654815</Real>
+ <Real>-0.000551126</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-ora">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Average calculated orientations"
+xaxis label "Restraint label"
+yaxis label ""
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>-5.65282</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>4</Real>
+ <Real>-6.6605</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>5</Real>
+ <Real>-5.05241</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>6</Real>
+ <Real>-4.79816</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">2</Int>
+ <Real>7</Real>
+ <Real>-1.77661</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">2</Int>
+ <Real>8</Real>
+ <Real>-5.81927</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">2</Int>
+ <Real>9</Real>
+ <Real>-3.85166</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-ort">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Calculated orientations"
+xaxis label "Time (ps)"
+yaxis label ""
+TYPE xy
+s0 legend "3"
+s1 legend "4"
+s2 legend "5"
+s3 legend "6"
+s4 legend "7"
+s5 legend "8"
+s6 legend "9"
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">8</Int>
+ <Real>0.000000</Real>
+ <Real>-4.89452</Real>
+ <Real>-5.87842</Real>
+ <Real>-5.30698</Real>
+ <Real>-5.01504</Real>
+ <Real>-0.544227</Real>
+ <Real>-4.75521</Real>
+ <Real>-5.82053</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">8</Int>
+ <Real>0.002000</Real>
+ <Real>-5.15825</Real>
+ <Real>-6.3131</Real>
+ <Real>-4.82974</Real>
+ <Real>-5.30595</Real>
+ <Real>-0.699448</Real>
+ <Real>-5.26383</Real>
+ <Real>-4.98295</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">8</Int>
+ <Real>0.004000</Real>
+ <Real>-5.50881</Real>
+ <Real>-6.5012</Real>
+ <Real>-4.6769</Real>
+ <Real>-5.30756</Real>
+ <Real>-1.18245</Real>
+ <Real>-5.6455</Real>
+ <Real>-4.25769</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">8</Int>
+ <Real>0.006000</Real>
+ <Real>-5.78819</Real>
+ <Real>-6.57865</Real>
+ <Real>-4.73666</Real>
+ <Real>-5.14671</Real>
+ <Real>-1.67991</Real>
+ <Real>-5.82657</Real>
+ <Real>-3.80163</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">8</Int>
+ <Real>0.008000</Real>
+ <Real>-5.94801</Real>
+ <Real>-6.63582</Real>
+ <Real>-4.8771</Real>
+ <Real>-4.94553</Real>
+ <Real>-2.03635</Real>
+ <Real>-5.89558</Real>
+ <Real>-3.55664</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">8</Int>
+ <Real>0.010000</Real>
+ <Real>-5.99537</Real>
+ <Real>-6.69487</Real>
+ <Real>-5.0156</Real>
+ <Real>-4.77013</Real>
+ <Real>-2.23404</Real>
+ <Real>-5.93982</Real>
+ <Real>-3.4359</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">8</Int>
+ <Real>0.012000</Real>
+ <Real>-5.95561</Real>
+ <Real>-6.75984</Real>
+ <Real>-5.1177</Real>
+ <Real>-4.63846</Real>
+ <Real>-2.30732</Real>
+ <Real>-6.0011</Real>
+ <Real>-3.37638</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">8</Int>
+ <Real>0.014000</Real>
+ <Real>-5.86272</Real>
+ <Real>-6.83544</Real>
+ <Real>-5.18525</Real>
+ <Real>-4.53827</Real>
+ <Real>-2.29768</Real>
+ <Real>-6.08155</Real>
+ <Real>-3.3403</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">8</Int>
+ <Real>0.016000</Real>
+ <Real>-5.75713</Real>
+ <Real>-6.9238</Real>
+ <Real>-5.23559</Real>
+ <Real>-4.45047</Real>
+ <Real>-2.24405</Real>
+ <Real>-6.16018</Real>
+ <Real>-3.3078</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">8</Int>
+ <Real>0.018000</Real>
+ <Real>-5.67512</Real>
+ <Real>-7.02144</Real>
+ <Real>-5.27937</Real>
+ <Real>-4.36782</Real>
+ <Real>-2.18139</Real>
+ <Real>-6.21335</Real>
+ <Real>-3.26937</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">8</Int>
+ <Real>0.020000</Real>
+ <Real>-5.63729</Real>
+ <Real>-7.12295</Real>
+ <Real>-5.31557</Real>
+ <Real>-4.29384</Real>
+ <Real>-2.1358</Real>
+ <Real>-6.22931</Real>
+ <Real>-3.21908</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-oda">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Average restraint deviation"
+xaxis label "Restraint label"
+yaxis label ""
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>1.07718</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>4</Real>
+ <Real>1.2095</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>5</Real>
+ <Real>2.07759</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>6</Real>
+ <Real>-2.22816</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">2</Int>
+ <Real>7</Real>
+ <Real>0.323394</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">2</Int>
+ <Real>8</Real>
+ <Real>-1.71927</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">2</Int>
+ <Real>9</Real>
+ <Real>-0.751661</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-odr">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "RMS orientation restraint deviations"
+xaxis label "Restraint label"
+yaxis label ""
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>1.1271</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>4</Real>
+ <Real>1.25451</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>5</Real>
+ <Real>2.08989</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>6</Real>
+ <Real>2.25577</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">2</Int>
+ <Real>7</Real>
+ <Real>0.70923</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">2</Int>
+ <Real>8</Real>
+ <Real>1.7722</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">2</Int>
+ <Real>9</Real>
+ <Real>1.10045</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-evisco">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Shear viscosity using Einstein relation"
+xaxis label "Time (ps)"
+yaxis label "(kg m\S-1\N s\S-1\N)"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">5</Int>
+ <Real>0.1</Real>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>0</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">5</Int>
+ <Real>0.3</Real>
+ <Real>0.000176958</Real>
+ <Real>0.0001997</Real>
+ <Real>0.000227414</Real>
+ <Real>0.000201357</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">5</Int>
+ <Real>0.5</Real>
+ <Real>0.00032058</Real>
+ <Real>0.000336305</Real>
+ <Real>0.000523275</Real>
+ <Real>0.000393386</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">5</Int>
+ <Real>0.7</Real>
+ <Real>0.000438803</Real>
+ <Real>0.000332506</Real>
+ <Real>0.000720448</Real>
+ <Real>0.000497252</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">5</Int>
+ <Real>0.9</Real>
+ <Real>0.000479678</Real>
+ <Real>0.00026701</Real>
+ <Real>0.000834344</Real>
+ <Real>0.000527011</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">5</Int>
+ <Real>1.1</Real>
+ <Real>0.000518115</Real>
+ <Real>0.0002171</Real>
+ <Real>0.000888733</Real>
+ <Real>0.000541316</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">5</Int>
+ <Real>1.3</Real>
+ <Real>0.000521</Real>
+ <Real>0.000157779</Real>
+ <Real>0.00086004</Real>
+ <Real>0.00051294</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">5</Int>
+ <Real>1.5</Real>
+ <Real>0.000545937</Real>
+ <Real>0.000116376</Real>
+ <Real>0.000702937</Real>
+ <Real>0.000455084</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">5</Int>
+ <Real>1.7</Real>
+ <Real>0.000564482</Real>
+ <Real>0.000149521</Real>
+ <Real>0.000433129</Real>
+ <Real>0.000382377</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">5</Int>
+ <Real>1.9</Real>
+ <Real>0.000643496</Real>
+ <Real>0.000253498</Real>
+ <Real>0.000142306</Real>
+ <Real>0.000346433</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">5</Int>
+ <Real>2.1</Real>
+ <Real>0.000680419</Real>
+ <Real>0.000327415</Real>
+ <Real>4.35872e-05</Real>
+ <Real>0.000350474</Real>
+ </Sequence>
+ <Sequence Name="Row11">
+ <Int Name="Length">5</Int>
+ <Real>2.3</Real>
+ <Real>0.000715131</Real>
+ <Real>0.000369339</Real>
+ <Real>-5.31824e-05</Real>
+ <Real>0.000343763</Real>
+ </Sequence>
+ <Sequence Name="Row12">
+ <Int Name="Length">5</Int>
+ <Real>2.5</Real>
+ <Real>0.000818337</Real>
+ <Real>0.000399551</Real>
+ <Real>-8.46781e-05</Real>
+ <Real>0.000377737</Real>
+ </Sequence>
+ <Sequence Name="Row13">
+ <Int Name="Length">5</Int>
+ <Real>2.7</Real>
+ <Real>0.000924901</Real>
+ <Real>0.000419762</Real>
+ <Real>7.73914e-06</Real>
+ <Real>0.000450801</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-vis"></File>
+ <File Name="-o"></File>
+ <File Name="-eviscoi"></File>
+ <File Name="-corr"></File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <OutputFiles Name="Files">
+ <File Name="-eviscoi">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Shear viscosity integral"
+xaxis label "Time (ps)"
+yaxis label "(kg m\S-1\N s\S-1\N ps)"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">5</Int>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>0</Real>
+ <Real>0</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">5</Int>
+ <Real>0.2</Real>
+ <Real>3.53916e-05</Real>
+ <Real>3.994e-05</Real>
+ <Real>4.54828e-05</Real>
+ <Real>4.02715e-05</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">5</Int>
+ <Real>0.4</Real>
+ <Real>9.95076e-05</Real>
+ <Real>0.000107201</Real>
+ <Real>0.000150138</Real>
+ <Real>0.000118949</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">5</Int>
+ <Real>0.6</Real>
+ <Real>0.000187268</Real>
+ <Real>0.000173702</Real>
+ <Real>0.000294227</Real>
+ <Real>0.000218399</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">5</Int>
+ <Real>0.8</Real>
+ <Real>0.000283204</Real>
+ <Real>0.000227104</Real>
+ <Real>0.000461096</Real>
+ <Real>0.000323801</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">5</Int>
+ <Real>1</Real>
+ <Real>0.000386827</Real>
+ <Real>0.000270524</Real>
+ <Real>0.000638843</Real>
+ <Real>0.000432065</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">5</Int>
+ <Real>1.2</Real>
+ <Real>0.000491027</Real>
+ <Real>0.00030208</Real>
+ <Real>0.000810851</Real>
+ <Real>0.000534652</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">5</Int>
+ <Real>1.4</Real>
+ <Real>0.000600214</Real>
+ <Real>0.000325355</Real>
+ <Real>0.000951438</Real>
+ <Real>0.000625669</Real>
+ </Sequence>
+ <Sequence Name="Row8">
+ <Int Name="Length">5</Int>
+ <Real>1.6</Real>
+ <Real>0.000713111</Real>
+ <Real>0.000355259</Real>
+ <Real>0.00103806</Real>
+ <Real>0.000702145</Real>
+ </Sequence>
+ <Sequence Name="Row9">
+ <Int Name="Length">5</Int>
+ <Real>1.8</Real>
+ <Real>0.00084181</Real>
+ <Real>0.000405959</Real>
+ <Real>0.00106653</Real>
+ <Real>0.000771431</Real>
+ </Sequence>
+ <Sequence Name="Row10">
+ <Int Name="Length">5</Int>
+ <Real>2</Real>
+ <Real>0.000977894</Real>
+ <Real>0.000471442</Real>
+ <Real>0.00107524</Real>
+ <Real>0.000841526</Real>
+ </Sequence>
+ <Sequence Name="Row11">
+ <Int Name="Length">5</Int>
+ <Real>2.2</Real>
+ <Real>0.00112092</Real>
+ <Real>0.00054531</Real>
+ <Real>0.00106461</Real>
+ <Real>0.000910279</Real>
+ </Sequence>
+ <Sequence Name="Row12">
+ <Int Name="Length">5</Int>
+ <Real>2.4</Real>
+ <Real>0.00128459</Real>
+ <Real>0.00062522</Real>
+ <Real>0.00104767</Real>
+ <Real>0.000985826</Real>
+ </Sequence>
+ <Sequence Name="Row13">
+ <Int Name="Length">5</Int>
+ <Real>2.6</Real>
+ <Real>0.00146957</Real>
+ <Real>0.000709173</Real>
+ <Real>0.00104922</Real>
+ <Real>0.00107599</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-vis"></File>
+ <File Name="-o"></File>
+ <File Name="-evisco"></File>
+ <File Name="-corr"></File>
+ </OutputFiles>
+</ReferenceData>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/broadcaststructs.h"
+#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/edsamhistory.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-/* We use the same defines as in broadcaststructs.cpp here */
-#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
-#define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
-#define snew_bc(cr, d, nr) { if (!MASTER(cr)) {snew((d), (nr)); }}
-
/* enum to identify the type of ED: none, normal ED, flooding */
enum {
eEDnone, eEDedsam, eEDflood, eEDnr
static void translate_and_rotate(rvec *x, int nat, rvec transvec, matrix rotmat);
static real rmsd_from_structure(rvec *x, struct gmx_edx *s);
static int read_edi_file(const char *fn, t_edpar *edi, int nr_mdatoms);
-static void crosscheck_edi_file_vs_checkpoint(gmx_edsam_t ed, edsamstate_t *EDstate);
-static void init_edsamstate(gmx_edsam_t ed, edsamstate_t *EDstate);
+static void crosscheck_edi_file_vs_checkpoint(gmx_edsam_t ed, edsamhistory_t *EDstate);
+static void init_edsamstate(gmx_edsam_t ed, edsamhistory_t *EDstate);
static void write_edo_legend(gmx_edsam_t ed, int nED, const gmx_output_env_t *oenv);
/* End function declarations */
struct t_do_edfit *loc;
gmx_bool bFirst;
- if (edi->buf->do_edfit != NULL)
+ if (edi->buf->do_edfit != nullptr)
{
bFirst = FALSE;
}
#endif
-gmx_edsam_t ed_open(int natoms, edsamstate_t *EDstate, int nfile, const t_filenm fnm[], unsigned long Flags, const gmx_output_env_t *oenv, t_commrec *cr)
+/* This function opens the ED input and output files, reads in all datasets it finds
+ * in the input file, and cross-checks whether the .edi file information is consistent
+ * with the essential dynamics data found in the checkpoint file (if present).
+ * gmx make_edi can be used to create an .edi input file.
+ */
+static gmx_edsam_t ed_open(
+ int natoms,
+ ObservablesHistory *oh,
+ const char *ediFileName,
+ const char *edoFileName,
+ gmx_bool bAppend,
+ const gmx_output_env_t *oenv,
+ t_commrec *cr)
{
gmx_edsam_t ed;
int nED;
-
/* Allocate space for the ED data structure */
snew(ed, 1);
if (MASTER(cr))
{
- fprintf(stderr, "ED sampling will be performed!\n");
snew(ed->edpar, 1);
+ // If we start from a checkpoint file, we already have an edsamHistory struct
+ if (oh->edsamHistory.get() == nullptr)
+ {
+ oh->edsamHistory = std::unique_ptr<edsamhistory_t>(new edsamhistory_t {});
+ }
+ edsamhistory_t *EDstate = oh->edsamHistory.get();
+
/* Read the edi input file: */
- nED = read_edi_file(ftp2fn(efEDI, nfile, fnm), ed->edpar, natoms);
+ nED = read_edi_file(ediFileName, ed->edpar, natoms);
/* Make sure the checkpoint was produced in a run using this .edi file */
if (EDstate->bFromCpt)
init_edsamstate(ed, EDstate);
/* The master opens the ED output file */
- /* TODO This file is never closed... */
- if (Flags & MD_APPENDFILES)
+ if (bAppend)
{
- ed->edo = gmx_fio_fopen(opt2fn("-eo", nfile, fnm), "a+");
+ ed->edo = gmx_fio_fopen(edoFileName, "a+");
}
else
{
- ed->edo = xvgropen(opt2fn("-eo", nfile, fnm),
+ ed->edo = xvgropen(edoFileName,
"Essential dynamics / flooding output",
"Time (ps)",
"RMSDs (nm), projections on EVs (nm), ...", oenv);
int i;
real totalmass = 0.0;
rvec com;
- gmx_mtop_atomlookup_t alook = NULL;
- t_atom *atom;
/* NOTE Init_edi is executed on the master process only
* The initialized data sets are then transmitted to the
* other nodes in broadcast_ed_data */
- alook = gmx_mtop_atomlookup_init(mtop);
-
/* evaluate masses (reference structure) */
snew(edi->sref.m, edi->sref.nr);
+ int molb = 0;
for (i = 0; i < edi->sref.nr; i++)
{
if (edi->fitmas)
{
- gmx_mtop_atomnr_to_atom(alook, edi->sref.anrs[i], &atom);
- edi->sref.m[i] = atom->m;
+ edi->sref.m[i] = mtopGetAtomMass(mtop, edi->sref.anrs[i], &molb);
}
else
{
snew(edi->sav.m, edi->sav.nr );
for (i = 0; i < edi->sav.nr; i++)
{
- gmx_mtop_atomnr_to_atom(alook, edi->sav.anrs[i], &atom);
- edi->sav.m[i] = atom->m;
+ edi->sav.m[i] = mtopGetAtomMass(mtop, edi->sav.anrs[i], &molb);
if (edi->pcamas)
{
- edi->sav.sqrtm[i] = sqrt(atom->m);
+ edi->sav.sqrtm[i] = sqrt(edi->sav.m[i]);
}
else
{
"For ED with mass-weighting, all average structure atoms need to have a mass >0.\n"
"Either make the covariance analysis non-mass-weighted, or exclude massless\n"
"atoms from the average structure by creating a proper index group.\n",
- i, edi->sav.anrs[i]+1, atom->m);
+ i, edi->sav.anrs[i] + 1, edi->sav.m[i]);
}
}
- gmx_mtop_atomlookup_destroy(alook);
-
/* put reference structure in origin */
get_center(edi->sref.x, edi->sref.m, edi->sref.nr, com);
com[XX] = -com[XX];
eof = fgets2 (line, STRLEN, file);
- if (eof == NULL)
+ if (eof == nullptr)
{
*bEOF = TRUE;
return -1;
}
eof = fgets2 (line, STRLEN, file);
- if (eof == NULL)
+ if (eof == nullptr)
{
*bEOF = TRUE;
return -1;
snew(edi->sref.anrs, edi->sref.nr);
snew(edi->sref.x, edi->sref.nr);
snew(edi->sref.x_old, edi->sref.nr);
- edi->sref.sqrtm = NULL;
+ edi->sref.sqrtm = nullptr;
read_edx(in, edi->sref.nr, edi->sref.anrs, edi->sref.x);
/* average positions. they define which atoms will be used for ED sampling */
{
snew(edi->star.anrs, edi->star.nr);
snew(edi->star.x, edi->star.nr);
- edi->star.sqrtm = NULL;
+ edi->star.sqrtm = nullptr;
read_edx(in, edi->star.nr, edi->star.anrs, edi->star.x);
}
}
snew(edi->sori.anrs, edi->sori.nr);
snew(edi->sori.x, edi->sori.nr);
- edi->sori.sqrtm = NULL;
+ edi->sori.sqrtm = nullptr;
read_edx(in, edi->sori.nr, edi->sori.anrs, edi->sori.x);
}
}
/* Terminate the edi group list with a NULL pointer: */
- last_edi->next_edi = NULL;
+ last_edi->next_edi = nullptr;
fprintf(stderr, "ED: Found %d ED group%s.\n", edi_nr, edi_nr > 1 ? "s" : "");
/* Allocate memory the first time this routine is called for each edi group */
- if (NULL == edi->buf->fit_to_ref)
+ if (nullptr == edi->buf->fit_to_ref)
{
snew(edi->buf->fit_to_ref, 1);
snew(edi->buf->fit_to_ref->xcopy, edi->sref.nr);
rvec vec_dum;
- if (edi->buf->do_radcon != NULL)
+ if (edi->buf->do_radcon != nullptr)
{
bFirst = FALSE;
}
int i;
- if (NULL == floodvecs->refproj0)
+ if (nullptr == floodvecs->refproj0)
{
snew(floodvecs->refproj0, floodvecs->neig);
}
/* Call on MASTER only. Check whether the essential dynamics / flooding
* groups of the checkpoint file are consistent with the provided .edi file. */
-static void crosscheck_edi_file_vs_checkpoint(gmx_edsam_t ed, edsamstate_t *EDstate)
+static void crosscheck_edi_file_vs_checkpoint(gmx_edsam_t ed, edsamhistory_t *EDstate)
{
- t_edpar *edi = NULL; /* points to a single edi data set */
+ t_edpar *edi = nullptr; /* points to a single edi data set */
int edinum;
- if (NULL == EDstate->nref || NULL == EDstate->nav)
+ if (nullptr == EDstate->nref || nullptr == EDstate->nav)
{
gmx_fatal(FARGS, "Essential dynamics and flooding can only be switched on (or off) at the\n"
"start of a new simulation. If a simulation runs with/without ED constraints,\n"
edi = ed->edpar;
edinum = 0;
- while (edi != NULL)
+ while (edi != nullptr)
{
/* Check number of atoms in the reference and average structures */
if (EDstate->nref[edinum] != edi->sref.nr)
* c) in any case, for subsequent checkpoint writing, we set the pointers in
* edsamstate to the x_old arrays, which contain the correct PBC representation of
* all ED structures at the last time step. */
-static void init_edsamstate(gmx_edsam_t ed, edsamstate_t *EDstate)
+static void init_edsamstate(gmx_edsam_t ed, edsamhistory_t *EDstate)
{
int i, nr_edi;
t_edpar *edi;
/* Makes a legend for the xvg output file. Call on MASTER only! */
static void write_edo_legend(gmx_edsam_t ed, int nED, const gmx_output_env_t *oenv)
{
- t_edpar *edi = NULL;
+ t_edpar *edi = nullptr;
int i;
int nr_edi, nsets, n_flood, n_edsam;
const char **setname;
char buf[STRLEN];
- char *LegendStr = NULL;
+ char *LegendStr = nullptr;
edi = ed->edpar;
/* Init routine for ED and flooding. Calls init_edi in a loop for every .edi-cycle
* contained in the input file, creates a NULL terminated list of t_edpar structures */
-void init_edsam(const gmx_mtop_t *mtop,
- const t_inputrec *ir,
- t_commrec *cr,
- gmx_edsam_t ed,
- rvec x[],
- matrix box,
- edsamstate_t *EDstate)
-{
- t_edpar *edi = NULL; /* points to a single edi data set */
- int i, nr_edi, avindex;
- rvec *x_pbc = NULL; /* positions of the whole MD system with pbc removed */
- rvec *xfit = NULL, *xstart = NULL; /* dummy arrays to determine initial RMSDs */
- rvec fit_transvec; /* translation ... */
- matrix fit_rotmat; /* ... and rotation from fit to reference structure */
- rvec *ref_x_old = NULL; /* helper pointer */
+gmx_edsam_t init_edsam(
+ const char *ediFileName,
+ const char *edoFileName,
+ const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ t_commrec *cr,
+ gmx_constr *constr,
+ rvec x[],
+ matrix box,
+ ObservablesHistory *oh,
+ const gmx_output_env_t *oenv,
+ gmx_bool bAppend)
+{
+ t_edpar *edi = nullptr; /* points to a single edi data set */
+ int i, avindex;
+ int nED = 0; /* Number of ED data sets */
+ rvec *x_pbc = nullptr; /* positions of the whole MD system with pbc removed */
+ rvec *xfit = nullptr, *xstart = nullptr; /* dummy arrays to determine initial RMSDs */
+ rvec fit_transvec; /* translation ... */
+ matrix fit_rotmat; /* ... and rotation from fit to reference structure */
+ rvec *ref_x_old = nullptr; /* helper pointer */
+
if (MASTER(cr))
{
fprintf(stderr, "ED: Initializing essential dynamics constraints.\n");
- if (NULL == ed)
+ if (oh->edsamHistory != nullptr && oh->edsamHistory->bFromCpt && !gmx_fexist(ediFileName) )
{
- gmx_fatal(FARGS, "The checkpoint file you provided is from an essential dynamics or\n"
- "flooding simulation. Please also provide the correct .edi file with -ei.\n");
+ gmx_fatal(FARGS, "The checkpoint file you provided is from an essential dynamics or flooding\n"
+ "simulation. Please also set the .edi file on the command line with -ei.\n");
}
}
+ /* Open input and output files, allocate space for ED data structure */
+ gmx_edsam_t ed = ed_open(mtop->natoms, oh, ediFileName, edoFileName, bAppend, oenv, cr);
+ saveEdsamPointer(constr, ed);
+
/* Needed for initializing radacc radius in do_edsam */
ed->bFirst = TRUE;
* as well, but will be done in the order given in the edi file, so
* expect different results for different order of edi file concatenation! */
edi = ed->edpar;
- while (edi != NULL)
+ while (edi != nullptr)
{
init_edi(mtop, edi);
init_flood(edi, ed, ir->delta_t);
* not before dd_partition_system which is called after init_edsam */
if (MASTER(cr))
{
+ edsamhistory_t *EDstate = oh->edsamHistory.get();
+
if (!EDstate->bFromCpt)
{
/* Remove PBC, make molecule(s) subject to ED whole. */
snew(x_pbc, mtop->natoms);
copy_rvecn(x, x_pbc, 0, mtop->natoms);
- do_pbc_first_mtop(NULL, ir->ePBC, box, mtop, x_pbc);
+ do_pbc_first_mtop(nullptr, ir->ePBC, box, mtop, x_pbc);
}
/* Reset pointer to first ED data set which contains the actual ED data */
edi = ed->edpar;
GMX_ASSERT(NULL != edi,
"The pointer to the essential dynamics parameters is undefined");
+ nED = EDstate->nED;
/* Loop over all ED/flooding data sets (usually only one, though) */
- for (nr_edi = 1; nr_edi <= EDstate->nED; nr_edi++)
+ for (int nr_edi = 1; nr_edi <= EDstate->nED; nr_edi++)
{
/* For multiple ED groups we use the output frequency that was specified
* in the first set */
if (PAR(cr))
{
/* First let everybody know how many ED data sets to expect */
- gmx_bcast(sizeof(EDstate->nED), &EDstate->nED, cr);
+ gmx_bcast(sizeof(nED), &nED, cr);
/* Broadcast the essential dynamics / flooding data to all nodes */
- broadcast_ed_data(cr, ed, EDstate->nED);
+ broadcast_ed_data(cr, ed, nED);
}
else
{
/* In the single-CPU case, point the local atom numbers pointers to the global
* one, so that we can use the same notation in serial and parallel case: */
-
/* Loop over all ED data sets (usually only one, though) */
edi = ed->edpar;
- for (nr_edi = 1; nr_edi <= EDstate->nED; nr_edi++)
+ for (int nr_edi = 1; nr_edi <= nED; nr_edi++)
{
edi->sref.anrs_loc = edi->sref.anrs;
edi->sav.anrs_loc = edi->sav.anrs;
/* Allocate space for ED buffer variables */
/* Again, loop over ED data sets */
edi = ed->edpar;
- for (nr_edi = 1; nr_edi <= EDstate->nED; nr_edi++)
+ for (int nr_edi = 1; nr_edi <= nED; nr_edi++)
{
/* Allocate space for ED buffer variables */
snew_bc(cr, edi->buf, 1); /* MASTER has already allocated edi->buf in init_edi() */
{
fflush(ed->edo);
}
+
+ return ed;
}
/* Loop over all ED groups (usually one) */
edi = ed->edpar;
edinr = 0;
- while (edi != NULL)
+ while (edi != nullptr)
{
edinr++;
if (bNeedDoEdsam(edi))
/* dx is the ED correction to the positions: */
rvec_sub(x_unsh, xs[edi->sav.anrs_loc[i]], dx);
- if (v != NULL)
+ if (v != nullptr)
{
/* dv is the ED correction to the velocity: */
svmul(dt_1, dx, dv);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
-struct gmx_output_env_t;
-struct t_filenm;
/*! \brief Abstract type for essential dynamics
*
- * The main type is defined only in edsam.c
+ * The main type is defined only in edsam.cpp
*/
typedef struct gmx_edsam *gmx_edsam_t;
-struct edsamstate_t;
-struct t_commrec;
-struct t_inputrec;
struct gmx_domdec_t;
struct gmx_mtop_t;
+struct gmx_output_env_t;
+struct ObservablesHistory;
+struct t_commrec;
+struct t_filenm;
+struct t_inputrec;
/*! \brief Applies essential dynamics constrains as defined in the .edi input file.
*
t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam_t ed);
-/*! \brief Reads in the .edi file containing the essential dynamics and flooding data.
- *
- * This function opens the ED input and output files, reads in all datasets it finds
- * in the input file, and cross-checks whether the .edi file information is consistent
- * with the essential dynamics data found in the checkpoint file (if present).
- * gmx make_edi can be used to create an .edi input file.
- *
- * \param natoms Number of atoms of the whole MD system.
- * \param EDstate Essential dynamics and flooding data stored in the checkpoint file.
- * \param nfile Number of entries (files) in the fnm structure.
- * \param fnm The filenames struct; it contains also the names of the
- * essential dynamics and flooding in + output files.
- * \param Flags Flags passed over from main, used to determine
- * whether we are appending.
- * \param oenv Needed to open the output xvgr file.
- * \param cr Data needed for MPI communication.
- * \returns Pointer to the initialized essential dynamics / flooding data.
- */
-gmx_edsam_t ed_open(int natoms, edsamstate_t *EDstate, int nfile, const t_filenm fnm[],
- unsigned long Flags, const gmx_output_env_t *oenv, t_commrec *cr);
-
/*! \brief Initializes the essential dynamics and flooding module.
*
+ * \param ediFileName Essential dynamics input file.
+ * \param edoFileName Output file for essential dynamics data.
* \param mtop Molecular topology.
* \param ir MD input parameter record.
* \param cr Data needed for MPI communication.
- * \param ed The essential dynamics data.
+ * \param constr Data structure keeping the constraint information.
* \param x Positions of the whole MD system.
* \param box The simulation box.
- * \param EDstate ED data stored in the checkpoint file.
+ * \param oh The observables history container.
+ * \param oenv The output environment information.
+ * \param bAppend Append to existing output files?
+ *
+ * \returns A pointer to the ED data structure.
*/
-void init_edsam(const gmx_mtop_t *mtop, const t_inputrec *ir, t_commrec *cr,
- gmx_edsam_t ed, rvec x[], matrix box, edsamstate_t *EDstate);
-
+gmx_edsam_t init_edsam(
+ const char *ediFileName,
+ const char *edoFileName,
+ const gmx_mtop_t *mtop,
+ const t_inputrec *ir,
+ t_commrec *cr,
+ struct gmx_constr *constr,
+ rvec x[],
+ matrix box,
+ ObservablesHistory *oh,
+ const gmx_output_env_t *oenv,
+ gmx_bool bAppend);
/*! \brief Make a selection of the home atoms for the ED groups.
*
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${EWALD_SOURCES} PARENT_SCOPE)
if (BUILD_TESTING)
-# add_subdirectory(tests)
+ add_subdirectory(tests)
endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "pme-internal.h"
-static void make_dft_mod(real *mod, real *data, int ndata)
+static void make_dft_mod(real *mod,
+ const double *data, int splineOrder, int ndata)
{
- int i, j;
- real sc, ss, arg;
-
- for (i = 0; i < ndata; i++)
+ for (int i = 0; i < ndata; i++)
{
- sc = ss = 0;
- for (j = 0; j < ndata; j++)
+ /* We use double precision, since this is only called once per grid.
+ * But for single precision bsp_mod, single precision also seems
+ * to give full accuracy.
+ */
+ double sc = 0;
+ double ss = 0;
+ for (int j = 0; j < splineOrder; j++)
{
- arg = (2.0*M_PI*i*j)/ndata;
- sc += data[j]*cos(arg);
- ss += data[j]*sin(arg);
+ double arg = (2.0*M_PI*i*(j + 1))/ndata;
+ sc += data[j]*cos(arg);
+ ss += data[j]*sin(arg);
}
- mod[i] = sc*sc+ss*ss;
+ mod[i] = sc*sc + ss*ss;
}
- for (i = 0; i < ndata; i++)
+ if (splineOrder % 2 == 0 && ndata % 2 == 0)
{
- if (mod[i] < 1e-7)
- {
- mod[i] = (mod[i-1]+mod[i+1])*0.5;
- }
+ /* Note that pme_order = splineOrder + 1 */
+ GMX_RELEASE_ASSERT(mod[ndata/2] < GMX_DOUBLE_EPS, "With even spline order and even grid size (ndata), dft_mod[ndata/2] should first come out as zero");
+ /* This factor causes a division by zero. But since this occurs in
+ * the tail of the distribution, the term with this factor can
+ * be ignored (see Essmann et al. JCP 103, 8577).
+ * Using the average of the neighbors probably originates from
+ * Tom Darden's original PME code. It seems to give slighlty better
+ * accuracy than using a large value.
+ */
+ mod[ndata/2] = (mod[ndata/2 - 1] + mod[ndata/2 + 1])*0.5;
}
}
void make_bspline_moduli(splinevec bsp_mod,
- int nx, int ny, int nz, int order)
+ int nx, int ny, int nz, int pme_order)
{
- int nmax = std::max(nx, std::max(ny, nz));
- real *data, *ddata, *bsp_data;
- int i, k, l;
- real div;
+ /* We use double precision, since this is only called once per grid.
+ * But for single precision bsp_mod, single precision also seems
+ * to give full accuracy.
+ */
+ double *data;
- snew(data, order);
- snew(ddata, order);
- snew(bsp_data, nmax);
+ /* In GROMACS we, confusingly, defined pme-order as the order
+ * of the cardinal B-spline + 1. This probably happened because
+ * the smooth PME paper only talks about "n" which is the number
+ * of points we spread to and that was chosen to be pme-order.
+ */
+ const int splineOrder = pme_order - 1;
- data[order-1] = 0;
- data[1] = 0;
- data[0] = 1;
+ snew(data, splineOrder);
- for (k = 3; k < order; k++)
+ data[0] = 1;
+ for (int k = 1; k < splineOrder; k++)
{
- div = 1.0/(k-1.0);
- data[k-1] = 0;
- for (l = 1; l < (k-1); l++)
- {
- data[k-l-1] = div*(l*data[k-l-2]+(k-l)*data[k-l-1]);
- }
- data[0] = div*data[0];
+ data[k] = 0;
}
- /* differentiate */
- ddata[0] = -data[0];
- for (k = 1; k < order; k++)
- {
- ddata[k] = data[k-1]-data[k];
- }
- div = 1.0/(order-1);
- data[order-1] = 0;
- for (l = 1; l < (order-1); l++)
- {
- data[order-l-1] = div*(l*data[order-l-2]+(order-l)*data[order-l-1]);
- }
- data[0] = div*data[0];
- for (i = 0; i < nmax; i++)
+ for (int k = 2; k <= splineOrder; k++)
{
- bsp_data[i] = 0;
- }
- for (i = 1; i <= order; i++)
- {
- bsp_data[i] = data[i-1];
+ double div = 1.0/k;
+ for (int m = k - 1; m > 0; m--)
+ {
+ data[m] = div*((k - m)*data[m - 1] + (m + 1)*data[m]);
+ }
+ data[0] = div*data[0];
}
- make_dft_mod(bsp_mod[XX], bsp_data, nx);
- make_dft_mod(bsp_mod[YY], bsp_data, ny);
- make_dft_mod(bsp_mod[ZZ], bsp_data, nz);
+ make_dft_mod(bsp_mod[XX], data, splineOrder, nx);
+ make_dft_mod(bsp_mod[YY], data, splineOrder, ny);
+ make_dft_mod(bsp_mod[ZZ], data, splineOrder, nz);
sfree(data);
- sfree(ddata);
- sfree(bsp_data);
}
/* Return the P3M optimal influence function */
if (order > 8)
{
- gmx_fatal(FARGS, "The current P3M code only supports orders up to 8");
+ GMX_THROW(gmx::InconsistentInputError("The current P3M code only supports orders up to 8"));
}
zarg = M_PI/n;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(*et)->ny = ir->nky+1;
(*et)->nz = ir->nkz+1;
(*et)->kmax = std::max((*et)->nx, std::max((*et)->ny, (*et)->nz));
- (*et)->eir = NULL;
- (*et)->tab_xy = NULL;
- (*et)->tab_qxyz = NULL;
+ (*et)->eir = nullptr;
+ (*et)->tab_xy = nullptr;
+ (*et)->tab_qxyz = nullptr;
}
//! Calculates wave vectors.
real tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
gmx_bool bFreeEnergy;
- if (cr != NULL)
+ if (cr != nullptr)
{
if (PAR(cr))
{
tensor dxdf_q = {{0}}, dxdf_lj = {{0}};
real vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
real L1_q, L1_lj, dipole_coeff, qqA, qqB, qqL, vr0_q, vr0_lj = 0;
- gmx_bool bMolPBC = fr->bMolPBC;
- gmx_bool bDoingLBRule = (fr->ljpme_combination_rule == eljpmeLB);
+ real chargecorr[2] = { 0, 0 };
+ gmx_bool bMolPBC = fr->bMolPBC;
+ gmx_bool bDoingLBRule = (fr->ljpme_combination_rule == eljpmeLB);
gmx_bool bNeedLongRangeCorrection;
/* This routine can be made faster by using tables instead of analytical interactions
}
break;
case eewg3DC:
- dipole_coeff = 2*M_PI*one_4pi_eps/vol;
- dipcorrA[ZZ] = 2*dipole_coeff*mutot[0][ZZ];
- dipcorrB[ZZ] = 2*dipole_coeff*mutot[1][ZZ];
+ dipole_coeff = 2*M_PI*one_4pi_eps/vol;
+ dipcorrA[ZZ] = 2*dipole_coeff*mutot[0][ZZ];
+ dipcorrB[ZZ] = 2*dipole_coeff*mutot[1][ZZ];
+ for (int q = 0; q < (bHaveChargeOrTypePerturbed ? 2 : 1); q++)
+ {
+ /* Avoid charge corrections with near-zero net charge */
+ if (fabs(fr->qsum[q]) > 1e-4)
+ {
+ chargecorr[q] = 2*dipole_coeff*fr->qsum[q];
+ }
+ }
break;
default:
gmx_incons("Unsupported Ewald geometry");
{
f[i][j] -= dipcorrA[j]*chargeA[i];
}
+ if (chargecorr[0] != 0)
+ {
+ f[i][ZZ] += chargecorr[0]*chargeA[i]*x[i][ZZ];
+ }
}
}
}
f[i][j] -= L1_q*dipcorrA[j]*chargeA[i]
+ lambda_q*dipcorrB[j]*chargeB[i];
}
+ if (chargecorr[0] != 0 || chargecorr[1] != 0)
+ {
+ f[i][ZZ] += (L1_q*chargecorr[0]*chargeA[i]
+ + lambda_q*chargecorr[1])*x[i][ZZ];
+ }
}
}
}
}
}
- /* Apply surface dipole correction:
- * correction = dipole_coeff * (dipole)^2
+ /* Apply surface and charged surface dipole correction:
+ * correction = dipole_coeff * ( (dipole)^2
+ * - qsum*sum_i q_i z_i^2 - qsum^2 * box_z^2 / 12 )
*/
if (dipole_coeff != 0)
{
else if (ewald_geometry == eewg3DC)
{
Vdipole[q] = dipole_coeff*mutot[q][ZZ]*mutot[q][ZZ];
+
+ if (chargecorr[q] != 0)
+ {
+ /* Here we use a non thread-parallelized loop,
+ * because this is the only loop over atoms for
+ * energies and they need reduction (unlike forces).
+ * We could implement a reduction over threads,
+ * but this case is rarely used.
+ */
+ const real *qPtr = (q == 0 ? chargeA : chargeB);
+ real sumQZ2 = 0;
+ for (int i = 0; i < numAtomsLocal; i++)
+ {
+ sumQZ2 += qPtr[i]*x[i][ZZ]*x[i][ZZ];
+ }
+ Vdipole[q] -= dipole_coeff*fr->qsum[q]*(sumQZ2 + fr->qsum[q]*box[ZZ][ZZ]*box[ZZ][ZZ]/12);
+ }
}
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
+#include "pme-gather.h"
+
#include "gromacs/math/vec.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/typetraits.h"
#include "pme-internal.h"
#include "pme-simd.h"
using namespace gmx; // TODO: Remove when this file is moved into gmx namespace
-#define DO_FSPLINE(order) \
- for (ithx = 0; (ithx < order); ithx++) \
- { \
- index_x = (i0+ithx)*pny*pnz; \
- tx = thx[ithx]; \
- dx = dthx[ithx]; \
- \
- for (ithy = 0; (ithy < order); ithy++) \
- { \
- index_xy = index_x+(j0+ithy)*pnz; \
- ty = thy[ithy]; \
- dy = dthy[ithy]; \
- fxy1 = fz1 = 0; \
- \
- for (ithz = 0; (ithz < order); ithz++) \
- { \
- gval = grid[index_xy+(k0+ithz)]; \
- fxy1 += thz[ithz]*gval; \
- fz1 += dthz[ithz]*gval; \
- } \
- fx += dx*ty*fxy1; \
- fy += tx*dy*fxy1; \
- fz += tx*ty*fz1; \
- } \
+/* Spline function. Goals: 1) Force compiler to instantiate function separately
+ for each compile-time value of order and once more for any possible (runtime)
+ value. 2) Allow overloading for specific compile-time values.
+ The Int template argument can be either int (runtime) or an object of type
+ integral_constant<int, N> (compile-time). Common runtime values can be
+ converted to compile-time values with a switch statement. For the compile
+ value the compiler is required to instantiate the function separately for
+ each value. The function can be overloaded for specific compile-time values
+ using integral_constant<int, N> where N is either a specific value or an
+ enable_if constrained non-type template parameter. The most specific overload
+ (specific value > int template parameter > general function) is called. Inside
+ the function the order argument can be used as regular int because
+ integral_constant has a proper conversion.
+
+ SIMD do_fspline() template funtions will be used for PME order 4 and 5
+ when the SIMD module has support for SIMD4 for the architecture used.
+ For SIMD4 without unaligned load/store support:
+ order 4 and 5 use the order 4+5 aligned SIMD template
+ For SIMD4 with unaligned load/store support:
+ order 4 uses the order 4 unaligned SIMD template
+ order 5 uses the order 4+5 aligned SIMD template
+ */
+struct do_fspline
+{
+ do_fspline (
+ const gmx_pme_t * pme,
+ const real * gmx_restrict grid,
+ const pme_atomcomm_t * gmx_restrict atc,
+ const splinedata_t * gmx_restrict spline,
+ int nn)
+ : pme(pme), grid(grid), atc(atc), spline(spline), nn(nn) {}
+
+ template <typename Int>
+ RVec operator()(Int order) const
+ {
+ static_assert(isIntegralConstant<Int, int>::value || std::is_same<Int, int>::value,
+ "'order' needs to be either of type integral_constant<int,N> or int.");
+
+ const int norder = nn*order;
+
+ /* Pointer arithmetic alert, next six statements */
+ const real *const gmx_restrict thx = spline->theta[XX] + norder;
+ const real *const gmx_restrict thy = spline->theta[YY] + norder;
+ const real *const gmx_restrict thz = spline->theta[ZZ] + norder;
+ const real *const gmx_restrict dthx = spline->dtheta[XX] + norder;
+ const real *const gmx_restrict dthy = spline->dtheta[YY] + norder;
+ const real *const gmx_restrict dthz = spline->dtheta[ZZ] + norder;
+
+ RVec f(0, 0, 0);
+
+ for (int ithx = 0; (ithx < order); ithx++)
+ {
+ const int index_x = (idxX + ithx)*gridNY*gridNZ;
+ const real tx = thx[ithx];
+ const real dx = dthx[ithx];
+
+ for (int ithy = 0; (ithy < order); ithy++)
+ {
+ const int index_xy = index_x + (idxY + ithy)*gridNZ;
+ const real ty = thy[ithy];
+ const real dy = dthy[ithy];
+ real fxy1 = 0, fz1 = 0;
+
+ for (int ithz = 0; (ithz < order); ithz++)
+ {
+ const real gval = grid[index_xy + (idxZ + ithz)];
+ fxy1 += thz[ithz]*gval;
+ fz1 += dthz[ithz]*gval;
+ }
+ f[XX] += dx*ty*fxy1;
+ f[YY] += tx*dy*fxy1;
+ f[ZZ] += tx*ty*fz1;
+ }
+ }
+
+ return f;
}
+#ifdef PME_SIMD4_UNALIGNED //TODO: Consider always have at least a dummy implementation of Simd (enough for first phase of two-phase lookup) and then use enable_if instead of #ifdef
+/* Gather for one charge with pme_order=4 with unaligned SIMD4 load+store.
+ * This code does not assume any memory alignment for the grid.
+ */
+ RVec
+ operator()(std::integral_constant<int, 4>) const
+ {
+ const int norder = nn*4;
+ /* Pointer arithmetic alert, next six statements */
+ const real *const gmx_restrict thx = spline->theta[XX] + norder;
+ const real *const gmx_restrict thy = spline->theta[YY] + norder;
+ const real *const gmx_restrict thz = spline->theta[ZZ] + norder;
+ const real *const gmx_restrict dthx = spline->dtheta[XX] + norder;
+ const real *const gmx_restrict dthy = spline->dtheta[YY] + norder;
+ const real *const gmx_restrict dthz = spline->dtheta[ZZ] + norder;
-void gather_f_bsplines(struct gmx_pme_t *pme, real *grid,
- gmx_bool bClearF, pme_atomcomm_t *atc,
- splinedata_t *spline,
- real scale)
-{
- /* sum forces for local particles */
- int nn, n, ithx, ithy, ithz, i0, j0, k0;
- int index_x, index_xy;
- int nx, ny, nz, pny, pnz;
- int *idxptr;
- real tx, ty, dx, dy, coefficient;
- real fx, fy, fz, gval;
- real fxy1, fz1;
- real *thx, *thy, *thz, *dthx, *dthy, *dthz;
- int norder;
- real rxx, ryx, ryy, rzx, rzy, rzz;
- int order;
+ Simd4Real fx_S = setZero();
+ Simd4Real fy_S = setZero();
+ Simd4Real fz_S = setZero();
+
+ /* With order 4 the z-spline is actually aligned */
+ const Simd4Real tz_S = load4(thz);
+ const Simd4Real dz_S = load4(dthz);
+
+ for (int ithx = 0; (ithx < 4); ithx++)
+ {
+ const int index_x = (idxX + ithx)*gridNY*gridNZ;
+ const Simd4Real tx_S = Simd4Real(thx[ithx]);
+ const Simd4Real dx_S = Simd4Real(dthx[ithx]);
+
+ for (int ithy = 0; (ithy < 4); ithy++)
+ {
+ const int index_xy = index_x + (idxY + ithy)*gridNZ;
+ const Simd4Real ty_S = Simd4Real(thy[ithy]);
+ const Simd4Real dy_S = Simd4Real(dthy[ithy]);
+
+ const Simd4Real gval_S = load4U(grid + index_xy + idxZ);
+
+ const Simd4Real fxy1_S = tz_S * gval_S;
+ const Simd4Real fz1_S = dz_S * gval_S;
+
+ fx_S = fma(dx_S * ty_S, fxy1_S, fx_S);
+ fy_S = fma(tx_S * dy_S, fxy1_S, fy_S);
+ fz_S = fma(tx_S * ty_S, fz1_S, fz_S);
+ }
+ }
+
+ return {
+ reduce(fx_S), reduce(fy_S), reduce(fz_S)
+ };
+ }
+#endif
#ifdef PME_SIMD4_SPREAD_GATHER
- // cppcheck-suppress unreadVariable cppcheck seems not to analyze code from pme-simd4.h
- struct pme_spline_work *work = pme->spline_work;
-#ifndef PME_SIMD4_UNALIGNED
- GMX_ALIGNED(real, GMX_SIMD4_WIDTH) thz_aligned[GMX_SIMD4_WIDTH*2];
- GMX_ALIGNED(real, GMX_SIMD4_WIDTH) dthz_aligned[GMX_SIMD4_WIDTH*2];
+/* Load order elements from unaligned memory into two 4-wide SIMD */
+ template<int order>
+ static inline void loadOrderU(const real* data, std::integral_constant<int, order>,
+ int offset, Simd4Real* S0, Simd4Real* S1)
+ {
+#ifdef PME_SIMD4_UNALIGNED //TODO: Extract into helper function
+ *S0 = load4U(data-offset);
+ *S1 = load4U(data-offset+4);
+#else
+ GMX_ALIGNED(real, GMX_SIMD4_WIDTH) buf_aligned[GMX_SIMD4_WIDTH*2];
+ /* Copy data to an aligned buffer */
+ for (int i = 0; i < order; i++)
+ {
+ buf_aligned[offset+i] = data[i];
+ }
+ *S0 = load4(buf_aligned);
+ *S1 = load4(buf_aligned+4);
#endif
+ }
#endif
- order = pme->pme_order;
- nx = pme->nkx;
- ny = pme->nky;
- nz = pme->nkz;
- pny = pme->pmegrid_ny;
- pnz = pme->pmegrid_nz;
-
- rxx = pme->recipbox[XX][XX];
- ryx = pme->recipbox[YY][XX];
- ryy = pme->recipbox[YY][YY];
- rzx = pme->recipbox[ZZ][XX];
- rzy = pme->recipbox[ZZ][YY];
- rzz = pme->recipbox[ZZ][ZZ];
-
- for (nn = 0; nn < spline->n; nn++)
+#ifdef PME_SIMD4_SPREAD_GATHER
+/* This code assumes that the grid is allocated 4-real aligned
+ * and that pme->pmegrid_nz is a multiple of 4.
+ * This code supports pme_order <= 5.
+ */
+ template <int Order>
+ typename std::enable_if<Order == 4 || Order == 5, RVec>::type
+ operator()(std::integral_constant<int, Order> order) const
{
- n = spline->ind[nn];
- coefficient = scale*atc->coefficient[n];
+ const int norder = nn*order;
+ GMX_ASSERT(gridNZ % 4 == 0, "For aligned SIMD4 operations the grid size has to be padded up to a multiple of 4");
+ /* Pointer arithmetic alert, next six statements */
+ const real *const gmx_restrict thx = spline->theta[XX] + norder;
+ const real *const gmx_restrict thy = spline->theta[YY] + norder;
+ const real *const gmx_restrict thz = spline->theta[ZZ] + norder;
+ const real *const gmx_restrict dthx = spline->dtheta[XX] + norder;
+ const real *const gmx_restrict dthy = spline->dtheta[YY] + norder;
+ const real *const gmx_restrict dthz = spline->dtheta[ZZ] + norder;
+
+ struct pme_spline_work *const work = pme->spline_work;
+
+ const int offset = idxZ & 3;
+
+ Simd4Real fx_S = setZero();
+ Simd4Real fy_S = setZero();
+ Simd4Real fz_S = setZero();
+
+ Simd4Real tz_S0, tz_S1, dz_S0, dz_S1;
+ loadOrderU(thz, order, offset, &tz_S0, &tz_S1);
+ loadOrderU(dthz, order, offset, &dz_S0, &dz_S1);
+
+ tz_S0 = selectByMask(tz_S0, work->mask_S0[offset]);
+ dz_S0 = selectByMask(dz_S0, work->mask_S0[offset]);
+ tz_S1 = selectByMask(tz_S1, work->mask_S1[offset]);
+ dz_S1 = selectByMask(dz_S1, work->mask_S1[offset]);
+
+ for (int ithx = 0; (ithx < order); ithx++)
+ {
+ const int index_x = (idxX + ithx)*gridNY*gridNZ;
+ const Simd4Real tx_S = Simd4Real(thx[ithx]);
+ const Simd4Real dx_S = Simd4Real(dthx[ithx]);
+
+ for (int ithy = 0; (ithy < order); ithy++)
+ {
+ const int index_xy = index_x + (idxY + ithy)*gridNZ;
+ const Simd4Real ty_S = Simd4Real(thy[ithy]);
+ const Simd4Real dy_S = Simd4Real(dthy[ithy]);
+
+ const Simd4Real gval_S0 = load4(grid + index_xy + idxZ - offset);
+ const Simd4Real gval_S1 = load4(grid + index_xy + idxZ - offset + 4);
+
+ const Simd4Real fxy1_S0 = tz_S0 * gval_S0;
+ const Simd4Real fz1_S0 = dz_S0 * gval_S0;
+ const Simd4Real fxy1_S1 = tz_S1 * gval_S1;
+ const Simd4Real fz1_S1 = dz_S1 * gval_S1;
+
+ const Simd4Real fxy1_S = fxy1_S0 + fxy1_S1;
+ const Simd4Real fz1_S = fz1_S0 + fz1_S1;
+
+ fx_S = fma(dx_S * ty_S, fxy1_S, fx_S);
+ fy_S = fma(tx_S * dy_S, fxy1_S, fy_S);
+ fz_S = fma(tx_S * ty_S, fz1_S, fz_S);
+ }
+ }
+
+ return {
+ reduce(fx_S), reduce(fy_S), reduce(fz_S)
+ };
+ }
+#endif
+ private:
+ const gmx_pme_t *const pme;
+ const real *const gmx_restrict grid;
+ const pme_atomcomm_t *const gmx_restrict atc;
+ const splinedata_t *const gmx_restrict spline;
+ const int nn;
+
+ const int gridNY = pme->pmegrid_ny;
+ const int gridNZ = pme->pmegrid_nz;
+
+ const int *const idxptr = atc->idx[spline->ind[nn]];
+ const int idxX = idxptr[XX];
+ const int idxY = idxptr[YY];
+ const int idxZ = idxptr[ZZ];
+};
+
+
+void gather_f_bsplines(const gmx_pme_t *pme, const real *grid,
+ gmx_bool bClearF, const pme_atomcomm_t *atc,
+ const splinedata_t *spline,
+ real scale)
+{
+ /* sum forces for local particles */
+
+ const int order = pme->pme_order;
+ const int nx = pme->nkx;
+ const int ny = pme->nky;
+ const int nz = pme->nkz;
+
+ const real rxx = pme->recipbox[XX][XX];
+ const real ryx = pme->recipbox[YY][XX];
+ const real ryy = pme->recipbox[YY][YY];
+ const real rzx = pme->recipbox[ZZ][XX];
+ const real rzy = pme->recipbox[ZZ][YY];
+ const real rzz = pme->recipbox[ZZ][ZZ];
+
+ /* Extract the buffer for force output */
+ rvec * gmx_restrict force = atc->f;
+
+ /* Note that unrolling this loop by templating this function on order
+ * deteriorates performance significantly with gcc5/6/7.
+ */
+ for (int nn = 0; nn < spline->n; nn++)
+ {
+ const int n = spline->ind[nn];
+ const real coefficient = scale*atc->coefficient[n];
if (bClearF)
{
- atc->f[n][XX] = 0;
- atc->f[n][YY] = 0;
- atc->f[n][ZZ] = 0;
+ force[n][XX] = 0;
+ force[n][YY] = 0;
+ force[n][ZZ] = 0;
}
if (coefficient != 0)
{
- fx = 0;
- fy = 0;
- fz = 0;
- idxptr = atc->idx[n];
- norder = nn*order;
-
- i0 = idxptr[XX];
- j0 = idxptr[YY];
- k0 = idxptr[ZZ];
-
- /* Pointer arithmetic alert, next six statements */
- thx = spline->theta[XX] + norder;
- thy = spline->theta[YY] + norder;
- thz = spline->theta[ZZ] + norder;
- dthx = spline->dtheta[XX] + norder;
- dthy = spline->dtheta[YY] + norder;
- dthz = spline->dtheta[ZZ] + norder;
+ RVec f;
+ const auto spline_func = do_fspline(pme, grid, atc, spline, nn);
switch (order)
{
case 4:
-#ifdef PME_SIMD4_SPREAD_GATHER
-#ifdef PME_SIMD4_UNALIGNED
-#define PME_GATHER_F_SIMD4_ORDER4
-#else
-#define PME_GATHER_F_SIMD4_ALIGNED
-#define PME_ORDER 4
-#endif
-#include "pme-simd4.h"
-#else
- DO_FSPLINE(4);
-#endif
+ f = spline_func(std::integral_constant<int, 4>());
break;
case 5:
-#ifdef PME_SIMD4_SPREAD_GATHER
-#define PME_GATHER_F_SIMD4_ALIGNED
-#define PME_ORDER 5
-#include "pme-simd4.h"
-#else
- DO_FSPLINE(5);
-#endif
+ f = spline_func(std::integral_constant<int, 5>());
break;
default:
- DO_FSPLINE(order);
+ f = spline_func(order);
break;
}
- atc->f[n][XX] += -coefficient*( fx*nx*rxx );
- atc->f[n][YY] += -coefficient*( fx*nx*ryx + fy*ny*ryy );
- atc->f[n][ZZ] += -coefficient*( fx*nx*rzx + fy*ny*rzy + fz*nz*rzz );
+ force[n][XX] += -coefficient*( f[XX]*nx*rxx );
+ force[n][YY] += -coefficient*( f[XX]*nx*ryx + f[YY]*ny*ryy );
+ force[n][ZZ] += -coefficient*( f[XX]*nx*rzx + f[YY]*ny*rzy + f[ZZ]*nz*rzz );
}
}
/* Since the energy and not forces are interpolated
}
-real gather_energy_bsplines(struct gmx_pme_t *pme, real *grid,
+real gather_energy_bsplines(gmx_pme_t *pme, real *grid,
pme_atomcomm_t *atc)
{
splinedata_t *spline;
- int n, ithx, ithy, ithz, i0, j0, k0;
- int index_x, index_xy;
- int * idxptr;
- real energy, pot, tx, ty, coefficient, gval;
- real *thx, *thy, *thz;
- int norder;
- int order;
+ int n, ithx, ithy, ithz, i0, j0, k0;
+ int index_x, index_xy;
+ int *idxptr;
+ real energy, pot, tx, ty, coefficient, gval;
+ real *thx, *thy, *thz;
+ int norder;
+ int order;
spline = &atc->spline[0];
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "pme-internal.h"
void
-gather_f_bsplines(struct gmx_pme_t *pme, real *grid,
- gmx_bool bClearF, pme_atomcomm_t *atc,
- splinedata_t *spline,
+gather_f_bsplines(const struct gmx_pme_t *pme, const real *grid,
+ gmx_bool bClearF, const pme_atomcomm_t *atc,
+ const splinedata_t *spline,
real scale);
real
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include "gromacs/ewald/pme.h"
+#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/math/vec.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/utility/fatalerror.h"
#endif
-int copy_pmegrid_to_fftgrid(struct gmx_pme_t *pme, real *pmegrid, real *fftgrid, int grid_index)
+int copy_pmegrid_to_fftgrid(const gmx_pme_t *pme, real *pmegrid, real *fftgrid, int grid_index)
{
ivec local_fft_ndata, local_fft_offset, local_fft_size;
ivec local_pme_size;
}
-void wrap_periodic_pmegrid(struct gmx_pme_t *pme, real *pmegrid)
+void wrap_periodic_pmegrid(const gmx_pme_t *pme, real *pmegrid)
{
int nx, ny, nz, pny, pnz, ny_x, overlap, ix, iy, iz;
}
grid->order = pme_order;
- if (ptr == NULL)
+ if (ptr == nullptr)
{
gridsize = grid->s[XX]*grid->s[YY]*grid->s[ZZ];
set_gridsize_alignment(&gridsize, pme_order);
}
env = getenv("GMX_PME_THREAD_DIVISION");
- if (env != NULL)
+ if (env != nullptr)
{
sscanf(env, "%20d %20d %20d", &nsub[XX], &nsub[YY], &nsub[ZZ]);
}
n_base[ZZ] = nz_base;
pmegrid_init(&grids->grid, 0, 0, 0, 0, 0, 0, n[XX], n[YY], n[ZZ], FALSE, pme_order,
- NULL);
+ nullptr);
grids->nthread = nthread;
}
else
{
- grids->grid_th = NULL;
+ grids->grid_th = nullptr;
}
- snew(grids->g2t, DIM);
tfac = 1;
for (d = DIM-1; d >= 0; d--)
{
{
grids->nthread_comm[d]++;
}
- if (debug != NULL)
+ if (debug != nullptr)
{
fprintf(debug, "pmegrid thread grid communication range in %c: %d\n",
'x'+d, grids->nthread_comm[d]);
void pmegrids_destroy(pmegrids_t *grids)
{
- int t;
-
- if (grids->grid.grid != NULL)
+ if (grids->grid.grid != nullptr)
{
- sfree(grids->grid.grid);
+ sfree_aligned(grids->grid.grid);
if (grids->nthread > 0)
{
- for (t = 0; t < grids->nthread; t++)
- {
- sfree(grids->grid_th[t].grid);
- }
+ sfree_aligned(grids->grid_all);
sfree(grids->grid_th);
}
+ for (int d = 0; d < DIM; d++)
+ {
+ sfree(grids->g2t[d]);
+ }
}
}
void
-make_gridindex5_to_localindex(int n, int local_start, int local_range,
- int **global_to_local,
- real **fraction_shift)
+make_gridindex_to_localindex(int n, int local_start, int local_range,
+ int **global_to_local,
+ real **fraction_shift)
{
/* Here we construct array for looking up the grid line index and
* fraction for particles. This is done because it is slighlty
* faster than the modulo operation and to because we need to take
* care of rounding issues, see below.
- * We use an array size of 5 times the grid size to allow for particles
- * to be out of the triclinic unit-cell by up to 2 box lengths, which
- * can be needed along dimension x for a very skewed unit-cell.
+ * We use an array size of c_pmeNeighborUnitcellCount times the grid size
+ * to allow for particles to be out of the triclinic unit-cell.
*/
- int * gtl;
- real * fsh;
+ const int arraySize = c_pmeNeighborUnitcellCount * n;
+ int * gtl;
+ real * fsh;
- snew(gtl, 5*n);
- snew(fsh, 5*n);
+ snew(gtl, arraySize);
+ snew(fsh, arraySize);
- for (int i = 0; i < 5*n; i++)
+ for (int i = 0; i < arraySize; i++)
{
/* Transform global grid index to the local grid index.
* Our local grid always runs from 0 to local_range-1.
sfree_aligned(newgrid->grid.grid);
newgrid->grid.grid = oldgrid->grid.grid;
- if (newgrid->grid_th != NULL && newgrid->nthread == oldgrid->nthread)
+ if (newgrid->grid_th != nullptr && newgrid->nthread == oldgrid->nthread)
{
sfree_aligned(newgrid->grid_all);
+ newgrid->grid_all = oldgrid->grid_all;
for (t = 0; t < newgrid->nthread; t++)
{
newgrid->grid_th[t].grid = oldgrid->grid_th[t].grid;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "pme-internal.h"
+
+/*! \brief
+ * We allow coordinates to be out the unit-cell by up to 2 box lengths,
+ * which might be needed along dimension x for a very skewed unit-cell.
+ */
+constexpr int c_pmeMaxUnitcellShift = 2;
+
+/*! \brief
+ * This affects the size of the lookup table of the modulo operation result,
+ * when working with PME local grid indices of the particles.
+ */
+constexpr int c_pmeNeighborUnitcellCount = 2*c_pmeMaxUnitcellShift + 1;
+
+
#if GMX_MPI
void
gmx_sum_qgrid_dd(struct gmx_pme_t *pme, real *grid, int direction);
#endif
int
-copy_pmegrid_to_fftgrid(struct gmx_pme_t *pme, real *pmegrid, real *fftgrid, int grid_index);
+copy_pmegrid_to_fftgrid(const gmx_pme_t *pme, real *pmegrid, real *fftgrid, int grid_index);
int
copy_fftgrid_to_pmegrid(struct gmx_pme_t *pme, const real *fftgrid, real *pmegrid, int grid_index,
int nthread, int thread);
void
-wrap_periodic_pmegrid(struct gmx_pme_t *pme, real *pmegrid);
+wrap_periodic_pmegrid(const gmx_pme_t *pme, real *pmegrid);
void
unwrap_periodic_pmegrid(struct gmx_pme_t *pme, real *pmegrid);
pmegrids_destroy(pmegrids_t *grids);
void
-make_gridindex5_to_localindex(int n, int local_start, int local_range,
- int **global_to_local,
- real **fraction_shift);
+make_gridindex_to_localindex(int n, int local_start, int local_range,
+ int **global_to_local,
+ real **fraction_shift);
void
set_grid_alignment(int *pmegrid_nz, int pme_order);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
-#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/math/gmxcomplex.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/gmxmpi.h"
+//! A repeat of typedef from parallel_3dfft.h
+typedef struct gmx_parallel_3dfft *gmx_parallel_3dfft_t;
+
struct t_commrec;
struct t_inputrec;
*/
#define PME_ORDER_MAX 12
-/*! \brief As gmx_pme_init, but takes most settings, except the grid, from pme_src */
+/*! \brief As gmx_pme_init, but takes most settings, except the grid/Ewald coefficients, from pme_src.
+ * This is only called when the PME cut-off/grid size changes.
+ */
int gmx_pme_reinit(struct gmx_pme_t **pmedata,
t_commrec * cr,
struct gmx_pme_t * pme_src,
const t_inputrec * ir,
- ivec grid_size);
+ ivec grid_size,
+ real ewaldcoeff_q,
+ real ewaldcoeff_lj);
+
/* The following three routines are for PME/PP node splitting in pme_pp.c */
/*! \brief Data structure for beta-spline interpolation */
typedef struct {
- int *thread_one;
int n;
int *ind;
splinevec theta;
ivec nc; /* The local spatial decomposition over the threads */
pmegrid_t *grid_th; /* Array of grids for each thread */
real *grid_all; /* Allocated array for the grids in *grid_th */
- int **g2t; /* The grid to thread index */
+ int *g2t[DIM]; /* The grid to thread index */
ivec nthread_comm; /* The number of threads to communicate with */
} pmegrids_t;
int nthread; /* The number of threads doing PME on our rank */
gmx_bool bPPnode; /* Node also does particle-particle forces */
+ bool doCoulomb; /* Apply PME to electrostatics */
+ bool doLJ; /* Apply PME to Lennard-Jones r^-6 interactions */
gmx_bool bFEP; /* Compute Free energy contribution */
gmx_bool bFEP_q;
gmx_bool bFEP_lj;
int nkx, nky, nkz; /* Grid dimensions */
gmx_bool bP3M; /* Do P3M: optimize the influence function */
int pme_order;
+ real ewaldcoeff_q; /* Ewald splitting coefficient for Coulomb */
+ real ewaldcoeff_lj; /* Ewald splitting coefficient for r^-6 */
real epsilon_r;
int ljpme_combination_rule; /* Type of combination rule in LJ-PME */
//! @endcond
-/*! \brief Check restrictions on pme_order and the PME grid nkx,nky,nkz.
- *
- * With bFatal=TRUE, a fatal error is generated on violation,
- * bValidSettings=NULL can be passed.
- * With bFatal=FALSE, *bValidSettings reports the validity of the settings.
- * bUseThreads tells if any MPI rank doing PME uses more than 1 threads.
- * If at calling you bUseThreads is unknown, pass TRUE for conservative
- * checking.
- */
-void gmx_pme_check_restrictions(int pme_order,
- int nkx, int nky, int nkz,
- int nnodes_major,
- int nnodes_minor,
- gmx_bool bUseThreads,
- gmx_bool bFatal,
- gmx_bool *bValidSettings);
-
/*! \brief Initialize the PME-only side of the PME <-> PP communication */
gmx_pme_pp_t gmx_pme_pp_init(t_commrec *cr);
real **sigmaA, real **sigmaB,
matrix box, rvec **x, rvec **f,
int *maxshift_x, int *maxshift_y,
- gmx_bool *bFreeEnergy_q, gmx_bool *bFreeEnergy_lj,
real *lambda_q, real *lambda_lj,
- gmx_bool *bEnerVir, int *pme_flags,
+ gmx_bool *bEnerVir,
gmx_int64_t *step,
ivec grid_size, real *ewaldcoeff_q, real *ewaldcoeff_lj);
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fft/calcgrid.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "pme-internal.h"
/*! \brief Parameters and settings for one PP-PME setup */
struct pme_setup_t {
real rcut_coulomb; /**< Coulomb cut-off */
- real rlist; /**< pair-list cut-off */
+ real rlistOuter; /**< cut-off for the outer pair-list */
+ real rlistInner; /**< cut-off for the inner pair-list */
real spacing; /**< (largest) PME grid spacing */
ivec grid; /**< the PME grid dimensions */
real grid_efficiency; /**< ineffiency factor for non-uniform grids <= 1 */
real cut_spacing; /**< the minimum cutoff / PME grid spacing ratio */
real rcut_vdw; /**< Vdw cutoff (does not change) */
real rcut_coulomb_start; /**< Initial electrostatics cutoff */
- real rbuf_coulomb; /**< the pairlist buffer size */
- real rbuf_vdw; /**< the pairlist buffer size */
+ real rbufOuter_coulomb; /**< the outer pairlist buffer size */
+ real rbufOuter_vdw; /**< the outer pairlist buffer size */
+ real rbufInner_coulomb; /**< the inner pairlist buffer size */
+ real rbufInner_vdw; /**< the inner pairlist buffer size */
matrix box_start; /**< the initial simulation box */
int n; /**< the count of setup as well as the allocation size */
pme_setup_t *setup; /**< the PME+cutoff setups */
* read bActive anywhere */
bool pme_loadbal_is_active(const pme_load_balancing_t *pme_lb)
{
- return pme_lb != NULL && pme_lb->bActive;
+ return pme_lb != nullptr && pme_lb->bActive;
}
void pme_loadbal_init(pme_load_balancing_t **pme_lb_p,
t_commrec *cr,
- FILE *fp_log,
+ const gmx::MDLogger &mdlog,
const t_inputrec *ir,
matrix box,
const interaction_const_t *ic,
- struct gmx_pme_t *pmedata,
+ const NbnxnListParameters *listParams,
+ gmx_pme_t *pmedata,
gmx_bool bUseGPU,
gmx_bool *bPrinting)
{
snew(pme_lb, 1);
- pme_lb->bSepPMERanks = !(cr->duty & DUTY_PME);
+ pme_lb->bSepPMERanks = !(cr->duty & DUTY_PME);
/* Initially we turn on balancing directly on based on PP/PME imbalance */
- pme_lb->bTriggerOnDLB = FALSE;
+ pme_lb->bTriggerOnDLB = FALSE;
/* Any number of stages >= 2 is supported */
- pme_lb->nstage = 2;
+ pme_lb->nstage = 2;
- pme_lb->cutoff_scheme = ir->cutoff_scheme;
+ pme_lb->cutoff_scheme = ir->cutoff_scheme;
- pme_lb->rbuf_coulomb = ic->rlist - ic->rcoulomb;
- pme_lb->rbuf_vdw = ic->rlist - ic->rvdw;
+ pme_lb->rbufOuter_coulomb = listParams->rlistOuter - ic->rcoulomb;
+ pme_lb->rbufOuter_vdw = listParams->rlistOuter - ic->rvdw;
+ pme_lb->rbufInner_coulomb = listParams->rlistInner - ic->rcoulomb;
+ pme_lb->rbufInner_vdw = listParams->rlistInner - ic->rvdw;
copy_mat(box, pme_lb->box_start);
if (ir->ePBC == epbcXY && ir->nwall == 2)
pme_lb->cur = 0;
pme_lb->setup[0].rcut_coulomb = ic->rcoulomb;
- pme_lb->setup[0].rlist = ic->rlist;
+ pme_lb->setup[0].rlistOuter = listParams->rlistOuter;
+ pme_lb->setup[0].rlistInner = listParams->rlistInner;
pme_lb->setup[0].grid[XX] = ir->nkx;
pme_lb->setup[0].grid[YY] = ir->nky;
pme_lb->setup[0].grid[ZZ] = ir->nkz;
if (!wallcycle_have_counter())
{
- md_print_warn(cr, fp_log, "NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("NOTE: Cycle counters unsupported or not enabled in kernel. Cannot use PME-PP balancing.");
}
/* Tune with GPUs and/or separate PME ranks.
dd_dlb_lock(cr->dd);
if (dd_dlb_is_locked(cr->dd))
{
- md_print_warn(cr, fp_log, "NOTE: DLB will not turn on during the first phase of PME tuning\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("NOTE: DLB will not turn on during the first phase of PME tuning");
}
}
real fac, sp;
real tmpr_coulomb, tmpr_vdw;
int d;
- gmx_bool grid_ok;
+ bool grid_ok;
/* Try to add a new setup with next larger cut-off to the list */
pme_lb->n++;
srenew(pme_lb->setup, pme_lb->n);
set = &pme_lb->setup[pme_lb->n-1];
- set->pmedata = NULL;
+ set->pmedata = nullptr;
get_pme_nnodes(dd, &npmeranks_x, &npmeranks_y);
fac *= 1.01;
clear_ivec(set->grid);
- sp = calc_grid(NULL, pme_lb->box_start,
- fac*pme_lb->setup[pme_lb->cur].spacing,
- &set->grid[XX],
- &set->grid[YY],
- &set->grid[ZZ]);
+ sp = calcFftGrid(nullptr, pme_lb->box_start,
+ fac*pme_lb->setup[pme_lb->cur].spacing,
+ minimalPmeGridSize(pme_order),
+ &set->grid[XX],
+ &set->grid[YY],
+ &set->grid[ZZ]);
/* As here we can't easily check if one of the PME ranks
* uses threading, we do a conservative grid check.
* This means we can't use pme_order or less grid lines
* per PME rank along x, which is not a strong restriction.
*/
- gmx_pme_check_restrictions(pme_order,
- set->grid[XX], set->grid[YY], set->grid[ZZ],
- npmeranks_x, npmeranks_y,
- TRUE,
- FALSE,
- &grid_ok);
+ grid_ok = gmx_pme_check_restrictions(pme_order,
+ set->grid[XX], set->grid[YY], set->grid[ZZ],
+ npmeranks_x,
+ true,
+ false);
}
while (sp <= 1.001*pme_lb->setup[pme_lb->cur].spacing || !grid_ok);
if (pme_lb->cutoff_scheme == ecutsVERLET)
{
/* Never decrease the Coulomb and VdW list buffers */
- set->rlist = std::max(set->rcut_coulomb + pme_lb->rbuf_coulomb,
- pme_lb->rcut_vdw + pme_lb->rbuf_vdw);
+ set->rlistOuter = std::max(set->rcut_coulomb + pme_lb->rbufOuter_coulomb,
+ pme_lb->rcut_vdw + pme_lb->rbufOuter_vdw);
+ set->rlistInner = std::max(set->rcut_coulomb + pme_lb->rbufInner_coulomb,
+ pme_lb->rcut_vdw + pme_lb->rbufInner_vdw);
}
else
{
/* TODO Remove these lines and pme_lb->cutoff_scheme */
- tmpr_coulomb = set->rcut_coulomb + pme_lb->rbuf_coulomb;
- tmpr_vdw = pme_lb->rcut_vdw + pme_lb->rbuf_vdw;
+ tmpr_coulomb = set->rcut_coulomb + pme_lb->rbufOuter_coulomb;
+ tmpr_vdw = pme_lb->rcut_vdw + pme_lb->rbufOuter_vdw;
/* Two (known) bugs with cutoff-scheme=group here:
* - This modification of rlist results in incorrect DD comunication.
* - We should set fr->bTwinRange = (fr->rlistlong > fr->rlist).
*/
- set->rlist = std::min(tmpr_coulomb, tmpr_vdw);
+ set->rlistOuter = std::min(tmpr_coulomb, tmpr_vdw);
+ set->rlistInner = set->rlistOuter;
}
- set->spacing = sp;
+ set->spacing = sp;
/* The grid efficiency is the size wrt a grid with uniform x/y/z spacing */
set->grid_efficiency = 1;
for (d = 0; d < DIM; d++)
pre,
desc, set->grid[XX], set->grid[YY], set->grid[ZZ], set->rcut_coulomb,
buft);
- if (fp_err != NULL)
+ if (fp_err != nullptr)
{
fprintf(fp_err, "\r%s\n", buf);
fflush(fp_err);
}
- if (fp_log != NULL)
+ if (fp_log != nullptr)
{
fprintf(fp_log, "%s\n", buf);
}
gmx_step_str(step, sbuf),
pmelblim_str[pme_lb->elimited],
pme_lb->setup[pme_loadbal_end(pme_lb)-1].rcut_coulomb);
- if (fp_err != NULL)
+ if (fp_err != nullptr)
{
fprintf(fp_err, "\r%s\n", buf);
fflush(fp_err);
}
- if (fp_log != NULL)
+ if (fp_log != nullptr)
{
fprintf(fp_log, "%s\n", buf);
}
t_commrec *cr,
FILE *fp_err,
FILE *fp_log,
+ const gmx::MDLogger &mdlog,
const t_inputrec *ir,
t_state *state,
double cycles,
* better overal performance can be obtained with a slightly
* shorter cut-off and better DD load balancing.
*/
- set_dd_dlb_max_cutoff(cr, pme_lb->setup[pme_lb->fastest].rlist);
+ set_dd_dlb_max_cutoff(cr, pme_lb->setup[pme_lb->fastest].rlistOuter);
}
}
cycles_fast = pme_lb->setup[pme_lb->fastest].cycles;
if (OK && ir->ePBC != epbcNONE)
{
- OK = (gmx::square(pme_lb->setup[pme_lb->cur+1].rlist)
+ OK = (gmx::square(pme_lb->setup[pme_lb->cur+1].rlistOuter)
<= max_cutoff2(ir->ePBC, state->box));
if (!OK)
{
if (DOMAINDECOMP(cr))
{
OK = change_dd_cutoff(cr, state, ir,
- pme_lb->setup[pme_lb->cur].rlist);
+ pme_lb->setup[pme_lb->cur].rlistOuter);
if (!OK)
{
/* Failed: do not use this setup */
if (DOMAINDECOMP(cr) && pme_lb->stage > 0)
{
- OK = change_dd_cutoff(cr, state, ir, pme_lb->setup[pme_lb->cur].rlist);
+ OK = change_dd_cutoff(cr, state, ir, pme_lb->setup[pme_lb->cur].rlistOuter);
if (!OK)
{
/* For some reason the chosen cut-off is incompatible with DD.
/* This should not happen, as we set limits on the DLB bounds.
* But we implement a complete failsafe solution anyhow.
*/
- md_print_warn(cr, fp_log, "The fastest PP/PME load balancing setting (cutoff %.3f nm) is no longer available due to DD DLB or box size limitations\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "The fastest PP/PME load balancing setting (cutoff %.3f nm) is no longer available due to DD DLB or box size limitations", pme_lb->fastest);
pme_lb->fastest = pme_lb->lower_limit;
pme_lb->start = pme_lb->lower_limit;
}
set = &pme_lb->setup[pme_lb->cur];
- ic->rcoulomb = set->rcut_coulomb;
- ic->rlist = set->rlist;
- ic->ewaldcoeff_q = set->ewaldcoeff_q;
+ NbnxnListParameters *listParams = nbv->listParams.get();
+
+ ic->rcoulomb = set->rcut_coulomb;
+ listParams->rlistOuter = set->rlistOuter;
+ listParams->rlistInner = set->rlistInner;
+ ic->ewaldcoeff_q = set->ewaldcoeff_q;
/* TODO: centralize the code that sets the potentials shifts */
if (ic->coulomb_modifier == eintmodPOTSHIFT)
{
}
/* We always re-initialize the tables whether they are used or not */
- init_interaction_const_tables(NULL, ic, rtab);
+ init_interaction_const_tables(nullptr, ic, rtab);
- nbnxn_gpu_pme_loadbal_update_param(nbv, ic);
+ nbnxn_gpu_pme_loadbal_update_param(nbv, ic, listParams);
/* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
* also sharing texture references. To keep the code simple, we don't
if (!pme_lb->bSepPMERanks)
{
- if (pme_lb->setup[pme_lb->cur].pmedata == NULL)
+ if (pme_lb->setup[pme_lb->cur].pmedata == nullptr)
{
/* Generate a new PME data structure,
* copying part of the old pointers.
*/
gmx_pme_reinit(&set->pmedata,
cr, pme_lb->setup[0].pmedata, ir,
- set->grid);
+ set->grid, set->ewaldcoeff_q, set->ewaldcoeff_lj);
}
*pmedata = set->pmedata;
}
if (debug)
{
- print_grid(NULL, debug, "", "switched to", set, -1);
+ print_grid(nullptr, debug, "", "switched to", set, -1);
}
if (pme_lb->stage == pme_lb->nstage)
t_commrec *cr,
FILE *fp_err,
FILE *fp_log,
+ const gmx::MDLogger &mdlog,
const t_inputrec *ir,
t_forcerec *fr,
t_state *state,
{
/* Unlock the DLB=auto, DLB is allowed to activate */
dd_dlb_unlock(cr->dd);
- md_print_warn(cr, fp_log, "NOTE: DLB can now turn on, when beneficial\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("NOTE: DLB can now turn on, when beneficial");
/* We don't deactivate the tuning yet, since we will balance again
* after DLB gets turned on, if it does within PMETune_period.
* This also ensures that we won't disable the currently
* optimal setting during a second round of PME balancing.
*/
- set_dd_dlb_max_cutoff(cr, fr->ic->rlist);
+ set_dd_dlb_max_cutoff(cr, fr->nbv->listParams->rlistOuter);
}
}
* but the first data collected is skipped anyhow.
*/
pme_load_balance(pme_lb, cr,
- fp_err, fp_log,
+ fp_err, fp_log, mdlog,
ir, state, pme_lb->cycles_c - cycles_prev,
fr->ic, fr->nbv, &fr->pmedata,
step);
/* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
fr->ewaldcoeff_q = fr->ic->ewaldcoeff_q;
fr->ewaldcoeff_lj = fr->ic->ewaldcoeff_lj;
- fr->rlist = fr->ic->rlist;
+ fr->rlist = fr->nbv->listParams->rlistOuter;
fr->rcoulomb = fr->ic->rcoulomb;
fr->rvdw = fr->ic->rvdw;
if (ir->eDispCorr != edispcNO)
{
- calc_enervirdiff(NULL, ir->eDispCorr, fr);
+ calc_enervirdiff(nullptr, ir->eDispCorr, fr);
}
}
{
/* Make sure DLB is allowed when we deactivate PME tuning */
dd_dlb_unlock(cr->dd);
- md_print_warn(cr, fp_log, "NOTE: DLB can now turn on, when beneficial\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("NOTE: DLB can now turn on, when beneficial");
}
*bPrinting = pme_lb->bBalance;
fprintf(fplog,
" %-7s %6.3f nm %6.3f nm %3d %3d %3d %5.3f nm %5.3f nm\n",
name,
- setup->rcut_coulomb, setup->rlist,
+ setup->rcut_coulomb, setup->rlistInner,
setup->grid[XX], setup->grid[YY], setup->grid[ZZ],
setup->spacing, 1/setup->ewaldcoeff_q);
}
/*! \brief Print all load-balancing settings */
static void print_pme_loadbal_settings(pme_load_balancing_t *pme_lb,
- t_commrec *cr,
FILE *fplog,
+ const gmx::MDLogger &mdlog,
gmx_bool bNonBondedOnGPU)
{
double pp_ratio, grid_ratio;
real pp_ratio_temporary;
- pp_ratio_temporary = pme_lb->setup[pme_lb->cur].rlist / pme_lb->setup[0].rlist;
+ pp_ratio_temporary = pme_lb->setup[pme_lb->cur].rlistInner / pme_lb->setup[0].rlistInner;
pp_ratio = gmx::power3(pp_ratio_temporary);
grid_ratio = pme_grid_points(&pme_lb->setup[pme_lb->cur])/
(double)pme_grid_points(&pme_lb->setup[0]);
if (pp_ratio > 1.5 && !bNonBondedOnGPU)
{
- md_print_warn(cr, fplog,
- "NOTE: PME load balancing increased the non-bonded workload by more than 50%%.\n"
- " For better performance, use (more) PME ranks (mdrun -npme),\n"
- " or if you are beyond the scaling limit, use fewer total ranks (or nodes).\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: PME load balancing increased the non-bonded workload by more than 50%.\n"
+ " For better performance, use (more) PME ranks (mdrun -npme),\n"
+ " or if you are beyond the scaling limit, use fewer total ranks (or nodes).");
}
else
{
}
void pme_loadbal_done(pme_load_balancing_t *pme_lb,
- t_commrec *cr,
FILE *fplog,
+ const gmx::MDLogger &mdlog,
gmx_bool bNonBondedOnGPU)
{
- if (fplog != NULL && (pme_lb->cur > 0 || pme_lb->elimited != epmelblimNO))
+ if (fplog != nullptr && (pme_lb->cur > 0 || pme_lb->elimited != epmelblimNO))
{
- print_pme_loadbal_settings(pme_lb, cr, fplog, bNonBondedOnGPU);
+ print_pme_loadbal_settings(pme_lb, fplog, mdlog, bNonBondedOnGPU);
}
/* TODO: Here we should free all pointers in pme_lb,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/interaction_const.h"
-#include "gromacs/mdtypes/state.h"
#include "gromacs/timing/wallcycle.h"
+struct NbnxnListParameters;
struct t_commrec;
struct t_inputrec;
+class t_state;
+
+namespace gmx
+{
+class MDLogger;
+}
/*! \brief Object to manage PME load balancing */
struct pme_load_balancing_t;
* usage.
*/
void pme_loadbal_init(pme_load_balancing_t **pme_lb_p,
- struct t_commrec *cr,
- FILE *fp_log,
+ t_commrec *cr,
+ const gmx::MDLogger &mdlog,
const t_inputrec *ir,
matrix box,
const interaction_const_t *ic,
- struct gmx_pme_t *pmedata,
+ const NbnxnListParameters *listParams,
+ gmx_pme_t *pmedata,
gmx_bool bUseGPU,
gmx_bool *bPrinting);
struct t_commrec *cr,
FILE *fp_err,
FILE *fp_log,
+ const gmx::MDLogger &mdlog,
const t_inputrec *ir,
t_forcerec *fr,
t_state *state,
/*! \brief Finish the PME load balancing and print the settings when fplog!=NULL */
void pme_loadbal_done(pme_load_balancing_t *pme_lb,
- struct t_commrec *cr,
FILE *fplog,
+ const gmx::MDLogger &mdlog,
gmx_bool bNonBondedOnGPU);
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void gmx_pmeonly_switch(int *npmedata, struct gmx_pme_t ***pmedata,
ivec grid_size,
+ real ewaldcoeff_q, real ewaldcoeff_lj,
t_commrec *cr, t_inputrec *ir,
struct gmx_pme_t **pme_ret)
{
int ind;
- struct gmx_pme_t *pme = NULL;
+ struct gmx_pme_t *pme = nullptr;
ind = 0;
while (ind < *npmedata)
srenew(*pmedata, *npmedata);
/* Generate a new PME data structure, copying part of the old pointers */
- gmx_pme_reinit(&((*pmedata)[ind]), cr, pme, ir, grid_size);
+ gmx_pme_reinit(&((*pmedata)[ind]), cr, pme, ir, grid_size, ewaldcoeff_q, ewaldcoeff_lj);
*pme_ret = (*pmedata)[ind];
}
int ret;
int natoms;
matrix box;
- rvec *x_pp = NULL, *f_pp = NULL;
- real *chargeA = NULL, *chargeB = NULL;
- real *c6A = NULL, *c6B = NULL;
- real *sigmaA = NULL, *sigmaB = NULL;
+ rvec *x_pp = nullptr, *f_pp = nullptr;
+ real *chargeA = nullptr, *chargeB = nullptr;
+ real *c6A = nullptr, *c6B = nullptr;
+ real *sigmaA = nullptr, *sigmaB = nullptr;
real lambda_q = 0;
real lambda_lj = 0;
int maxshift_x = 0, maxshift_y = 0;
float cycles;
int count;
gmx_bool bEnerVir;
- int pme_flags;
gmx_int64_t step;
ivec grid_switch;
&sigmaA, &sigmaB,
box, &x_pp, &f_pp,
&maxshift_x, &maxshift_y,
- &pme->bFEP_q, &pme->bFEP_lj,
&lambda_q, &lambda_lj,
&bEnerVir,
- &pme_flags,
&step,
grid_switch, &ewaldcoeff_q, &ewaldcoeff_lj);
if (ret == pmerecvqxSWITCHGRID)
{
/* Switch the PME grid to grid_switch */
- gmx_pmeonly_switch(&npmedata, &pmedata, grid_switch, cr, ir, &pme);
+ gmx_pmeonly_switch(&npmedata, &pmedata, grid_switch, ewaldcoeff_q, ewaldcoeff_lj, cr, ir, &pme);
}
if (ret == pmerecvqxRESETCOUNTERS)
gmx_pme_do(pme, 0, natoms, x_pp, f_pp,
chargeA, chargeB, c6A, c6B, sigmaA, sigmaB, box,
cr, maxshift_x, maxshift_y, mynrnb, wcycle,
- vir_q, ewaldcoeff_q, vir_lj, ewaldcoeff_lj,
+ vir_q, vir_lj,
&energy_q, &energy_lj, lambda_q, lambda_lj, &dvdlambda_q, &dvdlambda_lj,
- pme_flags | GMX_PME_DO_ALL_F | (bEnerVir ? GMX_PME_CALC_ENER_VIR : 0));
+ GMX_PME_DO_ALL_F | (bEnerVir ? GMX_PME_CALC_ENER_VIR : 0));
cycles = wallcycle_stop(wcycle, ewcPMEMESH);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* Some parts of the code(gmx_pme_send_q, gmx_pme_recv_q_x) assume
* that the six first flags are exactly in this order.
- * If more PP_PME_...-flags are to be introduced be aware of some of
- * the PME-specific flags in pme.h. Currently, they are also passed
- * through here.
*/
#define PP_PME_CHARGE (1<<0)
#define PP_PME_SIGMA (1<<4)
#define PP_PME_SIGMAB (1<<5)
#define PP_PME_COORD (1<<6)
-#define PP_PME_FEP_Q (1<<7)
-#define PP_PME_FEP_LJ (1<<8)
#define PP_PME_ENER_VIR (1<<9)
#define PP_PME_FINISH (1<<10)
#define PP_PME_SWITCHGRID (1<<11)
int *node; /**< The PP node ranks */
int node_peer; /**< The peer PP node rank */
int *nat; /**< The number of atom for each PP node */
- int flags_charge; /**< The flags sent along with the last charges */
//@{
/**< Vectors of A- and B-state parameters used to transfer vectors to PME ranks */
real *chargeA;
int maxshift_y; /**< Maximum shift in y direction */
real lambda_q; /**< Free-energy lambda for electrostatics */
real lambda_lj; /**< Free-energy lambda for Lennard-Jones */
- int flags; /**< Control flags */
+ unsigned int flags; /**< Control flags */
gmx_int64_t step; /**< MD integration step number */
//@{
/*! \brief Used in PME grid tuning */
snew(pme_pp->req, eCommType_NR*pme_pp->nnode);
snew(pme_pp->stat, eCommType_NR*pme_pp->nnode);
pme_pp->nalloc = 0;
- pme_pp->flags_charge = 0;
#else
GMX_UNUSED_VALUE(cr);
#endif
}
/*! \brief Send data to PME ranks */
-static void gmx_pme_send_coeffs_coords(t_commrec *cr, int flags,
+static void gmx_pme_send_coeffs_coords(t_commrec *cr, unsigned int flags,
real gmx_unused *chargeA, real gmx_unused *chargeB,
real gmx_unused *c6A, real gmx_unused *c6B,
real gmx_unused *sigmaA, real gmx_unused *sigmaB,
if (dd->pme_receive_vir_ener)
{
/* Peer PP node: communicate all data */
- if (dd->cnb == NULL)
+ if (dd->cnb == nullptr)
{
snew(dd->cnb, 1);
}
real *sigmaA, real *sigmaB,
int maxshift_x, int maxshift_y)
{
- int flags;
+ unsigned int flags = 0;
- flags = 0;
if (EEL_PME(ic->eeltype))
{
flags |= PP_PME_CHARGE;
gmx_pme_send_coeffs_coords(cr, flags,
chargeA, chargeB,
sqrt_c6A, sqrt_c6B, sigmaA, sigmaB,
- NULL, NULL, 0, 0, maxshift_x, maxshift_y, -1);
+ nullptr, nullptr, 0, 0, maxshift_x, maxshift_y, -1);
}
void gmx_pme_send_coordinates(t_commrec *cr, matrix box, rvec *x,
- gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj,
real lambda_q, real lambda_lj,
- gmx_bool bEnerVir, int pme_flags,
+ gmx_bool bEnerVir,
gmx_int64_t step)
{
- int flags;
-
- flags = pme_flags | PP_PME_COORD;
- if (bFreeEnergy_q)
- {
- flags |= PP_PME_FEP_Q;
- }
- if (bFreeEnergy_lj)
- {
- flags |= PP_PME_FEP_LJ;
- }
+ unsigned int flags = PP_PME_COORD;
if (bEnerVir)
{
flags |= PP_PME_ENER_VIR;
}
- gmx_pme_send_coeffs_coords(cr, flags, NULL, NULL, NULL, NULL, NULL, NULL,
+ gmx_pme_send_coeffs_coords(cr, flags, nullptr, nullptr, nullptr, nullptr, nullptr, nullptr,
box, x, lambda_q, lambda_lj, 0, 0, step);
}
void gmx_pme_send_finish(t_commrec *cr)
{
- int flags;
-
- flags = PP_PME_FINISH;
+ unsigned int flags = PP_PME_FINISH;
- gmx_pme_send_coeffs_coords(cr, flags, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, 0, 0, 0, 0, -1);
+ gmx_pme_send_coeffs_coords(cr, flags, nullptr, nullptr, nullptr, nullptr, nullptr, nullptr, nullptr, nullptr, 0, 0, 0, 0, -1);
}
void gmx_pme_send_switchgrid(t_commrec gmx_unused *cr,
rvec **f,
int *maxshift_x,
int *maxshift_y,
- gmx_bool *bFreeEnergy_q,
- gmx_bool *bFreeEnergy_lj,
real *lambda_q,
real *lambda_lj,
gmx_bool *bEnerVir,
- int *pme_flags,
gmx_int64_t *step,
ivec grid_size,
real *ewaldcoeff_q,
real *ewaldcoeff_lj)
{
- int nat = 0, status;
+ int status = -1;
+ int nat = 0;
- *pme_flags = 0;
#if GMX_MPI
- gmx_pme_comm_n_box_t cnb;
- int messages;
+ unsigned int flags = 0;
+ int messages = 0;
- cnb.flags = 0;
- messages = 0;
do
{
+ gmx_pme_comm_n_box_t cnb;
+ cnb.flags = 0;
/* Receive the send count, box and time step from the peer PP node */
MPI_Recv(&cnb, sizeof(cnb), MPI_BYTE,
pme_pp->node_peer, eCommType_CNB,
pme_pp->mpi_comm_mysim, MPI_STATUS_IGNORE);
+ /* We accumulate all received flags */
+ flags |= cnb.flags;
+
+ *step = cnb.step;
+
if (debug)
{
fprintf(debug, "PME only rank receiving:%s%s%s%s%s\n",
(cnb.flags & PP_PME_RESETCOUNTERS) ? " reset counters" : "");
}
+ if (cnb.flags & PP_PME_FINISH)
+ {
+ status = pmerecvqxFINISH;
+ }
+
if (cnb.flags & PP_PME_SWITCHGRID)
{
/* Special case, receive the new parameters and return */
copy_ivec(cnb.grid_size, grid_size);
*ewaldcoeff_q = cnb.ewaldcoeff_q;
*ewaldcoeff_lj = cnb.ewaldcoeff_lj;
- return pmerecvqxSWITCHGRID;
+
+ status = pmerecvqxSWITCHGRID;
}
if (cnb.flags & PP_PME_RESETCOUNTERS)
{
- /* Special case, receive the step and return */
- *step = cnb.step;
-
- return pmerecvqxRESETCOUNTERS;
+ /* Special case, receive the step (set above) and return */
+ status = pmerecvqxRESETCOUNTERS;
}
if (cnb.flags & (PP_PME_CHARGE | PP_PME_SQRTC6 | PP_PME_SIGMA))
}
}
}
-
- pme_pp->flags_charge = cnb.flags;
}
if (cnb.flags & PP_PME_COORD)
{
- if (!(pme_pp->flags_charge & (PP_PME_CHARGE | PP_PME_SQRTC6)))
- {
- gmx_incons("PME-only rank received coordinates before charges and/or C6-values"
- );
- }
-
/* The box, FE flag and lambda are sent along with the coordinates
* */
copy_mat(cnb.box, box);
- *bFreeEnergy_q = ((cnb.flags & GMX_PME_DO_COULOMB) &&
- (cnb.flags & PP_PME_FEP_Q));
- *bFreeEnergy_lj = ((cnb.flags & GMX_PME_DO_LJ) &&
- (cnb.flags & PP_PME_FEP_LJ));
*lambda_q = cnb.lambda_q;
*lambda_lj = cnb.lambda_lj;
*bEnerVir = (cnb.flags & PP_PME_ENER_VIR);
- *pme_flags = cnb.flags;
-
- if (*bFreeEnergy_q && !(pme_pp->flags_charge & PP_PME_CHARGEB))
- {
- gmx_incons("PME-only rank received free energy request, but "
- "did not receive B-state charges");
- }
-
- if (*bFreeEnergy_lj && !(pme_pp->flags_charge & PP_PME_SQRTC6B))
- {
- gmx_incons("PME-only rank received free energy request, but "
- "did not receive B-state C6-values");
- }
+ *step = cnb.step;
/* Receive the coordinates in place */
nat = 0;
}
}
}
+
+ status = pmerecvqxX;
}
/* Wait for the coordinates and/or charges to arrive */
MPI_Waitall(messages, pme_pp->req, pme_pp->stat);
messages = 0;
}
- while (!(cnb.flags & (PP_PME_COORD | PP_PME_FINISH)));
- status = ((cnb.flags & PP_PME_FINISH) ? pmerecvqxFINISH : pmerecvqxX);
-
- *step = cnb.step;
+ while (status == -1);
#else
GMX_UNUSED_VALUE(box);
GMX_UNUSED_VALUE(maxshift_x);
GMX_UNUSED_VALUE(maxshift_y);
- GMX_UNUSED_VALUE(bFreeEnergy_q);
- GMX_UNUSED_VALUE(bFreeEnergy_lj);
GMX_UNUSED_VALUE(lambda_q);
GMX_UNUSED_VALUE(lambda_lj);
GMX_UNUSED_VALUE(bEnerVir);
status = pmerecvqxX;
#endif
- *natoms = nat;
- *chargeA = pme_pp->chargeA;
- *chargeB = pme_pp->chargeB;
- *sqrt_c6A = pme_pp->sqrt_c6A;
- *sqrt_c6B = pme_pp->sqrt_c6B;
- *sigmaA = pme_pp->sigmaA;
- *sigmaB = pme_pp->sigmaB;
- *x = pme_pp->x;
- *f = pme_pp->f;
+ if (status == pmerecvqxX)
+ {
+ *natoms = nat;
+ *chargeA = pme_pp->chargeA;
+ *chargeB = pme_pp->chargeB;
+ *sqrt_c6A = pme_pp->sqrt_c6A;
+ *sqrt_c6B = pme_pp->sqrt_c6B;
+ *sigmaA = pme_pp->sigmaA;
+ *sigmaB = pme_pp->sigmaB;
+ *x = pme_pp->x;
+ *f = pme_pp->f;
+ }
return status;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
-#ifdef PME_GATHER_F_SIMD4_ORDER4
-/* Gather for one charge with pme_order=4 with unaligned SIMD4 load+store.
- * This code does not assume any memory alignment for the grid.
- */
-{
- Simd4Real fx_S, fy_S, fz_S;
-
- Simd4Real tx_S, ty_S, tz_S;
- Simd4Real dx_S, dy_S, dz_S;
-
- Simd4Real gval_S;
-
- Simd4Real fxy1_S;
- Simd4Real fz1_S;
-
- fx_S = setZero();
- fy_S = setZero();
- fz_S = setZero();
-
- /* With order 4 the z-spline is actually aligned */
- tz_S = load4(thz);
- dz_S = load4(dthz);
-
- for (ithx = 0; (ithx < 4); ithx++)
- {
- index_x = (i0+ithx)*pny*pnz;
- tx_S = Simd4Real(thx[ithx]);
- dx_S = Simd4Real(dthx[ithx]);
-
- for (ithy = 0; (ithy < 4); ithy++)
- {
- index_xy = index_x+(j0+ithy)*pnz;
- ty_S = Simd4Real(thy[ithy]);
- dy_S = Simd4Real(dthy[ithy]);
-
- gval_S = load4U(grid+index_xy+k0);
-
- fxy1_S = tz_S * gval_S;
- fz1_S = dz_S * gval_S;
-
- fx_S = fma(dx_S * ty_S, fxy1_S, fx_S);
- fy_S = fma(tx_S * dy_S, fxy1_S, fy_S);
- fz_S = fma(tx_S * ty_S, fz1_S, fz_S);
- }
- }
-
- fx += reduce(fx_S);
- fy += reduce(fy_S);
- fz += reduce(fz_S);
-}
-#undef PME_GATHER_F_SIMD4_ORDER4
-#endif
-
-
#ifdef PME_SPREAD_SIMD4_ALIGNED
/* This code assumes that the grid is allocated 4-real aligned
* and that pnz is a multiple of 4.
#undef PME_ORDER
#undef PME_SPREAD_SIMD4_ALIGNED
#endif
-
-
-#ifdef PME_GATHER_F_SIMD4_ALIGNED
-/* This code assumes that the grid is allocated 4-real aligned
- * and that pnz is a multiple of 4.
- * This code supports pme_order <= 5.
- */
-{
- int offset;
-
- Simd4Real fx_S, fy_S, fz_S;
-
- Simd4Real tx_S, ty_S, tz_S0, tz_S1;
- Simd4Real dx_S, dy_S, dz_S0, dz_S1;
-
- Simd4Real gval_S0;
- Simd4Real gval_S1;
-
- Simd4Real fxy1_S0;
- Simd4Real fz1_S0;
- Simd4Real fxy1_S1;
- Simd4Real fz1_S1;
- Simd4Real fxy1_S;
- Simd4Real fz1_S;
-
- offset = k0 & 3;
-
- fx_S = setZero();
- fy_S = setZero();
- fz_S = setZero();
-
-#ifdef PME_SIMD4_UNALIGNED
- tz_S0 = load4U(thz-offset);
- tz_S1 = load4U(thz-offset+4);
- dz_S0 = load4U(dthz-offset);
- dz_S1 = load4U(dthz-offset+4);
-#else
- {
- int i;
- /* Copy (d)thz to an aligned buffer (unused buffer parts are masked) */
- for (i = 0; i < PME_ORDER; i++)
- {
- thz_aligned[offset+i] = thz[i];
- dthz_aligned[offset+i] = dthz[i];
- }
- tz_S0 = load4(thz_aligned);
- tz_S1 = load4(thz_aligned+4);
- dz_S0 = load4(dthz_aligned);
- dz_S1 = load4(dthz_aligned+4);
- }
-#endif
- tz_S0 = selectByMask(tz_S0, work->mask_S0[offset]);
- dz_S0 = selectByMask(dz_S0, work->mask_S0[offset]);
- tz_S1 = selectByMask(tz_S1, work->mask_S1[offset]);
- dz_S1 = selectByMask(dz_S1, work->mask_S1[offset]);
-
- for (ithx = 0; (ithx < PME_ORDER); ithx++)
- {
- index_x = (i0+ithx)*pny*pnz;
- tx_S = Simd4Real(thx[ithx]);
- dx_S = Simd4Real(dthx[ithx]);
-
- for (ithy = 0; (ithy < PME_ORDER); ithy++)
- {
- index_xy = index_x+(j0+ithy)*pnz;
- ty_S = Simd4Real(thy[ithy]);
- dy_S = Simd4Real(dthy[ithy]);
-
- gval_S0 = load4(grid+index_xy+k0-offset);
- gval_S1 = load4(grid+index_xy+k0-offset+4);
-
- fxy1_S0 = tz_S0 * gval_S0;
- fz1_S0 = dz_S0 * gval_S0;
- fxy1_S1 = tz_S1 * gval_S1;
- fz1_S1 = dz_S1 * gval_S1;
-
- fxy1_S = fxy1_S0 + fxy1_S1;
- fz1_S = fz1_S0 + fz1_S1;
-
- fx_S = fma(dx_S * ty_S, fxy1_S, fx_S);
- fy_S = fma(tx_S * dy_S, fxy1_S, fy_S);
- fz_S = fma(tx_S * ty_S, fz1_S, fz_S);
- }
- }
-
- fx += reduce(fx_S);
- fy += reduce(fy_S);
- fz += reduce(fz_S);
-}
-#undef PME_ORDER
-#undef PME_GATHER_F_SIMD4_ALIGNED
-#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void free_work(struct pme_solve_work_t *work)
{
- sfree(work->mhx);
- sfree(work->mhy);
- sfree(work->mhz);
- sfree(work->m2);
- sfree_aligned(work->denom);
- sfree_aligned(work->tmp1);
- sfree_aligned(work->tmp2);
- sfree_aligned(work->eterm);
- sfree(work->m2inv);
+ if (work)
+ {
+ sfree(work->mhx);
+ sfree(work->mhy);
+ sfree(work->mhz);
+ sfree(work->m2);
+ sfree_aligned(work->denom);
+ sfree_aligned(work->tmp1);
+ sfree_aligned(work->tmp2);
+ sfree_aligned(work->eterm);
+ sfree(work->m2inv);
+ }
}
void pme_free_all_work(struct pme_solve_work_t **work, int nthread)
{
- int thread;
-
- for (thread = 0; thread < nthread; thread++)
+ if (*work)
{
- free_work(&(*work)[thread]);
+ for (int thread = 0; thread < nthread; thread++)
+ {
+ free_work(&(*work)[thread]);
+ }
}
- sfree(work);
- *work = NULL;
+ sfree(*work);
+ *work = nullptr;
}
void get_pme_ener_vir_q(struct pme_solve_work_t *work, int nthread,
}
#endif
-int solve_pme_yzx(struct gmx_pme_t *pme, t_complex *grid,
- real ewaldcoeff, real vol,
+int solve_pme_yzx(const gmx_pme_t *pme, t_complex *grid, real vol,
gmx_bool bEnerVir,
int nthread, int thread)
{
int kx, ky, kz, maxkx, maxky;
int nx, ny, nz, iyz0, iyz1, iyz, iy, iz, kxstart, kxend;
real mx, my, mz;
- real factor = M_PI*M_PI/(ewaldcoeff*ewaldcoeff);
+ real ewaldcoeff = pme->ewaldcoeff_q;
+ real factor = M_PI*M_PI/(ewaldcoeff*ewaldcoeff);
real ets2, struct2, vfactor, ets2vf;
real d1, d2, energy = 0;
real by, bz;
return local_ndata[YY]*local_ndata[XX];
}
-int solve_pme_lj_yzx(struct gmx_pme_t *pme, t_complex **grid, gmx_bool bLB,
- real ewaldcoeff, real vol,
+int solve_pme_lj_yzx(const gmx_pme_t *pme, t_complex **grid, gmx_bool bLB, real vol,
gmx_bool bEnerVir, int nthread, int thread)
{
/* do recip sum over local cells in grid */
int kx, ky, kz, maxkx, maxky;
int nx, ny, nz, iy, iyz0, iyz1, iyz, iz, kxstart, kxend;
real mx, my, mz;
- real factor = M_PI*M_PI/(ewaldcoeff*ewaldcoeff);
+ real ewaldcoeff = pme->ewaldcoeff_lj;
+ real factor = M_PI*M_PI/(ewaldcoeff*ewaldcoeff);
real ets2, ets2vf;
real eterm, vterm, d1, d2, energy = 0;
real by, bz;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void get_pme_ener_vir_lj(struct pme_solve_work_t *work, int nthread,
real *mesh_energy, matrix vir);
-int solve_pme_yzx(struct gmx_pme_t *pme, t_complex *grid,
- real ewaldcoeff, real vol,
+int solve_pme_yzx(const gmx_pme_t *pme, t_complex *grid,
+ real vol,
gmx_bool bEnerVir,
int nthread, int thread);
-int solve_pme_lj_yzx(struct gmx_pme_t *pme, t_complex **grid, gmx_bool bLB,
- real ewaldcoeff, real vol,
+int solve_pme_lj_yzx(const gmx_pme_t *pme, t_complex **grid, gmx_bool bLB,
+ real vol,
gmx_bool bEnerVir, int nthread, int thread);
#endif
#include <algorithm>
#include "gromacs/ewald/pme.h"
+#include "gromacs/fft/parallel_3dfft.h"
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
+#include "pme-grid.h"
#include "pme-internal.h"
#include "pme-simd.h"
#include "pme-spline-work.h"
/* TODO consider split of pme-spline from this file */
-static void calc_interpolation_idx(struct gmx_pme_t *pme, pme_atomcomm_t *atc,
+static void calc_interpolation_idx(const gmx_pme_t *pme, const pme_atomcomm_t *atc,
int start, int grid_index, int end, int thread)
{
int i;
int nx, ny, nz;
int *g2tx, *g2ty, *g2tz;
gmx_bool bThreads;
- int *thread_idx = NULL;
- thread_plist_t *tpl = NULL;
- int *tpl_n = NULL;
+ int *thread_idx = nullptr;
+ thread_plist_t *tpl = nullptr;
+ int *tpl_n = nullptr;
int thread_i;
nx = pme->nkx;
}
}
+ const real shift = c_pmeMaxUnitcellShift;
+
for (i = start; i < end; i++)
{
xptr = atc->x[i];
idxptr = atc->idx[i];
fptr = atc->fractx[i];
- /* Fractional coordinates along box vectors, add 2.0 to make 100% sure we are positive for triclinic boxes */
- tx = nx * ( xptr[XX] * rxx + xptr[YY] * ryx + xptr[ZZ] * rzx + 2.0 );
- ty = ny * ( xptr[YY] * ryy + xptr[ZZ] * rzy + 2.0 );
- tz = nz * ( xptr[ZZ] * rzz + 2.0 );
+ /* Fractional coordinates along box vectors, add a positive shift to ensure tx/ty/tz are positive for triclinic boxes */
+ tx = nx * ( xptr[XX] * rxx + xptr[YY] * ryx + xptr[ZZ] * rzx + shift );
+ ty = ny * ( xptr[YY] * ryy + xptr[ZZ] * rzy + shift );
+ tz = nz * ( xptr[ZZ] * rzz + shift );
- tix = (int)(tx);
- tiy = (int)(ty);
- tiz = (int)(tz);
+ tix = static_cast<int>(tx);
+ tiy = static_cast<int>(ty);
+ tiz = static_cast<int>(tz);
+#ifdef DEBUG
+ range_check(tix, 0, c_pmeNeighborUnitcellCount * nx);
+ range_check(tiy, 0, c_pmeNeighborUnitcellCount * ny);
+ range_check(tiz, 0, c_pmeNeighborUnitcellCount * nz);
+#endif
/* Because decomposition only occurs in x and y,
* we never have a fraction correction in z.
*/
}
}
-static void make_thread_local_ind(pme_atomcomm_t *atc,
+static void make_thread_local_ind(const pme_atomcomm_t *atc,
int thread, splinedata_t *spline)
{
int n, t, i, start, end;
}
-static void spread_coefficients_bsplines_thread(pmegrid_t *pmegrid,
- pme_atomcomm_t *atc,
+static void spread_coefficients_bsplines_thread(const pmegrid_t *pmegrid,
+ const pme_atomcomm_t *atc,
splinedata_t *spline,
struct pme_spline_work gmx_unused *work)
{
}
}
-static void copy_local_grid(struct gmx_pme_t *pme, pmegrids_t *pmegrids,
+static void copy_local_grid(const gmx_pme_t *pme, const pmegrids_t *pmegrids,
int grid_index, int thread, real *fftgrid)
{
ivec local_fft_ndata, local_fft_offset, local_fft_size;
ivec nf;
int offx, offy, offz, x, y, z, i0, i0t;
int d;
- pmegrid_t *pmegrid;
real *grid_th;
gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index],
fft_my = local_fft_size[YY];
fft_mz = local_fft_size[ZZ];
- pmegrid = &pmegrids->grid_th[thread];
+ const pmegrid_t *pmegrid = &pmegrids->grid_th[thread];
nsy = pmegrid->s[YY];
nsz = pmegrid->s[ZZ];
}
static void
-reduce_threadgrid_overlap(struct gmx_pme_t *pme,
+reduce_threadgrid_overlap(const gmx_pme_t *pme,
const pmegrids_t *pmegrids, int thread,
real *fftgrid, real *commbuf_x, real *commbuf_y,
int grid_index)
int thread_f;
const pmegrid_t *pmegrid, *pmegrid_g, *pmegrid_f;
const real *grid_th;
- real *commbuf = NULL;
+ real *commbuf = nullptr;
gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index],
local_fft_ndata,
}
-static void sum_fftgrid_dd(struct gmx_pme_t *pme, real *fftgrid, int grid_index)
+static void sum_fftgrid_dd(const gmx_pme_t *pme, real *fftgrid, int grid_index)
{
ivec local_fft_ndata, local_fft_offset, local_fft_size;
- pme_overlap_t *overlap;
int send_index0, send_nindex;
int recv_nindex;
#if GMX_MPI
if (pme->nnodes_minor > 1)
{
/* Major dimension */
- overlap = &pme->overlap[1];
+ const pme_overlap_t *overlap = &pme->overlap[1];
if (pme->nnodes_major > 1)
{
sendptr = overlap->sendbuf + send_index0*local_fft_ndata[ZZ];
recvptr = overlap->recvbuf;
- if (debug != NULL)
+ if (debug != nullptr)
{
fprintf(debug, "PME fftgrid comm y %2d x %2d x %2d\n",
local_fft_ndata[XX], send_nindex, local_fft_ndata[ZZ]);
if (pme->nnodes_major > 1)
{
/* Major dimension */
- overlap = &pme->overlap[0];
+ const pme_overlap_t *overlap = &pme->overlap[0];
ipulse = 0;
recvptr = overlap->recvbuf;
- if (debug != NULL)
+ if (debug != nullptr)
{
fprintf(debug, "PME fftgrid comm x %2d x %2d x %2d\n",
send_nindex, local_fft_ndata[YY], local_fft_ndata[ZZ]);
}
}
-void spread_on_grid(struct gmx_pme_t *pme,
- pme_atomcomm_t *atc, pmegrids_t *grids,
+void spread_on_grid(const gmx_pme_t *pme,
+ const pme_atomcomm_t *atc, const pmegrids_t *grids,
gmx_bool bCalcSplines, gmx_bool bSpread,
real *fftgrid, gmx_bool bDoSplines, int grid_index)
{
try
{
splinedata_t *spline;
- pmegrid_t *grid = NULL;
/* make local bsplines */
- if (grids == NULL || !pme->bUseThreads)
+ if (grids == nullptr || !pme->bUseThreads)
{
spline = &atc->spline[0];
spline->n = atc->n;
-
- if (bSpread)
- {
- grid = &grids->grid;
- }
}
else
{
/* Get the indices our thread should operate on */
make_thread_local_ind(atc, thread, spline);
}
-
- grid = &grids->grid_th[thread];
}
if (bCalcSplines)
if (bSpread)
{
/* put local atoms on grid. */
+ const pmegrid_t *grid = pme->bUseThreads ? &grids->grid_th[thread] : &grids->grid;
+
#ifdef PME_TIME_SPREAD
ct1a = omp_cyc_start();
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "pme-internal.h"
void
-spread_on_grid(struct gmx_pme_t *pme,
- pme_atomcomm_t *atc, pmegrids_t *grids,
+spread_on_grid(const gmx_pme_t *pme,
+ const pme_atomcomm_t *atc, const pmegrids_t *grids,
gmx_bool bCalcSplines, gmx_bool bSpread,
real *fftgrid, gmx_bool bDoSplines, int grid_index);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/gmxomp.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/unique_cptr.h"
#include "calculate-spline-moduli.h"
#include "pme-gather.h"
}
}
-int gmx_pme_destroy(FILE *log, struct gmx_pme_t **pmedata)
-{
- int i;
-
- if (NULL != log)
- {
- fprintf(log, "Destroying PME data structures.\n");
- }
-
- sfree((*pmedata)->nnx);
- sfree((*pmedata)->nny);
- sfree((*pmedata)->nnz);
-
- for (i = 0; i < (*pmedata)->ngrids; ++i)
- {
- pmegrids_destroy(&(*pmedata)->pmegrid[i]);
- sfree((*pmedata)->fftgrid[i]);
- sfree((*pmedata)->cfftgrid[i]);
- gmx_parallel_3dfft_destroy((*pmedata)->pfft_setup[i]);
- }
-
- sfree((*pmedata)->lb_buf1);
- sfree((*pmedata)->lb_buf2);
-
- pme_free_all_work(&(*pmedata)->solve_work, (*pmedata)->nthread);
-
- sfree(*pmedata);
- *pmedata = NULL;
-
- return 0;
-}
-
/*! \brief Round \p n up to the next multiple of \p f */
static int mult_up(int n, int f)
{
snew(atc->thread_plist[thread].n, atc->nthread+2*gmxCacheLineSize);
atc->thread_plist[thread].n += gmxCacheLineSize;
}
- snew(atc->spline[thread].thread_one, pme->nthread);
- atc->spline[thread].thread_one[thread] = 1;
}
}
+/*! \brief Destroy an atom communication data structure and its child structs */
+static void destroy_atomcomm(pme_atomcomm_t *atc)
+{
+ sfree(atc->pd);
+ if (atc->nslab > 1)
+ {
+ sfree(atc->node_dest);
+ sfree(atc->node_src);
+ for (int i = 0; i < atc->nthread; i++)
+ {
+ sfree(atc->count_thread[i]);
+ }
+ sfree(atc->count_thread);
+ sfree(atc->rcount);
+ sfree(atc->buf_index);
+
+ sfree(atc->x);
+ sfree(atc->coefficient);
+ sfree(atc->f);
+ }
+ sfree(atc->idx);
+ sfree(atc->fractx);
+
+ sfree(atc->thread_idx);
+ for (int i = 0; i < atc->nthread; i++)
+ {
+ if (atc->nthread > 1)
+ {
+ int *n_ptr = atc->thread_plist[i].n - gmxCacheLineSize;
+ sfree(n_ptr);
+ sfree(atc->thread_plist[i].i);
+ }
+ sfree(atc->spline[i].ind);
+ for (int d = 0; d < ZZ; d++)
+ {
+ sfree(atc->spline[i].theta[d]);
+ sfree(atc->spline[i].dtheta[d]);
+ }
+ sfree_aligned(atc->spline[i].ptr_dtheta_z);
+ sfree_aligned(atc->spline[i].ptr_theta_z);
+ }
+ if (atc->nthread > 1)
+ {
+ sfree(atc->thread_plist);
+ }
+ sfree(atc->spline);
+}
+
/*! \brief Initialize data structure for communication */
static void
init_overlap_comm(pme_overlap_t * ol,
snew(ol->recvbuf, norder*commplainsize);
}
-void gmx_pme_check_restrictions(int pme_order,
+/*! \brief Destroy data structure for communication */
+static void
+destroy_overlap_comm(const pme_overlap_t *ol)
+{
+ sfree(ol->s2g0);
+ sfree(ol->s2g1);
+ sfree(ol->send_id);
+ sfree(ol->recv_id);
+ sfree(ol->comm_data);
+ sfree(ol->sendbuf);
+ sfree(ol->recvbuf);
+}
+
+int minimalPmeGridSize(int pmeOrder)
+{
+ /* The actual grid size limitations are:
+ * serial: >= pme_order
+ * DD, no OpenMP: >= 2*(pme_order - 1)
+ * DD, OpenMP: >= pme_order + 1
+ * But we use the maximum for simplicity since in practice there is not
+ * much performance difference between pme_order and 2*(pme_order -1).
+ */
+ int minimalSize = 2*(pmeOrder - 1);
+
+ GMX_RELEASE_ASSERT(pmeOrder >= 3, "pmeOrder has to be >= 3");
+ GMX_RELEASE_ASSERT(minimalSize >= pmeOrder + 1, "The grid size should be >= pmeOrder + 1");
+
+ return minimalSize;
+}
+
+bool gmx_pme_check_restrictions(int pme_order,
int nkx, int nky, int nkz,
int nnodes_major,
- int nnodes_minor,
- gmx_bool bUseThreads,
- gmx_bool bFatal,
- gmx_bool *bValidSettings)
+ bool useThreads,
+ bool errorsAreFatal)
{
if (pme_order > PME_ORDER_MAX)
{
- if (!bFatal)
+ if (!errorsAreFatal)
{
- *bValidSettings = FALSE;
- return;
+ return false;
}
- gmx_fatal(FARGS, "pme_order (%d) is larger than the maximum allowed value (%d). Modify and recompile the code if you really need such a high order.",
- pme_order, PME_ORDER_MAX);
+
+ std::string message = gmx::formatString(
+ "pme_order (%d) is larger than the maximum allowed value (%d). Modify and recompile the code if you really need such a high order.",
+ pme_order, PME_ORDER_MAX);
+ GMX_THROW(InconsistentInputError(message));
}
- if (nkx <= pme_order*(nnodes_major > 1 ? 2 : 1) ||
- nky <= pme_order*(nnodes_minor > 1 ? 2 : 1) ||
- nkz <= pme_order)
+ const int minGridSize = minimalPmeGridSize(pme_order);
+ if (nkx < minGridSize ||
+ nky < minGridSize ||
+ nkz < minGridSize)
{
- if (!bFatal)
+ if (!errorsAreFatal)
{
- *bValidSettings = FALSE;
- return;
+ return false;
}
- gmx_fatal(FARGS, "The PME grid sizes need to be larger than pme_order (%d) and for dimensions with domain decomposition larger than 2*pme_order",
- pme_order);
+ std::string message = gmx::formatString(
+ "The PME grid sizes need to be >= 2*(pme_order-1) (%d)",
+ minGridSize);
+ GMX_THROW(InconsistentInputError(message));
}
/* Check for a limitation of the (current) sum_fftgrid_dd code.
* We only allow multiple communication pulses in dim 1, not in dim 0.
*/
- if (bUseThreads && (nkx < nnodes_major*pme_order &&
- nkx != nnodes_major*(pme_order - 1)))
+ if (useThreads && (nkx < nnodes_major*pme_order &&
+ nkx != nnodes_major*(pme_order - 1)))
{
- if (!bFatal)
+ if (!errorsAreFatal)
{
- *bValidSettings = FALSE;
- return;
+ return false;
}
gmx_fatal(FARGS, "The number of PME grid lines per rank along x is %g. But when using OpenMP threads, the number of grid lines per rank along x should be >= pme_order (%d) or = pmeorder-1. To resolve this issue, use fewer ranks along x (and possibly more along y and/or z) by specifying -dd manually.",
nkx/(double)nnodes_major, pme_order);
}
- if (bValidSettings != NULL)
- {
- *bValidSettings = TRUE;
- }
-
- return;
+ return true;
}
/*! \brief Round \p enumerator */
t_commrec * cr,
int nnodes_major,
int nnodes_minor,
- t_inputrec * ir,
+ const t_inputrec * ir,
int homenr,
gmx_bool bFreeEnergy_q,
gmx_bool bFreeEnergy_lj,
gmx_bool bReproducible,
+ real ewaldcoeff_q,
+ real ewaldcoeff_lj,
int nthread)
{
- struct gmx_pme_t *pme = NULL;
-
int use_threads, sum_use_threads, i;
ivec ndata;
{
fprintf(debug, "Creating PME data structures.\n");
}
- snew(pme, 1);
- pme->sum_qgrid_tmp = NULL;
- pme->sum_qgrid_dd_tmp = NULL;
+ gmx_pme_t *pmeRaw = nullptr;
+ snew(pmeRaw, 1);
+ unique_cptr<gmx_pme_t, gmx_pme_destroy> pme(pmeRaw);
+
+ pme->sum_qgrid_tmp = nullptr;
+ pme->sum_qgrid_dd_tmp = nullptr;
+
pme->buf_nalloc = 0;
pme->nnodes = 1;
gmx_fatal(FARGS, "pme does not (yet) work with pbc = screw");
}
- pme->bFEP_q = ((ir->efep != efepNO) && bFreeEnergy_q);
- pme->bFEP_lj = ((ir->efep != efepNO) && bFreeEnergy_lj);
- pme->bFEP = (pme->bFEP_q || pme->bFEP_lj);
- pme->nkx = ir->nkx;
- pme->nky = ir->nky;
- pme->nkz = ir->nkz;
- pme->bP3M = (ir->coulombtype == eelP3M_AD || getenv("GMX_PME_P3M") != NULL);
- pme->pme_order = ir->pme_order;
+ /* NOTE:
+ * It is likely that the current gmx_pme_do() routine supports calculating
+ * only Coulomb or LJ while gmx_pme_init() configures for both,
+ * but that has never been tested.
+ * It is likely that the current gmx_pme_do() routine supports calculating,
+ * not calculating free-energy for Coulomb and/or LJ while gmx_pme_init()
+ * configures with free-energy, but that has never been tested.
+ */
+ pme->doCoulomb = EEL_PME(ir->coulombtype);
+ pme->doLJ = EVDW_PME(ir->vdwtype);
+ pme->bFEP_q = ((ir->efep != efepNO) && bFreeEnergy_q);
+ pme->bFEP_lj = ((ir->efep != efepNO) && bFreeEnergy_lj);
+ pme->bFEP = (pme->bFEP_q || pme->bFEP_lj);
+ pme->nkx = ir->nkx;
+ pme->nky = ir->nky;
+ pme->nkz = ir->nkz;
+ pme->bP3M = (ir->coulombtype == eelP3M_AD || getenv("GMX_PME_P3M") != nullptr);
+ pme->pme_order = ir->pme_order;
+ pme->ewaldcoeff_q = ewaldcoeff_q;
+ pme->ewaldcoeff_lj = ewaldcoeff_lj;
/* Always constant electrostatics coefficients */
- pme->epsilon_r = ir->epsilon_r;
+ pme->epsilon_r = ir->epsilon_r;
/* Always constant LJ coefficients */
pme->ljpme_combination_rule = ir->ljpme_combination_rule;
gmx_pme_check_restrictions(pme->pme_order,
pme->nkx, pme->nky, pme->nkz,
pme->nnodes_major,
- pme->nnodes_minor,
pme->bUseThreads,
- TRUE,
- NULL);
+ true);
if (pme->nnodes > 1)
{
* (unless the coefficient distribution is inhomogeneous).
*/
- imbal = estimate_pme_load_imbalance(pme);
+ imbal = estimate_pme_load_imbalance(pme.get());
if (imbal >= 1.2 && pme->nodeid_major == 0 && pme->nodeid_minor == 0)
{
fprintf(stderr,
pme->pmegrid_start_iy = pme->overlap[1].s2g0[pme->nodeid_minor];
pme->pmegrid_start_iz = 0;
- make_gridindex5_to_localindex(pme->nkx,
- pme->pmegrid_start_ix,
- pme->pmegrid_nx - (pme->pme_order-1),
- &pme->nnx, &pme->fshx);
- make_gridindex5_to_localindex(pme->nky,
- pme->pmegrid_start_iy,
- pme->pmegrid_ny - (pme->pme_order-1),
- &pme->nny, &pme->fshy);
- make_gridindex5_to_localindex(pme->nkz,
- pme->pmegrid_start_iz,
- pme->pmegrid_nz_base,
- &pme->nnz, &pme->fshz);
+ make_gridindex_to_localindex(pme->nkx,
+ pme->pmegrid_start_ix,
+ pme->pmegrid_nx - (pme->pme_order-1),
+ &pme->nnx, &pme->fshx);
+ make_gridindex_to_localindex(pme->nky,
+ pme->pmegrid_start_iy,
+ pme->pmegrid_ny - (pme->pme_order-1),
+ &pme->nny, &pme->fshy);
+ make_gridindex_to_localindex(pme->nkz,
+ pme->pmegrid_start_iz,
+ pme->pmegrid_nz_base,
+ &pme->nnz, &pme->fshz);
pme->spline_work = make_pme_spline_work(pme->pme_order);
/* It doesn't matter if we allocate too many grids here,
* we only allocate and use the ones we need.
*/
- if (EVDW_PME(ir->vdwtype))
+ if (pme->doLJ)
{
pme->ngrids = ((ir->ljpme_combination_rule == eljpmeLB) ? DO_Q_AND_LJ_LB : DO_Q_AND_LJ);
}
for (i = 0; i < pme->ngrids; ++i)
{
- if ((i < DO_Q && EEL_PME(ir->coulombtype) && (i == 0 ||
- bFreeEnergy_q)) ||
- (i >= DO_Q && EVDW_PME(ir->vdwtype) && (i == 2 ||
- bFreeEnergy_lj ||
- ir->ljpme_combination_rule == eljpmeLB)))
+ if ((i < DO_Q && pme->doCoulomb && (i == 0 ||
+ bFreeEnergy_q)) ||
+ (i >= DO_Q && pme->doLJ && (i == 2 ||
+ bFreeEnergy_lj ||
+ ir->ljpme_combination_rule == eljpmeLB)))
{
pmegrids_init(&pme->pmegrid[i],
pme->pmegrid_nx, pme->pmegrid_ny, pme->pmegrid_nz,
}
/* Use atc[0] for spreading */
- init_atomcomm(pme, &pme->atc[0], nnodes_major > 1 ? 0 : 1, TRUE);
+ init_atomcomm(pme.get(), &pme->atc[0], nnodes_major > 1 ? 0 : 1, TRUE);
if (pme->ndecompdim >= 2)
{
- init_atomcomm(pme, &pme->atc[1], 1, FALSE);
+ init_atomcomm(pme.get(), &pme->atc[1], 1, FALSE);
}
if (pme->nnodes == 1)
pme_realloc_atomcomm_things(&pme->atc[0]);
}
- pme->lb_buf1 = NULL;
- pme->lb_buf2 = NULL;
+ pme->lb_buf1 = nullptr;
+ pme->lb_buf2 = nullptr;
pme->lb_buf_nalloc = 0;
pme_init_all_work(&pme->solve_work, pme->nthread, pme->nkx);
- *pmedata = pme;
+ // no exception was thrown during the init, so we hand over the PME structure handle
+ *pmedata = pme.release();
return 0;
}
t_commrec * cr,
struct gmx_pme_t * pme_src,
const t_inputrec * ir,
- ivec grid_size)
+ ivec grid_size,
+ real ewaldcoeff_q,
+ real ewaldcoeff_lj)
{
- t_inputrec irc;
int homenr;
int ret;
- irc = *ir;
- irc.nkx = grid_size[XX];
- irc.nky = grid_size[YY];
- irc.nkz = grid_size[ZZ];
+ // Create a copy of t_inputrec fields that are used in gmx_pme_init().
+ // TODO: This would be better as just copying a sub-structure that contains
+ // all the PME parameters and nothing else.
+ t_inputrec irc;
+ irc.ePBC = ir->ePBC;
+ irc.coulombtype = ir->coulombtype;
+ irc.vdwtype = ir->vdwtype;
+ irc.efep = ir->efep;
+ irc.pme_order = ir->pme_order;
+ irc.epsilon_r = ir->epsilon_r;
+ irc.ljpme_combination_rule = ir->ljpme_combination_rule;
+ irc.nkx = grid_size[XX];
+ irc.nky = grid_size[YY];
+ irc.nkz = grid_size[ZZ];
if (pme_src->nnodes == 1)
{
homenr = -1;
}
- ret = gmx_pme_init(pmedata, cr, pme_src->nnodes_major, pme_src->nnodes_minor,
- &irc, homenr, pme_src->bFEP_q, pme_src->bFEP_lj, FALSE, pme_src->nthread);
+ try
+ {
+ ret = gmx_pme_init(pmedata, cr, pme_src->nnodes_major, pme_src->nnodes_minor,
+ &irc, homenr, pme_src->bFEP_q, pme_src->bFEP_lj, FALSE, ewaldcoeff_q, ewaldcoeff_lj, pme_src->nthread);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
if (ret == 0)
{
atc = &pme->atc_energy;
atc->nthread = 1;
- if (atc->spline == NULL)
+ if (atc->spline == nullptr)
{
snew(atc->spline, atc->nthread);
}
grid = &pme->pmegrid[PME_GRID_QA];
/* Only calculate the spline coefficients, don't actually spread */
- spread_on_grid(pme, atc, NULL, TRUE, FALSE, pme->fftgrid[PME_GRID_QA], FALSE, PME_GRID_QA);
+ spread_on_grid(pme, atc, nullptr, TRUE, FALSE, pme->fftgrid[PME_GRID_QA], FALSE, PME_GRID_QA);
*V = gather_energy_bsplines(pme, grid->grid.grid, atc);
}
matrix box, t_commrec *cr,
int maxshift_x, int maxshift_y,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- matrix vir_q, real ewaldcoeff_q,
- matrix vir_lj, real ewaldcoeff_lj,
+ matrix vir_q, matrix vir_lj,
real *energy_q, real *energy_lj,
real lambda_q, real lambda_lj,
real *dvdlambda_q, real *dvdlambda_lj,
{
int d, i, j, npme, grid_index, max_grid_index;
int n_d;
- pme_atomcomm_t *atc = NULL;
- pmegrids_t *pmegrid = NULL;
- real *grid = NULL;
+ pme_atomcomm_t *atc = nullptr;
+ pmegrids_t *pmegrid = nullptr;
+ real *grid = nullptr;
rvec *f_d;
- real *coefficient = NULL;
+ real *coefficient = nullptr;
real energy_AB[4];
matrix vir_AB[4];
real scale, lambda;
* that don't yet have them.
*/
- bDoSplines = pme->bFEP || ((flags & GMX_PME_DO_COULOMB) && (flags & GMX_PME_DO_LJ));
+ bDoSplines = pme->bFEP || (pme->doCoulomb && pme->doLJ);
/* We need a maximum of four separate PME calculations:
* grid_index=0: Coulomb PME with charges from state A
* If grid_index < 2 we should be doing electrostatic PME
* If grid_index >= 2 we should be doing LJ-PME
*/
- if ((grid_index < DO_Q && (!(flags & GMX_PME_DO_COULOMB) ||
+ if ((grid_index < DO_Q && (!pme->doCoulomb ||
(grid_index == 1 && !pme->bFEP_q))) ||
- (grid_index >= DO_Q && (!(flags & GMX_PME_DO_LJ) ||
+ (grid_index >= DO_Q && (!pme->doLJ ||
(grid_index == 3 && !pme->bFEP_lj))))
{
continue;
fprintf(debug, "PME: number of ranks = %d, rank = %d\n",
cr->nnodes, cr->nodeid);
fprintf(debug, "Grid = %p\n", (void*)grid);
- if (grid == NULL)
+ if (grid == nullptr)
{
gmx_fatal(FARGS, "No grid!");
}
if (flags & GMX_PME_SPREAD)
{
- wallcycle_start(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_start(wcycle, ewcPME_SPREAD);
/* Spread the coefficients on a grid */
spread_on_grid(pme, &pme->atc[0], pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
}
- wallcycle_stop(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_stop(wcycle, ewcPME_SPREAD);
/* TODO If the OpenMP and single-threaded implementations
converge, then spread_on_grid() and
if (grid_index < DO_Q)
{
loop_count =
- solve_pme_yzx(pme, cfftgrid, ewaldcoeff_q,
+ solve_pme_yzx(pme, cfftgrid,
box[XX][XX]*box[YY][YY]*box[ZZ][ZZ],
bCalcEnerVir,
pme->nthread, thread);
else
{
loop_count =
- solve_pme_lj_yzx(pme, &cfftgrid, FALSE, ewaldcoeff_lj,
+ solve_pme_lj_yzx(pme, &cfftgrid, FALSE,
box[XX][XX]*box[YY][YY]*box[ZZ][ZZ],
bCalcEnerVir,
pme->nthread, thread);
/* Note: this wallcycle region is closed below
outside an OpenMP region, so take care if
refactoring code here. */
- wallcycle_start(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_start(wcycle, ewcPME_GATHER);
}
copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
/* Note: this wallcycle region is opened above inside an OpenMP
region, so take care if refactoring code here. */
- wallcycle_stop(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_stop(wcycle, ewcPME_GATHER);
}
if (bCalcEnerVir)
/* For Lorentz-Berthelot combination rules in LJ-PME, we need to calculate
* seven terms. */
- if ((flags & GMX_PME_DO_LJ) && pme->ljpme_combination_rule == eljpmeLB)
+ if (pme->doLJ && pme->ljpme_combination_rule == eljpmeLB)
{
/* Loop over A- and B-state if we are doing FEP */
for (fep_state = 0; fep_state < fep_states_lj; ++fep_state)
{
- real *local_c6 = NULL, *local_sigma = NULL, *RedistC6 = NULL, *RedistSigma = NULL;
+ real *local_c6 = nullptr, *local_sigma = nullptr, *RedistC6 = nullptr, *RedistSigma = nullptr;
if (pme->nnodes == 1)
{
- if (pme->lb_buf1 == NULL)
+ if (pme->lb_buf1 == nullptr)
{
pme->lb_buf_nalloc = pme->atc[0].n;
snew(pme->lb_buf1, pme->lb_buf_nalloc);
if (flags & GMX_PME_SPREAD)
{
- wallcycle_start(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_start(wcycle, ewcPME_SPREAD);
/* Spread the c6 on a grid */
spread_on_grid(pme, &pme->atc[0], pmegrid, bFirst, TRUE, fftgrid, bDoSplines, grid_index);
#endif
copy_pmegrid_to_fftgrid(pme, grid, fftgrid, grid_index);
}
- wallcycle_stop(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_stop(wcycle, ewcPME_SPREAD);
}
/*Here we start a large thread parallel region*/
#pragma omp parallel num_threads(pme->nthread) private(thread)
}
loop_count =
- solve_pme_lj_yzx(pme, &pme->cfftgrid[2], TRUE, ewaldcoeff_lj,
+ solve_pme_lj_yzx(pme, &pme->cfftgrid[2], TRUE,
box[XX][XX]*box[YY][YY]*box[ZZ][ZZ],
bCalcEnerVir,
pme->nthread, thread);
if (bBackFFT)
{
- bFirst = !(flags & GMX_PME_DO_COULOMB);
+ bFirst = !pme->doCoulomb;
calc_initial_lb_coeffs(pme, local_c6, local_sigma);
for (grid_index = 8; grid_index >= 2; --grid_index)
{
npme = static_cast<int>(ntot*std::log(ntot)/std::log(2.0));
inc_nrnb(nrnb, eNR_FFT, 2*npme);
}
- wallcycle_start(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_start(wcycle, ewcPME_GATHER);
}
copy_fftgrid_to_pmegrid(pme, fftgrid, grid, grid_index, pme->nthread, thread);
inc_nrnb(nrnb, eNR_GATHERFBSP,
pme->pme_order*pme->pme_order*pme->pme_order*pme->atc[0].n);
}
- wallcycle_stop(wcycle, ewcPME_SPREADGATHER);
+ wallcycle_stop(wcycle, ewcPME_GATHER);
bFirst = FALSE;
} /* for (grid_index = 8; grid_index >= 2; --grid_index) */
if (bCalcEnerVir)
{
- if (flags & GMX_PME_DO_COULOMB)
+ if (pme->doCoulomb)
{
if (!pme->bFEP_q)
{
*energy_q = 0;
}
- if (flags & GMX_PME_DO_LJ)
+ if (pme->doLJ)
{
if (!pme->bFEP_lj)
{
}
return 0;
}
+
+void gmx_pme_destroy(gmx_pme_t *pme)
+{
+ if (!pme)
+ {
+ return;
+ }
+
+ sfree(pme->nnx);
+ sfree(pme->nny);
+ sfree(pme->nnz);
+ sfree(pme->fshx);
+ sfree(pme->fshy);
+ sfree(pme->fshz);
+
+ for (int i = 0; i < pme->ngrids; ++i)
+ {
+ pmegrids_destroy(&pme->pmegrid[i]);
+ }
+ if (pme->pfft_setup)
+ {
+ for (int i = 0; i < pme->ngrids; ++i)
+ {
+ gmx_parallel_3dfft_destroy(pme->pfft_setup[i]);
+ }
+ }
+ sfree(pme->fftgrid);
+ sfree(pme->cfftgrid);
+ sfree(pme->pfft_setup);
+
+ for (int i = 0; i < std::max(1, pme->ndecompdim); i++) //pme->atc[0] is always allocated
+ {
+ destroy_atomcomm(&pme->atc[i]);
+ }
+
+ for (int i = 0; i < DIM; i++)
+ {
+ sfree(pme->bsp_mod[i]);
+ }
+
+ destroy_overlap_comm(&pme->overlap[0]);
+ destroy_overlap_comm(&pme->overlap[1]);
+
+ sfree(pme->lb_buf1);
+ sfree(pme->lb_buf2);
+
+ sfree(pme->bufv);
+ sfree(pme->bufr);
+
+ pme_free_all_work(&pme->solve_work, pme->nthread);
+
+ sfree(pme->sum_qgrid_tmp);
+ sfree(pme->sum_qgrid_dd_tmp);
+
+ sfree(pme);
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
GMX_SUM_GRID_FORWARD, GMX_SUM_GRID_BACKWARD
};
+/*! \brief Return the smallest allowed PME grid size for \p pmeOrder */
+int minimalPmeGridSize(int pmeOrder);
+
+/*! \brief Check restrictions on pme_order and the PME grid nkx,nky,nkz.
+ *
+ * With errorsAreFatal=true, an exception or fatal error is generated
+ * on violation of restrictions.
+ * With errorsAreFatal=false, false is returned on violation of restrictions.
+ * When all restrictions are obeyed, true is returned.
+ * Argument useThreads tells if any MPI rank doing PME uses more than 1 threads.
+ * If at calling useThreads is unknown, pass true for conservative checking.
+ */
+bool gmx_pme_check_restrictions(int pme_order,
+ int nkx, int nky, int nkz,
+ int nnodes_major,
+ bool useThreads,
+ bool errorsAreFatal);
+
/*! \brief Initialize \p pmedata
*
- * Return value 0 indicates all well, non zero is an error code.
+ * \returns 0 indicates all well, non zero is an error code.
+ * \throws gmx::InconsistentInputError if input grid sizes/PME order are inconsistent.
*/
int gmx_pme_init(struct gmx_pme_t **pmedata, struct t_commrec *cr,
int nnodes_major, int nnodes_minor,
- t_inputrec *ir, int homenr,
+ const t_inputrec *ir, int homenr,
gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj,
- gmx_bool bReproducible, int nthread);
+ gmx_bool bReproducible,
+ real ewaldcoeff_q, real ewaldcoeff_lj,
+ int nthread);
-/*! \brief Destroy the pme data structures resepectively.
- *
- * \return 0 indicates all well, non zero is an error code.
- */
-int gmx_pme_destroy(FILE *log, struct gmx_pme_t **pmedata);
+/*! \brief Destroys the PME data structure.*/
+void gmx_pme_destroy(gmx_pme_t *pme);
//@{
/*! \brief Flag values that control what gmx_pme_do() will calculate
/* This forces the grid to be backtransformed even without GMX_PME_CALC_F */
#define GMX_PME_CALC_POT (1<<4)
-/* These values label bits used for sending messages to PME nodes using the
- * routines in pme_pp.c and shouldn't conflict with the flags used there
- */
-#define GMX_PME_DO_COULOMB (1<<13)
-#define GMX_PME_DO_LJ (1<<14)
-
#define GMX_PME_DO_ALL_F (GMX_PME_SPREAD | GMX_PME_SOLVE | GMX_PME_CALC_F)
//@}
matrix box, t_commrec *cr,
int maxshift_x, int maxshift_y,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- matrix vir_q, real ewaldcoeff_q,
- matrix vir_lj, real ewaldcoeff_lj,
+ matrix vir_q, matrix vir_lj,
real *energy_q, real *energy_lj,
real lambda_q, real lambda_lj,
real *dvdlambda_q, real *dvdlambda_lj,
/*! \brief Send the coordinates to our PME-only node and request a PME calculation */
void gmx_pme_send_coordinates(struct t_commrec *cr, matrix box, rvec *x,
- gmx_bool bFreeEnergy_q, gmx_bool bFreeEnergy_lj,
real lambda_q, real lambda_lj,
- gmx_bool bEnerVir, int pme_flags,
+ gmx_bool bEnerVir,
gmx_int64_t step);
/*! \brief Tell our PME-only node to finish */
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2016,2017, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+file(GLOB EWALD_TEST_SOURCES *.cpp)
+gmx_add_unit_test(EwaldUnitTests ewald-test
+ ${EWALD_TEST_SOURCES})
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements PME B-spline moduli computation tests.
+ *
+ * \author Aleksei Iupinov <a.yupinov@gmail.com>
+ * \ingroup module_ewald
+ */
+
+#include "gmxpre.h"
+
+#include <string>
+
+#include <gmock/gmock.h>
+
+#include "gromacs/ewald/pme-internal.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+#include "pmetestcommon.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+/*! \brief Moduli algorithm type */
+enum class ModuliType
+{
+ PME,
+ P3M
+};
+
+/*! \brief Convenience typedef of input parameters - grid dimensions, PME interpolation order, moduli type */
+typedef std::tuple<IVec, int, ModuliType> BSplineModuliInputParameters;
+
+/*! \brief Test fixture for testing PME B-spline moduli creation */
+class PmeBSplineModuliTest : public ::testing::TestWithParam<BSplineModuliInputParameters>
+{
+ public:
+ //! Default constructor
+ PmeBSplineModuliTest() = default;
+ //! The whole logic being tested is contained here
+ void runTest()
+ {
+ /* Getting the input */
+ const BSplineModuliInputParameters parameters = GetParam();
+ int pmeOrder;
+ IVec gridSize;
+ ModuliType moduliType;
+ std::tie(gridSize, pmeOrder, moduliType) = parameters;
+
+ /* Describing the test in case it fails */
+ SCOPED_TRACE(formatString("Testing B-spline moduli creation (%s) for PME order %d, grid size %d %d %d",
+ (moduliType == ModuliType::P3M) ? "P3M" : "plain",
+ pmeOrder,
+ gridSize[XX], gridSize[YY], gridSize[ZZ]));
+
+ /* Storing the input where it's needed */
+ t_inputrec inputRec;
+ inputRec.nkx = gridSize[XX];
+ inputRec.nky = gridSize[YY];
+ inputRec.nkz = gridSize[ZZ];
+ inputRec.coulombtype = (moduliType == ModuliType::P3M) ? eelP3M_AD : eelPME;
+ inputRec.pme_order = pmeOrder;
+
+ /* PME initialization call which checks the inputs and computes the B-spline moduli according to the grid sizes. */
+ PmeSafePointer pme = pmeInitEmpty(&inputRec);
+
+ /* Setting up the checker */
+ TestReferenceData refData;
+ TestReferenceChecker checker(refData.rootChecker());
+ auto singlePrecisionUlps = 6;
+ /* P3M moduli use polynomial expansions that are strongly affected by rounding errors. */
+ auto doublePrecisionUlps = (moduliType == ModuliType::P3M) ? 10 : singlePrecisionUlps;
+ auto tolerance = relativeToleranceAsPrecisionDependentUlp(1.0, singlePrecisionUlps, doublePrecisionUlps);
+ checker.setDefaultTolerance(tolerance);
+
+ /* Perform a correctness check */
+ const char *dimString[] = { "X", "Y", "Z" };
+ for (int i = 0; i < DIM; i++)
+ {
+ checker.checkSequenceArray(gridSize[i], pme->bsp_mod[i], dimString[i]);
+ }
+ }
+};
+
+// Different aliases are needed to reuse the test class without instantiating tests more than once
+//! Failure test alias
+using PmeBSplineModuliFailureTest = PmeBSplineModuliTest;
+TEST_P(PmeBSplineModuliFailureTest, Throws)
+{
+ EXPECT_THROW(runTest(), InconsistentInputError);
+}
+//! Correctness test alias
+using PmeBSplineModuliCorrectnessTest = PmeBSplineModuliTest;
+TEST_P(PmeBSplineModuliCorrectnessTest, ReproducesValues)
+{
+ EXPECT_NO_THROW(runTest());
+}
+
+/* Invalid input instances */
+
+//! Sane interpolation order
+const int sanePmeOrder = 4;
+//! Sane grid size
+const IVec saneGridSize = {32, 25, 47};
+/*! \brief Hand-picked invalid input for the exception tests */
+static std::vector<BSplineModuliInputParameters> const invalidInputs
+{
+ /* Invalid grid sizes */
+ BSplineModuliInputParameters {
+ IVec {
+ -1, 10, 10
+ }, sanePmeOrder, ModuliType::P3M
+ },
+ BSplineModuliInputParameters {
+ IVec {
+ 40, 0, 20
+ }, sanePmeOrder, ModuliType::P3M
+ },
+ BSplineModuliInputParameters {
+ IVec {
+ 64, 2, 64
+ }, sanePmeOrder, ModuliType::PME
+ },
+ /* Invalid interpolation orders */
+ BSplineModuliInputParameters {
+ saneGridSize, 8 + 1, ModuliType::P3M // P3M only supports orders up to 8
+ },
+ BSplineModuliInputParameters {
+ saneGridSize, PME_ORDER_MAX + 1, ModuliType::PME
+ },
+};
+
+/*! \brief Instantiation of the PME B-spline moduli creation test with invalid input */
+INSTANTIATE_TEST_CASE_P(InsaneInput, PmeBSplineModuliFailureTest, ::testing::ValuesIn(invalidInputs));
+
+/* Valid input instances */
+
+//! A couple of valid inputs for grid sizes. It is good to test both even and odd dimensions.
+static std::vector<IVec> const sampleGridSizes
+{
+ IVec {
+ 64, 32, 64
+ },
+ IVec {
+ 57, 84, 29
+ }
+};
+
+/*! \brief Instantiation of the PME B-spline moduli creation test with valid input - up to order of 8 */
+INSTANTIATE_TEST_CASE_P(SaneInput1, PmeBSplineModuliCorrectnessTest, ::testing::Combine(
+ ::testing::ValuesIn(sampleGridSizes),
+ ::testing::Range(3, 8 + 1),
+ ::testing::Values(ModuliType::PME, ModuliType::P3M)
+ ));
+}
+}
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements PME force gathering tests.
+ *
+ * \author Aleksei Iupinov <a.yupinov@gmail.com>
+ * \ingroup module_ewald
+ */
+
+#include "gmxpre.h"
+
+#include <string>
+
+#include <gmock/gmock.h>
+
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+#include "pmetestcommon.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+/* Valid input instances */
+
+//! A couple of valid inputs for boxes.
+static std::vector<Matrix3x3> const c_sampleBoxes
+{
+ // normal box
+ Matrix3x3 {{
+ 8.0f, 0.0f, 0.0f,
+ 0.0f, 3.4f, 0.0f,
+ 0.0f, 0.0f, 2.0f
+ }},
+ // triclinic box
+ Matrix3x3 {{
+ 7.0f, 0.0f, 0.0f,
+ 0.0f, 4.1f, 0.0f,
+ 3.5f, 2.0f, 12.2f
+ }},
+};
+
+//! A couple of valid inputs for grid sizes
+static std::vector<IVec> const c_sampleGridSizes
+{
+ IVec {
+ 16, 12, 14
+ },
+ IVec {
+ 13, 15, 11
+ }
+};
+//! Random charges
+static std::vector<real> const c_sampleChargesFull
+{
+ 4.95f, 3.11f, 3.97f, 1.08f, 2.09f, 1.1f, 4.13f, 3.31f, 2.8f, 5.83f, 5.09f, 6.1f, 2.86f, 0.24f, 5.76f, 5.19f, 0.72f
+};
+
+//! All the input atom gridline indices
+static std::vector<IVec> const c_sampleGridLineIndicesFull
+{
+ IVec {
+ 4, 2, 6
+ },
+ IVec {
+ 1, 4, 10
+ },
+ IVec {
+ 0, 6, 6
+ },
+ IVec {
+ 0, 1, 4
+ },
+ IVec {
+ 6, 3, 0
+ },
+ IVec {
+ 7, 2, 2
+ },
+ IVec {
+ 8, 3, 1
+ },
+ IVec {
+ 4, 0, 3
+ },
+ IVec {
+ 0, 0, 0
+ },
+ IVec {
+ 8, 5, 8
+ },
+ IVec {
+ 4, 4, 2
+ },
+ IVec {
+ 7, 1, 7
+ },
+ IVec {
+ 8, 5, 5
+ },
+ IVec {
+ 2, 6, 5
+ },
+ IVec {
+ 1, 6, 2
+ },
+ IVec {
+ 7, 1, 8
+ },
+ IVec {
+ 3, 5, 1
+ },
+};
+
+// Spline values/derivatives below are also generated randomly, so they are bogus,
+// but that should not affect the reproducibility, which we're after
+
+//! A lot of bogus input spline values - should have at list (max PME order = 5) * (DIM = 3) * (total unique atom number in all test cases = 16) values
+static std::vector<real> const c_sampleSplineValuesFull
+{
+ 0.12f, 0.81f, 0.29f, 0.22f, 0.13f, 0.19f, 0.12f, 0.8f, 0.44f, 0.38f, 0.32f, 0.36f, 0.27f, 0.11f, 0.17f, 0.94f, 0.07f, 0.9f, 0.98f, 0.96f, 0.07f, 0.94f, 0.77f, 0.24f, 0.84f, 0.16f, 0.77f, 0.57f, 0.52f, 0.27f, 0.39f, 0.45f, 0.6f, 0.59f, 0.44f, 0.91f, 0.97f, 0.43f, 0.24f, 0.52f, 0.73f, 0.55f, 0.99f, 0.39f, 0.97f, 0.35f, 0.1f, 0.68f, 0.19f, 0.1f, 0.77f, 0.2f, 0.43f, 0.69f, 0.76f, 0.32f, 0.31f, 0.94f, 0.53f, 0.6f, 0.93f, 0.57f, 0.94f, 0.88f, 0.75f, 0.77f, 0.91f, 0.72f, 0.07f, 0.78f, 0.09f, 0.02f, 0.48f, 0.97f, 0.89f, 0.39f, 0.48f, 0.19f, 0.02f, 0.92f, 0.8f, 0.41f, 0.53f, 0.32f, 0.38f, 0.58f, 0.36f, 0.46f, 0.92f, 0.91f, 0.01f, 0.86f, 0.54f, 0.86f, 0.94f, 0.37f, 0.35f, 0.81f, 0.89f, 0.48f,
+ 0.34f, 0.18f, 0.11f, 0.02f, 0.87f, 0.95f, 0.66f, 0.67f, 0.38f, 0.45f, 0.04f, 0.94f, 0.54f, 0.76f, 0.58f, 0.83f, 0.31f, 0.73f, 0.71f, 0.06f, 0.35f, 0.32f, 0.35f, 0.61f, 0.27f, 0.98f, 0.83f, 0.11f, 0.3f, 0.42f, 0.95f, 0.69f, 0.58f, 0.29f, 0.1f, 0.68f, 0.94f, 0.62f, 0.51f, 0.47f, 0.04f, 0.47f, 0.34f, 0.71f, 0.52f, 0.19f, 0.69f, 0.5f, 0.59f, 0.05f, 0.74f, 0.11f, 0.4f, 0.81f, 0.24f, 0.53f, 0.71f, 0.07f, 0.17f, 0.41f, 0.23f, 0.78f, 0.27f, 0.1f, 0.71f, 0.36f, 0.67f, 0.6f, 0.94f, 0.69f, 0.19f, 0.58f, 0.68f, 0.5f, 0.62f, 0.38f, 0.29f, 0.44f, 0.04f, 0.89f, 0.0f, 0.76f, 0.22f, 0.16f, 0.08f, 0.62f, 0.51f, 0.62f, 0.83f, 0.72f, 0.96f, 0.99f, 0.4f, 0.79f, 0.83f, 0.21f, 0.43f, 0.32f, 0.44f, 0.72f,
+ 0.21f, 0.4f, 0.93f, 0.07f, 0.11f, 0.41f, 0.24f, 0.04f, 0.36f, 0.15f, 0.92f, 0.08f, 0.99f, 0.35f, 0.42f, 0.7f, 0.17f, 0.39f, 0.69f, 0.0f, 0.86f, 0.89f, 0.59f, 0.81f, 0.77f, 0.15f, 0.89f, 0.17f, 0.76f, 0.67f, 0.58f, 0.78f, 0.26f, 0.19f, 0.69f, 0.18f, 0.46f, 0.6f, 0.69f, 0.23f, 0.34f, 0.3f, 0.64f, 0.34f, 0.6f, 0.99f, 0.69f, 0.57f, 0.75f, 0.07f, 0.36f, 0.75f, 0.81f, 0.8f, 0.42f, 0.09f, 0.94f, 0.66f, 0.35f, 0.67f, 0.34f, 0.66f, 0.02f, 0.47f, 0.78f, 0.21f, 0.02f, 0.18f, 0.42f, 0.2f, 0.46f, 0.34f, 0.4f, 0.46f, 0.96f, 0.86f, 0.25f, 0.25f, 0.22f, 0.37f, 0.59f, 0.19f, 0.45f, 0.61f, 0.04f, 0.71f, 0.77f, 0.51f, 0.77f, 0.15f, 0.78f, 0.36f, 0.62f, 0.24f, 0.86f, 0.2f, 0.77f, 0.08f, 0.09f, 0.3f,
+ 0.0f, 0.6f, 0.99f, 0.69f,
+};
+
+//! A lot of bogus input spline derivatives - should have at list (max PME order = 5) * (DIM = 3) * (total unique atom number in all test cases = 16) values
+static std::vector<real> const c_sampleSplineDerivativesFull
+{
+ 0.82f, 0.88f, 0.83f, 0.11f, 0.93f, 0.32f, 0.71f, 0.37f, 0.69f, 0.88f, 0.11f, 0.38f, 0.25f, 0.5f, 0.36f, 0.81f, 0.78f, 0.31f, 0.66f, 0.32f, 0.27f, 0.35f, 0.53f, 0.83f, 0.08f, 0.08f, 0.94f, 0.71f, 0.65f, 0.24f, 0.13f, 0.01f, 0.33f, 0.65f, 0.24f, 0.53f, 0.45f, 0.84f, 0.33f, 0.97f, 0.31f, 0.7f, 0.03f, 0.31f, 0.41f, 0.76f, 0.12f, 0.3f, 0.57f, 0.65f, 0.87f, 0.99f, 0.42f, 0.97f, 0.32f, 0.39f, 0.73f, 0.23f, 0.03f, 0.67f, 0.97f, 0.57f, 0.42f, 0.38f, 0.54f, 0.17f, 0.53f, 0.54f, 0.18f, 0.8f, 0.76f, 0.13f, 0.29f, 0.83f, 0.77f, 0.56f, 0.4f, 0.87f, 0.36f, 0.18f, 0.59f, 0.04f, 0.05f, 0.61f, 0.26f, 0.91f, 0.62f, 0.16f, 0.89f, 0.23f, 0.26f, 0.59f, 0.33f, 0.2f, 0.49f, 0.41f, 0.25f, 0.4f, 0.16f, 0.83f,
+ 0.44f, 0.82f, 0.21f, 0.95f, 0.14f, 0.8f, 0.37f, 0.31f, 0.41f, 0.53f, 0.15f, 0.85f, 0.78f, 0.17f, 0.92f, 0.03f, 0.13f, 0.2f, 0.03f, 0.33f, 0.87f, 0.38f, 0, 0.08f, 0.79f, 0.36f, 0.53f, 0.05f, 0.07f, 0.94f, 0.23f, 0.85f, 0.13f, 0.27f, 0.23f, 0.22f, 0.26f, 0.38f, 0.15f, 0.48f, 0.18f, 0.33f, 0.23f, 0.62f, 0.1f, 0.36f, 0.99f, 0.07f, 0.02f, 0.04f, 0.09f, 0.29f, 0.52f, 0.29f, 0.83f, 0.97f, 0.61f, 0.81f, 0.49f, 0.56f, 0.08f, 0.09f, 0.03f, 0.65f, 0.46f, 0.1f, 0.06f, 0.06f, 0.39f, 0.29f, 0.04f, 0.03f, 0.1f, 0.83f, 0.94f, 0.59f, 0.97f, 0.82f, 0.2f, 0.66f, 0.23f, 0.11f, 0.03f, 0.16f, 0.27f, 0.53f, 0.94f, 0.46f, 0.43f, 0.29f, 0.97f, 0.64f, 0.46f, 0.37f, 0.43f, 0.48f, 0.37f, 0.93f, 0.5f, 0.2f,
+ 0.92f, 0.09f, 0.74f, 0.55f, 0.44f, 0.05f, 0.13f, 0.17f, 0.79f, 0.44f, 0.11f, 0.6f, 0.64f, 0.05f, 0.96f, 0.3f, 0.45f, 0.47f, 0.42f, 0.74f, 0.91f, 0.06f, 0.89f, 0.24f, 0.26f, 0.68f, 0.4f, 0.88f, 0.5f, 0.65f, 0.48f, 0.15f, 0.0f, 0.41f, 0.67f, 0.4f, 0.31f, 0.73f, 0.77f, 0.36f, 0.26f, 0.74f, 0.46f, 0.56f, 0.78f, 0.92f, 0.32f, 0.9f, 0.06f, 0.55f, 0.6f, 0.13f, 0.38f, 0.93f, 0.5f, 0.92f, 0.96f, 0.82f, 0.0f, 0.04f, 0.9f, 0.55f, 0.97f, 1.0f, 0.23f, 0.46f, 0.52f, 0.49f, 0.0f, 0.32f, 0.16f, 0.4f, 0.62f, 0.36f, 0.03f, 0.63f, 0.16f, 0.58f, 0.97f, 0.03f, 0.44f, 0.07f, 0.22f, 0.75f, 0.32f, 0.61f, 0.94f, 0.33f, 0.7f, 0.57f, 0.5f, 0.84f, 0.7f, 0.47f, 0.18f, 0.09f, 0.25f, 0.77f, 0.94f, 0.85f,
+ 0.09f, 0.83f, 0.02f, 0.91f,
+};
+
+//! 2 c_sample grids - only non-zero values have to be listed
+static std::vector<SparseRealGridValuesInput> const c_sampleGrids
+{
+ SparseRealGridValuesInput {{
+ IVec {
+ 0, 0, 0
+ }, 3.5f
+ }, {
+ IVec {
+ 7, 0, 0
+ }, -2.5f
+ },
+ {
+ IVec {
+ 3, 5, 7
+ }, -0.006f
+ }, {
+ IVec {
+ 1, 6, 7
+ }, -2.76f
+ }, {
+ IVec {
+ 3, 1, 2
+ }, 0.6f
+ }, {
+ IVec {
+ 6, 2, 4
+ }, 7.1f
+ }, {
+ IVec {
+ 4, 5, 6
+ }, 4.1f
+ }, {
+ IVec {
+ 4, 4, 6
+ }, -3.7f
+ }, },
+ SparseRealGridValuesInput {{
+ IVec {
+ 0, 4, 0
+ }, 6.f
+ }, {
+ IVec {
+ 4, 2, 7
+ }, 13.76f
+ }, {
+ IVec {
+ 0, 6, 7
+ }, 3.6f
+ }, {
+ IVec {
+ 3, 2, 8
+ }, 0.61f
+ },
+ {
+ IVec {
+ 5, 4, 3
+ }, 2.1f
+ },
+ {
+ IVec {
+ 2, 5, 10
+ }, 3.6f
+ }, {
+ IVec {
+ 5, 3, 6
+ }, 2.1f
+ }, {
+ IVec {
+ 6, 6, 6
+ }, 6.1f
+ }, }
+};
+
+//! Input forces for reduction
+static std::vector<RVec> const c_sampleForcesFull {
+ RVec {
+ 0.02f, 0.87f, 0.95f
+ }, RVec {
+ 0.66f, 0.67f, 0.38f
+ }, RVec {
+ 0.45f, 0.04f, 0.94f
+ }, RVec {
+ 0.54f, 0.76f, 0.58f
+ },
+ RVec {
+ 0.83f, 0.31f, 0.73f
+ }, RVec {
+ 0.71f, 0.06f, 0.35f
+ }, RVec {
+ 0.32f, 0.35f, 0.61f
+ }, RVec {
+ 0.27f, 0.98f, 0.83f
+ },
+ RVec {
+ 0.11f, 0.3f, 0.42f
+ }, RVec {
+ 0.95f, 0.69f, 0.58f
+ }, RVec {
+ 0.29f, 0.1f, 0.68f
+ }, RVec {
+ 0.94f, 0.62f, 0.51f
+ },
+ RVec {
+ 0.47f, 0.04f, 0.47f
+ }, RVec {
+ 0.34f, 0.71f, 0.52f
+ }
+};
+
+//! PME orders to test
+static std::vector<int> const pmeOrders {
+ 3, 4, 5
+};
+//! Atom counts to test
+static std::vector<size_t> const atomCounts {
+ 1, 2, 13
+};
+
+/* Helper structures for test input */
+
+//! A structure for all the spline data which depends in size both on the PME order and atom count
+struct AtomAndPmeOrderSizedData
+{
+ //! Spline values
+ SplineParamsVector splineValues;
+ //! Spline derivatives
+ SplineParamsVector splineDerivatives;
+};
+
+//! A structure for all the input atom data which depends in size on atom count - including a range of spline data for different PME orders
+struct AtomSizedData
+{
+ //! Gridline indices
+ GridLineIndicesVector gridLineIndices;
+ //! Charges
+ ChargesVector charges;
+ //! Coordinates
+ CoordinatesVector coordinates;
+ //! Spline data for different orders
+ std::map<int, AtomAndPmeOrderSizedData> splineDataByPmeOrder;
+};
+
+//! A range of the test input data sets, uniquely identified by the atom count
+typedef std::map<size_t, AtomSizedData> InputDataByAtomCount;
+
+/*! \brief Convenience typedef of the test input parameters - unit cell box, PME interpolation order, grid dimensions,
+ * grid values, overwriting/reducing the input forces, atom count.
+ *
+ * The rest of the atom-related input data - gridline indices, spline theta values, spline dtheta values, atom charges -
+ * is looked up in the inputAtomDataSets_ test fixture variable.
+ */
+typedef std::tuple<Matrix3x3, int, IVec, SparseRealGridValuesInput, PmeGatherInputHandling, size_t> GatherInputParameters;
+
+//! Test fixture
+class PmeGatherTest : public ::testing::TestWithParam<GatherInputParameters>
+{
+ private:
+ //! Storage of all the input atom datasets
+ static InputDataByAtomCount s_inputAtomDataSets_;
+
+ public:
+ //! Default constructor
+ PmeGatherTest() = default;
+ //! Sets the input atom data references once
+ static void SetUpTestCase()
+ {
+ auto gridLineIndicesIt = c_sampleGridLineIndicesFull.begin();
+ auto chargesIt = c_sampleChargesFull.begin();
+ for (auto atomCount : atomCounts)
+ {
+ AtomSizedData atomData;
+ atomData.gridLineIndices = GridLineIndicesVector::fromVector(gridLineIndicesIt, gridLineIndicesIt + atomCount);
+ gridLineIndicesIt += atomCount;
+ atomData.charges = ChargesVector::fromVector(chargesIt, chargesIt + atomCount);
+ chargesIt += atomCount;
+ atomData.coordinates.resize(atomCount, RVec {1e6, 1e7, -1e8});
+ /* The coordinates are intentionally bogus in this test - only the size matters; the gridline indices are fed directly as inputs */
+ for (auto pmeOrder : pmeOrders)
+ {
+ AtomAndPmeOrderSizedData splineData;
+ const size_t dimSize = atomCount * pmeOrder;
+ for (int dimIndex = 0; dimIndex < DIM; dimIndex++)
+ {
+ splineData.splineValues[dimIndex] = SplineParamsDimVector::fromVector(c_sampleSplineValuesFull.begin() + dimIndex * dimSize,
+ c_sampleSplineValuesFull.begin() + (dimIndex + 1) * dimSize);
+ splineData.splineDerivatives[dimIndex] = SplineParamsDimVector::fromVector(c_sampleSplineDerivativesFull.begin() + dimIndex * dimSize,
+ c_sampleSplineDerivativesFull.begin() + (dimIndex + 1) * dimSize);
+ }
+ atomData.splineDataByPmeOrder[pmeOrder] = splineData;
+ }
+ s_inputAtomDataSets_[atomCount] = atomData;
+ }
+ }
+ //! The test
+ void runTest()
+ {
+ /* Getting the input */
+ Matrix3x3 box;
+ int pmeOrder;
+ IVec gridSize;
+ size_t atomCount;
+ SparseRealGridValuesInput nonZeroGridValues;
+ PmeGatherInputHandling inputForceTreatment;
+ std::tie(box, pmeOrder, gridSize, nonZeroGridValues, inputForceTreatment, atomCount) = GetParam();
+ auto inputAtomData = s_inputAtomDataSets_[atomCount];
+ auto inputAtomSplineData = inputAtomData.splineDataByPmeOrder[pmeOrder];
+
+ /* Storing the input where it's needed, running the test */
+ t_inputrec inputRec;
+ inputRec.nkx = gridSize[XX];
+ inputRec.nky = gridSize[YY];
+ inputRec.nkz = gridSize[ZZ];
+ inputRec.pme_order = pmeOrder;
+ inputRec.coulombtype = eelPME;
+
+ TestReferenceData refData;
+ const std::map<CodePath, std::string> modesToTest = {{CodePath::CPU, "CPU"}};
+ for (const auto &mode : modesToTest)
+ {
+ /* Describing the test uniquely */
+ SCOPED_TRACE(formatString("Testing force gathering with %s for PME grid size %d %d %d"
+ ", order %d, %zu atoms, %s",
+ mode.second.c_str(),
+ gridSize[XX], gridSize[YY], gridSize[ZZ],
+ pmeOrder,
+ atomCount,
+ (inputForceTreatment == PmeGatherInputHandling::ReduceWith) ? "with reduction" : "without reduction"
+ ));
+
+ PmeSafePointer pmeSafe = pmeInitAtoms(&inputRec, inputAtomData.coordinates, inputAtomData.charges, box);
+
+ /* Setting some more inputs */
+ pmeSetRealGrid(pmeSafe.get(), mode.first, nonZeroGridValues);
+
+ pmeSetGridLineIndices(pmeSafe.get(), mode.first, inputAtomData.gridLineIndices);
+
+ for (int dimIndex = 0; dimIndex < DIM; dimIndex++)
+ {
+ pmeSetSplineData(pmeSafe.get(), mode.first, inputAtomSplineData.splineValues[dimIndex], PmeSplineDataType::Values, dimIndex);
+ pmeSetSplineData(pmeSafe.get(), mode.first, inputAtomSplineData.splineDerivatives[dimIndex], PmeSplineDataType::Derivatives, dimIndex);
+ }
+
+ /* Explicitly copying the c_sample forces to be able to modify them */
+ auto inputForcesFull(c_sampleForcesFull);
+ GMX_RELEASE_ASSERT(inputForcesFull.size() >= atomCount, "Bad input forces size");
+ auto forces = ForcesVector::fromVector(inputForcesFull.begin(), inputForcesFull.begin() + atomCount);
+
+ /* Running the force gathering itself */
+ pmePerformGather(pmeSafe.get(), mode.first, inputForceTreatment, forces);
+
+ /* Check the output forces correctness */
+ TestReferenceChecker forceChecker(refData.rootChecker());
+ const auto ulpTolerance = 3 * pmeOrder;
+ forceChecker.setDefaultTolerance(relativeToleranceAsUlp(1.0, ulpTolerance));
+ forceChecker.checkSequence(forces.begin(), forces.end(), "Forces");
+ }
+ }
+};
+
+// An instance of static atom data
+InputDataByAtomCount PmeGatherTest::s_inputAtomDataSets_;
+
+//! Test for PME force gathering
+TEST_P(PmeGatherTest, ReproducesOutputs)
+{
+ EXPECT_NO_THROW(runTest());
+}
+
+//! Instantiation of the PME gathering test
+INSTANTIATE_TEST_CASE_P(SaneInput, PmeGatherTest, ::testing::Combine(::testing::ValuesIn(c_sampleBoxes),
+ ::testing::ValuesIn(pmeOrders),
+ ::testing::ValuesIn(c_sampleGridSizes),
+ ::testing::ValuesIn(c_sampleGrids),
+ ::testing::Values(PmeGatherInputHandling::Overwrite, PmeGatherInputHandling::ReduceWith),
+ ::testing::ValuesIn(atomCounts)));
+
+}
+}
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements PME solving tests.
+ *
+ * \author Aleksei Iupinov <a.yupinov@gmail.com>
+ * \ingroup module_ewald
+ */
+
+#include "gmxpre.h"
+
+#include <string>
+
+#include <gmock/gmock.h>
+
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+#include "pmetestcommon.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+/*! \brief Convenience typedef of the test input parameters - unit cell box, complex grid dimensions, complex grid values,
+ * electrostatic constant epsilon_r, Ewald splitting parameters ewaldcoeff_q and ewaldcoeff_lj, solver type
+ * Output: transformed local grid (Fourier space); optionally reciprocal energy and virial matrix.
+ * TODO:
+ * Implement and test Lorentz-Berthelot
+ */
+typedef std::tuple<Matrix3x3, IVec, SparseComplexGridValuesInput, double, double, double, PmeSolveAlgorithm> SolveInputParameters;
+
+//! Test fixture
+class PmeSolveTest : public ::testing::TestWithParam<SolveInputParameters>
+{
+ public:
+ //! Default constructor
+ PmeSolveTest() = default;
+
+ //! The test
+ void runTest()
+ {
+ /* Getting the input */
+ Matrix3x3 box;
+ IVec gridSize;
+ SparseComplexGridValuesInput nonZeroGridValues;
+ double epsilon_r;
+ double ewaldCoeff_q;
+ double ewaldCoeff_lj;
+ PmeSolveAlgorithm method;
+ std::tie(box, gridSize, nonZeroGridValues, epsilon_r, ewaldCoeff_q, ewaldCoeff_lj, method) = GetParam();
+
+ /* Storing the input where it's needed, running the test */
+ t_inputrec inputRec;
+ inputRec.nkx = gridSize[XX];
+ inputRec.nky = gridSize[YY];
+ inputRec.nkz = gridSize[ZZ];
+ inputRec.pme_order = 4;
+ inputRec.coulombtype = eelPME;
+ inputRec.epsilon_r = epsilon_r;
+ switch (method)
+ {
+ case PmeSolveAlgorithm::Coulomb:
+ break;
+
+ case PmeSolveAlgorithm::LennardJones:
+ inputRec.vdwtype = evdwPME;
+ break;
+
+ default:
+ GMX_THROW(InternalError("Unknown PME solver"));
+ }
+
+ TestReferenceData refData;
+ const std::map<CodePath, std::string> modesToTest = {{CodePath::CPU, "CPU"}};
+ for (const auto &mode : modesToTest)
+ {
+ std::map<GridOrdering, std::string> gridOrderingsToTest = {{GridOrdering::YZX, "YZX"}};
+ for (const auto &gridOrdering : gridOrderingsToTest)
+ {
+ for (bool computeEnergyAndVirial : {false, true})
+ {
+ /* Describing the test*/
+ SCOPED_TRACE(formatString("Testing solving (%s, %s, %s energy/virial) with %s for PME grid size %d %d %d, Ewald coefficients %g %g",
+ (method == PmeSolveAlgorithm::LennardJones) ? "Lennard-Jones" : "Coulomb",
+ gridOrdering.second.c_str(), computeEnergyAndVirial ? "with" : "without",
+ mode.second.c_str(),
+ gridSize[XX], gridSize[YY], gridSize[ZZ],
+ ewaldCoeff_q, ewaldCoeff_lj
+ ));
+
+ /* Running the test */
+ PmeSafePointer pmeSafe = pmeInitEmpty(&inputRec, box, ewaldCoeff_q, ewaldCoeff_lj);
+ pmeSetComplexGrid(pmeSafe.get(), mode.first, gridOrdering.first, nonZeroGridValues);
+ const real cellVolume = box[0] * box[4] * box[8];
+ //FIXME - this is box[XX][XX] * box[YY][YY] * box[ZZ][ZZ], should be stored in the PME structure
+ pmePerformSolve(pmeSafe.get(), mode.first, method, cellVolume, gridOrdering.first, computeEnergyAndVirial);
+
+ /* Check the outputs */
+ TestReferenceChecker checker(refData.rootChecker());
+ const auto ulpTolerance = 200;
+ checker.setDefaultTolerance(relativeToleranceAsUlp(10.0, ulpTolerance));
+
+ SparseComplexGridValuesOutput nonZeroGridValuesOutput = pmeGetComplexGrid(pmeSafe.get(), mode.first, gridOrdering.first);
+ /* Transformed grid */
+ TestReferenceChecker gridValuesChecker(checker.checkCompound("NonZeroGridValues", "ComplexSpaceGrid"));
+ const auto ulpToleranceGrid = 50;
+ gridValuesChecker.setDefaultTolerance(relativeToleranceAsUlp(1.0, ulpToleranceGrid));
+ for (const auto &point : nonZeroGridValuesOutput)
+ {
+ // we want an additional safeguard for denormal numbers as they cause an exception in string conversion;
+ // however, using GMX_REAL_MIN causes an "unused item warning" for single precision builds
+ if (fabs(point.second.re) >= GMX_FLOAT_MIN)
+ {
+ gridValuesChecker.checkReal(point.second.re, (point.first + " re").c_str());
+ }
+ if (fabs(point.second.im) >= GMX_FLOAT_MIN)
+ {
+ gridValuesChecker.checkReal(point.second.im, (point.first + " im").c_str());
+ }
+ }
+
+ if (computeEnergyAndVirial)
+ {
+ real energy;
+ Matrix3x3 virial;
+ std::tie(energy, virial) = pmeGetReciprocalEnergyAndVirial(pmeSafe.get(), mode.first, method);
+ /* Energy */
+ checker.checkReal(energy, "Energy");
+ /* Virial */
+ TestReferenceChecker virialChecker(checker.checkCompound("Matrix", "Virial"));
+ virialChecker.setDefaultTolerance(relativeToleranceAsUlp(1000, 30));
+ for (int i = 0; i < DIM; i++)
+ {
+ for (int j = 0; j <= i; j++)
+ {
+ std::string valueId = formatString("Cell %d %d", i, j);
+ virialChecker.checkReal(virial[i * DIM + j], valueId.c_str());
+ }
+ }
+ }
+ }
+ }
+ }
+ }
+};
+
+/*! \brief Test for PME solving */
+TEST_P(PmeSolveTest, ReproducesOutputs)
+{
+ EXPECT_NO_THROW(runTest());
+}
+
+/* Valid input instances */
+
+//! A couple of valid inputs for boxes.
+static std::vector<Matrix3x3> const c_sampleBoxes
+{
+ // normal box
+ Matrix3x3 {{
+ 8.0f, 0.0f, 0.0f,
+ 0.0f, 3.4f, 0.0f,
+ 0.0f, 0.0f, 2.0f
+ }},
+ // triclinic box
+ Matrix3x3 {{
+ 7.0f, 0.0f, 0.0f,
+ 0.0f, 4.1f, 0.0f,
+ 3.5f, 2.0f, 12.2f
+ }},
+};
+
+//! A couple of valid inputs for grid sizes
+static std::vector<IVec> const c_sampleGridSizes
+{
+ IVec {
+ 16, 12, 28
+ },
+ IVec {
+ 9, 7, 23
+ }
+};
+
+//! Moved out from instantiations for readability
+const auto c_inputBoxes = ::testing::ValuesIn(c_sampleBoxes);
+//! Moved out from instantiations for readability
+const auto c_inputGridSizes = ::testing::ValuesIn(c_sampleGridSizes);
+
+//! 2 sample complex grids - only non-zero values have to be listed
+static std::vector<SparseComplexGridValuesInput> const c_sampleGrids
+{
+ SparseComplexGridValuesInput {{
+ IVec {
+ 0, 0, 0
+ }, t_complex {
+ 3.5f, 6.7f
+ }
+ }, {
+ IVec {
+ 7, 0, 0
+ }, t_complex {
+ -2.5f, -0.7f
+ }
+ }, {
+ IVec {
+ 3, 5, 7
+ }, t_complex {
+ -0.006f, 1e-8f
+ }
+ }, {
+ IVec {
+ 3, 1, 2
+ }, t_complex {
+ 0.6f, 7.9f
+ }
+ }, {
+ IVec {
+ 6, 2, 4
+ }, t_complex {
+ 30.1f, 2.45f
+ }
+ }, },
+ SparseComplexGridValuesInput {{
+ IVec {
+ 0, 4, 0
+ }, t_complex {
+ 0.0f, 0.3f
+ }
+ }, {
+ IVec {
+ 4, 2, 7
+ }, t_complex {
+ 13.76f, -40.0f
+ }
+ }, {
+ IVec {
+ 0, 6, 7
+ }, t_complex {
+ 3.6f, 0.0f
+ }
+ }, {
+ IVec {
+ 2, 5, 10
+ }, t_complex {
+ 3.6f, 10.65f
+ }
+ }, }
+};
+
+//! Moved out from instantiations for readability
+const auto c_inputGrids = ::testing::ValuesIn(c_sampleGrids);
+//! Moved out from instantiations for readability
+const auto c_inputEpsilon_r = ::testing::Values(1.2);
+//! Moved out from instantiations for readability
+const auto c_inputEwaldCoeff_q = ::testing::Values(2.0);
+//! Moved out from instantiations for readability
+const auto c_inputEwaldCoeff_lj = ::testing::Values(0.7);
+//! Moved out from instantiations for readability
+const auto c_inputMethods = ::testing::Values(PmeSolveAlgorithm::Coulomb, PmeSolveAlgorithm::LennardJones);
+
+//! Instantiation of the PME solving test
+INSTANTIATE_TEST_CASE_P(SaneInput, PmeSolveTest, ::testing::Combine(c_inputBoxes, c_inputGridSizes, c_inputGrids,
+ c_inputEpsilon_r, c_inputEwaldCoeff_q, c_inputEwaldCoeff_lj, c_inputMethods));
+
+//! A few more instances to check that different ewaldCoeff_q actually affects results of the Coulomb solver
+INSTANTIATE_TEST_CASE_P(DifferentEwaldCoeffQ, PmeSolveTest, ::testing::Combine(c_inputBoxes, c_inputGridSizes, c_inputGrids,
+ c_inputEpsilon_r, ::testing::Values(0.4), c_inputEwaldCoeff_lj,
+ ::testing::Values(PmeSolveAlgorithm::Coulomb)));
+
+//! A few more instances to check that different ewaldCoeff_lj actually affects results of the Lennard-Jones solver.
+//! The value has to be approximately larger than 1 / (box dimensions) to have a meaningful output grid.
+//! Previous value of 0.3 caused one of the grid cells to be less or greater than GMX_FLOAT_MIN, depending on the architecture.
+INSTANTIATE_TEST_CASE_P(DifferentEwaldCoeffLJ, PmeSolveTest, ::testing::Combine(c_inputBoxes, c_inputGridSizes, c_inputGrids,
+ c_inputEpsilon_r, c_inputEwaldCoeff_q, ::testing::Values(2.35),
+ ::testing::Values(PmeSolveAlgorithm::LennardJones)));
+
+//! A few more instances to check that different epsilon_r actually affects results of all solvers
+INSTANTIATE_TEST_CASE_P(DifferentEpsilonR, PmeSolveTest, ::testing::Combine(c_inputBoxes, c_inputGridSizes, c_inputGrids,
+ testing::Values(1.9), c_inputEwaldCoeff_q, c_inputEwaldCoeff_lj,
+ c_inputMethods));
+
+}
+}
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements PME spline computation and charge spreading tests.
+ *
+ * \author Aleksei Iupinov <a.yupinov@gmail.com>
+ * \ingroup module_ewald
+ */
+
+#include "gmxpre.h"
+
+#include <string>
+
+#include <gmock/gmock.h>
+
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+#include "pmetestcommon.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! PME spline and spread code path being tested
+enum class PmeSplineAndSpreadOptions
+{
+ SplineOnly,
+ SpreadOnly,
+ SplineAndSpreadUnified
+};
+
+/*! \brief Convenience typedef of input parameters - unit cell box, PME interpolation order, grid dimensions,
+ * particle coordinates, particle charges
+ * TODO: consider inclusion of local grid offsets/sizes or PME nodes counts to test the PME DD
+ */
+typedef std::tuple<Matrix3x3, int, IVec, CoordinatesVector, ChargesVector> SplineAndSpreadInputParameters;
+
+/*! \brief Test fixture for testing both atom spline parameter computation and charge spreading.
+ * These 2 stages of PME are tightly coupled in the code.
+ */
+class PmeSplineAndSpreadTest : public ::testing::TestWithParam<SplineAndSpreadInputParameters>
+{
+ public:
+ //! Default constructor
+ PmeSplineAndSpreadTest() = default;
+ //! The test
+ void runTest()
+ {
+ /* Getting the input */
+ Matrix3x3 box;
+ int pmeOrder;
+ IVec gridSize;
+ CoordinatesVector coordinates;
+ ChargesVector charges;
+
+ std::tie(box, pmeOrder, gridSize, coordinates, charges) = GetParam();
+ const size_t atomCount = coordinates.size();
+
+ /* Storing the input where it's needed */
+ t_inputrec inputRec;
+ inputRec.nkx = gridSize[XX];
+ inputRec.nky = gridSize[YY];
+ inputRec.nkz = gridSize[ZZ];
+ inputRec.pme_order = pmeOrder;
+ inputRec.coulombtype = eelPME;
+
+ TestReferenceData refData;
+
+ const std::map<CodePath, std::string> modesToTest = {{CodePath::CPU, "CPU"}};
+ const std::map<PmeSplineAndSpreadOptions, std::string> optionsToTest = {{PmeSplineAndSpreadOptions::SplineAndSpreadUnified, "spline computation and charge spreading (fused)"},
+ {PmeSplineAndSpreadOptions::SplineOnly, "spline computation"},
+ {PmeSplineAndSpreadOptions::SpreadOnly, "charge spreading"}};
+ for (const auto &mode : modesToTest)
+ {
+ for (const auto &option : optionsToTest)
+ {
+ /* Describing the test uniquely in case it fails */
+
+ SCOPED_TRACE(formatString("Testing %s with %s for PME grid size %d %d %d"
+ ", order %d, %zu atoms",
+ option.second.c_str(), mode.second.c_str(),
+ gridSize[XX], gridSize[YY], gridSize[ZZ],
+ pmeOrder,
+ atomCount));
+
+ /* Running the test */
+
+ PmeSafePointer pmeSafe = pmeInitAtoms(&inputRec, coordinates, charges, box);
+
+ const bool computeSplines = (option.first == PmeSplineAndSpreadOptions::SplineOnly) || (option.first == PmeSplineAndSpreadOptions::SplineAndSpreadUnified);
+ const bool spreadCharges = (option.first == PmeSplineAndSpreadOptions::SpreadOnly) || (option.first == PmeSplineAndSpreadOptions::SplineAndSpreadUnified);
+
+ if (!computeSplines)
+ {
+ // Here we should set up the results of the spline computation so that the spread can run.
+ // What is lazy and works is running the separate spline so that it will set it up for us:
+ pmePerformSplineAndSpread(pmeSafe.get(), mode.first, true, false);
+ // We know that it is tested in another iteration.
+ // TODO: Clean alternative: read and set the reference gridline indices, spline params
+ }
+
+ pmePerformSplineAndSpread(pmeSafe.get(), mode.first, computeSplines, spreadCharges);
+
+ /* Outputs correctness check */
+ /* All tolerances were picked empirically for single precision on CPU */
+
+ TestReferenceChecker rootChecker(refData.rootChecker());
+
+ const auto maxGridSize = std::max(std::max(gridSize[XX], gridSize[YY]), gridSize[ZZ]);
+ const auto ulpToleranceSplineValues = 2 * (pmeOrder - 2) * maxGridSize;
+ /* 2 is empiric, the rest follows from the amount of operations */
+
+ if (computeSplines)
+ {
+ const char *dimString[] = { "X", "Y", "Z" };
+
+ /* Spline values */
+ SCOPED_TRACE(formatString("Testing spline values with tolerance of %ld", ulpToleranceSplineValues));
+ TestReferenceChecker splineValuesChecker(rootChecker.checkCompound("Splines", "Values"));
+ splineValuesChecker.setDefaultTolerance(relativeToleranceAsUlp(1.0, ulpToleranceSplineValues));
+ for (int i = 0; i < DIM; i++)
+ {
+ auto splineValuesDim = pmeGetSplineData(pmeSafe.get(), mode.first, PmeSplineDataType::Values, i);
+ splineValuesChecker.checkSequence(splineValuesDim.begin(), splineValuesDim.end(), dimString[i]);
+ }
+
+ /* Spline derivatives */
+ const auto ulpToleranceSplineDerivatives = 4 * ulpToleranceSplineValues;
+ /* 4 is just a wild guess since the derivatives are deltas of neighbor spline values which could differ greatly */
+ SCOPED_TRACE(formatString("Testing spline derivatives with tolerance of %ld", ulpToleranceSplineDerivatives));
+ TestReferenceChecker splineDerivativesChecker(rootChecker.checkCompound("Splines", "Derivatives"));
+ splineDerivativesChecker.setDefaultTolerance(relativeToleranceAsUlp(1.0, ulpToleranceSplineDerivatives));
+ for (int i = 0; i < DIM; i++)
+ {
+ auto splineDerivativesDim = pmeGetSplineData(pmeSafe.get(), mode.first, PmeSplineDataType::Derivatives, i);
+ splineDerivativesChecker.checkSequence(splineDerivativesDim.begin(), splineDerivativesDim.end(), dimString[i]);
+ }
+
+ /* Particle gridline indices */
+ auto gridLineIndices = pmeGetGridlineIndices(pmeSafe.get(), mode.first);
+ rootChecker.checkSequence(gridLineIndices.begin(), gridLineIndices.end(), "Gridline indices");
+ }
+
+ if (spreadCharges)
+ {
+ /* The wrapped grid */
+ SparseRealGridValuesOutput nonZeroGridValues = pmeGetRealGrid(pmeSafe.get(), mode.first);
+ TestReferenceChecker gridValuesChecker(rootChecker.checkCompound("NonZeroGridValues", "RealSpaceGrid"));
+ const auto ulpToleranceGrid = 2 * ulpToleranceSplineValues * (int)(ceil(sqrt(atomCount)));
+ /* 2 is empiric; sqrt(atomCount) assumes all the input charges may spread onto the same cell */
+ SCOPED_TRACE(formatString("Testing grid values with tolerance of %ld", ulpToleranceGrid));
+ gridValuesChecker.setDefaultTolerance(relativeToleranceAsUlp(1.0, ulpToleranceGrid));
+ for (const auto &point : nonZeroGridValues)
+ {
+ gridValuesChecker.checkReal(point.second, point.first.c_str());
+ }
+ }
+ }
+ }
+ }
+};
+
+
+/*! \brief Test for PME B-spline moduli computation */
+TEST_P(PmeSplineAndSpreadTest, ReproducesOutputs)
+{
+ EXPECT_NO_THROW(runTest());
+}
+
+/* Valid input instances */
+
+//! A couple of valid inputs for boxes.
+static std::vector<Matrix3x3> const sampleBoxes
+{
+ // normal box
+ Matrix3x3 {{
+ 8.0f, 0.0f, 0.0f,
+ 0.0f, 3.4f, 0.0f,
+ 0.0f, 0.0f, 2.0f
+ }},
+ // triclinic box
+ Matrix3x3 {{
+ 7.0f, 0.0f, 0.0f,
+ 0.0f, 4.1f, 0.0f,
+ 3.5f, 2.0f, 12.2f
+ }},
+};
+
+//! A couple of valid inputs for grid sizes.
+static std::vector<IVec> const sampleGridSizes
+{
+ IVec {
+ 16, 12, 14
+ },
+ IVec {
+ 19, 17, 11
+ }
+};
+
+//! Random charges
+static std::vector<real> const sampleChargesFull
+{
+ 4.95f, 3.11f, 3.97f, 1.08f, 2.09f, 1.1f, 4.13f, 3.31f, 2.8f, 5.83f, 5.09f, 6.1f, 2.86f, 0.24f, 5.76f, 5.19f, 0.72f
+};
+//! 1 charge
+static auto const sampleCharges1 = ChargesVector::fromVector(sampleChargesFull.begin(), sampleChargesFull.begin() + 1);
+//! 2 charges
+static auto const sampleCharges2 = ChargesVector::fromVector(sampleChargesFull.begin() + 1, sampleChargesFull.begin() + 3);
+//! 13 charges
+static auto const sampleCharges13 = ChargesVector::fromVector(sampleChargesFull.begin() + 3, sampleChargesFull.begin() + 16);
+
+//! Random coordinate vectors
+static CoordinatesVector const sampleCoordinatesFull
+{
+ {
+ 5.59f, 1.37f, 0.95f
+ }, {
+ 16.0f, 1.02f, 0.22f // 2 box lengths in x
+ }, {
+ 0.034f, 1.65f, 0.22f
+ }, {
+ 0.33f, 0.92f, 1.56f
+ }, {
+ 1.16f, 0.75f, 0.39f
+ }, {
+ 0.5f, 1.63f, 1.14f
+ }, {
+ 16.0001f, 1.52f, 1.19f // > 2 box lengths in x
+ }, {
+ 1.43f, 1.1f, 4.1f // > 2 box lengths in z
+ }, {
+ -1.08f, 1.19f, 0.08f // negative x
+ }, {
+ 1.6f, 0.93f, 0.53f
+ }, {
+ 1.32f, -1.48f, 0.16f // negative y
+ }, {
+ 0.87f, 0.0f, 0.33f
+ }, {
+ 0.95f, 7.7f, -0.48f // > 2 box lengths in y, negative z
+ }, {
+ 1.23f, 0.91f, 0.68f
+ }, {
+ 0.19f, 1.45f, 0.94f
+ }, {
+ 1.28f, 0.46f, 0.38f
+ }, {
+ 1.21f, 0.23f, 1.0f
+ }
+};
+//! 1 coordinate vector
+static CoordinatesVector const sampleCoordinates1(sampleCoordinatesFull.begin(), sampleCoordinatesFull.begin() + 1);
+//! 2 coordinate vectors
+static CoordinatesVector const sampleCoordinates2(sampleCoordinatesFull.begin() + 1, sampleCoordinatesFull.begin() + 3);
+//! 13 coordinate vectors
+static CoordinatesVector const sampleCoordinates13(sampleCoordinatesFull.begin() + 3, sampleCoordinatesFull.begin() + 16);
+
+//! moved out from instantiantions for readability
+auto inputBoxes = ::testing::ValuesIn(sampleBoxes);
+//! moved out from instantiantions for readability
+auto inputPmeOrders = ::testing::Range(3, 5 + 1);
+//! moved out from instantiantions for readability
+auto inputGridSizes = ::testing::ValuesIn(sampleGridSizes);
+
+/*! \brief Instantiation of the PME spline computation test with valid input and 1 atom */
+INSTANTIATE_TEST_CASE_P(SaneInput1, PmeSplineAndSpreadTest, ::testing::Combine(inputBoxes, inputPmeOrders, inputGridSizes,
+ ::testing::Values(sampleCoordinates1),
+ ::testing::Values(sampleCharges1)
+ ));
+/*! \brief Instantiation of the PME spline computation test with valid input and 2 atoms */
+INSTANTIATE_TEST_CASE_P(SaneInput2, PmeSplineAndSpreadTest, ::testing::Combine(inputBoxes, inputPmeOrders, inputGridSizes,
+ ::testing::Values(sampleCoordinates2),
+ ::testing::Values(sampleCharges2)
+ ));
+/*! \brief Instantiation of the PME spline computation test with valid input and 13 atoms */
+INSTANTIATE_TEST_CASE_P(SaneInput13, PmeSplineAndSpreadTest, ::testing::Combine(inputBoxes, inputPmeOrders, inputGridSizes,
+ ::testing::Values(sampleCoordinates13),
+ ::testing::Values(sampleCharges13)
+ ));
+}
+}
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements common routines for PME tests.
+ *
+ * \author Aleksei Iupinov <a.yupinov@gmail.com>
+ * \ingroup module_ewald
+ */
+#include "gmxpre.h"
+
+#include "pmetestcommon.h"
+
+#include <cstring>
+
+#include "gromacs/ewald/pme.h"
+#include "gromacs/ewald/pme-gather.h"
+#include "gromacs/ewald/pme-grid.h"
+#include "gromacs/ewald/pme-internal.h"
+#include "gromacs/ewald/pme-solve.h"
+#include "gromacs/ewald/pme-spread.h"
+#include "gromacs/fft/parallel_3dfft.h"
+#include "gromacs/math/invertmatrix.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+namespace test
+{
+
+//! PME initialization - internal
+static PmeSafePointer pmeInitInternal(const t_inputrec *inputRec,
+ size_t atomCount,
+ const Matrix3x3 &box,
+ real ewaldCoeff_q = 1.0f,
+ real ewaldCoeff_lj = 1.0f
+ )
+{
+ gmx_pme_t *pmeDataRaw = nullptr;
+ gmx_pme_init(&pmeDataRaw, nullptr, 1, 1, inputRec,
+ atomCount, false, false, true, ewaldCoeff_q, ewaldCoeff_lj, 1);
+ PmeSafePointer pme(pmeDataRaw); // taking ownership
+
+ // TODO get rid of this with proper matrix type
+ matrix boxTemp;
+ for (int i = 0; i < DIM; i++)
+ {
+ for (int j = 0; j < DIM; j++)
+ {
+ boxTemp[i][j] = box[i * DIM + j];
+ }
+ }
+ const char *boxError = check_box(-1, boxTemp);
+ GMX_RELEASE_ASSERT(boxError == nullptr, boxError);
+ invertBoxMatrix(boxTemp, pme->recipbox);
+
+ return pme;
+}
+
+//! Simple PME initialization based on input, no atom data
+PmeSafePointer pmeInitEmpty(const t_inputrec *inputRec,
+ const Matrix3x3 &box,
+ real ewaldCoeff_q,
+ real ewaldCoeff_lj
+ )
+{
+ return pmeInitInternal(inputRec, 0, box, ewaldCoeff_q, ewaldCoeff_lj);
+ // hiding the fact that PME actually needs to know the number of atoms in advance
+}
+
+//! PME initialization with atom data
+PmeSafePointer pmeInitAtoms(const t_inputrec *inputRec,
+ const CoordinatesVector &coordinates,
+ const ChargesVector &charges,
+ const Matrix3x3 &box
+ )
+{
+ const size_t atomCount = coordinates.size();
+ GMX_RELEASE_ASSERT(atomCount == charges.size(), "Mismatch in atom data");
+ PmeSafePointer pmeSafe = pmeInitInternal(inputRec, atomCount, box);
+ pme_atomcomm_t *atc = &(pmeSafe->atc[0]);
+ atc->x = const_cast<rvec *>(as_rvec_array(coordinates.data()));
+ atc->coefficient = const_cast<real *>(charges.data());
+ /* With decomposition there would be more boilerplate atc code here, e.g. do_redist_pos_coeffs */
+ return pmeSafe;
+}
+
+//! Getting local PME real grid pointer for test I/O
+static real *pmeGetRealGridInternal(const gmx_pme_t *pme)
+{
+ const size_t gridIndex = 0;
+ return pme->fftgrid[gridIndex];
+}
+
+//! Getting local PME real grid dimensions
+static void pmeGetRealGridSizesInternal(const gmx_pme_t *pme,
+ IVec &gridSize,
+ IVec &paddedGridSize)
+{
+ const size_t gridIndex = 0;
+ IVec gridOffsetUnused;
+ gmx_parallel_3dfft_real_limits(pme->pfft_setup[gridIndex], gridSize, gridOffsetUnused, paddedGridSize);
+}
+
+//! Getting local PME complex grid pointer for test I/O
+static t_complex *pmeGetComplexGridInternal(const gmx_pme_t *pme)
+{
+ const size_t gridIndex = 0;
+ return pme->cfftgrid[gridIndex];
+}
+
+//! Getting local PME complex grid dimensions
+static void pmeGetComplexGridSizesInternal(const gmx_pme_t *pme,
+ IVec &gridSize,
+ IVec &paddedGridSize)
+{
+ const size_t gridIndex = 0;
+ IVec gridOffsetUnused, complexOrderUnused;
+ gmx_parallel_3dfft_complex_limits(pme->pfft_setup[gridIndex], complexOrderUnused, gridSize, gridOffsetUnused, paddedGridSize); //TODO: what about YZX ordering?
+}
+
+//! Getting the PME grid memory buffer and its sizes - template definition
+template<typename ValueType> static void pmeGetGridAndSizesInternal(const gmx_pme_t *, ValueType * &, IVec &, IVec &)
+{
+ GMX_THROW(InternalError("Deleted function call"));
+ // explicitly deleting general template does not compile in clang/icc, see https://llvm.org/bugs/show_bug.cgi?id=17537
+}
+
+//! Getting the PME real grid memory buffer and its sizes
+template<> void pmeGetGridAndSizesInternal<real>(const gmx_pme_t *pme, real * &grid, IVec &gridSize, IVec &paddedGridSize)
+{
+ grid = pmeGetRealGridInternal(pme);
+ pmeGetRealGridSizesInternal(pme, gridSize, paddedGridSize);
+}
+
+//! Getting the PME complex grid memory buffer and its sizes
+template<> void pmeGetGridAndSizesInternal<t_complex>(const gmx_pme_t *pme, t_complex * &grid, IVec &gridSize, IVec &paddedGridSize)
+{
+ grid = pmeGetComplexGridInternal(pme);
+ pmeGetComplexGridSizesInternal(pme, gridSize, paddedGridSize);
+}
+
+//! PME spline calculation and charge spreading
+void pmePerformSplineAndSpread(gmx_pme_t *pme, CodePath mode, // TODO const qualifiers
+ bool computeSplines, bool spreadCharges)
+{
+ GMX_RELEASE_ASSERT(pme != nullptr, "PME data is not initialized");
+ pme_atomcomm_t *atc = &(pme->atc[0]);
+ const size_t gridIndex = 0;
+ const bool computeSplinesForZeroCharges = true;
+ real *fftgrid = spreadCharges ? pme->fftgrid[gridIndex] : nullptr;
+
+ switch (mode)
+ {
+ case CodePath::CPU:
+ spread_on_grid(pme, atc, &pme->pmegrid[gridIndex], computeSplines, spreadCharges,
+ fftgrid, computeSplinesForZeroCharges, gridIndex);
+ if (spreadCharges && !pme->bUseThreads)
+ {
+ wrap_periodic_pmegrid(pme, pme->pmegrid[gridIndex].grid.grid);
+ copy_pmegrid_to_fftgrid(pme, pme->pmegrid[gridIndex].grid.grid, fftgrid, gridIndex);
+ }
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+}
+
+//! Getting the internal spline data buffer pointer
+static real *pmeGetSplineDataInternal(const gmx_pme_t *pme, PmeSplineDataType type, int dimIndex)
+{
+ GMX_ASSERT((0 <= dimIndex) && (dimIndex < DIM), "Invalid dimension index");
+ const pme_atomcomm_t *atc = &(pme->atc[0]);
+ const size_t threadIndex = 0;
+ real *splineBuffer = nullptr;
+ switch (type)
+ {
+ case PmeSplineDataType::Values:
+ splineBuffer = atc->spline[threadIndex].theta[dimIndex];
+ break;
+
+ case PmeSplineDataType::Derivatives:
+ splineBuffer = atc->spline[threadIndex].dtheta[dimIndex];
+ break;
+
+ default:
+ GMX_THROW(InternalError("Unknown spline data type"));
+ }
+ return splineBuffer;
+}
+
+//! PME solving
+void pmePerformSolve(const gmx_pme_t *pme, CodePath mode,
+ PmeSolveAlgorithm method, real cellVolume,
+ GridOrdering gridOrdering, bool computeEnergyAndVirial)
+{
+ t_complex *h_grid = pmeGetComplexGridInternal(pme);
+ const bool useLorentzBerthelot = false;
+ const size_t threadIndex = 0;
+ switch (mode)
+ {
+ case CodePath::CPU:
+ if (gridOrdering != GridOrdering::YZX)
+ {
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ switch (method)
+ {
+ case PmeSolveAlgorithm::Coulomb:
+ solve_pme_yzx(pme, h_grid, cellVolume,
+ computeEnergyAndVirial, pme->nthread, threadIndex);
+ break;
+
+ case PmeSolveAlgorithm::LennardJones:
+ solve_pme_lj_yzx(pme, &h_grid, useLorentzBerthelot,
+ cellVolume, computeEnergyAndVirial, pme->nthread, threadIndex);
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+}
+
+//! PME force gathering
+void pmePerformGather(gmx_pme_t *pme, CodePath mode,
+ PmeGatherInputHandling inputTreatment, ForcesVector &forces)
+{
+ pme_atomcomm_t *atc = &(pme->atc[0]);
+ const size_t atomCount = atc->n;
+ GMX_RELEASE_ASSERT(forces.size() == atomCount, "Invalid force buffer size");
+ const bool forceReductionWithInput = (inputTreatment == PmeGatherInputHandling::ReduceWith);
+ const real scale = 1.0;
+ const size_t threadIndex = 0;
+ const size_t gridIndex = 0;
+ real *grid = pme->pmegrid[gridIndex].grid.grid;
+ switch (mode)
+ {
+ case CodePath::CPU:
+ atc->f = as_rvec_array(forces.begin());
+ if (atc->nthread == 1)
+ {
+ // something which is normally done in serial spline computation (make_thread_local_ind())
+ atc->spline[threadIndex].n = atomCount;
+ }
+ copy_fftgrid_to_pmegrid(pme, pme->fftgrid[gridIndex], grid, gridIndex, pme->nthread, threadIndex);
+ unwrap_periodic_pmegrid(pme, grid);
+ gather_f_bsplines(pme, grid, !forceReductionWithInput, atc, &atc->spline[threadIndex], scale);
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+}
+
+//! Setting atom spline values/derivatives to be used in spread/gather
+void pmeSetSplineData(const gmx_pme_t *pme, CodePath mode,
+ const SplineParamsDimVector &splineValues, PmeSplineDataType type, int dimIndex)
+{
+ const pme_atomcomm_t *atc = &(pme->atc[0]);
+ const size_t atomCount = atc->n;
+ const size_t pmeOrder = pme->pme_order;
+ const size_t dimSize = pmeOrder * atomCount;
+ GMX_RELEASE_ASSERT(dimSize == splineValues.size(), "Mismatch in spline data");
+ real *splineBuffer = pmeGetSplineDataInternal(pme, type, dimIndex);
+
+ switch (mode)
+ {
+ case CodePath::CPU:
+ std::copy(splineValues.begin(), splineValues.end(), splineBuffer);
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+}
+
+//! Setting gridline indices to be used in spread/gather
+void pmeSetGridLineIndices(const gmx_pme_t *pme, CodePath mode,
+ const GridLineIndicesVector &gridLineIndices)
+{
+ const pme_atomcomm_t *atc = &(pme->atc[0]);
+ const size_t atomCount = atc->n;
+ GMX_RELEASE_ASSERT(atomCount == gridLineIndices.size(), "Mismatch in gridline indices size");
+
+ IVec paddedGridSizeUnused, gridSize;
+ pmeGetRealGridSizesInternal(pme, gridSize, paddedGridSizeUnused);
+
+ for (const auto &index : gridLineIndices)
+ {
+ for (int i = 0; i < DIM; i++)
+ {
+ GMX_RELEASE_ASSERT((0 <= index[i]) && (index[i] < gridSize[i]), "Invalid gridline index");
+ }
+ }
+
+ switch (mode)
+ {
+ case CodePath::CPU:
+ // incompatible IVec and ivec assignment?
+ //std::copy(gridLineIndices.begin(), gridLineIndices.end(), atc->idx);
+ memcpy(atc->idx, gridLineIndices.data(), atomCount * sizeof(gridLineIndices[0]));
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+}
+
+//! Getting plain index into the complex 3d grid
+inline size_t pmeGetGridPlainIndexInternal(const IVec &index, const IVec &paddedGridSize, GridOrdering gridOrdering)
+{
+ size_t result;
+ switch (gridOrdering)
+ {
+ case GridOrdering::YZX:
+ result = (index[YY] * paddedGridSize[ZZ] + index[ZZ]) * paddedGridSize[XX] + index[XX];
+ break;
+
+ case GridOrdering::XYZ:
+ result = (index[XX] * paddedGridSize[YY] + index[YY]) * paddedGridSize[ZZ] + index[ZZ];
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ return result;
+}
+
+//! Setting real or complex grid
+template<typename ValueType>
+static void pmeSetGridInternal(const gmx_pme_t *pme, CodePath mode,
+ GridOrdering gridOrdering,
+ const SparseGridValuesInput<ValueType> &gridValues)
+{
+ IVec gridSize, paddedGridSize;
+ ValueType *grid;
+ pmeGetGridAndSizesInternal<ValueType>(pme, grid, gridSize, paddedGridSize);
+
+ switch (mode)
+ {
+ case CodePath::CPU:
+ std::memset(grid, 0, paddedGridSize[XX] * paddedGridSize[YY] * paddedGridSize[ZZ] * sizeof(ValueType));
+ for (const auto &gridValue : gridValues)
+ {
+ for (int i = 0; i < DIM; i++)
+ {
+ GMX_RELEASE_ASSERT((0 <= gridValue.first[i]) && (gridValue.first[i] < gridSize[i]), "Invalid grid value index");
+ }
+ const size_t gridValueIndex = pmeGetGridPlainIndexInternal(gridValue.first, paddedGridSize, gridOrdering);
+ grid[gridValueIndex] = gridValue.second;
+ }
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+}
+
+//! Setting real grid to be used in gather
+void pmeSetRealGrid(const gmx_pme_t *pme, CodePath mode,
+ const SparseRealGridValuesInput &gridValues)
+{
+ pmeSetGridInternal<real>(pme, mode, GridOrdering::XYZ, gridValues);
+}
+
+//! Setting complex grid to be used in solve
+void pmeSetComplexGrid(const gmx_pme_t *pme, CodePath mode,
+ GridOrdering gridOrdering,
+ const SparseComplexGridValuesInput &gridValues)
+{
+ pmeSetGridInternal<t_complex>(pme, mode, gridOrdering, gridValues);
+}
+
+//! Getting the single dimension's spline values or derivatives
+SplineParamsDimVector pmeGetSplineData(const gmx_pme_t *pme, CodePath mode,
+ PmeSplineDataType type, int dimIndex)
+{
+ GMX_RELEASE_ASSERT(pme != nullptr, "PME data is not initialized");
+ const pme_atomcomm_t *atc = &(pme->atc[0]);
+ const size_t atomCount = atc->n;
+ const size_t pmeOrder = pme->pme_order;
+ const size_t dimSize = pmeOrder * atomCount;
+
+ real *sourceBuffer = pmeGetSplineDataInternal(pme, type, dimIndex);
+ SplineParamsDimVector result;
+ switch (mode)
+ {
+ case CodePath::CPU:
+ result = SplineParamsDimVector::fromArray(sourceBuffer, dimSize);
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ return result;
+}
+
+//! Getting the gridline indices
+GridLineIndicesVector pmeGetGridlineIndices(const gmx_pme_t *pme, CodePath mode)
+{
+ GMX_RELEASE_ASSERT(pme != nullptr, "PME data is not initialized");
+ const pme_atomcomm_t *atc = &(pme->atc[0]);
+ const size_t atomCount = atc->n;
+
+ GridLineIndicesVector gridLineIndices;
+ switch (mode)
+ {
+ case CodePath::CPU:
+ gridLineIndices = GridLineIndicesVector::fromArray(reinterpret_cast<IVec *>(atc->idx), atomCount);
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ return gridLineIndices;
+}
+
+//! Getting real or complex grid - only non zero values
+template<typename ValueType>
+static SparseGridValuesOutput<ValueType> pmeGetGridInternal(const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering)
+{
+ IVec gridSize, paddedGridSize;
+ ValueType *grid;
+ pmeGetGridAndSizesInternal<ValueType>(pme, grid, gridSize, paddedGridSize);
+ SparseGridValuesOutput<ValueType> gridValues;
+ switch (mode)
+ {
+ case CodePath::CPU:
+ gridValues.clear();
+ for (int ix = 0; ix < gridSize[XX]; ix++)
+ {
+ for (int iy = 0; iy < gridSize[YY]; iy++)
+ {
+ for (int iz = 0; iz < gridSize[ZZ]; iz++)
+ {
+ IVec temp(ix, iy, iz);
+ const size_t gridValueIndex = pmeGetGridPlainIndexInternal(temp, paddedGridSize, gridOrdering);
+ const ValueType value = grid[gridValueIndex];
+ if (value != ValueType {})
+ {
+ auto key = formatString("Cell %d %d %d", ix, iy, iz);
+ gridValues[key] = value;
+ }
+ }
+ }
+ }
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ return gridValues;
+}
+
+//! Getting the real grid (spreading output of pmePerformSplineAndSpread())
+SparseRealGridValuesOutput pmeGetRealGrid(const gmx_pme_t *pme, CodePath mode)
+{
+ return pmeGetGridInternal<real>(pme, mode, GridOrdering::XYZ);
+}
+
+//! Getting the complex grid output of pmePerformSolve()
+SparseComplexGridValuesOutput pmeGetComplexGrid(const gmx_pme_t *pme, CodePath mode,
+ GridOrdering gridOrdering)
+{
+ return pmeGetGridInternal<t_complex>(pme, mode, gridOrdering);
+}
+
+//! Getting the reciprocal energy and virial
+PmeSolveOutput pmeGetReciprocalEnergyAndVirial(const gmx_pme_t *pme, CodePath mode,
+ PmeSolveAlgorithm method)
+{
+ real energy = 0.0f;
+ Matrix3x3 virial;
+ matrix virialTemp; //TODO get rid of
+ switch (mode)
+ {
+ case CodePath::CPU:
+ switch (method)
+ {
+ case PmeSolveAlgorithm::Coulomb:
+ get_pme_ener_vir_q(pme->solve_work, pme->nthread, &energy, virialTemp);
+ break;
+
+ case PmeSolveAlgorithm::LennardJones:
+ get_pme_ener_vir_lj(pme->solve_work, pme->nthread, &energy, virialTemp);
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ break;
+
+ default:
+ GMX_THROW(InternalError("Test not implemented for this mode"));
+ }
+ for (int i = 0; i < DIM; i++)
+ {
+ for (int j = 0; j < DIM; j++)
+ {
+ virial[i * DIM + j] = virialTemp[i][j];
+ }
+ }
+ return std::make_tuple(energy, virial);
+}
+
+}
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Describes common routines and types for PME tests.
+ *
+ * \author Aleksei Iupinov <a.yupinov@gmail.com>
+ * \ingroup module_ewald
+ */
+#ifndef GMX_EWALD_PME_TEST_COMMON_H
+#define GMX_EWALD_PME_TEST_COMMON_H
+
+#include <array>
+#include <map>
+#include <vector>
+
+#include "gromacs/ewald/pme.h"
+#include "gromacs/math/gmxcomplex.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/unique_cptr.h"
+
+struct t_inputrec;
+
+namespace gmx
+{
+namespace test
+{
+
+// Convenience typedefs
+//! A safe pointer type for PME.
+typedef gmx::unique_cptr<gmx_pme_t, gmx_pme_destroy> PmeSafePointer;
+//! Charges
+typedef ConstArrayRef<real> ChargesVector;
+//! Coordinates
+typedef std::vector<RVec> CoordinatesVector;
+//! Forces
+typedef ArrayRef<RVec> ForcesVector;
+//! Gridline indices
+typedef ConstArrayRef<IVec> GridLineIndicesVector;
+//! Type of spline data
+enum class PmeSplineDataType
+{
+ Values, // theta
+ Derivatives, // dtheta
+};
+/*! \brief Spline parameters (theta or dtheta).
+ * A reference to a single dimension's spline data; this means (atomCount * pmeOrder) values or derivatives.
+ */
+typedef ConstArrayRef<real> SplineParamsDimVector;
+/*! \brief Spline parameters (theta or dtheta) in all 3 dimensions
+ */
+typedef std::array<SplineParamsDimVector, DIM> SplineParamsVector;
+
+//! Non-zero grid values for test input; keys are 3d indices (IVec)
+template<typename ValueType>using SparseGridValuesInput = std::map<IVec, ValueType>;
+//! Non-zero real grid values
+typedef SparseGridValuesInput<real> SparseRealGridValuesInput;
+//! Non-zero complex grid values
+typedef SparseGridValuesInput<t_complex> SparseComplexGridValuesInput;
+//! Non-zero grid values for test output; keys are string representations of the cells' 3d indices (IVec); this allows for better sorting.
+template<typename ValueType>using SparseGridValuesOutput = std::map<std::string, ValueType>;
+//! Non-zero real grid values
+typedef SparseGridValuesOutput<real> SparseRealGridValuesOutput;
+//! Non-zero complex grid values
+typedef SparseGridValuesOutput<t_complex> SparseComplexGridValuesOutput;
+//! TODO: make proper C++ matrix for the whole Gromacs, get rid of this
+typedef std::array<real, DIM * DIM> Matrix3x3;
+//! PME code path being tested
+enum class CodePath
+{
+ CPU, // serial CPU code
+};
+//! PME gathering input forces treatment
+enum class PmeGatherInputHandling
+{
+ Overwrite,
+ ReduceWith,
+};
+//! PME solver type
+enum class PmeSolveAlgorithm
+{
+ Coulomb,
+ LennardJones,
+};
+//! PME grid dimension ordering (from major to minor)
+enum class GridOrdering
+{
+ YZX,
+ XYZ
+};
+//! PME solver results - reciprocal energy and virial
+typedef std::tuple<real, Matrix3x3> PmeSolveOutput;
+
+// PME stages
+
+//! Simple PME initialization (no atom data)
+PmeSafePointer pmeInitEmpty(const t_inputrec *inputRec,
+ const Matrix3x3 &box = {{1.0f, 0.0f, 0.0f, 0.0f, 1.0f, 0.0f, 0.0f, 0.0f, 1.0f}},
+ real ewaldCoeff_q = 0.0f, real ewaldCoeff_lj = 0.0f);
+//! PME initialization with atom data and system box; lacks Ewald coefficients
+PmeSafePointer pmeInitAtoms(const t_inputrec *inputRec,
+ const CoordinatesVector &coordinates,
+ const ChargesVector &charges,
+ const Matrix3x3 &box
+ );
+//! PME spline computation and charge spreading
+void pmePerformSplineAndSpread(gmx_pme_t *pme, CodePath mode,
+ bool computeSplines, bool spreadCharges);
+//! PME solving
+void pmePerformSolve(const gmx_pme_t *pme, CodePath mode,
+ PmeSolveAlgorithm method, real cellVolume,
+ GridOrdering gridOrdering, bool computeEnergyAndVirial);
+//! PME force gathering
+void pmePerformGather(gmx_pme_t *pme, CodePath mode,
+ PmeGatherInputHandling inputTreatment, ForcesVector &forces);
+
+// PME state setters
+
+//! Setting atom spline values or derivatives to be used in spread/gather
+void pmeSetSplineData(const gmx_pme_t *pme, CodePath mode,
+ const SplineParamsDimVector &splineValues, PmeSplineDataType type, int dimIndex);
+//! Setting gridline indices be used in spread/gather
+void pmeSetGridLineIndices(const gmx_pme_t *pme, CodePath mode,
+ const GridLineIndicesVector &gridLineIndices);
+//! Setting real grid to be used in gather
+void pmeSetRealGrid(const gmx_pme_t *pme, CodePath mode,
+ const SparseRealGridValuesInput &gridValues);
+void pmeSetComplexGrid(const gmx_pme_t *pme, CodePath mode, GridOrdering gridOrdering,
+ const SparseComplexGridValuesInput &gridValues);
+
+// PME state getters
+
+//! Getting the single dimension's spline values or derivatives
+SplineParamsDimVector pmeGetSplineData(const gmx_pme_t *pme, CodePath mode,
+ PmeSplineDataType type, int dimIndex);
+//! Getting the gridline indices
+GridLineIndicesVector pmeGetGridlineIndices(const gmx_pme_t *pme, CodePath mode);
+//! Getting the real grid (spreading output of pmePerformSplineAndSpread())
+SparseRealGridValuesOutput pmeGetRealGrid(const gmx_pme_t *pme, CodePath mode);
+//! Getting the complex grid output of pmePerformSolve()
+SparseComplexGridValuesOutput pmeGetComplexGrid(const gmx_pme_t *pme, CodePath mode,
+ GridOrdering gridOrdering);
+//! Getting the reciprocal energy and virial
+PmeSolveOutput pmeGetReciprocalEnergyAndVirial(const gmx_pme_t *pme, CodePath mode,
+ PmeSolveAlgorithm method);
+}
+}
+
+#endif
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.018817131631578641</Real>
+ <Real Name="Cell 3 1 2 im">0.24775889296163411</Real>
+ <Real Name="Cell 3 5 7 re">-1.119109555041644e-18</Real>
+ <Real Name="Cell 3 5 7 im">1.8651825641876716e-24</Real>
+ <Real Name="Cell 6 2 4 re">0.00014622573978042473</Real>
+ <Real Name="Cell 6 2 4 im">1.1902095179213895e-05</Real>
+ <Real Name="Cell 7 0 0 re">-1.6418289569939666</Real>
+ <Real Name="Cell 7 0 0 im">-0.45971210012946007</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">4.18620154095722</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">5.2163287107129568</Real>
+ <Real Name="Cell 1 0">0.71788757122964064</Real>
+ <Real Name="Cell 1 1">-1.5300517107974831</Real>
+ <Real Name="Cell 2 0">2.4408178106438716</Real>
+ <Real Name="Cell 2 1">1.9143668566123748</Real>
+ <Real Name="Cell 2 2">4.4157467245717141</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.040960646891504318</Real>
+ <Real Name="Cell 0 0 0 im">-0.078410378960130159</Real>
+ <Real Name="Cell 3 1 2 re">-1.3292554554983258e-14</Real>
+ <Real Name="Cell 3 1 2 im">-1.7501863013212537e-13</Real>
+ <Real Name="Cell 7 0 0 re">3.8478547590276771e-09</Real>
+ <Real Name="Cell 7 0 0 im">1.0773993141797484e-09</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.33435589928707093</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.16717786512572544</Real>
+ <Real Name="Cell 1 0">-3.2035473334097224e-12</Real>
+ <Real Name="Cell 1 1">0.16717794964102289</Real>
+ <Real Name="Cell 2 0">-1.0892061239107136e-11</Real>
+ <Real Name="Cell 2 1">-8.5427928890925915e-12</Real>
+ <Real Name="Cell 2 2">0.16717794961448998</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.0073185487574843394</Real>
+ <Real Name="Cell 0 6 7 re">0.0017113607923287439</Real>
+ <Real Name="Cell 2 5 10 re">0.053679757843731919</Real>
+ <Real Name="Cell 2 5 10 im">0.15880261547309443</Real>
+ <Real Name="Cell 4 2 7 re">1.8806856946202906</Real>
+ <Real Name="Cell 4 2 7 im">-5.4671094864454624</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">246.45436864462314</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">192.88102601012326</Real>
+ <Real Name="Cell 1 0">271.42730351185259</Real>
+ <Real Name="Cell 1 1">115.25885143338239</Real>
+ <Real Name="Cell 2 0">183.08288439538768</Real>
+ <Real Name="Cell 2 1">159.24069411835538</Real>
+ <Real Name="Cell 2 2">-16.391759814440562</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-4.178818756469648e-13</Real>
+ <Real Name="Cell 0 6 7 re">-1.0069137884249014e-27</Real>
+ <Real Name="Cell 2 5 10 re">-5.6094174367698197e-19</Real>
+ <Real Name="Cell 2 5 10 im">-1.6594526428986948e-18</Real>
+ <Real Name="Cell 4 2 7 re">-2.2152312932810136e-08</Real>
+ <Real Name="Cell 4 2 7 im">6.4396257454452892e-08</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-2.8806661919058218e-06</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-1.8705530331608101e-05</Real>
+ <Real Name="Cell 1 0">-1.7197688691957962e-05</Real>
+ <Real Name="Cell 1 1">-1.3240622263816033e-05</Real>
+ <Real Name="Cell 2 0">-1.1629584411980756e-05</Real>
+ <Real Name="Cell 2 1">-9.9276940353995703e-06</Real>
+ <Real Name="Cell 2 2">-5.2730666430580063e-06</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.52012107052982537</Real>
+ <Real Name="Cell 3 1 2 im">6.8482605725216255</Real>
+ <Real Name="Cell 3 5 7 re">-0.0036980789183935344</Real>
+ <Real Name="Cell 3 5 7 im">6.1634647729559887e-09</Real>
+ <Real Name="Cell 6 2 4 re">15.260222121080961</Real>
+ <Real Name="Cell 6 2 4 im">1.2421111113117829</Real>
+ <Real Name="Cell 7 0 0 re">-2.8812686235380811</Real>
+ <Real Name="Cell 7 0 0 im">-0.80675520085170338</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">520.6731680619182</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">171.22464074353465</Real>
+ <Real Name="Cell 1 0">-373.95782882517159</Real>
+ <Real Name="Cell 1 1">229.20286440584107</Real>
+ <Real Name="Cell 2 0">-313.85265632355726</Real>
+ <Real Name="Cell 2 1">356.06528628658498</Real>
+ <Real Name="Cell 2 2">10.654363487499289</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.0063639096934527042</Real>
+ <Real Name="Cell 0 0 0 im">-0.012182341066375335</Real>
+ <Real Name="Cell 3 1 2 re">-9.9228430546493259e-06</Real>
+ <Real Name="Cell 3 1 2 im">-0.00013065076327181465</Real>
+ <Real Name="Cell 3 5 7 re">2.5759085022798612e-11</Real>
+ <Real Name="Cell 3 5 7 im">-4.2931807737236158e-17</Real>
+ <Real Name="Cell 6 2 4 re">-1.3138496192640048e-06</Real>
+ <Real Name="Cell 6 2 4 im">-1.0694124880568754e-07</Real>
+ <Real Name="Cell 7 0 0 re">0.00057663643475955946</Real>
+ <Real Name="Cell 7 0 0 im">0.00016145819898305986</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.053802892914868977</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.020691662312509726</Real>
+ <Real Name="Cell 1 0">-0.0023237899154683532</Real>
+ <Real Name="Cell 1 1">0.02527149273778484</Real>
+ <Real Name="Cell 2 0">0.000600553079798094</Real>
+ <Real Name="Cell 2 1">-0.00016167607048479874</Real>
+ <Real Name="Cell 2 2">0.026646993387493604</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.069611755622628294</Real>
+ <Real Name="Cell 0 6 7 re">0.79383865861583514</Real>
+ <Real Name="Cell 2 5 10 re">0.88080833512750023</Real>
+ <Real Name="Cell 2 5 10 im">2.6057246337798414</Real>
+ <Real Name="Cell 4 2 7 re">19.096438888541929</Real>
+ <Real Name="Cell 4 2 7 im">-55.512902822367884</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">2517.0732535091583</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">1955.3066474629525</Real>
+ <Real Name="Cell 1 0">2721.0324266903935</Real>
+ <Real Name="Cell 1 1">1103.5308168016663</Real>
+ <Real Name="Cell 2 0">1875.3173351098101</Real>
+ <Real Name="Cell 2 1">1534.4704563076873</Real>
+ <Real Name="Cell 2 2">-113.42604196736495</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-7.0537221329547844e-09</Real>
+ <Real Name="Cell 0 6 7 re">-5.7463804790685012e-07</Real>
+ <Real Name="Cell 2 5 10 re">-4.1614840083045064e-11</Real>
+ <Real Name="Cell 2 5 10 im">-1.2311056743065747e-10</Real>
+ <Real Name="Cell 4 2 7 re">-2.2493407131842702e-07</Real>
+ <Real Name="Cell 4 2 7 im">6.5387810342123984e-07</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-3.1321432926615869e-05</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-0.00018890242348857845</Real>
+ <Real Name="Cell 1 0">-0.00017462064584253123</Real>
+ <Real Name="Cell 1 1">-0.00013613472585420061</Real>
+ <Real Name="Cell 2 0">-0.00011809371439078819</Real>
+ <Real Name="Cell 2 1">-9.3982474514113124e-05</Real>
+ <Real Name="Cell 2 2">-6.9661560924232365e-05</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.012194838340975378</Real>
+ <Real Name="Cell 0 6 7 re">6.975795431873326e-17</Real>
+ <Real Name="Cell 2 5 10 re">1.5478395335267946e-29</Real>
+ <Real Name="Cell 2 5 10 im">4.5790252439711993e-29</Real>
+ <Real Name="Cell 4 2 7 re">5.7327906140725394e-14</Real>
+ <Real Name="Cell 4 2 7 im">-1.6665088717192258e-13</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">0.0018292258312883258</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-0.00091461291090054464</Real>
+ <Real Name="Cell 1 0">5.5807272795043997e-12</Real>
+ <Real Name="Cell 1 1">0.0071615797758995967</Real>
+ <Real Name="Cell 2 0">3.3205328244435521e-11</Real>
+ <Real Name="Cell 2 1">3.9061162844133993e-11</Real>
+ <Real Name="Cell 2 2">-0.00091461268319907444</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-5.4292848213686879e-16</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-8.1439275556636247e-17</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">4.0719637778318123e-17</Real>
+ <Real Name="Cell 1 0">-2.215406351573413e-112</Real>
+ <Real Name="Cell 1 1">-2.3047772408403365e-15</Real>
+ <Real Name="Cell 2 0">-1.3181668161597632e-111</Real>
+ <Real Name="Cell 2 1">-1.5507844461013891e-111</Real>
+ <Real Name="Cell 2 2">4.0719637778318123e-17</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.058526893274896463</Real>
+ <Real Name="Cell 3 1 2 im">0.77060407346768123</Real>
+ <Real Name="Cell 3 5 7 re">-1.6754581199058096e-16</Real>
+ <Real Name="Cell 3 5 7 im">2.7924301585993392e-22</Real>
+ <Real Name="Cell 6 2 4 re">0.00075718908137880822</Real>
+ <Real Name="Cell 6 2 4 im">6.1631669832991787e-05</Real>
+ <Real Name="Cell 7 0 0 re">-27.942228597744055</Real>
+ <Real Name="Cell 7 0 0 im">-7.8238238741294062</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">43.811954836969655</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">24.403587715787729</Real>
+ <Real Name="Cell 1 0">2.2029901722547436</Real>
+ <Real Name="Cell 1 1">-20.146106627765938</Real>
+ <Real Name="Cell 2 0">7.4901667957596416</Real>
+ <Real Name="Cell 2 1">5.9835608562785838</Real>
+ <Real Name="Cell 2 2">-1.5618699365008126</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.040960646891504318</Real>
+ <Real Name="Cell 0 0 0 im">-0.078410378960130159</Real>
+ <Real Name="Cell 3 1 2 re">-4.1343810365053865e-14</Real>
+ <Real Name="Cell 3 1 2 im">-5.4436015474703515e-13</Real>
+ <Real Name="Cell 7 0 0 re">0.0073924880067034026</Real>
+ <Real Name="Cell 7 0 0 im">0.0020698966066268229</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.3443209679114585</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.15510734808993293</Real>
+ <Real Name="Cell 1 0">-9.9639879528132092e-12</Real>
+ <Real Name="Cell 1 1">0.17216048394791436</Real>
+ <Real Name="Cell 2 0">-3.3877559989804848e-11</Real>
+ <Real Name="Cell 2 1">-2.6570634540835225e-11</Real>
+ <Real Name="Cell 2 2">0.1721604838653891</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.17992679246372756</Real>
+ <Real Name="Cell 0 6 7 re">3.1968338340529017e-14</Real>
+ <Real Name="Cell 2 5 10 re">1.4964328935770195e-27</Real>
+ <Real Name="Cell 2 5 10 im">4.4269472688716676e-27</Real>
+ <Real Name="Cell 4 2 7 re">5.8210622825280826e-13</Real>
+ <Real Name="Cell 4 2 7 im">-1.6921692400294715e-12</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">0.026989020017818024</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-0.013494509960742423</Real>
+ <Real Name="Cell 1 0">5.6666575255782654e-11</Real>
+ <Real Name="Cell 1 1">0.06534006396863376</Real>
+ <Real Name="Cell 2 0">3.3716613222916207e-10</Real>
+ <Real Name="Cell 2 1">3.9636410829671391e-10</Real>
+ <Real Name="Cell 2 2">-0.013494507645153258</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-3.36295522544755e-10</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-5.0444330386190764e-11</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">2.5222165193095382e-11</Real>
+ <Real Name="Cell 1 0">-2.2495184669680253e-111</Real>
+ <Real Name="Cell 1 1">-8.0991543667196338e-10</Real>
+ <Real Name="Cell 2 0">-1.3384635253888647e-110</Real>
+ <Real Name="Cell 2 1">8.1762240348126863e-110</Real>
+ <Real Name="Cell 2 2">2.5222165193095382e-11</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.16722545997013091</Real>
+ <Real Name="Cell 3 1 2 im">2.2018018286947507</Real>
+ <Real Name="Cell 3 5 7 re">-7.965262272963144e-05</Real>
+ <Real Name="Cell 3 5 7 im">1.3275436925529491e-10</Real>
+ <Real Name="Cell 6 2 4 re">1.8922041838381742</Real>
+ <Real Name="Cell 6 2 4 im">0.1540166206604045</Real>
+ <Real Name="Cell 7 0 0 re">-0.082605078044972122</Real>
+ <Real Name="Cell 7 0 0 im">-0.023129421458700488</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">74.938609442792128</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">131.28949617469087</Real>
+ <Real Name="Cell 1 0">95.826683673140366</Real>
+ <Real Name="Cell 1 1">17.066209311548512</Real>
+ <Real Name="Cell 2 0">0.28439471667197097</Real>
+ <Real Name="Cell 2 1">0.22350643167596149</Real>
+ <Real Name="Cell 2 2">-37.437308226605346</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.0063639096934527042</Real>
+ <Real Name="Cell 0 0 0 im">-0.012182341066375335</Real>
+ <Real Name="Cell 3 1 2 re">-3.1903187316269281e-06</Real>
+ <Real Name="Cell 3 1 2 im">-4.2005862137679066e-05</Real>
+ <Real Name="Cell 3 5 7 re">7.4468604604379845e-21</Real>
+ <Real Name="Cell 3 5 7 im">-1.2411433917415391e-26</Real>
+ <Real Name="Cell 6 2 4 re">-1.1742988941980482e-10</Real>
+ <Real Name="Cell 6 2 4 im">-9.5582468781340022e-12</Real>
+ <Real Name="Cell 7 0 0 re">7.4608679756532561e-13</Real>
+ <Real Name="Cell 7 0 0 im">2.089042997606721e-13</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.052281447439372866</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.02472611767566462</Real>
+ <Real Name="Cell 1 0">-0.00080506035697563581</Real>
+ <Real Name="Cell 1 1">0.025682559278230224</Real>
+ <Real Name="Cell 2 0">-3.29941854498715e-06</Real>
+ <Real Name="Cell 2 1">-1.8777213593421415e-06</Real>
+ <Real Name="Cell 2 2">0.026140716022377927</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-1.5498022019739996</Real>
+ <Real Name="Cell 0 0 0 im">-2.9667641307498531</Real>
+ <Real Name="Cell 3 1 2 re">-0.01941158897436121</Real>
+ <Real Name="Cell 3 1 2 im">-0.25558591442507311</Real>
+ <Real Name="Cell 3 5 7 re">1.7720564655953271e-14</Real>
+ <Real Name="Cell 3 5 7 im">-2.9534273990373024e-20</Real>
+ <Real Name="Cell 6 2 4 re">-0.0028355851140043973</Real>
+ <Real Name="Cell 6 2 4 im">-0.00023080344107898613</Real>
+ <Real Name="Cell 7 0 0 re">0.98439186309649662</Real>
+ <Real Name="Cell 7 0 0 im">0.27562971697307287</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-16.094465920337093</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">4.8742582912547263</Real>
+ <Real Name="Cell 1 0">-0.57680403129439006</Real>
+ <Real Name="Cell 1 1">7.5948376541956275</Real>
+ <Real Name="Cell 2 0">-1.9611337614092448</Real>
+ <Real Name="Cell 2 1">-1.5381440834517075</Real>
+ <Real Name="Cell 2 2">2.8175429297438925</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-0.014734386660503283</Real>
+ <Real Name="Cell 0 6 7 re">-1.9260433175085867e-12</Real>
+ <Real Name="Cell 2 5 10 re">-1.413009482353229e-21</Real>
+ <Real Name="Cell 2 5 10 im">-4.1801530129700011e-21</Real>
+ <Real Name="Cell 4 2 7 re">-2.8112014428689828e-10</Real>
+ <Real Name="Cell 4 2 7 im">8.1720970817089197e-10</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.0022101946504346128</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.0011050803459824404</Real>
+ <Real Name="Cell 1 0">-1.9975569870376849e-08</Real>
+ <Real Name="Cell 1 1">-0.0056561825503867015</Real>
+ <Real Name="Cell 2 0">-1.1885464406244038e-07</Real>
+ <Real Name="Cell 2 1">-1.3974988391173238e-07</Real>
+ <Real Name="Cell 2 2">0.0011042651858169206</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-1.5498022019739996</Real>
+ <Real Name="Cell 0 0 0 im">-2.9667641307498531</Real>
+ <Real Name="Cell 3 1 2 re">-0.060375832961279227</Real>
+ <Real Name="Cell 3 1 2 im">-0.79494844533157683</Real>
+ <Real Name="Cell 3 5 7 re">7.6208799660687442e-13</Real>
+ <Real Name="Cell 3 5 7 im">-1.2701466422516263e-18</Real>
+ <Real Name="Cell 6 2 4 re">-0.010822157027959465</Real>
+ <Real Name="Cell 6 2 4 im">-0.00088087325244235457</Real>
+ <Real Name="Cell 7 0 0 re">1.642150584269557</Real>
+ <Real Name="Cell 7 0 0 im">0.45980215576509176</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-21.508655755976211</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">8.1769429198299068</Real>
+ <Real Name="Cell 1 0">-1.4219812694541607</Real>
+ <Real Name="Cell 1 1">9.3048524361756808</Real>
+ <Real Name="Cell 2 0">-4.834736451754865</Real>
+ <Real Name="Cell 2 1">-4.9282166403949645</Real>
+ <Real Name="Cell 2 2">-6.0016091693463043</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-0.10980031377406475</Real>
+ <Real Name="Cell 0 6 7 re">-1.104282829889803e-10</Real>
+ <Real Name="Cell 2 5 10 re">-3.9568265111014019e-20</Real>
+ <Real Name="Cell 2 5 10 im">-1.1705611652820699e-19</Real>
+ <Real Name="Cell 4 2 7 re">-2.8544874197050347e-09</Real>
+ <Real Name="Cell 4 2 7 im">8.2979284076276372e-09</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.016470419312996247</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.0082350372497414174</Real>
+ <Real Name="Cell 1 0">-2.0283147278850997e-07</Real>
+ <Real Name="Cell 1 1">-0.022453844836226242</Real>
+ <Real Name="Cell 2 0">-1.206847296948174e-06</Real>
+ <Real Name="Cell 2 1">-1.419058922419327e-06</Real>
+ <Real Name="Cell 2 2">0.0082267526649127572</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.24078724347789371</Real>
+ <Real Name="Cell 0 0 0 im">-0.46093556725010454</Real>
+ <Real Name="Cell 3 1 2 re">-0.033844124579137755</Real>
+ <Real Name="Cell 3 1 2 im">-0.44561429463090468</Real>
+ <Real Name="Cell 3 5 7 re">0.00013337714155882522</Real>
+ <Real Name="Cell 3 5 7 im">-2.222952326481159e-10</Real>
+ <Real Name="Cell 6 2 4 re">-1.4748639396178393</Real>
+ <Real Name="Cell 6 2 4 im">-0.12004706566765375</Real>
+ <Real Name="Cell 7 0 0 re">0.072971802679737227</Real>
+ <Real Name="Cell 7 0 0 im">0.020432104402369752</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-50.292058479806066</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-53.039180547663896</Real>
+ <Real Name="Cell 1 0">-44.367827409532083</Real>
+ <Real Name="Cell 1 1">-0.10395647320044596</Real>
+ <Real Name="Cell 2 0">-0.11740041231477359</Real>
+ <Real Name="Cell 2 1">-0.10348396692396387</Real>
+ <Real Name="Cell 2 2">25.127119580840922</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-0.0057362984570354389</Real>
+ <Real Name="Cell 0 6 7 re">-0.0069394141749721059</Real>
+ <Real Name="Cell 2 5 10 re">-0.10030703953351935</Real>
+ <Real Name="Cell 2 5 10 im">-0.2967416558520477</Real>
+ <Real Name="Cell 4 2 7 re">-0.98747845589181826</Real>
+ <Real Name="Cell 4 2 7 im">2.870576858913505</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-131.95802432517937</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-37.20016196088654</Real>
+ <Real Name="Cell 1 0">-90.173425803606264</Real>
+ <Real Name="Cell 1 1">-20.045771494967298</Real>
+ <Real Name="Cell 2 0">-60.362280008302307</Real>
+ <Real Name="Cell 2 1">-55.408444753903993</Real>
+ <Real Name="Cell 2 2">29.593848348790942</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.24078724347789371</Real>
+ <Real Name="Cell 0 0 0 im">-0.46093556725010454</Real>
+ <Real Name="Cell 3 1 2 re">-0.10526532449299339</Real>
+ <Real Name="Cell 3 1 2 im">-1.3859934008147894</Real>
+ <Real Name="Cell 3 5 7 re">0.0020302261986413928</Real>
+ <Real Name="Cell 3 5 7 im">-3.3837102810922127e-09</Real>
+ <Real Name="Cell 6 2 4 re">-6.6640634797260141</Real>
+ <Real Name="Cell 6 2 4 im">-0.54242377528829877</Real>
+ <Real Name="Cell 7 0 0 re">0.23325414914067172</Real>
+ <Real Name="Cell 7 0 0 im">0.065311160647145622</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-215.20970930906984</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">8.3297521257045215</Real>
+ <Real Name="Cell 1 0">102.94721396484063</Real>
+ <Real Name="Cell 1 1">-15.233403449790623</Real>
+ <Real Name="Cell 2 0">80.797987021631059</Real>
+ <Real Name="Cell 2 1">-91.960023311736748</Real>
+ <Real Name="Cell 2 2">37.691308119304068</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-0.029904417511235334</Real>
+ <Real Name="Cell 0 6 7 re">-0.27370127182526427</Real>
+ <Real Name="Cell 2 5 10 re">-0.6991498586593593</Real>
+ <Real Name="Cell 2 5 10 im">-2.06831831257441</Real>
+ <Real Name="Cell 4 2 7 re">-10.026833319693612</Real>
+ <Real Name="Cell 4 2 7 im">29.147770793339333</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-1329.4143993872051</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-381.37902032167398</Real>
+ <Real Name="Cell 1 0">-881.13528084607606</Real>
+ <Real Name="Cell 1 1">-107.89864126422562</Real>
+ <Real Name="Cell 2 0">-614.45788958812147</Real>
+ <Real Name="Cell 2 1">-490.1935785693114</Real>
+ <Real Name="Cell 2 2">278.73579683973628</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">8.2210755780125459e-34</Real>
+ <Real Name="Cell 3 1 2 im">1.0824415878263353e-32</Real>
+ <Real Name="Cell 7 0 0 re">-5.3044697270927454e-20</Real>
+ <Real Name="Cell 7 0 0 im">-1.4852514982922861e-20</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">7.1504251744240444e-20</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">3.41272626726192e-18</Real>
+ <Real Name="Cell 1 0">5.9287266918327695e-31</Real>
+ <Real Name="Cell 1 1">-3.5752125871655224e-20</Real>
+ <Real Name="Cell 2 0">2.0157671317638854e-30</Real>
+ <Real Name="Cell 2 1">1.5809937844887388e-30</Real>
+ <Real Name="Cell 2 2">-3.5752125866744843e-20</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">4.898432637853757e-38</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">7.3476492487499718e-39</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-3.6738246243749859e-39</Real>
+ <Real Name="Cell 1 0">0</Real>
+ <Real Name="Cell 1 1">6.3099551402707054e-37</Real>
+ <Real Name="Cell 2 0">0</Real>
+ <Real Name="Cell 2 1">0</Real>
+ <Real Name="Cell 2 2">-3.6738246243749859e-39</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">2.556999772227411e-33</Real>
+ <Real Name="Cell 3 1 2 im">3.3667162736272229e-32</Real>
+ <Real Name="Cell 7 0 0 re">-1.0926105068604317</Real>
+ <Real Name="Cell 7 0 0 im">-0.30593093671094795</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">1.4728389596008808</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">6.4146764633054083</Real>
+ <Real Name="Cell 1 0">1.84401087871763e-30</Real>
+ <Real Name="Cell 1 1">-0.73641947980044042</Real>
+ <Real Name="Cell 2 0">6.2696371634985231e-30</Real>
+ <Real Name="Cell 2 1">4.917362343247014e-30</Real>
+ <Real Name="Cell 2 2">-0.73641947980044042</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">2.7045303395891825e-21</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">4.0567956705863441e-22</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-2.0283978352931721e-22</Real>
+ <Real Name="Cell 1 0">0</Real>
+ <Real Name="Cell 1 1">1.9685468212785548e-20</Real>
+ <Real Name="Cell 2 0">0</Real>
+ <Real Name="Cell 2 1">0</Real>
+ <Real Name="Cell 2 2">-2.0283978352931721e-22</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">1.4765194649429009e-07</Real>
+ <Real Name="Cell 3 1 2 im">1.9440839083925106e-06</Real>
+ <Real Name="Cell 6 2 4 re">2.8973305349725333e-25</Real>
+ <Real Name="Cell 6 2 4 im">2.3582923119190961e-26</Real>
+ <Real Name="Cell 7 0 0 re">-1.9143774765849531e-29</Real>
+ <Real Name="Cell 7 0 0 im">-5.3602568431532371e-30</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">1.5446854233119991e-05</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.00017895573959435024</Real>
+ <Real Name="Cell 1 0">0.00010624017864812442</Real>
+ <Real Name="Cell 1 1">5.2738464577355206e-05</Real>
+ <Real Name="Cell 2 0">4.3541015979734419e-07</Real>
+ <Real Name="Cell 2 1">2.4779440564845181e-07</Real>
+ <Real Name="Cell 2 2">-7.7224115666698012e-06</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">8.4622953690730811e-28</Real>
+ <Real Name="Cell 4 2 7 re">1.4391546043716599e-17</Real>
+ <Real Name="Cell 4 2 7 im">-4.1835888966074777e-17</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">1.8714632354986221e-15</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">3.7666982290146189e-14</Real>
+ <Real Name="Cell 1 0">3.2953537029348404e-14</Real>
+ <Real Name="Cell 1 1">2.7195337232381974e-14</Real>
+ <Real Name="Cell 2 0">2.2284153843094576e-14</Real>
+ <Real Name="Cell 2 1">1.9023058601221014e-14</Real>
+ <Real Name="Cell 2 2">1.1928221773909695e-14</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">4.5924160406040909e-07</Real>
+ <Real Name="Cell 3 1 2 im">6.0466809528496931e-06</Real>
+ <Real Name="Cell 3 5 7 re">-4.7703059370503073e-21</Real>
+ <Real Name="Cell 3 5 7 im">7.9505097776562864e-27</Real>
+ <Real Name="Cell 6 2 4 re">1.0063968348774453e-13</Real>
+ <Real Name="Cell 6 2 4 im">8.1916021999667744e-15</Real>
+ <Real Name="Cell 7 0 0 re">-0.024375179191018694</Real>
+ <Real Name="Cell 7 0 0 im">-0.0068250500572553229</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">0.032905785796259142</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.17994239387577421</Real>
+ <Real Name="Cell 1 0">0.00033043861081358196</Real>
+ <Real Name="Cell 1 1">-0.016264838330712152</Real>
+ <Real Name="Cell 2 0">-0.056174983204850239</Real>
+ <Real Name="Cell 2 1">7.7074954253368213e-07</Real>
+ <Real Name="Cell 2 2">-0.00033672708354701251</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">7.9977633138124044e-16</Real>
+ <Real Name="Cell 0 6 7 re">7.6137551246740057e-12</Real>
+ <Real Name="Cell 2 5 10 re">5.378627596651949e-26</Real>
+ <Real Name="Cell 2 5 10 im">1.5911773158340167e-25</Real>
+ <Real Name="Cell 4 2 7 re">1.4613142447013661e-16</Real>
+ <Real Name="Cell 4 2 7 im">-4.2480064546339484e-16</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">2.7428640483431204e-11</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-1.3322349180734567e-11</Real>
+ <Real Name="Cell 1 0">3.3460945005926606e-13</Real>
+ <Real Name="Cell 1 1">9.089404609722578e-11</Real>
+ <Real Name="Cell 2 0">2.262727808888106e-13</Real>
+ <Real Name="Cell 2 1">-2.6231426231809359e-10</Real>
+ <Real Name="Cell 2 2">6.4698667840508995e-10</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>0.057799991083145486</Real>
+ <Real>0.72439999160766533</Real>
+ <Real>0.21780001730918919</Real>
+ <Real>0.23120004539489969</Real>
+ <Real>0.71759997596740277</Real>
+ <Real>0.051199978637697541</Real>
+ <Real>0.5</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>0.49980165541637689</Real>
+ <Real>0.50019832490943372</Real>
+ <Real>1.9674189388751984e-08</Real>
+ <Real>0.0098000146865899751</Real>
+ <Real>0.62040007553099485</Real>
+ <Real>0.36979990978241517</Real>
+ <Real>0.01280001373291384</Real>
+ <Real>0.6344000583648608</Real>
+ <Real>0.35279992790222536</Real>
+ <Real>0.31999996185302848</Real>
+ <Real>0.66000002861022722</Real>
+ <Real>0.020000009536744301</Real>
+ <Real>0.064799962234502573</Real>
+ <Real>0.73039997062682005</Real>
+ <Real>0.20480006713867738</Real>
+ <Real>0.033799997520446823</Real>
+ <Real>0.69239999542236319</Real>
+ <Real>0.27380000705718999</Real>
+ <Real>0.0050000023841860752</Real>
+ <Real>0.59000001907348576</Real>
+ <Real>0.40499997854232817</Real>
+ <Real>0.14579997940063549</Real>
+ <Real>0.74840000305175636</Real>
+ <Real>0.10580001754760815</Real>
+ <Real>0.19220000295639039</Real>
+ <Real>0.7355999988555908</Real>
+ <Real>0.07219999818801881</Real>
+ <Real>0.09680002517700359</Real>
+ <Real>0.7464000068664518</Real>
+ <Real>0.15679996795654461</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>0.28346023183768659</Real>
+ <Real>0.68602074496934773</Real>
+ <Real>0.03051902319296566</Real>
+ <Real>0.062283763229400151</Real>
+ <Real>0.72837372425978641</Real>
+ <Real>0.20934251251081343</Real>
+ <Real>0.030519075166579968</Real>
+ <Real>0.68602085139144819</Real>
+ <Real>0.28346007344197183</Real>
+ <Real>0.20179944632183019</Real>
+ <Real>0.73169544279752741</Real>
+ <Real>0.06650511088064244</Real>
+ <Real>0.0069204181366000162</Real>
+ <Real>0.60380624729966226</Real>
+ <Real>0.38927333456373775</Real>
+ <Real>0.31999993268181826</Real>
+ <Real>0.66000005048863186</Real>
+ <Real>0.020000016829549865</Real>
+ <Real>0.25750869847450536</Real>
+ <Real>0.70262972869771734</Real>
+ <Real>0.039861572827777289</Real>
+ <Real>0.024982681258888664</Real>
+ <Real>0.67356397004906354</Real>
+ <Real>0.30145334869204782</Real>
+ <Real>0.5</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>0.33910152816638917</Real>
+ <Real>0.64532779089322467</Real>
+ <Real>0.015570680940386146</Real>
+ <Real>0.31065743749553704</Real>
+ <Real>0.6669204166516397</Real>
+ <Real>0.022422145852823244</Real>
+ <Real>0.38927333456373775</Real>
+ <Real>0.60380624729966226</Real>
+ <Real>0.0069204181366000162</Real>
+ <Real>0.070865057959422981</Real>
+ <Real>0.73474048840351802</Real>
+ <Real>0.19439445363705898</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>0.0032000320435372487</Real>
+ <Real>0.57360033645613839</Real>
+ <Real>0.42319963150032436</Real>
+ <Real>0.036450027036671884</Real>
+ <Real>0.69710004606245946</Real>
+ <Real>0.26644992690086866</Real>
+ <Real>0.00020000200272107804</Real>
+ <Real>0.51960009613036107</Real>
+ <Real>0.48019990186691786</Real>
+ <Real>0.22444973163612758</Real>
+ <Real>0.72110013618453195</Real>
+ <Real>0.054450132179340471</Real>
+ <Real>0.045000200271829272</Real>
+ <Real>0.71000026702836294</Real>
+ <Real>0.24499953269980779</Real>
+ <Real>0.096800005507469256</Real>
+ <Real>0.74640000150203689</Real>
+ <Real>0.15679999299049385</Real>
+ <Real>0.042050058078785923</Real>
+ <Real>0.7059000841140346</Real>
+ <Real>0.25204985780717948</Real>
+ <Real>0.38720002202987702</Real>
+ <Real>0.60559998097419676</Real>
+ <Real>0.0071999969959262167</Real>
+ <Real>0.23804993666410867</Real>
+ <Real>0.7139000348806297</Real>
+ <Real>0.048050028455261629</Real>
+ <Real>0.06479997296333595</Real>
+ <Real>0.73039997897147568</Real>
+ <Real>0.20480004806518837</Real>
+ <Real>0.028799987983704867</Real>
+ <Real>0.68239997396468866</Real>
+ <Real>0.28880003805160648</Real>
+ <Real>0.088200007009506365</Real>
+ <Real>0.74360000267028781</Real>
+ <Real>0.16819999032020583</Real>
+ <Real>0.057800011348724922</Real>
+ <Real>0.72440001068115123</Real>
+ <Real>0.21779997797012385</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>-0.3399999737739563</Real>
+ <Real>-0.3200000524520874</Real>
+ <Real>0.6600000262260437</Real>
+ <Real>-0.68000006675720215</Real>
+ <Real>0.3600001335144043</Real>
+ <Real>0.31999993324279785</Real>
+ <Real>-1</Real>
+ <Real>1</Real>
+ <Real>0</Real>
+ <Real>-0.9998016357421875</Real>
+ <Real>0.999603271484375</Real>
+ <Real>0.0001983642578125</Real>
+ <Real>-0.1400001049041748</Real>
+ <Real>-0.71999979019165039</Real>
+ <Real>0.8599998950958252</Real>
+ <Real>-0.16000008583068848</Real>
+ <Real>-0.67999982833862305</Real>
+ <Real>0.83999991416931152</Real>
+ <Real>-0.79999995231628418</Real>
+ <Real>0.59999990463256836</Real>
+ <Real>0.20000004768371582</Real>
+ <Real>-0.3599998950958252</Real>
+ <Real>-0.28000020980834961</Real>
+ <Real>0.6400001049041748</Real>
+ <Real>-0.25999999046325684</Real>
+ <Real>-0.48000001907348633</Real>
+ <Real>0.74000000953674316</Real>
+ <Real>-0.10000002384185791</Real>
+ <Real>-0.79999995231628418</Real>
+ <Real>0.89999997615814209</Real>
+ <Real>-0.53999996185302734</Real>
+ <Real>0.079999923706054688</Real>
+ <Real>0.46000003814697266</Real>
+ <Real>-0.62000000476837158</Real>
+ <Real>0.24000000953674316</Real>
+ <Real>0.37999999523162842</Real>
+ <Real>-0.44000005722045898</Real>
+ <Real>-0.11999988555908203</Real>
+ <Real>0.55999994277954102</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>-0.75294120864472092</Real>
+ <Real>0.50588241728944183</Real>
+ <Real>0.24705879135527908</Real>
+ <Real>-0.35294125071858673</Real>
+ <Real>-0.29411749856282654</Real>
+ <Real>0.64705874928141327</Real>
+ <Real>-0.24705900172460815</Real>
+ <Real>-0.5058819965507837</Real>
+ <Real>0.75294099827539185</Real>
+ <Real>-0.63529433544118774</Real>
+ <Real>0.27058867088237548</Real>
+ <Real>0.36470566455881226</Real>
+ <Real>-0.11764708357286224</Real>
+ <Real>-0.76470583285427551</Real>
+ <Real>0.88235291642713776</Real>
+ <Real>-0.79999991585226837</Real>
+ <Real>0.59999983170453675</Real>
+ <Real>0.20000008414773163</Real>
+ <Real>-0.71764712564672806</Real>
+ <Real>0.43529425129345611</Real>
+ <Real>0.28235287435327194</Real>
+ <Real>-0.22352933256684082</Real>
+ <Real>-0.55294133486631836</Real>
+ <Real>0.77647066743315918</Real>
+ <Real>-1</Real>
+ <Real>1</Real>
+ <Real>0</Real>
+ <Real>-0.823530847226003</Real>
+ <Real>0.64706169445200601</Real>
+ <Real>0.176469152773997</Real>
+ <Real>-0.78823529164271378</Real>
+ <Real>0.57647058328542755</Real>
+ <Real>0.21176470835728622</Real>
+ <Real>-0.88235291642713776</Real>
+ <Real>0.76470583285427551</Real>
+ <Real>0.11764708357286224</Real>
+ <Real>-0.37647060432236401</Real>
+ <Real>-0.24705879135527198</Real>
+ <Real>0.62352939567763599</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>-0.080000400543212891</Real>
+ <Real>-0.83999919891357422</Real>
+ <Real>0.91999959945678711</Real>
+ <Real>-0.27000010013580322</Real>
+ <Real>-0.45999979972839355</Real>
+ <Real>0.72999989986419678</Real>
+ <Real>-0.020000100135803223</Real>
+ <Real>-0.95999979972839355</Real>
+ <Real>0.97999989986419678</Real>
+ <Real>-0.66999959945678711</Real>
+ <Real>0.33999919891357422</Real>
+ <Real>0.33000040054321289</Real>
+ <Real>-0.30000066757202148</Real>
+ <Real>-0.39999866485595703</Real>
+ <Real>0.69999933242797852</Real>
+ <Real>-0.4400000125169754</Real>
+ <Real>-0.11999997496604919</Real>
+ <Real>0.5599999874830246</Real>
+ <Real>-0.29000020027160645</Real>
+ <Real>-0.41999959945678711</Real>
+ <Real>0.70999979972839355</Real>
+ <Real>-0.88000002503395081</Real>
+ <Real>0.76000005006790161</Real>
+ <Real>0.11999997496604919</Real>
+ <Real>-0.68999990820884705</Real>
+ <Real>0.37999981641769409</Real>
+ <Real>0.31000009179115295</Real>
+ <Real>-0.35999992489814758</Real>
+ <Real>-0.28000015020370483</Real>
+ <Real>0.64000007510185242</Real>
+ <Real>-0.23999994993209839</Real>
+ <Real>-0.52000010013580322</Real>
+ <Real>0.76000005006790161</Real>
+ <Real>-0.42000001668930054</Real>
+ <Real>-0.15999996662139893</Real>
+ <Real>0.57999998331069946</Real>
+ <Real>-0.34000003337860107</Real>
+ <Real>-0.31999993324279785</Real>
+ <Real>0.65999996662139893</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">7</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">0</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">4</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 3 10">5.6623669355262653e-05</Real>
+ <Real Name="Cell 0 3 11">0.010149697050426341</Real>
+ <Real Name="Cell 0 3 12">0.007488398765799556</Real>
+ <Real Name="Cell 0 4 10">0.00013703866529058128</Real>
+ <Real Name="Cell 0 4 11">0.02456394918823649</Real>
+ <Real Name="Cell 0 4 12">0.018123166225599462</Real>
+ <Real Name="Cell 0 5 10">0.022687329577496734</Real>
+ <Real Name="Cell 0 5 11">0.0010927770632069087</Real>
+ <Real Name="Cell 0 5 12">0.00080624577962836266</Real>
+ <Real Name="Cell 0 5 6">0.038010113433341118</Real>
+ <Real Name="Cell 0 5 7">0.32045712249755282</Real>
+ <Real Name="Cell 0 5 8">0.16598105861316068</Real>
+ <Real Name="Cell 0 5 9">0.30037466664767609</Real>
+ <Real Name="Cell 0 6 10">0.082238852604420473</Real>
+ <Real Name="Cell 0 6 6">0.058957914436500745</Real>
+ <Real Name="Cell 0 6 7">0.497064646805428</Real>
+ <Real Name="Cell 0 6 8">0.4514325111168781</Real>
+ <Real Name="Cell 0 6 9">1.08911485499034</Real>
+ <Real Name="Cell 0 7 10">0.0074748367848824267</Real>
+ <Real Name="Cell 0 7 6">0.00067573567214182734</Real>
+ <Real Name="Cell 0 7 7">0.0056970182276166216</Real>
+ <Real Name="Cell 0 7 8">0.032100787939127552</Real>
+ <Real Name="Cell 0 7 9">0.098991602183492719</Real>
+ <Real Name="Cell 1 0 2">0.024540565786750318</Real>
+ <Real Name="Cell 1 0 3">0.073595948046277712</Real>
+ <Real Name="Cell 1 0 4">0.0049534769926253023</Real>
+ <Real Name="Cell 1 1 2">0.024540565786750318</Real>
+ <Real Name="Cell 1 1 3">0.073595948046277712</Real>
+ <Real Name="Cell 1 1 4">0.0049534769926253023</Real>
+ <Real Name="Cell 1 3 10">0.0010238823471539209</Real>
+ <Real Name="Cell 1 3 11">0.13074669381137438</Real>
+ <Real Name="Cell 1 3 12">0.094844263370290671</Real>
+ <Real Name="Cell 1 4 10">0.0023154748502671177</Real>
+ <Real Name="Cell 1 4 11">0.31459714509427167</Real>
+ <Real Name="Cell 1 4 12">0.22902528850437476</Real>
+ <Real Name="Cell 1 5 10">0.022790068545680862</Real>
+ <Real Name="Cell 1 5 11">0.013858268451161514</Real>
+ <Real Name="Cell 1 5 12">0.01015017752588509</Real>
+ <Real Name="Cell 1 5 6">0.14547470847027352</Real>
+ <Real Name="Cell 1 5 7">1.2264771100795671</Real>
+ <Real Name="Cell 1 5 8">0.37971512665726326</Real>
+ <Real Name="Cell 1 5 9">0.30867345161902582</Real>
+ <Real Name="Cell 1 6 10">0.082304121783941267</Real>
+ <Real Name="Cell 1 6 6">0.22564745642516129</Real>
+ <Real Name="Cell 1 6 7">1.9024726950852704</Real>
+ <Real Name="Cell 1 6 8">0.96563446440803302</Real>
+ <Real Name="Cell 1 6 9">1.2711641691167428</Real>
+ <Real Name="Cell 1 7 10">0.0074807692176505243</Real>
+ <Real Name="Cell 1 7 6">0.0025862182726760627</Real>
+ <Real Name="Cell 1 7 7">0.021835169148112558</Real>
+ <Real Name="Cell 1 7 8">0.11677582478108178</Real>
+ <Real Name="Cell 1 7 9">0.17393479356687258</Real>
+ <Real Name="Cell 13 4 0">0.0011101808418038936</Real>
+ <Real Name="Cell 13 4 1">0.0085603195748374158</Real>
+ <Real Name="Cell 13 4 2">0.0017983092800505994</Real>
+ <Real Name="Cell 13 5 0">0.0022897486430743653</Real>
+ <Real Name="Cell 13 5 1">0.017655664187933528</Real>
+ <Real Name="Cell 13 5 2">0.0037090139540988942</Real>
+ <Real Name="Cell 13 6 0">6.9386375596519858e-05</Real>
+ <Real Name="Cell 13 6 1">0.00053502053618650989</Real>
+ <Real Name="Cell 13 6 2">0.00011239444822480495</Real>
+ <Real Name="Cell 14 4 0">0.055023284000462663</Real>
+ <Real Name="Cell 14 4 1">0.42427042276793414</Real>
+ <Real Name="Cell 14 4 2">0.089128616267700259</Real>
+ <Real Name="Cell 14 5 0">0.11348555580624049</Real>
+ <Real Name="Cell 14 5 1">0.87505799798432204</Real>
+ <Real Name="Cell 14 5 2">0.1838278237863091</Real>
+ <Real Name="Cell 14 6 0">0.003438958867283791</Real>
+ <Real Name="Cell 14 6 1">0.026516929314719953</Real>
+ <Real Name="Cell 14 6 2">0.0055705443760856732</Real>
+ <Real Name="Cell 15 4 0">0.030599320369454324</Real>
+ <Real Name="Cell 15 4 1">0.23594350692428107</Real>
+ <Real Name="Cell 15 4 2">0.04956583622378094</Real>
+ <Real Name="Cell 15 5 0">0.063111116366510248</Real>
+ <Real Name="Cell 15 5 1">0.48663362263056564</Real>
+ <Real Name="Cell 15 5 2">0.10222956653786006</Real>
+ <Real Name="Cell 15 6 0">0.0019124595347036657</Real>
+ <Real Name="Cell 15 6 1">0.014746484693797416</Real>
+ <Real Name="Cell 15 6 2">0.0030978680224661675</Real>
+ <Real Name="Cell 2 0 2">0.50271860606288887</Real>
+ <Real Name="Cell 2 0 3">1.5076283381240179</Real>
+ <Real Name="Cell 2 0 4">0.10147300883509652</Real>
+ <Real Name="Cell 2 1 2">0.5047764048326977</Real>
+ <Real Name="Cell 2 1 3">1.5334184619673425</Real>
+ <Real Name="Cell 2 1 4">0.10922713407267229</Real>
+ <Real Name="Cell 2 2 2">0.022432594190590932</Real>
+ <Real Name="Cell 2 2 3">0.28837614886492213</Real>
+ <Real Name="Cell 2 2 4">0.088415117807521301</Real>
+ <Real Name="Cell 2 3 0">1.0101863480419877e-05</Real>
+ <Real Name="Cell 2 3 1">0.00015938430774211805</Real>
+ <Real Name="Cell 2 3 10">0.03729190653598248</Real>
+ <Real Name="Cell 2 3 11">0.45618055990310158</Real>
+ <Real Name="Cell 2 3 12">0.14540410722102243</Real>
+ <Real Name="Cell 2 3 2">0.018528685636693628</Real>
+ <Real Name="Cell 2 3 3">0.31609512046265792</Real>
+ <Real Name="Cell 2 3 4">0.1153625735577145</Real>
+ <Real Name="Cell 2 3 5">0.0074180447991776845</Real>
+ <Real Name="Cell 2 3 6">0.0031394075351794978</Real>
+ <Real Name="Cell 2 4 0">0.00088138724545949656</Real>
+ <Real Name="Cell 2 4 1">0.013906275435475911</Real>
+ <Real Name="Cell 2 4 10">0.071078767034347068</Real>
+ <Real Name="Cell 2 4 11">0.88791266956615367</Real>
+ <Real Name="Cell 2 4 12">0.29130323596519359</Real>
+ <Real Name="Cell 2 4 2">0.0084857720442544186</Real>
+ <Real Name="Cell 2 4 3">0.070515847026058828</Real>
+ <Real Name="Cell 2 4 4">0.027625108536345405</Real>
+ <Real Name="Cell 2 4 5">0.015925083165855905</Real>
+ <Real Name="Cell 2 4 6">0.0067396905037282002</Real>
+ <Real Name="Cell 2 5 0">0.00056822954982062139</Real>
+ <Real Name="Cell 2 5 1">0.008965363035475387</Real>
+ <Real Name="Cell 2 5 10">0.0017255256521228211</Real>
+ <Real Name="Cell 2 5 11">0.02330827131049042</Real>
+ <Real Name="Cell 2 5 12">0.0084189784020007839</Real>
+ <Real Name="Cell 2 5 2">0.0030936745465869725</Real>
+ <Real Name="Cell 2 5 4">2.2596343831713116e-05</Real>
+ <Real Name="Cell 2 5 5">0.00053540801653051829</Real>
+ <Real Name="Cell 2 5 6">0.014505103615625918</Real>
+ <Real Name="Cell 2 5 7">0.12038318703711517</Real>
+ <Real Name="Cell 2 5 8">0.035951287063896872</Real>
+ <Real Name="Cell 2 5 9">0.0080604032936843015</Real>
+ <Real Name="Cell 2 6 1">0.0031905603848251464</Real>
+ <Real Name="Cell 2 6 10">3.2372497043954596e-09</Real>
+ <Real Name="Cell 2 6 2">0.0049901942107793643</Real>
+ <Real Name="Cell 2 6 3">5.932857406782298e-05</Real>
+ <Real Name="Cell 2 6 6">0.022147561134276194</Real>
+ <Real Name="Cell 2 6 7">0.18679797109805318</Real>
+ <Real Name="Cell 2 6 8">0.23828713894708675</Real>
+ <Real Name="Cell 2 6 9">0.18118497683324633</Real>
+ <Real Name="Cell 2 7 1">0.086021452109728128</Real>
+ <Real Name="Cell 2 7 10">2.9423943070631154e-10</Real>
+ <Real Name="Cell 2 7 2">0.13454180474453697</Real>
+ <Real Name="Cell 2 7 3">0.0015995716981841053</Real>
+ <Real Name="Cell 2 7 6">0.00025384034107059551</Real>
+ <Real Name="Cell 2 7 7">0.0021712678064379127</Real>
+ <Real Name="Cell 2 7 8">0.081491318690849343</Real>
+ <Real Name="Cell 2 7 9">0.074864630216865194</Real>
+ <Real Name="Cell 2 8 1">0.038498874570059433</Real>
+ <Real Name="Cell 2 8 2">0.06021414354505631</Real>
+ <Real Name="Cell 2 8 3">0.00071588782407037044</Real>
+ <Real Name="Cell 3 0 2">0.19879312362478679</Real>
+ <Real Name="Cell 3 0 3">0.5961707861742187</Real>
+ <Real Name="Cell 3 0 4">0.040126098669622232</Real>
+ <Real Name="Cell 3 1 2">0.21466027875317184</Real>
+ <Real Name="Cell 3 1 3">0.79503177385004864</Real>
+ <Real Name="Cell 3 1 4">0.09991615678155788</Real>
+ <Real Name="Cell 3 2 2">0.16791813106015502</Real>
+ <Real Name="Cell 3 2 3">2.1269408189763399</Real>
+ <Real Name="Cell 3 2 4">0.64480275193967729</Real>
+ <Real Name="Cell 3 3 0">0.00063950892592356222</Real>
+ <Real Name="Cell 3 3 1">0.010089988609606101</Real>
+ <Real Name="Cell 3 3 10">0.025452215343283555</Real>
+ <Real Name="Cell 3 3 11">0.28688742759245028</Real>
+ <Real Name="Cell 3 3 12">0.080441621921961484</Real>
+ <Real Name="Cell 3 3 2">0.086826077747086727</Real>
+ <Real Name="Cell 3 3 3">1.3272237357284817</Real>
+ <Real Name="Cell 3 3 4">0.79581183811150646</Real>
+ <Real Name="Cell 3 3 5">0.15916407654768858</Real>
+ <Real Name="Cell 3 3 6">0.016114766398237244</Real>
+ <Real Name="Cell 3 4 0">0.055797132059747637</Real>
+ <Real Name="Cell 3 4 1">0.88035116338443908</Real>
+ <Real Name="Cell 3 4 10">0.048436885524032317</Real>
+ <Real Name="Cell 3 4 11">0.54596165014164655</Real>
+ <Real Name="Cell 3 4 12">0.15308457750534166</Real>
+ <Real Name="Cell 3 4 2">0.31522661556836007</Real>
+ <Real Name="Cell 3 4 3">0.27398777795327972</Real>
+ <Real Name="Cell 3 4 4">1.0124189061732707</Real>
+ <Real Name="Cell 3 4 5">0.41213787182227002</Real>
+ <Real Name="Cell 3 4 6">0.034595233924539864</Real>
+ <Real Name="Cell 3 5 0">0.035972359930240401</Real>
+ <Real Name="Cell 3 5 1">0.56756158865585526</Real>
+ <Real Name="Cell 3 5 10">0.0011687010863065466</Real>
+ <Real Name="Cell 3 5 11">0.013173142052778681</Real>
+ <Real Name="Cell 3 5 12">0.0036936749770689519</Real>
+ <Real Name="Cell 3 5 2">0.1958482700028199</Real>
+ <Real Name="Cell 3 5 3">0.0031270837041210611</Real>
+ <Real Name="Cell 3 5 4">0.052610770806788179</Real>
+ <Real Name="Cell 3 5 5">0.021492155630256263</Real>
+ <Real Name="Cell 3 5 6">0.0011631063639692884</Real>
+ <Real Name="Cell 3 6 1">0.035962755702326245</Real>
+ <Real Name="Cell 3 6 2">0.056247528228260152</Real>
+ <Real Name="Cell 3 6 3">0.0006687286112860752</Real>
+ <Real Name="Cell 3 7 1">0.96960035048860149</Real>
+ <Real Name="Cell 3 7 2">1.5165028935952978</Real>
+ <Real Name="Cell 3 7 3">0.018029750035056202</Real>
+ <Real Name="Cell 3 8 1">0.43394434017377931</Real>
+ <Real Name="Cell 3 8 2">0.67871040599482013</Real>
+ <Real Name="Cell 3 8 3">0.0080692091112776632</Real>
+ <Real Name="Cell 4 1 2">0.0033332923269083705</Real>
+ <Real Name="Cell 4 1 3">0.04177571839298766</Real>
+ <Real Name="Cell 4 1 4">0.012560395377580517</Real>
+ <Real Name="Cell 4 2 2">0.034803053196972543</Real>
+ <Real Name="Cell 4 2 3">0.4377835401891883</Real>
+ <Real Name="Cell 4 2 4">0.13200408043466716</Real>
+ <Real Name="Cell 4 3 0">0.00038119006176646992</Real>
+ <Real Name="Cell 4 3 1">0.0060143075810304616</Real>
+ <Real Name="Cell 4 3 2">0.014060101366706755</Real>
+ <Real Name="Cell 4 3 3">0.21059581558386664</Real>
+ <Real Name="Cell 4 3 4">0.75488543362632587</Real>
+ <Real Name="Cell 4 3 5">0.25512450276702403</Real>
+ <Real Name="Cell 4 3 6">0.0022781167300332033</Real>
+ <Real Name="Cell 4 4 0">0.033258819938330797</Real>
+ <Real Name="Cell 4 4 1">0.52474813211099514</Real>
+ <Real Name="Cell 4 4 2">0.1818911746733872</Real>
+ <Real Name="Cell 4 4 3">0.12930160007977831</Real>
+ <Real Name="Cell 4 4 4">1.9149130085007566</Real>
+ <Real Name="Cell 4 4 5">0.69299270525738577</Real>
+ <Real Name="Cell 4 4 6">0.0048906685480422209</Real>
+ <Real Name="Cell 4 5 0">0.021441930750053368</Real>
+ <Real Name="Cell 4 5 1">0.33830464011672068</Real>
+ <Real Name="Cell 4 5 2">0.11673865854400045</Real>
+ <Real Name="Cell 4 5 3">0.0064496111881862817</Real>
+ <Real Name="Cell 4 5 4">0.10828690342773702</Real>
+ <Real Name="Cell 4 5 5">0.039047766821141347</Real>
+ <Real Name="Cell 4 5 6">0.00016442634048088761</Real>
+ <Real Name="Cell 4 6 1">0.010083755583954317</Real>
+ <Real Name="Cell 4 6 2">0.015771492361433749</Real>
+ <Real Name="Cell 4 6 3">0.00018750776286506287</Real>
+ <Real Name="Cell 4 7 1">0.27187051596858192</Real>
+ <Real Name="Cell 4 7 2">0.42521893060562377</Real>
+ <Real Name="Cell 4 7 3">0.0050554410818283964</Real>
+ <Real Name="Cell 4 8 1">0.12167556623225267</Real>
+ <Real Name="Cell 4 8 2">0.19030660228007695</Real>
+ <Real Name="Cell 4 8 3">0.0022625611092610995</Real>
+ <Real Name="Cell 5 3 3">0.0012625752032468175</Real>
+ <Real Name="Cell 5 3 4">0.021195022858288406</Real>
+ <Real Name="Cell 5 3 5">0.0075679301049474106</Real>
+ <Real Name="Cell 5 4 3">0.0034450209945261568</Real>
+ <Real Name="Cell 5 4 4">0.057832039262687311</Real>
+ <Real Name="Cell 5 4 5">0.020649604102476335</Real>
+ <Real Name="Cell 5 5 3">0.00019544284800053645</Real>
+ <Real Name="Cell 5 5 4">0.0032809258570957118</Real>
+ <Real Name="Cell 5 5 5">0.0011714928420709493</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>0.023382024515234419</Real>
+ <Real>0.66948591982610428</Real>
+ <Real>0.30713205565866131</Real>
+ <Real>0.030012519422176642</Real>
+ <Real>0.68497504042982427</Real>
+ <Real>0.28501244014799909</Real>
+ <Real>0.330078125</Real>
+ <Real>0.65234375</Real>
+ <Real>0.017578125</Real>
+ <Real>0.49976447018752879</Real>
+ <Real>0.50023550206879008</Real>
+ <Real>2.7743681130232289e-08</Real>
+ <Real>0.18225710646138371</Real>
+ <Real>0.73923591165094016</Real>
+ <Real>0.078506981887676131</Real>
+ <Real>0.15961255758703274</Real>
+ <Real>0.74577498674987708</Real>
+ <Real>0.094612455663090178</Real>
+ <Real>0.019999988675119096</Real>
+ <Real>0.65999996602534927</Real>
+ <Real>0.32000004529953163</Real>
+ <Real>0.3741123922437507</Real>
+ <Real>0.61677509093879102</Real>
+ <Real>0.0091125168174582827</Real>
+ <Real>0.43594452067539102</Real>
+ <Real>0.56186094732433545</Real>
+ <Real>0.0021945320002735302</Real>
+ <Real>0.27658205230720379</Real>
+ <Real>0.6905859236977987</Real>
+ <Real>0.032832023994997545</Real>
+ <Real>0.0031007776826630362</Real>
+ <Real>0.5725483993351439</Real>
+ <Real>0.42435082298219307</Real>
+ <Real>0.15056328435726465</Real>
+ <Real>0.747623436947912</Real>
+ <Real>0.1018132786948234</Real>
+ <Real>0.46080006523132555</Real>
+ <Real>0.53839993748664394</Real>
+ <Real>0.0007999972820305068</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>0.080000018232009792</Real>
+ <Real>0.74000000911600228</Real>
+ <Real>0.17999997265198792</Real>
+ <Real>0.031250026296172552</Real>
+ <Real>0.68750005259232294</Real>
+ <Real>0.28124992111150449</Real>
+ <Real>0.3612502145767475</Real>
+ <Real>0.62749982328969989</Real>
+ <Real>0.011249962133552631</Real>
+ <Real>0.080000123416718763</Real>
+ <Real>0.7400000617082404</Real>
+ <Real>0.17999981487504085</Real>
+ <Real>0.12500001753077744</Real>
+ <Real>0.74999999999999878</Real>
+ <Real>0.12499998246922378</Real>
+ <Real>0.0012499940395428412</Real>
+ <Real>0.54749989271162902</Real>
+ <Real>0.45125011324882813</Real>
+ <Real>0.061250033133174432</Real>
+ <Real>0.72750002839985095</Real>
+ <Real>0.21124993846697457</Real>
+ <Real>0.079999955121217034</Real>
+ <Real>0.73999997756059277</Real>
+ <Real>0.18000006731819018</Real>
+ <Real>0.5</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>0.12500101678715228</Real>
+ <Real>0.74999999999586464</Real>
+ <Real>0.12499898321698313</Real>
+ <Real>0.10124999842222977</Real>
+ <Real>0.74749999964938441</Real>
+ <Real>0.15125000192838584</Real>
+ <Real>0.28124997370383537</Real>
+ <Real>0.68750001753077561</Real>
+ <Real>0.031250008765389033</Real>
+ <Real>0.24500001595301041</Real>
+ <Real>0.70999999088399368</Real>
+ <Real>0.04499999316299591</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>0.088200132179309776</Real>
+ <Real>0.74360005035390486</Real>
+ <Real>0.16819981746678536</Real>
+ <Real>0.36551256726980519</Real>
+ <Real>0.62397494413852073</Real>
+ <Real>0.010512488591674085</Real>
+ <Real>0.2664500574350388</Real>
+ <Real>0.6970999638080535</Real>
+ <Real>0.036449978756907697</Real>
+ <Real>0.10351235680585091</Real>
+ <Real>0.74797497167577376</Real>
+ <Real>0.14851267151837533</Real>
+ <Real>0.10125023603453087</Real>
+ <Real>0.74750005245181228</Real>
+ <Real>0.15124971151365685</Real>
+ <Real>0.15680000550746923</Real>
+ <Real>0.74639999881982799</Real>
+ <Real>0.096799995672702838</Real>
+ <Real>0.0036125133752946681</Real>
+ <Real>0.57777513060567287</Real>
+ <Real>0.41861235601903246</Real>
+ <Real>0.0072000023603441266</Real>
+ <Real>0.60560001494884452</Real>
+ <Real>0.38719998269081135</Real>
+ <Real>0.017112486657502868</Real>
+ <Real>0.65077495456337409</Real>
+ <Real>0.33211255877912305</Real>
+ <Real>0.20479996223449881</Real>
+ <Real>0.73040001652240405</Real>
+ <Real>0.064800021243097139</Real>
+ <Real>0.03379998977184373</Real>
+ <Real>0.69239998111724699</Real>
+ <Real>0.27380002911090928</Real>
+ <Real>0.34445001088380822</Real>
+ <Real>0.64109999134540541</Real>
+ <Real>0.014449997770786371</Real>
+ <Real>0.41405002386570011</Real>
+ <Real>0.58189997849464348</Real>
+ <Real>0.0040499976396564108</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>-0.2162499688565731</Real>
+ <Real>-0.56750006228685379</Real>
+ <Real>0.7837500311434269</Real>
+ <Real>-0.24500007927417755</Real>
+ <Real>-0.5099998414516449</Real>
+ <Real>0.75499992072582245</Real>
+ <Real>-0.8125</Real>
+ <Real>0.625</Real>
+ <Real>0.1875</Real>
+ <Real>-0.99976444244384766</Real>
+ <Real>0.99952888488769531</Real>
+ <Real>0.00023555755615234375</Real>
+ <Real>-0.60375012457370758</Real>
+ <Real>0.20750024914741516</Real>
+ <Real>0.39624987542629242</Real>
+ <Real>-0.56500010192394257</Real>
+ <Real>0.13000020384788513</Real>
+ <Real>0.43499989807605743</Real>
+ <Real>-0.19999994337558746</Real>
+ <Real>-0.60000011324882507</Real>
+ <Real>0.80000005662441254</Real>
+ <Real>-0.86499987542629242</Real>
+ <Real>0.72999975085258484</Real>
+ <Real>0.13500012457370758</Real>
+ <Real>-0.93374998867511749</Real>
+ <Real>0.86749997735023499</Real>
+ <Real>0.066250011324882507</Real>
+ <Real>-0.74375002831220627</Real>
+ <Real>0.48750005662441254</Real>
+ <Real>0.25624997168779373</Real>
+ <Real>-0.078749954700469971</Real>
+ <Real>-0.84250009059906006</Real>
+ <Real>0.92125004529953003</Real>
+ <Real>-0.54875000566244125</Real>
+ <Real>0.097500011324882507</Real>
+ <Real>0.45124999433755875</Real>
+ <Real>-0.96000006794929504</Real>
+ <Real>0.92000013589859009</Real>
+ <Real>0.039999932050704956</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>-0.40000004558002189</Real>
+ <Real>-0.19999990883995622</Real>
+ <Real>0.59999995441997811</Real>
+ <Real>-0.25000010518466809</Real>
+ <Real>-0.49999978963066383</Real>
+ <Real>0.74999989481533191</Real>
+ <Real>-0.85000025244319488</Real>
+ <Real>0.70000050488638976</Real>
+ <Real>0.14999974755680512</Real>
+ <Real>-0.4000003085416779</Real>
+ <Real>-0.19999938291664421</Real>
+ <Real>0.5999996914583221</Real>
+ <Real>-0.50000003506155366</Real>
+ <Real>7.0123107320796407e-08</Real>
+ <Real>0.49999996493844634</Real>
+ <Real>-0.049999880790714712</Real>
+ <Real>-0.90000023841857058</Real>
+ <Real>0.95000011920928529</Real>
+ <Real>-0.35000009466619986</Real>
+ <Real>-0.29999981066760029</Real>
+ <Real>0.64999990533380014</Real>
+ <Real>-0.39999988780302687</Real>
+ <Real>-0.20000022439394627</Real>
+ <Real>0.60000011219697313</Real>
+ <Real>-1</Real>
+ <Real>1</Real>
+ <Real>0</Real>
+ <Real>-0.50000203357016915</Real>
+ <Real>4.0671403382930293e-06</Real>
+ <Real>0.49999796642983085</Real>
+ <Real>-0.44999999649384392</Real>
+ <Real>-0.10000000701231215</Real>
+ <Real>0.55000000350615608</Real>
+ <Real>-0.74999996493844634</Real>
+ <Real>0.49999992987689268</Real>
+ <Real>0.25000003506155366</Real>
+ <Real>-0.7000000227900145</Real>
+ <Real>0.400000045580029</Real>
+ <Real>0.2999999772099855</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>-0.42000031471252441</Real>
+ <Real>-0.15999937057495117</Real>
+ <Real>0.57999968528747559</Real>
+ <Real>-0.8550000786781311</Real>
+ <Real>0.71000015735626221</Real>
+ <Real>0.1449999213218689</Real>
+ <Real>-0.7300000786781311</Real>
+ <Real>0.46000015735626221</Real>
+ <Real>0.2699999213218689</Real>
+ <Real>-0.45499968528747559</Real>
+ <Real>-0.090000629425048828</Real>
+ <Real>0.54500031471252441</Real>
+ <Real>-0.45000052452087402</Real>
+ <Real>-0.099998950958251953</Real>
+ <Real>0.54999947547912598</Real>
+ <Real>-0.56000000983476639</Real>
+ <Real>0.12000001966953278</Real>
+ <Real>0.43999999016523361</Real>
+ <Real>-0.085000157356262207</Real>
+ <Real>-0.82999968528747559</Real>
+ <Real>0.91499984264373779</Real>
+ <Real>-0.12000001966953278</Real>
+ <Real>-0.75999996066093445</Real>
+ <Real>0.87999998033046722</Real>
+ <Real>-0.18499992787837982</Real>
+ <Real>-0.63000014424324036</Real>
+ <Real>0.81500007212162018</Real>
+ <Real>-0.63999994099140167</Real>
+ <Real>0.27999988198280334</Real>
+ <Real>0.36000005900859833</Real>
+ <Real>-0.25999996066093445</Real>
+ <Real>-0.4800000786781311</Real>
+ <Real>0.74000003933906555</Real>
+ <Real>-0.83000001311302185</Real>
+ <Real>0.6600000262260437</Real>
+ <Real>0.16999998688697815</Real>
+ <Real>-0.9100000262260437</Real>
+ <Real>0.8200000524520874</Real>
+ <Real>0.089999973773956299</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">8</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">16</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">9</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">0</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">5</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 4 10">0.00033979852581477555</Real>
+ <Real Name="Cell 0 4 8">0.00017818256489556583</Real>
+ <Real Name="Cell 0 4 9">0.0015022263680871451</Real>
+ <Real Name="Cell 0 5 10">0.0031431356861857176</Real>
+ <Real Name="Cell 0 5 8">0.0016481883699655609</Real>
+ <Real Name="Cell 0 5 9">0.01389559090917796</Real>
+ <Real Name="Cell 0 6 10">0.00076454639268285103</Real>
+ <Real Name="Cell 0 6 8">0.00040091061873570724</Real>
+ <Real Name="Cell 0 6 9">0.0033800080443555183</Real>
+ <Real Name="Cell 0 7 5">0.084015665878839491</Real>
+ <Real Name="Cell 0 7 6">0.17346451942957417</Real>
+ <Real Name="Cell 0 7 7">0.12703198776749894</Real>
+ <Real Name="Cell 0 7 8">0.024522774730782425</Real>
+ <Real Name="Cell 0 8 5">0.20537165214239544</Real>
+ <Real Name="Cell 0 8 6">0.54034620040982984</Real>
+ <Real Name="Cell 0 8 7">1.1510578006413572</Real>
+ <Real Name="Cell 0 8 8">0.22683533523454369</Real>
+ <Real Name="Cell 0 9 5">0.0093350774777616521</Real>
+ <Real Name="Cell 0 9 6">0.055832087480720508</Real>
+ <Real Name="Cell 0 9 7">0.27828266895736808</Real>
+ <Real Name="Cell 0 9 8">0.055176101276372402</Real>
+ <Real Name="Cell 1 10 6">0.0010883693853612156</Real>
+ <Real Name="Cell 1 10 7">0.0028474464087142122</Real>
+ <Real Name="Cell 1 10 8">0.00014888734255858396</Real>
+ <Real Name="Cell 1 4 10">0.0097292827856903189</Real>
+ <Real Name="Cell 1 4 8">0.0051018130734727116</Real>
+ <Real Name="Cell 1 4 9">0.043012503094870161</Real>
+ <Real Name="Cell 1 5 10">0.089995846366223098</Real>
+ <Real Name="Cell 1 5 8">0.047191760755966275</Real>
+ <Real Name="Cell 1 5 9">0.39786556785521332</Real>
+ <Real Name="Cell 1 6 10">0.021890877952912662</Real>
+ <Real Name="Cell 1 6 8">0.011479075055175422</Real>
+ <Real Name="Cell 1 6 9">0.096778095203887429</Real>
+ <Real Name="Cell 1 7 5">0.41718059718172407</Real>
+ <Real Name="Cell 1 7 6">0.79357651466241896</Real>
+ <Real Name="Cell 1 7 7">0.14112497270190399</Real>
+ <Real Name="Cell 1 7 8">0.024545887635769155</Real>
+ <Real Name="Cell 1 8 5">1.0197749144608135</Real>
+ <Real Name="Cell 1 8 6">2.0912342252936194</Real>
+ <Real Name="Cell 1 8 7">1.2777345644176898</Real>
+ <Real Name="Cell 1 8 8">0.23183008622566867</Real>
+ <Real Name="Cell 1 9 5">0.046353417022564243</Real>
+ <Real Name="Cell 1 9 6">0.18547491543672612</Real>
+ <Real Name="Cell 1 9 7">0.43892226002306806</Real>
+ <Real Name="Cell 1 9 8">0.063532735899987328</Real>
+ <Real Name="Cell 16 5 0">8.7594955501962249e-05</Real>
+ <Real Name="Cell 16 5 1">0.00041696984940586026</Real>
+ <Real Name="Cell 16 5 2">5.4076473314515499e-05</Real>
+ <Real Name="Cell 16 6 0">0.038366765938295154</Real>
+ <Real Name="Cell 16 6 1">0.18263362911489175</Real>
+ <Real Name="Cell 16 6 2">0.023685603611956891</Real>
+ <Real Name="Cell 16 7 0">0.031621937657192963</Real>
+ <Real Name="Cell 16 7 1">0.15052687117976654</Real>
+ <Real Name="Cell 16 7 2">0.019521704852446232</Real>
+ <Real Name="Cell 17 5 0">0.00040927936853095821</Real>
+ <Real Name="Cell 17 5 1">0.0019482532490978466</Real>
+ <Real Name="Cell 17 5 2">0.00025266734509671985</Real>
+ <Real Name="Cell 17 6 0">0.1792651830897814</Real>
+ <Real Name="Cell 17 6 1">0.85333882491652924</Real>
+ <Real Name="Cell 17 6 2">0.11066880317507713</Real>
+ <Real Name="Cell 17 7 0">0.14775059364886992</Real>
+ <Real Name="Cell 17 7 1">0.70332295313530524</Real>
+ <Real Name="Cell 17 7 2">0.091213369410045014</Real>
+ <Real Name="Cell 18 5 0">5.1923069018054873e-05</Real>
+ <Real Name="Cell 18 5 1">0.00024716439599839095</Real>
+ <Real Name="Cell 18 5 2">3.2054545151286616e-05</Real>
+ <Real Name="Cell 18 6 0">0.022742408217434739</Real>
+ <Real Name="Cell 18 6 1">0.10825850044912612</Real>
+ <Real Name="Cell 18 6 2">0.014039954972639695</Real>
+ <Real Name="Cell 18 7 0">0.018744321999481783</Real>
+ <Real Name="Cell 18 7 1">0.089226794814272023</Real>
+ <Real Name="Cell 18 7 2">0.011571748882056981</Real>
+ <Real Name="Cell 2 0 1">0.022753288764355752</Real>
+ <Real Name="Cell 2 0 2">0.86529040215781761</Real>
+ <Real Name="Cell 2 0 3">0.44158707635031469</Real>
+ <Real Name="Cell 2 1 1">0.022753288764355752</Real>
+ <Real Name="Cell 2 1 2">0.86529040215781761</Real>
+ <Real Name="Cell 2 1 3">0.44158707635031469</Real>
+ <Real Name="Cell 2 10 6">0.0021509785485837041</Real>
+ <Real Name="Cell 2 10 7">0.0056274976361570823</Real>
+ <Real Name="Cell 2 10 8">0.00029425072434655059</Real>
+ <Real Name="Cell 2 3 2">0.00071647563036925078</Real>
+ <Real Name="Cell 2 3 3">0.0012231120937252554</Real>
+ <Real Name="Cell 2 3 4">2.0606519624561914e-05</Real>
+ <Real Name="Cell 2 4 10">0.010870740615147208</Real>
+ <Real Name="Cell 2 4 2">0.0157624518101704</Real>
+ <Real Name="Cell 2 4 3">0.026910992269419991</Real>
+ <Real Name="Cell 2 4 4">0.00050551465829993657</Real>
+ <Real Name="Cell 2 4 5">2.0630529598032113e-05</Real>
+ <Real Name="Cell 2 4 8">0.022590889607581807</Real>
+ <Real Name="Cell 2 4 9">0.091953470864929776</Real>
+ <Real Name="Cell 2 5 10">0.079730129199632044</Real>
+ <Real Name="Cell 2 5 2">0.0064482734385521989</Real>
+ <Real Name="Cell 2 5 3">0.011026798734413678</Real>
+ <Real Name="Cell 2 5 4">0.00057062638631341807</Real>
+ <Real Name="Cell 2 5 5">0.00015230934427263969</Real>
+ <Real Name="Cell 2 5 8">0.14315096256908022</Real>
+ <Real Name="Cell 2 5 9">0.61584734032591548</Real>
+ <Real Name="Cell 2 6 10">0.016449866071848479</Real>
+ <Real Name="Cell 2 6 3">3.8044669821726105e-06</Real>
+ <Real Name="Cell 2 6 4">7.7935315495623989e-05</Real>
+ <Real Name="Cell 2 6 5">3.0818446322078073e-05</Real>
+ <Real Name="Cell 2 6 8">0.02551618044207965</Real>
+ <Real Name="Cell 2 6 9">0.11661769417980841</Real>
+ <Real Name="Cell 2 7 5">0.056812724572056175</Real>
+ <Real Name="Cell 2 7 6">0.10574143245003807</Real>
+ <Real Name="Cell 2 7 7">0.0023833534014874617</Real>
+ <Real Name="Cell 2 7 8">1.3613453599533678e-09</Real>
+ <Real Name="Cell 2 8 5">0.13887556547966037</Real>
+ <Real Name="Cell 2 8 6">0.32754967899868059</Real>
+ <Real Name="Cell 2 8 7">0.18653193978312091</Real>
+ <Real Name="Cell 2 8 8">0.0094487677124567102</Real>
+ <Real Name="Cell 2 9 5">0.0063125273132716301</Real>
+ <Real Name="Cell 2 9 6">0.13172622800644337</Real>
+ <Real Name="Cell 2 9 7">0.31415511253401474</Real>
+ <Real Name="Cell 2 9 8">0.016412705198223475</Real>
+ <Real Name="Cell 3 0 1">0.029325255333130615</Real>
+ <Real Name="Cell 3 0 2">1.1152173315857687</Real>
+ <Real Name="Cell 3 0 3">0.56913327562870597</Real>
+ <Real Name="Cell 3 1 1">0.029325255333130615</Real>
+ <Real Name="Cell 3 1 2">1.1152173315857687</Real>
+ <Real Name="Cell 3 1 3">0.56913327562870597</Real>
+ <Real Name="Cell 3 10 0">0.010145751826232199</Real>
+ <Real Name="Cell 3 10 1">0.85337020047029799</Real>
+ <Real Name="Cell 3 10 2">0.54561578384185616</Real>
+ <Real Name="Cell 3 10 6">5.7960499812135745e-05</Real>
+ <Real Name="Cell 3 10 7">0.00015163915786052019</Real>
+ <Real Name="Cell 3 10 8">7.9289117338890878e-06</Real>
+ <Real Name="Cell 3 11 0">0.0024678865771531875</Real>
+ <Real Name="Cell 3 11 1">0.2075766191755235</Real>
+ <Real Name="Cell 3 11 2">0.13271740648581237</Real>
+ <Real Name="Cell 3 2 2">0.24260448267074416</Real>
+ <Real Name="Cell 3 2 3">0.34095286828095939</Real>
+ <Real Name="Cell 3 2 4">0.0023730166056101336</Real>
+ <Real Name="Cell 3 3 2">0.71940994058169738</Real>
+ <Real Name="Cell 3 3 3">1.0159824779923214</Real>
+ <Real Name="Cell 3 3 4">0.0073472068525608069</Real>
+ <Real Name="Cell 3 4 10">0.015998248299614531</Real>
+ <Real Name="Cell 3 4 2">0.40433187211438543</Real>
+ <Real Name="Cell 3 4 3">0.68135139693612101</Real>
+ <Real Name="Cell 3 4 4">0.023405432983189891</Real>
+ <Real Name="Cell 3 4 5">0.0038093594277436656</Real>
+ <Real Name="Cell 3 4 8">0.050562339096890584</Real>
+ <Real Name="Cell 3 4 9">0.18032587950135495</Real>
+ <Real Name="Cell 3 5 0">0.0076351676149998314</Real>
+ <Real Name="Cell 3 5 1">0.056368147040608489</Real>
+ <Real Name="Cell 3 5 10">0.095988708996469344</Real>
+ <Real Name="Cell 3 5 2">0.15888080548132233</Real>
+ <Real Name="Cell 3 5 3">0.30371763843954619</Real>
+ <Real Name="Cell 3 5 4">0.11086210523037408</Real>
+ <Real Name="Cell 3 5 5">0.028123419410124081</Real>
+ <Real Name="Cell 3 5 8">0.3033715668651783</Real>
+ <Real Name="Cell 3 5 9">1.0819464761279529</Real>
+ <Real Name="Cell 3 6 0">0.045810999265179453</Real>
+ <Real Name="Cell 3 6 1">0.33820883481113989</Real>
+ <Real Name="Cell 3 6 10">0.015997988033247611</Real>
+ <Real Name="Cell 3 6 2">0.068522407341301245</Real>
+ <Real Name="Cell 3 6 3">0.014934082496857223</Real>
+ <Real Name="Cell 3 6 4">0.024701645567436741</Real>
+ <Real Name="Cell 3 6 5">0.0056905247384739233</Real>
+ <Real Name="Cell 3 6 8">0.05056151652706585</Real>
+ <Real Name="Cell 3 6 9">0.18032294588258366</Real>
+ <Real Name="Cell 3 7 0">0.0076351654733934201</Real>
+ <Real Name="Cell 3 7 1">0.05636813122977221</Real>
+ <Real Name="Cell 3 7 2">0.011405569215818359</Real>
+ <Real Name="Cell 3 8 6">0.0018611834196012062</Real>
+ <Real Name="Cell 3 8 7">0.0048693211288215509</Real>
+ <Real Name="Cell 3 8 8">0.00025460717389303762</Real>
+ <Real Name="Cell 3 9 0">0.0010968374532188702</Real>
+ <Real Name="Cell 3 9 1">0.0922561889318676</Real>
+ <Real Name="Cell 3 9 2">0.058985458843749838</Real>
+ <Real Name="Cell 3 9 6">0.0032329178496899079</Real>
+ <Real Name="Cell 3 9 7">0.008458121336913935</Real>
+ <Real Name="Cell 3 9 8">0.00044225844076897785</Real>
+ <Real Name="Cell 4 0 1">0.00011453939191042932</Real>
+ <Real Name="Cell 4 0 2">0.004355846643336595</Real>
+ <Real Name="Cell 4 0 3">0.0022229364609438027</Real>
+ <Real Name="Cell 4 1 1">0.00011453939191042932</Real>
+ <Real Name="Cell 4 1 2">0.004355846643336595</Real>
+ <Real Name="Cell 4 1 3">0.0022229364609438027</Real>
+ <Real Name="Cell 4 10 0">0.016726649891858267</Real>
+ <Real Name="Cell 4 10 1">1.4068966810823802</Real>
+ <Real Name="Cell 4 10 2">0.89952172575305001</Real>
+ <Real Name="Cell 4 11 0">0.0040686462132976968</Real>
+ <Real Name="Cell 4 11 1">0.34221824997802897</Real>
+ <Real Name="Cell 4 11 2">0.21880267040476464</Real>
+ <Real Name="Cell 4 2 2">0.28345967841462172</Real>
+ <Real Name="Cell 4 2 3">0.398370175742504</Real>
+ <Real Name="Cell 4 2 4">0.0027726384792803398</Real>
+ <Real Name="Cell 4 3 2">0.82825849042288924</Real>
+ <Real Name="Cell 4 3 3">1.166075644183495</Real>
+ <Real Name="Cell 4 3 4">0.0082306813353532505</Real>
+ <Real Name="Cell 4 4 10">0.00076059307614952955</Real>
+ <Real Name="Cell 4 4 2">0.20260276249046691</Real>
+ <Real Name="Cell 4 4 3">0.46522211219696519</Real>
+ <Real Name="Cell 4 4 4">0.11061191382510344</Real>
+ <Real Name="Cell 4 4 5">0.0028233504976611979</Real>
+ <Real Name="Cell 4 4 8">0.0024038484908342275</Real>
+ <Real Name="Cell 4 4 9">0.0085731020565926342</Real>
+ <Real Name="Cell 4 5 0">0.030968285418697873</Real>
+ <Real Name="Cell 4 5 1">0.22862954084299197</Real>
+ <Real Name="Cell 4 5 10">0.0045635213358331071</Real>
+ <Real Name="Cell 4 5 2">0.11760920316189255</Real>
+ <Real Name="Cell 4 5 3">1.7244611989533951</Real>
+ <Real Name="Cell 4 5 4">1.2262834578844777</Real>
+ <Real Name="Cell 4 5 5">0.020843995347149334</Real>
+ <Real Name="Cell 4 5 8">0.014422973624171607</Real>
+ <Real Name="Cell 4 5 9">0.051438193925714422</Real>
+ <Real Name="Cell 4 6 0">0.18580968645308085</Real>
+ <Real Name="Cell 4 6 1">1.3717770526714039</Real>
+ <Real Name="Cell 4 6 10">0.00076058070249505633</Real>
+ <Real Name="Cell 4 6 2">0.2805028021484528</Real>
+ <Real Name="Cell 4 6 3">0.47016370063536744</Real>
+ <Real Name="Cell 4 6 4">0.35093367474363762</Real>
+ <Real Name="Cell 4 6 5">0.0042175977764954617</Real>
+ <Real Name="Cell 4 6 8">0.0024038093839956771</Real>
+ <Real Name="Cell 4 6 9">0.0085729625856903382</Real>
+ <Real Name="Cell 4 7 0">0.030968276732329478</Real>
+ <Real Name="Cell 4 7 1">0.22862947671414563</Real>
+ <Real Name="Cell 4 7 2">0.046261056816129208</Real>
+ <Real Name="Cell 4 9 0">0.0018082855152078731</Real>
+ <Real Name="Cell 4 9 1">0.1520968577834364</Real>
+ <Real Name="Cell 4 9 2">0.0972455403688324</Real>
+ <Real Name="Cell 5 10 0">0.00024712716301057887</Real>
+ <Real Name="Cell 5 10 1">0.020786133965422622</Real>
+ <Real Name="Cell 5 10 2">0.013289944704344794</Real>
+ <Real Name="Cell 5 11 0">6.011203692829193e-05</Real>
+ <Real Name="Cell 5 11 1">0.0050560886844819245</Real>
+ <Real Name="Cell 5 11 2">0.0032326905594280381</Real>
+ <Real Name="Cell 5 2 2">0.00042118684737507846</Real>
+ <Real Name="Cell 5 2 3">0.00059192996812694541</Real>
+ <Real Name="Cell 5 2 4">4.1198059157139e-06</Real>
+ <Real Name="Cell 5 3 2">0.001220582197244095</Real>
+ <Real Name="Cell 5 3 3">0.001715388753503997</Real>
+ <Real Name="Cell 5 3 4">1.1939028457703049e-05</Real>
+ <Real Name="Cell 5 4 2">0.00049015578742989607</Real>
+ <Real Name="Cell 5 4 3">0.066129974627542984</Real>
+ <Real Name="Cell 5 4 4">0.047834785417711266</Real>
+ <Real Name="Cell 5 5 0">0.0032888372766258409</Real>
+ <Real Name="Cell 5 5 1">0.024280496846889963</Real>
+ <Real Name="Cell 5 5 2">0.0098159243010806398</Real>
+ <Real Name="Cell 5 5 3">0.78417040521923786</Real>
+ <Real Name="Cell 5 5 4">0.56815083145775247</Real>
+ <Real Name="Cell 5 6 0">0.019733020892273433</Real>
+ <Real Name="Cell 5 6 1">0.14568296064985509</Real>
+ <Real Name="Cell 5 6 2">0.030901317814393377</Real>
+ <Real Name="Cell 5 6 3">0.22770576410086152</Real>
+ <Real Name="Cell 5 6 4">0.16497845154645666</Real>
+ <Real Name="Cell 5 7 0">0.0032888363541320131</Real>
+ <Real Name="Cell 5 7 1">0.024280490036395375</Real>
+ <Real Name="Cell 5 7 2">0.0049129322484586218</Real>
+ <Real Name="Cell 5 9 0">2.6716435877812135e-05</Real>
+ <Real Name="Cell 5 9 1">0.0022471484254082343</Real>
+ <Real Name="Cell 5 9 2">0.0014367500164200787</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>0.00021708683077646437</Real>
+ <Real>0.10685313751771594</Real>
+ <Real>0.56622690927004382</Real>
+ <Real>0.31478347546866026</Real>
+ <Real>0.011919390912803422</Real>
+ <Real>0.00555681060650858</Real>
+ <Real>0.24823626950660688</Real>
+ <Real>0.59218767283768492</Real>
+ <Real>0.15299780777998639</Real>
+ <Real>0.0010214392692131807</Real>
+ <Real>0.0055706031003877185</Real>
+ <Real>0.24842522267954437</Real>
+ <Real>0.59213916477497697</Real>
+ <Real>0.15284743306593457</Real>
+ <Real>0.0010175763791563232</Real>
+ <Real>7.9004320672188935e-05</Real>
+ <Real>0.088529908212318653</Real>
+ <Real>0.54771436432265241</Real>
+ <Real>0.34733817457128247</Real>
+ <Real>0.016338548573074076</Real>
+ <Real>0.0012959629629042319</Real>
+ <Real>0.16290908840719873</Real>
+ <Real>0.5949639220172942</Real>
+ <Real>0.23611429987157478</Real>
+ <Real>0.0047167267410280055</Real>
+ <Real>0.0030707289787711557</Real>
+ <Real>0.20766465349097596</Real>
+ <Real>0.59868195490802356</Real>
+ <Real>0.18838975650061909</Real>
+ <Real>0.0021929061216100672</Real>
+ <Real>0.0094664469245116546</Real>
+ <Real>0.292875904454512</Real>
+ <Real>0.57662973675080809</Real>
+ <Real>0.12064508407747568</Real>
+ <Real>0.00038282779269252336</Real>
+ <Real>2.4732795142422786e-06</Real>
+ <Real>0.058324774366595201</Real>
+ <Real>0.49997145574959673</Real>
+ <Real>0.41284792733169456</Real>
+ <Real>0.028853369272599252</Real>
+ <Real>0.0001122461656009853</Real>
+ <Real>0.094134504932700883</Real>
+ <Real>0.55402979196571256</Real>
+ <Real>0.33690993174225514</Real>
+ <Real>0.014813525193730359</Real>
+ <Real>0.0029041821408254892</Real>
+ <Real>0.20429690725194238</Real>
+ <Real>0.59883901780490834</Real>
+ <Real>0.1916318736441007</Real>
+ <Real>0.0023280191582231232</Real>
+ <Real>0.0067521400006586548</Real>
+ <Real>0.26361111244989777</Real>
+ <Real>0.58773820865348103</Real>
+ <Real>0.14115472132129334</Real>
+ <Real>0.00074381757466905163</Real>
+ <Real>4.5824991688022811e-05</Real>
+ <Real>0.08113201123186245</Real>
+ <Real>0.53835170637041108</Real>
+ <Real>0.36182499545693908</Real>
+ <Real>0.018645461949099336</Real>
+ <Real>0.00045614602247217174</Real>
+ <Real>0.12555140868204157</Real>
+ <Real>0.57972350108592152</Real>
+ <Real>0.28554029601040781</Real>
+ <Real>0.0087286481991568354</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>4.0445689790761521e-07</Real>
+ <Real>0.051775860314962917</Real>
+ <Real>0.48537868893172431</Real>
+ <Real>0.42973098647302688</Real>
+ <Real>0.033114059823387824</Real>
+ <Real>0.040349760360540596</Real>
+ <Real>0.45431917497727448</Real>
+ <Real>0.46231551720983821</Real>
+ <Real>0.043015547281948473</Real>
+ <Real>1.7039818940569402e-10</Real>
+ <Real>0.015128431656919935</Real>
+ <Real>0.33912518267111513</Real>
+ <Real>0.55271819213710216</Real>
+ <Real>0.092923758682779953</Real>
+ <Real>0.00010443485208280977</Real>
+ <Real>9.2885392266106725e-06</Real>
+ <Real>0.066031433813125914</Real>
+ <Real>0.51483976179875901</Real>
+ <Real>0.39438014636383906</Real>
+ <Real>0.024739369485049234</Real>
+ <Real>0.013022673519183717</Real>
+ <Real>0.32362472920489493</Real>
+ <Real>0.56155215775990919</Real>
+ <Real>0.1016316085083009</Real>
+ <Real>0.00016883100771119422</Real>
+ <Real>0.0039663616904885837</Real>
+ <Real>0.22407360111788807</Real>
+ <Real>0.59703848434694429</Real>
+ <Real>0.17329435021010889</Real>
+ <Real>0.001627202634570212</Real>
+ <Real>0.0033463234311831495</Real>
+ <Real>0.21299812095041259</Real>
+ <Real>0.59830465286561263</Real>
+ <Real>0.18335801078383104</Real>
+ <Real>0.0019928919689605092</Real>
+ <Real>0.0011600005621822387</Real>
+ <Real>0.15817872363342664</Real>
+ <Real>0.5937405609424351</Real>
+ <Real>0.24181947217421018</Real>
+ <Real>0.005101242687745782</Real>
+ <Real>2.6188756138822681e-05</Real>
+ <Real>0.074880580528960364</Real>
+ <Real>0.52940638875946033</Real>
+ <Real>0.37477740365364631</Real>
+ <Real>0.020909438301794151</Real>
+ <Real>0.00012302926676329543</Real>
+ <Real>0.095721497307896308</Real>
+ <Real>0.55570684053130115</Real>
+ <Real>0.33403649747337788</Real>
+ <Real>0.014412135420661361</Real>
+ <Real>0.0080438175486878816</Real>
+ <Real>0.27835174040155514</Real>
+ <Real>0.58255814246999404</Real>
+ <Real>0.13050795912816038</Real>
+ <Real>0.0005383404516025815</Real>
+ <Real>7.6674538268946279e-05</Real>
+ <Real>0.08808460996980419</Real>
+ <Real>0.54718509906177959</Real>
+ <Real>0.34818620507411202</Real>
+ <Real>0.016467411356035154</Real>
+ <Real>0.020350910822734453</Real>
+ <Real>0.37168637272872385</Real>
+ <Real>0.53159022896744179</Real>
+ <Real>0.076342335409551182</Real>
+ <Real>3.015207154867334e-05</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>8.0781071366164143e-05</Real>
+ <Real>0.088863912709195345</Real>
+ <Real>0.54810860714010579</Real>
+ <Real>0.34670402655589716</Real>
+ <Real>0.016242672523435472</Real>
+ <Real>0.0038814058076428711</Real>
+ <Real>0.22262305120967962</Real>
+ <Real>0.59724025827145955</Real>
+ <Real>0.1745837324097608</Real>
+ <Real>0.0016715523014573224</Real>
+ <Real>0.009543753462321709</Real>
+ <Real>0.29362203367646711</Real>
+ <Real>0.57630387159140495</Real>
+ <Real>0.1201544165903765</Real>
+ <Real>0.00037592467942967011</Real>
+ <Real>0.0067501440370550166</Real>
+ <Real>0.26358696701753564</Real>
+ <Real>0.5877459756955512</Real>
+ <Real>0.14117271390405697</Real>
+ <Real>0.00074419934580130292</Real>
+ <Real>0.00031590729140079595</Real>
+ <Real>0.11563401680596481</Real>
+ <Real>0.5731545365365911</Real>
+ <Real>0.30060725043776265</Real>
+ <Real>0.010288288928280482</Real>
+ <Real>0.028347089724108751</Real>
+ <Real>0.41069974749995353</Real>
+ <Real>0.50175891727755573</Real>
+ <Real>0.059191285976777946</Real>
+ <Real>2.9595216040380113e-06</Real>
+ <Real>0.00098188613037316231</Real>
+ <Real>0.15144140556262448</Real>
+ <Real>0.59167601560811955</Real>
+ <Real>0.25019950958578069</Real>
+ <Real>0.0057011831131020489</Real>
+ <Real>0.01850916350611969</Real>
+ <Real>0.36100761805514159</Real>
+ <Real>0.53889806957339226</Real>
+ <Real>0.081537796519681793</Real>
+ <Real>4.735234566460818e-05</Real>
+ <Real>0.006209064902512571</Real>
+ <Real>0.25686322541125284</Real>
+ <Real>0.58981468383641034</Real>
+ <Real>0.14625615092505842</Real>
+ <Real>0.00085687492476571407</Real>
+ <Real>0.0038355399988331635</Real>
+ <Real>0.22183168789484034</Real>
+ <Real>0.5973458516518555</Real>
+ <Real>0.17529074144732165</Real>
+ <Real>0.0016961790071493039</Real>
+ <Real>9.7026072122114408e-05</Real>
+ <Real>0.091721283461048936</Real>
+ <Real>0.55138735537598849</Real>
+ <Real>0.34134544531642963</Real>
+ <Real>0.015448889774410696</Real>
+ <Real>0.03002027414372372</Real>
+ <Real>0.41767831776931053</Real>
+ <Real>0.49589560078901784</Real>
+ <Real>0.056404209820706527</Real>
+ <Real>1.59747724137161e-06</Real>
+ <Real>0.004214083962815713</Real>
+ <Real>0.22819550614322012</Real>
+ <Real>0.59640775379533539</Real>
+ <Real>0.16967606301236299</Real>
+ <Real>0.001506593086265755</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>-0.0032320813985638091</Real>
+ <Real>-0.32416132360442773</Real>
+ <Real>-0.27678859468033556</Real>
+ <Real>0.5389894857682096</Real>
+ <Real>0.065192513915117434</Real>
+ <Real>-0.036781240901433088</Real>
+ <Real>-0.50429111252355241</Real>
+ <Real>0.12925157857804453</Real>
+ <Real>0.40149514402030057</Real>
+ <Real>0.010325630826640411</Real>
+ <Real>-0.036849690391817888</Real>
+ <Real>-0.50443110165396199</Real>
+ <Real>0.12970760425672057</Real>
+ <Real>0.40127685801571628</Real>
+ <Real>0.010296329773342997</Real>
+ <Real>-0.0015144164319307073</Real>
+ <Real>-0.28671745992113595</Real>
+ <Real>-0.33943376678124004</Real>
+ <Real>0.54507757905361098</Real>
+ <Real>0.082588064080695744</Real>
+ <Real>-0.012343878077116547</Real>
+ <Real>-0.41544815555149472</Real>
+ <Real>-0.099545525862192785</Real>
+ <Real>0.49481103068733606</Real>
+ <Real>0.032526528803468034</Real>
+ <Real>-0.023574272347497677</Real>
+ <Real>-0.46862126184458164</Real>
+ <Real>0.026278876914052063</Real>
+ <Real>0.44760312109563155</Real>
+ <Real>0.018313536182395652</Real>
+ <Real>-0.054846312535409794</Real>
+ <Real>-0.5308051855327709</Real>
+ <Real>0.2310953731700971</Real>
+ <Real>0.34961006039975789</Real>
+ <Real>0.0049460644983257609</Real>
+ <Real>-0.00011270990432847568</Real>
+ <Real>-0.21395558471812193</Real>
+ <Real>-0.44523204146839401</Real>
+ <Real>0.53278167670846766</Real>
+ <Real>0.12651865938237672</Real>
+ <Real>-0.0019707694277898893</Real>
+ <Real>-0.29864603181250143</Real>
+ <Real>-0.32005930312994324</Real>
+ <Real>0.54393977940855043</Real>
+ <Real>0.07673632496168413</Real>
+ <Real>-0.022608672803415615</Real>
+ <Real>-0.46514479473883608</Real>
+ <Real>0.01726906146395546</Real>
+ <Real>0.45133095250225974</Real>
+ <Real>0.01915345357603648</Real>
+ <Real>-0.042568491442497081</Real>
+ <Real>-0.51490723558017959</Real>
+ <Real>0.1656596194149379</Real>
+ <Real>0.38367643368065152</Real>
+ <Real>0.0081396739270872612</Real>
+ <Real>-0.0010065468105848374</Real>
+ <Real>-0.2702759651770702</Real>
+ <Real>-0.36524056546538103</Real>
+ <Real>0.54533521370431204</Real>
+ <Real>0.091187863748724007</Real>
+ <Real>-0.0056407272445787252</Real>
+ <Real>-0.35815197346276556</Real>
+ <Real>-0.21516582446249533</Real>
+ <Real>0.52735047829160231</Real>
+ <Real>0.051608046878237321</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>-2.8984203206300032e-05</Real>
+ <Real>-0.19601731158403063</Real>
+ <Real>-0.46759172313762626</Real>
+ <Real>0.52335131784016975</Real>
+ <Real>0.14028670108469343</Real>
+ <Real>-0.16270013029218783</Real>
+ <Real>-0.50390284243168182</Real>
+ <Real>0.49590616097256179</Real>
+ <Real>0.17069672651867335</Real>
+ <Real>8.5232634550106489e-08</Real>
+ <Real>-0.07795655011881443</Real>
+ <Real>-0.54424675415103807</Real>
+ <Real>0.3242301455679914</Real>
+ <Real>0.29610617179238913</Real>
+ <Real>0.0018669869094719406</Real>
+ <Real>-0.00030406591916461119</Real>
+ <Real>-0.23401130135135068</Real>
+ <Real>-0.41833282598860178</Real>
+ <Real>0.53991581970791414</Real>
+ <Real>0.11273237355120293</Real>
+ <Real>-0.069667831943294664</Real>
+ <Real>-0.54137398919008151</Real>
+ <Real>0.29442815351047347</Real>
+ <Real>0.31393698832247624</Real>
+ <Real>0.0026766793004264337</Real>
+ <Real>-0.028562841964611067</Real>
+ <Real>-0.48441063880862106</Real>
+ <Real>0.069151399193913665</Real>
+ <Real>0.42918048589648011</Real>
+ <Real>0.014641595682838331</Real>
+ <Real>-0.025143927553512784</Real>
+ <Real>-0.47396109287771809</Real>
+ <Real>0.040399870863204346</Real>
+ <Real>0.44165924712079685</Real>
+ <Real>0.017045902447229689</Real>
+ <Real>-0.011359280676947803</Real>
+ <Real>-0.40889456223730591</Real>
+ <Real>-0.11363739643448467</Real>
+ <Real>0.49939560228867841</Real>
+ <Real>0.034495637060059994</Real>
+ <Real>-0.00066159670659626552</Real>
+ <Real>-0.25572387049812095</Real>
+ <Real>-0.38719548605006293</Real>
+ <Real>0.54420897042087379</Real>
+ <Real>0.099371982833906358</Real>
+ <Real>-0.002111122856071995</Real>
+ <Real>-0.30194495620125406</Real>
+ <Real>-0.31460518178652813</Real>
+ <Real>0.54348972360110648</Real>
+ <Real>0.075171537242747735</Real>
+ <Real>-0.048540454602101754</Real>
+ <Real>-0.52362041615793031</Real>
+ <Real>0.1992492406188362</Real>
+ <Real>0.36652458564452561</Real>
+ <Real>0.006387044496670261</Real>
+ <Real>-0.0014807971091969363</Real>
+ <Real>-0.28575065546727157</Real>
+ <Real>-0.34098018220316317</Real>
+ <Real>0.54513551924492898</Real>
+ <Real>0.083076115534702732</Real>
+ <Real>-0.097374461581833008</Real>
+ <Real>-0.54459752168524922</Real>
+ <Real>0.38205377972520166</Real>
+ <Real>0.25918285193267654</Real>
+ <Real>0.00073535160920408949</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>-0.0015398888964354171</Real>
+ <Real>-0.28744075781890077</Real>
+ <Real>-0.33827449641384477</Real>
+ <Real>0.54503082187013352</Real>
+ <Real>0.082224321259047425</Real>
+ <Real>-0.028102759671169996</Real>
+ <Real>-0.48309062848886392</Real>
+ <Real>0.065429417681321655</Real>
+ <Real>0.43082408878862832</Real>
+ <Real>0.014939881690083917</Real>
+ <Real>-0.055181892379010555</Real>
+ <Real>-0.53113661988609029</Real>
+ <Real>0.23269793928045979</Real>
+ <Real>0.34874155061339374</Real>
+ <Real>0.0048790223712473569</Real>
+ <Real>-0.042559053512507009</Real>
+ <Real>-0.51489178900580035</Real>
+ <Real>0.16560354559645685</Real>
+ <Real>0.38370448987451528</Real>
+ <Real>0.0081428070473352349</Real>
+ <Real>-0.0042822983182703679</Real>
+ <Real>-0.34061516921592089</Real>
+ <Real>-0.24754270553705771</Real>
+ <Real>0.53406011199495973</Real>
+ <Real>0.058380061076289277</Real>
+ <Real>-0.12484999797808245</Real>
+ <Real>-0.53377567857897978</Real>
+ <Real>0.44223030167724925</Real>
+ <Real>0.21626642429477083</Real>
+ <Real>0.00012895058504219708</Real>
+ <Real>-0.010024276215463116</Real>
+ <Real>-0.3992261265440199</Real>
+ <Real>-0.13397926508654767</Real>
+ <Real>0.5057340146670074</Real>
+ <Real>0.037495653179023217</Real>
+ <Real>-0.090687467643976075</Real>
+ <Real>-0.54536264560477932</Real>
+ <Real>0.36381929882182451</Real>
+ <Real>0.27119920974659328</Real>
+ <Real>0.0010316046803375766</Real>
+ <Real>-0.03997392842591032</Real>
+ <Real>-0.51044064189409244</Real>
+ <Real>0.14985404179605111</Real>
+ <Real>0.39150955579381641</Real>
+ <Real>0.0090509727301352396</Real>
+ <Real>-0.027853326369114029</Real>
+ <Real>-0.48236434897080954</Real>
+ <Real>0.063393336696226488</Real>
+ <Real>0.43171967899643182</Real>
+ <Real>0.01510465964726525</Real>
+ <Real>-0.0017667435669507293</Real>
+ <Real>-0.29356366588737742</Real>
+ <Real>-0.32838065167620528</Real>
+ <Real>0.54451927528234589</Real>
+ <Real>0.079191785848187535</Real>
+ <Real>-0.13033713529174909</Real>
+ <Real>-0.53038126048484435</Real>
+ <Real>0.45185513192345894</Real>
+ <Real>0.20878205877461156</Real>
+ <Real>8.120507852295045e-05</Real>
+ <Real>-0.02989059562152363</Real>
+ <Real>-0.48808251440715034</Real>
+ <Real>0.079656692066635837</Real>
+ <Real>0.42449654157427391</Real>
+ <Real>0.013819876387764206</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">4</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">11</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">10</Int>
+ <Int Name="Z">13</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 1 1">3.7704475772332836e-12</Real>
+ <Real Name="Cell 0 1 2">4.1477133035177474e-09</Real>
+ <Real Name="Cell 0 1 3">2.5582908655476696e-08</Real>
+ <Real Name="Cell 0 1 4">3.3829757874947194e-08</Real>
+ <Real Name="Cell 0 1 5">6.4603687662248064e-06</Real>
+ <Real Name="Cell 0 1 6">3.2017871951316145e-05</Real>
+ <Real Name="Cell 0 1 7">1.6792686507051745e-05</Real>
+ <Real Name="Cell 0 1 8">5.7473001870377429e-07</Real>
+ <Real Name="Cell 0 2 1">4.8266741918272822e-07</Real>
+ <Real Name="Cell 0 2 2">0.00053096244801467359</Real>
+ <Real Name="Cell 0 2 3">0.0032749524407888154</Real>
+ <Real Name="Cell 0 2 4">0.0020719973337249863</Real>
+ <Real Name="Cell 0 2 5">0.00025757699814518356</Real>
+ <Real Name="Cell 0 2 6">0.00079567188140728133</Real>
+ <Real Name="Cell 0 2 7">0.00041731282101649115</Real>
+ <Real Name="Cell 0 2 8">1.4282539326117711e-05</Real>
+ <Real Name="Cell 0 3 0">5.9308385507673237e-05</Real>
+ <Real Name="Cell 0 3 1">0.00086487526256287279</Real>
+ <Real Name="Cell 0 3 2">0.0060423246113045946</Real>
+ <Real Name="Cell 0 3 3">0.03084302397776225</Real>
+ <Real Name="Cell 0 3 4">0.019422851526003437</Real>
+ <Real Name="Cell 0 3 5">0.0011883525860937917</Real>
+ <Real Name="Cell 0 3 6">0.0013806462286454566</Real>
+ <Real Name="Cell 0 3 7">0.00072411930842997173</Real>
+ <Real Name="Cell 0 3 8">2.4782997259131731e-05</Real>
+ <Real Name="Cell 0 4 0">0.0033505374835231649</Real>
+ <Real Name="Cell 0 4 1">0.049784065033905686</Real>
+ <Real Name="Cell 0 4 2">0.080933655815938046</Real>
+ <Real Name="Cell 0 4 3">0.054644122832690413</Real>
+ <Real Name="Cell 0 4 4">0.019527025676968034</Real>
+ <Real Name="Cell 0 4 5">0.0008560121097811158</Real>
+ <Real Name="Cell 0 4 6">0.00024987402338172405</Real>
+ <Real Name="Cell 0 4 7">0.00013105356118873863</Real>
+ <Real Name="Cell 0 4 8">4.4853106524421048e-06</Real>
+ <Real Name="Cell 0 5 0">0.0089274230026671394</Real>
+ <Real Name="Cell 0 5 1">0.13703939232835463</Real>
+ <Real Name="Cell 0 5 2">0.26577483197529306</Real>
+ <Real Name="Cell 0 5 3">0.14873924017072424</Real>
+ <Real Name="Cell 0 5 4">0.015998679751913502</Real>
+ <Real Name="Cell 0 5 5">6.3343314471152033e-05</Real>
+ <Real Name="Cell 0 5 6">4.1509215280147159e-07</Real>
+ <Real Name="Cell 0 5 7">2.1770692331242828e-07</Real>
+ <Real Name="Cell 0 5 8">7.4510236378646352e-09</Real>
+ <Real Name="Cell 0 6 0">0.0025912432931190481</Real>
+ <Real Name="Cell 0 6 1">0.042459640802408681</Real>
+ <Real Name="Cell 0 6 2">0.11482320272947122</Real>
+ <Real Name="Cell 0 6 3">0.088052030731030725</Real>
+ <Real Name="Cell 0 6 4">0.0095850018575592954</Real>
+ <Real Name="Cell 0 6 5">1.5331411773910054e-06</Real>
+ <Real Name="Cell 0 7 0">2.4331306290502165e-05</Real>
+ <Real Name="Cell 0 7 1">0.00058897507594114025</Real>
+ <Real Name="Cell 0 7 2">0.0038121348078564952</Real>
+ <Real Name="Cell 0 7 3">0.0041951495960878982</Real>
+ <Real Name="Cell 0 7 4">0.00050248095884609619</Real>
+ <Real Name="Cell 0 7 5">2.2634706839362255e-07</Real>
+ <Real Name="Cell 0 8 1">6.1074452018871705e-09</Real>
+ <Real Name="Cell 0 8 2">1.879009645235996e-07</Real>
+ <Real Name="Cell 0 8 3">3.6880084227612454e-07</Real>
+ <Real Name="Cell 0 8 4">7.6891813895612386e-08</Real>
+ <Real Name="Cell 0 8 5">2.4056985427358033e-10</Real>
+ <Real Name="Cell 1 0 0">3.1834405547852001e-07</Real>
+ <Real Name="Cell 1 0 1">1.3169596737122512e-05</Real>
+ <Real Name="Cell 1 0 2">3.0240302103668306e-05</Real>
+ <Real Name="Cell 1 0 3">7.4986776519795489e-06</Real>
+ <Real Name="Cell 1 0 4">4.3932708527073875e-08</Real>
+ <Real Name="Cell 1 1 0">2.2506953819454378e-06</Real>
+ <Real Name="Cell 1 1 1">9.3109189283570784e-05</Real>
+ <Real Name="Cell 1 1 2">0.00021382119147760439</Real>
+ <Real Name="Cell 1 1 3">5.3151286276529188e-05</Real>
+ <Real Name="Cell 1 1 4">2.6147223784414513e-06</Real>
+ <Real Name="Cell 1 1 5">0.00081200969282870764</Real>
+ <Real Name="Cell 1 1 6">0.0040248081786522305</Real>
+ <Real Name="Cell 1 1 7">0.0021109254886737261</Real>
+ <Real Name="Cell 1 1 8">7.2246465452580259e-05</Real>
+ <Real Name="Cell 1 11 0">1.1133774308742727e-10</Real>
+ <Real Name="Cell 1 11 1">4.6059386153095683e-09</Real>
+ <Real Name="Cell 1 11 2">1.0576252103854932e-08</Real>
+ <Real Name="Cell 1 11 3">2.6225897155722595e-09</Real>
+ <Real Name="Cell 1 11 4">1.5365038331781313e-11</Real>
+ <Real Name="Cell 1 2 0">1.5933124147544389e-06</Real>
+ <Real Name="Cell 1 2 1">6.847155838658876e-05</Real>
+ <Real Name="Cell 1 2 2">0.002964983056401943</Real>
+ <Real Name="Cell 1 2 3">0.017391875758012421</Real>
+ <Real Name="Cell 1 2 4">0.011032773402513961</Real>
+ <Real Name="Cell 1 2 5">0.020693324497262969</Real>
+ <Real Name="Cell 1 2 6">0.10001997324122575</Real>
+ <Real Name="Cell 1 2 7">0.05245832882452281</Real>
+ <Real Name="Cell 1 2 8">0.0017953873130321419</Real>
+ <Real Name="Cell 1 3 0">7.7925862541051509e-07</Real>
+ <Real Name="Cell 1 3 1">4.4794798301202857e-05</Real>
+ <Real Name="Cell 1 3 2">0.026496668647201942</Real>
+ <Real Name="Cell 1 3 3">0.16281171882666379</Real>
+ <Real Name="Cell 1 3 4">0.1030182021058587</Real>
+ <Real Name="Cell 1 3 5">0.039835757980574718</Real>
+ <Real Name="Cell 1 3 6">0.17355420251935791</Real>
+ <Real Name="Cell 1 3 7">0.091025453512976043</Real>
+ <Real Name="Cell 1 3 8">0.0031153478973161095</Real>
+ <Real Name="Cell 1 4 0">3.9001134110377136e-05</Real>
+ <Real Name="Cell 1 4 1">0.0088255421886861748</Real>
+ <Real Name="Cell 1 4 2">0.13934239827875922</Real>
+ <Real Name="Cell 1 4 3">0.28195206608718143</Real>
+ <Real Name="Cell 1 4 4">0.10703120678706325</Real>
+ <Real Name="Cell 1 4 5">0.010607481556243276</Real>
+ <Real Name="Cell 1 4 6">0.031410426478957823</Real>
+ <Real Name="Cell 1 4 7">0.016474094396903022</Real>
+ <Real Name="Cell 1 4 8">0.00056382619760595549</Real>
+ <Real Name="Cell 1 5 0">0.00010391754263288176</Real>
+ <Real Name="Cell 1 5 1">0.053329144205845461</Real>
+ <Real Name="Cell 1 5 2">0.73955327542646399</Real>
+ <Real Name="Cell 1 5 3">0.90614399566507098</Real>
+ <Real Name="Cell 1 5 4">0.11386071510771985</Real>
+ <Real Name="Cell 1 5 5">0.00037699078141340778</Real>
+ <Real Name="Cell 1 5 6">5.2179179616621858e-05</Real>
+ <Real Name="Cell 1 5 7">2.7366859572347577e-05</Real>
+ <Real Name="Cell 1 5 8">9.3663129525308548e-07</Real>
+ <Real Name="Cell 1 6 0">3.0162750807754859e-05</Real>
+ <Real Name="Cell 1 6 1">0.034291164685054908</Real>
+ <Real Name="Cell 1 6 2">0.49584680636659995</Real>
+ <Real Name="Cell 1 6 3">0.62252280037563723</Real>
+ <Real Name="Cell 1 6 4">0.079047345328780008</Real>
+ <Real Name="Cell 1 6 5">5.8504469572490606e-05</Real>
+ <Real Name="Cell 1 7 0">2.8322277974299722e-07</Real>
+ <Real Name="Cell 1 7 1">0.0017794006626936547</Real>
+ <Real Name="Cell 1 7 2">0.028789258332702738</Real>
+ <Real Name="Cell 1 7 3">0.039957074289487533</Real>
+ <Real Name="Cell 1 7 4">0.005931307709881122</Real>
+ <Real Name="Cell 1 7 5">9.6274538062489295e-06</Real>
+ <Real Name="Cell 1 8 1">2.7236609877597162e-07</Real>
+ <Real Name="Cell 1 8 2">8.3795844206217942e-06</Real>
+ <Real Name="Cell 1 8 3">1.6446950126544283e-05</Real>
+ <Real Name="Cell 1 8 4">3.4290481021564943e-06</Real>
+ <Real Name="Cell 1 8 5">1.072839305563524e-08</Real>
+ <Real Name="Cell 13 3 0">9.6671911172593367e-07</Real>
+ <Real Name="Cell 13 3 1">1.4006069016374246e-05</Real>
+ <Real Name="Cell 13 3 2">1.7111454457301455e-05</Real>
+ <Real Name="Cell 13 3 3">2.0185968985987524e-06</Real>
+ <Real Name="Cell 13 3 4">1.009283889116871e-10</Real>
+ <Real Name="Cell 13 4 0">5.4613333209970765e-05</Real>
+ <Real Name="Cell 13 4 1">0.00079125167266781986</Real>
+ <Real Name="Cell 13 4 2">0.00096668572354528944</Real>
+ <Real Name="Cell 13 4 3">0.00011403757689549133</Real>
+ <Real Name="Cell 13 4 4">5.7017965892270016e-09</Real>
+ <Real Name="Cell 13 5 0">0.00014551585515716774</Real>
+ <Real Name="Cell 13 5 1">0.00210827021581199</Real>
+ <Real Name="Cell 13 5 2">0.0025757098397399493</Real>
+ <Real Name="Cell 13 5 3">0.00030385026048857015</Real>
+ <Real Name="Cell 13 5 4">1.5192293856587216e-08</Real>
+ <Real Name="Cell 13 6 0">4.2236934847362106e-05</Real>
+ <Real Name="Cell 13 6 1">0.00061193930826099977</Real>
+ <Real Name="Cell 13 6 2">0.00074761673612338999</Real>
+ <Real Name="Cell 13 6 3">8.8194538263534265e-05</Real>
+ <Real Name="Cell 13 6 4">4.4096632982680613e-09</Real>
+ <Real Name="Cell 13 7 0">3.9659718609677362e-07</Real>
+ <Real Name="Cell 13 7 1">5.7459995285021488e-06</Real>
+ <Real Name="Cell 13 7 2">7.0199860595212811e-06</Real>
+ <Real Name="Cell 13 7 3">8.2813077773815883e-07</Real>
+ <Real Name="Cell 13 7 4">4.1405941554410773e-11</Real>
+ <Real Name="Cell 14 3 0">6.5376459709579301e-05</Real>
+ <Real Name="Cell 14 3 1">0.00094719054959386271</Real>
+ <Real Name="Cell 14 3 2">0.0011571989208973236</Real>
+ <Real Name="Cell 14 3 3">0.00013651195803454481</Real>
+ <Real Name="Cell 14 3 4">6.8254994353606008e-09</Real>
+ <Real Name="Cell 14 4 0">0.0036933441522977819</Real>
+ <Real Name="Cell 14 4 1">0.053510096646325826</Real>
+ <Real Name="Cell 14 4 2">0.065374201762032624</Real>
+ <Real Name="Cell 14 4 3">0.0077120364755959752</Real>
+ <Real Name="Cell 14 4 4">3.8559626107143182e-07</Real>
+ <Real Name="Cell 14 5 0">0.0098408227647459531</Real>
+ <Real Name="Cell 14 5 1">0.14257630903237381</Real>
+ <Real Name="Cell 14 5 2">0.1741879192402527</Real>
+ <Real Name="Cell 14 5 3">0.020548527562583081</Real>
+ <Real Name="Cell 14 5 4">1.0274115564323738e-06</Real>
+ <Real Name="Cell 14 6 0">0.0028563635867038988</Real>
+ <Real Name="Cell 14 6 1">0.041383712234474755</Real>
+ <Real Name="Cell 14 6 2">0.050559190187226349</Real>
+ <Real Name="Cell 14 6 3">0.0059643453899414839</Real>
+ <Real Name="Cell 14 6 4">2.9821296740201686e-07</Real>
+ <Real Name="Cell 14 7 0">2.6820737940617965e-05</Real>
+ <Real Name="Cell 14 7 1">0.00038858557993718518</Real>
+ <Real Name="Cell 14 7 2">0.000474741659925114</Real>
+ <Real Name="Cell 14 7 3">5.6004125467636519e-05</Real>
+ <Real Name="Cell 14 7 4">2.8001658774866164e-09</Real>
+ <Real Name="Cell 15 1 1">7.6601823228135412e-15</Real>
+ <Real Name="Cell 15 1 2">8.4266494830885169e-12</Real>
+ <Real Name="Cell 15 1 3">5.1975194094234499e-11</Real>
+ <Real Name="Cell 15 1 4">3.2876712459450888e-11</Real>
+ <Real Name="Cell 15 1 5">1.5402349936074849e-12</Real>
+ <Real Name="Cell 15 2 1">9.8060518187462104e-10</Real>
+ <Real Name="Cell 15 2 2">1.0787231688139069e-06</Real>
+ <Real Name="Cell 15 2 3">6.6535158707587536e-06</Real>
+ <Real Name="Cell 15 2 4">4.2086563011333431e-06</Real>
+ <Real Name="Cell 15 2 5">1.9717055709470061e-07</Real>
+ <Real Name="Cell 15 3 0">0.00018847553517622293</Real>
+ <Real Name="Cell 15 3 1">0.0027306906377961228</Real>
+ <Real Name="Cell 15 3 2">0.0033462406249134642</Real>
+ <Real Name="Cell 15 3 3">0.00045593813310929726</Real>
+ <Real Name="Cell 15 3 4">3.9475345922646997e-05</Real>
+ <Real Name="Cell 15 3 5">1.848397836179248e-06</Real>
+ <Real Name="Cell 15 4 0">0.01064764012591983</Real>
+ <Real Name="Cell 15 4 1">0.15426638748479837</Real>
+ <Real Name="Cell 15 4 2">0.18848768996618698</Real>
+ <Real Name="Cell 15 4 3">0.02229998784533575</Real>
+ <Real Name="Cell 15 4 4">3.7354193397897755e-05</Real>
+ <Real Name="Cell 15 4 5">1.6365198090804252e-06</Real>
+ <Real Name="Cell 15 5 0">0.028370369784463605</Real>
+ <Real Name="Cell 15 5 1">0.41104137132755258</Real>
+ <Real Name="Cell 15 5 2">0.50223200245331323</Real>
+ <Real Name="Cell 15 5 3">0.059315774696959159</Real>
+ <Real Name="Cell 15 5 4">1.3800156742702871e-05</Real>
+ <Real Name="Cell 15 5 5">1.2633423271277674e-07</Real>
+ <Real Name="Cell 15 6 0">0.0082346865837247263</Real>
+ <Real Name="Cell 15 6 1">0.11930896409852028</Real>
+ <Real Name="Cell 15 6 2">0.14579682111395517</Real>
+ <Real Name="Cell 15 6 3">0.017240345022343992</Real>
+ <Real Name="Cell 15 6 4">6.0435229746471657e-06</Real>
+ <Real Name="Cell 15 6 5">1.4681523879443191e-10</Real>
+ <Real Name="Cell 15 7 0">7.7322219031669351e-05</Real>
+ <Real Name="Cell 15 7 1">0.001120394193835168</Real>
+ <Real Name="Cell 15 7 2">0.0013704608458003386</Real>
+ <Real Name="Cell 15 7 3">0.00016361124598818271</Real>
+ <Real Name="Cell 15 7 4">2.5323952396839405e-07</Real>
+ <Real Name="Cell 15 7 5">6.9436034378439443e-12</Real>
+ <Real Name="Cell 2 0 0">0.0012908810309318257</Real>
+ <Real Name="Cell 2 0 1">0.013801752046572177</Real>
+ <Real Name="Cell 2 0 13">1.7703621935103908e-05</Real>
+ <Real Name="Cell 2 0 2">0.026169915314852705</Real>
+ <Real Name="Cell 2 0 3">0.0062965454712082414</Real>
+ <Real Name="Cell 2 0 4">3.6843875649614558e-05</Real>
+ <Real Name="Cell 2 1 0">0.0025032045215755533</Real>
+ <Real Name="Cell 2 1 1">0.079753716118418819</Real>
+ <Real Name="Cell 2 1 13">1.0641682686758067e-05</Real>
+ <Real Name="Cell 2 1 2">0.17981638582869913</Real>
+ <Real Name="Cell 2 1 3">0.044474238980637716</Real>
+ <Real Name="Cell 2 1 4">0.00026870853789524239</Real>
+ <Real Name="Cell 2 1 5">0.0029655463051386222</Real>
+ <Real Name="Cell 2 1 6">0.014699091884626855</Real>
+ <Real Name="Cell 2 1 7">0.0077093581463567743</Real>
+ <Real Name="Cell 2 1 8">0.00026385293084516882</Real>
+ <Real Name="Cell 2 10 0">2.8303130614497391e-07</Real>
+ <Real Name="Cell 2 10 1">1.7094159110736354e-06</Real>
+ <Real Name="Cell 2 10 13">3.9194472100577706e-09</Real>
+ <Real Name="Cell 2 10 2">1.8196732584500806e-06</Real>
+ <Real Name="Cell 2 10 3">2.4995583653365001e-07</Real>
+ <Real Name="Cell 2 10 4">1.4415302549321039e-10</Real>
+ <Real Name="Cell 2 11 0">0.00017646383836175032</Real>
+ <Real Name="Cell 2 11 1">0.00047881111138060319</Real>
+ <Real Name="Cell 2 11 13">3.0494805458591623e-06</Real>
+ <Real Name="Cell 2 11 2">0.00014827079101254026</Real>
+ <Real Name="Cell 2 11 3">3.5532162123108468e-06</Real>
+ <Real Name="Cell 2 11 4">1.288882879193024e-08</Real>
+ <Real Name="Cell 2 2 0">0.0013683038824244772</Real>
+ <Real Name="Cell 2 2 1">0.055657457193022675</Real>
+ <Real Name="Cell 2 2 13">4.5913956452464588e-07</Real>
+ <Real Name="Cell 2 2 2">0.12932801231006824</Real>
+ <Real Name="Cell 2 2 3">0.041358631561558841</Real>
+ <Real Name="Cell 2 2 4">0.0064907477596851566</Real>
+ <Real Name="Cell 2 2 5">0.073982245856878584</Real>
+ <Real Name="Cell 2 2 6">0.36528517924623594</Real>
+ <Real Name="Cell 2 2 7">0.19158423489485196</Real>
+ <Real Name="Cell 2 2 8">0.0065569741243146802</Real>
+ <Real Name="Cell 2 3 0">0.0001003766833421703</Real>
+ <Real Name="Cell 2 3 1">0.0046053771947082156</Real>
+ <Real Name="Cell 2 3 2">0.025962601198358828</Real>
+ <Real Name="Cell 2 3 3">0.093568636080465103</Real>
+ <Real Name="Cell 2 3 4">0.057596781970915147</Real>
+ <Real Name="Cell 2 3 5">0.13055779831653314</Real>
+ <Real Name="Cell 2 3 6">0.63384118113411592</Real>
+ <Real Name="Cell 2 3 7">0.33243609276184499</Real>
+ <Real Name="Cell 2 3 8">0.011377631669035961</Real>
+ <Real Name="Cell 2 4 0">2.1693299673592877e-05</Real>
+ <Real Name="Cell 2 4 1">0.0069400541388516639</Real>
+ <Real Name="Cell 2 4 2">0.096387485876494594</Real>
+ <Real Name="Cell 2 4 3">0.17808015494994614</Real>
+ <Real Name="Cell 2 4 4">0.062277014946357616</Real>
+ <Real Name="Cell 2 4 5">0.025520667214395141</Real>
+ <Real Name="Cell 2 4 6">0.11471472041783777</Real>
+ <Real Name="Cell 2 4 7">0.060165408264794155</Real>
+ <Real Name="Cell 2 4 8">0.0020591622551177071</Real>
+ <Real Name="Cell 2 5 0">1.9598590559306782e-06</Real>
+ <Real Name="Cell 2 5 1">0.036474634233574756</Real>
+ <Real Name="Cell 2 5 2">0.54259195103350411</Real>
+ <Real Name="Cell 2 5 3">0.69914663409168787</Real>
+ <Real Name="Cell 2 5 4">0.094771303511015995</Real>
+ <Real Name="Cell 2 5 5">0.00030616079898533355</Real>
+ <Real Name="Cell 2 5 6">0.00019056474783501627</Real>
+ <Real Name="Cell 2 5 7">9.9947119363666856e-05</Real>
+ <Real Name="Cell 2 5 8">3.4206920826603155e-06</Real>
+ <Real Name="Cell 2 6 0">8.465206252254226e-11</Real>
+ <Real Name="Cell 2 6 1">0.025220455762166569</Real>
+ <Real Name="Cell 2 6 2">0.40880078972991263</Real>
+ <Real Name="Cell 2 6 3">0.56732930576004903</Real>
+ <Real Name="Cell 2 6 4">0.084187596685747504</Real>
+ <Real Name="Cell 2 6 5">0.00013649763653189972</Real>
+ <Real Name="Cell 2 7 0">2.702937398317187e-10</Real>
+ <Real Name="Cell 2 7 1">0.0016079459149824856</Real>
+ <Real Name="Cell 2 7 2">0.032106518158682609</Real>
+ <Real Name="Cell 2 7 3">0.051900574397716726</Real>
+ <Real Name="Cell 2 7 4">0.0092082761525901537</Real>
+ <Real Name="Cell 2 7 5">2.2808109313890465e-05</Real>
+ <Real Name="Cell 2 8 0">3.6857498320737797e-08</Real>
+ <Real Name="Cell 2 8 1">1.3680823343505409e-06</Real>
+ <Real Name="Cell 2 8 2">2.1046448276938429e-05</Real>
+ <Real Name="Cell 2 8 3">3.9364841011200986e-05</Real>
+ <Real Name="Cell 2 8 4">8.1734740220907526e-06</Real>
+ <Real Name="Cell 2 8 5">2.5571886923640475e-08</Real>
+ <Real Name="Cell 2 9 0">1.3834851631882297e-07</Real>
+ <Real Name="Cell 2 9 1">2.6983860357172753e-06</Real>
+ <Real Name="Cell 2 9 2">4.0280452624402109e-06</Real>
+ <Real Name="Cell 2 9 3">6.0946207367363441e-07</Real>
+ <Real Name="Cell 2 9 4">3.5393964534100044e-10</Real>
+ <Real Name="Cell 3 0 0">0.073598597350954489</Real>
+ <Real Name="Cell 3 0 1">0.25895739820523322</Real>
+ <Real Name="Cell 3 0 13">0.001245374784747947</Real>
+ <Real Name="Cell 3 0 2">0.20617723416988132</Real>
+ <Real Name="Cell 3 0 3">0.037563056636917141</Real>
+ <Real Name="Cell 3 0 4">0.00021684508540157531</Real>
+ <Real Name="Cell 3 1 0">0.054460723103019075</Real>
+ <Real Name="Cell 3 1 1">0.57918491788543014</Real>
+ <Real Name="Cell 3 1 13">0.00074859728331063097</Real>
+ <Real Name="Cell 3 1 2">1.097401072556955</Real>
+ <Real Name="Cell 3 1 3">0.26425853833690915</Real>
+ <Real Name="Cell 3 1 4">0.0015562925275854991</Real>
+ <Real Name="Cell 3 1 5">0.0011768905418317172</Real>
+ <Real Name="Cell 3 1 6">0.0058334054564500677</Real>
+ <Real Name="Cell 3 1 7">0.003059495935508741</Real>
+ <Real Name="Cell 3 1 8">0.00010471130724084337</Real>
+ <Real Name="Cell 3 10 0">0.0013447135706338926</Real>
+ <Real Name="Cell 3 10 1">0.025959568194080906</Real>
+ <Real Name="Cell 3 10 13">2.7571650272749616e-07</Real>
+ <Real Name="Cell 3 10 2">0.038699930850046207</Real>
+ <Real Name="Cell 3 10 3">0.0058536957875895404</Real>
+ <Real Name="Cell 3 10 4">3.3994106358534032e-06</Real>
+ <Real Name="Cell 3 11 0">0.012435411509110801</Real>
+ <Real Name="Cell 3 11 1">0.033978426480946601</Real>
+ <Real Name="Cell 3 11 13">0.00021451803434990806</Real>
+ <Real Name="Cell 3 11 2">0.010672162987863991</Real>
+ <Real Name="Cell 3 11 3">0.00023129296207515817</Real>
+ <Real Name="Cell 3 11 4">1.4755088738748664e-07</Real>
+ <Real Name="Cell 3 2 0">0.010834472210292486</Real>
+ <Real Name="Cell 3 2 1">0.39037372957947158</Real>
+ <Real Name="Cell 3 2 13">3.229852277885253e-05</Real>
+ <Real Name="Cell 3 2 2">0.90592883136236979</Real>
+ <Real Name="Cell 3 2 3">0.23059569527913507</Real>
+ <Real Name="Cell 3 2 4">0.0018050886134847197</Real>
+ <Real Name="Cell 3 2 5">0.029257574237216415</Real>
+ <Real Name="Cell 3 2 6">0.14496518386988957</Real>
+ <Real Name="Cell 3 2 7">0.076031126955147368</Real>
+ <Real Name="Cell 3 2 8">0.0026021667824651564</Real>
+ <Real Name="Cell 3 3 0">0.0028266087590039942</Real>
+ <Real Name="Cell 3 3 1">0.15306608054300855</Real>
+ <Real Name="Cell 3 3 2">0.40626716994816375</Real>
+ <Real Name="Cell 3 3 3">0.12264118748953037</Real>
+ <Real Name="Cell 3 3 4">0.0036208997307676846</Real>
+ <Real Name="Cell 3 3 5">0.050850313040567675</Real>
+ <Real Name="Cell 3 3 6">0.2515429275204078</Real>
+ <Real Name="Cell 3 3 7">0.1319288655829173</Real>
+ <Real Name="Cell 3 3 8">0.0045152679621689642</Real>
+ <Real Name="Cell 3 4 0">0.0011766071466203342</Real>
+ <Real Name="Cell 3 4 1">0.073439108391376462</Real>
+ <Real Name="Cell 3 4 2">0.2179748889236045</Real>
+ <Real Name="Cell 3 4 3">0.080359776056964052</Real>
+ <Real Name="Cell 3 4 4">0.0040188011837243541</Real>
+ <Real Name="Cell 3 4 5">0.0092755341314021047</Real>
+ <Real Name="Cell 3 4 6">0.045525089663560954</Real>
+ <Real Name="Cell 3 4 7">0.023876932236096826</Real>
+ <Real Name="Cell 3 4 8">0.00081718846504268844</Real>
+ <Real Name="Cell 3 5 0">9.74415967473093e-05</Real>
+ <Real Name="Cell 3 5 1">0.0095721178488858503</Real>
+ <Real Name="Cell 3 5 2">0.065249832423662155</Real>
+ <Real Name="Cell 3 5 3">0.071583868329026634</Real>
+ <Real Name="Cell 3 5 4">0.010559758829523262</Real>
+ <Real Name="Cell 3 5 5">4.3834830096599138e-05</Real>
+ <Real Name="Cell 3 5 6">7.5626538602050164e-05</Real>
+ <Real Name="Cell 3 5 7">3.9664496012998495e-05</Real>
+ <Real Name="Cell 3 5 8">1.3575181389739834e-06</Real>
+ <Real Name="Cell 3 6 0">1.1129915568376659e-07</Real>
+ <Real Name="Cell 3 6 1">0.002030139159326027</Real>
+ <Real Name="Cell 3 6 2">0.043022839749956548</Real>
+ <Real Name="Cell 3 6 3">0.072214276536706506</Real>
+ <Real Name="Cell 3 6 4">0.013294439866378269</Real>
+ <Real Name="Cell 3 6 5">3.5090074605446344e-05</Real>
+ <Real Name="Cell 3 7 0">6.3740557011882817e-06</Real>
+ <Real Name="Cell 3 7 1">0.00032657514172532197</Real>
+ <Real Name="Cell 3 7 2">0.0055137970717333796</Real>
+ <Real Name="Cell 3 7 3">0.0099137159308061544</Real>
+ <Real Name="Cell 3 7 4">0.0019781397947032518</Real>
+ <Real Name="Cell 3 7 5">5.8820820362405976e-06</Real>
+ <Real Name="Cell 3 8 0">0.00086917198840454687</Real>
+ <Real Name="Cell 3 8 1">0.016952727811193911</Real>
+ <Real Name="Cell 3 8 2">0.025311275338046373</Real>
+ <Real Name="Cell 3 8 3">0.0038390534153474407</Real>
+ <Real Name="Cell 3 8 4">4.3333937600640824e-06</Real>
+ <Real Name="Cell 3 8 5">6.6008085724512386e-09</Real>
+ <Real Name="Cell 3 9 0">0.0032625289425569242</Real>
+ <Real Name="Cell 3 9 1">0.063633226968848128</Real>
+ <Real Name="Cell 3 9 2">0.094989195405288995</Real>
+ <Real Name="Cell 3 9 3">0.014372309206184548</Real>
+ <Real Name="Cell 3 9 4">8.3465899567890004e-06</Real>
+ <Real Name="Cell 4 0 0">0.21208332364093133</Real>
+ <Real Name="Cell 4 0 1">0.60805146227571971</Real>
+ <Real Name="Cell 4 0 13">0.0036504664849270206</Real>
+ <Real Name="Cell 4 0 2">0.25759965785165739</Real>
+ <Real Name="Cell 4 0 3">0.024121820296595573</Real>
+ <Real Name="Cell 4 0 4">0.00013186522454339343</Real>
+ <Real Name="Cell 4 1 0">0.1339229042933362</Real>
+ <Real Name="Cell 4 1 1">0.63518242938678626</Real>
+ <Real Name="Cell 4 1 13">0.0021943027327198995</Real>
+ <Real Name="Cell 4 1 2">0.7785262725674873</Real>
+ <Real Name="Cell 4 1 3">0.17048796327818375</Real>
+ <Real Name="Cell 4 1 4">0.0010246029357946658</Real>
+ <Real Name="Cell 4 1 5">2.3510099532532993e-05</Real>
+ <Real Name="Cell 4 1 6">0.00011653076295108855</Real>
+ <Real Name="Cell 4 1 7">6.1117883588286066e-05</Real>
+ <Real Name="Cell 4 1 8">2.0917607413846612e-06</Real>
+ <Real Name="Cell 4 10 0">0.011437196930540057</Real>
+ <Real Name="Cell 4 10 1">0.22228830893121732</Real>
+ <Real Name="Cell 4 10 13">8.0818550758735646e-07</Real>
+ <Real Name="Cell 4 10 2">0.33167235070659445</Real>
+ <Real Name="Cell 4 10 3">0.050178345658876453</Real>
+ <Real Name="Cell 4 10 4">2.9140417648520178e-05</Real>
+ <Real Name="Cell 4 11 0">0.036607760811500203</Real>
+ <Real Name="Cell 4 11 1">0.10262942510457841</Real>
+ <Real Name="Cell 4 11 13">0.00062879938183849895</Real>
+ <Real Name="Cell 4 11 2">0.035764885315914687</Real>
+ <Real Name="Cell 4 11 3">0.0013444610869341829</Real>
+ <Real Name="Cell 4 11 4">6.6084303392542545e-07</Real>
+ <Real Name="Cell 4 2 0">0.015170162593397993</Real>
+ <Real Name="Cell 4 2 1">0.47986874050893052</Real>
+ <Real Name="Cell 4 2 13">9.4674050222332066e-05</Real>
+ <Real Name="Cell 4 2 2">1.1594214344599676</Real>
+ <Real Name="Cell 4 2 3">0.31297903039943076</Real>
+ <Real Name="Cell 4 2 4">0.0024800112415277946</Real>
+ <Real Name="Cell 4 2 5">0.0005842463595196562</Real>
+ <Real Name="Cell 4 2 6">0.0028958905057806972</Real>
+ <Real Name="Cell 4 2 7">0.0015188324038607369</Real>
+ <Real Name="Cell 4 2 8">5.1982068236206017e-05</Real>
+ <Real Name="Cell 4 3 0">0.0095503653278588528</Real>
+ <Real Name="Cell 4 3 1">0.5598798524948827</Real>
+ <Real Name="Cell 4 3 2">1.5519204324548681</Real>
+ <Real Name="Cell 4 3 3">0.48023680763631632</Real>
+ <Real Name="Cell 4 3 4">0.0060696965563888745</Real>
+ <Real Name="Cell 4 3 5">0.001013784152379558</Real>
+ <Real Name="Cell 4 3 6">0.0050249360305466692</Real>
+ <Real Name="Cell 4 3 7">0.0026354710771304257</Real>
+ <Real Name="Cell 4 3 8">9.0199048306914141e-05</Real>
+ <Real Name="Cell 4 4 0">0.0041999333775353236</Real>
+ <Real Name="Cell 4 4 1">0.34220996425764427</Real>
+ <Real Name="Cell 4 4 2">1.1348563699444243</Real>
+ <Real Name="Cell 4 4 3">0.43671940766042799</Real>
+ <Real Name="Cell 4 4 4">0.011807119078425752</Real>
+ <Real Name="Cell 4 4 5">0.00020145117966054654</Real>
+ <Real Name="Cell 4 4 6">0.00090942991559854415</Real>
+ <Real Name="Cell 4 4 7">0.00047697646789274229</Real>
+ <Real Name="Cell 4 4 8">1.6324528788061371e-05</Real>
+ <Real Name="Cell 4 5 0">0.00051621780997905271</Real>
+ <Real Name="Cell 4 5 1">0.062248659565771566</Real>
+ <Real Name="Cell 4 5 2">0.27697084243004816</Real>
+ <Real Name="Cell 4 5 3">0.20478194223402993</Real>
+ <Real Name="Cell 4 5 4">0.028778419042058846</Real>
+ <Real Name="Cell 4 5 5">0.00014053565658219612</Real>
+ <Real Name="Cell 4 5 6">1.5107501627376874e-06</Real>
+ <Real Name="Cell 4 5 7">7.9235602890492953e-07</Real>
+ <Real Name="Cell 4 5 8">2.7118400329890425e-08</Real>
+ <Real Name="Cell 4 6 0">3.3485271342159279e-06</Real>
+ <Real Name="Cell 4 6 1">0.0015015418570646112</Real>
+ <Real Name="Cell 4 6 2">0.040245233940218117</Real>
+ <Real Name="Cell 4 6 3">0.085984835311039107</Real>
+ <Real Name="Cell 4 6 4">0.020451539892035284</Real>
+ <Real Name="Cell 4 6 5">0.00010754361606928727</Real>
+ <Real Name="Cell 4 7 0">5.4639661148476695e-05</Real>
+ <Real Name="Cell 4 7 1">0.0011277569505600041</Real>
+ <Real Name="Cell 4 7 2">0.0040056399488043069</Real>
+ <Real Name="Cell 4 7 3">0.0056170540076213079</Real>
+ <Real Name="Cell 4 7 4">0.0012896037684901921</Real>
+ <Real Name="Cell 4 7 5">6.7706960941369075e-06</Real>
+ <Real Name="Cell 4 8 0">0.0074507135099742871</Real>
+ <Real Name="Cell 4 8 1">0.1453206870644014</Real>
+ <Real Name="Cell 4 8 2">0.21692907739696357</Real>
+ <Real Name="Cell 4 8 3">0.03282244542471896</Real>
+ <Real Name="Cell 4 8 4">1.9075348084881309e-05</Real>
+ <Real Name="Cell 4 8 5">4.3944649588989032e-11</Real>
+ <Real Name="Cell 4 9 0">0.027967040808127171</Real>
+ <Real Name="Cell 4 9 1">0.5454765572120418</Real>
+ <Real Name="Cell 4 9 2">0.81426609572047715</Real>
+ <Real Name="Cell 4 9 3">0.12320226583533885</Real>
+ <Real Name="Cell 4 9 4">7.1548613373304825e-05</Real>
+ <Real Name="Cell 5 0 0">0.067604105140985124</Real>
+ <Real Name="Cell 5 0 1">0.18366847344578174</Real>
+ <Real Name="Cell 5 0 13">0.0011681699277809241</Real>
+ <Real Name="Cell 5 0 2">0.057378284797746031</Real>
+ <Real Name="Cell 5 0 3">0.0015062233055636589</Real>
+ <Real Name="Cell 5 0 4">5.7979556015132922e-06</Real>
+ <Real Name="Cell 5 1 0">0.041035834540160486</Real>
+ <Real Name="Cell 5 1 1">0.12852887244782626</Real>
+ <Real Name="Cell 5 1 13">0.00070218928879226092</Real>
+ <Real Name="Cell 5 1 2">0.078294224714775762</Real>
+ <Real Name="Cell 5 1 3">0.012424480032800451</Real>
+ <Real Name="Cell 5 1 4">8.6429115961081471e-05</Real>
+ <Real Name="Cell 5 10 0">0.0094205460288156861</Real>
+ <Real Name="Cell 5 10 1">0.18348935856747964</Real>
+ <Real Name="Cell 5 10 13">2.586239347574194e-07</Real>
+ <Real Name="Cell 5 10 2">0.27385744062045808</Real>
+ <Real Name="Cell 5 10 3">0.041434236681951224</Real>
+ <Real Name="Cell 5 10 4">2.4062495747350859e-05</Real>
+ <Real Name="Cell 5 11 0">0.011836119172707184</Real>
+ <Real Name="Cell 5 11 1">0.03520835528903675</Real>
+ <Real Name="Cell 5 11 13">0.00020121935963634903</Real>
+ <Real Name="Cell 5 11 2">0.014974307221056467</Real>
+ <Real Name="Cell 5 11 3">0.00096339397717289501</Real>
+ <Real Name="Cell 5 11 4">5.0963218860785206e-07</Real>
+ <Real Name="Cell 5 2 0">0.0043448458824475508</Real>
+ <Real Name="Cell 5 2 1">0.14371337306210846</Real>
+ <Real Name="Cell 5 2 13">3.0296231691923133e-05</Real>
+ <Real Name="Cell 5 2 2">0.36438594370345451</Real>
+ <Real Name="Cell 5 2 3">0.10358801651008759</Real>
+ <Real Name="Cell 5 2 4">0.00094879611698496286</Real>
+ <Real Name="Cell 5 3 0">0.0045994193383868112</Real>
+ <Real Name="Cell 5 3 1">0.32190185793324017</Real>
+ <Real Name="Cell 5 3 2">0.98659694247371699</Real>
+ <Real Name="Cell 5 3 3">0.3416942845154689</Real>
+ <Real Name="Cell 5 3 4">0.005662296150676962</Real>
+ <Real Name="Cell 5 3 5">1.5636548562492185e-08</Real>
+ <Real Name="Cell 5 4 0">0.003027394838257735</Real>
+ <Real Name="Cell 5 4 1">0.36614831194380887</Real>
+ <Real Name="Cell 5 4 2">1.3960881027314547</Real>
+ <Real Name="Cell 5 4 3">0.64277123858546115</Real>
+ <Real Name="Cell 5 4 4">0.033276089985935321</Real>
+ <Real Name="Cell 5 4 5">0.00011115889121853726</Real>
+ <Real Name="Cell 5 5 0">0.00065924413613634679</Real>
+ <Real Name="Cell 5 5 1">0.10468817425661922</Real>
+ <Real Name="Cell 5 5 2">0.68236393796811101</Real>
+ <Real Name="Cell 5 5 3">0.84263027527448631</Real>
+ <Real Name="Cell 5 5 4">0.16801514412785501</Real>
+ <Real Name="Cell 5 5 5">0.00086669353930324223</Real>
+ <Real Name="Cell 5 6 0">6.5800211159975458e-06</Real>
+ <Real Name="Cell 5 6 1">0.0070381532222178701</Real>
+ <Real Name="Cell 5 6 2">0.2391230718154575</Real>
+ <Real Name="Cell 5 6 3">0.52601752916053368</Real>
+ <Real Name="Cell 5 6 4">0.12598030816764566</Real>
+ <Real Name="Cell 5 6 5">0.00066390894846348738</Real>
+ <Real Name="Cell 5 7 0">4.5118317447611442e-05</Real>
+ <Real Name="Cell 5 7 1">0.0012577507985554381</Real>
+ <Real Name="Cell 5 7 2">0.01606446908013251</Real>
+ <Real Name="Cell 5 7 3">0.033090167773294703</Real>
+ <Real Name="Cell 5 7 4">0.0079004154620033878</Real>
+ <Real Name="Cell 5 7 5">4.1646844882794823e-05</Real>
+ <Real Name="Cell 5 8 0">0.0061523744893062738</Real>
+ <Real Name="Cell 5 8 1">0.11999753846430328</Real>
+ <Real Name="Cell 5 8 2">0.17912763775000046</Real>
+ <Real Name="Cell 5 8 3">0.027102848762240124</Real>
+ <Real Name="Cell 5 8 4">1.573973688110895e-05</Real>
+ <Real Name="Cell 5 9 0">0.023093588040791941</Real>
+ <Real Name="Cell 5 9 1">0.45042344610530621</Real>
+ <Real Name="Cell 5 9 2">0.67237452468293513</Real>
+ <Real Name="Cell 5 9 3">0.10173340799312046</Real>
+ <Real Name="Cell 5 9 4">5.9080766301625985e-05</Real>
+ <Real Name="Cell 6 0 0">0.00082077079294070991</Real>
+ <Real Name="Cell 6 0 1">0.0022101622765118975</Real>
+ <Real Name="Cell 6 0 13">1.4191386433891566e-05</Real>
+ <Real Name="Cell 6 0 2">0.00064857064479032693</Real>
+ <Real Name="Cell 6 0 3">6.2758129908261011e-06</Real>
+ <Real Name="Cell 6 1 0">0.00049725206412809043</Real>
+ <Real Name="Cell 6 1 1">0.001538913388734903</Real>
+ <Real Name="Cell 6 1 13">8.5304708758598335e-06</Real>
+ <Real Name="Cell 6 1 2">0.00093970364184294691</Real>
+ <Real Name="Cell 6 1 3">0.00016020194894869811</Real>
+ <Real Name="Cell 6 1 4">1.3889741843526278e-06</Real>
+ <Real Name="Cell 6 10 0">0.00065752523856780272</Real>
+ <Real Name="Cell 6 10 1">0.012821491220844288</Real>
+ <Real Name="Cell 6 10 13">3.1418649906252384e-09</Real>
+ <Real Name="Cell 6 10 2">0.0191388343876954</Real>
+ <Real Name="Cell 6 10 3">0.0028957747538766441</Real>
+ <Real Name="Cell 6 10 4">1.6816944677570216e-06</Real>
+ <Real Name="Cell 6 11 0">0.00015524606453695252</Real>
+ <Real Name="Cell 6 11 1">0.00065116667085300781</Real>
+ <Real Name="Cell 6 11 13">2.4444916982276238e-06</Real>
+ <Real Name="Cell 6 11 2">0.00051545295777129837</Real>
+ <Real Name="Cell 6 11 3">6.2168088676848042e-05</Real>
+ <Real Name="Cell 6 11 4">3.5475768471150243e-08</Real>
+ <Real Name="Cell 6 2 0">9.4888854677418292e-05</Real>
+ <Real Name="Cell 6 2 1">0.0042754320625026879</Real>
+ <Real Name="Cell 6 2 13">3.680505046449241e-07</Real>
+ <Real Name="Cell 6 2 2">0.01150399473725236</Real>
+ <Real Name="Cell 6 2 3">0.0034615879184730618</Real>
+ <Real Name="Cell 6 2 4">3.8952932259370093e-05</Real>
+ <Real Name="Cell 6 3 0">0.00025235343711598303</Real>
+ <Real Name="Cell 6 3 1">0.028404078858073042</Real>
+ <Real Name="Cell 6 3 2">0.10361448352320463</Real>
+ <Real Name="Cell 6 3 3">0.041763769805479703</Real>
+ <Real Name="Cell 6 3 4">0.00089467169660995124</Real>
+ <Real Name="Cell 6 3 5">9.9160631673552472e-09</Real>
+ <Real Name="Cell 6 4 0">0.00043161630972750076</Real>
+ <Real Name="Cell 6 4 1">0.065388034760294478</Real>
+ <Real Name="Cell 6 4 2">0.27666855689441577</Real>
+ <Real Name="Cell 6 4 3">0.16175737992964104</Real>
+ <Real Name="Cell 6 4 4">0.015779899068777317</Real>
+ <Real Name="Cell 6 4 5">7.0492448031671362e-05</Real>
+ <Real Name="Cell 6 5 0">0.00012699520016769497</Real>
+ <Real Name="Cell 6 5 1">0.024539070735279885</Real>
+ <Real Name="Cell 6 5 2">0.27104489843692597</Real>
+ <Real Name="Cell 6 5 3">0.4663662096198079</Real>
+ <Real Name="Cell 6 5 4">0.10499762880490854</Real>
+ <Real Name="Cell 6 5 5">0.0005496217946129589</Real>
+ <Real Name="Cell 6 6 0">1.3763408648738738e-06</Real>
+ <Real Name="Cell 6 6 1">0.0040311205726970365</Real>
+ <Real Name="Cell 6 6 2">0.14995136281498866</Real>
+ <Real Name="Cell 6 6 3">0.33286271704947562</Real>
+ <Real Name="Cell 6 6 4">0.079875180015346631</Real>
+ <Real Name="Cell 6 6 5">0.00042102405425504402</Real>
+ <Real Name="Cell 6 7 0">3.1532566547884657e-06</Real>
+ <Real Name="Cell 6 7 1">0.00030105640434455741</Real>
+ <Real Name="Cell 6 7 2">0.009446190571854576</Real>
+ <Real Name="Cell 6 7 3">0.020872285203432872</Real>
+ <Real Name="Cell 6 7 4">0.0050100570477663066</Real>
+ <Real Name="Cell 6 7 5">2.6410735267336944e-05</Real>
+ <Real Name="Cell 6 8 0">0.00042998092346156037</Real>
+ <Real Name="Cell 6 8 1">0.0083864615997738361</Real>
+ <Real Name="Cell 6 8 2">0.012518982261419167</Real>
+ <Real Name="Cell 6 8 3">0.0018941805248498551</Real>
+ <Real Name="Cell 6 8 4">1.1000283891925967e-06</Real>
+ <Real Name="Cell 6 9 0">0.0016139788514304538</Real>
+ <Real Name="Cell 6 9 1">0.031479470185329379</Real>
+ <Real Name="Cell 6 9 2">0.046991323356162476</Real>
+ <Real Name="Cell 6 9 3">0.0071100068423672969</Real>
+ <Real Name="Cell 6 9 4">4.1290728477833956e-06</Real>
+ <Real Name="Cell 7 2 0">7.3333269531007198e-09</Real>
+ <Real Name="Cell 7 2 1">1.1310571632229732e-06</Real>
+ <Real Name="Cell 7 2 2">4.4189988416612641e-06</Real>
+ <Real Name="Cell 7 2 3">1.8686431659857344e-06</Real>
+ <Real Name="Cell 7 2 4">4.2579927034904449e-08</Real>
+ <Real Name="Cell 7 3 0">4.6677641699840157e-07</Real>
+ <Real Name="Cell 7 3 1">7.1997585733344011e-05</Real>
+ <Real Name="Cell 7 3 2">0.00028144060590160649</Real>
+ <Real Name="Cell 7 3 3">0.00011931010941132857</Real>
+ <Real Name="Cell 7 3 4">2.79875471101822e-06</Real>
+ <Real Name="Cell 7 3 5">4.6644478371396267e-10</Real>
+ <Real Name="Cell 7 4 0">1.3111594641865414e-06</Real>
+ <Real Name="Cell 7 4 1">0.00023230344530564693</Real>
+ <Real Name="Cell 7 4 2">0.001964553166613188</Real>
+ <Real Name="Cell 7 4 3">0.002952912988906251</Real>
+ <Real Name="Cell 7 4 4">0.00063663389408771494</Real>
+ <Real Name="Cell 7 4 5">3.3159162180257156e-06</Real>
+ <Real Name="Cell 7 5 0">4.0182136311688975e-07</Real>
+ <Real Name="Cell 7 5 1">0.00029647813676396455</Real>
+ <Real Name="Cell 7 5 2">0.0093992676557784309</Real>
+ <Real Name="Cell 7 5 3">0.020520958255432858</Real>
+ <Real Name="Cell 7 5 4">0.004906738741398583</Real>
+ <Real Name="Cell 7 5 5">2.5853830777996006e-05</Real>
+ <Real Name="Cell 7 6 0">4.3673388694017694e-09</Real>
+ <Real Name="Cell 7 6 1">0.0001803088715674896</Real>
+ <Real Name="Cell 7 6 2">0.0070172253096031775</Real>
+ <Real Name="Cell 7 6 3">0.015642247173435798</Real>
+ <Real Name="Cell 7 6 4">0.0037569228451156912</Real>
+ <Real Name="Cell 7 6 5">1.9804681617185402e-05</Real>
+ <Real Name="Cell 7 7 1">1.1268476522822571e-05</Real>
+ <Real Name="Cell 7 7 2">0.00044002372886475029</Real>
+ <Real Name="Cell 7 7 3">0.0009811645043648991</Real>
+ <Real Name="Cell 7 7 4">0.00023566925439787439</Real>
+ <Real Name="Cell 7 7 5">1.2423428019353165e-06</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>0.00043168598745147113</Real>
+ <Real>0.12397212138337553</Real>
+ <Real>0.57875978626183999</Real>
+ <Real>0.28787707086482694</Real>
+ <Real>0.0089593355025060009</Real>
+ <Real>2.412283597558329e-05</Real>
+ <Real>0.074060428119428312</Real>
+ <Real>0.5281551619863365</Real>
+ <Real>0.3765290805515803</Real>
+ <Real>0.021231206506679284</Real>
+ <Real>0.0033016690086745014</Real>
+ <Real>0.21215288599464993</Real>
+ <Real>0.59837477660759653</Real>
+ <Real>0.18414717639524303</Real>
+ <Real>0.0020234919938359637</Real>
+ <Real>0.0025586095786372461</Real>
+ <Real>0.19690898092691589</Real>
+ <Real>0.59895530494502436</Real>
+ <Real>0.19892677511393422</Real>
+ <Real>0.0026503294354883137</Real>
+ <Real>0.00039076566299572229</Real>
+ <Real>0.12120264109770255</Real>
+ <Real>0.5769963210853325</Real>
+ <Real>0.2920308692972568</Real>
+ <Real>0.009379402856712335</Real>
+ <Real>0.040630434871156813</Real>
+ <Real>0.45518549365190381</Real>
+ <Real>0.46146147760918327</Real>
+ <Real>0.042722593803103726</Real>
+ <Real>6.4652349062851777e-11</Real>
+ <Real>9.9173825171589586e-07</Real>
+ <Real>0.054580451594272536</Real>
+ <Real>0.49187307297977795</Real>
+ <Real>0.42235622694042391</Real>
+ <Real>0.031189256747273925</Real>
+ <Real>0.0035886370244400901</Real>
+ <Real>0.21746702452323663</Real>
+ <Real>0.59787057097020369</Real>
+ <Real>0.17923611426248856</Real>
+ <Real>0.0018376532196310062</Real>
+ <Real>0.026799462318528058</Real>
+ <Real>0.40392471542377728</Real>
+ <Real>0.50729578665061448</Real>
+ <Real>0.061975074125176763</Real>
+ <Real>4.9614819032708608e-06</Real>
+ <Real>2.1494937337497418e-07</Real>
+ <Real>0.05019469086708727</Real>
+ <Real>0.48154173346733414</Real>
+ <Real>0.43398971515956575</Real>
+ <Real>0.034273645556639379</Real>
+ <Real>5.537920060640921e-05</Real>
+ <Real>0.083542305116125995</Real>
+ <Real>0.54153929048313976</Real>
+ <Real>0.35700971710986118</Real>
+ <Real>0.017853308090266577</Real>
+ <Real>9.1124858730694142e-05</Real>
+ <Real>0.090721181941133183</Real>
+ <Real>0.55025864959373116</Real>
+ <Real>0.3432075990130844</Real>
+ <Real>0.015721444593320491</Real>
+ <Real>0.018987348346149579</Real>
+ <Real>0.36385552673261401</Real>
+ <Real>0.53698509539530281</Real>
+ <Real>0.080129839254891311</Real>
+ <Real>4.2190271042138495e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>0.00015195084349147622</Real>
+ <Real>0.099586358951448004</Real>
+ <Real>0.55959855329798436</Real>
+ <Real>0.32717756091340827</Real>
+ <Real>0.01348557599366784</Real>
+ <Real>2.4260362260629302e-05</Real>
+ <Real>0.074116427316521308</Real>
+ <Real>0.52824119730101549</Real>
+ <Real>0.37640907510647797</Real>
+ <Real>0.021209039913724623</Real>
+ <Real>2.9799899041508872e-09</Real>
+ <Real>0.044459798525464958</Real>
+ <Real>0.46644097736487722</Real>
+ <Real>0.45009197937107209</Real>
+ <Real>0.039007241758595698</Real>
+ <Real>0.0027408920796075957</Real>
+ <Real>0.20087746981344573</Real>
+ <Real>0.59893243346414637</Real>
+ <Real>0.19497658318626196</Real>
+ <Real>0.0024726214565381982</Real>
+ <Real>0.00010852418716670213</Real>
+ <Real>0.093564473503081363</Real>
+ <Real>0.55341578786571499</Real>
+ <Real>0.33795038178000431</Real>
+ <Real>0.014960832664032583</Real>
+ <Real>8.70688143407287e-06</Real>
+ <Real>0.065574009020506169</Real>
+ <Real>0.51401843463678332</Real>
+ <Real>0.39543783225030044</Real>
+ <Real>0.024961017210975898</Real>
+ <Real>0.0026918827551873068</Real>
+ <Real>0.19982682442644864</Real>
+ <Real>0.59894752670430673</Real>
+ <Real>0.19601515417024337</Real>
+ <Real>0.0025186119438139094</Real>
+ <Real>0.00015096524582485841</Real>
+ <Real>0.099462640452621973</Real>
+ <Real>0.55947807717550002</Real>
+ <Real>0.32739415018595958</Real>
+ <Real>0.013514166940093513</Real>
+ <Real>0.00010548375296443968</Real>
+ <Real>0.093089590287530832</Real>
+ <Real>0.55289950737145288</Real>
+ <Real>0.33882057290998219</Real>
+ <Real>0.015084845678069543</Real>
+ <Real>0.012967061736831292</Real>
+ <Real>0.32319192962601168</Real>
+ <Real>0.56178721913659135</Real>
+ <Real>0.10188280823098855</Real>
+ <Real>0.00017098126957707798</Real>
+ <Real>0.0093924113694081966</Real>
+ <Real>0.29215749184002215</Real>
+ <Real>0.57694155886402931</Real>
+ <Real>0.12111896985329024</Real>
+ <Real>0.00038956807325003957</Real>
+ <Real>0.0064292944800659483</Real>
+ <Real>0.25964388571917835</Real>
+ <Real>0.58898204094315654</Real>
+ <Real>0.14413606898777964</Real>
+ <Real>0.00080870986981941974</Real>
+ <Real>0.00063228945691469213</Real>
+ <Real>0.13563675482476231</Real>
+ <Real>0.58520218545915026</Real>
+ <Real>0.27113574277694441</Real>
+ <Real>0.0073930274822284784</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>0.0051677772656301057</Real>
+ <Real>0.24277874193839083</Real>
+ <Real>0.59352018741180557</Real>
+ <Real>0.15739494285160488</Real>
+ <Real>0.0011383505325685479</Real>
+ <Real>0.0073630099847195752</Real>
+ <Real>0.27079302072734218</Real>
+ <Real>0.58532264913373744</Real>
+ <Real>0.13588426274984747</Real>
+ <Real>0.00063705740435331104</Real>
+ <Real>0.037212443309160612</Real>
+ <Real>0.44421545919804756</Real>
+ <Real>0.47206292117996462</Real>
+ <Real>0.046509151178613553</Real>
+ <Real>2.5134213594333823e-08</Real>
+ <Real>0.030775118026428579</Real>
+ <Real>0.42071682716898717</Real>
+ <Real>0.49329128362289443</Real>
+ <Real>0.055215591102667598</Real>
+ <Real>1.1800790222950388e-06</Real>
+ <Real>0.00035249786697384835</Real>
+ <Real>0.11844678361245713</Real>
+ <Real>0.57514570201795168</Real>
+ <Real>0.29623697037588936</Real>
+ <Real>0.0098180461267279116</Real>
+ <Real>0.030884113789831424</Real>
+ <Real>0.42115016817053519</Real>
+ <Real>0.49291730315772098</Real>
+ <Real>0.055047286957198585</Real>
+ <Real>1.1279247137839807e-06</Real>
+ <Real>0.0030967576983704373</Real>
+ <Real>0.20818071823371087</Real>
+ <Real>0.5986522754924074</Real>
+ <Real>0.18789742938665951</Real>
+ <Real>0.0021728191888517098</Real>
+ <Real>0.022343511730447432</Real>
+ <Real>0.38242826198506941</Real>
+ <Real>0.52386869352108667</Real>
+ <Real>0.071341485967975876</Real>
+ <Real>1.8046795420541908e-05</Real>
+ <Real>0.010145481949927834</Real>
+ <Real>0.29929464095801378</Real>
+ <Real>0.57375984196142316</Real>
+ <Real>0.11647346532187075</Real>
+ <Real>0.0003265698087644401</Real>
+ <Real>0.0014617904290638469</Real>
+ <Real>0.1682872607776017</Real>
+ <Real>0.59613993352686223</Real>
+ <Real>0.2297980712357692</Real>
+ <Real>0.0043129440307029107</Real>
+ <Real>0.00093350652545619761</Real>
+ <Real>0.14948506602626943</Real>
+ <Real>0.59100241651365182</Real>
+ <Real>0.25269117265923857</Real>
+ <Real>0.0058878382753838965</Real>
+ <Real>2.2511326449719818e-05</Real>
+ <Real>0.073388012440734784</Real>
+ <Real>0.52711510749250323</Real>
+ <Real>0.37797470767964925</Real>
+ <Real>0.021499661060662919</Real>
+ <Real>0.0077812058733808722</Real>
+ <Real>0.27548781880963463</Real>
+ <Real>0.58363198148677997</Real>
+ <Real>0.13252480522712207</Real>
+ <Real>0.00057418860308248792</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>-0.0054123159943235263</Real>
+ <Real>-0.35543045994849493</Real>
+ <Real>-0.22027447567701353</Real>
+ <Real>0.52848959517680594</Real>
+ <Real>0.052627656443025993</Real>
+ <Real>-0.00062205452524004593</Real>
+ <Real>-0.25376770847962776</Real>
+ <Real>-0.39008172763611693</Real>
+ <Real>0.54395479881207742</Real>
+ <Real>0.10051669182890735</Real>
+ <Real>-0.024891858917245911</Real>
+ <Real>-0.47312831449340104</Real>
+ <Real>0.038174033354594794</Real>
+ <Real>0.44260431243999732</Real>
+ <Real>0.01724182761605484</Real>
+ <Real>-0.020559388675760314</Real>
+ <Real>-0.45723030077824783</Real>
+ <Real>-0.0027515317099742753</Real>
+ <Real>0.45943152045773322</Real>
+ <Real>0.021109700706249193</Real>
+ <Real>-0.0050227837091489976</Real>
+ <Real>-0.35059378814664566</Real>
+ <Real>-0.22927643071818149</Real>
+ <Real>0.53042536071289603</Real>
+ <Real>0.054467641861080135</Real>
+ <Real>-0.16354820572788292</Real>
+ <Real>-0.50307919348273278</Real>
+ <Real>0.49680304535368675</Real>
+ <Real>0.1698243126523564</Real>
+ <Real>4.1204572502199554e-08</Real>
+ <Real>-5.6794329827889662e-05</Real>
+ <Real>-0.20380268688822553</Real>
+ <Real>-0.45809886799216037</Real>
+ <Real>0.52783297396830886</Real>
+ <Real>0.13412537524190493</Real>
+ <Real>-0.026497465234508667</Real>
+ <Real>-0.47828050014666967</Real>
+ <Real>0.052093413976694869</Real>
+ <Real>0.43664453342465404</Real>
+ <Real>0.016040017979829454</Real>
+ <Real>-0.11970209227194881</Real>
+ <Real>-0.53662234959272781</Real>
+ <Real>0.4325409594380264</Real>
+ <Real>0.22359349898992603</Real>
+ <Real>0.00018998343672421792</Real>
+ <Real>-1.8040946492467145e-05</Real>
+ <Real>-0.19155920806570498</Real>
+ <Real>-0.47287224461691968</Real>
+ <Real>0.52049427721692421</Real>
+ <Real>0.14395521641219289</Real>
+ <Real>-0.001160158143288331</Real>
+ <Real>-0.27572281668186399</Real>
+ <Real>-0.35680733132162235</Real>
+ <Real>0.54542374526199011</Real>
+ <Real>0.088266560884784587</Real>
+ <Real>-0.0016855235775882218</Real>
+ <Real>-0.29143371186306077</Real>
+ <Real>-0.33183866640415738</Real>
+ <Real>0.54472056270785008</Real>
+ <Real>0.080237339136956284</Real>
+ <Real>-0.092439038491503631</Real>
+ <Real>-0.54524494322339256</Real>
+ <Real>0.36875305699126182</Real>
+ <Real>0.26798486965366852</Real>
+ <Real>0.0009460550699658196</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>-0.0024733439646709445</Real>
+ <Real>-0.30983851881908325</Real>
+ <Real>-0.30138592749241133</Real>
+ <Real>0.54218078730075636</Real>
+ <Real>0.07151700297540918</Real>
+ <Real>-0.00062471242253069026</Real>
+ <Real>-0.25390162851379605</Real>
+ <Real>-0.38988463303054299</Real>
+ <Real>0.54397300129259696</Real>
+ <Real>0.10043797267427278</Real>
+ <Real>-7.289005458467352e-07</Real>
+ <Real>-0.17497413775377094</Real>
+ <Real>-0.4914265549325933</Real>
+ <Real>0.50777843872868289</Real>
+ <Real>0.15862298285822721</Real>
+ <Real>-0.021648416398585668</Real>
+ <Real>-0.46153114918445864</Real>
+ <Real>0.0080465180715674767</Real>
+ <Real>0.45509407700458371</Real>
+ <Real>0.020038970506893111</Real>
+ <Real>-0.0019215517592169318</Real>
+ <Real>-0.29745274240975228</Real>
+ <Real>-0.32202193698478676</Real>
+ <Real>0.5440883082356982</Real>
+ <Real>0.077307922918057798</Real>
+ <Real>-0.00028967042316330595</Real>
+ <Real>-0.2328515765720254</Real>
+ <Real>-0.41993880385606597</Real>
+ <Real>0.53959101912086138</Real>
+ <Real>0.11348903173039328</Real>
+ <Real>-0.021357444482793631</Real>
+ <Real>-0.46040374597745926</Real>
+ <Real>0.0051976929501876823</Real>
+ <Real>0.45624562996317708</Real>
+ <Real>0.020317867546888163</Real>
+ <Real>-0.0024613020578055349</Real>
+ <Real>-0.30958887167136379</Real>
+ <Real>-0.30180765951720046</Real>
+ <Real>0.54222714227971447</Real>
+ <Real>0.071630690966655336</Real>
+ <Real>-0.0018810327659186724</Real>
+ <Real>-0.29645523625782155</Real>
+ <Real>-0.32365838815836168</Real>
+ <Real>0.54420661615386279</Real>
+ <Real>0.077788041028239135</Real>
+ <Real>-0.069444581465373606</Real>
+ <Real>-0.5412697447426873</Real>
+ <Real>0.29357544069077202</Real>
+ <Real>0.31443667870801228</Real>
+ <Real>0.0027022068092765858</Real>
+ <Real>-0.054524288877065188</Real>
+ <Real>-0.53048257613609351</Real>
+ <Real>0.22954925309162344</Real>
+ <Real>0.3504463777332944</Real>
+ <Real>0.0050112341882408307</Real>
+ <Real>-0.04103265979952906</Real>
+ <Real>-0.51231766614035856</Real>
+ <Real>0.15639997126635846</Real>
+ <Real>0.38828369508647514</Real>
+ <Real>0.0086666595870540392</Real>
+ <Real>-0.0072059979806885803</Real>
+ <Real>-0.37492576008690903</Real>
+ <Real>-0.18296626785233178</Real>
+ <Real>0.51953380788814496</Real>
+ <Real>0.045564218031784426</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>-0.034832530108168232</Real>
+ <Real>-0.50014496344496462</Real>
+ <Real>0.11598741843099425</Real>
+ <Real>0.40779017390557831</Real>
+ <Real>0.011199901216560273</Real>
+ <Real>-0.045425396100255505</Real>
+ <Real>-0.51933118858727911</Real>
+ <Real>0.18218527922514327</Real>
+ <Real>0.37532459171257293</Real>
+ <Real>0.0072467137498184323</Real>
+ <Real>-0.15311696790993051</Real>
+ <Real>-0.51278384813801825</Real>
+ <Real>0.48492220750431003</Real>
+ <Real>0.18097500104515701</Real>
+ <Real>3.6074984818065711e-06</Real>
+ <Real>-0.13278743328419851</Real>
+ <Real>-0.52875151750440053</Real>
+ <Real>0.45593004025726047</Real>
+ <Real>0.20554420513547464</Real>
+ <Real>6.4705395863929661e-05</Real>
+ <Real>-0.0046491606241226236</Real>
+ <Real>-0.34569837253547919</Real>
+ <Real>-0.23828863536588613</Real>
+ <Real>0.53226903083470045</Real>
+ <Real>0.056367137690787474</Real>
+ <Real>-0.13313999577356062</Real>
+ <Real>-0.52851141417561998</Real>
+ <Real>0.45650536422465193</Real>
+ <Real>0.20508349717179866</Real>
+ <Real>6.2548552730021432e-05</Real>
+ <Real>-0.023723982790674208</Real>
+ <Real>-0.46914679562135475</Real>
+ <Real>0.027653117742020838</Real>
+ <Real>0.44703008254271953</Real>
+ <Real>0.018187578127288623</Real>
+ <Real>-0.1044409359397518</Real>
+ <Real>-0.54291528648973197</Real>
+ <Real>0.39965376922055962</Real>
+ <Real>0.24720206478708404</Real>
+ <Real>0.00050038842184013438</Real>
+ <Real>-0.057771240463032621</Real>
+ <Real>-0.53353552805699944</Real>
+ <Real>0.24477502703072435</Real>
+ <Real>0.3421414919616802</Real>
+ <Real>0.0043902495276275291</Real>
+ <Real>-0.013510487389683298</Real>
+ <Real>-0.42267040103937348</Real>
+ <Real>-0.083712754882333984</Real>
+ <Real>0.48947866244152172</Real>
+ <Real>0.030414980869869036</Real>
+ <Real>-0.0096515085445540213</Real>
+ <Real>-0.39634333796672683</Real>
+ <Real>-0.13994616469967064</Real>
+ <Real>0.50752837747773805</Real>
+ <Real>0.038412633733213512</Real>
+ <Real>-0.00059061979071704568</Real>
+ <Real>-0.25215556429754155</Real>
+ <Real>-0.39244859365573209</Real>
+ <Real>0.54372635936695712</Real>
+ <Real>0.10146841837703359</Real>
+ <Real>-0.047346988432876699</Real>
+ <Real>-0.52203952869624104</Real>
+ <Real>0.19282346856287375</Real>
+ <Real>0.36985960269448226</Real>
+ <Real>0.0067034458717617042</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">4</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">16</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">10</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">16</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">15</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 1 3">4.9479740823536002e-11</Real>
+ <Real Name="Cell 0 1 4">1.6626245726929841e-08</Real>
+ <Real Name="Cell 0 1 5">8.0732574400883411e-08</Real>
+ <Real Name="Cell 0 1 6">4.1582460178790155e-08</Real>
+ <Real Name="Cell 0 1 7">1.3781484180727238e-09</Real>
+ <Real Name="Cell 0 2 1">1.0513678870843961e-07</Real>
+ <Real Name="Cell 0 2 2">4.9392564698635728e-06</Real>
+ <Real Name="Cell 0 2 3">1.2117639002150265e-05</Real>
+ <Real Name="Cell 0 2 4">1.7536520861008393e-05</Real>
+ <Real Name="Cell 0 2 5">6.9627005449864914e-05</Real>
+ <Real Name="Cell 0 2 6">3.5850450440278356e-05</Real>
+ <Real Name="Cell 0 2 7">1.1881750466189399e-06</Real>
+ <Real Name="Cell 0 3 1">6.890511259260331e-05</Real>
+ <Real Name="Cell 0 3 2">0.0032371164019809355</Real>
+ <Real Name="Cell 0 3 3">0.0079140174146799629</Real>
+ <Real Name="Cell 0 3 4">0.0021834273903276508</Real>
+ <Real Name="Cell 0 3 5">0.00042687162378168933</Real>
+ <Real Name="Cell 0 3 6">0.00021204848948456936</Real>
+ <Real Name="Cell 0 3 7">7.027825892969387e-06</Real>
+ <Real Name="Cell 0 4 0">3.2167211187803997e-08</Real>
+ <Real Name="Cell 0 4 1">0.00038763225198604065</Real>
+ <Real Name="Cell 0 4 2">0.018190611663084513</Real>
+ <Real Name="Cell 0 4 3">0.044469469501171137</Real>
+ <Real Name="Cell 0 4 4">0.011844526987928358</Real>
+ <Real Name="Cell 0 4 5">0.00033669619657422108</Real>
+ <Real Name="Cell 0 4 6">0.00012949010409253451</Real>
+ <Real Name="Cell 0 4 7">4.2916311671771559e-06</Real>
+ <Real Name="Cell 0 5 0">0.00024233607822658125</Real>
+ <Real Name="Cell 0 5 1">0.0037765131373025777</Real>
+ <Real Name="Cell 0 5 2">0.016272564369407355</Real>
+ <Real Name="Cell 0 5 3">0.027701280279014685</Real>
+ <Real Name="Cell 0 5 4">0.0069693389359114545</Real>
+ <Real Name="Cell 0 5 5">6.0995882083439624e-05</Real>
+ <Real Name="Cell 0 5 6">5.7324384981392963e-06</Real>
+ <Real Name="Cell 0 5 7">1.8998758163759294e-07</Real>
+ <Real Name="Cell 0 6 0">0.0019020740106302041</Real>
+ <Real Name="Cell 0 6 1">0.035868393150081966</Real>
+ <Real Name="Cell 0 6 2">0.10233676223180677</Real>
+ <Real Name="Cell 0 6 3">0.055815489098793872</Real>
+ <Real Name="Cell 0 6 4">0.0032087988755052166</Real>
+ <Real Name="Cell 0 6 5">2.0553897142033654e-06</Real>
+ <Real Name="Cell 0 7 0">0.0014678570402335413</Real>
+ <Real Name="Cell 0 7 1">0.042571933720211924</Real>
+ <Real Name="Cell 0 7 2">0.18630208183056671</Real>
+ <Real Name="Cell 0 7 3">0.11973476726953122</Real>
+ <Real Name="Cell 0 7 4">0.0066958984413124914</Real>
+ <Real Name="Cell 0 7 5">4.2578291011704643e-11</Real>
+ <Real Name="Cell 0 8 0">9.3912967498973072e-05</Real>
+ <Real Name="Cell 0 8 1">0.0068458528441489377</Real>
+ <Real Name="Cell 0 8 2">0.041899673524474955</Real>
+ <Real Name="Cell 0 8 3">0.029404662179499844</Real>
+ <Real Name="Cell 0 8 4">0.0016953604960386203</Real>
+ <Real Name="Cell 0 8 5">4.1085899845168109e-11</Real>
+ <Real Name="Cell 0 9 0">9.5131650091012236e-09</Real>
+ <Real Name="Cell 0 9 1">3.6285186665321725e-05</Real>
+ <Real Name="Cell 0 9 2">0.00028568707151635465</Real>
+ <Real Name="Cell 0 9 3">0.00022660623541248136</Real>
+ <Real Name="Cell 0 9 4">1.5674494662014633e-05</Real>
+ <Real Name="Cell 0 9 5">3.5607113691946983e-12</Real>
+ <Real Name="Cell 1 1 3">1.5346986279876964e-08</Real>
+ <Real Name="Cell 1 1 4">5.1569139371013472e-06</Real>
+ <Real Name="Cell 1 1 5">2.5040586127729852e-05</Real>
+ <Real Name="Cell 1 1 6">1.2897509874260841e-05</Real>
+ <Real Name="Cell 1 1 7">4.2745625809211247e-07</Real>
+ <Real Name="Cell 1 2 1">4.908276528799683e-07</Real>
+ <Real Name="Cell 1 2 2">2.305875697609859e-05</Real>
+ <Real Name="Cell 1 2 3">6.9603101001052036e-05</Real>
+ <Real Name="Cell 1 2 4">0.0044609989034486448</Real>
+ <Real Name="Cell 1 2 5">0.021588929177202544</Real>
+ <Real Name="Cell 1 2 6">0.011119629203325362</Real>
+ <Real Name="Cell 1 2 7">0.00036853277392025576</Real>
+ <Real Name="Cell 1 3 1">0.00032168126020138337</Real>
+ <Real Name="Cell 1 3 2">0.015112371846259442</Real>
+ <Real Name="Cell 1 3 3">0.0370234145072037</Real>
+ <Real Name="Cell 1 3 4">0.036094968664250326</Real>
+ <Real Name="Cell 1 3 5">0.12776456595038849</Real>
+ <Real Name="Cell 1 3 6">0.065770458871125426</Real>
+ <Real Name="Cell 1 3 7">0.002179800171981933</Real>
+ <Real Name="Cell 1 4 0">4.8678827312710805e-17</Real>
+ <Real Name="Cell 1 4 1">0.0018076006566280362</Real>
+ <Real Name="Cell 1 4 2">0.084919877693199725</Real>
+ <Real Name="Cell 1 4 3">0.20765106553513776</Real>
+ <Real Name="Cell 1 4 4">0.071112994047407924</Real>
+ <Real Name="Cell 1 4 5">0.078375959818312566</Real>
+ <Real Name="Cell 1 4 6">0.040163566296262367</Real>
+ <Real Name="Cell 1 4 7">0.0013311226684847726</Real>
+ <Real Name="Cell 1 5 0">4.5872681735427457e-07</Real>
+ <Real Name="Cell 1 5 1">0.0025523108623422409</Real>
+ <Real Name="Cell 1 5 2">0.060390993794884447</Real>
+ <Real Name="Cell 1 5 3">0.12908264854096432</Real>
+ <Real Name="Cell 1 5 4">0.033337207319746556</Real>
+ <Real Name="Cell 1 5 5">0.0036848225515440768</Real>
+ <Real Name="Cell 1 5 6">0.0017780136580532566</Real>
+ <Real Name="Cell 1 5 7">5.8927891702945559e-05</Real>
+ <Real Name="Cell 1 6 0">1.8525444276679718e-05</Real>
+ <Real Name="Cell 1 6 1">0.060823493091753299</Real>
+ <Real Name="Cell 1 6 2">0.44043882770688458</Real>
+ <Real Name="Cell 1 6 3">0.32095086007456436</Real>
+ <Real Name="Cell 1 6 4">0.019502188148647608</Real>
+ <Real Name="Cell 1 6 5">9.59576136152423e-06</Real>
+ <Real Name="Cell 1 7 0">4.2023530924477262e-05</Real>
+ <Real Name="Cell 1 7 1">0.14104940189413367</Real>
+ <Real Name="Cell 1 7 2">1.0323580255566671</Real>
+ <Real Name="Cell 1 7 3">0.75697807028691433</Real>
+ <Real Name="Cell 1 7 4">0.045197615958555579</Real>
+ <Real Name="Cell 1 7 5">2.7359215279061732e-09</Real>
+ <Real Name="Cell 1 8 0">1.0284025479409903e-05</Real>
+ <Real Name="Cell 1 8 1">0.037435108584675789</Real>
+ <Real Name="Cell 1 8 2">0.28746524151708852</Real>
+ <Real Name="Cell 1 8 3">0.22225728405777784</Real>
+ <Real Name="Cell 1 8 4">0.014707046825307692</Real>
+ <Real Name="Cell 1 8 5">2.6400260604375077e-09</Real>
+ <Real Name="Cell 1 9 0">5.7700982496756358e-08</Real>
+ <Real Name="Cell 1 9 1">0.00052685468719330345</Real>
+ <Real Name="Cell 1 9 2">0.0053948153781404285</Real>
+ <Real Name="Cell 1 9 3">0.0052660358440288603</Real>
+ <Real Name="Cell 1 9 4">0.00047848296623588478</Real>
+ <Real Name="Cell 1 9 5">2.2879797798746884e-10</Real>
+ <Real Name="Cell 16 4 0">3.0591957622616733e-08</Real>
+ <Real Name="Cell 16 4 1">4.1716619052455725e-07</Real>
+ <Real Name="Cell 16 4 2">4.8825442595734692e-07</Real>
+ <Real Name="Cell 16 4 3">5.4526553078207448e-08</Real>
+ <Real Name="Cell 16 4 4">1.117254821698738e-12</Real>
+ <Real Name="Cell 16 5 0">0.00023039676378848261</Real>
+ <Real Name="Cell 16 5 1">0.0031417976399055404</Real>
+ <Real Name="Cell 16 5 2">0.0036771834295040396</Real>
+ <Real Name="Cell 16 5 3">0.00041065503308857382</Real>
+ <Real Name="Cell 16 5 4">8.4143649262955958e-09</Real>
+ <Real Name="Cell 16 6 0">0.001806023234463245</Real>
+ <Real Name="Cell 16 6 1">0.024627774463274996</Real>
+ <Real Name="Cell 16 6 2">0.028824531221126104</Real>
+ <Real Name="Cell 16 6 3">0.003219023214180718</Real>
+ <Real Name="Cell 16 6 4">6.5958125063309245e-08</Real>
+ <Real Name="Cell 16 7 0">0.0013893857976795517</Real>
+ <Real Name="Cell 16 7 1">0.018946312215024717</Real>
+ <Real Name="Cell 16 7 2">0.022174905360675456</Real>
+ <Real Name="Cell 16 7 3">0.0024764161672109941</Real>
+ <Real Name="Cell 16 7 4">5.0742028372502962e-08</Real>
+ <Real Name="Cell 16 8 0">8.7701479171100279e-05</Real>
+ <Real Name="Cell 16 8 1">0.0011959382403866987</Real>
+ <Real Name="Cell 16 8 2">0.0013997350511703885</Real>
+ <Real Name="Cell 16 8 3">0.00015631753345280895</Real>
+ <Real Name="Cell 16 8 4">3.2029627421287572e-09</Real>
+ <Real Name="Cell 17 4 0">3.4272375809873896e-07</Real>
+ <Real Name="Cell 17 4 1">4.6735408806467023e-06</Real>
+ <Real Name="Cell 17 4 2">5.4699471618230825e-06</Real>
+ <Real Name="Cell 17 4 3">6.1086464023204118e-07</Real>
+ <Real Name="Cell 17 4 4">1.251668088620264e-11</Real>
+ <Real Name="Cell 17 5 0">0.0025811504354660533</Real>
+ <Real Name="Cell 17 5 1">0.035197770198861576</Real>
+ <Real Name="Cell 17 5 2">0.041195733196437261</Real>
+ <Real Name="Cell 17 5 3">0.0046005959461132223</Real>
+ <Real Name="Cell 17 5 4">9.4266696009746056e-08</Real>
+ <Real Name="Cell 17 6 0">0.020232999723799272</Real>
+ <Real Name="Cell 17 6 1">0.27590661316233178</Real>
+ <Real Name="Cell 17 6 2">0.32292316128979293</Real>
+ <Real Name="Cell 17 6 3">0.03606293349973367</Real>
+ <Real Name="Cell 17 6 4">7.3893330978373592e-07</Real>
+ <Real Name="Cell 17 7 0">0.015565382506862265</Real>
+ <Real Name="Cell 17 7 1">0.21225680960164375</Real>
+ <Real Name="Cell 17 7 2">0.24842695568707113</Real>
+ <Real Name="Cell 17 7 3">0.027743456823291383</Real>
+ <Real Name="Cell 17 7 4">5.6846635550123161e-07</Real>
+ <Real Name="Cell 17 8 0">0.00098252556776936206</Real>
+ <Real Name="Cell 17 8 1">0.01339817651604942</Real>
+ <Real Name="Cell 17 8 2">0.015681325889552945</Real>
+ <Real Name="Cell 17 8 3">0.001751235837292897</Real>
+ <Real Name="Cell 17 8 4">3.5883006951508512e-08</Real>
+ <Real Name="Cell 18 2 1">3.6609907086066561e-10</Real>
+ <Real Name="Cell 18 2 2">1.71990910752863e-08</Real>
+ <Real Name="Cell 18 2 3">4.2046546896215035e-08</Real>
+ <Real Name="Cell 18 2 4">1.1150275906698594e-08</Real>
+ <Real Name="Cell 18 2 5">8.0643776011556709e-11</Real>
+ <Real Name="Cell 18 3 1">2.3993597300805377e-07</Real>
+ <Real Name="Cell 18 3 2">1.1272032573864506e-05</Real>
+ <Real Name="Cell 18 3 3">2.7556691464567284e-05</Real>
+ <Real Name="Cell 18 3 4">7.307727639659058e-06</Real>
+ <Real Name="Cell 18 3 5">5.2852750537956458e-08</Real>
+ <Real Name="Cell 18 4 0">3.4744914772034036e-07</Real>
+ <Real Name="Cell 18 4 1">6.0862336662597547e-06</Real>
+ <Real Name="Cell 18 4 2">6.8885497424581494e-05</Real>
+ <Real Name="Cell 18 4 3">0.00015546664610137969</Real>
+ <Real Name="Cell 18 4 4">4.1063807551389755e-05</Real>
+ <Real Name="Cell 18 4 5">2.969917069995424e-07</Real>
+ <Real Name="Cell 18 5 0">0.0026167387692974447</Real>
+ <Real Name="Cell 18 5 1">0.035684104200557266</Real>
+ <Real Name="Cell 18 5 2">0.041802541230034788</Real>
+ <Real Name="Cell 18 5 3">0.0047558371250823756</Real>
+ <Real Name="Cell 18 5 4">2.4176673527483894e-05</Real>
+ <Real Name="Cell 18 5 5">1.7364058883811605e-07</Real>
+ <Real Name="Cell 18 6 0">0.020511970341053575</Real>
+ <Real Name="Cell 18 6 1">0.27972077860183842</Real>
+ <Real Name="Cell 18 6 2">0.32744890776861246</Real>
+ <Real Name="Cell 18 6 3">0.036615402865375603</Real>
+ <Real Name="Cell 18 6 4">4.6687138830384599e-06</Real>
+ <Real Name="Cell 18 6 5">7.1571025525842582e-09</Real>
+ <Real Name="Cell 18 7 0">0.015780001074489215</Real>
+ <Real Name="Cell 18 7 1">0.21520604100121718</Real>
+ <Real Name="Cell 18 7 2">0.25201515923428436</Real>
+ <Real Name="Cell 18 7 3">0.028242825454598955</Real>
+ <Real Name="Cell 18 7 4">7.2228046199710238e-06</Real>
+ <Real Name="Cell 18 8 0">0.00099607408809970375</Real>
+ <Real Name="Cell 18 8 1">0.01358845932780222</Real>
+ <Real Name="Cell 18 8 2">0.01593741447618845</Real>
+ <Real Name="Cell 18 8 3">0.0018039767480669806</Real>
+ <Real Name="Cell 18 8 4">1.6629136614134367e-06</Real>
+ <Real Name="Cell 18 9 0">9.5554951885286652e-12</Real>
+ <Real Name="Cell 18 9 1">3.1151376234511103e-08</Real>
+ <Real Name="Cell 18 9 2">2.2374718276577056e-07</Real>
+ <Real Name="Cell 18 9 3">1.6044081225890489e-07</Real>
+ <Real Name="Cell 18 9 4">9.1260685272821227e-09</Real>
+ <Real Name="Cell 2 0 0">0.00015445186807673834</Real>
+ <Real Name="Cell 2 0 1">0.0045548659421078665</Real>
+ <Real Name="Cell 2 0 10">5.0484629021891178e-10</Real>
+ <Real Name="Cell 2 0 2">0.0087315455428858494</Real>
+ <Real Name="Cell 2 0 3">0.0017724924323999545</Real>
+ <Real Name="Cell 2 0 4">4.969733034487073e-06</Real>
+ <Real Name="Cell 2 1 0">0.00091702206667114829</Real>
+ <Real Name="Cell 2 1 1">0.02705214160316986</Real>
+ <Real Name="Cell 2 1 10">9.1556297509847007e-11</Real>
+ <Real Name="Cell 2 1 2">0.051859984281513956</Real>
+ <Real Name="Cell 2 1 3">0.010527666868546792</Real>
+ <Real Name="Cell 2 1 4">5.4067366072504947e-05</Real>
+ <Real Name="Cell 2 1 5">0.00011920801347780539</Real>
+ <Real Name="Cell 2 1 6">6.1399782060948146e-05</Real>
+ <Real Name="Cell 2 1 7">2.0349448337947681e-06</Real>
+ <Real Name="Cell 2 15 0">1.3415134170144429e-09</Real>
+ <Real Name="Cell 2 15 1">4.7521702804424301e-09</Real>
+ <Real Name="Cell 2 15 10">1.1652762451484694e-11</Real>
+ <Real Name="Cell 2 15 2">1.8318510524348346e-09</Real>
+ <Real Name="Cell 2 15 3">3.4380928522370846e-11</Real>
+ <Real Name="Cell 2 16 0">2.0838605945675685e-07</Real>
+ <Real Name="Cell 2 16 1">5.2795214152132265e-06</Real>
+ <Real Name="Cell 2 16 10">2.9043424475043593e-10</Real>
+ <Real Name="Cell 2 16 2">9.9396508980883738e-06</Real>
+ <Real Name="Cell 2 16 3">2.0093413862421701e-06</Real>
+ <Real Name="Cell 2 16 4">5.6314147488440349e-09</Real>
+ <Real Name="Cell 2 2 0">0.00056195091754646348</Real>
+ <Real Name="Cell 2 2 1">0.016577957740282697</Real>
+ <Real Name="Cell 2 2 10">1.5365116311398331e-13</Real>
+ <Real Name="Cell 2 2 2">0.031791611977287269</Real>
+ <Real Name="Cell 2 2 3">0.006542409977773834</Real>
+ <Real Name="Cell 2 2 4">0.021191353091345382</Real>
+ <Real Name="Cell 2 2 5">0.10277562215279767</Real>
+ <Real Name="Cell 2 2 6">0.052936017598657584</Real>
+ <Real Name="Cell 2 2 7">0.0017544341676510784</Real>
+ <Real Name="Cell 2 3 0">2.5046602068380665e-05</Real>
+ <Real Name="Cell 2 3 1">0.00089910276643434582</Real>
+ <Real Name="Cell 2 3 2">0.0089341095659474616</Real>
+ <Real Name="Cell 2 3 3">0.019036980132589476</Real>
+ <Real Name="Cell 2 3 4">0.1300658791051732</Real>
+ <Real Name="Cell 2 3 5">0.60793288056058503</Real>
+ <Real Name="Cell 2 3 6">0.31310631897981711</Real>
+ <Real Name="Cell 2 3 7">0.010377139215315263</Real>
+ <Real Name="Cell 2 4 0">1.9971795888534043e-07</Real>
+ <Real Name="Cell 2 4 1">0.00090689893895242271</Real>
+ <Real Name="Cell 2 4 2">0.042257317076231343</Real>
+ <Real Name="Cell 2 4 3">0.10349468451861138</Real>
+ <Real Name="Cell 2 4 4">0.10383407971439287</Real>
+ <Real Name="Cell 2 4 5">0.37141846770980802</Real>
+ <Real Name="Cell 2 4 6">0.1912023515719371</Real>
+ <Real Name="Cell 2 4 7">0.0063369318991148881</Real>
+ <Real Name="Cell 2 5 0">4.3300548837069532e-07</Real>
+ <Real Name="Cell 2 5 1">0.0014647168090771909</Real>
+ <Real Name="Cell 2 5 2">0.031411138793115134</Real>
+ <Real Name="Cell 2 5 3">0.065192602942507033</Real>
+ <Real Name="Cell 2 5 4">0.019668212383341096</Real>
+ <Real Name="Cell 2 5 5">0.016549469416744719</Real>
+ <Real Name="Cell 2 5 6">0.0084643975596968239</Real>
+ <Real Name="Cell 2 5 7">0.00028053164860084045</Real>
+ <Real Name="Cell 2 6 0">1.1564073487337495e-05</Real>
+ <Real Name="Cell 2 6 1">0.038780054382099659</Real>
+ <Real Name="Cell 2 6 2">0.28457861246858152</Real>
+ <Real Name="Cell 2 6 3">0.21031175059436169</Real>
+ <Real Name="Cell 2 6 4">0.013056399157831716</Real>
+ <Real Name="Cell 2 6 5">4.7735698990094365e-06</Real>
+ <Real Name="Cell 2 7 0">2.6210941095015262e-05</Real>
+ <Real Name="Cell 2 7 1">0.09687377922004041</Real>
+ <Real Name="Cell 2 7 2">0.75012528681155177</Real>
+ <Real Name="Cell 2 7 3">0.58502414895287624</Real>
+ <Real Name="Cell 2 7 4">0.039312117542748368</Real>
+ <Real Name="Cell 2 7 5">7.7166352246466984e-09</Real>
+ <Real Name="Cell 2 8 0">6.414357407535341e-06</Real>
+ <Real Name="Cell 2 8 1">0.031935527165092181</Real>
+ <Real Name="Cell 2 8 2">0.28179723453710215</Real>
+ <Real Name="Cell 2 8 3">0.24755128063814402</Real>
+ <Real Name="Cell 2 8 4">0.019904712380116096</Real>
+ <Real Name="Cell 2 8 5">7.4461631608083059e-09</Real>
+ <Real Name="Cell 2 9 0">3.5989285544223758e-08</Real>
+ <Real Name="Cell 2 9 1">0.0010727579703914717</Real>
+ <Real Name="Cell 2 9 2">0.012247960886355646</Real>
+ <Real Name="Cell 2 9 3">0.012724512135907948</Real>
+ <Real Name="Cell 2 9 4">0.0012284964703332458</Real>
+ <Real Name="Cell 2 9 5">6.4532206726602809e-10</Real>
+ <Real Name="Cell 3 0 0">0.015899136314447414</Real>
+ <Real Name="Cell 3 0 1">0.11672610427978347</Real>
+ <Real Name="Cell 3 0 10">0.00011789103208376422</Real>
+ <Real Name="Cell 3 0 2">0.15013454964738263</Real>
+ <Real Name="Cell 3 0 3">0.027063028371588197</Real>
+ <Real Name="Cell 3 0 4">7.4904413298601993e-05</Real>
+ <Real Name="Cell 3 1 0">0.016283157315938795</Real>
+ <Real Name="Cell 3 1 1">0.41646885582143139</Real>
+ <Real Name="Cell 3 1 10">2.1380104432427704e-05</Real>
+ <Real Name="Cell 3 1 2">0.78503708116938986</Real>
+ <Real Name="Cell 3 1 3">0.15874452985591544</Real>
+ <Real Name="Cell 3 1 4">0.00045735091069704136</Real>
+ <Real Name="Cell 3 1 5">6.033386787915789e-05</Real>
+ <Real Name="Cell 3 1 6">3.1075816386824106e-05</Real>
+ <Real Name="Cell 3 1 7">1.0299315386746828e-06</Real>
+ <Real Name="Cell 3 10 0">6.1613480093664233e-08</Real>
+ <Real Name="Cell 3 10 1">1.0545672672824666e-06</Real>
+ <Real Name="Cell 3 10 2">1.4445971479036167e-06</Real>
+ <Real Name="Cell 3 10 3">1.9672812754632667e-07</Real>
+ <Real Name="Cell 3 10 4">4.9765045164443508e-11</Real>
+ <Real Name="Cell 3 11 0">4.0593710056290399e-05</Real>
+ <Real Name="Cell 3 11 1">0.00069479597350841766</Real>
+ <Real Name="Cell 3 11 2">0.0009517650631160118</Real>
+ <Real Name="Cell 3 11 3">0.00012961326900204912</Real>
+ <Real Name="Cell 3 11 4">3.278743241369594e-08</Real>
+ <Real Name="Cell 3 12 0">0.00022833991480983664</Real>
+ <Real Name="Cell 3 12 1">0.0039082324128820361</Real>
+ <Real Name="Cell 3 12 2">0.0053536854140586766</Real>
+ <Real Name="Cell 3 12 3">0.00072907558242674489</Real>
+ <Real Name="Cell 3 12 4">1.8442954619804386e-07</Real>
+ <Real Name="Cell 3 13 0">0.00013361944893374375</Real>
+ <Real Name="Cell 3 13 1">0.0022870108441145694</Real>
+ <Real Name="Cell 3 13 2">0.003132857850923247</Real>
+ <Real Name="Cell 3 13 3">0.00042663884514470895</Real>
+ <Real Name="Cell 3 13 4">1.0792407604516389e-07</Real>
+ <Real Name="Cell 3 14 0">5.5155400250989383e-06</Real>
+ <Real Name="Cell 3 14 1">9.4403172211883734e-05</Real>
+ <Real Name="Cell 3 14 2">0.00012931802224600355</Real>
+ <Real Name="Cell 3 14 3">1.7610786793653479e-05</Real>
+ <Real Name="Cell 3 14 4">4.4548871129837326e-09</Real>
+ <Real Name="Cell 3 15 0">0.00031326842318178026</Real>
+ <Real Name="Cell 3 15 1">0.00110972046314576</Real>
+ <Real Name="Cell 3 15 10">2.7211375395801689e-06</Real>
+ <Real Name="Cell 3 15 2">0.00042777141355565513</Real>
+ <Real Name="Cell 3 15 3">8.0285885546328847e-06</Real>
+ <Real Name="Cell 3 16 0">0.0078105603778430722</Real>
+ <Real Name="Cell 3 16 1">0.027736536769341732</Real>
+ <Real Name="Cell 3 16 10">6.7821817312454626e-05</Real>
+ <Real Name="Cell 3 16 2">0.010810927299283632</Real>
+ <Real Name="Cell 3 16 3">0.00023037720704507705</Real>
+ <Real Name="Cell 3 16 4">8.4877359583721074e-08</Real>
+ <Real Name="Cell 3 2 0">0.0085779551026819879</Real>
+ <Real Name="Cell 3 2 1">0.25355917668716771</Real>
+ <Real Name="Cell 3 2 10">3.5880414596141041e-08</Real>
+ <Real Name="Cell 3 2 2">0.48680327118079653</Real>
+ <Real Name="Cell 3 2 3">0.099040713430520774</Real>
+ <Real Name="Cell 3 2 4">0.010993044079633829</Real>
+ <Real Name="Cell 3 2 5">0.052017037966696912</Real>
+ <Real Name="Cell 3 2 6">0.026792114042239482</Real>
+ <Real Name="Cell 3 2 7">0.00088795875533525604</Real>
+ <Real Name="Cell 3 3 0">0.0009104641725514442</Real>
+ <Real Name="Cell 3 3 1">0.030150891559067361</Real>
+ <Real Name="Cell 3 3 2">0.062042893425351207</Real>
+ <Real Name="Cell 3 3 3">0.014338561585781928</Real>
+ <Real Name="Cell 3 3 4">0.063567726507331238</Real>
+ <Real Name="Cell 3 3 5">0.30767181898838308</Real>
+ <Real Name="Cell 3 3 6">0.15847017939758667</Real>
+ <Real Name="Cell 3 3 7">0.0052521045197773354</Real>
+ <Real Name="Cell 3 4 0">0.00081540986631094747</Real>
+ <Real Name="Cell 3 4 1">0.030405860406687836</Real>
+ <Real Name="Cell 3 4 2">0.068229856996604762</Real>
+ <Real Name="Cell 3 4 3">0.019460753443483872</Real>
+ <Real Name="Cell 3 4 4">0.039647222187578213</Real>
+ <Real Name="Cell 3 4 5">0.187889199111751</Real>
+ <Real Name="Cell 3 4 6">0.096771828347541097</Real>
+ <Real Name="Cell 3 4 7">0.0032072643508282497</Real>
+ <Real Name="Cell 3 5 0">0.00044548212654713673</Real>
+ <Real Name="Cell 3 5 1">0.017766924610801954</Real>
+ <Real Name="Cell 3 5 2">0.042441962324856898</Real>
+ <Real Name="Cell 3 5 3">0.013041415153522374</Real>
+ <Real Name="Cell 3 5 4">0.0023293644925800119</Real>
+ <Real Name="Cell 3 5 5">0.0083210574797234864</Real>
+ <Real Name="Cell 3 5 6">0.0042840227694801473</Real>
+ <Real Name="Cell 3 5 7">0.00014198340303486998</Real>
+ <Real Name="Cell 3 6 0">2.6971571752651984e-05</Real>
+ <Real Name="Cell 3 6 1">0.0033135486103988165</Real>
+ <Real Name="Cell 3 6 2">0.019783289891593309</Real>
+ <Real Name="Cell 3 6 3">0.014275744590630378</Real>
+ <Real Name="Cell 3 6 4">0.00096128929981621888</Real>
+ <Real Name="Cell 3 6 5">1.4876692606671744e-07</Real>
+ <Real Name="Cell 3 7 0">1.2079912201636798e-06</Real>
+ <Real Name="Cell 3 7 1">0.0074313122805206612</Real>
+ <Real Name="Cell 3 7 2">0.070089498398585748</Real>
+ <Real Name="Cell 3 7 3">0.064763477013715876</Real>
+ <Real Name="Cell 3 7 4">0.0055410748938068063</Real>
+ <Real Name="Cell 3 7 5">2.37476017279155e-09</Real>
+ <Real Name="Cell 3 8 0">2.938249761202904e-07</Real>
+ <Real Name="Cell 3 8 1">0.004350597372893018</Real>
+ <Real Name="Cell 3 8 2">0.047379857080942452</Real>
+ <Real Name="Cell 3 8 3">0.047972123742179094</Real>
+ <Real Name="Cell 3 8 4">0.0045209288150333425</Real>
+ <Real Name="Cell 3 8 5">2.2915235979947213e-09</Real>
+ <Real Name="Cell 3 9 0">1.6485752654186814e-09</Real>
+ <Real Name="Cell 3 9 1">0.00029940412546229471</Real>
+ <Real Name="Cell 3 9 2">0.0035485178617052564</Real>
+ <Real Name="Cell 3 9 3">0.0037576292463859535</Real>
+ <Real Name="Cell 3 9 4">0.00036906100862140552</Real>
+ <Real Name="Cell 3 9 5">1.9859499631032996e-10</Real>
+ <Real Name="Cell 4 0 0">0.133126185601043</Real>
+ <Real Name="Cell 4 0 1">0.5474492739278628</Real>
+ <Real Name="Cell 4 0 10">0.0011309851892542036</Real>
+ <Real Name="Cell 4 0 2">0.34307522180441824</Real>
+ <Real Name="Cell 4 0 3">0.036888979430054356</Real>
+ <Real Name="Cell 4 0 4">9.4073701897767642e-05</Real>
+ <Real Name="Cell 4 1 0">0.040980752596047623</Real>
+ <Real Name="Cell 4 1 1">0.59605381702291205</Real>
+ <Real Name="Cell 4 1 10">0.00020510959171689182</Real>
+ <Real Name="Cell 4 1 2">1.0146150749870528</Real>
+ <Real Name="Cell 4 1 3">0.20004366591318026</Real>
+ <Real Name="Cell 4 1 4">0.00055982924098096117</Real>
+ <Real Name="Cell 4 1 5">1.9377939534407772e-06</Real>
+ <Real Name="Cell 4 1 6">9.9808832434271717e-07</Real>
+ <Real Name="Cell 4 1 7">3.3079183852411305e-08</Real>
+ <Real Name="Cell 4 10 0">3.7337017077065266e-06</Real>
+ <Real Name="Cell 4 10 1">6.3905489525316407e-05</Real>
+ <Real Name="Cell 4 10 2">8.7540824343573307e-05</Real>
+ <Real Name="Cell 4 10 3">1.1921484465039313e-05</Real>
+ <Real Name="Cell 4 10 4">3.0157010094562396e-09</Real>
+ <Real Name="Cell 4 11 0">0.0024599292935394601</Real>
+ <Real Name="Cell 4 11 1">0.042103788145911869</Real>
+ <Real Name="Cell 4 11 2">0.057675801400756836</Real>
+ <Real Name="Cell 4 11 3">0.0078544059364720059</Real>
+ <Real Name="Cell 4 11 4">1.9868783942771841e-06</Real>
+ <Real Name="Cell 4 12 0">0.013837120197836682</Real>
+ <Real Name="Cell 4 12 1">0.23683411506554683</Real>
+ <Real Name="Cell 4 12 2">0.32442680307308097</Real>
+ <Real Name="Cell 4 12 3">0.044181090615489978</Real>
+ <Real Name="Cell 4 12 4">1.1176205443100524e-05</Real>
+ <Real Name="Cell 4 13 0">0.0080971755516537659</Real>
+ <Real Name="Cell 4 13 1">0.13859006634965235</Real>
+ <Real Name="Cell 4 13 2">0.18984736278833814</Real>
+ <Real Name="Cell 4 13 3">0.025853793395035699</Real>
+ <Real Name="Cell 4 13 4">6.5400673102689055e-06</Real>
+ <Real Name="Cell 4 14 0">0.00033423499499346147</Real>
+ <Real Name="Cell 4 14 1">0.0057207170373203553</Real>
+ <Real Name="Cell 4 14 2">0.0078365143433406607</Real>
+ <Real Name="Cell 4 14 3">0.0010671921895267365</Real>
+ <Real Name="Cell 4 14 4">2.6996072281749859e-07</Real>
+ <Real Name="Cell 4 15 0">0.0030053341684876602</Real>
+ <Real Name="Cell 4 15 1">0.010646080417197543</Real>
+ <Real Name="Cell 4 15 10">2.6105176965471934e-05</Real>
+ <Real Name="Cell 4 15 2">0.004103816249348192</Real>
+ <Real Name="Cell 4 15 3">7.7022099013043731e-05</Real>
+ <Real Name="Cell 4 16 0">0.074908465129061255</Real>
+ <Real Name="Cell 4 16 1">0.26544132891853162</Real>
+ <Real Name="Cell 4 16 10">0.00065064720812851602</Real>
+ <Real Name="Cell 4 16 2">0.10247108226089444</Real>
+ <Real Name="Cell 4 16 3">0.0019577232995084013</Real>
+ <Real Name="Cell 4 16 4">1.0659889146341705e-07</Real>
+ <Real Name="Cell 4 2 0">0.01267023835150325</Real>
+ <Real Name="Cell 4 2 1">0.38451543644451536</Real>
+ <Real Name="Cell 4 2 10">3.4421801875228903e-07</Real>
+ <Real Name="Cell 4 2 2">0.75113671344938193</Real>
+ <Real Name="Cell 4 2 3">0.15607059201749374</Real>
+ <Real Name="Cell 4 2 4">0.00083355352107825564</Real>
+ <Real Name="Cell 4 2 5">0.0016706752268287968</Real>
+ <Real Name="Cell 4 2 6">0.00086050502671124369</Real>
+ <Real Name="Cell 4 2 7">2.8519323681349135e-05</Real>
+ <Real Name="Cell 4 3 0">0.0096787987704337903</Real>
+ <Real Name="Cell 4 3 1">0.34092837648570989</Real>
+ <Real Name="Cell 4 3 2">0.72087715415569853</Real>
+ <Real Name="Cell 4 3 3">0.16348296129708256</Real>
+ <Real Name="Cell 4 3 4">0.0027460129719335206</Real>
+ <Real Name="Cell 4 3 5">0.0098817212592206966</Real>
+ <Real Name="Cell 4 3 6">0.0050897210179259734</Real>
+ <Real Name="Cell 4 3 7">0.0001686862907852668</Real>
+ <Real Name="Cell 4 4 0">0.0085097959371298847</Real>
+ <Real Name="Cell 4 4 1">0.31786585796828204</Real>
+ <Real Name="Cell 4 4 2">0.70063491826719182</Real>
+ <Real Name="Cell 4 4 3">0.16863468706298085</Real>
+ <Real Name="Cell 4 4 4">0.0022699270810111055</Real>
+ <Real Name="Cell 4 4 5">0.006034398630144518</Real>
+ <Real Name="Cell 4 4 6">0.0031081028024071596</Real>
+ <Real Name="Cell 4 4 7">0.00010301042655791835</Real>
+ <Real Name="Cell 4 5 0">0.0038281445627319885</Real>
+ <Real Name="Cell 4 5 1">0.1672464291750031</Real>
+ <Real Name="Cell 4 5 2">0.40977193731401379</Real>
+ <Real Name="Cell 4 5 3">0.11308303333443409</Real>
+ <Real Name="Cell 4 5 4">0.0011849364518967463</Real>
+ <Real Name="Cell 4 5 5">0.00026713874151849747</Real>
+ <Real Name="Cell 4 5 6">0.00013759358898932756</Real>
+ <Real Name="Cell 4 5 7">4.5602012528184056e-06</Real>
+ <Real Name="Cell 4 6 0">0.00038022745951561422</Real>
+ <Real Name="Cell 4 6 1">0.021746648116490682</Real>
+ <Real Name="Cell 4 6 2">0.061283321782474177</Real>
+ <Real Name="Cell 4 6 3">0.01997256380053733</Real>
+ <Real Name="Cell 4 6 4">0.00036493206183265368</Real>
+ <Real Name="Cell 4 6 5">2.5074219693784609e-09</Real>
+ <Real Name="Cell 4 7 0">2.5291074077738082e-06</Real>
+ <Real Name="Cell 4 7 1">0.00040782063721388217</Real>
+ <Real Name="Cell 4 7 2">0.0036335952348797609</Real>
+ <Real Name="Cell 4 7 3">0.0037755058749347013</Real>
+ <Real Name="Cell 4 7 4">0.00039978329539623408</Real>
+ <Real Name="Cell 4 7 5">7.494760396823547e-09</Real>
+ <Real Name="Cell 4 8 1">0.00010068752756718856</Real>
+ <Real Name="Cell 4 8 2">0.0013118448451629389</Real>
+ <Real Name="Cell 4 8 3">0.0014892706048971367</Real>
+ <Real Name="Cell 4 8 4">0.00016035669040550973</Real>
+ <Real Name="Cell 4 8 5">2.4565311284381348e-09</Real>
+ <Real Name="Cell 4 9 1">4.0350330391010803e-06</Real>
+ <Real Name="Cell 4 9 2">4.9561160559909242e-05</Real>
+ <Real Name="Cell 4 9 3">5.3875236214470152e-05</Real>
+ <Real Name="Cell 4 9 4">5.4807985715573241e-06</Real>
+ <Real Name="Cell 4 9 5">3.3015749952792959e-11</Real>
+ <Real Name="Cell 5 0 0">0.11770311353212747</Real>
+ <Real Name="Cell 5 0 1">0.42621899606965957</Real>
+ <Real Name="Cell 5 0 10">0.0010193009370130027</Real>
+ <Real Name="Cell 5 0 2">0.18042927066502606</Real>
+ <Real Name="Cell 5 0 3">0.0071063720035356888</Real>
+ <Real Name="Cell 5 0 4">1.149275196397271e-05</Real>
+ <Real Name="Cell 5 1 0">0.023415618988298772</Real>
+ <Real Name="Cell 5 1 1">0.13843144777727917</Real>
+ <Real Name="Cell 5 1 10">0.00018485511659551137</Real>
+ <Real Name="Cell 5 1 2">0.15001699133198049</Real>
+ <Real Name="Cell 5 1 3">0.025124513971455879</Real>
+ <Real Name="Cell 5 1 4">6.9272258088587743e-05</Real>
+ <Real Name="Cell 5 10 0">1.0264868325268343e-05</Real>
+ <Real Name="Cell 5 10 1">0.00017569197718318345</Real>
+ <Real Name="Cell 5 10 2">0.0002406713512002004</Real>
+ <Real Name="Cell 5 10 3">3.2775105740980442e-05</Real>
+ <Real Name="Cell 5 10 4">8.290907039133046e-09</Real>
+ <Real Name="Cell 5 11 0">0.0067629533006169336</Real>
+ <Real Name="Cell 5 11 1">0.11575371444931457</Real>
+ <Real Name="Cell 5 11 2">0.15856502561817157</Real>
+ <Real Name="Cell 5 11 3">0.021593702181585284</Real>
+ <Real Name="Cell 5 11 4">5.4624195214844321e-06</Real>
+ <Real Name="Cell 5 12 0">0.038041661587088091</Real>
+ <Real Name="Cell 5 12 1">0.65111548709460387</Real>
+ <Real Name="Cell 5 12 2">0.89192942431883637</Real>
+ <Real Name="Cell 5 12 3">0.12146473209112615</Real>
+ <Real Name="Cell 5 12 4">3.0726149604501696e-05</Real>
+ <Real Name="Cell 5 13 0">0.022261135824737127</Real>
+ <Real Name="Cell 5 13 1">0.38101832809328512</Real>
+ <Real Name="Cell 5 13 2">0.52193729801698308</Real>
+ <Real Name="Cell 5 13 3">0.071078464667106572</Real>
+ <Real Name="Cell 5 13 4">1.7980260619035756e-05</Real>
+ <Real Name="Cell 5 14 0">0.00091889456681103372</Real>
+ <Real Name="Cell 5 14 1">0.015727664315820143</Real>
+ <Real Name="Cell 5 14 2">0.021544513772333559</Real>
+ <Real Name="Cell 5 14 3">0.002933974955909309</Real>
+ <Real Name="Cell 5 14 4">7.4218871502139319e-07</Real>
+ <Real Name="Cell 5 15 0">0.0027085588415147145</Real>
+ <Real Name="Cell 5 15 1">0.0095947850138700681</Real>
+ <Real Name="Cell 5 15 10">2.3527303093458172e-05</Real>
+ <Real Name="Cell 5 15 2">0.0036985663367070055</Real>
+ <Real Name="Cell 5 15 3">6.9416203183415799e-05</Real>
+ <Real Name="Cell 5 16 0">0.067508709566095532</Real>
+ <Real Name="Cell 5 16 1">0.23915301021901</Real>
+ <Real Name="Cell 5 16 10">0.00058639610422097819</Real>
+ <Real Name="Cell 5 16 2">0.092206199549789175</Real>
+ <Real Name="Cell 5 16 3">0.0017347788936183891</Real>
+ <Real Name="Cell 5 16 4">1.3022923457980471e-08</Real>
+ <Real Name="Cell 5 2 0">0.0042767928502442046</Real>
+ <Real Name="Cell 5 2 1">0.14260649828480482</Real>
+ <Real Name="Cell 5 2 10">3.1022665228917236e-07</Real>
+ <Real Name="Cell 5 2 2">0.29417368623015311</Real>
+ <Real Name="Cell 5 2 3">0.06501877277952775</Real>
+ <Real Name="Cell 5 2 4">0.00025889350787007895</Real>
+ <Real Name="Cell 5 3 0">0.013202573969039771</Real>
+ <Real Name="Cell 5 3 1">0.46852986001851926</Real>
+ <Real Name="Cell 5 3 2">0.99437149801590496</Real>
+ <Real Name="Cell 5 3 3">0.22638233528685536</Real>
+ <Real Name="Cell 5 3 4">0.00099699195104319149</Real>
+ <Real Name="Cell 5 4 0">0.010738487310442526</Real>
+ <Real Name="Cell 5 4 1">0.44377346459425671</Real>
+ <Real Name="Cell 5 4 2">1.0421726448235411</Real>
+ <Real Name="Cell 5 4 3">0.27062400088295574</Real>
+ <Real Name="Cell 5 4 4">0.0020911778684610375</Real>
+ <Real Name="Cell 5 5 0">0.007706342132584568</Real>
+ <Real Name="Cell 5 5 1">0.45090850981172659</Real>
+ <Real Name="Cell 5 5 2">1.2437763994756306</Real>
+ <Real Name="Cell 5 5 3">0.37929625939321432</Real>
+ <Real Name="Cell 5 5 4">0.0043466021115814669</Real>
+ <Real Name="Cell 5 5 5">2.6303807303724975e-09</Real>
+ <Real Name="Cell 5 6 0">0.0018732571429053411</Real>
+ <Real Name="Cell 5 6 1">0.12811614078768885</Real>
+ <Real Name="Cell 5 6 2">0.42113163177770868</Real>
+ <Real Name="Cell 5 6 3">0.19109116801872655</Real>
+ <Real Name="Cell 5 6 4">0.010313112016963737</Real>
+ <Real Name="Cell 5 6 5">1.9277819425816929e-07</Real>
+ <Real Name="Cell 5 7 0">2.2397250310540012e-05</Real>
+ <Real Name="Cell 5 7 1">0.016498265772688772</Real>
+ <Real Name="Cell 5 7 2">0.20926295352574414</Real>
+ <Real Name="Cell 5 7 3">0.24163402265709524</Real>
+ <Real Name="Cell 5 7 4">0.026909873769326405</Real>
+ <Real Name="Cell 5 7 5">5.7478378791358553e-07</Real>
+ <Real Name="Cell 5 8 1">0.0048797522262633841</Real>
+ <Real Name="Cell 5 8 2">0.066709536978584269</Real>
+ <Real Name="Cell 5 8 3">0.078217059554019447</Real>
+ <Real Name="Cell 5 8 4">0.0087550729578455798</Real>
+ <Real Name="Cell 5 8 5">1.871152283239253e-07</Real>
+ <Real Name="Cell 5 9 1">6.1883226488395235e-05</Real>
+ <Real Name="Cell 5 9 2">0.0008459858604220222</Real>
+ <Real Name="Cell 5 9 3">0.00099192003757619224</Real>
+ <Real Name="Cell 5 9 4">0.00011102862146499881</Real>
+ <Real Name="Cell 5 9 5">2.372926639897037e-09</Real>
+ <Real Name="Cell 6 0 0">0.0092672473304723311</Real>
+ <Real Name="Cell 6 0 1">0.032828991604000851</Real>
+ <Real Name="Cell 6 0 10">8.0497665752031437e-05</Real>
+ <Real Name="Cell 6 0 2">0.012656103725794182</Real>
+ <Real Name="Cell 6 0 3">0.00023783273117372765</Real>
+ <Real Name="Cell 6 0 4">9.2006474688292464e-10</Real>
+ <Real Name="Cell 6 1 0">0.0016828704520302244</Real>
+ <Real Name="Cell 6 1 1">0.0060309907631398429</Real>
+ <Real Name="Cell 6 1 10">1.4598637995825225e-05</Real>
+ <Real Name="Cell 6 1 2">0.0024580205988672965</Real>
+ <Real Name="Cell 6 1 3">7.986935820788236e-05</Real>
+ <Real Name="Cell 6 1 4">1.5644908672818736e-07</Real>
+ <Real Name="Cell 6 10 0">3.077313387497189e-06</Real>
+ <Real Name="Cell 6 10 1">5.2670843534422768e-05</Real>
+ <Real Name="Cell 6 10 2">7.215106395590838e-05</Real>
+ <Real Name="Cell 6 10 3">9.8256761292374825e-06</Real>
+ <Real Name="Cell 6 10 4">2.4855378965956516e-09</Real>
+ <Real Name="Cell 6 11 0">0.0020274713782519696</Real>
+ <Real Name="Cell 6 11 1">0.034701902044914017</Real>
+ <Real Name="Cell 6 11 2">0.047536340522018154</Real>
+ <Real Name="Cell 6 11 3">0.0064735938838535977</Real>
+ <Real Name="Cell 6 11 4">1.6375832781226253e-06</Real>
+ <Real Name="Cell 6 12 0">0.011404541273696604</Real>
+ <Real Name="Cell 6 12 1">0.19519845182140685</Real>
+ <Real Name="Cell 6 12 2">0.26739226175970099</Real>
+ <Real Name="Cell 6 12 3">0.036414012759682479</Real>
+ <Real Name="Cell 6 12 4">9.2114178699611053e-06</Real>
+ <Real Name="Cell 6 13 0">0.0066736843692114306</Real>
+ <Real Name="Cell 6 13 1">0.11422580054309768</Real>
+ <Real Name="Cell 6 13 2">0.15647201539526656</Real>
+ <Real Name="Cell 6 13 3">0.021308671865219956</Real>
+ <Real Name="Cell 6 13 4">5.3903172413271835e-06</Real>
+ <Real Name="Cell 6 14 0">0.0002754761641886042</Real>
+ <Real Name="Cell 6 14 1">0.0047150095275937127</Real>
+ <Real Name="Cell 6 14 2">0.0064588476498539452</Real>
+ <Real Name="Cell 6 14 3">0.00087957878506592189</Real>
+ <Real Name="Cell 6 14 4">2.2250137034514399e-07</Real>
+ <Real Name="Cell 6 15 0">0.00021390411445406103</Real>
+ <Real Name="Cell 6 15 1">0.00075773284313115517</Real>
+ <Real Name="Cell 6 15 10">1.8580312365981586e-06</Real>
+ <Real Name="Cell 6 15 2">0.00029208837736029468</Real>
+ <Real Name="Cell 6 15 3">5.4820339300467294e-06</Real>
+ <Real Name="Cell 6 16 0">0.0053313607452783532</Real>
+ <Real Name="Cell 6 16 1">0.018885785929965981</Real>
+ <Real Name="Cell 6 16 10">4.6309697050020013e-05</Real>
+ <Real Name="Cell 6 16 2">0.0072800324366607532</Real>
+ <Real Name="Cell 6 16 3">0.00013663495876952339</Real>
+ <Real Name="Cell 6 16 4">1.0425642885710289e-12</Real>
+ <Real Name="Cell 6 2 0">0.000441853028377094</Real>
+ <Real Name="Cell 6 2 1">0.01555300880687302</Real>
+ <Real Name="Cell 6 2 10">2.4499655064112745e-08</Real>
+ <Real Name="Cell 6 2 2">0.032931750790930366</Real>
+ <Real Name="Cell 6 2 3">0.0074768432810286131</Real>
+ <Real Name="Cell 6 2 4">3.2392740238761398e-05</Real>
+ <Real Name="Cell 6 3 0">0.0019384982510236421</Real>
+ <Real Name="Cell 6 3 1">0.06932217380582581</Real>
+ <Real Name="Cell 6 3 2">0.14795579575142345</Real>
+ <Real Name="Cell 6 3 3">0.03395516263297587</Real>
+ <Real Name="Cell 6 3 4">0.0001564748433145119</Real>
+ <Real Name="Cell 6 4 0">0.0025748826827637818</Real>
+ <Real Name="Cell 6 4 1">0.14003142058267803</Real>
+ <Real Name="Cell 6 4 2">0.37483042120721527</Real>
+ <Real Name="Cell 6 4 3">0.11089791762978085</Real>
+ <Real Name="Cell 6 4 4">0.0011561635790623495</Real>
+ <Real Name="Cell 6 5 0">0.0047163429111931835</Real>
+ <Real Name="Cell 6 5 1">0.31297523144855305</Real>
+ <Real Name="Cell 6 5 2">0.89878293689175737</Real>
+ <Real Name="Cell 6 5 3">0.28375940459773341</Real>
+ <Real Name="Cell 6 5 4">0.0036058250999567924</Real>
+ <Real Name="Cell 6 5 5">8.0010596015756409e-09</Real>
+ <Real Name="Cell 6 6 0">0.0015020804722975806</Real>
+ <Real Name="Cell 6 6 1">0.11610434921520267</Real>
+ <Real Name="Cell 6 6 2">0.49885769654057188</Real>
+ <Real Name="Cell 6 6 3">0.33606894310218988</Real>
+ <Real Name="Cell 6 6 4">0.02848942916901959</Real>
+ <Real Name="Cell 6 6 5">5.8639032910087906e-07</Real>
+ <Real Name="Cell 6 7 0">1.9206630021634376e-05</Real>
+ <Real Name="Cell 6 7 1">0.046886823666419664</Real>
+ <Real Name="Cell 6 7 2">0.62703525524630166</Real>
+ <Real Name="Cell 6 7 3">0.73201149524177678</Real>
+ <Real Name="Cell 6 7 4">0.081819273809129872</Real>
+ <Real Name="Cell 6 7 5">1.7483702233724723e-06</Real>
+ <Real Name="Cell 6 8 1">0.014843170021902385</Real>
+ <Real Name="Cell 6 8 2">0.2029162452401258</Real>
+ <Real Name="Cell 6 8 3">0.23791968520962989</Real>
+ <Real Name="Cell 6 8 4">0.026631072735217923</Real>
+ <Real Name="Cell 6 8 5">5.6916478930034905e-07</Real>
+ <Real Name="Cell 6 9 1">0.00018823563363062559</Real>
+ <Real Name="Cell 6 9 2">0.0025733093362375341</Real>
+ <Real Name="Cell 6 9 3">0.0030172101129711214</Real>
+ <Real Name="Cell 6 9 4">0.00033772548877227903</Real>
+ <Real Name="Cell 6 9 5">7.2179389305722861e-09</Real>
+ <Real Name="Cell 7 1 0">1.0773145471598899e-09</Real>
+ <Real Name="Cell 7 1 1">3.8141521969526777e-08</Real>
+ <Real Name="Cell 7 1 2">8.080434242132067e-08</Real>
+ <Real Name="Cell 7 1 3">1.8348171588560835e-08</Real>
+ <Real Name="Cell 7 1 4">7.9496898678689158e-11</Real>
+ <Real Name="Cell 7 10 0">3.1550755703541391e-08</Real>
+ <Real Name="Cell 7 10 1">5.400180962412764e-07</Real>
+ <Real Name="Cell 7 10 2">7.3974285552856636e-07</Real>
+ <Real Name="Cell 7 10 3">1.007396609117612e-07</Real>
+ <Real Name="Cell 7 10 4">2.5483462063369444e-11</Real>
+ <Real Name="Cell 7 11 0">2.078704574290248e-05</Real>
+ <Real Name="Cell 7 11 1">0.00035578801896344253</Real>
+ <Real Name="Cell 7 11 2">0.0004873756026747601</Real>
+ <Real Name="Cell 7 11 3">6.6371783901905606e-05</Real>
+ <Real Name="Cell 7 11 4">1.6789641952675067e-08</Real>
+ <Real Name="Cell 7 12 0">0.00011692728374668503</Real>
+ <Real Name="Cell 7 12 1">0.0020013101987430676</Real>
+ <Real Name="Cell 7 12 2">0.0027414913157932067</Real>
+ <Real Name="Cell 7 12 3">0.0003733417679961367</Real>
+ <Real Name="Cell 7 12 4">9.4441858303794197e-08</Real>
+ <Real Name="Cell 7 13 0">6.8423250628621554e-05</Real>
+ <Real Name="Cell 7 13 1">0.0011711222986319954</Real>
+ <Real Name="Cell 7 13 2">0.0016042598560921941</Real>
+ <Real Name="Cell 7 13 3">0.00021847131433476552</Real>
+ <Real Name="Cell 7 13 4">5.5265278842470988e-08</Real>
+ <Real Name="Cell 7 14 0">2.8243731021273011e-06</Real>
+ <Real Name="Cell 7 14 1">4.8341554795616413e-05</Real>
+ <Real Name="Cell 7 14 2">6.6220595261723376e-05</Real>
+ <Real Name="Cell 7 14 3">9.0180530466554547e-06</Real>
+ <Real Name="Cell 7 14 4">2.2812386960602466e-09</Real>
+ <Real Name="Cell 7 2 0">2.3110214396946787e-07</Real>
+ <Real Name="Cell 7 2 1">8.1819998854132056e-06</Real>
+ <Real Name="Cell 7 2 2">1.7333894566670802e-05</Real>
+ <Real Name="Cell 7 2 3">3.9359923276026833e-06</Real>
+ <Real Name="Cell 7 2 4">1.7053425828141122e-08</Real>
+ <Real Name="Cell 7 3 0">2.5128684631689892e-06</Real>
+ <Real Name="Cell 7 3 1">0.00013720015137355153</Real>
+ <Real Name="Cell 7 3 2">0.00036781153932398478</Real>
+ <Real Name="Cell 7 3 3">0.0001089526884296779</Real>
+ <Real Name="Cell 7 3 4">1.1371153924886989e-06</Real>
+ <Real Name="Cell 7 4 0">0.00011298322969292173</Real>
+ <Real Name="Cell 7 4 1">0.0075806403487128924</Real>
+ <Real Name="Cell 7 4 2">0.021786790641868229</Real>
+ <Real Name="Cell 7 4 3">0.0068351556180775023</Real>
+ <Real Name="Cell 7 4 4">7.8983874108971293e-05</Real>
+ <Real Name="Cell 7 5 0">0.0003372762779307707</Real>
+ <Real Name="Cell 7 5 1">0.022742425957312278</Real>
+ <Real Name="Cell 7 5 2">0.066146734292249557</Real>
+ <Real Name="Cell 7 5 3">0.021574675957909142</Real>
+ <Real Name="Cell 7 5 4">0.00036097574257915857</Real>
+ <Real Name="Cell 7 5 5">2.6573351482076121e-09</Real>
+ <Real Name="Cell 7 6 0">0.00011037493197617212</Real>
+ <Real Name="Cell 7 6 1">0.01249895073187695</Real>
+ <Real Name="Cell 7 6 2">0.090769979471857484</Real>
+ <Real Name="Cell 7 6 3">0.088107099680242829</Real>
+ <Real Name="Cell 7 6 4">0.009189916967116336</Real>
+ <Real Name="Cell 7 6 5">1.9475365885062688e-07</Real>
+ <Real Name="Cell 7 7 0">1.418214949500247e-06</Real>
+ <Real Name="Cell 7 7 1">0.015238651847434075</Real>
+ <Real Name="Cell 7 7 2">0.20729355128070057</Real>
+ <Real Name="Cell 7 7 3">0.24281667874999768</Real>
+ <Real Name="Cell 7 7 4">0.02717057122721802</Real>
+ <Real Name="Cell 7 7 5">5.8067379547233111e-07</Real>
+ <Real Name="Cell 7 8 1">0.0049297567290031482</Real>
+ <Real Name="Cell 7 8 2">0.067393132593677282</Real>
+ <Real Name="Cell 7 8 3">0.079018576718705533</Real>
+ <Real Name="Cell 7 8 4">0.0088447892076484232</Real>
+ <Real Name="Cell 7 8 5">1.8903266255286361e-07</Real>
+ <Real Name="Cell 7 9 1">6.2517365236635327e-05</Real>
+ <Real Name="Cell 7 9 2">0.00085465496908036667</Real>
+ <Real Name="Cell 7 9 3">0.0010020845840401809</Real>
+ <Real Name="Cell 7 9 4">0.0001121663700122217</Real>
+ <Real Name="Cell 7 9 5">2.3972428369423224e-09</Real>
+ <Real Name="Cell 8 5 1">9.2329734511730085e-07</Real>
+ <Real Name="Cell 8 5 2">1.2622103650023891e-05</Real>
+ <Real Name="Cell 8 5 3">1.4799440643814777e-05</Real>
+ <Real Name="Cell 8 5 4">1.6565463251967153e-06</Real>
+ <Real Name="Cell 8 5 5">3.5404050355808568e-11</Real>
+ <Real Name="Cell 8 6 1">6.7667616668507533e-05</Real>
+ <Real Name="Cell 8 6 2">0.00092506241446137347</Real>
+ <Real Name="Cell 8 6 3">0.0010846374482607873</Real>
+ <Real Name="Cell 8 6 4">0.00012140676275073122</Real>
+ <Real Name="Cell 8 6 5">2.5947304199006742e-09</Real>
+ <Real Name="Cell 8 7 1">0.00020175647550532561</Real>
+ <Real Name="Cell 8 7 2">0.0027581484549467567</Real>
+ <Real Name="Cell 8 7 3">0.0032339343327874434</Real>
+ <Real Name="Cell 8 7 4">0.0003619840887125341</Real>
+ <Real Name="Cell 8 7 5">7.7363987410724327e-09</Real>
+ <Real Name="Cell 8 8 1">6.5679843053759093e-05</Real>
+ <Real Name="Cell 8 8 2">0.00089788819509334318</Real>
+ <Real Name="Cell 8 8 3">0.0010527756241362162</Real>
+ <Real Name="Cell 8 8 4">0.00011784037203787135</Real>
+ <Real Name="Cell 8 8 5">2.5185087806588107e-09</Real>
+ <Real Name="Cell 8 9 1">8.3292766004440302e-07</Real>
+ <Real Name="Cell 8 9 2">1.1386688496019285e-05</Real>
+ <Real Name="Cell 8 9 3">1.3350914015519671e-05</Real>
+ <Real Name="Cell 8 9 4">1.4944083416875408e-06</Real>
+ <Real Name="Cell 8 9 5">3.1938803869528501e-11</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>0.006550665150801457</Real>
+ <Real>0.3748146491843859</Real>
+ <Real>0.57071867995278003</Real>
+ <Real>0.047916005712032542</Real>
+ <Real>0.052405348767599988</Real>
+ <Real>0.58065069913736744</Real>
+ <Real>0.36148262217966726</Real>
+ <Real>0.0054613299153652957</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0.66666666666666663</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>0.16656750421064892</Real>
+ <Real>0.66666662732219051</Real>
+ <Real>0.16676586846585964</Real>
+ <Real>1.30088532538745e-12</Real>
+ <Real>0.00045733436139501672</Real>
+ <Real>0.24509473072115898</Real>
+ <Real>0.64843864037767174</Real>
+ <Real>0.10600929453977423</Real>
+ <Real>0.00068266776530006841</Real>
+ <Real>0.25741872001902455</Real>
+ <Real>0.64311464249673911</Real>
+ <Real>0.098783969718936201</Real>
+ <Real>0.085333318074545181</Real>
+ <Real>0.63066665045420167</Real>
+ <Real>0.2826666971842452</Real>
+ <Real>0.0013333342870078769</Real>
+ <Real>0.0077759932022114535</Real>
+ <Real>0.38813859684244745</Real>
+ <Real>0.56039472180429584</Real>
+ <Real>0.043690688151045189</Real>
+ <Real>0.0029293330109914262</Real>
+ <Real>0.32167866038576759</Real>
+ <Real>0.60785467065874721</Real>
+ <Real>0.06753733594449364</Real>
+ <Real>0.00016666678587598462</Real>
+ <Real>0.22116668061415373</Real>
+ <Real>0.65716666225592246</Real>
+ <Real>0.12149999034404779</Real>
+ <Real>0.02624399443817178</Real>
+ <Real>0.50373464367930043</Real>
+ <Real>0.45379869117991101</Real>
+ <Real>0.016222670702616706</Real>
+ <Real>0.039721334249814354</Real>
+ <Real>0.54970266925779976</Real>
+ <Real>0.40143066350332895</Real>
+ <Real>0.0091453329890569101</Real>
+ <Real>0.014197338872274482</Real>
+ <Real>0.44087470383707628</Real>
+ <Real>0.51565863292948289</Real>
+ <Real>0.02926932436116628</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>0.071142963187526845</Real>
+ <Real>0.61316861326413319</Real>
+ <Real>0.31317509255387399</Real>
+ <Real>0.0025133309944659421</Real>
+ <Real>0.0073275030978816038</Real>
+ <Real>0.38343854596171534</Real>
+ <Real>0.56408164950151107</Real>
+ <Real>0.045152301438891845</Real>
+ <Real>0.0025133374147378422</Real>
+ <Real>0.31317523045133716</Real>
+ <Real>0.6131685285777202</Real>
+ <Real>0.071142903556204715</Real>
+ <Real>0.042734015047808917</Real>
+ <Real>0.55791123556566391</Real>
+ <Real>0.39126981916643305</Real>
+ <Real>0.0080849302200940651</Real>
+ <Real>0.00027138900362524455</Real>
+ <Real>0.23159645957882208</Real>
+ <Real>0.65363999740434231</Real>
+ <Real>0.11449215401321031</Real>
+ <Real>0.085333306406062043</Real>
+ <Real>0.63066663805643286</Real>
+ <Real>0.28266672052121627</Real>
+ <Real>0.0013333350162886739</Real>
+ <Real>0.061600125763086246</Real>
+ <Real>0.59819855067527716</Real>
+ <Real>0.33644964700691471</Real>
+ <Real>0.0037516765547217332</Real>
+ <Real>0.0018614540225098352</Real>
+ <Real>0.29782965214144619</Real>
+ <Real>0.62228566621641879</Real>
+ <Real>0.078023227619625074</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0.66666666666666663</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>0.093086856262166257</Real>
+ <Real>0.63827304965955856</Real>
+ <Real>0.2677241791203871</Real>
+ <Real>0.00091591495788805532</Real>
+ <Real>0.081623718615090907</Real>
+ <Real>0.62657059413828775</Real>
+ <Real>0.29022294752086536</Real>
+ <Real>0.0015827397257558828</Real>
+ <Real>0.11449215401321031</Real>
+ <Real>0.65363999740434231</Real>
+ <Real>0.23159645957882208</Real>
+ <Real>0.00027138900362524455</Real>
+ <Real>0.0088928703984411054</Real>
+ <Real>0.3990884155919483</Real>
+ <Real>0.55161516194314397</Real>
+ <Real>0.040403552066466536</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>8.5334615078031984e-05</Real>
+ <Real>0.20961089513657627</Real>
+ <Real>0.66052260642482619</Real>
+ <Real>0.12978116382351942</Real>
+ <Real>0.0032805036499513811</Real>
+ <Real>0.32827523282138604</Real>
+ <Real>0.60360812354317706</Real>
+ <Real>0.064836139985485555</Real>
+ <Real>1.3333533605942498e-06</Real>
+ <Real>0.17686271867720754</Real>
+ <Real>0.66627066272130631</Real>
+ <Real>0.15686528524812551</Real>
+ <Real>0.050127076764796274</Real>
+ <Real>0.57573496773679889</Real>
+ <Real>0.36814843368880035</Real>
+ <Real>0.0059895218096044133</Real>
+ <Real>0.0045000300408078141</Real>
+ <Real>0.34816711060208322</Real>
+ <Real>0.59016635624543157</Real>
+ <Real>0.057166503111677383</Real>
+ <Real>0.014197334544976585</Real>
+ <Real>0.44087467479769382</Real>
+ <Real>0.51565865928665788</Real>
+ <Real>0.029269331370671631</Real>
+ <Real>0.0040648417547602001</Real>
+ <Real>0.34152229961697517</Real>
+ <Real>0.59476107577337534</Real>
+ <Real>0.059651782854889167</Real>
+ <Real>0.11357867635981268</Real>
+ <Real>0.65313067213408094</Real>
+ <Real>0.2330026516863507</Real>
+ <Real>0.0002879998197555918</Real>
+ <Real>0.054751478149118946</Real>
+ <Real>0.58546212298784195</Real>
+ <Real>0.3548212277858061</Real>
+ <Real>0.004965171077232872</Real>
+ <Real>0.0077759951334009786</Real>
+ <Real>0.38813861667887345</Real>
+ <Real>0.56039470614019771</Real>
+ <Real>0.043690682047527844</Real>
+ <Real>0.0023039985580447344</Real>
+ <Real>0.30855463394228649</Real>
+ <Real>0.61597868637339115</Real>
+ <Real>0.073162681126277593</Real>
+ <Real>0.012348001471996365</Real>
+ <Real>0.42782267760483422</Real>
+ <Real>0.527310657063643</Real>
+ <Real>0.032518663859526398</Real>
+ <Real>0.0065506685959499985</Real>
+ <Real>0.37481468891684211</Real>
+ <Real>0.57071864975706676</Real>
+ <Real>0.047915992730141049</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>-0.057799991083145486</Real>
+ <Real>-0.66660000052451984</Real>
+ <Real>0.50659997429847614</Real>
+ <Real>0.21780001730918919</Real>
+ <Real>-0.23120004539489969</Real>
+ <Real>-0.48639993057250308</Real>
+ <Real>0.66639999732970523</Real>
+ <Real>0.051199978637697541</Real>
+ <Real>-0.5</Real>
+ <Real>0</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>-0.49980165541637689</Real>
+ <Real>-0.00039666949305683374</Real>
+ <Real>0.50019830523524433</Real>
+ <Real>1.9674189388751984e-08</Real>
+ <Real>-0.0098000146865899751</Real>
+ <Real>-0.61060006084440488</Real>
+ <Real>0.25060016574857968</Real>
+ <Real>0.36979990978241517</Real>
+ <Real>-0.01280001373291384</Real>
+ <Real>-0.62160004463194696</Real>
+ <Real>0.28160013046263543</Real>
+ <Real>0.35279992790222536</Real>
+ <Real>-0.31999996185302848</Real>
+ <Real>-0.34000006675719874</Real>
+ <Real>0.64000001907348292</Real>
+ <Real>0.020000009536744301</Real>
+ <Real>-0.064799962234502573</Real>
+ <Real>-0.66560000839231748</Real>
+ <Real>0.52559990348814267</Real>
+ <Real>0.20480006713867738</Real>
+ <Real>-0.033799997520446823</Real>
+ <Real>-0.65859999790191637</Real>
+ <Real>0.4185999883651732</Real>
+ <Real>0.27380000705718999</Real>
+ <Real>-0.0050000023841860752</Real>
+ <Real>-0.58500001668929968</Real>
+ <Real>0.18500004053115759</Real>
+ <Real>0.40499997854232817</Real>
+ <Real>-0.14579997940063549</Real>
+ <Real>-0.60260002365112086</Real>
+ <Real>0.64259998550414821</Real>
+ <Real>0.10580001754760815</Real>
+ <Real>-0.19220000295639039</Real>
+ <Real>-0.54339999589920041</Real>
+ <Real>0.66340000066757199</Real>
+ <Real>0.07219999818801881</Real>
+ <Real>-0.09680002517700359</Real>
+ <Real>-0.64959998168944821</Real>
+ <Real>0.5896000389099072</Real>
+ <Real>0.15679996795654461</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>-0.28346023183768659</Real>
+ <Real>-0.40256051313166114</Real>
+ <Real>0.65550172177638211</Real>
+ <Real>0.03051902319296566</Real>
+ <Real>-0.062283763229400151</Real>
+ <Real>-0.66608996103038631</Real>
+ <Real>0.51903121174897304</Real>
+ <Real>0.20934251251081343</Real>
+ <Real>-0.030519075166579968</Real>
+ <Real>-0.65550177622486827</Real>
+ <Real>0.40256077794947637</Real>
+ <Real>0.28346007344197183</Real>
+ <Real>-0.20179944632183019</Real>
+ <Real>-0.52989599647569718</Real>
+ <Real>0.66519033191688492</Real>
+ <Real>0.06650511088064244</Real>
+ <Real>-0.0069204181366000162</Real>
+ <Real>-0.59688582916306221</Real>
+ <Real>0.21453291273592451</Real>
+ <Real>0.38927333456373775</Real>
+ <Real>-0.31999993268181826</Real>
+ <Real>-0.34000011780681361</Real>
+ <Real>0.64000003365908198</Real>
+ <Real>0.020000016829549865</Real>
+ <Real>-0.25750869847450536</Real>
+ <Real>-0.44512103022321198</Real>
+ <Real>0.66276815586994009</Real>
+ <Real>0.039861572827777289</Real>
+ <Real>-0.024982681258888664</Real>
+ <Real>-0.64858128879017485</Real>
+ <Real>0.37211062135701573</Real>
+ <Real>0.30145334869204782</Real>
+ <Real>-0.5</Real>
+ <Real>0</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>-0.33910152816638917</Real>
+ <Real>-0.30622626272683551</Real>
+ <Real>0.62975710995283851</Real>
+ <Real>0.015570680940386146</Real>
+ <Real>-0.31065743749553704</Real>
+ <Real>-0.35626297915610267</Real>
+ <Real>0.6444982707988165</Real>
+ <Real>0.022422145852823244</Real>
+ <Real>-0.38927333456373775</Real>
+ <Real>-0.21453291273592451</Real>
+ <Real>0.59688582916306221</Real>
+ <Real>0.0069204181366000162</Real>
+ <Real>-0.070865057959422981</Real>
+ <Real>-0.66387543044409503</Real>
+ <Real>0.54034603476645904</Real>
+ <Real>0.19439445363705898</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>-0.0032000320435372487</Real>
+ <Real>-0.57040030441260114</Real>
+ <Real>0.15040070495581404</Real>
+ <Real>0.42319963150032436</Real>
+ <Real>-0.036450027036671884</Real>
+ <Real>-0.66065001902578757</Real>
+ <Real>0.43065011916159079</Real>
+ <Real>0.26644992690086866</Real>
+ <Real>-0.00020000200272107804</Real>
+ <Real>-0.51940009412763999</Real>
+ <Real>0.039400194263443211</Real>
+ <Real>0.48019990186691786</Real>
+ <Real>-0.22444973163612758</Real>
+ <Real>-0.49665040454840437</Real>
+ <Real>0.66665000400519148</Real>
+ <Real>0.054450132179340471</Real>
+ <Real>-0.045000200271829272</Real>
+ <Real>-0.66500006675653367</Real>
+ <Real>0.46500073432855515</Real>
+ <Real>0.24499953269980779</Real>
+ <Real>-0.096800005507469256</Real>
+ <Real>-0.64959999599456764</Real>
+ <Real>0.58960000851154304</Real>
+ <Real>0.15679999299049385</Real>
+ <Real>-0.042050058078785923</Real>
+ <Real>-0.66385002603524867</Real>
+ <Real>0.45385022630685512</Real>
+ <Real>0.25204985780717948</Real>
+ <Real>-0.38720002202987702</Real>
+ <Real>-0.21839995894431974</Real>
+ <Real>0.59839998397827054</Real>
+ <Real>0.0071999969959262167</Real>
+ <Real>-0.23804993666410867</Real>
+ <Real>-0.47585009821652102</Real>
+ <Real>0.66585000642536807</Real>
+ <Real>0.048050028455261629</Real>
+ <Real>-0.06479997296333595</Real>
+ <Real>-0.66560000600813973</Real>
+ <Real>0.52559993090628732</Real>
+ <Real>0.20480004806518837</Real>
+ <Real>-0.028799987983704867</Real>
+ <Real>-0.65359998598098379</Real>
+ <Real>0.39359993591308218</Real>
+ <Real>0.28880003805160648</Real>
+ <Real>-0.088200007009506365</Real>
+ <Real>-0.65539999566078144</Real>
+ <Real>0.57540001235008198</Real>
+ <Real>0.16819999032020583</Real>
+ <Real>-0.057800011348724922</Real>
+ <Real>-0.66659999933242631</Real>
+ <Real>0.50660003271102738</Real>
+ <Real>0.21779997797012385</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">7</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">0</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">4</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 3 10">4.2950315356913931e-08</Real>
+ <Real Name="Cell 0 3 11">0.00010550061121302938</Real>
+ <Real Name="Cell 0 3 12">0.00033245189212343837</Real>
+ <Real Name="Cell 0 3 13">6.5320994399638903e-05</Real>
+ <Real Name="Cell 0 4 0">0.00033509649733611701</Real>
+ <Real Name="Cell 0 4 1">0.010405865891297168</Real>
+ <Real Name="Cell 0 4 10">3.7018116939038949e-07</Real>
+ <Real Name="Cell 0 4 11">0.0009092911031199979</Real>
+ <Real Name="Cell 0 4 12">0.0028653440415890041</Real>
+ <Real Name="Cell 0 4 13">0.00056299009429063333</Real>
+ <Real Name="Cell 0 4 2">0.012170975474346139</Real>
+ <Real Name="Cell 0 4 3">0.00069083745196048469</Real>
+ <Real Name="Cell 0 5 0">0.0024765732197673551</Real>
+ <Real Name="Cell 0 5 1">0.076905873381982126</Real>
+ <Real Name="Cell 0 5 10">0.010822923401325766</Real>
+ <Real Name="Cell 0 5 11">0.00064049772304074779</Real>
+ <Real Name="Cell 0 5 12">0.0014634708398500113</Real>
+ <Real Name="Cell 0 5 13">0.00028754647754684209</Real>
+ <Real Name="Cell 0 5 2">0.089951139918889741</Real>
+ <Real Name="Cell 0 5 3">0.0051057219229048911</Real>
+ <Real Name="Cell 0 5 6">0.00032345861862233</Real>
+ <Real Name="Cell 0 5 7">0.01120690928221869</Real>
+ <Real Name="Cell 0 5 8">0.015286641915757749</Real>
+ <Real Name="Cell 0 5 9">0.01777714420179741</Real>
+ <Real Name="Cell 0 6 0">0.0011100077091752976</Real>
+ <Real Name="Cell 0 6 1">0.034469448209118014</Real>
+ <Real Name="Cell 0 6 10">0.141295526322989</Real>
+ <Real Name="Cell 0 6 11">0.0023025081221303549</Real>
+ <Real Name="Cell 0 6 12">1.1744824887884069e-05</Real>
+ <Real Name="Cell 0 6 13">2.3076531038101656e-06</Real>
+ <Real Name="Cell 0 6 2">0.040316376661963943</Real>
+ <Real Name="Cell 0 6 3">0.0022884002177259023</Real>
+ <Real Name="Cell 0 6 6">0.0018466373740537478</Real>
+ <Real Name="Cell 0 6 7">0.063980665027010677</Real>
+ <Real Name="Cell 0 6 8">0.098097835327591698</Real>
+ <Real Name="Cell 0 6 9">0.22583047424257968</Real>
+ <Real Name="Cell 0 7 0">5.2358910319006335e-06</Real>
+ <Real Name="Cell 0 7 1">0.00016259191108390975</Real>
+ <Real Name="Cell 0 7 10">0.099092240692514502</Real>
+ <Real Name="Cell 0 7 11">0.0016121626020337491</Real>
+ <Real Name="Cell 0 7 2">0.00019017179183371629</Real>
+ <Real Name="Cell 0 7 3">1.0794352217871204e-05</Real>
+ <Real Name="Cell 0 7 6">0.00065429698252113082</Real>
+ <Real Name="Cell 0 7 7">0.022669505477933588</Real>
+ <Real Name="Cell 0 7 8">0.04143357897276008</Real>
+ <Real Name="Cell 0 7 9">0.15669012808529104</Real>
+ <Real Name="Cell 0 8 10">0.0020475738534051391</Real>
+ <Real Name="Cell 0 8 11">3.3312618306866694e-05</Real>
+ <Real Name="Cell 0 8 6">7.6671727402196969e-07</Real>
+ <Real Name="Cell 0 8 7">2.6564544706433857e-05</Real>
+ <Real Name="Cell 0 8 8">0.00031153957215634021</Real>
+ <Real Name="Cell 0 8 9">0.0032041511249004512</Real>
+ <Real Name="Cell 1 0 2">0.00016305839833258049</Real>
+ <Real Name="Cell 1 0 3">0.001743597055019892</Real>
+ <Real Name="Cell 1 0 4">0.0010567126779587096</Real>
+ <Real Name="Cell 1 0 5">1.4787049969606595e-05</Real>
+ <Real Name="Cell 1 1 2">0.00065223359333032194</Real>
+ <Real Name="Cell 1 1 3">0.0069743882200795681</Real>
+ <Real Name="Cell 1 1 4">0.0042268507118348383</Real>
+ <Real Name="Cell 1 1 5">5.9148199878426382e-05</Real>
+ <Real Name="Cell 1 2 2">0.00016305839833258049</Real>
+ <Real Name="Cell 1 2 3">0.001743597055019892</Real>
+ <Real Name="Cell 1 2 4">0.0010567126779587096</Real>
+ <Real Name="Cell 1 2 5">1.4787049969606595e-05</Real>
+ <Real Name="Cell 1 3 10">2.8025545948817311e-06</Real>
+ <Real Name="Cell 1 3 11">0.0060537351499214079</Real>
+ <Real Name="Cell 1 3 12">0.019047031424992478</Real>
+ <Real Name="Cell 1 3 13">0.0037394622186376499</Real>
+ <Real Name="Cell 1 4 10">2.3546749634256062e-05</Real>
+ <Real Name="Cell 1 4 11">0.052145725306194969</Real>
+ <Real Name="Cell 1 4 12">0.16411917917245875</Real>
+ <Real Name="Cell 1 4 13">0.032226347293359915</Real>
+ <Real Name="Cell 1 5 10">0.043400797755306655</Real>
+ <Real Name="Cell 1 5 11">0.027327314932316479</Real>
+ <Real Name="Cell 1 5 12">0.083808096907543345</Real>
+ <Real Name="Cell 1 5 13">0.016458352473098174</Real>
+ <Real Name="Cell 1 5 6">0.0044763366943537776</Real>
+ <Real Name="Cell 1 5 7">0.15509217117998589</Real>
+ <Real Name="Cell 1 5 8">0.19713755876117658</Real>
+ <Real Name="Cell 1 5 9">0.079837052192902352</Real>
+ <Real Name="Cell 1 6 10">0.57452511785829974</Real>
+ <Real Name="Cell 1 6 11">0.0094140243493374201</Real>
+ <Real Name="Cell 1 6 12">0.00067225770348083511</Real>
+ <Real Name="Cell 1 6 13">0.00013205790877515966</Real>
+ <Real Name="Cell 1 6 6">0.025555573921168157</Real>
+ <Real Name="Cell 1 6 7">0.88542708978291407</Real>
+ <Real Name="Cell 1 6 8">1.1784841813340943</Real>
+ <Real Name="Cell 1 6 9">0.98995069746548714</Real>
+ <Real Name="Cell 1 7 10">0.41423879995353341</Real>
+ <Real Name="Cell 1 7 11">0.0064524890955536948</Real>
+ <Real Name="Cell 1 7 6">0.0090548015209451459</Real>
+ <Real Name="Cell 1 7 7">0.31372293657985123</Real>
+ <Real Name="Cell 1 7 8">0.46056101525849008</Real>
+ <Real Name="Cell 1 7 9">0.71898136715916283</Real>
+ <Real Name="Cell 1 8 10">0.010241143735164637</Real>
+ <Real Name="Cell 1 8 11">0.00013332979322199908</Real>
+ <Real Name="Cell 1 8 6">1.0610583457374935e-05</Real>
+ <Real Name="Cell 1 8 7">0.0003676435394808515</Real>
+ <Real Name="Cell 1 8 8">0.0038757666132998151</Real>
+ <Real Name="Cell 1 8 9">0.021534174455808238</Real>
+ <Real Name="Cell 13 4 0">2.3157560649486199e-06</Real>
+ <Real Name="Cell 13 4 1">7.1911963390779827e-05</Real>
+ <Real Name="Cell 13 4 2">8.4110130947704685e-05</Real>
+ <Real Name="Cell 13 4 3">4.7741800704841749e-06</Real>
+ <Real Name="Cell 13 5 0">1.7114889291764152e-05</Real>
+ <Real Name="Cell 13 5 1">0.0005314744980334967</Real>
+ <Real Name="Cell 13 5 2">0.0006216266044919938</Real>
+ <Real Name="Cell 13 5 3">3.5284184116817302e-05</Real>
+ <Real Name="Cell 13 6 0">7.6709458472318317e-06</Real>
+ <Real Name="Cell 13 6 1">0.00023820849928380913</Real>
+ <Real Name="Cell 13 6 2">0.00027861494976489938</Real>
+ <Real Name="Cell 13 6 3">1.5814479486823714e-05</Real>
+ <Real Name="Cell 13 7 0">3.6183745604395287e-08</Real>
+ <Real Name="Cell 13 7 1">1.1236262008029312e-06</Real>
+ <Real Name="Cell 13 7 2">1.3142228695972977e-06</Real>
+ <Real Name="Cell 13 7 3">7.4596681297607286e-08</Real>
+ <Real Name="Cell 14 4 0">0.00087321973061572802</Real>
+ <Real Name="Cell 14 4 1">0.027116390301470762</Real>
+ <Real Name="Cell 14 4 2">0.031716046003246838</Real>
+ <Real Name="Cell 14 4 3">0.0018002363453387589</Real>
+ <Real Name="Cell 14 5 0">0.0064536413152841681</Real>
+ <Real Name="Cell 14 5 1">0.20040712621959006</Real>
+ <Real Name="Cell 14 5 2">0.23440146582542237</Real>
+ <Real Name="Cell 14 5 3">0.013304875334599011</Real>
+ <Real Name="Cell 14 6 0">0.002892541821513587</Real>
+ <Real Name="Cell 14 6 1">0.089823088331024092</Real>
+ <Real Name="Cell 14 6 2">0.1050594555539329</Real>
+ <Real Name="Cell 14 6 3">0.0059632859118166903</Real>
+ <Real Name="Cell 14 7 0">1.364407981806975e-05</Real>
+ <Real Name="Cell 14 7 1">0.00042369426695193784</Real>
+ <Real Name="Cell 14 7 2">0.00049556400068598912</Real>
+ <Real Name="Cell 14 7 3">2.812873727655301e-05</Real>
+ <Real Name="Cell 15 4 0">0.00218158335506652</Real>
+ <Real Name="Cell 15 4 1">0.067745452441234991</Real>
+ <Real Name="Cell 15 4 2">0.079236869740012594</Real>
+ <Real Name="Cell 15 4 3">0.0044975686055645364</Real>
+ <Real Name="Cell 15 5 0">0.016123268839866908</Real>
+ <Real Name="Cell 15 5 1">0.50068136972705513</Real>
+ <Real Name="Cell 15 5 2">0.58561014864764749</Real>
+ <Real Name="Cell 15 5 3">0.033239851956539723</Real>
+ <Real Name="Cell 15 6 0">0.0072264985208227907</Real>
+ <Real Name="Cell 15 6 1">0.22440692477878199</Real>
+ <Real Name="Cell 15 6 2">0.26247226384497674</Real>
+ <Real Name="Cell 15 6 3">0.014898203545571202</Real>
+ <Real Name="Cell 15 7 0">3.408729370477176e-05</Real>
+ <Real Name="Cell 15 7 1">0.0010585243645006683</Real>
+ <Real Name="Cell 15 7 2">0.0012380780430882019</Real>
+ <Real Name="Cell 15 7 3">7.0274620339026402e-05</Real>
+ <Real Name="Cell 2 0 2">0.017905921567627086</Real>
+ <Real Name="Cell 2 0 3">0.19146951295972336</Real>
+ <Real Name="Cell 2 0 4">0.11604072237023297</Real>
+ <Real Name="Cell 2 0 5">0.0016238093816689579</Real>
+ <Real Name="Cell 2 1 2">0.071627978687475655</Real>
+ <Real Name="Cell 2 1 3">0.76612365439178398</Real>
+ <Real Name="Cell 2 1 4">0.46453686083666401</Real>
+ <Real Name="Cell 2 1 5">0.0065266351492525082</Real>
+ <Real Name="Cell 2 2 2">0.018101186649385214</Real>
+ <Real Name="Cell 2 2 3">0.20275496433660919</Real>
+ <Real Name="Cell 2 2 4">0.13330799619841771</Real>
+ <Real Name="Cell 2 2 5">0.0030848862702219353</Real>
+ <Real Name="Cell 2 3 0">1.8487129301657384e-09</Real>
+ <Real Name="Cell 2 3 1">1.4303483163258406e-07</Real>
+ <Real Name="Cell 2 3 10">0.0004615992069788358</Real>
+ <Real Name="Cell 2 3 11">0.032045543747876895</Real>
+ <Real Name="Cell 2 3 12">0.061960981387845254</Real>
+ <Real Name="Cell 2 3 13">0.0082635562051842672</Real>
+ <Real Name="Cell 2 3 2">0.00040426756626450538</Real>
+ <Real Name="Cell 2 3 3">0.029021040438571837</Real>
+ <Real Name="Cell 2 3 4">0.048547918921529709</Real>
+ <Real Name="Cell 2 3 5">0.0048291117556227489</Real>
+ <Real Name="Cell 2 3 6">0.00031668189191720006</Real>
+ <Real Name="Cell 2 3 7">3.7613795394796753e-05</Real>
+ <Real Name="Cell 2 4 0">1.5776445017470423e-06</Real>
+ <Real Name="Cell 2 4 1">0.00012206228019578449</Real>
+ <Real Name="Cell 2 4 10">0.0031716627891397215</Real>
+ <Real Name="Cell 2 4 11">0.23592451154391614</Real>
+ <Real Name="Cell 2 4 12">0.47588837217928692</Real>
+ <Real Name="Cell 2 4 13">0.066689110487020989</Real>
+ <Real Name="Cell 2 4 2">0.00042908263949965344</Real>
+ <Real Name="Cell 2 4 3">0.021417492478982808</Real>
+ <Real Name="Cell 2 4 4">0.039000460498604186</Real>
+ <Real Name="Cell 2 4 5">0.005366082958354652</Real>
+ <Real Name="Cell 2 4 6">0.0024309546849622674</Real>
+ <Real Name="Cell 2 4 7">0.00028873590334019044</Real>
+ <Real Name="Cell 2 5 0">4.4526222460492609e-06</Real>
+ <Real Name="Cell 2 5 1">0.00034449917177247066</Real>
+ <Real Name="Cell 2 5 10">0.012458044870967803</Real>
+ <Real Name="Cell 2 5 11">0.10636772459500912</Real>
+ <Real Name="Cell 2 5 12">0.2224033505685204</Real>
+ <Real Name="Cell 2 5 13">0.032450949223171502</Real>
+ <Real Name="Cell 2 5 2">0.00060017237238862682</Real>
+ <Real Name="Cell 2 5 3">0.0016800179022782619</Real>
+ <Real Name="Cell 2 5 4">0.0029892977034694191</Real>
+ <Real Name="Cell 2 5 5">0.0008846745247210895</Real>
+ <Real Name="Cell 2 5 6">0.0043949292092120259</Real>
+ <Real Name="Cell 2 5 7">0.11339270338521788</Real>
+ <Real Name="Cell 2 5 8">0.14139810979965023</Real>
+ <Real Name="Cell 2 5 9">0.026782256867452288</Real>
+ <Real Name="Cell 2 6 0">7.7992520956755581e-07</Real>
+ <Real Name="Cell 2 6 1">6.8710797878527758e-05</Real>
+ <Real Name="Cell 2 6 10">0.17749440017109669</Real>
+ <Real Name="Cell 2 6 11">0.0028511069165586466</Real>
+ <Real Name="Cell 2 6 12">0.0013479180531386348</Real>
+ <Real Name="Cell 2 6 13">0.00022636363927053141</Real>
+ <Real Name="Cell 2 6 2">0.00015040505928594613</Real>
+ <Real Name="Cell 2 6 3">2.7074545361823401e-05</Real>
+ <Real Name="Cell 2 6 4">4.4187184652806337e-08</Real>
+ <Real Name="Cell 2 6 5">3.075974601799134e-06</Real>
+ <Real Name="Cell 2 6 6">0.018668576880988243</Real>
+ <Real Name="Cell 2 6 7">0.64660068531865333</Real>
+ <Real Name="Cell 2 6 8">0.85684341929464791</Real>
+ <Real Name="Cell 2 6 9">0.42339525096833763</Real>
+ <Real Name="Cell 2 7 1">0.0013388699831736112</Real>
+ <Real Name="Cell 2 7 10">0.16974581175417192</Real>
+ <Real Name="Cell 2 7 11">0.0016140825169375986</Real>
+ <Real Name="Cell 2 7 2">0.0076991305061531231</Real>
+ <Real Name="Cell 2 7 3">0.0027466445845383304</Real>
+ <Real Name="Cell 2 7 4">3.3949534031249405e-06</Real>
+ <Real Name="Cell 2 7 6">0.0066124382975103896</Real>
+ <Real Name="Cell 2 7 7">0.22910253676411832</Real>
+ <Real Name="Cell 2 7 8">0.37541443403161301</Real>
+ <Real Name="Cell 2 7 9">0.47215876123032374</Real>
+ <Real Name="Cell 2 8 1">0.0027974367006971803</Real>
+ <Real Name="Cell 2 8 10">0.010233903838170607</Real>
+ <Real Name="Cell 2 8 11">3.3352290106902824e-05</Real>
+ <Real Name="Cell 2 8 2">0.016086573388042858</Real>
+ <Real Name="Cell 2 8 3">0.0057388428011104012</Real>
+ <Real Name="Cell 2 8 4">7.0934200978550121e-06</Real>
+ <Real Name="Cell 2 8 6">7.7485771775539345e-06</Real>
+ <Real Name="Cell 2 8 7">0.00026853543929615</Real>
+ <Real Name="Cell 2 8 8">0.0098372127559782519</Real>
+ <Real Name="Cell 2 8 9">0.03798666708747394</Real>
+ <Real Name="Cell 2 9 1">0.00035074733727529048</Real>
+ <Real Name="Cell 2 9 2">0.0020169617351246572</Real>
+ <Real Name="Cell 2 9 3">0.00071954580099320561</Real>
+ <Real Name="Cell 2 9 4">8.8938498979355444e-07</Real>
+ <Real Name="Cell 3 0 2">0.033835623551399498</Real>
+ <Real Name="Cell 3 0 3">0.36180714506131645</Real>
+ <Real Name="Cell 3 0 4">0.21927439947297753</Real>
+ <Real Name="Cell 3 0 5">0.0030684040891095399</Real>
+ <Real Name="Cell 3 1 2">0.13547578806272392</Real>
+ <Real Name="Cell 3 1 3">1.4548553583155341</Real>
+ <Real Name="Cell 3 1 4">0.88871065525324011</Real>
+ <Real Name="Cell 3 1 5">0.013248617212529085</Real>
+ <Real Name="Cell 3 2 2">0.039846669436794921</Real>
+ <Real Name="Cell 3 2 3">0.70699584092402734</Real>
+ <Real Name="Cell 3 2 4">0.74580508783692068</Real>
+ <Real Name="Cell 3 2 5">0.047400400734869452</Real>
+ <Real Name="Cell 3 3 0">9.907626368103328e-07</Real>
+ <Real Name="Cell 3 3 1">7.6655258169972478e-05</Real>
+ <Real Name="Cell 3 3 10">0.0013607745040133191</Real>
+ <Real Name="Cell 3 3 11">0.068679049113872598</Real>
+ <Real Name="Cell 3 3 12">0.10047643482955704</Real>
+ <Real Name="Cell 3 3 13">0.0081217677233436109</Real>
+ <Real Name="Cell 3 3 2">0.0099245124668976836</Real>
+ <Real Name="Cell 3 3 3">0.62597286133171748</Real>
+ <Real Name="Cell 3 3 4">1.0117086746774517</Real>
+ <Real Name="Cell 3 3 5">0.11191982717448912</Real>
+ <Real Name="Cell 3 3 6">0.0079065491239385614</Real>
+ <Real Name="Cell 3 3 7">0.0007219698154281415</Real>
+ <Real Name="Cell 3 4 0">0.00084549158552165945</Real>
+ <Real Name="Cell 3 4 1">0.06541564382903689</Real>
+ <Real Name="Cell 3 4 10">0.0093310404836781744</Real>
+ <Real Name="Cell 3 4 11">0.47227468323239086</Real>
+ <Real Name="Cell 3 4 12">0.69322650053967994</Real>
+ <Real Name="Cell 3 4 13">0.056530832247206016</Real>
+ <Real Name="Cell 3 4 2">0.11373511827223479</Real>
+ <Real Name="Cell 3 4 3">0.2713214863338036</Real>
+ <Real Name="Cell 3 4 4">0.56777188224543784</Real>
+ <Real Name="Cell 3 4 5">0.24918693562109068</Real>
+ <Real Name="Cell 3 4 6">0.064412785716560533</Real>
+ <Real Name="Cell 3 4 7">0.0055420785021559355</Real>
+ <Real Name="Cell 3 5 0">0.0023862502853921287</Real>
+ <Real Name="Cell 3 5 1">0.18462407128491792</Real>
+ <Real Name="Cell 3 5 10">0.0039864403175846079</Real>
+ <Real Name="Cell 3 5 11">0.19870325951005169</Real>
+ <Real Name="Cell 3 5 12">0.29268796973393935</Real>
+ <Real Name="Cell 3 5 13">0.02408787913335474</Real>
+ <Real Name="Cell 3 5 2">0.31312980743875407</Real>
+ <Real Name="Cell 3 5 3">0.048982155403907664</Real>
+ <Real Name="Cell 3 5 4">0.09032005003050933</Real>
+ <Real Name="Cell 3 5 5">0.11393087437246284</Real>
+ <Real Name="Cell 3 5 6">0.031671845299420832</Real>
+ <Real Name="Cell 3 5 7">0.005147299718395862</Real>
+ <Real Name="Cell 3 5 8">0.0032617667856080631</Real>
+ <Real Name="Cell 3 5 9">0.00050312708544542246</Real>
+ <Real Name="Cell 3 6 0">0.00041797768844334745</Real>
+ <Real Name="Cell 3 6 1">0.032756603588485769</Real>
+ <Real Name="Cell 3 6 10">0.0090198896928035868</Real>
+ <Real Name="Cell 3 6 11">0.0006954273694937792</Real>
+ <Real Name="Cell 3 6 12">0.0010506061416214218</Real>
+ <Real Name="Cell 3 6 13">9.2091458578066684e-05</Real>
+ <Real Name="Cell 3 6 2">0.057218516634815794</Real>
+ <Real Name="Cell 3 6 3">0.0061742764829265896</Real>
+ <Real Name="Cell 3 6 4">0.00063892872883243156</Real>
+ <Real Name="Cell 3 6 5">0.0011691232506900651</Real>
+ <Real Name="Cell 3 6 6">0.00065436683019917815</Real>
+ <Real Name="Cell 3 6 7">0.014744811996528273</Real>
+ <Real Name="Cell 3 6 8">0.028310947770342914</Real>
+ <Real Name="Cell 3 6 9">0.03937391518615449</Real>
+ <Real Name="Cell 3 7 1">0.06682967732992437</Real>
+ <Real Name="Cell 3 7 10">0.017633890675406386</Real>
+ <Real Name="Cell 3 7 11">1.2590923308017436e-14</Real>
+ <Real Name="Cell 3 7 2">0.38430199639517298</Real>
+ <Real Name="Cell 3 7 3">0.13709872775665843</Real>
+ <Real Name="Cell 3 7 4">0.00016945905377844923</Real>
+ <Real Name="Cell 3 7 6">0.00015064357459036907</Real>
+ <Real Name="Cell 3 7 7">0.005219515757859906</Real>
+ <Real Name="Cell 3 7 8">0.026314989565077548</Real>
+ <Real Name="Cell 3 7 9">0.075295027623240238</Real>
+ <Real Name="Cell 3 8 1">0.13963401555641472</Real>
+ <Real Name="Cell 3 8 10">0.0020459728853106465</Real>
+ <Real Name="Cell 3 8 11">2.6017017251355131e-16</Real>
+ <Real Name="Cell 3 8 2">0.8029610958330442</Real>
+ <Real Name="Cell 3 8 3">0.28645426177698968</Real>
+ <Real Name="Cell 3 8 4">0.00035406796945404429</Real>
+ <Real Name="Cell 3 8 6">1.7652691964710824e-07</Real>
+ <Real Name="Cell 3 8 7">6.1335399578891201e-06</Real>
+ <Real Name="Cell 3 8 8">0.0023143351570314823</Real>
+ <Real Name="Cell 3 8 9">0.0086905438166314207</Real>
+ <Real Name="Cell 3 9 1">0.017507548655976035</Real>
+ <Real Name="Cell 3 9 2">0.10067661807285928</Real>
+ <Real Name="Cell 3 9 3">0.035916119047268574</Real>
+ <Real Name="Cell 3 9 4">4.4393639888089178e-05</Real>
+ <Real Name="Cell 4 0 2">0.003759398397327105</Real>
+ <Real Name="Cell 4 0 3">0.040199560655909627</Real>
+ <Real Name="Cell 4 0 4">0.024363074754668708</Real>
+ <Real Name="Cell 4 0 5">0.00034092332885271202</Real>
+ <Real Name="Cell 4 1 2">0.015193497585489754</Real>
+ <Real Name="Cell 4 1 3">0.16971872256758302</Real>
+ <Real Name="Cell 4 1 4">0.11103523591878797</Real>
+ <Real Name="Cell 4 1 5">0.0025040799245339661</Real>
+ <Real Name="Cell 4 2 2">0.010774116469313418</Real>
+ <Real Name="Cell 4 2 3">0.44234432435298821</Real>
+ <Real Name="Cell 4 2 4">0.63727074972356412</Real>
+ <Real Name="Cell 4 2 5">0.051877374562982616</Real>
+ <Real Name="Cell 4 3 0">2.6212263938109493e-06</Real>
+ <Real Name="Cell 4 3 1">0.00020280416163694063</Real>
+ <Real Name="Cell 4 3 10">0.00025152815444910053</Real>
+ <Real Name="Cell 4 3 11">0.012555021993817085</Real>
+ <Real Name="Cell 4 3 12">0.018126946298234189</Real>
+ <Real Name="Cell 4 3 13">0.0014132514788792942</Real>
+ <Real Name="Cell 4 3 2">0.010964643545717887</Real>
+ <Real Name="Cell 4 3 3">0.64937886636400888</Real>
+ <Real Name="Cell 4 3 4">1.0947645822609935</Real>
+ <Real Name="Cell 4 3 5">0.22696988079589014</Real>
+ <Real Name="Cell 4 3 6">0.018986475771994395</Real>
+ <Real Name="Cell 4 3 7">0.00065039989094193716</Real>
+ <Real Name="Cell 4 4 0">0.0022368878047817477</Real>
+ <Real Name="Cell 4 4 1">0.17306790325161722</Real>
+ <Real Name="Cell 4 4 10">0.0017246649920512828</Real>
+ <Real Name="Cell 4 4 11">0.086086613065623985</Real>
+ <Real Name="Cell 4 4 12">0.12429188995494535</Real>
+ <Real Name="Cell 4 4 13">0.009690308251679448</Real>
+ <Real Name="Cell 4 4 2">0.29546793821926287</Real>
+ <Real Name="Cell 4 4 3">0.21778462395380638</Real>
+ <Real Name="Cell 4 4 4">1.0702655289755327</Real>
+ <Real Name="Cell 4 4 5">1.3620142626691392</Real>
+ <Real Name="Cell 4 4 6">0.17323593075235827</Real>
+ <Real Name="Cell 4 4 7">0.0049926841487913168</Real>
+ <Real Name="Cell 4 5 0">0.0063132197338868438</Real>
+ <Real Name="Cell 4 5 1">0.48845351106786289</Real>
+ <Real Name="Cell 4 5 10">0.00072341221284664622</Real>
+ <Real Name="Cell 4 5 11">0.036109103820914271</Real>
+ <Real Name="Cell 4 5 12">0.052134340040297669</Real>
+ <Real Name="Cell 4 5 13">0.0040646081226336514</Real>
+ <Real Name="Cell 4 5 2">0.82807302039068265</Real>
+ <Real Name="Cell 4 5 3">0.096427224677649734</Real>
+ <Real Name="Cell 4 5 4">0.44314477578098654</Real>
+ <Real Name="Cell 4 5 5">0.74771601172012381</Real>
+ <Real Name="Cell 4 5 6">0.093262715335143395</Real>
+ <Real Name="Cell 4 5 7">0.0023125750286696629</Real>
+ <Real Name="Cell 4 6 0">0.0011058290939381999</Real>
+ <Real Name="Cell 4 6 1">0.086161005084866182</Real>
+ <Real Name="Cell 4 6 10">2.4748757046975492e-06</Real>
+ <Real Name="Cell 4 6 11">0.00012353336338230507</Real>
+ <Real Name="Cell 4 6 12">0.00017835752459645737</Real>
+ <Real Name="Cell 4 6 13">1.3905488065011144e-05</Real>
+ <Real Name="Cell 4 6 2">0.14849427470411145</Real>
+ <Real Name="Cell 4 6 3">0.015341219620302503</Real>
+ <Real Name="Cell 4 6 4">0.0047129237984894004</Real>
+ <Real Name="Cell 4 6 5">0.0082573902547324607</Real>
+ <Real Name="Cell 4 6 6">0.00092902517735477625</Real>
+ <Real Name="Cell 4 6 7">1.2611698688655134e-05</Real>
+ <Real Name="Cell 4 7 1">0.096488725265258452</Real>
+ <Real Name="Cell 4 7 2">0.55485543594657594</Real>
+ <Real Name="Cell 4 7 3">0.19794321931890207</Real>
+ <Real Name="Cell 4 7 4">0.0002446650760113426</Real>
+ <Real Name="Cell 4 8 1">0.20160366925301407</Real>
+ <Real Name="Cell 4 8 2">1.1593156763579595</Real>
+ <Real Name="Cell 4 8 3">0.4135828223322302</Real>
+ <Real Name="Cell 4 8 4">0.00051120353104834994</Real>
+ <Real Name="Cell 4 9 1">0.025277408478197247</Real>
+ <Real Name="Cell 4 9 2">0.14535695711817775</Real>
+ <Real Name="Cell 4 9 3">0.051855712638529596</Real>
+ <Real Name="Cell 4 9 4">6.4095561939345712e-05</Real>
+ <Real Name="Cell 5 1 2">8.8492741942662414e-06</Real>
+ <Real Name="Cell 5 1 3">0.00050633578934437329</Real>
+ <Real Name="Cell 5 1 4">0.00077098173194170767</Real>
+ <Real Name="Cell 5 1 5">6.4729538939222294e-05</Real>
+ <Real Name="Cell 5 2 2">0.00039740630658555734</Real>
+ <Real Name="Cell 5 2 3">0.022750462154480639</Real>
+ <Real Name="Cell 5 2 4">0.034650097639080731</Real>
+ <Real Name="Cell 5 2 5">0.0029103125984534517</Real>
+ <Real Name="Cell 5 3 0">4.2852838115120977e-07</Real>
+ <Real Name="Cell 5 3 1">3.315522050373283e-05</Real>
+ <Real Name="Cell 5 3 2">0.00061946880637814728</Real>
+ <Real Name="Cell 5 3 3">0.033262285423226325</Real>
+ <Real Name="Cell 5 3 4">0.085134873931137597</Real>
+ <Real Name="Cell 5 3 5">0.064773341660101735</Real>
+ <Real Name="Cell 5 3 6">0.0062512313254760874</Real>
+ <Real Name="Cell 5 3 7">2.3250889570295768e-05</Real>
+ <Real Name="Cell 5 4 0">0.00036569519979781667</Real>
+ <Real Name="Cell 5 4 1">0.028293820245653564</Real>
+ <Real Name="Cell 5 4 2">0.048021229942312067</Real>
+ <Real Name="Cell 5 4 3">0.013066835389676628</Real>
+ <Real Name="Cell 5 4 4">0.34406729851412915</Real>
+ <Real Name="Cell 5 4 5">0.58777937539560787</Real>
+ <Real Name="Cell 5 4 6">0.060307381408057831</Real>
+ <Real Name="Cell 5 4 7">0.00017848149948917534</Real>
+ <Real Name="Cell 5 5 0">0.0010321099462458419</Real>
+ <Real Name="Cell 5 5 1">0.079854297537884616</Real>
+ <Real Name="Cell 5 5 2">0.1353600240158695</Real>
+ <Real Name="Cell 5 5 3">0.015534435322056188</Real>
+ <Real Name="Cell 5 5 4">0.18967111273463377</Real>
+ <Real Name="Cell 5 5 5">0.33014801992429144</Real>
+ <Real Name="Cell 5 5 6">0.03377003312867459</Real>
+ <Real Name="Cell 5 5 7">8.2671333995383551e-05</Real>
+ <Real Name="Cell 5 6 0">0.00018078528149042571</Real>
+ <Real Name="Cell 5 6 1">0.01403436574102454</Real>
+ <Real Name="Cell 5 6 2">0.023979854487134824</Real>
+ <Real Name="Cell 5 6 3">0.0024182058042573097</Real>
+ <Real Name="Cell 5 6 4">0.002111616708676785</Real>
+ <Real Name="Cell 5 6 5">0.0036790495014350443</Real>
+ <Real Name="Cell 5 6 6">0.00037259678061122691</Real>
+ <Real Name="Cell 5 6 7">4.5085064986571803e-07</Real>
+ <Real Name="Cell 5 7 1">0.0075226597282771999</Real>
+ <Real Name="Cell 5 7 2">0.043258822536376432</Real>
+ <Real Name="Cell 5 7 3">0.015432471310635028</Real>
+ <Real Name="Cell 5 7 4">1.9075100320442366e-05</Real>
+ <Real Name="Cell 5 8 1">0.015717855113053587</Real>
+ <Real Name="Cell 5 8 2">0.09038504060368785</Real>
+ <Real Name="Cell 5 8 3">0.032244625818329896</Real>
+ <Real Name="Cell 5 8 4">3.9855539653970006e-05</Real>
+ <Real Name="Cell 5 9 1">0.0019707312151901065</Real>
+ <Real Name="Cell 5 9 2">0.011332629014755418</Real>
+ <Real Name="Cell 5 9 3">0.0040428856332651517</Real>
+ <Real Name="Cell 5 9 4">4.997154861740327e-06</Real>
+ <Real Name="Cell 6 3 3">1.9464033267581281e-06</Real>
+ <Real Name="Cell 6 3 4">0.00016353407592266335</Real>
+ <Real Name="Cell 6 3 5">0.00028479458890517983</Real>
+ <Real Name="Cell 6 3 6">2.8563579002759801e-05</Real>
+ <Real Name="Cell 6 4 3">1.8901514155576222e-05</Real>
+ <Real Name="Cell 6 4 4">0.0015880786928779277</Real>
+ <Real Name="Cell 6 4 5">0.0027656390017523321</Real>
+ <Real Name="Cell 6 4 6">0.00027738079021567288</Real>
+ <Real Name="Cell 6 5 3">1.0630931416268054e-05</Real>
+ <Real Name="Cell 6 5 4">0.00089319593809584867</Real>
+ <Real Name="Cell 6 5 5">0.0015555007026308136</Real>
+ <Real Name="Cell 6 5 6">0.00015600952033269309</Real>
+ <Real Name="Cell 6 6 3">1.1854319510832442e-07</Real>
+ <Real Name="Cell 6 6 4">9.959832888925606e-06</Real>
+ <Real Name="Cell 6 6 5">1.7345048713316886e-05</Real>
+ <Real Name="Cell 6 6 6">1.7396280987434627e-06</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>0.0016854540244076904</Real>
+ <Real>0.29311731353696457</Real>
+ <Real>0.62495897970942083</Real>
+ <Real>0.08023825272920683</Real>
+ <Real>0.0024510232125503567</Real>
+ <Real>0.31182615608828101</Real>
+ <Real>0.61399469745996438</Real>
+ <Real>0.071728123239204175</Real>
+ <Real>0.089396158854166657</Real>
+ <Real>0.63480631510416663</Real>
+ <Real>0.27469889322916663</Real>
+ <Real>0.0010986328125</Real>
+ <Real>0.16654891563009322</Real>
+ <Real>0.66666661118583959</Real>
+ <Real>0.16678447318188874</Real>
+ <Real>2.1784112419024706e-12</Real>
+ <Real>0.036679250243501299</Real>
+ <Real>0.54076108468440021</Real>
+ <Real>0.41219020447440313</Real>
+ <Real>0.010369460597695286</Real>
+ <Real>0.030060370435004882</Real>
+ <Real>0.51859816391065605</Real>
+ <Real>0.43762266279761575</Real>
+ <Real>0.013718802856723243</Real>
+ <Real>0.0013333322008454032</Real>
+ <Real>0.28266663042704326</Real>
+ <Real>0.63066668591896469</Real>
+ <Real>0.085333351453146619</Real>
+ <Real>0.10786905756209218</Real>
+ <Real>0.64967182393728695</Real>
+ <Real>0.24204905486544184</Real>
+ <Real>0.00041006363517895783</Real>
+ <Real>0.13568773041454193</Real>
+ <Real>0.66242299043599051</Real>
+ <Real>0.2018408165595105</Real>
+ <Real>4.8462589956979473e-05</Real>
+ <Real>0.068569303078043639</Real>
+ <Real>0.6094158238958427</Real>
+ <Real>0.31921047128639002</Real>
+ <Real>0.0028044017397236948</Real>
+ <Real>8.1395367348647448e-05</Real>
+ <Real>0.20889823559751874</Real>
+ <Real>0.66070929740338646</Real>
+ <Real>0.13031107163174604</Real>
+ <Real>0.027540534381201576</Real>
+ <Real>0.50898335071154721</Real>
+ <Real>0.44816170109574205</Real>
+ <Real>0.015314413811509116</Real>
+ <Real>0.14745603131103738</Real>
+ <Real>0.66509867193952754</Real>
+ <Real>0.18743463013712769</Real>
+ <Real>1.0666612307322972e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>0.010666670313068831</Real>
+ <Real>0.41466669674948081</Real>
+ <Real>0.53866664114185348</Real>
+ <Real>0.035999991795596688</Real>
+ <Real>0.0026041699536889272</Real>
+ <Real>0.31510423569410645</Real>
+ <Real>0.61197912393538834</Real>
+ <Real>0.07031247041681625</Real>
+ <Real>0.10235425786179789</Real>
+ <Real>0.64585423387961782</Real>
+ <Real>0.25122901109856532</Real>
+ <Real>0.00056249716001883718</Real>
+ <Real>0.010666691350019937</Real>
+ <Real>0.41466687030416455</Real>
+ <Real>0.53866649388328902</Real>
+ <Real>0.035999944462526537</Real>
+ <Real>0.020833337716027845</Real>
+ <Real>0.47916668858013739</Real>
+ <Real>0.47916664475319531</Real>
+ <Real>0.02083332895063943</Real>
+ <Real>2.0833184322081997e-05</Real>
+ <Real>0.19285410154860061</Real>
+ <Real>0.66422917814054716</Real>
+ <Real>0.14289588712653006</Real>
+ <Real>0.0071458391316396429</Real>
+ <Real>0.38147922973802206</Real>
+ <Real>0.56560411779523667</Real>
+ <Real>0.045770813335101523</Real>
+ <Real>0.010666657690911333</Real>
+ <Real>0.41466659261666311</Real>
+ <Real>0.53866672949696659</Real>
+ <Real>0.036000020195458941</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0.66666666666666663</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>0.020833587530638329</Real>
+ <Real>0.47916793764698851</Real>
+ <Real>0.47916539568427707</Real>
+ <Real>0.020833079138096039</Real>
+ <Real>0.015187499645001698</Real>
+ <Real>0.44735416440081327</Real>
+ <Real>0.5097291687572123</Real>
+ <Real>0.027729167196972774</Real>
+ <Real>0.070312490138938491</Real>
+ <Real>0.61197915242290968</Real>
+ <Real>0.31510418967581139</Real>
+ <Real>0.0026041677623403724</Real>
+ <Real>0.057166672250220395</Real>
+ <Real>0.59016667726402305</Real>
+ <Real>0.34816665151130699</Real>
+ <Real>0.0044999989744494255</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>0.012348027757665452</Real>
+ <Real>0.42782287292924226</Real>
+ <Real>0.52731048558104343</Real>
+ <Real>0.032518613732048778</Real>
+ <Real>0.10417109125784305</Real>
+ <Real>0.64716599950200826</Real>
+ <Real>0.24815480590058539</Real>
+ <Real>0.00050810333956326215</Real>
+ <Real>0.064836187630456954</Real>
+ <Real>0.60360820054940012</Real>
+ <Real>0.32827511468795989</Real>
+ <Real>0.0032804971321829571</Real>
+ <Real>0.015699363256675682</Real>
+ <Real>0.45058077634622828</Real>
+ <Real>0.50674004282499185</Real>
+ <Real>0.026979817572104103</Real>
+ <Real>0.015187553107800395</Real>
+ <Real>0.44735450563823331</Real>
+ <Real>0.50972885392100609</Real>
+ <Real>0.027729087332960128</Real>
+ <Real>0.02926933487542473</Real>
+ <Real>0.51565867246524488</Real>
+ <Real>0.44087466027800237</Real>
+ <Real>0.014197332381327967</Real>
+ <Real>0.00010235473511721623</Real>
+ <Real>0.21247219451474078</Real>
+ <Real>0.65974870412142894</Real>
+ <Real>0.12767674662871301</Real>
+ <Real>0.00028800014162065922</Real>
+ <Real>0.23300267843691519</Real>
+ <Real>0.65313066237084039</Real>
+ <Real>0.11357865905062374</Real>
+ <Real>0.001055269599152589</Real>
+ <Real>0.27311330846590165</Real>
+ <Real>0.63560750214911865</Real>
+ <Real>0.090223919785827028</Real>
+ <Real>0.043690654581706838</Real>
+ <Real>0.56039463565174574</Real>
+ <Real>0.38813870594278954</Real>
+ <Real>0.0077760038237577982</Real>
+ <Real>0.0029293320036731184</Real>
+ <Real>0.32167864075795827</Real>
+ <Real>0.60785468313399849</Real>
+ <Real>0.067537344104370053</Real>
+ <Real>0.095297837850113781</Real>
+ <Real>0.64022317055664446</Real>
+ <Real>0.2636601584493915</Real>
+ <Real>0.00081883314385018213</Real>
+ <Real>0.12559517752556038</Real>
+ <Real>0.65893117106870747</Real>
+ <Real>0.21535215151194756</Real>
+ <Real>0.00012149989378455396</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>-0.023382024515234419</Real>
+ <Real>-0.64610389531086987</Real>
+ <Real>0.36235386416744297</Real>
+ <Real>0.30713205565866131</Real>
+ <Real>-0.030012519422176642</Real>
+ <Real>-0.65496252100764762</Real>
+ <Real>0.39996260028182518</Real>
+ <Real>0.28501244014799909</Real>
+ <Real>-0.330078125</Real>
+ <Real>-0.322265625</Real>
+ <Real>0.634765625</Real>
+ <Real>0.017578125</Real>
+ <Real>-0.49976447018752879</Real>
+ <Real>-0.0004710318812612968</Real>
+ <Real>0.50023547432510895</Real>
+ <Real>2.7743681130232289e-08</Real>
+ <Real>-0.18225710646138371</Real>
+ <Real>-0.55697880518955645</Real>
+ <Real>0.66072892976326403</Real>
+ <Real>0.078506981887676131</Real>
+ <Real>-0.15961255758703274</Real>
+ <Real>-0.58616242916284433</Real>
+ <Real>0.6511625310867869</Real>
+ <Real>0.094612455663090178</Real>
+ <Real>-0.019999988675119096</Real>
+ <Real>-0.63999997735023018</Real>
+ <Real>0.33999992072581764</Real>
+ <Real>0.32000004529953163</Real>
+ <Real>-0.3741123922437507</Real>
+ <Real>-0.24266269869504031</Real>
+ <Real>0.60766257412133273</Real>
+ <Real>0.0091125168174582827</Real>
+ <Real>-0.43594452067539102</Real>
+ <Real>-0.12591642664894442</Real>
+ <Real>0.55966641532406192</Real>
+ <Real>0.0021945320002735302</Real>
+ <Real>-0.27658205230720379</Real>
+ <Real>-0.41400387139059491</Real>
+ <Real>0.65775389970280118</Real>
+ <Real>0.032832023994997545</Real>
+ <Real>-0.0031007776826630362</Real>
+ <Real>-0.56944762165248086</Real>
+ <Real>0.14819757635295083</Real>
+ <Real>0.42435082298219307</Real>
+ <Real>-0.15056328435726465</Real>
+ <Real>-0.59706015259064737</Real>
+ <Real>0.64581015825308863</Real>
+ <Real>0.1018132786948234</Real>
+ <Real>-0.46080006523132555</Real>
+ <Real>-0.077599872255318392</Real>
+ <Real>0.53759994020461344</Real>
+ <Real>0.0007999972820305068</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>-0.080000018232009792</Real>
+ <Real>-0.65999999088399253</Real>
+ <Real>0.56000003646401431</Real>
+ <Real>0.17999997265198792</Real>
+ <Real>-0.031250026296172552</Real>
+ <Real>-0.65625002629615037</Real>
+ <Real>0.40625013148081845</Real>
+ <Real>0.28124992111150449</Real>
+ <Real>-0.3612502145767475</Real>
+ <Real>-0.26624960871295239</Real>
+ <Real>0.61624986115614722</Real>
+ <Real>0.011249962133552631</Real>
+ <Real>-0.080000123416718763</Real>
+ <Real>-0.65999993829152159</Real>
+ <Real>0.56000024683319949</Real>
+ <Real>0.17999981487504085</Real>
+ <Real>-0.12500001753077744</Real>
+ <Real>-0.62499998246922139</Real>
+ <Real>0.62500001753077505</Real>
+ <Real>0.12499998246922378</Real>
+ <Real>-0.0012499940395428412</Real>
+ <Real>-0.54624989867208618</Real>
+ <Real>0.096249779462800888</Real>
+ <Real>0.45125011324882813</Real>
+ <Real>-0.061250033133174432</Real>
+ <Real>-0.6662499952666765</Real>
+ <Real>0.51625008993287635</Real>
+ <Real>0.21124993846697457</Real>
+ <Real>-0.079999955121217034</Real>
+ <Real>-0.66000002243937572</Real>
+ <Real>0.55999991024240259</Real>
+ <Real>0.18000006731819018</Real>
+ <Real>-0.5</Real>
+ <Real>0</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>-0.12500101678715228</Real>
+ <Real>-0.62499898320871239</Real>
+ <Real>0.62500101677888154</Real>
+ <Real>0.12499898321698313</Real>
+ <Real>-0.10124999842222977</Real>
+ <Real>-0.64625000122715459</Real>
+ <Real>0.59624999772099851</Real>
+ <Real>0.15125000192838584</Real>
+ <Real>-0.28124997370383537</Real>
+ <Real>-0.40625004382694024</Real>
+ <Real>0.65625000876538653</Real>
+ <Real>0.031250008765389033</Real>
+ <Real>-0.24500001595301041</Real>
+ <Real>-0.46499997493098327</Real>
+ <Real>0.66499999772099772</Real>
+ <Real>0.04499999316299591</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>-0.088200132179309776</Real>
+ <Real>-0.65539991817459509</Real>
+ <Real>0.5754002328871195</Real>
+ <Real>0.16819981746678536</Real>
+ <Real>-0.36551256726980519</Real>
+ <Real>-0.25846237686871554</Real>
+ <Real>0.61346245554684664</Real>
+ <Real>0.010512488591674085</Real>
+ <Real>-0.2664500574350388</Real>
+ <Real>-0.4306499063730147</Real>
+ <Real>0.6606499850511458</Real>
+ <Real>0.036449978756907697</Real>
+ <Real>-0.10351235680585091</Real>
+ <Real>-0.64446261486992285</Real>
+ <Real>0.59946230015739843</Real>
+ <Real>0.14851267151837533</Real>
+ <Real>-0.10125023603453087</Real>
+ <Real>-0.64624981641728141</Real>
+ <Real>0.59625034093815543</Real>
+ <Real>0.15124971151365685</Real>
+ <Real>-0.15680000550746923</Real>
+ <Real>-0.58959999331235879</Real>
+ <Real>0.64960000314712518</Real>
+ <Real>0.096799995672702838</Real>
+ <Real>-0.0036125133752946681</Real>
+ <Real>-0.5741626172303782</Real>
+ <Real>0.15916277458664041</Real>
+ <Real>0.41861235601903246</Real>
+ <Real>-0.0072000023603441266</Real>
+ <Real>-0.5984000125885004</Real>
+ <Real>0.21840003225803317</Real>
+ <Real>0.38719998269081135</Real>
+ <Real>-0.017112486657502868</Real>
+ <Real>-0.63366246790587122</Real>
+ <Real>0.31866239578425104</Real>
+ <Real>0.33211255877912305</Real>
+ <Real>-0.20479996223449881</Real>
+ <Real>-0.52560005428790524</Real>
+ <Real>0.66559999527930691</Real>
+ <Real>0.064800021243097139</Real>
+ <Real>-0.03379998977184373</Real>
+ <Real>-0.65859999134540326</Real>
+ <Real>0.41859995200633771</Real>
+ <Real>0.27380002911090928</Real>
+ <Real>-0.34445001088380822</Real>
+ <Real>-0.29664998046159718</Real>
+ <Real>0.62664999357461904</Real>
+ <Real>0.014449997770786371</Real>
+ <Real>-0.41405002386570011</Real>
+ <Real>-0.16784995462894337</Real>
+ <Real>0.57784998085498707</Real>
+ <Real>0.0040499976396564108</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">8</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">16</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">9</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">0</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">5</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 10 5">3.9368318824602623e-05</Real>
+ <Real Name="Cell 0 10 6">0.00065323622565822059</Real>
+ <Real Name="Cell 0 10 7">0.011266406490666068</Real>
+ <Real Name="Cell 0 10 8">0.012548465905978405</Real>
+ <Real Name="Cell 0 10 9">0.0006680865255725832</Real>
+ <Real Name="Cell 0 4 0">6.3139563990237878e-07</Real>
+ <Real Name="Cell 0 4 10">1.0238491228872584e-05</Real>
+ <Real Name="Cell 0 4 8">2.3975471254174857e-07</Real>
+ <Real Name="Cell 0 4 9">8.3067961889104249e-06</Real>
+ <Real Name="Cell 0 5 0">2.4568921903458716e-05</Real>
+ <Real Name="Cell 0 5 1">4.1265985540490265e-07</Real>
+ <Real Name="Cell 0 5 10">0.00039802123933402675</Real>
+ <Real Name="Cell 0 5 2">3.5281336914636707e-07</Real>
+ <Real Name="Cell 0 5 3">1.1361525443963153e-08</Real>
+ <Real Name="Cell 0 5 8">9.320461940030214e-06</Real>
+ <Real Name="Cell 0 5 9">0.00032292661487872077</Real>
+ <Real Name="Cell 0 6 0">0.00024871377117768114</Real>
+ <Real Name="Cell 0 6 1">0.0038200183144798611</Real>
+ <Real Name="Cell 0 6 10">0.00051704360580639367</Real>
+ <Real Name="Cell 0 6 2">0.0032660156157182964</Real>
+ <Real Name="Cell 0 6 3">0.0001051743577862276</Real>
+ <Real Name="Cell 0 6 8">1.2107608270648624e-05</Real>
+ <Real Name="Cell 0 6 9">0.00041949304425843595</Real>
+ <Real Name="Cell 0 7 0">0.00074893221896923598</Real>
+ <Real Name="Cell 0 7 1">0.01315692850260362</Real>
+ <Real Name="Cell 0 7 10">3.4554888209782736e-05</Real>
+ <Real Name="Cell 0 7 2">0.011248829300506514</Real>
+ <Real Name="Cell 0 7 3">0.00036224211293842058</Real>
+ <Real Name="Cell 0 7 5">0.0010629440119686352</Real>
+ <Real Name="Cell 0 7 6">0.0072561820654140803</Real>
+ <Real Name="Cell 0 7 7">0.0062467776977057988</Real>
+ <Real Name="Cell 0 7 8">0.0037279204515623492</Real>
+ <Real Name="Cell 0 7 9">0.00022598774775221378</Real>
+ <Real Name="Cell 0 8 0">0.00016065965189781533</Real>
+ <Real Name="Cell 0 8 1">0.0028304552586849185</Real>
+ <Real Name="Cell 0 8 2">0.0024199651188624291</Real>
+ <Real Name="Cell 0 8 3">7.7929289748803488e-05</Real>
+ <Real Name="Cell 0 8 5">0.0092515508159670638</Real>
+ <Real Name="Cell 0 8 6">0.066631000313149322</Real>
+ <Real Name="Cell 0 8 7">0.15411420389413394</Real>
+ <Real Name="Cell 0 8 8">0.14461562717965634</Real>
+ <Real Name="Cell 0 8 9">0.0076953826676021374</Real>
+ <Real Name="Cell 0 9 5">0.0047635649214000271</Real>
+ <Real Name="Cell 0 9 6">0.037819174251502052</Real>
+ <Real Name="Cell 0 9 7">0.18012859510030349</Real>
+ <Real Name="Cell 0 9 8">0.1877983288061168</Real>
+ <Real Name="Cell 0 9 9">0.0099965661534688662</Real>
+ <Real Name="Cell 1 10 5">0.00072757552739804489</Real>
+ <Real Name="Cell 1 10 6">0.0080458297148575109</Real>
+ <Real Name="Cell 1 10 7">0.061586495423043654</Real>
+ <Real Name="Cell 1 10 8">0.058344215405201398</Real>
+ <Real Name="Cell 1 10 9">0.0027552792692082466</Real>
+ <Real Name="Cell 1 11 6">3.5863226380796118e-06</Real>
+ <Real Name="Cell 1 11 7">3.3387739675550008e-05</Real>
+ <Real Name="Cell 1 11 8">1.8158076814044073e-05</Real>
+ <Real Name="Cell 1 11 9">1.814560904838949e-07</Real>
+ <Real Name="Cell 1 4 0">0.00010980601729090598</Real>
+ <Real Name="Cell 1 4 10">0.0017805760348364051</Real>
+ <Real Name="Cell 1 4 8">4.1695742648786474e-05</Real>
+ <Real Name="Cell 1 4 9">0.0014446349456777325</Real>
+ <Real Name="Cell 1 5 0">0.0042687077726072898</Real>
+ <Real Name="Cell 1 5 10">0.069219874713131208</Real>
+ <Real Name="Cell 1 5 8">0.0016209215589522048</Real>
+ <Real Name="Cell 1 5 9">0.056160168389108561</Real>
+ <Real Name="Cell 1 6 0">0.0055452017148019759</Real>
+ <Real Name="Cell 1 6 10">0.089919054759559719</Real>
+ <Real Name="Cell 1 6 8">0.002105634184176365</Real>
+ <Real Name="Cell 1 6 9">0.072954036360432378</Real>
+ <Real Name="Cell 1 7 0">0.00037059509721009369</Real>
+ <Real Name="Cell 1 7 10">0.0060094406936914797</Real>
+ <Real Name="Cell 1 7 5">0.019644528219461749</Real>
+ <Real Name="Cell 1 7 6">0.1324355491257436</Real>
+ <Real Name="Cell 1 7 7">0.067583526693952761</Real>
+ <Real Name="Cell 1 7 8">0.015191941497319769</Real>
+ <Real Name="Cell 1 7 9">0.0056680092178851066</Real>
+ <Real Name="Cell 1 8 5">0.17098017302101526</Real>
+ <Real Name="Cell 1 8 6">1.1672436600278535</Real>
+ <Real Name="Cell 1 8 7">0.99356085528681715</Real>
+ <Real Name="Cell 1 8 8">0.58332648146984811</Real>
+ <Real Name="Cell 1 8 9">0.030836309309274869</Real>
+ <Real Name="Cell 1 9 5">0.088036608203257066</Real>
+ <Real Name="Cell 1 9 6">0.61884324706600524</Real>
+ <Real Name="Cell 1 9 7">0.95017516286955628</Real>
+ <Real Name="Cell 1 9 8">0.77316589815987258</Real>
+ <Real Name="Cell 1 9 9">0.04022287807020241</Real>
+ <Real Name="Cell 16 5 0">5.132404320263556e-08</Real>
+ <Real Name="Cell 16 5 1">9.0421214202722412e-07</Real>
+ <Real Name="Cell 16 5 2">7.7307770085524097e-07</Real>
+ <Real Name="Cell 16 5 3">2.4895150627876361e-08</Real>
+ <Real Name="Cell 16 6 0">0.0004751099057475562</Real>
+ <Real Name="Cell 16 6 1">0.0083703488417352472</Real>
+ <Real Name="Cell 16 6 2">0.0071564290470788501</Real>
+ <Real Name="Cell 16 6 3">0.00023045597989392565</Real>
+ <Real Name="Cell 16 7 0">0.0016363762019424991</Real>
+ <Real Name="Cell 16 7 1">0.028829202424270801</Real>
+ <Real Name="Cell 16 7 2">0.02464821305946872</Real>
+ <Real Name="Cell 16 7 3">0.00079373777842075372</Real>
+ <Real Name="Cell 16 8 0">0.00035203426278849478</Real>
+ <Real Name="Cell 16 8 1">0.0062020377772305695</Real>
+ <Real Name="Cell 16 8 2">0.0053025798732244849</Real>
+ <Real Name="Cell 16 8 3">0.00017075712378488035</Real>
+ <Real Name="Cell 17 5 0">8.8543667906245702e-07</Real>
+ <Real Name="Cell 17 5 1">1.5599367201908655e-05</Real>
+ <Real Name="Cell 17 5 2">1.3337050422936156e-05</Real>
+ <Real Name="Cell 17 5 3">4.2948836687859664e-07</Real>
+ <Real Name="Cell 17 6 0">0.0081965431966044069</Real>
+ <Real Name="Cell 17 6 1">0.14440432628736768</Real>
+ <Real Name="Cell 17 6 2">0.1234619171442481</Real>
+ <Real Name="Cell 17 6 3">0.0039758009068327537</Real>
+ <Real Name="Cell 17 7 0">0.028230580046554082</Real>
+ <Real Name="Cell 17 7 1">0.49735819046413043</Real>
+ <Real Name="Cell 17 7 2">0.42522822744173738</Real>
+ <Real Name="Cell 17 7 3">0.013693475780863551</Real>
+ <Real Name="Cell 17 8 0">0.0060732559071581234</Real>
+ <Real Name="Cell 17 8 1">0.10699686521596845</Real>
+ <Real Name="Cell 17 8 2">0.091479517599077478</Real>
+ <Real Name="Cell 17 8 3">0.0029458828879361811</Real>
+ <Real Name="Cell 18 5 0">7.4718189186791356e-07</Real>
+ <Real Name="Cell 18 5 1">1.3163634366497968e-05</Real>
+ <Real Name="Cell 18 5 2">1.1254562638515077e-05</Real>
+ <Real Name="Cell 18 5 3">3.6242674161567493e-07</Real>
+ <Real Name="Cell 18 6 0">0.006916709909624107</Real>
+ <Real Name="Cell 18 6 1">0.12185659376970091</Real>
+ <Real Name="Cell 18 6 2">0.10418419634835555</Real>
+ <Real Name="Cell 18 6 3">0.0033550072111344278</Real>
+ <Real Name="Cell 18 7 0">0.023822571061826277</Real>
+ <Real Name="Cell 18 7 1">0.4196991636719602</Real>
+ <Real Name="Cell 18 7 2">0.35883179336096283</Real>
+ <Real Name="Cell 18 7 3">0.011555334652531795</Real>
+ <Real Name="Cell 18 8 0">0.0051249591820764166</Real>
+ <Real Name="Cell 18 8 1">0.090290047912465352</Real>
+ <Real Name="Cell 18 8 2">0.077195626342492399</Real>
+ <Real Name="Cell 18 8 3">0.0024859037370804538</Real>
+ <Real Name="Cell 2 0 1">0.00014557358688998794</Real>
+ <Real Name="Cell 2 0 2">0.037675759798917609</Real>
+ <Real Name="Cell 2 0 3">0.087681540353607479</Real>
+ <Real Name="Cell 2 0 4">0.012446316692004146</Real>
+ <Real Name="Cell 2 1 1">0.00058229434755995176</Real>
+ <Real Name="Cell 2 1 2">0.15070303919567044</Real>
+ <Real Name="Cell 2 1 3">0.35072616141442992</Real>
+ <Real Name="Cell 2 1 4">0.049785266768016583</Real>
+ <Real Name="Cell 2 10 5">0.00064063291182019783</Real>
+ <Real Name="Cell 2 10 6">0.016067367864742034</Real>
+ <Real Name="Cell 2 10 7">0.11883665557286413</Real>
+ <Real Name="Cell 2 10 8">0.070160664175803231</Real>
+ <Real Name="Cell 2 10 9">0.0012445288545738981</Real>
+ <Real Name="Cell 2 11 6">2.5466645187382811e-05</Real>
+ <Real Name="Cell 2 11 7">0.00023708790472383055</Real>
+ <Real Name="Cell 2 11 8">0.00012894135474551734</Real>
+ <Real Name="Cell 2 11 9">1.2885282055708898e-06</Real>
+ <Real Name="Cell 2 2 1">0.00014557358688998794</Real>
+ <Real Name="Cell 2 2 2">0.037675759798917609</Real>
+ <Real Name="Cell 2 2 3">0.087681540353607479</Real>
+ <Real Name="Cell 2 2 4">0.012446316692004146</Real>
+ <Real Name="Cell 2 3 2">1.3896653536189814e-06</Real>
+ <Real Name="Cell 2 3 3">8.6333372981770328e-06</Real>
+ <Real Name="Cell 2 3 4">3.3104398920091251e-06</Real>
+ <Real Name="Cell 2 3 5">6.7782107158832729e-09</Real>
+ <Real Name="Cell 2 4 0">0.00026588867300879549</Real>
+ <Real Name="Cell 2 4 10">0.0053821817531829273</Real>
+ <Real Name="Cell 2 4 2">0.0001681493323822428</Real>
+ <Real Name="Cell 2 4 3">0.0010446335924586734</Real>
+ <Real Name="Cell 2 4 4">0.00040065824666590978</Real>
+ <Real Name="Cell 2 4 5">1.0005046766266776e-06</Real>
+ <Real Name="Cell 2 4 6">2.0037391255016578e-08</Real>
+ <Real Name="Cell 2 4 8">0.00026740416852910425</Real>
+ <Real Name="Cell 2 4 9">0.005369692940826034</Real>
+ <Real Name="Cell 2 5 0">0.0098320650706891308</Real>
+ <Real Name="Cell 2 5 10">0.18405744802597662</Real>
+ <Real Name="Cell 2 5 2">0.00032657092309448137</Real>
+ <Real Name="Cell 2 5 3">0.002028857162055594</Real>
+ <Real Name="Cell 2 5 4">0.00078076349230173754</Real>
+ <Real Name="Cell 2 5 5">6.9049276028999028e-06</Real>
+ <Real Name="Cell 2 5 6">5.90209753493568e-07</Real>
+ <Real Name="Cell 2 5 8">0.0075615432205544814</Real>
+ <Real Name="Cell 2 5 9">0.17239936614469817</Real>
+ <Real Name="Cell 2 6 0">0.012553689412396613</Real>
+ <Real Name="Cell 2 6 10">0.22819022739728018</Real>
+ <Real Name="Cell 2 6 2">3.7520901401691251e-05</Real>
+ <Real Name="Cell 2 6 3">0.00023312888358377476</Real>
+ <Real Name="Cell 2 6 4">9.2584842394106341e-05</Real>
+ <Real Name="Cell 2 6 5">6.235725654716531e-06</Real>
+ <Real Name="Cell 2 6 6">6.7250324459062679e-07</Real>
+ <Real Name="Cell 2 6 8">0.0085949831085865291</Real>
+ <Real Name="Cell 2 6 9">0.20820549639964436</Real>
+ <Real Name="Cell 2 7 0">0.00082191945841264958</Real>
+ <Real Name="Cell 2 7 10">0.014398556691109307</Real>
+ <Real Name="Cell 2 7 3">1.5867786277437549e-09</Real>
+ <Real Name="Cell 2 7 4">1.7424887022582369e-07</Real>
+ <Real Name="Cell 2 7 5">0.017297408182217682</Real>
+ <Real Name="Cell 2 7 6">0.11631939446940248</Real>
+ <Real Name="Cell 2 7 7">0.051166371516509511</Real>
+ <Real Name="Cell 2 7 8">0.004350396420061289</Real>
+ <Real Name="Cell 2 7 9">0.012883157212519267</Real>
+ <Real Name="Cell 2 8 5">0.15054866743208792</Real>
+ <Real Name="Cell 2 8 6">1.0205236077305906</Real>
+ <Real Name="Cell 2 8 7">0.58836363111277346</Real>
+ <Real Name="Cell 2 8 8">0.16949681681354267</Real>
+ <Real Name="Cell 2 8 9">0.007940732393002168</Real>
+ <Real Name="Cell 2 9 5">0.077516555376348481</Real>
+ <Real Name="Cell 2 9 6">0.55583195367941296</Real>
+ <Real Name="Cell 2 9 7">0.65387235798750443</Real>
+ <Real Name="Cell 2 9 8">0.33673831836642315</Real>
+ <Real Name="Cell 2 9 9">0.011490181362325803</Real>
+ <Real Name="Cell 3 0 1">0.0007106854132024348</Real>
+ <Real Name="Cell 3 0 2">0.18393180722162297</Real>
+ <Real Name="Cell 3 0 3">0.42805836599685543</Real>
+ <Real Name="Cell 3 0 4">0.06076250444931288</Real>
+ <Real Name="Cell 3 1 1">0.0028427416528097392</Real>
+ <Real Name="Cell 3 1 2">0.73572722888649189</Real>
+ <Real Name="Cell 3 1 3">1.7122334639874217</Real>
+ <Real Name="Cell 3 1 4">0.24305001779725152</Real>
+ <Real Name="Cell 3 10 0">6.5570188040891774e-05</Real>
+ <Real Name="Cell 3 10 1">0.053048687244270525</Real>
+ <Real Name="Cell 3 10 2">0.14870096974930153</Real>
+ <Real Name="Cell 3 10 3">0.025858924893137996</Real>
+ <Real Name="Cell 3 10 5">2.1891467943153414e-05</Real>
+ <Real Name="Cell 3 10 6">0.005069015919674757</Real>
+ <Real Name="Cell 3 10 7">0.045882618052900351</Real>
+ <Real Name="Cell 3 10 8">0.024920722707758577</Real>
+ <Real Name="Cell 3 10 9">0.0002490342357977776</Real>
+ <Real Name="Cell 3 11 0">8.5178018613957072e-05</Real>
+ <Real Name="Cell 3 11 1">0.068912141394508755</Real>
+ <Real Name="Cell 3 11 2">0.19316787625072074</Real>
+ <Real Name="Cell 3 11 3">0.033591667977389404</Real>
+ <Real Name="Cell 3 11 6">1.1020147532851824e-05</Real>
+ <Real Name="Cell 3 11 7">0.00010259473397798729</Real>
+ <Real Name="Cell 3 11 8">5.5796621106787217e-05</Real>
+ <Real Name="Cell 3 11 9">5.5758309825069386e-07</Real>
+ <Real Name="Cell 3 12 0">5.6925928823842461e-06</Real>
+ <Real Name="Cell 3 12 1">0.0046055164465631029</Real>
+ <Real Name="Cell 3 12 2">0.012909740040254374</Real>
+ <Real Name="Cell 3 12 3">0.002244988708908149</Real>
+ <Real Name="Cell 3 2 1">0.0007106854132024348</Real>
+ <Real Name="Cell 3 2 2">0.18942652991974782</Real>
+ <Real Name="Cell 3 2 3">0.45688625679255385</Real>
+ <Real Name="Cell 3 2 4">0.070184047364540661</Real>
+ <Real Name="Cell 3 2 5">5.3155561969079468e-06</Real>
+ <Real Name="Cell 3 3 2">0.056902195211874916</Real>
+ <Real Name="Cell 3 3 3">0.29870638450310633</Real>
+ <Real Name="Cell 3 3 4">0.097685539114643061</Real>
+ <Real Name="Cell 3 3 5">5.5738095444132192e-05</Real>
+ <Real Name="Cell 3 4 0">0.00031241653195321204</Real>
+ <Real Name="Cell 3 4 10">0.014581302981169915</Real>
+ <Real Name="Cell 3 4 2">0.054857381864426749</Real>
+ <Real Name="Cell 3 4 3">0.30848794008616515</Real>
+ <Real Name="Cell 3 4 4">0.10862308496535618</Real>
+ <Real Name="Cell 3 4 5">0.00060665047137282849</Real>
+ <Real Name="Cell 3 4 6">5.1425232362682741e-05</Real>
+ <Real Name="Cell 3 4 8">0.001597885638944696</Real>
+ <Real Name="Cell 3 4 9">0.020744207761907191</Real>
+ <Real Name="Cell 3 5 0">0.0077011097984351403</Real>
+ <Real Name="Cell 3 5 1">0.0011315118479777613</Real>
+ <Real Name="Cell 3 5 10">0.3431046101807379</Real>
+ <Real Name="Cell 3 5 2">0.04326939362003096</Real>
+ <Real Name="Cell 3 5 3">0.26114887521319613</Real>
+ <Real Name="Cell 3 5 4">0.10888606815620945</Real>
+ <Real Name="Cell 3 5 5">0.014214859401284977</Real>
+ <Real Name="Cell 3 5 6">0.0015147517623348083</Real>
+ <Real Name="Cell 3 5 8">0.036932215827313292</Real>
+ <Real Name="Cell 3 5 9">0.48339016841571658</Real>
+ <Real Name="Cell 3 6 0">0.0088956228781327841</Real>
+ <Real Name="Cell 3 6 1">0.026024768218852169</Real>
+ <Real Name="Cell 3 6 10">0.34876910664290012</Real>
+ <Real Name="Cell 3 6 2">0.034427350744566008</Real>
+ <Real Name="Cell 3 6 3">0.032277765916131164</Real>
+ <Real Name="Cell 3 6 4">0.02249274539694604</Real>
+ <Real Name="Cell 3 6 5">0.016118700053854015</Real>
+ <Real Name="Cell 3 6 6">0.0017259549997094888</Real>
+ <Real Name="Cell 3 6 8">0.037064708019645544</Real>
+ <Real Name="Cell 3 6 9">0.48798485732281677</Real>
+ <Real Name="Cell 3 7 0">0.0012673314288160686</Real>
+ <Real Name="Cell 3 7 1">0.026024765838498866</Real>
+ <Real Name="Cell 3 7 10">0.015738573073123159</Real>
+ <Real Name="Cell 3 7 2">0.029653418460105309</Real>
+ <Real Name="Cell 3 7 3">0.0016928027465487241</Real>
+ <Real Name="Cell 3 7 4">0.00068193632655410771</Real>
+ <Real Name="Cell 3 7 5">0.001481545973791003</Real>
+ <Real Name="Cell 3 7 6">0.004064771454758016</Real>
+ <Real Name="Cell 3 7 7">0.0016353091483799825</Real>
+ <Real Name="Cell 3 7 8">0.0016300334474656998</Real>
+ <Real Name="Cell 3 7 9">0.021682918306723812</Real>
+ <Real Name="Cell 3 8 0">3.8414476296381054e-05</Real>
+ <Real Name="Cell 3 8 1">0.0011315113719071008</Real>
+ <Real Name="Cell 3 8 2">0.0012892772678749086</Real>
+ <Real Name="Cell 3 8 3">7.0136272809158856e-05</Real>
+ <Real Name="Cell 3 8 5">0.0051444926824162412</Real>
+ <Real Name="Cell 3 8 6">0.036566636221130641</Real>
+ <Real Name="Cell 3 8 7">0.032901800624634298</Real>
+ <Real Name="Cell 3 8 8">0.010197182131828483</Real>
+ <Real Name="Cell 3 8 9">0.00010146007541164779</Real>
+ <Real Name="Cell 3 9 0">1.6866918218498779e-06</Real>
+ <Real Name="Cell 3 9 1">0.0013645955518532642</Real>
+ <Real Name="Cell 3 9 2">0.0038251027955094122</Real>
+ <Real Name="Cell 3 9 3">0.00066518090678473662</Real>
+ <Real Name="Cell 3 9 5">0.0026488667000631413</Real>
+ <Real Name="Cell 3 9 6">0.030448663600165269</Real>
+ <Real Name="Cell 3 9 7">0.12512696986734462</Real>
+ <Real Name="Cell 3 9 8">0.064087943874734418</Real>
+ <Real Name="Cell 3 9 9">0.00064021195201485737</Real>
+ <Real Name="Cell 4 0 1">0.00021654641549095449</Real>
+ <Real Name="Cell 4 0 2">0.056044169204399329</Real>
+ <Real Name="Cell 4 0 3">0.13042972749340867</Real>
+ <Real Name="Cell 4 0 4">0.01851438384736331</Real>
+ <Real Name="Cell 4 1 1">0.00086618566196381796</Real>
+ <Real Name="Cell 4 1 2">0.22417667681759731</Real>
+ <Real Name="Cell 4 1 3">0.52171890997363468</Real>
+ <Real Name="Cell 4 1 4">0.074057535389453241</Real>
+ <Real Name="Cell 4 10 0">0.00039491495173132397</Real>
+ <Real Name="Cell 4 10 1">0.31950068145932792</Real>
+ <Real Name="Cell 4 10 2">0.89559353183986712</Real>
+ <Real Name="Cell 4 10 3">0.15574266875106305</Real>
+ <Real Name="Cell 4 10 6">1.9684868577027566e-05</Real>
+ <Real Name="Cell 4 10 7">0.00018326105426731579</Real>
+ <Real Name="Cell 4 10 8">9.9667372896329544e-05</Real>
+ <Real Name="Cell 4 10 9">9.95989389172576e-07</Real>
+ <Real Name="Cell 4 11 0">0.00051300864180110078</Real>
+ <Real Name="Cell 4 11 1">0.41504280841077901</Real>
+ <Real Name="Cell 4 11 2">1.1634080182600961</Real>
+ <Real Name="Cell 4 11 3">0.2023152950177963</Real>
+ <Real Name="Cell 4 11 6">4.4074060640941977e-08</Real>
+ <Real Name="Cell 4 11 7">4.1031814803816576e-07</Real>
+ <Real Name="Cell 4 11 8">2.2315342466053253e-07</Real>
+ <Real Name="Cell 4 11 9">2.2300020223328006e-09</Real>
+ <Real Name="Cell 4 12 0">3.4285246245913893e-05</Real>
+ <Real Name="Cell 4 12 1">0.027738021798229848</Real>
+ <Real Name="Cell 4 12 2">0.077752550620741795</Real>
+ <Real Name="Cell 4 12 3">0.013521077704747895</Real>
+ <Real Name="Cell 4 2 1">0.00021654641549095449</Real>
+ <Real Name="Cell 4 2 2">0.080828050451617339</Real>
+ <Real Name="Cell 4 2 3">0.26045758537460462</Real>
+ <Real Name="Cell 4 2 4">0.061010140886432751</Real>
+ <Real Name="Cell 4 2 5">2.3975752878673684e-05</Real>
+ <Real Name="Cell 4 3 2">0.25620735053901378</Real>
+ <Real Name="Cell 4 3 3">1.3445201560158522</Real>
+ <Real Name="Cell 4 3 4">0.43953908991547852</Real>
+ <Real Name="Cell 4 3 5">0.00024921440496203633</Real>
+ <Real Name="Cell 4 4 0">0.00014789846741481761</Real>
+ <Real Name="Cell 4 4 10">0.0073823420171066452</Real>
+ <Real Name="Cell 4 4 2">0.19306673998131624</Real>
+ <Real Name="Cell 4 4 3">1.0561141440806694</Real>
+ <Real Name="Cell 4 4 4">0.36770226921625809</Real>
+ <Real Name="Cell 4 4 5">0.0033188803820038302</Real>
+ <Real Name="Cell 4 4 6">0.0001626491915834907</Real>
+ <Real Name="Cell 4 4 8">0.0008309899274023155</Real>
+ <Real Name="Cell 4 4 9">0.010658624871962234</Real>
+ <Real Name="Cell 4 5 0">0.0039679759770219532</Real>
+ <Real Name="Cell 4 5 1">0.016681845189954903</Real>
+ <Real Name="Cell 4 5 10">0.16979224505330873</Real>
+ <Real Name="Cell 4 5 2">0.10283084654977119</Real>
+ <Real Name="Cell 4 5 3">0.65328282906837465</Real>
+ <Real Name="Cell 4 5 4">0.63580125168951207</Real>
+ <Real Name="Cell 4 5 5">0.12378525434862332</Real>
+ <Real Name="Cell 4 5 6">0.0047909000751974766</Real>
+ <Real Name="Cell 4 5 8">0.019112585824847043</Real>
+ <Real Name="Cell 4 5 9">0.24514603116434824</Real>
+ <Real Name="Cell 4 6 0">0.01642751737502629</Real>
+ <Real Name="Cell 4 6 1">0.38368237620069789</Real>
+ <Real Name="Cell 4 6 10">0.16979134431366882</Real>
+ <Real Name="Cell 4 6 2">0.44667355482426851</Real>
+ <Real Name="Cell 4 6 3">0.28045412600392</Real>
+ <Real Name="Cell 4 6 4">0.66333327151699706</Real>
+ <Real Name="Cell 4 6 5">0.16818306217873083</Real>
+ <Real Name="Cell 4 6 6">0.0054588996979611799</Real>
+ <Real Name="Cell 4 6 8">0.01911248443350453</Real>
+ <Real Name="Cell 4 6 9">0.24514473067652107</Real>
+ <Real Name="Cell 4 7 0">0.013173796818948985</Real>
+ <Real Name="Cell 4 7 1">0.3836823411072206</Real>
+ <Real Name="Cell 4 7 10">0.0073821618691786604</Real>
+ <Real Name="Cell 4 7 2">0.43718664122512013</Real>
+ <Real Name="Cell 4 7 3">0.039821594929706855</Real>
+ <Real Name="Cell 4 7 4">0.051177852907122678</Real>
+ <Real Name="Cell 4 7 5">0.012303131733254044</Real>
+ <Real Name="Cell 4 7 6">0.00029696307708921546</Real>
+ <Real Name="Cell 4 7 8">0.0008309696491338133</Real>
+ <Real Name="Cell 4 7 9">0.0106583647743968</Real>
+ <Real Name="Cell 4 8 0">0.00056634347026476351</Real>
+ <Real Name="Cell 4 8 1">0.016681838171259455</Real>
+ <Real Name="Cell 4 8 2">0.019007776037038855</Real>
+ <Real Name="Cell 4 8 3">0.0010340169634934541</Real>
+ <Real Name="Cell 4 8 6">8.0198943008146383e-06</Real>
+ <Real Name="Cell 4 8 7">7.4663149460643202e-05</Real>
+ <Real Name="Cell 4 8 8">4.0605899538555062e-05</Real>
+ <Real Name="Cell 4 8 9">4.0578018566091689e-07</Real>
+ <Real Name="Cell 4 9 0">1.0158577233239914e-05</Real>
+ <Real Name="Cell 4 9 1">0.0082186615990308808</Real>
+ <Real Name="Cell 4 9 2">0.023037760466904516</Real>
+ <Real Name="Cell 4 9 3">0.0040062396272475273</Real>
+ <Real Name="Cell 4 9 6">5.0605444244849411e-05</Real>
+ <Real Name="Cell 4 9 7">0.0004711236464539991</Real>
+ <Real Name="Cell 4 9 8">0.00025622277651484457</Real>
+ <Real Name="Cell 4 9 9">2.5604684788728845e-06</Real>
+ <Real Name="Cell 5 0 1">5.1993448696228794e-08</Real>
+ <Real Name="Cell 5 0 2">1.3456374374266296e-05</Real>
+ <Real Name="Cell 5 0 3">3.1316571689799778e-05</Real>
+ <Real Name="Cell 5 0 4">4.4453595065413668e-06</Real>
+ <Real Name="Cell 5 1 1">2.0797379478491518e-07</Real>
+ <Real Name="Cell 5 1 2">5.3825497497065185e-05</Real>
+ <Real Name="Cell 5 1 3">0.00012526628675919911</Real>
+ <Real Name="Cell 5 1 4">1.7781438026165467e-05</Real>
+ <Real Name="Cell 5 10 0">0.00014713396409819641</Real>
+ <Real Name="Cell 5 10 1">0.11903677383977188</Real>
+ <Real Name="Cell 5 10 2">0.33367241727012076</Real>
+ <Real Name="Cell 5 10 3">0.058025243491328232</Real>
+ <Real Name="Cell 5 11 0">0.00019113227988435427</Real>
+ <Real Name="Cell 5 11 1">0.15463302517214483</Real>
+ <Real Name="Cell 5 11 2">0.43345239991493939</Real>
+ <Real Name="Cell 5 11 3">0.075376865887611208</Real>
+ <Real Name="Cell 5 12 0">1.2773697648389128e-05</Real>
+ <Real Name="Cell 5 12 1">0.010334389937690541</Real>
+ <Real Name="Cell 5 12 2">0.028968366331590625</Real>
+ <Real Name="Cell 5 12 3">0.0050375650576349254</Real>
+ <Real Name="Cell 5 2 1">5.1993448696228794e-08</Real>
+ <Real Name="Cell 5 2 2">0.0069979202004532481</Real>
+ <Real Name="Cell 5 2 3">0.036675087605562665</Real>
+ <Real Name="Cell 5 2 4">0.011980377411494514</Real>
+ <Real Name="Cell 5 2 5">6.7567213147013654e-06</Real>
+ <Real Name="Cell 5 3 2">0.072145578843287039</Real>
+ <Real Name="Cell 5 3 3">0.37854881086515846</Real>
+ <Real Name="Cell 5 3 4">0.12373178241247922</Real>
+ <Real Name="Cell 5 3 5">6.9952146412871448e-05</Real>
+ <Real Name="Cell 5 4 0">1.2993518591326576e-06</Real>
+ <Real Name="Cell 5 4 10">6.48570603357018e-05</Real>
+ <Real Name="Cell 5 4 2">0.047461531839977013</Real>
+ <Real Name="Cell 5 4 3">0.2593289702602522</Real>
+ <Real Name="Cell 5 4 4">0.10214709961083704</Real>
+ <Real Name="Cell 5 4 5">0.0037084177585585878</Real>
+ <Real Name="Cell 5 4 6">3.2079146666437109e-05</Real>
+ <Real Name="Cell 5 4 8">7.3006051108176207e-06</Real>
+ <Real Name="Cell 5 4 9">9.3640619035881791e-05</Real>
+ <Real Name="Cell 5 5 0">0.00046157513356384074</Real>
+ <Real Name="Cell 5 5 1">0.012715584339562609</Real>
+ <Real Name="Cell 5 5 10">0.0014916981435483157</Real>
+ <Real Name="Cell 5 5 2">0.024738827199646898</Real>
+ <Real Name="Cell 5 5 3">0.36110379307448548</Real>
+ <Real Name="Cell 5 5 4">0.95358495979718705</Real>
+ <Real Name="Cell 5 5 5">0.18763322273448055</Real>
+ <Real Name="Cell 5 5 6">0.0009449047036770153</Real>
+ <Real Name="Cell 5 5 8">0.00016791231416005478</Real>
+ <Real Name="Cell 5 5 9">0.0021537136720895821</Real>
+ <Real Name="Cell 5 6 0">0.0099587605161680463</Real>
+ <Real Name="Cell 5 6 1">0.2924583916605063</Real>
+ <Real Name="Cell 5 6 10">0.0014916902301618813</Real>
+ <Real Name="Cell 5 6 2">0.33454656561073542</Real>
+ <Real Name="Cell 5 6 3">0.46685456419554205</Real>
+ <Real Name="Cell 5 6 4">1.3797609665697212</Real>
+ <Real Name="Cell 5 6 5">0.27521282678161574</Real>
+ <Real Name="Cell 5 6 6">0.0010766536393042895</Real>
+ <Real Name="Cell 5 6 8">0.00016791142339335724</Real>
+ <Real Name="Cell 5 6 9">0.0021537022467428188</Real>
+ <Real Name="Cell 5 7 0">0.0099301742793222406</Real>
+ <Real Name="Cell 5 7 1">0.29245836491082339</Real>
+ <Real Name="Cell 5 7 10">6.4855477658414885e-05</Real>
+ <Real Name="Cell 5 7 2">0.33325287008517934</Real>
+ <Real Name="Cell 5 7 3">0.053887296781903044</Real>
+ <Real Name="Cell 5 7 4">0.11130775837033037</Real>
+ <Real Name="Cell 5 7 5">0.022013802141037347</Real>
+ <Real Name="Cell 5 7 6">5.8569747637333812e-05</Real>
+ <Real Name="Cell 5 7 8">7.3004269574781102e-06</Real>
+ <Real Name="Cell 5 7 9">9.3638333966529074e-05</Real>
+ <Real Name="Cell 5 8 0">0.00043169014454399443</Real>
+ <Real Name="Cell 5 8 1">0.012715578989626023</Real>
+ <Real Name="Cell 5 8 2">0.014488503912746004</Real>
+ <Real Name="Cell 5 8 3">0.00078816999906920922</Real>
+ <Real Name="Cell 5 9 0">3.7847939951920602e-06</Real>
+ <Real Name="Cell 5 9 1">0.0030620371686249331</Real>
+ <Real Name="Cell 5 9 2">0.0085832076161716959</Real>
+ <Real Name="Cell 5 9 3">0.0014926097755985647</Real>
+ <Real Name="Cell 6 10 0">2.4926471293158858e-07</Real>
+ <Real Name="Cell 6 10 1">0.0002016642958091611</Real>
+ <Real Name="Cell 6 10 2">0.00056528592710597284</Real>
+ <Real Name="Cell 6 10 3">9.8302562228245956e-05</Real>
+ <Real Name="Cell 6 11 0">3.2380377412748318e-07</Real>
+ <Real Name="Cell 6 11 1">0.00026196913041473801</Real>
+ <Real Name="Cell 6 11 2">0.00073432663013277657</Real>
+ <Real Name="Cell 6 11 3">0.00012769854297284291</Real>
+ <Real Name="Cell 6 12 0">2.1640360856964461e-08</Real>
+ <Real Name="Cell 6 12 1">1.7507845703268913e-05</Real>
+ <Real Name="Cell 6 12 2">4.90763064938692e-05</Real>
+ <Real Name="Cell 6 12 3">8.5343123571898908e-06</Real>
+ <Real Name="Cell 6 2 2">3.9747493701031309e-07</Real>
+ <Real Name="Cell 6 2 3">2.0853398265340585e-06</Real>
+ <Real Name="Cell 6 2 4">6.8153160450628412e-07</Real>
+ <Real Name="Cell 6 2 5">3.8451446608248141e-10</Real>
+ <Real Name="Cell 6 3 2">4.1033779584782283e-06</Real>
+ <Real Name="Cell 6 3 3">2.1528244131565571e-05</Real>
+ <Real Name="Cell 6 3 4">7.0358694436746982e-06</Real>
+ <Real Name="Cell 6 3 5">3.9695790549881638e-09</Real>
+ <Real Name="Cell 6 4 2">2.7846445770653399e-06</Real>
+ <Real Name="Cell 6 4 3">0.00076804086733975113</Real>
+ <Real Name="Cell 6 4 4">0.002349562731018647</Real>
+ <Real Name="Cell 6 4 5">0.00045389420229477798</Real>
+ <Real Name="Cell 6 5 0">1.0860024762991741e-05</Real>
+ <Real Name="Cell 6 5 1">0.00031988569683235593</Real>
+ <Real Name="Cell 6 5 2">0.00038394367077000782</Real>
+ <Real Name="Cell 6 5 3">0.040343690042915749</Real>
+ <Real Name="Cell 6 5 4">0.12520941339310562</Real>
+ <Real Name="Cell 6 5 5">0.024230928563847662</Real>
+ <Real Name="Cell 6 6 0">0.00024978052842572604</Real>
+ <Real Name="Cell 6 6 1">0.0073573698158498589</Real>
+ <Real Name="Cell 6 6 2">0.0084120041315793974</Real>
+ <Real Name="Cell 6 6 3">0.060242390521747839</Real>
+ <Real Name="Cell 6 6 4">0.18564294970091513</Real>
+ <Real Name="Cell 6 6 5">0.035926236314377316</Real>
+ <Real Name="Cell 6 7 0">0.00024978050557957035</Real>
+ <Real Name="Cell 6 7 1">0.0073573691429086293</Real>
+ <Real Name="Cell 6 7 2">0.0083855330326609578</Real>
+ <Real Name="Cell 6 7 3">0.0052941796826830286</Real>
+ <Real Name="Cell 6 7 4">0.015022925983743229</Real>
+ <Real Name="Cell 6 7 5">0.0029072862174129633</Real>
+ <Real Name="Cell 6 8 0">1.0860020193760609e-05</Real>
+ <Real Name="Cell 6 8 1">0.00031988556224410989</Real>
+ <Real Name="Cell 6 8 2">0.00036448699850678612</Real>
+ <Real Name="Cell 6 8 3">1.9827976649894474e-05</Real>
+ <Real Name="Cell 6 9 0">6.4119497799102226e-09</Real>
+ <Real Name="Cell 6 9 1">5.18750256272409e-06</Real>
+ <Real Name="Cell 6 9 2">1.4541107456667027e-05</Real>
+ <Real Name="Cell 6 9 3">2.5286815964881614e-06</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>0.00055680649486861621</Real>
+ <Real>0.13155676367522579</Real>
+ <Real>0.58312216819554608</Real>
+ <Real>0.27685812037771235</Real>
+ <Real>0.0079061412566471846</Real>
+ <Real>0.0089089101651006128</Real>
+ <Real>0.28736974193084774</Real>
+ <Real>0.57897075870228831</Real>
+ <Real>0.12431368289967992</Real>
+ <Real>0.00043690630208344738</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0</Real>
+ <Real>0.041633615792825124</Real>
+ <Real>0.45823414137123475</Real>
+ <Real>0.4584325056212426</Real>
+ <Real>0.041699737214697399</Real>
+ <Real>6.4512288017413517e-17</Real>
+ <Real>1.6006714642896532e-05</Real>
+ <Real>0.070293332330147548</Real>
+ <Real>0.5221574156457981</Real>
+ <Real>0.38474124976356439</Real>
+ <Real>0.022791995545847068</Real>
+ <Real>2.7306725260463809e-05</Real>
+ <Real>0.07530679536916321</Real>
+ <Real>0.53004920643788322</Real>
+ <Real>0.3738720599463905</Real>
+ <Real>0.02074463152130257</Real>
+ <Real>0.017066662597656615</Real>
+ <Real>0.35206664066314697</Real>
+ <Real>0.5447333499272653</Real>
+ <Real>0.086066680081686067</Real>
+ <Real>6.666673024497716e-05</Real>
+ <Real>0.00069983918426549322</Real>
+ <Real>0.13904326676503828</Real>
+ <Real>0.58680435526295316</Real>
+ <Real>0.26646202753774184</Real>
+ <Real>0.006990511250001127</Real>
+ <Real>0.00019040663873036857</Real>
+ <Real>0.10406770362683616</Real>
+ <Real>0.5637877706041462</Real>
+ <Real>0.31945971181953425</Real>
+ <Real>0.012494407310752881</Real>
+ <Real>4.1666706403110725e-06</Real>
+ <Real>0.060983338602384092</Real>
+ <Real>0.50535834372838317</Real>
+ <Real>0.40631665389537802</Real>
+ <Real>0.027337497103214377</Real>
+ <Real>0.0035429389988709558</Real>
+ <Real>0.21663888845184356</Real>
+ <Real>0.5979589752382396</Real>
+ <Real>0.17999359002553345</Real>
+ <Real>0.0018656072855123651</Real>
+ <Real>0.0061568068560727456</Real>
+ <Real>0.25619410909844714</Real>
+ <Real>0.59001017262631739</Real>
+ <Real>0.14677010479610444</Real>
+ <Real>0.00086880662305831996</Real>
+ <Real>0.0015617074790447547</Real>
+ <Real>0.17135053108134043</Real>
+ <Real>0.59671157761250604</Real>
+ <Real>0.22627847883524646</Real>
+ <Real>0.0040977049918622353</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>0.013391617172245837</Real>
+ <Real>0.32646347852484026</Real>
+ <Real>0.55999463520774495</Real>
+ <Real>0.099995033965726746</Real>
+ <Real>0.00015523512944212931</Real>
+ <Real>0.00064654452700266306</Real>
+ <Real>0.13637341505766881</Real>
+ <Real>0.58555883494629768</Real>
+ <Real>0.27011715754497401</Real>
+ <Real>0.0073040479240566785</Real>
+ <Real>0.00015523565817055968</Real>
+ <Real>0.099995099319446945</Real>
+ <Real>0.5599946983171572</Real>
+ <Real>0.32646336449927055</Real>
+ <Real>0.013391602205954676</Real>
+ <Real>0.0067871694226328706</Real>
+ <Real>0.26403411642505714</Real>
+ <Real>0.58760174928538256</Real>
+ <Real>0.14083980990471962</Real>
+ <Real>0.00073715496220775755</Real>
+ <Real>7.9820311975637406e-06</Real>
+ <Real>0.064974183875945363</Real>
+ <Real>0.51293039122777406</Real>
+ <Real>0.39683182136468764</Real>
+ <Real>0.025255621500395283</Real>
+ <Real>0.017066659486061366</Real>
+ <Real>0.35206662077810369</Real>
+ <Real>0.54473336261674044</Real>
+ <Real>0.086066690340230678</Real>
+ <Real>6.6666778863712974e-05</Real>
+ <Real>0.011051788298338951</Real>
+ <Real>0.30742184274810441</Real>
+ <Real>0.56991289942021961</Real>
+ <Real>0.11134864536861958</Real>
+ <Real>0.00026482416471736544</Real>
+ <Real>0.00010402239381387114</Real>
+ <Real>0.092858260504505463</Real>
+ <Real>0.55264643128266311</Real>
+ <Real>0.33924559891274259</Real>
+ <Real>0.015145686906274896</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0</Real>
+ <Real>0.019164974400796734</Real>
+ <Real>0.36489953061317437</Real>
+ <Real>0.53627727048142182</Real>
+ <Real>0.079617816820449078</Real>
+ <Real>4.0407684157884067e-05</Real>
+ <Real>0.016084673911882248</Real>
+ <Real>0.34565295698911602</Real>
+ <Real>0.54875914803294235</Real>
+ <Real>0.08941942896195168</Real>
+ <Real>8.3792104107546423e-05</Real>
+ <Real>0.025255621500395283</Real>
+ <Real>0.39683182136468764</Real>
+ <Real>0.51293039122777406</Real>
+ <Real>0.064974183875945363</Real>
+ <Real>7.9820311975637406e-06</Real>
+ <Real>0.00083697607326539626</Real>
+ <Real>0.14538926247215167</Real>
+ <Real>0.58947935175907284</Real>
+ <Real>0.25799620909470156</Real>
+ <Real>0.006298200600808445</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>1.7067008466108632e-06</Real>
+ <Real>0.056678590590662367</Real>
+ <Real>0.4964877539430167</Real>
+ <Real>0.41698229408180587</Real>
+ <Real>0.029849654683668386</Real>
+ <Real>0.00022143407849568522</Real>
+ <Real>0.1072864642102718</Real>
+ <Real>0.56659546340401901</Real>
+ <Real>0.3140640443829672</Real>
+ <Real>0.011832593924246375</Real>
+ <Real>6.6668001820736845e-09</Real>
+ <Real>0.045101324376820941</Real>
+ <Real>0.46822942234059373</Real>
+ <Real>0.44823725565695222</Real>
+ <Real>0.038431990958832915</Real>
+ <Real>0.0083962803385882814</Real>
+ <Real>0.28210008780463808</Real>
+ <Real>0.58110471898080385</Real>
+ <Real>0.1279047767269117</Real>
+ <Real>0.00049413614905794139</Real>
+ <Real>0.00033750300408412384</Real>
+ <Real>0.1173168960890562</Real>
+ <Real>0.57435849488551072</Real>
+ <Real>0.29798297751749492</Real>
+ <Real>0.010004128503854031</Real>
+ <Real>0.0015617068443743462</Real>
+ <Real>0.17135051200737639</Real>
+ <Real>0.59671157426940269</Real>
+ <Real>0.22627850057854337</Real>
+ <Real>0.0040977063003031534</Real>
+ <Real>0.00029470123073821155</Real>
+ <Real>0.11391109924980138</Real>
+ <Real>0.57188208654989214</Real>
+ <Real>0.30332392449946483</Real>
+ <Real>0.010588188470103232</Real>
+ <Real>0.024987309509989539</Real>
+ <Real>0.39556278684045149</Real>
+ <Real>0.5139211628158693</Real>
+ <Real>0.065520100840899334</Real>
+ <Real>8.6399927902244245e-06</Real>
+ <Real>0.0094446287242976913</Real>
+ <Real>0.29266458295212366</Real>
+ <Real>0.5767216570041318</Real>
+ <Real>0.12078433044702153</Real>
+ <Real>0.00038480087242524205</Real>
+ <Real>0.00069983941600817838</Real>
+ <Real>0.1390432781007275</Real>
+ <Real>0.58680436039658534</Real>
+ <Real>0.26646201213876175</Real>
+ <Real>0.0069905099479172436</Real>
+ <Real>0.00013823988464359079</Real>
+ <Real>0.097817691333339188</Real>
+ <Real>0.55785075794125749</Real>
+ <Real>0.33029240051099151</Real>
+ <Real>0.013900910329768222</Real>
+ <Real>0.0012965402060794952</Real>
+ <Real>0.16292851360064831</Real>
+ <Real>0.59496857499371825</Real>
+ <Real>0.23609116507560096</Real>
+ <Real>0.0047152061239528892</Real>
+ <Real>0.0005568068853187883</Real>
+ <Real>0.13155678562547082</Real>
+ <Real>0.58312217987233406</Real>
+ <Real>0.27685808921624516</Real>
+ <Real>0.0079061384006310718</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>-0.006550665150801457</Real>
+ <Real>-0.36826398403358446</Real>
+ <Real>-0.19590403076839413</Real>
+ <Real>0.52280267424074744</Real>
+ <Real>0.047916005712032542</Real>
+ <Real>-0.052405348767599988</Real>
+ <Real>-0.5282453503697675</Real>
+ <Real>0.21916807695770019</Real>
+ <Real>0.35602129226430196</Real>
+ <Real>0.0054613299153652957</Real>
+ <Real>-0.16666666666666666</Real>
+ <Real>-0.5</Real>
+ <Real>0.5</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>-0.16656750421064892</Real>
+ <Real>-0.50009912311154159</Real>
+ <Real>0.4999007588563309</Real>
+ <Real>0.16676586846455876</Real>
+ <Real>1.30088532538745e-12</Real>
+ <Real>-0.00045733436139501672</Real>
+ <Real>-0.24463739635976395</Real>
+ <Real>-0.40334390965651279</Real>
+ <Real>0.54242934583789748</Real>
+ <Real>0.10600929453977423</Real>
+ <Real>-0.00068266776530006841</Real>
+ <Real>-0.25673605225372448</Real>
+ <Real>-0.38569592247771456</Real>
+ <Real>0.54433067277780289</Real>
+ <Real>0.098783969718936201</Real>
+ <Real>-0.085333318074545181</Real>
+ <Real>-0.54533333237965653</Real>
+ <Real>0.34799995326995647</Real>
+ <Real>0.28133336289723732</Real>
+ <Real>0.0013333342870078769</Real>
+ <Real>-0.0077759932022114535</Real>
+ <Real>-0.380362603640236</Real>
+ <Real>-0.17225612496184839</Real>
+ <Real>0.51670403365325068</Real>
+ <Real>0.043690688151045189</Real>
+ <Real>-0.0029293330109914262</Real>
+ <Real>-0.31874932737477618</Real>
+ <Real>-0.28617601027297962</Real>
+ <Real>0.54031733471425358</Real>
+ <Real>0.06753733594449364</Real>
+ <Real>-0.00016666678587598462</Real>
+ <Real>-0.22100001382827775</Real>
+ <Real>-0.43599998164176873</Real>
+ <Real>0.53566667191187467</Real>
+ <Real>0.12149999034404779</Real>
+ <Real>-0.02624399443817178</Real>
+ <Real>-0.47749064924112866</Real>
+ <Real>0.049935952499389424</Real>
+ <Real>0.43757602047729433</Real>
+ <Real>0.016222670702616706</Real>
+ <Real>-0.039721334249814354</Real>
+ <Real>-0.50998133500798537</Real>
+ <Real>0.1482720057544708</Real>
+ <Real>0.39228533051427206</Real>
+ <Real>0.0091453329890569101</Real>
+ <Real>-0.014197338872274482</Real>
+ <Real>-0.4266773649648018</Real>
+ <Real>-0.074783929092406609</Real>
+ <Real>0.48638930856831658</Real>
+ <Real>0.02926932436116628</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>-0.071142963187526845</Real>
+ <Real>-0.5420256500766063</Real>
+ <Real>0.2999935207102592</Real>
+ <Real>0.31066176155940806</Real>
+ <Real>0.0025133309944659421</Real>
+ <Real>-0.0073275030978816038</Real>
+ <Real>-0.37611104286383373</Real>
+ <Real>-0.18064310353979574</Real>
+ <Real>0.51892934806261926</Real>
+ <Real>0.045152301438891845</Real>
+ <Real>-0.0025133374147378422</Real>
+ <Real>-0.3106618930365993</Real>
+ <Real>-0.29999329812638303</Real>
+ <Real>0.54202562502151552</Real>
+ <Real>0.071142903556204715</Real>
+ <Real>-0.042734015047808917</Real>
+ <Real>-0.51517722051785497</Real>
+ <Real>0.16664141639923086</Real>
+ <Real>0.38318488894633901</Real>
+ <Real>0.0080849302200940651</Real>
+ <Real>-0.00027138900362524455</Real>
+ <Real>-0.23132507057519683</Real>
+ <Real>-0.42204353782552023</Real>
+ <Real>0.53914784339113198</Real>
+ <Real>0.11449215401321031</Real>
+ <Real>-0.085333306406062043</Real>
+ <Real>-0.54533333165037079</Real>
+ <Real>0.34799991753521659</Real>
+ <Real>0.28133338550492759</Real>
+ <Real>0.0013333350162886739</Real>
+ <Real>-0.061600125763086246</Real>
+ <Real>-0.5365984249121909</Real>
+ <Real>0.26174890366836245</Real>
+ <Real>0.33269797045219296</Real>
+ <Real>0.0037516765547217332</Real>
+ <Real>-0.0018614540225098352</Real>
+ <Real>-0.29596819811893638</Real>
+ <Real>-0.3244560140749726</Real>
+ <Real>0.54426243859679369</Real>
+ <Real>0.078023227619625074</Real>
+ <Real>-0.16666666666666666</Real>
+ <Real>-0.5</Real>
+ <Real>0.5</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>-0.093086856262166257</Real>
+ <Real>-0.54518619339739227</Real>
+ <Real>0.37054887053917146</Real>
+ <Real>0.26680826416249903</Real>
+ <Real>0.00091591495788805532</Real>
+ <Real>-0.081623718615090907</Real>
+ <Real>-0.54494687552319687</Real>
+ <Real>0.33634764661742239</Real>
+ <Real>0.28864020779510946</Real>
+ <Real>0.0015827397257558828</Real>
+ <Real>-0.11449215401321031</Real>
+ <Real>-0.53914784339113198</Real>
+ <Real>0.42204353782552023</Real>
+ <Real>0.23132507057519683</Real>
+ <Real>0.00027138900362524455</Real>
+ <Real>-0.0088928703984411054</Real>
+ <Real>-0.39019554519350719</Real>
+ <Real>-0.15252674635119567</Real>
+ <Real>0.51121160987667746</Real>
+ <Real>0.040403552066466536</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>-8.5334615078031984e-05</Real>
+ <Real>-0.20952556052149823</Real>
+ <Real>-0.45091171128824992</Real>
+ <Real>0.53074144260130673</Real>
+ <Real>0.12978116382351942</Real>
+ <Real>-0.0032805036499513811</Real>
+ <Real>-0.32499472917143468</Real>
+ <Real>-0.27533289072179101</Real>
+ <Real>0.53877198355769151</Real>
+ <Real>0.064836139985485555</Real>
+ <Real>-1.3333533605942498e-06</Real>
+ <Real>-0.17686138532384696</Real>
+ <Real>-0.48940794404409876</Real>
+ <Real>0.50940537747318082</Real>
+ <Real>0.15686528524812551</Real>
+ <Real>-0.050127076764796274</Real>
+ <Real>-0.52560789097200256</Real>
+ <Real>0.20758653404799854</Real>
+ <Real>0.36215891187919591</Real>
+ <Real>0.0059895218096044133</Real>
+ <Real>-0.0045000300408078141</Real>
+ <Real>-0.34366708056127543</Real>
+ <Real>-0.24199924564334835</Real>
+ <Real>0.5329998531337542</Real>
+ <Real>0.057166503111677383</Real>
+ <Real>-0.014197334544976585</Real>
+ <Real>-0.42667734025271725</Real>
+ <Real>-0.074783984488964061</Real>
+ <Real>0.48638932791598627</Real>
+ <Real>0.029269331370671631</Real>
+ <Real>-0.0040648417547602001</Real>
+ <Real>-0.33745745786221498</Real>
+ <Real>-0.25323877615640017</Real>
+ <Real>0.53510929291848619</Real>
+ <Real>0.059651782854889167</Real>
+ <Real>-0.11357867635981268</Real>
+ <Real>-0.53955199577426827</Real>
+ <Real>0.42012802044773023</Real>
+ <Real>0.23271465186659512</Real>
+ <Real>0.0002879998197555918</Real>
+ <Real>-0.054751478149118946</Real>
+ <Real>-0.53071064483872299</Real>
+ <Real>0.23064089520203584</Real>
+ <Real>0.34985605670857323</Real>
+ <Real>0.004965171077232872</Real>
+ <Real>-0.0077759951334009786</Real>
+ <Real>-0.38036262154547246</Real>
+ <Real>-0.17225608946132426</Real>
+ <Real>0.51670402409266991</Real>
+ <Real>0.043690682047527844</Real>
+ <Real>-0.0023039985580447344</Real>
+ <Real>-0.30625063538424174</Real>
+ <Real>-0.30742405243110466</Real>
+ <Real>0.5428160052471136</Real>
+ <Real>0.073162681126277593</Real>
+ <Real>-0.012348001471996365</Real>
+ <Real>-0.41547467613283784</Real>
+ <Real>-0.099487979458808773</Real>
+ <Real>0.4947919932041166</Real>
+ <Real>0.032518663859526398</Real>
+ <Real>-0.0065506685959499985</Real>
+ <Real>-0.36826402032089212</Real>
+ <Real>-0.19590396084022466</Real>
+ <Real>0.52280265702692574</Real>
+ <Real>0.047915992730141049</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">7</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">0</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">4</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 3 0">2.4038114646503656e-07</Real>
+ <Real Name="Cell 0 3 10">1.3744169255185129e-11</Real>
+ <Real Name="Cell 0 3 11">4.5643625464317996e-07</Real>
+ <Real Name="Cell 0 3 12">3.9982471074940497e-06</Real>
+ <Real Name="Cell 0 3 13">3.3579846389930545e-06</Real>
+ <Real Name="Cell 0 4 0">3.3761656553106184e-05</Real>
+ <Real Name="Cell 0 4 1">0.0030613639575252432</Real>
+ <Real Name="Cell 0 4 10">3.3505806257523221e-10</Real>
+ <Real Name="Cell 0 4 11">1.1127092829720778e-05</Real>
+ <Real Name="Cell 0 4 12">9.7470054730924369e-05</Real>
+ <Real Name="Cell 0 4 13">8.1861610287863737e-05</Real>
+ <Real Name="Cell 0 4 2">0.010660903694456762</Real>
+ <Real Name="Cell 0 4 3">0.0040427124373237184</Real>
+ <Real Name="Cell 0 4 4">7.3209996452955803e-05</Real>
+ <Real Name="Cell 0 5 0">0.00058563158095855294</Real>
+ <Real Name="Cell 0 5 1">0.063152608416313441</Real>
+ <Real Name="Cell 0 5 10">0.00068239171632767097</Real>
+ <Real Name="Cell 0 5 11">0.00016835571402374467</Real>
+ <Real Name="Cell 0 5 12">0.00016777058988978752</Real>
+ <Real Name="Cell 0 5 13">0.00014042018665552742</Real>
+ <Real Name="Cell 0 5 2">0.21992284671839957</Real>
+ <Real Name="Cell 0 5 3">0.083396760083518956</Real>
+ <Real Name="Cell 0 5 4">0.0015102425919624064</Real>
+ <Real Name="Cell 0 5 6">1.1612402470787594e-06</Real>
+ <Real Name="Cell 0 5 7">0.00014592617066762326</Real>
+ <Real Name="Cell 0 5 8">0.00054267958666784138</Real>
+ <Real Name="Cell 0 5 9">0.00054067388179342612</Real>
+ <Real Name="Cell 0 6 0">0.00089235766783298377</Real>
+ <Real Name="Cell 0 6 1">0.097712565492877948</Real>
+ <Real Name="Cell 0 6 10">0.026448413158310487</Real>
+ <Real Name="Cell 0 6 11">0.0058102635075056005</Real>
+ <Real Name="Cell 0 6 12">5.2288557836028981e-05</Real>
+ <Real Name="Cell 0 6 13">2.5074028305439302e-05</Real>
+ <Real Name="Cell 0 6 2">0.34027455242530774</Real>
+ <Real Name="Cell 0 6 3">0.12903523046642151</Real>
+ <Real Name="Cell 0 6 4">0.0023367154877349532</Real>
+ <Real Name="Cell 0 6 6">1.8246119276179033e-05</Real>
+ <Real Name="Cell 0 6 7">0.0022928815309455307</Real>
+ <Real Name="Cell 0 6 8">0.0087541406888681124</Real>
+ <Real Name="Cell 0 6 9">0.016129790823298878</Real>
+ <Real Name="Cell 0 7 0">0.00014070976948887473</Real>
+ <Real Name="Cell 0 7 1">0.015438373512183686</Real>
+ <Real Name="Cell 0 7 10">0.058798419436105316</Real>
+ <Real Name="Cell 0 7 11">0.012923025924008376</Real>
+ <Real Name="Cell 0 7 12">4.9972017340616792e-05</Real>
+ <Real Name="Cell 0 7 13">3.8925633356598415e-08</Real>
+ <Real Name="Cell 0 7 2">0.053762641585906677</Real>
+ <Real Name="Cell 0 7 3">0.020387286672117096</Real>
+ <Real Name="Cell 0 7 4">0.00036919598118612611</Real>
+ <Real Name="Cell 0 7 6">2.3584270703226314e-05</Real>
+ <Real Name="Cell 0 7 7">0.002963695342430731</Real>
+ <Real Name="Cell 0 7 8">0.011670900942034709</Real>
+ <Real Name="Cell 0 7 9">0.032796874107813463</Real>
+ <Real Name="Cell 0 8 0">1.0899084515889616e-07</Real>
+ <Real Name="Cell 0 8 1">1.1958478116022732e-05</Real>
+ <Real Name="Cell 0 8 10">0.014083454466678687</Real>
+ <Real Name="Cell 0 8 11">0.0030974648587453659</Real>
+ <Real Name="Cell 0 8 12">1.1966475344471613e-05</Real>
+ <Real Name="Cell 0 8 2">4.1644242663079643e-05</Real>
+ <Real Name="Cell 0 8 3">1.5791878679524813e-05</Real>
+ <Real Name="Cell 0 8 4">2.8597715025184313e-07</Real>
+ <Real Name="Cell 0 8 6">2.987478939556591e-06</Real>
+ <Real Name="Cell 0 8 7">0.00037541874964836414</Real>
+ <Real Name="Cell 0 8 8">0.0015742548438927978</Real>
+ <Real Name="Cell 0 8 9">0.0073756061587431469</Real>
+ <Real Name="Cell 0 9 10">7.3657209093621774e-05</Real>
+ <Real Name="Cell 0 9 11">1.6212117812662444e-05</Real>
+ <Real Name="Cell 0 9 12">6.263248073312284e-08</Real>
+ <Real Name="Cell 0 9 6">3.6700961328170883e-10</Real>
+ <Real Name="Cell 0 9 7">4.6119920144976405e-08</Real>
+ <Real Name="Cell 0 9 8">1.2326576585445708e-06</Real>
+ <Real Name="Cell 0 9 9">3.5823429323979585e-05</Real>
+ <Real Name="Cell 1 0 2">4.5707299525594552e-07</Real>
+ <Real Name="Cell 1 0 3">1.4163508322049627e-05</Real>
+ <Real Name="Cell 1 0 4">2.7910456079410612e-05</Real>
+ <Real Name="Cell 1 0 5">5.8453600780912934e-06</Real>
+ <Real Name="Cell 1 0 6">1.8622445886520021e-08</Real>
+ <Real Name="Cell 1 1 2">5.0278029478154015e-06</Real>
+ <Real Name="Cell 1 1 3">0.00015579859154254589</Real>
+ <Real Name="Cell 1 1 4">0.00030701501687351674</Real>
+ <Real Name="Cell 1 1 5">6.4298960859004233e-05</Real>
+ <Real Name="Cell 1 1 6">2.0484690475172022e-07</Real>
+ <Real Name="Cell 1 2 2">5.0278029478154015e-06</Real>
+ <Real Name="Cell 1 2 3">0.00015579859154254589</Real>
+ <Real Name="Cell 1 2 4">0.00030701501687351674</Real>
+ <Real Name="Cell 1 2 5">6.4298960859004233e-05</Real>
+ <Real Name="Cell 1 2 6">2.0484690475172022e-07</Real>
+ <Real Name="Cell 1 3 0">5.6796490194329426e-05</Real>
+ <Real Name="Cell 1 3 10">3.407168468900614e-09</Real>
+ <Real Name="Cell 1 3 11">0.00010787402532512448</Real>
+ <Real Name="Cell 1 3 12">0.0009448005288780081</Real>
+ <Real Name="Cell 1 3 13">0.00079345244766444755</Real>
+ <Real Name="Cell 1 3 2">4.5707299525594552e-07</Real>
+ <Real Name="Cell 1 3 3">1.4163508322049627e-05</Real>
+ <Real Name="Cell 1 3 4">2.7910456079410612e-05</Real>
+ <Real Name="Cell 1 3 5">5.8453600780912934e-06</Real>
+ <Real Name="Cell 1 3 6">1.8622445886520021e-08</Real>
+ <Real Name="Cell 1 4 0">0.0013861356368472467</Real>
+ <Real Name="Cell 1 4 1">0.0001698625654470248</Real>
+ <Real Name="Cell 1 4 10">8.2207399247739423e-08</Real>
+ <Real Name="Cell 1 4 11">0.0026296046984274108</Real>
+ <Real Name="Cell 1 4 12">0.023031817788568786</Real>
+ <Real Name="Cell 1 4 13">0.019342615035822668</Real>
+ <Real Name="Cell 1 4 2">0.0005915299443807338</Real>
+ <Real Name="Cell 1 4 3">0.00022431357901120738</Real>
+ <Real Name="Cell 1 4 4">4.0621232843936084e-06</Real>
+ <Real Name="Cell 1 5 0">0.0024069621894676333</Real>
+ <Real Name="Cell 1 5 1">0.0035040799555692546</Real>
+ <Real Name="Cell 1 5 10">0.0076432154207601924</Real>
+ <Real Name="Cell 1 5 11">0.0061536880635841172</Real>
+ <Real Name="Cell 1 5 12">0.039513031863137441</Real>
+ <Real Name="Cell 1 5 13">0.03317880385175679</Real>
+ <Real Name="Cell 1 5 2">0.012202619310315087</Real>
+ <Real Name="Cell 1 5 3">0.0046273451357963071</Real>
+ <Real Name="Cell 1 5 4">8.3797184744239381e-05</Real>
+ <Real Name="Cell 1 5 6">4.8320975061311598e-05</Real>
+ <Real Name="Cell 1 5 7">0.0060722101833934825</Real>
+ <Real Name="Cell 1 5 8">0.022282153065727051</Real>
+ <Real Name="Cell 1 5 9">0.012425762410203248</Real>
+ <Real Name="Cell 1 6 0">0.00047350706084050632</Real>
+ <Real Name="Cell 1 6 1">0.0054216706282934077</Real>
+ <Real Name="Cell 1 6 10">0.29518569263643696</Real>
+ <Real Name="Cell 1 6 11">0.064893807832174882</Real>
+ <Real Name="Cell 1 6 12">0.0073012826320099072</Real>
+ <Real Name="Cell 1 6 13">0.0059244976754494342</Real>
+ <Real Name="Cell 1 6 2">0.018880443238126255</Real>
+ <Real Name="Cell 1 6 3">0.0071596372022988131</Real>
+ <Real Name="Cell 1 6 4">0.00012965478557058568</Real>
+ <Real Name="Cell 1 6 6">0.00075924880895913863</Real>
+ <Real Name="Cell 1 6 7">0.095410292219511583</Real>
+ <Real Name="Cell 1 6 8">0.35281345240034301</Real>
+ <Real Name="Cell 1 6 9">0.28136158282034168</Real>
+ <Real Name="Cell 1 7 0">8.4656226811274288e-06</Real>
+ <Real Name="Cell 1 7 1">0.00085661220537424179</Real>
+ <Real Name="Cell 1 7 10">0.66128563932136208</Real>
+ <Real Name="Cell 1 7 11">0.14322294829521243</Real>
+ <Real Name="Cell 1 7 12">0.00056045021066088998</Real>
+ <Real Name="Cell 1 7 13">9.1970942121584555e-06</Real>
+ <Real Name="Cell 1 7 2">0.0029830690998182978</Real>
+ <Real Name="Cell 1 7 3">0.001131207156247181</Real>
+ <Real Name="Cell 1 7 4">2.0485175035412225e-05</Real>
+ <Real Name="Cell 1 7 6">0.00098137741897652954</Real>
+ <Real Name="Cell 1 7 7">0.12332387659649466</Real>
+ <Real Name="Cell 1 7 8">0.46083830155109629</Real>
+ <Real Name="Cell 1 7 9">0.50442664771633416</Real>
+ <Real Name="Cell 1 8 0">6.0474562403535729e-09</Real>
+ <Real Name="Cell 1 8 1">6.6352704213313889e-07</Real>
+ <Real Name="Cell 1 8 10">0.16204687577379562</Real>
+ <Real Name="Cell 1 8 11">0.034666836127424466</Real>
+ <Real Name="Cell 1 8 12">0.00013170721423765898</Real>
+ <Real Name="Cell 1 8 2">2.3106687061696157e-06</Real>
+ <Real Name="Cell 1 8 3">8.762267613226581e-07</Real>
+ <Real Name="Cell 1 8 4">1.5867702460401362e-08</Real>
+ <Real Name="Cell 1 8 6">0.00012431354812034582</Real>
+ <Real Name="Cell 1 8 7">0.01562174597442814</Real>
+ <Real Name="Cell 1 8 8">0.05995896538780851</Real>
+ <Real Name="Cell 1 8 9">0.10483377652624837</Real>
+ <Real Name="Cell 1 9 10">0.0010858577236716744</Real>
+ <Real Name="Cell 1 9 11">0.00020202509648595602</Real>
+ <Real Name="Cell 1 9 12">6.8935499557641082e-07</Real>
+ <Real Name="Cell 1 9 6">1.5271828904707491e-08</Real>
+ <Real Name="Cell 1 9 7">1.9191242023435899e-06</Real>
+ <Real Name="Cell 1 9 8">4.6403858752887685e-05</Real>
+ <Real Name="Cell 1 9 9">0.00068372122755422046</Real>
+ <Real Name="Cell 13 4 0">2.0378662739711926e-09</Real>
+ <Real Name="Cell 13 4 1">2.2359473591691984e-07</Real>
+ <Real Name="Cell 13 4 2">7.7864702768786007e-07</Real>
+ <Real Name="Cell 13 4 3">2.9527009279294114e-07</Real>
+ <Real Name="Cell 13 4 4">5.3470838653924772e-09</Real>
+ <Real Name="Cell 13 5 0">4.2038964523823106e-08</Real>
+ <Real Name="Cell 13 5 1">4.6125161846894896e-06</Real>
+ <Real Name="Cell 13 5 2">1.6062641200574176e-05</Real>
+ <Real Name="Cell 13 5 3">6.0911008314983672e-06</Real>
+ <Real Name="Cell 13 5 4">1.1030452380229092e-07</Real>
+ <Real Name="Cell 13 6 0">6.5044582912678825e-08</Real>
+ <Real Name="Cell 13 6 1">7.1366931799923446e-06</Real>
+ <Real Name="Cell 13 6 2">2.4852843289593539e-05</Real>
+ <Real Name="Cell 13 6 3">9.4244260664261451e-06</Real>
+ <Real Name="Cell 13 6 4">1.7066813670055601e-07</Real>
+ <Real Name="Cell 13 7 0">1.0276903086976353e-08</Real>
+ <Real Name="Cell 13 7 1">1.1275820504641901e-06</Real>
+ <Real Name="Cell 13 7 2">3.9266953601016551e-06</Real>
+ <Real Name="Cell 13 7 3">1.4890388868364316e-06</Real>
+ <Real Name="Cell 13 7 4">2.6965195599164326e-08</Real>
+ <Real Name="Cell 13 8 0">7.9604318789868479e-12</Real>
+ <Real Name="Cell 13 8 1">8.7341877457846162e-10</Real>
+ <Real Name="Cell 13 8 2">3.0415963504837989e-09</Real>
+ <Real Name="Cell 13 8 3">1.1534012263719127e-09</Real>
+ <Real Name="Cell 13 8 4">2.0887090289167917e-11</Real>
+ <Real Name="Cell 14 4 0">5.6200506292808043e-06</Real>
+ <Real Name="Cell 14 4 1">0.0006166320883484646</Real>
+ <Real Name="Cell 14 4 2">0.0021473615682432389</Real>
+ <Real Name="Cell 14 4 3">0.00081429919715734415</Real>
+ <Real Name="Cell 14 4 4">1.4746248282501894e-05</Real>
+ <Real Name="Cell 14 5 0">0.00011593553121914285</Real>
+ <Real Name="Cell 14 5 1">0.012720449235276224</Real>
+ <Real Name="Cell 14 5 2">0.044297733340119452</Real>
+ <Real Name="Cell 14 5 3">0.016798106675747038</Real>
+ <Real Name="Cell 14 5 4">0.0003041990616977784</Real>
+ <Real Name="Cell 14 6 0">0.0001793806854742009</Real>
+ <Real Name="Cell 14 6 1">0.019681653065017058</Real>
+ <Real Name="Cell 14 6 2">0.068539451951827077</Real>
+ <Real Name="Cell 14 6 3">0.025990788660540647</Real>
+ <Real Name="Cell 14 6 4">0.0004706705151918625</Real>
+ <Real Name="Cell 14 7 0">2.8341759417053756e-05</Real>
+ <Real Name="Cell 14 7 1">0.0031096585154863762</Real>
+ <Real Name="Cell 14 7 2">0.010829084818469932</Real>
+ <Real Name="Cell 14 7 3">0.0041064882617057206</Real>
+ <Real Name="Cell 14 7 4">7.4364921011448918e-05</Real>
+ <Real Name="Cell 14 8 0">2.1953368953727255e-08</Real>
+ <Real Name="Cell 14 8 1">2.4087241623219196e-06</Real>
+ <Real Name="Cell 14 8 2">8.3881487720211001e-06</Real>
+ <Real Name="Cell 14 8 3">3.1808629304477868e-06</Real>
+ <Real Name="Cell 14 8 4">5.7602653531692198e-08</Real>
+ <Real Name="Cell 15 4 0">3.9556900032567638e-05</Real>
+ <Real Name="Cell 15 4 1">0.0043401840098360595</Real>
+ <Real Name="Cell 15 4 2">0.015114270758739695</Real>
+ <Real Name="Cell 15 4 3">0.0057314700637626104</Real>
+ <Real Name="Cell 15 4 4">0.00010379192424481706</Real>
+ <Real Name="Cell 15 5 0">0.00081601581928188659</Real>
+ <Real Name="Cell 15 5 1">0.089533275046948274</Real>
+ <Real Name="Cell 15 5 2">0.31179096506265502</Real>
+ <Real Name="Cell 15 5 3">0.11823399295496491</Real>
+ <Real Name="Cell 15 5 4">0.0021411144965289711</Real>
+ <Real Name="Cell 15 6 0">0.0012625764981737295</Real>
+ <Real Name="Cell 15 6 1">0.13852992332707656</Real>
+ <Real Name="Cell 15 6 2">0.48241705066140106</Real>
+ <Real Name="Cell 15 6 3">0.18293696918957586</Real>
+ <Real Name="Cell 15 6 4">0.003312828966472173</Real>
+ <Real Name="Cell 15 7 0">0.00019948434951215846</Real>
+ <Real Name="Cell 15 7 1">0.021887427560106986</Real>
+ <Real Name="Cell 15 7 2">0.076220848149766346</Real>
+ <Real Name="Cell 15 7 3">0.028903644534247382</Real>
+ <Real Name="Cell 15 7 4">0.00052341979466404118</Real>
+ <Real Name="Cell 15 8 0">1.5451946581338766e-07</Real>
+ <Real Name="Cell 15 8 1">1.6953879454141424e-05</Real>
+ <Real Name="Cell 15 8 2">5.904024435374262e-05</Real>
+ <Real Name="Cell 15 8 3">2.2388602035267616e-05</Real>
+ <Real Name="Cell 15 8 4">4.0543805699760518e-07</Real>
+ <Real Name="Cell 2 0 2">0.0002498155385930853</Real>
+ <Real Name="Cell 2 0 3">0.0077411365286613881</Real>
+ <Real Name="Cell 2 0 4">0.015254599790898316</Real>
+ <Real Name="Cell 2 0 5">0.0031948108755827896</Real>
+ <Real Name="Cell 2 0 6">1.0178191224044032e-05</Real>
+ <Real Name="Cell 2 1 2">0.0027479747018518933</Real>
+ <Real Name="Cell 2 1 3">0.085153394284706016</Real>
+ <Real Name="Cell 2 1 4">0.16780455354843349</Real>
+ <Real Name="Cell 2 1 5">0.035144797811848927</Real>
+ <Real Name="Cell 2 1 6">0.00011201373799807559</Real>
+ <Real Name="Cell 2 10 1">1.3481074899302508e-06</Real>
+ <Real Name="Cell 2 10 2">2.134127947885331e-05</Real>
+ <Real Name="Cell 2 10 3">2.7726913477769916e-05</Real>
+ <Real Name="Cell 2 10 4">3.5349199420325544e-06</Real>
+ <Real Name="Cell 2 10 5">4.6614218264628964e-10</Real>
+ <Real Name="Cell 2 2 2">0.0027486297415234874</Real>
+ <Real Name="Cell 2 2 3">0.085308822265046866</Real>
+ <Real Name="Cell 2 2 4">0.16849458031331255</Real>
+ <Real Name="Cell 2 2 5">0.035472955034300369</Real>
+ <Real Name="Cell 2 2 6">0.00012141928533497429</Real>
+ <Real Name="Cell 2 3 0">0.00027510852556740777</Real>
+ <Real Name="Cell 2 3 1">4.9613992191374375e-11</Real>
+ <Real Name="Cell 2 3 10">2.3536826227928812e-06</Real>
+ <Real Name="Cell 2 3 11">0.00094277543386799543</Real>
+ <Real Name="Cell 2 3 12">0.0061486684252402106</Real>
+ <Real Name="Cell 2 3 13">0.0044073670860994476</Real>
+ <Real Name="Cell 2 3 2">0.00025303841064216971</Real>
+ <Real Name="Cell 2 3 3">0.0086421238685155007</Real>
+ <Real Name="Cell 2 3 4">0.019479403438330288</Real>
+ <Real Name="Cell 2 3 5">0.0053164228319110959</Real>
+ <Real Name="Cell 2 3 6">8.5628043126115337e-05</Real>
+ <Real Name="Cell 2 3 7">4.5173708911601381e-06</Real>
+ <Real Name="Cell 2 3 8">1.9012113989656424e-07</Real>
+ <Real Name="Cell 2 4 0">0.0065819138380779707</Real>
+ <Real Name="Cell 2 4 1">4.0386069305842674e-07</Real>
+ <Real Name="Cell 2 4 10">4.4890760674972554e-05</Real>
+ <Real Name="Cell 2 4 11">0.020502107996210002</Real>
+ <Real Name="Cell 2 4 12">0.1394226434741048</Real>
+ <Real Name="Cell 2 4 13">0.1026889737422</Real>
+ <Real Name="Cell 2 4 2">5.5558396599689873e-06</Real>
+ <Real Name="Cell 2 4 3">0.0014458595847623476</Real>
+ <Real Name="Cell 2 4 4">0.0073969820473805568</Real>
+ <Real Name="Cell 2 4 5">0.0040318988355889287</Real>
+ <Real Name="Cell 2 4 6">0.00030950036166268774</Real>
+ <Real Name="Cell 2 4 7">9.7076422866899026e-05</Real>
+ <Real Name="Cell 2 4 8">4.0856242750959616e-06</Real>
+ <Real Name="Cell 2 5 0">0.011180900719946847</Real>
+ <Real Name="Cell 2 5 1">3.1882266299411025e-06</Real>
+ <Real Name="Cell 2 5 10">0.0079732336948385458</Real>
+ <Real Name="Cell 2 5 11">0.034640590509580328</Real>
+ <Real Name="Cell 2 5 12">0.22998794327069275</Real>
+ <Real Name="Cell 2 5 13">0.17197978768373776</Real>
+ <Real Name="Cell 2 5 2">1.6750999695524604e-05</Real>
+ <Real Name="Cell 2 5 3">0.00055440887141524503</Real>
+ <Real Name="Cell 2 5 4">0.0028797840437215266</Real>
+ <Real Name="Cell 2 5 5">0.0016393547862294613</Real>
+ <Real Name="Cell 2 5 6">0.00043149799449147363</Real>
+ <Real Name="Cell 2 5 7">0.014138303521287764</Real>
+ <Real Name="Cell 2 5 8">0.051184175386311287</Real>
+ <Real Name="Cell 2 5 9">0.023925472939702819</Real>
+ <Real Name="Cell 2 6 0">0.0019768338428955939</Real>
+ <Real Name="Cell 2 6 1">2.4758505367869834e-06</Real>
+ <Real Name="Cell 2 6 10">0.31946219153207484</Real>
+ <Real Name="Cell 2 6 11">0.07137754822777681</Real>
+ <Real Name="Cell 2 6 12">0.039661433119773763</Real>
+ <Real Name="Cell 2 6 13">0.029959251247611205</Real>
+ <Real Name="Cell 2 6 2">1.2252595311538765e-05</Real>
+ <Real Name="Cell 2 6 3">2.1046343352777652e-05</Real>
+ <Real Name="Cell 2 6 4">7.7301320396013998e-05</Real>
+ <Real Name="Cell 2 6 5">5.0149728482387922e-05</Real>
+ <Real Name="Cell 2 6 6">0.0017925603415350079</Real>
+ <Real Name="Cell 2 6 7">0.2197532064734799</Real>
+ <Real Name="Cell 2 6 8">0.80885660483650923</Real>
+ <Real Name="Cell 2 6 9">0.48302447295309703</Real>
+ <Real Name="Cell 2 7 0">2.9679017361548918e-06</Real>
+ <Real Name="Cell 2 7 1">8.4222334570356772e-06</Real>
+ <Real Name="Cell 2 7 10">0.78126224197119498</Real>
+ <Real Name="Cell 2 7 11">0.15315390894632977</Real>
+ <Real Name="Cell 2 7 12">0.00060241082218086761</Real>
+ <Real Name="Cell 2 7 13">4.2643245949186972e-05</Real>
+ <Real Name="Cell 2 7 2">0.00013161200922329601</Real>
+ <Real Name="Cell 2 7 3">0.0001703925362663897</Real>
+ <Real Name="Cell 2 7 4">2.16860031509523e-05</Real>
+ <Real Name="Cell 2 7 5">9.8273197151913112e-09</Real>
+ <Real Name="Cell 2 7 6">0.0022601333230167424</Real>
+ <Real Name="Cell 2 7 7">0.28401257306799099</Real>
+ <Real Name="Cell 2 7 8">1.0592075495997366</Real>
+ <Real Name="Cell 2 7 9">0.85758572457001703</Real>
+ <Real Name="Cell 2 8 1">4.9190690254313615e-05</Real>
+ <Real Name="Cell 2 8 10">0.22977231345145957</Real>
+ <Real Name="Cell 2 8 11">0.040432136181128647</Real>
+ <Real Name="Cell 2 8 12">0.00013176422876454407</Real>
+ <Real Name="Cell 2 8 2">0.00077871555222152754</Real>
+ <Real Name="Cell 2 8 3">0.001011719037822199</Real>
+ <Real Name="Cell 2 8 4">0.00012898463456450065</Real>
+ <Real Name="Cell 2 8 5">1.7008922428143823e-08</Real>
+ <Real Name="Cell 2 8 6">0.00028629174278980263</Real>
+ <Real Name="Cell 2 8 7">0.035976585464035656</Real>
+ <Real Name="Cell 2 8 8">0.141038481060279</Real>
+ <Real Name="Cell 2 8 9">0.20442217635953042</Real>
+ <Real Name="Cell 2 9 1">3.019602449530798e-05</Real>
+ <Real Name="Cell 2 9 10">0.0038374796374183165</Real>
+ <Real Name="Cell 2 9 11">0.00043799089807709237</Real>
+ <Real Name="Cell 2 9 12">6.8965340936608935e-07</Real>
+ <Real Name="Cell 2 9 2">0.00047801959615105283</Real>
+ <Real Name="Cell 2 9 3">0.00062105029814599059</Real>
+ <Real Name="Cell 2 9 4">7.9178055129780698e-05</Real>
+ <Real Name="Cell 2 9 5">1.0441037432565514e-08</Real>
+ <Real Name="Cell 2 9 6">3.5170732223681197e-08</Real>
+ <Real Name="Cell 2 9 7">4.4197422153861985e-06</Real>
+ <Real Name="Cell 2 9 8">0.0003323640374771887</Real>
+ <Real Name="Cell 2 9 9">0.0035614219337351239</Real>
+ <Real Name="Cell 3 0 2">0.0013533780477245978</Real>
+ <Real Name="Cell 3 0 3">0.041937680503510946</Real>
+ <Real Name="Cell 3 0 4">0.082641938928603803</Real>
+ <Real Name="Cell 3 0 5">0.017307918194345771</Real>
+ <Real Name="Cell 3 0 6">5.514044741068652e-05</Real>
+ <Real Name="Cell 3 1 2">0.014887572973361067</Real>
+ <Real Name="Cell 3 1 3">0.46141240727683552</Real>
+ <Real Name="Cell 3 1 4">0.90949536388352359</Real>
+ <Real Name="Cell 3 1 5">0.19059317407922791</Real>
+ <Real Name="Cell 3 1 6">0.00061242970207887545</Real>
+ <Real Name="Cell 3 10 1">0.00026784048902184389</Real>
+ <Real Name="Cell 3 10 2">0.0042400615489968478</Real>
+ <Real Name="Cell 3 10 3">0.0055087521732680817</Real>
+ <Real Name="Cell 3 10 4">0.00070231394232224994</Real>
+ <Real Name="Cell 3 10 5">9.2612607738090323e-08</Real>
+ <Real Name="Cell 3 2 2">0.014959237424696927</Real>
+ <Real Name="Cell 3 2 3">0.47836591519652877</Real>
+ <Real Name="Cell 3 2 4">0.98467672257792527</Real>
+ <Real Name="Cell 3 2 5">0.22630570493329041</Real>
+ <Real Name="Cell 3 2 6">0.0016333719273454875</Real>
+ <Real Name="Cell 3 3 0">0.00031315856721966481</Real>
+ <Real Name="Cell 3 3 1">2.1787936619969193e-07</Real>
+ <Real Name="Cell 3 3 10">1.939211492020101e-05</Real>
+ <Real Name="Cell 3 3 11">0.0040783965173197372</Real>
+ <Real Name="Cell 3 3 12">0.018242282177917079</Real>
+ <Real Name="Cell 3 3 13">0.00905056858982233</Real>
+ <Real Name="Cell 3 3 2">0.0016644761398509245</Real>
+ <Real Name="Cell 3 3 3">0.11969193086264861</Real>
+ <Real Name="Cell 3 3 4">0.43486486106665123</Real>
+ <Real Name="Cell 3 3 5">0.18887955664491532</Real>
+ <Real Name="Cell 3 3 6">0.0059690091133855856</Real>
+ <Real Name="Cell 3 3 7">0.00028786531821870198</Real>
+ <Real Name="Cell 3 3 8">1.1625272812067771e-05</Real>
+ <Real Name="Cell 3 4 0">0.0066056535086816415</Real>
+ <Real Name="Cell 3 4 1">0.0017735503221979446</Real>
+ <Real Name="Cell 3 4 10">0.0003692607488595925</Real>
+ <Real Name="Cell 3 4 11">0.078863863673193813</Real>
+ <Real Name="Cell 3 4 12">0.35794419826055957</Real>
+ <Real Name="Cell 3 4 13">0.18123526493388614</Real>
+ <Real Name="Cell 3 4 2">0.0088885526611963833</Real>
+ <Real Name="Cell 3 4 3">0.072429371397158188</Real>
+ <Real Name="Cell 3 4 4">0.336693633529348</Real>
+ <Real Name="Cell 3 4 5">0.19322521924102548</Real>
+ <Real Name="Cell 3 4 6">0.025278943128235698</Real>
+ <Real Name="Cell 3 4 7">0.0062597711796156608</Real>
+ <Real Name="Cell 3 4 8">0.0002498222808438753</Real>
+ <Real Name="Cell 3 5 0">0.010456678835921987</Real>
+ <Real Name="Cell 3 5 1">0.014001066367590452</Real>
+ <Real Name="Cell 3 5 10">0.0013577282177660427</Real>
+ <Real Name="Cell 3 5 11">0.11741462944841109</Real>
+ <Real Name="Cell 3 5 12">0.53796261051252425</Real>
+ <Real Name="Cell 3 5 13">0.27635376183063376</Real>
+ <Real Name="Cell 3 5 2">0.068585276590653846</Real>
+ <Real Name="Cell 3 5 3">0.053721460399325863</Real>
+ <Real Name="Cell 3 5 4">0.10284390550374783</Real>
+ <Real Name="Cell 3 5 5">0.087722090247097248</Real>
+ <Real Name="Cell 3 5 6">0.035108251849537024</Real>
+ <Real Name="Cell 3 5 7">0.013502937599793575</Real>
+ <Real Name="Cell 3 5 8">0.01311313478406596</Real>
+ <Real Name="Cell 3 5 9">0.0054071704127621901</Real>
+ <Real Name="Cell 3 6 0">0.00172806584954548</Real>
+ <Real Name="Cell 3 6 1">0.010833852564152676</Real>
+ <Real Name="Cell 3 6 10">0.050683918175936468</Real>
+ <Real Name="Cell 3 6 11">0.02544845109710072</Real>
+ <Real Name="Cell 3 6 12">0.082392746409420833</Real>
+ <Real Name="Cell 3 6 13">0.043130178809524591</Real>
+ <Real Name="Cell 3 6 2">0.053061317410684164</Real>
+ <Real Name="Cell 3 6 3">0.028024881422337892</Real>
+ <Real Name="Cell 3 6 4">0.004676743891157676</Real>
+ <Real Name="Cell 3 6 5">0.0081684258795971434</Real>
+ <Real Name="Cell 3 6 6">0.0064409760279563249</Real>
+ <Real Name="Cell 3 6 7">0.056312160193815408</Real>
+ <Real Name="Cell 3 6 8">0.2023202100726163</Real>
+ <Real Name="Cell 3 6 9">0.1156369039316627</Real>
+ <Real Name="Cell 3 7 0">3.7770252083125348e-06</Real>
+ <Real Name="Cell 3 7 1">0.0023315142692650974</Real>
+ <Real Name="Cell 3 7 10">0.18740171023266458</Real>
+ <Real Name="Cell 3 7 11">0.023804825511154818</Real>
+ <Real Name="Cell 3 7 12">0.00010732079533397955</Real>
+ <Real Name="Cell 3 7 13">3.4916774113249023e-05</Real>
+ <Real Name="Cell 3 7 2">0.029370905937156751</Real>
+ <Real Name="Cell 3 7 3">0.03552520913646505</Real>
+ <Real Name="Cell 3 7 4">0.0043676781559706182</Real>
+ <Real Name="Cell 3 7 5">1.6062853555129327e-05</Real>
+ <Real Name="Cell 3 7 6">0.00057264054241721544</Real>
+ <Real Name="Cell 3 7 7">0.070652283704718336</Real>
+ <Real Name="Cell 3 7 8">0.27157898124136376</Real>
+ <Real Name="Cell 3 7 9">0.26311915734455293</Real>
+ <Real Name="Cell 3 8 1">0.0097731513484277718</Real>
+ <Real Name="Cell 3 8 10">0.088130184446009577</Real>
+ <Real Name="Cell 3 8 11">0.0094279804995700926</Real>
+ <Real Name="Cell 3 8 12">1.1985480188262105e-05</Real>
+ <Real Name="Cell 3 8 2">0.15471433537300527</Real>
+ <Real Name="Cell 3 8 3">0.20100720741268732</Real>
+ <Real Name="Cell 3 8 4">0.025626523000660064</Real>
+ <Real Name="Cell 3 8 5">3.3793136933942519e-06</Real>
+ <Real Name="Cell 3 8 6">7.1217533257907862e-05</Real>
+ <Real Name="Cell 3 8 7">0.0089494858734831401</Real>
+ <Real Name="Cell 3 8 8">0.040307942312643112</Real>
+ <Real Name="Cell 3 8 9">0.096877478985862658</Real>
+ <Real Name="Cell 3 9 1">0.0059993123899618073</Real>
+ <Real Name="Cell 3 9 10">0.0031001231431427479</Real>
+ <Real Name="Cell 3 9 11">0.00027571527994622148</Real>
+ <Real Name="Cell 3 9 12">6.273195200417625e-08</Real>
+ <Real Name="Cell 3 9 2">0.094972398975208247</Real>
+ <Real Name="Cell 3 9 3">0.12338957895055563</Real>
+ <Real Name="Cell 3 9 4">0.015731007478384532</Real>
+ <Real Name="Cell 3 9 5">2.0744136448484635e-06</Real>
+ <Real Name="Cell 3 9 6">8.7490221249028777e-09</Real>
+ <Real Name="Cell 3 9 7">1.0994827024180016e-06</Real>
+ <Real Name="Cell 3 9 8">0.00030958684791900621</Real>
+ <Real Name="Cell 3 9 9">0.0031987041013290607</Real>
+ <Real Name="Cell 4 0 2">0.00076686615718124702</Real>
+ <Real Name="Cell 4 0 3">0.023763196058110423</Real>
+ <Real Name="Cell 4 0 4">0.046827496747665655</Real>
+ <Real Name="Cell 4 0 5">0.0098072055600581555</Real>
+ <Real Name="Cell 4 0 6">3.1244295030631789e-05</Real>
+ <Real Name="Cell 4 1 2">0.0084369710052495175</Real>
+ <Real Name="Cell 4 1 3">0.26173615957935237</Real>
+ <Real Name="Cell 4 1 4">0.5166139512741964</Real>
+ <Real Name="Cell 4 1 5">0.10859689364135737</Real>
+ <Real Name="Cell 4 1 6">0.00036418042192934647</Real>
+ <Real Name="Cell 4 10 1">0.0011303673247218093</Real>
+ <Real Name="Cell 4 10 2">0.017894333479224256</Real>
+ <Real Name="Cell 4 10 3">0.023248589036680915</Real>
+ <Real Name="Cell 4 10 4">0.0029639758163407626</Real>
+ <Real Name="Cell 4 10 5">3.908530260929958e-07</Real>
+ <Real Name="Cell 4 2 2">0.008686409294217148</Real>
+ <Real Name="Cell 4 2 3">0.32071395875766134</Real>
+ <Real Name="Cell 4 2 4">0.77810281278405968</Real>
+ <Real Name="Cell 4 2 5">0.23278332028139342</Real>
+ <Real Name="Cell 4 2 6">0.0039127688598208071</Real>
+ <Real Name="Cell 4 3 0">0.00015910319588090428</Real>
+ <Real Name="Cell 4 3 1">1.6184654078290555e-06</Real>
+ <Real Name="Cell 4 3 10">1.5586288861135836e-05</Real>
+ <Real Name="Cell 4 3 11">0.0031031078765990437</Real>
+ <Real Name="Cell 4 3 12">0.013125466256572916</Real>
+ <Real Name="Cell 4 3 13">0.0059820443778905554</Real>
+ <Real Name="Cell 4 3 2">0.0018278250082883571</Real>
+ <Real Name="Cell 4 3 3">0.28164543316785084</Real>
+ <Real Name="Cell 4 3 4">1.2074457782232799</Real>
+ <Real Name="Cell 4 3 5">0.58025820985662313</Real>
+ <Real Name="Cell 4 3 6">0.024585509569928304</Real>
+ <Real Name="Cell 4 3 7">0.0010026045412059243</Real>
+ <Real Name="Cell 4 3 8">3.2087665641407865e-05</Real>
+ <Real Name="Cell 4 4 0">0.0030853443950048004</Real>
+ <Real Name="Cell 4 4 1">0.013174399648705735</Real>
+ <Real Name="Cell 4 4 10">0.00029676269513131184</Real>
+ <Real Name="Cell 4 4 11">0.059117515083456057</Real>
+ <Real Name="Cell 4 4 12">0.25021085588296993</Real>
+ <Real Name="Cell 4 4 13">0.11415216192660219</Real>
+ <Real Name="Cell 4 4 2">0.065100835266032595</Real>
+ <Real Name="Cell 4 4 3">0.21478052886756377</Real>
+ <Real Name="Cell 4 4 4">0.94038480253223422</Real>
+ <Real Name="Cell 4 4 5">0.80944917342994382</Real>
+ <Real Name="Cell 4 4 6">0.23376990800002562</Real>
+ <Real Name="Cell 4 4 7">0.023065186355986048</Real>
+ <Real Name="Cell 4 4 8">0.00068955059782948279</Real>
+ <Real Name="Cell 4 5 0">0.004798342901198416</Real>
+ <Real Name="Cell 4 5 1">0.10400361440328074</Real>
+ <Real Name="Cell 4 5 10">0.00043992577564243735</Real>
+ <Real Name="Cell 4 5 11">0.086921578831488683</Real>
+ <Real Name="Cell 4 5 12">0.36806423480986006</Real>
+ <Real Name="Cell 4 5 13">0.1680501289700761</Real>
+ <Real Name="Cell 4 5 2">0.50926274540764782</Real>
+ <Real Name="Cell 4 5 3">0.30214533699332163</Real>
+ <Real Name="Cell 4 5 4">0.33869835233892948</Real>
+ <Real Name="Cell 4 5 5">0.78472963900816495</Real>
+ <Real Name="Cell 4 5 6">0.40277446022214047</Real>
+ <Real Name="Cell 4 5 7">0.038417733156320043</Real>
+ <Real Name="Cell 4 5 8">0.0011702489626882104</Real>
+ <Real Name="Cell 4 5 9">3.3170379202719005e-05</Real>
+ <Real Name="Cell 4 6 0">0.0009037361550058888</Real>
+ <Real Name="Cell 4 6 1">0.080470813530078358</Real>
+ <Real Name="Cell 4 6 10">0.0021284353207737293</Real>
+ <Real Name="Cell 4 6 11">0.013088971885849303</Real>
+ <Real Name="Cell 4 6 12">0.054715711240088886</Real>
+ <Real Name="Cell 4 6 13">0.025009393346210419</Real>
+ <Real Name="Cell 4 6 2">0.39405478450098691</Real>
+ <Real Name="Cell 4 6 3">0.20555007022122307</Real>
+ <Real Name="Cell 4 6 4">0.037925494791216811</Real>
+ <Real Name="Cell 4 6 5">0.13473382504984843</Real>
+ <Real Name="Cell 4 6 6">0.076590053558302409</Real>
+ <Real Name="Cell 4 6 7">0.0069819792230342197</Real>
+ <Real Name="Cell 4 6 8">0.0015666228178196177</Real>
+ <Real Name="Cell 4 6 9">0.0026147941586366959</Real>
+ <Real Name="Cell 4 7 0">1.5099930957770617e-05</Real>
+ <Real Name="Cell 4 7 1">0.012051206924945433</Real>
+ <Real Name="Cell 4 7 10">0.011516783749394587</Real>
+ <Real Name="Cell 4 7 11">0.0009930158800500685</Real>
+ <Real Name="Cell 4 7 12">2.8212300505386193e-05</Real>
+ <Real Name="Cell 4 7 13">1.306479956504001e-05</Real>
+ <Real Name="Cell 4 7 2">0.13478115830021317</Real>
+ <Real Name="Cell 4 7 3">0.15554439685539487</Real>
+ <Real Name="Cell 4 7 4">0.0186707494745777</Real>
+ <Real Name="Cell 4 7 5">0.00031442734625891687</Real>
+ <Real Name="Cell 4 7 6">0.00017491231550959222</Real>
+ <Real Name="Cell 4 7 7">0.00042794379399261126</Real>
+ <Real Name="Cell 4 7 8">0.0026849645069519238</Real>
+ <Real Name="Cell 4 7 9">0.012623790572206965</Real>
+ <Real Name="Cell 4 8 1">0.041245634609495797</Real>
+ <Real Name="Cell 4 8 10">0.0067084644222185014</Real>
+ <Real Name="Cell 4 8 11">0.00057505421163516694</Real>
+ <Real Name="Cell 4 8 12">1.8542341069229676e-20</Real>
+ <Real Name="Cell 4 8 2">0.65294097248095295</Real>
+ <Real Name="Cell 4 8 3">0.84831079917252827</Real>
+ <Real Name="Cell 4 8 4">0.10815162543933221</Real>
+ <Real Name="Cell 4 8 5">1.4261718954247822e-05</Real>
+ <Real Name="Cell 4 8 6">4.2157266739233652e-07</Real>
+ <Real Name="Cell 4 8 7">5.297663511458808e-05</Real>
+ <Real Name="Cell 4 8 8">0.00086830204501830706</Real>
+ <Real Name="Cell 4 8 9">0.0070828376641636102</Real>
+ <Real Name="Cell 4 9 1">0.025318900518653355</Real>
+ <Real Name="Cell 4 9 10">0.00027512004946931234</Real>
+ <Real Name="Cell 4 9 11">2.3588855861020139e-05</Real>
+ <Real Name="Cell 4 9 12">9.7050533789972903e-23</Real>
+ <Real Name="Cell 4 9 2">0.40081205401048664</Real>
+ <Real Name="Cell 4 9 3">0.52074109021476223</Real>
+ <Real Name="Cell 4 9 4">0.066389577257193896</Real>
+ <Real Name="Cell 4 9 5">8.754648748802647e-06</Real>
+ <Real Name="Cell 4 9 6">5.1789895346597485e-11</Real>
+ <Real Name="Cell 4 9 7">6.5122207703702547e-09</Real>
+ <Real Name="Cell 4 9 8">2.770613703961507e-05</Real>
+ <Real Name="Cell 4 9 9">0.00028740011938470101</Real>
+ <Real Name="Cell 5 0 2">2.9992946735227256e-05</Real>
+ <Real Name="Cell 5 0 3">0.00092940373878204225</Real>
+ <Real Name="Cell 5 0 4">0.0018314729402836519</Real>
+ <Real Name="Cell 5 0 5">0.0003835701852660163</Real>
+ <Real Name="Cell 5 0 6">1.2219974344388517e-06</Real>
+ <Real Name="Cell 5 1 2">0.00033046971762233006</Real>
+ <Real Name="Cell 5 1 3">0.010352752555218342</Real>
+ <Real Name="Cell 5 1 4">0.020719372033899675</Real>
+ <Real Name="Cell 5 1 5">0.0044914048273539823</Real>
+ <Real Name="Cell 5 1 6">2.1213171466930127e-05</Real>
+ <Real Name="Cell 5 10 1">0.00051328857140607879</Real>
+ <Real Name="Cell 5 10 2">0.0081256390439943607</Real>
+ <Real Name="Cell 5 10 3">0.010556953295497832</Real>
+ <Real Name="Cell 5 10 4">0.001345911969656533</Real>
+ <Real Name="Cell 5 10 5">1.7748247583358853e-07</Real>
+ <Real Name="Cell 5 2 2">0.00042503049761861712</Real>
+ <Real Name="Cell 5 2 3">0.032703865613726443</Real>
+ <Real Name="Cell 5 2 4">0.1198054196327147</Real>
+ <Real Name="Cell 5 2 5">0.051543614203844831</Real>
+ <Real Name="Cell 5 2 6">0.0013653475482235263</Real>
+ <Real Name="Cell 5 3 0">1.0478137381352539e-05</Real>
+ <Real Name="Cell 5 3 1">1.1925338701493142e-06</Real>
+ <Real Name="Cell 5 3 10">1.0486520487610103e-06</Real>
+ <Real Name="Cell 5 3 11">0.00020834496473269646</Real>
+ <Real Name="Cell 5 3 12">0.00087927827538165188</Real>
+ <Real Name="Cell 5 3 13">0.00039927150222563102</Real>
+ <Real Name="Cell 5 3 2">0.00042914116232236206</Real>
+ <Real Name="Cell 5 3 3">0.095817735328040526</Real>
+ <Real Name="Cell 5 3 4">0.42958675268253299</Real>
+ <Real Name="Cell 5 3 5">0.22331365927731023</Real>
+ <Real Name="Cell 5 3 6">0.016927445309520558</Real>
+ <Real Name="Cell 5 3 7">0.0006011246604854854</Real>
+ <Real Name="Cell 5 3 8">9.6588133525963907e-06</Real>
+ <Real Name="Cell 5 4 0">0.00022736396648894211</Real>
+ <Real Name="Cell 5 4 1">0.0097072929232629133</Real>
+ <Real Name="Cell 5 4 10">1.9966248447142645e-05</Real>
+ <Real Name="Cell 5 4 11">0.0039668709306190765</Real>
+ <Real Name="Cell 5 4 12">0.016741385783003594</Real>
+ <Real Name="Cell 5 4 13">0.007602096444401873</Real>
+ <Real Name="Cell 5 4 2">0.047727228811153079</Real>
+ <Real Name="Cell 5 4 3">0.081126347901379861</Real>
+ <Real Name="Cell 5 4 4">0.37492099196718037</Real>
+ <Real Name="Cell 5 4 5">0.69145938642903793</Real>
+ <Real Name="Cell 5 4 6">0.30866312059123402</Real>
+ <Real Name="Cell 5 4 7">0.015269161322852913</Real>
+ <Real Name="Cell 5 4 8">0.00020756388439212154</Real>
+ <Real Name="Cell 5 5 0">0.00051356638486853984</Real>
+ <Real Name="Cell 5 5 1">0.07663298343844574</Real>
+ <Real Name="Cell 5 5 10">2.9343543415895534e-05</Real>
+ <Real Name="Cell 5 5 11">0.0058299409468949587</Real>
+ <Real Name="Cell 5 5 12">0.024604100357978109</Real>
+ <Real Name="Cell 5 5 13">0.011172476775428245</Real>
+ <Real Name="Cell 5 5 2">0.3751983968642334</Real>
+ <Real Name="Cell 5 5 3">0.20368239449029452</Real>
+ <Real Name="Cell 5 5 4">0.2567859638381379</Real>
+ <Real Name="Cell 5 5 5">1.0614725158761387</Real>
+ <Real Name="Cell 5 5 6">0.56310714350494162</Real>
+ <Real Name="Cell 5 5 7">0.026993608795061689</Real>
+ <Real Name="Cell 5 5 8">0.0003295287312268396</Real>
+ <Real Name="Cell 5 6 0">0.0002140769377791569</Real>
+ <Real Name="Cell 5 6 1">0.059291114666230459</Real>
+ <Real Name="Cell 5 6 10">4.3564569918325488e-06</Real>
+ <Real Name="Cell 5 6 11">0.00086553578891611501</Real>
+ <Real Name="Cell 5 6 12">0.0036528207760416526</Real>
+ <Real Name="Cell 5 6 13">0.0016587095114775768</Real>
+ <Real Name="Cell 5 6 2">0.29031561707846099</Real>
+ <Real Name="Cell 5 6 3">0.15096981418490443</Real>
+ <Real Name="Cell 5 6 4">0.046422024623153361</Real>
+ <Real Name="Cell 5 6 5">0.20320308833555883</Real>
+ <Real Name="Cell 5 6 6">0.10943887270321667</Real>
+ <Real Name="Cell 5 6 7">0.0050200480887681118</Real>
+ <Real Name="Cell 5 6 8">5.3696181792110319e-05</Real>
+ <Real Name="Cell 5 7 0">1.0877150318557831e-05</Real>
+ <Real Name="Cell 5 7 1">0.0069202221642068462</Real>
+ <Real Name="Cell 5 7 10">2.210991775501217e-09</Real>
+ <Real Name="Cell 5 7 11">4.392772645944315e-07</Real>
+ <Real Name="Cell 5 7 12">1.8538818834547332e-06</Real>
+ <Real Name="Cell 5 7 13">8.4182928804259133e-07</Real>
+ <Real Name="Cell 5 7 2">0.068291339707546764</Real>
+ <Real Name="Cell 5 7 3">0.074308954028088195</Real>
+ <Real Name="Cell 5 7 4">0.0086693554299629369</Real>
+ <Real Name="Cell 5 7 5">0.0004824106975018388</Real>
+ <Real Name="Cell 5 7 6">0.00025712296653383537</Real>
+ <Real Name="Cell 5 7 7">1.0100512277499371e-05</Real>
+ <Real Name="Cell 5 7 8">5.0316984878272066e-08</Real>
+ <Real Name="Cell 5 8 1">0.018729232880697003</Real>
+ <Real Name="Cell 5 8 2">0.29649400831692124</Real>
+ <Real Name="Cell 5 8 3">0.38520950552315175</Real>
+ <Real Name="Cell 5 8 4">0.049110578572909701</Real>
+ <Real Name="Cell 5 8 5">6.4761048799977059e-06</Real>
+ <Real Name="Cell 5 9 1">0.011497061169908271</Real>
+ <Real Name="Cell 5 9 2">0.18200477146312666</Real>
+ <Real Name="Cell 5 9 3">0.23646335525008316</Real>
+ <Real Name="Cell 5 9 4">0.030146847419696182</Real>
+ <Real Name="Cell 5 9 5">3.9753990151306307e-06</Real>
+ <Real Name="Cell 6 1 2">9.9111874813813196e-09</Real>
+ <Real Name="Cell 6 1 3">2.341716672622359e-06</Real>
+ <Real Name="Cell 6 1 4">1.0379600902308469e-05</Real>
+ <Real Name="Cell 6 1 5">4.9280863802325025e-06</Real>
+ <Real Name="Cell 6 1 6">1.4072961741042381e-07</Real>
+ <Real Name="Cell 6 10 1">1.3465894431817205e-05</Real>
+ <Real Name="Cell 6 10 2">0.00021317247967891209</Real>
+ <Real Name="Cell 6 10 3">0.00027695691374809945</Real>
+ <Real Name="Cell 6 10 4">3.5309394183989422e-05</Real>
+ <Real Name="Cell 6 10 5">4.6561727967675297e-09</Real>
+ <Real Name="Cell 6 2 2">1.7217811865984706e-06</Real>
+ <Real Name="Cell 6 2 3">0.0004068377638012711</Real>
+ <Real Name="Cell 6 2 4">0.0018033520229420754</Real>
+ <Real Name="Cell 6 2 5">0.00085623240294104171</Real>
+ <Real Name="Cell 6 2 6">2.4452816325099927e-05</Real>
+ <Real Name="Cell 6 3 0">2.0323635686115184e-10</Real>
+ <Real Name="Cell 6 3 1">7.0645470620626314e-08</Real>
+ <Real Name="Cell 6 3 2">7.3538547650126887e-06</Real>
+ <Real Name="Cell 6 3 3">0.0016644367202467631</Real>
+ <Real Name="Cell 6 3 4">0.0080125679505275854</Real>
+ <Real Name="Cell 6 3 5">0.0066819870402248334</Real>
+ <Real Name="Cell 6 3 6">0.0017866716080254419</Real>
+ <Real Name="Cell 6 3 7">6.1094898083865543e-05</Real>
+ <Real Name="Cell 6 3 8">1.0011219042551309e-07</Real>
+ <Real Name="Cell 6 4 0">1.6543554007912385e-06</Real>
+ <Real Name="Cell 6 4 1">0.00057505811296606568</Real>
+ <Real Name="Cell 6 4 2">0.0028185353415214804</Real>
+ <Real Name="Cell 6 4 3">0.002285292053276467</Real>
+ <Real Name="Cell 6 4 4">0.021122824558270289</Real>
+ <Real Name="Cell 6 4 5">0.089917622258439356</Real>
+ <Real Name="Cell 6 4 6">0.046925173936249204</Real>
+ <Real Name="Cell 6 4 7">0.0016843951040598887</Real>
+ <Real Name="Cell 6 4 8">2.151369361965925e-06</Real>
+ <Real Name="Cell 6 5 0">1.3060097293069452e-05</Real>
+ <Real Name="Cell 6 5 1">0.00453972278321438</Real>
+ <Real Name="Cell 6 5 2">0.022225643441520882</Real>
+ <Real Name="Cell 6 5 3">0.011659178781222565</Real>
+ <Real Name="Cell 6 5 4">0.033179542517396708</Real>
+ <Real Name="Cell 6 5 5">0.16367654423662631</Real>
+ <Real Name="Cell 6 5 6">0.086880911286593199</Real>
+ <Real Name="Cell 6 5 7">0.003109000125058479</Real>
+ <Real Name="Cell 6 5 8">3.4155171952247187e-06</Real>
+ <Real Name="Cell 6 6 0">1.0104026364285639e-05</Real>
+ <Real Name="Cell 6 6 1">0.0035122775525201397</Real>
+ <Real Name="Cell 6 6 2">0.017196374370792692</Real>
+ <Real Name="Cell 6 6 3">0.0089399750953563402</Real>
+ <Real Name="Cell 6 6 4">0.0066678841890918366</Real>
+ <Real Name="Cell 6 6 5">0.031957789114167946</Real>
+ <Real Name="Cell 6 6 6">0.016969506353613825</Real>
+ <Real Name="Cell 6 6 7">0.00060479950181667604</Real>
+ <Real Name="Cell 6 6 8">5.5655308581459313e-07</Real>
+ <Real Name="Cell 6 7 0">6.4305192211866531e-07</Real>
+ <Real Name="Cell 6 7 1">0.00030608591805945587</Real>
+ <Real Name="Cell 6 7 2">0.0024012991500714019</Real>
+ <Real Name="Cell 6 7 3">0.0022658165305128935</Real>
+ <Real Name="Cell 6 7 4">0.00025067967617652283</Real>
+ <Real Name="Cell 6 7 5">7.6024187062631148e-05</Real>
+ <Real Name="Cell 6 7 6">4.0326760005420027e-05</Real>
+ <Real Name="Cell 6 7 7">1.419355404539194e-06</Real>
+ <Real Name="Cell 6 7 8">5.215282030910293e-10</Real>
+ <Real Name="Cell 6 8 1">0.00049135298701372696</Real>
+ <Real Name="Cell 6 8 2">0.0077783867361881235</Real>
+ <Real Name="Cell 6 8 3">0.010105797838626564</Real>
+ <Real Name="Cell 6 8 4">0.0012883939043035436</Real>
+ <Real Name="Cell 6 8 5">1.6989769400969864e-07</Real>
+ <Real Name="Cell 6 9 1">0.00030162022031004468</Real>
+ <Real Name="Cell 6 9 2">0.0047748131852920787</Real>
+ <Real Name="Cell 6 9 3">0.0062035095970835365</Real>
+ <Real Name="Cell 6 9 4">0.00079088896075296873</Real>
+ <Real Name="Cell 6 9 5">1.042928022251796e-07</Real>
+ <Real Name="Cell 7 3 3">1.2658790457362825e-09</Real>
+ <Real Name="Cell 7 3 4">4.8930122638409664e-07</Real>
+ <Real Name="Cell 7 3 5">2.4564999208928818e-06</Real>
+ <Real Name="Cell 7 3 6">1.3029175315370689e-06</Real>
+ <Real Name="Cell 7 3 7">4.5481201021914433e-08</Real>
+ <Real Name="Cell 7 4 3">3.5212298537689984e-08</Real>
+ <Real Name="Cell 7 4 4">1.3610637537864738e-05</Real>
+ <Real Name="Cell 7 4 5">6.8331179715500328e-05</Real>
+ <Real Name="Cell 7 4 6">3.6242578819043961e-05</Real>
+ <Real Name="Cell 7 4 7">1.2651268963101061e-06</Real>
+ <Real Name="Cell 7 5 3">6.527819550970732e-08</Real>
+ <Real Name="Cell 7 5 4">2.5232032417807118e-05</Real>
+ <Real Name="Cell 7 5 5">0.00012667551662675413</Real>
+ <Real Name="Cell 7 5 6">6.718817697723447e-05</Real>
+ <Real Name="Cell 7 5 7">2.3453510367556405e-06</Real>
+ <Real Name="Cell 7 6 3">1.2753946523246451e-08</Real>
+ <Real Name="Cell 7 6 4">4.9297930130693912e-06</Real>
+ <Real Name="Cell 7 6 5">2.4749654187698651e-05</Real>
+ <Real Name="Cell 7 6 6">1.3127115562418353e-05</Real>
+ <Real Name="Cell 7 6 7">4.5823082987295304e-07</Real>
+ <Real Name="Cell 7 7 3">3.0333132690454403e-11</Real>
+ <Real Name="Cell 7 7 4">1.1724689713050891e-08</Real>
+ <Real Name="Cell 7 7 5">5.8862920833952816e-08</Real>
+ <Real Name="Cell 7 7 6">3.1220652954126433e-08</Real>
+ <Real Name="Cell 7 7 7">1.089825532830857e-09</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>9.1119845071837208e-05</Real>
+ <Real>0.090720315044499733</Real>
+ <Real>0.55025766250121055</Real>
+ <Real>0.34320921934036525</Real>
+ <Real>0.015721683268852503</Real>
+ <Real>0.00015012522034442169</Real>
+ <Real>0.099356795254623917</Real>
+ <Real>0.5593747949437492</Real>
+ <Real>0.32757960274142961</Real>
+ <Real>0.013538681839852794</Real>
+ <Real>0.018158594767252602</Real>
+ <Real>0.35888417561848956</Real>
+ <Real>0.54030736287434888</Real>
+ <Real>0.082598368326822907</Real>
+ <Real>5.14984130859375e-05</Real>
+ <Real>0.041627420943636896</Real>
+ <Real>0.4582155406899513</Real>
+ <Real>0.45845109823303443</Real>
+ <Real>0.041705940133377188</Real>
+ <Real>1.2828530710933453e-16</Real>
+ <Real>0.0055362754759460259</Real>
+ <Real>0.24795438899936029</Real>
+ <Real>0.59225974451466756</Real>
+ <Real>0.15322236664250746</Real>
+ <Real>0.0010272243675186511</Real>
+ <Real>0.0042460280899123074</Real>
+ <Real>0.22871588718952912</Real>
+ <Real>0.59632216273624739</Real>
+ <Real>0.16922400252321107</Real>
+ <Real>0.001491919461100034</Real>
+ <Real>6.6666591167482021e-05</Real>
+ <Real>0.08606665073633292</Real>
+ <Real>0.54473331362803623</Real>
+ <Real>0.3520666975458463</Real>
+ <Real>0.017066671498617049</Real>
+ <Real>0.023326680338390325</Real>
+ <Real>0.3874518449014549</Real>
+ <Real>0.52012998426866952</Real>
+ <Real>0.069077650831027043</Real>
+ <Real>1.3839660458076671e-05</Real>
+ <Real>0.03167460418448273</Real>
+ <Real>0.42425323879349275</Real>
+ <Real>0.4902205011964671</Real>
+ <Real>0.053850853163774005</Real>
+ <Real>8.0266178337075683e-07</Real>
+ <Real>0.012749605276410803</Real>
+ <Real>0.32148691284470338</Real>
+ <Real>0.56270704376016845</Real>
+ <Real>0.10287678115211603</Real>
+ <Real>0.00017965696660134908</Real>
+ <Real>1.6024703728835248e-06</Real>
+ <Real>0.056417033443933631</Real>
+ <Real>0.49592335056242809</Real>
+ <Real>0.41764574336232119</Real>
+ <Real>0.030012270160944085</Real>
+ <Real>0.0037782170994077558</Real>
+ <Real>0.22083430910594309</Real>
+ <Real>0.59747439343876341</Real>
+ <Real>0.17618542306945406</Real>
+ <Real>0.00172765728643163</Real>
+ <Real>0.035389450019532316</Real>
+ <Real>0.43796494184012003</Real>
+ <Real>0.47790194087639981</Real>
+ <Real>0.0487435605980059</Real>
+ <Real>1.0666594187603302e-07</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>0.0010666671528536498</Real>
+ <Real>0.15473335174766273</Real>
+ <Real>0.59273333898525471</Real>
+ <Real>0.24606664375510937</Real>
+ <Real>0.0053999983591193996</Real>
+ <Real>0.00016276069058524602</Real>
+ <Real>0.10091149120354556</Real>
+ <Real>0.56087242706002582</Real>
+ <Real>0.32486973469163882</Real>
+ <Real>0.013183586354204581</Real>
+ <Real>0.021750286255291018</Real>
+ <Real>0.37931159553620664</Real>
+ <Real>0.52614729621290934</Real>
+ <Real>0.072769728387591756</Real>
+ <Real>2.1093608001061349e-05</Real>
+ <Real>0.0010666699577817054</Real>
+ <Real>0.1547334579841988</Real>
+ <Real>0.59273337159244333</Real>
+ <Real>0.24606651157306803</Real>
+ <Real>0.0053999888925081634</Real>
+ <Real>0.0026041673971157779</Real>
+ <Real>0.19791668273654572</Real>
+ <Real>0.59895833333333259</Real>
+ <Real>0.1979166505967882</Real>
+ <Real>0.0026041659362177087</Real>
+ <Real>2.6041418314877162e-07</Real>
+ <Real>0.05064476867914669</Real>
+ <Real>0.48264733964105189</Real>
+ <Real>0.43276985381443817</Real>
+ <Real>0.033937777451180033</Real>
+ <Real>0.00062526109313582761</Real>
+ <Real>0.13526982710338351</Real>
+ <Real>0.58502241326374205</Real>
+ <Real>0.27164474245602177</Real>
+ <Real>0.0074377560837167568</Real>
+ <Real>0.0010666654698994566</Real>
+ <Real>0.15473328800575983</Real>
+ <Real>0.59273331942090102</Real>
+ <Real>0.24606672306434757</Real>
+ <Real>0.0054000040390921661</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0</Real>
+ <Real>0.0026042090329703206</Real>
+ <Real>0.1979175987206947</Real>
+ <Real>0.59895833333074866</Real>
+ <Real>0.1979157346147063</Real>
+ <Real>0.0026041243008799383</Real>
+ <Real>0.0017085936967502549</Real>
+ <Real>0.17564479015142287</Real>
+ <Real>0.59739739561463689</Real>
+ <Real>0.22143646002330059</Real>
+ <Real>0.0038127605138894532</Real>
+ <Real>0.01318359128473468</Real>
+ <Real>0.32486977267499179</Real>
+ <Real>0.56087240624223145</Real>
+ <Real>0.10091146929006924</Real>
+ <Real>0.0001627605079728152</Real>
+ <Real>0.010004167969495891</Real>
+ <Real>0.29798334548041105</Real>
+ <Real>0.57435832781814944</Real>
+ <Real>0.11731665883449849</Real>
+ <Real>0.00033749989744494643</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>0.0012965438860746193</Real>
+ <Real>0.16292863742177591</Real>
+ <Real>0.59496860464339196</Real>
+ <Real>0.23609101761611412</Real>
+ <Real>0.0047151964326433184</Real>
+ <Real>0.022266572805360645</Real>
+ <Real>0.38202776345099154</Real>
+ <Real>0.52416325209613102</Real>
+ <Real>0.071523992911451742</Real>
+ <Real>1.8418736065012962e-05</Real>
+ <Real>0.011832605517855912</Real>
+ <Real>0.31406414072290789</Real>
+ <Real>0.56659541417064396</Real>
+ <Real>0.10728640609669558</Real>
+ <Real>0.00022143349189650375</Real>
+ <Real>0.0017858013352502983</Real>
+ <Real>0.17781228386651252</Real>
+ <Real>0.59769371581562036</Real>
+ <Real>0.21903219671569593</Real>
+ <Real>0.0036760022669208082</Real>
+ <Real>0.0017086017161747019</Real>
+ <Real>0.17564501834717935</Real>
+ <Real>0.59739742855015188</Real>
+ <Real>0.22143620551433324</Real>
+ <Real>0.0038127458721607366</Real>
+ <Real>0.0040977069545237296</Real>
+ <Real>0.22627851145019215</Real>
+ <Real>0.59671157259785013</Real>
+ <Real>0.17135050247039479</Real>
+ <Real>0.0015617065270392145</Real>
+ <Real>2.1750421477804795e-06</Real>
+ <Real>0.057733270813550459</Real>
+ <Real>0.49873314137135216</Real>
+ <Real>0.41432536200431536</Real>
+ <Real>0.029206050768634195</Real>
+ <Real>8.6400056648268334e-06</Real>
+ <Real>0.065520111244055546</Real>
+ <Real>0.51392118159705458</Real>
+ <Real>0.39556276272059754</Real>
+ <Real>0.024987304432627432</Real>
+ <Real>4.880619993386894e-05</Real>
+ <Real>0.08191627610789852</Real>
+ <Real>0.53940408234591719</Real>
+ <Real>0.36024771006311429</Real>
+ <Real>0.018383125283136074</Real>
+ <Real>0.0069905040885420225</Real>
+ <Real>0.26646194284335506</Real>
+ <Real>0.5868043834979163</Real>
+ <Real>0.13904332911133552</Real>
+ <Real>0.00069984045885097335</Real>
+ <Real>0.00019040655142945676</Real>
+ <Real>0.10406769412736623</Real>
+ <Real>0.56378776207543602</Real>
+ <Real>0.31945972792224575</Real>
+ <Real>0.012494409323522462</Real>
+ <Real>0.019774301666309266</Real>
+ <Real>0.36842563881228446</Real>
+ <Real>0.53386063089545432</Real>
+ <Real>0.077904628220022559</Real>
+ <Real>3.4800405929288513e-05</Real>
+ <Real>0.028572903710531138</Real>
+ <Real>0.41166191232062643</Real>
+ <Real>0.50096022420001085</Real>
+ <Real>0.058802226022017991</Real>
+ <Real>2.7337468135370829e-06</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">65</Int>
+ <Real>-0.0016854540244076904</Real>
+ <Real>-0.2914318595125569</Real>
+ <Real>-0.33184166617245625</Real>
+ <Real>0.54472072698021401</Real>
+ <Real>0.08023825272920683</Real>
+ <Real>-0.0024510232125503567</Real>
+ <Real>-0.30937513287573065</Real>
+ <Real>-0.30216854137168336</Real>
+ <Real>0.54226657422076019</Real>
+ <Real>0.071728123239204175</Real>
+ <Real>-0.089396158854166657</Real>
+ <Real>-0.54541015625</Real>
+ <Real>0.360107421875</Real>
+ <Real>0.27360026041666663</Real>
+ <Real>0.0010986328125</Real>
+ <Real>-0.16654891563009322</Real>
+ <Real>-0.50011769555574637</Real>
+ <Real>0.49988213800395087</Real>
+ <Real>0.16678447317971032</Real>
+ <Real>2.1784112419024706e-12</Real>
+ <Real>-0.036679250243501299</Real>
+ <Real>-0.50408183444089893</Real>
+ <Real>0.12857088020999707</Real>
+ <Real>0.40182074387670785</Real>
+ <Real>0.010369460597695286</Real>
+ <Real>-0.030060370435004882</Real>
+ <Real>-0.48853779347565118</Real>
+ <Real>0.080975501113040305</Real>
+ <Real>0.42390385994089252</Real>
+ <Real>0.013718802856723243</Real>
+ <Real>-0.0013333322008454032</Real>
+ <Real>-0.28133329822619785</Real>
+ <Real>-0.34800005549192142</Real>
+ <Real>0.54533333446581811</Real>
+ <Real>0.085333351453146619</Real>
+ <Real>-0.10786905756209218</Real>
+ <Real>-0.54180276637519476</Real>
+ <Real>0.40762276907184514</Real>
+ <Real>0.24163899123026289</Real>
+ <Real>0.00041006363517895783</Real>
+ <Real>-0.13568773041454193</Real>
+ <Real>-0.52673526002144855</Real>
+ <Real>0.46058217387648004</Real>
+ <Real>0.20179235396955353</Real>
+ <Real>4.8462589956979473e-05</Real>
+ <Real>-0.068569303078043639</Real>
+ <Real>-0.54084652081779905</Real>
+ <Real>0.29020535260945268</Real>
+ <Real>0.31640606954666634</Real>
+ <Real>0.0028044017397236948</Real>
+ <Real>-8.1395367348647448e-05</Real>
+ <Real>-0.20881684023017011</Real>
+ <Real>-0.45181106180586772</Real>
+ <Real>0.53039822577164042</Real>
+ <Real>0.13031107163174604</Real>
+ <Real>-0.027540534381201576</Real>
+ <Real>-0.48144281633034564</Real>
+ <Real>0.060821649615805162</Real>
+ <Real>0.43284728728423294</Real>
+ <Real>0.015314413811509116</Real>
+ <Real>-0.14745603131103738</Real>
+ <Real>-0.51764264062849019</Real>
+ <Real>0.47766404180239985</Real>
+ <Real>0.18742396352482035</Real>
+ <Real>1.0666612307322972e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">65</Int>
+ <Real>-0.010666670313068831</Real>
+ <Real>-0.40400002643641197</Real>
+ <Real>-0.12399994439237266</Real>
+ <Real>0.50266664934625682</Real>
+ <Real>0.035999991795596688</Real>
+ <Real>-0.0026041699536889272</Real>
+ <Real>-0.3125000657404175</Real>
+ <Real>-0.29687488824128189</Real>
+ <Real>0.54166665351857213</Real>
+ <Real>0.07031247041681625</Real>
+ <Real>-0.10235425786179789</Real>
+ <Real>-0.54349997601781996</Real>
+ <Real>0.3946252227810525</Real>
+ <Real>0.2506665139385465</Real>
+ <Real>0.00056249716001883718</Real>
+ <Real>-0.010666691350019937</Real>
+ <Real>-0.40400017895414458</Real>
+ <Real>-0.12399962357912447</Real>
+ <Real>0.5026665494207625</Real>
+ <Real>0.035999944462526537</Real>
+ <Real>-0.020833337716027845</Real>
+ <Real>-0.45833335086410953</Real>
+ <Real>4.3826942075497755e-08</Real>
+ <Real>0.45833331580255587</Real>
+ <Real>0.02083332895063943</Real>
+ <Real>-2.0833184322081997e-05</Real>
+ <Real>-0.19283326836427853</Real>
+ <Real>-0.47137507659194655</Real>
+ <Real>0.52133329101401715</Real>
+ <Real>0.14289588712653006</Real>
+ <Real>-0.0071458391316396429</Real>
+ <Real>-0.37433339060638243</Real>
+ <Real>-0.18412488805721461</Real>
+ <Real>0.51983330446013509</Real>
+ <Real>0.045770813335101523</Real>
+ <Real>-0.010666657690911333</Real>
+ <Real>-0.40399993492575176</Real>
+ <Real>-0.12400013688030348</Real>
+ <Real>0.5026667093015077</Real>
+ <Real>0.036000020195458941</Real>
+ <Real>-0.16666666666666666</Real>
+ <Real>-0.5</Real>
+ <Real>0.5</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>-0.020833587530638329</Real>
+ <Real>-0.45833435011635015</Real>
+ <Real>2.5419627114331433e-06</Real>
+ <Real>0.45833231654618101</Real>
+ <Real>0.020833079138096039</Real>
+ <Real>-0.015187499645001698</Real>
+ <Real>-0.43216666475581156</Real>
+ <Real>-0.062375004356399033</Real>
+ <Real>0.48200000156023953</Real>
+ <Real>0.027729167196972774</Real>
+ <Real>-0.070312490138938491</Real>
+ <Real>-0.5416666622839712</Real>
+ <Real>0.29687496274709829</Real>
+ <Real>0.31250002191347104</Real>
+ <Real>0.0026041677623403724</Real>
+ <Real>-0.057166672250220395</Real>
+ <Real>-0.53300000501380262</Real>
+ <Real>0.24200002575271606</Real>
+ <Real>0.34366665253685758</Real>
+ <Real>0.0044999989744494255</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">65</Int>
+ <Real>-0.012348027757665452</Real>
+ <Real>-0.41547484517157679</Real>
+ <Real>-0.099487612651801172</Real>
+ <Real>0.49479187184899465</Real>
+ <Real>0.032518613732048778</Real>
+ <Real>-0.10417109125784305</Real>
+ <Real>-0.54299490824416519</Real>
+ <Real>0.3990111936014229</Real>
+ <Real>0.24764670256102214</Real>
+ <Real>0.00050810333956326215</Real>
+ <Real>-0.064836187630456954</Real>
+ <Real>-0.53877201291894317</Real>
+ <Real>0.27533308586144023</Real>
+ <Real>0.32499461755577691</Real>
+ <Real>0.0032804971321829571</Real>
+ <Real>-0.015699363256675682</Real>
+ <Real>-0.43488141308955258</Real>
+ <Real>-0.05615926647876357</Real>
+ <Real>0.47976022525288775</Real>
+ <Real>0.026979817572104103</Real>
+ <Real>-0.015187553107800395</Real>
+ <Real>-0.43216695253043291</Real>
+ <Real>-0.062374348282772774</Real>
+ <Real>0.48199976658804594</Real>
+ <Real>0.027729087332960128</Real>
+ <Real>-0.02926933487542473</Real>
+ <Real>-0.48638933758982017</Real>
+ <Real>0.07478401218724251</Real>
+ <Real>0.4266773278966744</Real>
+ <Real>0.014197332381327967</Real>
+ <Real>-0.00010235473511721623</Real>
+ <Real>-0.21236983977962356</Real>
+ <Real>-0.44727650960668819</Real>
+ <Real>0.53207195749271596</Real>
+ <Real>0.12767674662871301</Real>
+ <Real>-0.00028800014162065922</Real>
+ <Real>-0.23271467829529452</Real>
+ <Real>-0.4201279839339252</Real>
+ <Real>0.53955200332021669</Real>
+ <Real>0.11357865905062374</Real>
+ <Real>-0.001055269599152589</Real>
+ <Real>-0.27205803886674906</Real>
+ <Real>-0.362494193683217</Real>
+ <Real>0.54538358236329165</Real>
+ <Real>0.090223919785827028</Real>
+ <Real>-0.043690654581706838</Real>
+ <Real>-0.5167039810700389</Real>
+ <Real>0.1722559297089562</Real>
+ <Real>0.38036270211903173</Real>
+ <Real>0.0077760038237577982</Real>
+ <Real>-0.0029293320036731184</Real>
+ <Real>-0.31874930875428514</Real>
+ <Real>-0.28617604237604022</Real>
+ <Real>0.54031733902962842</Real>
+ <Real>0.067537344104370053</Real>
+ <Real>-0.095297837850113781</Real>
+ <Real>-0.54492533270653065</Real>
+ <Real>0.37656301210725296</Real>
+ <Real>0.26284132530554133</Real>
+ <Real>0.00081883314385018213</Real>
+ <Real>-0.12559517752556038</Real>
+ <Real>-0.53333599354314709</Real>
+ <Real>0.44357901955675993</Real>
+ <Real>0.21523065161816302</Real>
+ <Real>0.00012149989378455396</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">8</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">16</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">9</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">0</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">8</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">5</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">2</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 10 10">0.00015550983169098254</Real>
+ <Real Name="Cell 0 10 5">4.3426126663572067e-05</Real>
+ <Real Name="Cell 0 10 6">0.00088464215043542534</Real>
+ <Real Name="Cell 0 10 7">0.0086945875355958491</Real>
+ <Real Name="Cell 0 10 8">0.025455958139809647</Real>
+ <Real Name="Cell 0 10 9">0.0092660282857752862</Real>
+ <Real Name="Cell 0 11 10">3.4127007305411425e-06</Real>
+ <Real Name="Cell 0 11 5">7.0042171467523923e-08</Real>
+ <Real Name="Cell 0 11 6">2.9628828187509245e-06</Real>
+ <Real Name="Cell 0 11 7">0.00016696707557498287</Real>
+ <Real Name="Cell 0 11 8">0.00055515856763483772</Real>
+ <Real Name="Cell 0 11 9">0.00020334366972394322</Real>
+ <Real Name="Cell 0 4 0">2.4782500924767428e-08</Real>
+ <Real Name="Cell 0 4 1">4.9495470489457263e-10</Real>
+ <Real Name="Cell 0 4 10">6.2453921981723285e-08</Real>
+ <Real Name="Cell 0 4 8">1.3609835892991086e-10</Real>
+ <Real Name="Cell 0 4 9">1.7102637568963844e-08</Real>
+ <Real Name="Cell 0 5 0">3.5955159511056679e-06</Real>
+ <Real Name="Cell 0 5 1">9.9720147587043648e-08</Real>
+ <Real Name="Cell 0 5 10">9.0597190062202705e-06</Real>
+ <Real Name="Cell 0 5 2">7.3629030380415593e-08</Real>
+ <Real Name="Cell 0 5 3">2.1143165193135773e-08</Real>
+ <Real Name="Cell 0 5 4">1.9270103447810681e-10</Real>
+ <Real Name="Cell 0 5 8">1.9742761543038636e-08</Real>
+ <Real Name="Cell 0 5 9">2.480950526780083e-06</Real>
+ <Real Name="Cell 0 6 0">0.00011210345636214471</Real>
+ <Real Name="Cell 0 6 1">0.0054302508112420425</Real>
+ <Real Name="Cell 0 6 10">3.4704848283661825e-05</Real>
+ <Real Name="Cell 0 6 2">0.014319209371003115</Real>
+ <Real Name="Cell 0 6 3">0.0041118755415084935</Real>
+ <Real Name="Cell 0 6 4">3.7476066769376444e-05</Real>
+ <Real Name="Cell 0 6 8">7.5628123077685048e-08</Real>
+ <Real Name="Cell 0 6 9">9.5037176729276018e-06</Real>
+ <Real Name="Cell 0 7 0">0.00094282750206276238</Real>
+ <Real Name="Cell 0 7 1">0.051748072135720614</Real>
+ <Real Name="Cell 0 7 10">1.5081448409904753e-05</Real>
+ <Real Name="Cell 0 7 2">0.13646282703871002</Real>
+ <Real Name="Cell 0 7 3">0.03918639264831611</Real>
+ <Real Name="Cell 0 7 4">0.00035714890991096</Real>
+ <Real Name="Cell 0 7 5">5.6734116452706757e-06</Real>
+ <Real Name="Cell 0 7 6">0.0001060318666387177</Real>
+ <Real Name="Cell 0 7 7">0.00018577684805835015</Real>
+ <Real Name="Cell 0 7 8">0.00013198988979525449</Real>
+ <Real Name="Cell 0 7 9">4.4122180077160772e-05</Real>
+ <Real Name="Cell 0 8 0">0.00084039357703873129</Real>
+ <Real Name="Cell 0 8 1">0.046400250389460058</Real>
+ <Real Name="Cell 0 8 10">9.8105074830821197e-05</Real>
+ <Real Name="Cell 0 8 2">0.1223605578196465</Real>
+ <Real Name="Cell 0 8 3">0.035136813207215088</Real>
+ <Real Name="Cell 0 8 4">0.00032024061636204578</Real>
+ <Real Name="Cell 0 8 5">0.00013980408764832462</Real>
+ <Real Name="Cell 0 8 6">0.0026522709054171735</Real>
+ <Real Name="Cell 0 8 7">0.0085045456266330741</Real>
+ <Real Name="Cell 0 8 8">0.016450615831675057</Real>
+ <Real Name="Cell 0 8 9">0.0058270205505329981</Real>
+ <Real Name="Cell 0 9 0">6.5893758678858019e-05</Real>
+ <Real Name="Cell 0 9 1">0.0036387037416742698</Real>
+ <Real Name="Cell 0 9 10">0.0003745973650160777</Real>
+ <Real Name="Cell 0 9 2">0.0095955051940054253</Real>
+ <Real Name="Cell 0 9 3">0.0027554260918586323</Real>
+ <Real Name="Cell 0 9 4">2.511324361697313e-05</Real>
+ <Real Name="Cell 0 9 5">0.00024136519195419676</Real>
+ <Real Name="Cell 0 9 6">0.0046789839158270074</Real>
+ <Real Name="Cell 0 9 7">0.024635992322006244</Real>
+ <Real Name="Cell 0 9 8">0.061857964260082388</Real>
+ <Real Name="Cell 0 9 9">0.022320564367285724</Real>
+ <Real Name="Cell 1 10 10">0.0017141079969648463</Real>
+ <Real Name="Cell 1 10 5">0.0025382285947518376</Real>
+ <Real Name="Cell 1 10 6">0.048247038404428705</Real>
+ <Real Name="Cell 1 10 7">0.15462771578528062</Real>
+ <Real Name="Cell 1 10 8">0.29427874360022516</Real>
+ <Real Name="Cell 1 10 9">0.10312733858731694</Real>
+ <Real Name="Cell 1 11 10">3.7887304515044594e-05</Real>
+ <Real Name="Cell 1 11 5">4.0939189404270194e-06</Real>
+ <Real Name="Cell 1 11 6">0.00011172440368499215</Real>
+ <Real Name="Cell 1 11 7">0.0023841117211727608</Real>
+ <Real Name="Cell 1 11 8">0.006947588599328495</Real>
+ <Real Name="Cell 1 11 9">0.0023942642345253242</Real>
+ <Real Name="Cell 1 12 10">9.329730763337878e-11</Real>
+ <Real Name="Cell 1 12 6">4.9854709314695529e-09</Real>
+ <Real Name="Cell 1 12 7">1.3232568615832114e-07</Real>
+ <Real Name="Cell 1 12 8">2.3872552524370354e-07</Real>
+ <Real Name="Cell 1 12 9">4.5203337348631021e-08</Real>
+ <Real Name="Cell 1 4 0">2.4673837951688867e-05</Real>
+ <Real Name="Cell 1 4 1">4.9278449415045374e-07</Real>
+ <Real Name="Cell 1 4 10">6.2180082434070194e-05</Real>
+ <Real Name="Cell 1 4 8">1.3550161317138827e-07</Real>
+ <Real Name="Cell 1 4 9">1.7027648226630303e-05</Real>
+ <Real Name="Cell 1 5 0">0.0035792474168576823</Real>
+ <Real Name="Cell 1 5 1">7.1484772763707945e-05</Real>
+ <Real Name="Cell 1 5 10">0.0090199951702175703</Real>
+ <Real Name="Cell 1 5 2">6.4913122068130159e-10</Real>
+ <Real Name="Cell 1 5 3">1.8640322383679289e-10</Real>
+ <Real Name="Cell 1 5 4">1.6988986150032878e-12</Real>
+ <Real Name="Cell 1 5 8">1.9656196140597609e-05</Real>
+ <Real Name="Cell 1 5 9">0.0024700723889715089</Real>
+ <Real Name="Cell 1 6 0">0.013711804127807739</Real>
+ <Real Name="Cell 1 6 1">0.00032170603230259896</Real>
+ <Real Name="Cell 1 6 10">0.034552679137933105</Real>
+ <Real Name="Cell 1 6 2">0.00012624158990232677</Real>
+ <Real Name="Cell 1 6 3">3.6251282622607455e-05</Real>
+ <Real Name="Cell 1 6 4">3.3039800799563351e-07</Real>
+ <Real Name="Cell 1 6 8">7.5296519066979278e-05</Real>
+ <Real Name="Cell 1 6 9">0.0094620470513557698</Real>
+ <Real Name="Cell 1 7 0">0.0057002046593389059</Real>
+ <Real Name="Cell 1 7 1">0.0005699015900104392</Real>
+ <Real Name="Cell 1 7 10">0.01435158026542112</Real>
+ <Real Name="Cell 1 7 2">0.0012030890673907467</Real>
+ <Real Name="Cell 1 7 3">0.00034547665183791649</Real>
+ <Real Name="Cell 1 7 4">3.1487105922443774e-06</Real>
+ <Real Name="Cell 1 7 5">0.00033160718613902687</Real>
+ <Real Name="Cell 1 7 6">0.0061819564689130644</Real>
+ <Real Name="Cell 1 7 7">0.0093115623782872824</Real>
+ <Real Name="Cell 1 7 8">0.0025441918147471143</Real>
+ <Real Name="Cell 1 7 9">0.0043707850923373091</Real>
+ <Real Name="Cell 1 8 0">0.00013231921531607838</Real>
+ <Real Name="Cell 1 8 1">0.0004115704522771027</Real>
+ <Real Name="Cell 1 8 10">0.001391297974239166</Real>
+ <Real Name="Cell 1 8 2">0.0010787600739862384</Real>
+ <Real Name="Cell 1 8 3">0.00030977458660269358</Real>
+ <Real Name="Cell 1 8 4">2.8233182093637914e-06</Real>
+ <Real Name="Cell 1 8 5">0.0081714571433293172</Real>
+ <Real Name="Cell 1 8 6">0.15277487153700511</Real>
+ <Real Name="Cell 1 8 7">0.27281437736389635</Real>
+ <Real Name="Cell 1 8 8">0.20745788862970044</Real>
+ <Real Name="Cell 1 8 9">0.064284699775528434</Real>
+ <Real Name="Cell 1 9 0">5.8093520701670787e-07</Real>
+ <Real Name="Cell 1 9 1">3.20796863591307e-05</Real>
+ <Real Name="Cell 1 9 10">0.0041250735354785009</Real>
+ <Real Name="Cell 1 9 2">8.4596279041795978e-05</Real>
+ <Real Name="Cell 1 9 3">2.4292498397222629e-05</Real>
+ <Real Name="Cell 1 9 4">2.2140438900426894e-07</Real>
+ <Real Name="Cell 1 9 5">0.014107637016354499</Real>
+ <Real Name="Cell 1 9 6">0.26493976039377909</Real>
+ <Real Name="Cell 1 9 7">0.58270645262046239</Real>
+ <Real Name="Cell 1 9 8">0.7303095158019538</Real>
+ <Real Name="Cell 1 9 9">0.24652753833462215</Real>
+ <Real Name="Cell 16 5 0">1.2686634193219325e-11</Real>
+ <Real Name="Cell 16 5 1">7.0056564132425547e-10</Real>
+ <Real Name="Cell 16 5 2">1.847438463614937e-09</Real>
+ <Real Name="Cell 16 5 3">5.3050673652159387e-10</Real>
+ <Real Name="Cell 16 5 4">4.8350942723800296e-12</Real>
+ <Real Name="Cell 16 6 0">2.4672682811038984e-06</Real>
+ <Real Name="Cell 16 6 1">0.00013624444114534139</Real>
+ <Real Name="Cell 16 6 2">0.00035928570597587275</Real>
+ <Real Name="Cell 16 6 3">0.00010317176518191451</Real>
+ <Real Name="Cell 16 6 4">9.4031833445362313e-07</Real>
+ <Real Name="Cell 16 7 0">2.3513197969169036e-05</Real>
+ <Real Name="Cell 16 7 1">0.0012984167718542109</Real>
+ <Real Name="Cell 16 7 2">0.0034240118907229635</Real>
+ <Real Name="Cell 16 7 3">0.00098323241056930718</Real>
+ <Real Name="Cell 16 7 4">8.9612837490680154e-06</Real>
+ <Real Name="Cell 16 8 0">2.1083309514137262e-05</Real>
+ <Real Name="Cell 16 8 1">0.0011642364732880575</Real>
+ <Real Name="Cell 16 8 2">0.0030701694668183736</Real>
+ <Real Name="Cell 16 8 3">0.00088162372738686146</Real>
+ <Real Name="Cell 16 8 4">8.0352115085894583e-06</Real>
+ <Real Name="Cell 16 9 0">1.6533514520905978e-06</Real>
+ <Real Name="Cell 16 9 1">9.1299331463920487e-05</Real>
+ <Real Name="Cell 16 9 2">0.00024076244494369601</Real>
+ <Real Name="Cell 16 9 3">6.9136862450137955e-05</Real>
+ <Real Name="Cell 16 9 4">6.3012064622365306e-07</Real>
+ <Real Name="Cell 17 5 0">6.8337625976730206e-10</Real>
+ <Real Name="Cell 17 5 1">3.7736559626313675e-08</Real>
+ <Real Name="Cell 17 5 2">9.9513832288961041e-08</Real>
+ <Real Name="Cell 17 5 3">2.8576193170230312e-08</Real>
+ <Real Name="Cell 17 5 4">2.6044643434642201e-10</Real>
+ <Real Name="Cell 17 6 0">0.00013290148861424918</Real>
+ <Real Name="Cell 17 6 1">0.0073389218279622621</Real>
+ <Real Name="Cell 17 6 2">0.019353227830031898</Real>
+ <Real Name="Cell 17 6 3">0.0055574342201251655</Real>
+ <Real Name="Cell 17 6 4">5.0651040820029641e-05</Real>
+ <Real Name="Cell 17 7 0">0.0012665582563992407</Real>
+ <Real Name="Cell 17 7 1">0.069940315426065283</Real>
+ <Real Name="Cell 17 7 2">0.18443729074584936</Real>
+ <Real Name="Cell 17 7 3">0.052962643754319312</Real>
+ <Real Name="Cell 17 7 4">0.00048270711347732289</Real>
+ <Real Name="Cell 17 8 0">0.0011356702636691541</Real>
+ <Real Name="Cell 17 8 1">0.062712580380500038</Real>
+ <Real Name="Cell 17 8 2">0.16537726989933088</Real>
+ <Real Name="Cell 17 8 3">0.047489406265512978</Real>
+ <Real Name="Cell 17 8 4">0.00043282345053456971</Real>
+ <Real Name="Cell 17 9 0">8.9059171581883523e-05</Real>
+ <Real Name="Cell 17 9 1">0.0049179155562328672</Real>
+ <Real Name="Cell 17 9 2">0.012968872327539139</Real>
+ <Real Name="Cell 17 9 3">0.0037241154551830398</Real>
+ <Real Name="Cell 17 9 4">3.3941980501701931e-05</Real>
+ <Real Name="Cell 18 5 0">1.7817407185594997e-09</Real>
+ <Real Name="Cell 18 5 1">9.8389084934625136e-08</Real>
+ <Real Name="Cell 18 5 2">2.5945859914641824e-07</Real>
+ <Real Name="Cell 18 5 3">7.4505612720814332e-08</Real>
+ <Real Name="Cell 18 5 4">6.7905200165523386e-10</Real>
+ <Real Name="Cell 18 6 0">0.00034650895525959808</Real>
+ <Real Name="Cell 18 6 1">0.019134489476789897</Real>
+ <Real Name="Cell 18 6 2">0.050458928836755956</Real>
+ <Real Name="Cell 18 6 3">0.014489685146634573</Real>
+ <Real Name="Cell 18 6 4">0.0001320605165552523</Real>
+ <Real Name="Cell 18 7 0">0.0033022487767173491</Real>
+ <Real Name="Cell 18 7 1">0.18235270260331951</Real>
+ <Real Name="Cell 18 7 2">0.4808762760570231</Real>
+ <Real Name="Cell 18 7 3">0.13808747024920706</Real>
+ <Real Name="Cell 18 7 4">0.0012585437479401581</Real>
+ <Real Name="Cell 18 8 0">0.0029609895320705923</Real>
+ <Real Name="Cell 18 8 1">0.16350810616090253</Real>
+ <Real Name="Cell 18 8 2">0.43118181454558763</Real>
+ <Real Name="Cell 18 8 3">0.12381730801168178</Real>
+ <Real Name="Cell 18 8 4">0.00112848398629982</Real>
+ <Real Name="Cell 18 9 0">0.00023220056316069793</Real>
+ <Real Name="Cell 18 9 1">0.01282229265611453</Real>
+ <Real Name="Cell 18 9 2">0.033813243538258521</Real>
+ <Real Name="Cell 18 9 3">0.0097097434279847603</Real>
+ <Real Name="Cell 18 9 4">8.8495624283213583e-05</Real>
+ <Real Name="Cell 2 0 1">3.9292058112330904e-07</Real>
+ <Real Name="Cell 2 0 2">0.00065947750194411507</Real>
+ <Real Name="Cell 2 0 3">0.0043425418447414453</Real>
+ <Real Name="Cell 2 0 4">0.0029002204592476952</Real>
+ <Real Name="Cell 2 0 5">0.0001479957111780785</Real>
+ <Real Name="Cell 2 1 1">4.3221263923563998e-06</Real>
+ <Real Name="Cell 2 1 2">0.0072542525213852667</Real>
+ <Real Name="Cell 2 1 3">0.047767960292155902</Real>
+ <Real Name="Cell 2 1 4">0.03190242505172465</Real>
+ <Real Name="Cell 2 1 5">0.0016279528229588636</Real>
+ <Real Name="Cell 2 10 10">0.001758654452341847</Real>
+ <Real Name="Cell 2 10 5">0.0068672598755057579</Real>
+ <Real Name="Cell 2 10 6">0.13123735197393818</Real>
+ <Real Name="Cell 2 10 7">0.33347730662196901</Real>
+ <Real Name="Cell 2 10 8">0.42320893379436209</Real>
+ <Real Name="Cell 2 10 9">0.1243441659049266</Real>
+ <Real Name="Cell 2 11 10">4.3945984061377063e-05</Real>
+ <Real Name="Cell 2 11 5">1.1076230616618764e-05</Real>
+ <Real Name="Cell 2 11 6">0.00056454698758130945</Real>
+ <Real Name="Cell 2 11 7">0.011139324794365892</Real>
+ <Real Name="Cell 2 11 8">0.022431536967245164</Real>
+ <Real Name="Cell 2 11 9">0.0053215522648599181</Real>
+ <Real Name="Cell 2 12 10">1.8439162152466346e-09</Real>
+ <Real Name="Cell 2 12 6">9.8532218392640596e-08</Real>
+ <Real Name="Cell 2 12 7">2.6152681635763627e-06</Real>
+ <Real Name="Cell 2 12 8">4.7181411570836046e-06</Real>
+ <Real Name="Cell 2 12 9">8.933930553273993e-07</Real>
+ <Real Name="Cell 2 2 1">4.3221263923563998e-06</Real>
+ <Real Name="Cell 2 2 2">0.0072542525213852667</Real>
+ <Real Name="Cell 2 2 3">0.047767960292155902</Real>
+ <Real Name="Cell 2 2 4">0.03190242505172465</Real>
+ <Real Name="Cell 2 2 5">0.0016279528229588636</Real>
+ <Real Name="Cell 2 3 1">3.9292058112330904e-07</Real>
+ <Real Name="Cell 2 3 2">0.0006594786390550268</Real>
+ <Real Name="Cell 2 3 3">0.0043425613541622351</Real>
+ <Real Name="Cell 2 3 4">0.002900247227253652</Real>
+ <Real Name="Cell 2 3 5">0.00014799936377039711</Real>
+ <Real Name="Cell 2 3 6">9.4060931347646326e-13</Real>
+ <Real Name="Cell 2 4 0">0.00016286091159007881</Real>
+ <Real Name="Cell 2 4 1">3.0554060667551216e-06</Real>
+ <Real Name="Cell 2 4 10">0.00043287157139199658</Real>
+ <Real Name="Cell 2 4 2">7.0500780842455004e-07</Real>
+ <Real Name="Cell 2 4 3">1.2095824598073633e-05</Real>
+ <Real Name="Cell 2 4 4">1.6596209552755588e-05</Real>
+ <Real Name="Cell 2 4 5">2.2649746362181506e-06</Real>
+ <Real Name="Cell 2 4 6">7.9309811414025573e-10</Real>
+ <Real Name="Cell 2 4 7">8.2102384453819349e-12</Real>
+ <Real Name="Cell 2 4 8">1.4856905085206247e-06</Real>
+ <Real Name="Cell 2 4 9">0.00012858310075115464</Real>
+ <Real Name="Cell 2 5 0">0.022713126018715672</Real>
+ <Real Name="Cell 2 5 1">0.00043863498422933272</Real>
+ <Real Name="Cell 2 5 10">0.058945017792247499</Real>
+ <Real Name="Cell 2 5 2">3.918477825382228e-06</Real>
+ <Real Name="Cell 2 5 3">6.7229367502926626e-05</Real>
+ <Real Name="Cell 2 5 4">9.2249428376030805e-05</Real>
+ <Real Name="Cell 2 5 5">1.2624897489633455e-05</Real>
+ <Real Name="Cell 2 5 6">2.4821393577762971e-08</Real>
+ <Real Name="Cell 2 5 7">8.4401903833257802e-10</Real>
+ <Real Name="Cell 2 5 8">0.00016967262949766116</Real>
+ <Real Name="Cell 2 5 9">0.016905063209985773</Real>
+ <Real Name="Cell 2 6 0">0.086199474502687612</Real>
+ <Real Name="Cell 2 6 1">0.0016762059085993247</Real>
+ <Real Name="Cell 2 6 10">0.22239284100034434</Real>
+ <Real Name="Cell 2 6 2">2.2696691620227494e-06</Real>
+ <Real Name="Cell 2 6 3">3.8940775278365286e-05</Real>
+ <Real Name="Cell 2 6 4">5.3452750651731918e-05</Real>
+ <Real Name="Cell 2 6 5">7.4200936559415253e-06</Real>
+ <Real Name="Cell 2 6 6">7.5274853939563912e-08</Real>
+ <Real Name="Cell 2 6 7">2.8706503330635104e-09</Real>
+ <Real Name="Cell 2 6 8">0.0006093806941790469</Real>
+ <Real Name="Cell 2 6 9">0.063210997069653524</Real>
+ <Real Name="Cell 2 7 0">0.03552752161528154</Real>
+ <Real Name="Cell 2 7 1">0.00069456350851879287</Real>
+ <Real Name="Cell 2 7 10">0.091245747123739521</Real>
+ <Real Name="Cell 2 7 2">9.2105777170667837e-08</Real>
+ <Real Name="Cell 2 7 3">1.5802757535347617e-06</Real>
+ <Real Name="Cell 2 7 4">2.1770663223537598e-06</Real>
+ <Real Name="Cell 2 7 5">0.00089751788198473407</Real>
+ <Real Name="Cell 2 7 6">0.016719364950284844</Real>
+ <Real Name="Cell 2 7 7">0.024580750421086251</Real>
+ <Real Name="Cell 2 7 8">0.0049817569477990957</Real>
+ <Real Name="Cell 2 7 9">0.026192331122416344</Real>
+ <Real Name="Cell 2 8 0">0.00077084317989471794</Real>
+ <Real Name="Cell 2 8 1">1.5197999913429375e-05</Real>
+ <Real Name="Cell 2 8 10">0.0030439057283585735</Real>
+ <Real Name="Cell 2 8 3">2.7920465551620358e-13</Real>
+ <Real Name="Cell 2 8 4">1.5260076121888002e-10</Real>
+ <Real Name="Cell 2 8 5">0.022108143442723001</Real>
+ <Real Name="Cell 2 8 6">0.4125334748725602</Real>
+ <Real Name="Cell 2 8 7">0.65165981446654364</Real>
+ <Real Name="Cell 2 8 8">0.26707709406119018</Real>
+ <Real Name="Cell 2 8 9">0.065678747925043662</Real>
+ <Real Name="Cell 2 9 10">0.0041586734287708278</Real>
+ <Real Name="Cell 2 9 5">0.038168670001167894</Real>
+ <Real Name="Cell 2 9 6">0.71491700908692968</Real>
+ <Real Name="Cell 2 9 7">1.2770505140092818</Real>
+ <Real Name="Cell 2 9 8">0.90599739157466841</Real>
+ <Real Name="Cell 2 9 9">0.26194858839602447</Real>
+ <Real Name="Cell 3 0 1">5.2628228014874394e-06</Real>
+ <Real Name="Cell 3 0 2">0.0088331164134419892</Real>
+ <Real Name="Cell 3 0 3">0.058164497699718098</Real>
+ <Real Name="Cell 3 0 4">0.038845881573913013</Real>
+ <Real Name="Cell 3 0 5">0.0019822713309739027</Real>
+ <Real Name="Cell 3 1 1">5.7891050816361839e-05</Real>
+ <Real Name="Cell 3 1 2">0.0971642805478619</Real>
+ <Real Name="Cell 3 1 3">0.63980947469689908</Real>
+ <Real Name="Cell 3 1 4">0.42730469731304321</Real>
+ <Real Name="Cell 3 1 5">0.02180498464071293</Real>
+ <Real Name="Cell 3 10 0">1.5873347162863456e-07</Real>
+ <Real Name="Cell 3 10 1">0.0012037300810579638</Real>
+ <Real Name="Cell 3 10 10">0.00022504749244868863</Real>
+ <Real Name="Cell 3 10 2">0.009441717570913815</Real>
+ <Real Name="Cell 3 10 3">0.0072672464590233252</Real>
+ <Real Name="Cell 3 10 4">0.0004590646966100127</Real>
+ <Real Name="Cell 3 10 5">0.0020250425788630472</Real>
+ <Real Name="Cell 3 10 6">0.041505512327973393</Real>
+ <Real Name="Cell 3 10 7">0.16041866540205424</Real>
+ <Real Name="Cell 3 10 8">0.21049031363048248</Real>
+ <Real Name="Cell 3 10 9">0.042836460156395077</Real>
+ <Real Name="Cell 3 11 0">6.080567326801825e-07</Real>
+ <Real Name="Cell 3 11 1">0.0046111016952326252</Real>
+ <Real Name="Cell 3 11 10">1.299609722080837e-05</Real>
+ <Real Name="Cell 3 11 2">0.036168174728078359</Real>
+ <Real Name="Cell 3 11 3">0.027838477241861104</Real>
+ <Real Name="Cell 3 11 4">0.0017585287881976169</Real>
+ <Real Name="Cell 3 11 5">3.2661991854950146e-06</Real>
+ <Real Name="Cell 3 11 6">0.00057427342265683144</Real>
+ <Real Name="Cell 3 11 7">0.013836785822932495</Real>
+ <Real Name="Cell 3 11 8">0.025073948443592176</Real>
+ <Real Name="Cell 3 11 9">0.004843850920990639</Real>
+ <Real Name="Cell 3 12 0">2.5242806966547337e-07</Real>
+ <Real Name="Cell 3 12 1">0.0019142481900138316</Real>
+ <Real Name="Cell 3 12 10">2.776053042473103e-09</Real>
+ <Real Name="Cell 3 12 2">0.01501482022851703</Real>
+ <Real Name="Cell 3 12 3">0.011556837865464914</Real>
+ <Real Name="Cell 3 12 4">0.0007300338991384314</Real>
+ <Real Name="Cell 3 12 6">1.4834224157735271e-07</Real>
+ <Real Name="Cell 3 12 7">3.9373389540956572e-06</Real>
+ <Real Name="Cell 3 12 8">7.1032566478014289e-06</Real>
+ <Real Name="Cell 3 12 9">1.3450212590240926e-06</Real>
+ <Real Name="Cell 3 13 0">5.5396055947692468e-09</Real>
+ <Real Name="Cell 3 13 1">4.2008719542286094e-05</Real>
+ <Real Name="Cell 3 13 2">0.00032950448915041591</Real>
+ <Real Name="Cell 3 13 3">0.00025361808527162813</Real>
+ <Real Name="Cell 3 13 4">1.6020801004412256e-05</Real>
+ <Real Name="Cell 3 2 1">5.7891050816361839e-05</Real>
+ <Real Name="Cell 3 2 2">0.09721678263018102</Real>
+ <Real Name="Cell 3 2 3">0.64056589440933942</Real>
+ <Real Name="Cell 3 2 4">0.42822520071010828</Real>
+ <Real Name="Cell 3 2 5">0.021913032438109804</Real>
+ <Real Name="Cell 3 2 6">5.0231996614006669e-09</Real>
+ <Real Name="Cell 3 3 1">5.2628228014874394e-06</Real>
+ <Real Name="Cell 3 3 2">0.010397691800003023</Real>
+ <Real Name="Cell 3 3 3">0.080708066485339736</Real>
+ <Real Name="Cell 3 3 4">0.066281637762740306</Real>
+ <Real Name="Cell 3 3 5">0.0052029917471760924</Real>
+ <Real Name="Cell 3 3 6">1.5024314242510404e-07</Real>
+ <Real Name="Cell 3 4 0">0.00042627683636924086</Real>
+ <Real Name="Cell 3 4 1">3.5400118501063598e-06</Real>
+ <Real Name="Cell 3 4 10">0.0016403087931345433</Real>
+ <Real Name="Cell 3 4 2">0.0034808370906558397</Real>
+ <Real Name="Cell 3 4 3">0.051432846937786748</Real>
+ <Real Name="Cell 3 4 4">0.063834141187148558</Real>
+ <Real Name="Cell 3 4 5">0.007715147612600063</Real>
+ <Real Name="Cell 3 4 6">8.0719946226841859e-06</Real>
+ <Real Name="Cell 3 4 7">2.8905201917854722e-07</Real>
+ <Real Name="Cell 3 4 8">1.7251012675847173e-05</Real>
+ <Real Name="Cell 3 4 9">0.0007024471648445108</Real>
+ <Real Name="Cell 3 5 0">0.038843463774114781</Real>
+ <Real Name="Cell 3 5 1">0.00040617331381915986</Real>
+ <Real Name="Cell 3 5 10">0.14090827988121804</Real>
+ <Real Name="Cell 3 5 2">0.0032375401801130123</Real>
+ <Real Name="Cell 3 5 3">0.053378565968710129</Real>
+ <Real Name="Cell 3 5 4">0.072116871072104641</Real>
+ <Real Name="Cell 3 5 5">0.010959943190772807</Real>
+ <Real Name="Cell 3 5 6">0.00076349338601510212</Real>
+ <Real Name="Cell 3 5 7">2.9714777332976491e-05</Real>
+ <Real Name="Cell 3 5 8">0.0013464653227093061</Real>
+ <Real Name="Cell 3 5 9">0.057834307728261175</Real>
+ <Real Name="Cell 3 6 0">0.12844990304803641</Real>
+ <Real Name="Cell 3 6 1">0.0020584050051700854</Real>
+ <Real Name="Cell 3 6 10">0.45387946717560984</Real>
+ <Real Name="Cell 3 6 2">0.0036705613989806126</Real>
+ <Real Name="Cell 3 6 3">0.026615293169202178</Real>
+ <Real Name="Cell 3 6 4">0.036360670942867442</Real>
+ <Real Name="Cell 3 6 5">0.00948331127843852</Real>
+ <Real Name="Cell 3 6 6">0.0025919335890815512</Real>
+ <Real Name="Cell 3 6 7">0.00010106494234577331</Real>
+ <Real Name="Cell 3 6 8">0.0041346253583830614</Real>
+ <Real Name="Cell 3 6 9">0.1825406702977076</Real>
+ <Real Name="Cell 3 7 0">0.046854556628265369</Real>
+ <Real Name="Cell 3 7 1">0.0024852906899019353</Real>
+ <Real Name="Cell 3 7 10">0.16105010198619132</Real>
+ <Real Name="Cell 3 7 2">0.0066179651088454708</Real>
+ <Real Name="Cell 3 7 3">0.0034829970604281163</Real>
+ <Real Name="Cell 3 7 4">0.0018415011223243494</Real>
+ <Real Name="Cell 3 7 5">0.0021945009003438366</Real>
+ <Real Name="Cell 3 7 6">0.0058904838841050437</Real>
+ <Real Name="Cell 3 7 7">0.0072126942384354003</Real>
+ <Real Name="Cell 3 7 8">0.002542452620295974</Real>
+ <Real Name="Cell 3 7 9">0.063390368677478146</Real>
+ <Real Name="Cell 3 8 0">0.00081167656518140406</Real>
+ <Real Name="Cell 3 8 1">0.00064814940457490655</Real>
+ <Real Name="Cell 3 8 10">0.0026967484413552428</Real>
+ <Real Name="Cell 3 8 2">0.0021666629694003666</Real>
+ <Real Name="Cell 3 8 3">0.00080328969882139376</Real>
+ <Real Name="Cell 3 8 4">2.0642453325401946e-05</Real>
+ <Real Name="Cell 3 8 5">0.0065496328757935858</Real>
+ <Real Name="Cell 3 8 6">0.12168226372182953</Real>
+ <Real Name="Cell 3 8 7">0.18480653103918754</Real>
+ <Real Name="Cell 3 8 8">0.04895768729010485</Real>
+ <Real Name="Cell 3 8 9">0.008200171024165535</Real>
+ <Real Name="Cell 3 9 0">8.2631323967394557e-08</Real>
+ <Real Name="Cell 3 9 1">1.6680051643878867e-05</Real>
+ <Real Name="Cell 3 9 10">0.00042522376422769737</Real>
+ <Real Name="Cell 3 9 2">9.3595902306118088e-05</Real>
+ <Real Name="Cell 3 9 3">6.066457974084798e-05</Real>
+ <Real Name="Cell 3 9 4">3.3465468049840549e-06</Real>
+ <Real Name="Cell 3 9 5">0.011255316288033328</Real>
+ <Real Name="Cell 3 9 6">0.21255370244104035</Real>
+ <Real Name="Cell 3 9 7">0.39282391120328353</Real>
+ <Real Name="Cell 3 9 8">0.23309730265154127</Real>
+ <Real Name="Cell 3 9 9">0.046568625001872858</Real>
+ <Real Name="Cell 4 0 1">6.0811406856676172e-06</Real>
+ <Real Name="Cell 4 0 2">0.010206580314244826</Real>
+ <Real Name="Cell 4 0 3">0.067208512763000036</Real>
+ <Real Name="Cell 4 0 4">0.044886039264514691</Real>
+ <Real Name="Cell 4 0 5">0.0022904952903622221</Real>
+ <Real Name="Cell 4 1 1">6.6892547542343791e-05</Real>
+ <Real Name="Cell 4 1 2">0.11227238345669309</Real>
+ <Real Name="Cell 4 1 3">0.7392936403930005</Real>
+ <Real Name="Cell 4 1 4">0.49374643190966166</Real>
+ <Real Name="Cell 4 1 5">0.025195448193984445</Real>
+ <Real Name="Cell 4 10 0">2.6365335974922171e-06</Real>
+ <Real Name="Cell 4 10 1">0.019993733952006879</Real>
+ <Real Name="Cell 4 10 10">1.0585583797748487e-05</Real>
+ <Real Name="Cell 4 10 2">0.15682518210139279</Real>
+ <Real Name="Cell 4 10 3">0.12070761921781678</Real>
+ <Real Name="Cell 4 10 4">0.007624979682083209</Real>
+ <Real Name="Cell 4 10 5">1.985737245315617e-05</Real>
+ <Real Name="Cell 4 10 6">0.00093562871576644273</Real>
+ <Real Name="Cell 4 10 7">0.015549876791515571</Real>
+ <Real Name="Cell 4 10 8">0.027164212367843568</Real>
+ <Real Name="Cell 4 10 9">0.0051288401348717925</Real>
+ <Real Name="Cell 4 11 0">1.0099709837149708e-05</Real>
+ <Real Name="Cell 4 11 1">0.076589546087524898</Real>
+ <Real Name="Cell 4 11 10">1.4640578091548502e-06</Real>
+ <Real Name="Cell 4 11 2">0.60074669099182854</Real>
+ <Real Name="Cell 4 11 3">0.4623919567695568</Real>
+ <Real Name="Cell 4 11 4">0.029208837837853406</Real>
+ <Real Name="Cell 4 11 5">3.2028034575442935e-08</Real>
+ <Real Name="Cell 4 11 6">7.883068954859417e-05</Real>
+ <Real Name="Cell 4 11 7">0.002077371059295864</Real>
+ <Real Name="Cell 4 11 8">0.0037463004093973139</Real>
+ <Real Name="Cell 4 11 9">0.00070934849014010672</Real>
+ <Real Name="Cell 4 12 0">4.1927835370487033e-06</Real>
+ <Real Name="Cell 4 12 1">0.031795308293375013</Real>
+ <Real Name="Cell 4 12 10">4.2438335557221526e-10</Real>
+ <Real Name="Cell 4 12 2">0.24939338620027793</Real>
+ <Real Name="Cell 4 12 3">0.19195693888907472</Real>
+ <Real Name="Cell 4 12 4">0.012125728005809607</Real>
+ <Real Name="Cell 4 12 6">2.2677512745800168e-08</Real>
+ <Real Name="Cell 4 12 7">6.0191253257744655e-07</Real>
+ <Real Name="Cell 4 12 8">1.0858956387227687e-06</Real>
+ <Real Name="Cell 4 12 9">2.0561733745263642e-07</Real>
+ <Real Name="Cell 4 13 0">9.2011824082289251e-08</Real>
+ <Real Name="Cell 4 13 1">0.00069775705983416022</Real>
+ <Real Name="Cell 4 13 2">0.0054730086052806022</Real>
+ <Real Name="Cell 4 13 3">0.004212549476109796</Real>
+ <Real Name="Cell 4 13 4">0.00026610254077785972</Real>
+ <Real Name="Cell 4 2 1">6.6892547542343791e-05</Real>
+ <Real Name="Cell 4 2 2">0.11292212713501221</Real>
+ <Real Name="Cell 4 2 3">0.74865477245871004</Real>
+ <Real Name="Cell 4 2 4">0.50513819461116538</Real>
+ <Real Name="Cell 4 2 5">0.026532602268906705</Real>
+ <Real Name="Cell 4 2 6">6.2165005286672365e-08</Real>
+ <Real Name="Cell 4 3 1">6.0811406856676172e-06</Real>
+ <Real Name="Cell 4 3 2">0.029564030388621168</Real>
+ <Real Name="Cell 4 3 3">0.34611113551190642</Real>
+ <Real Name="Cell 4 3 4">0.38429990929763463</Real>
+ <Real Name="Cell 4 3 5">0.04213246917556733</Real>
+ <Real Name="Cell 4 3 6">1.8551466278606118e-06</Real>
+ <Real Name="Cell 4 4 0">0.000587015315588387</Real>
+ <Real Name="Cell 4 4 1">3.0184743439997748e-06</Real>
+ <Real Name="Cell 4 4 10">0.0024701099633055688</Real>
+ <Real Name="Cell 4 4 2">0.039929919870704746</Real>
+ <Real Name="Cell 4 4 3">0.58252826879948949</Real>
+ <Real Name="Cell 4 4 4">0.71603854793436361</Real>
+ <Real Name="Cell 4 4 5">0.085451240682146615</Real>
+ <Real Name="Cell 4 4 6">7.9870149908774731e-05</Real>
+ <Real Name="Cell 4 4 7">2.5408575582109795e-06</Real>
+ <Real Name="Cell 4 4 8">2.9321126629228444e-05</Real>
+ <Real Name="Cell 4 4 9">0.0011197097060561922</Real>
+ <Real Name="Cell 4 5 0">0.044911610496675393</Real>
+ <Real Name="Cell 4 5 1">0.00061070818274139803</Real>
+ <Real Name="Cell 4 5 10">0.18847039345735117</Real>
+ <Real Name="Cell 4 5 2">0.023496837590293872</Real>
+ <Real Name="Cell 4 5 3">0.36467203383387659</Real>
+ <Real Name="Cell 4 5 4">0.51332372955600192</Real>
+ <Real Name="Cell 4 5 5">0.10248792206783859</Real>
+ <Real Name="Cell 4 5 6">0.0086736152554076178</Real>
+ <Real Name="Cell 4 5 7">0.00026120217665877185</Real>
+ <Real Name="Cell 4 5 8">0.0022300016249293744</Real>
+ <Real Name="Cell 4 5 9">0.085300750479011755</Real>
+ <Real Name="Cell 4 6 0">0.13668149835813465</Real>
+ <Real Name="Cell 4 6 1">0.029253119243852786</Real>
+ <Real Name="Cell 4 6 10">0.57162559989159067</Real>
+ <Real Name="Cell 4 6 2">0.10551829686535634</Real>
+ <Real Name="Cell 4 6 3">0.19834120985432607</Real>
+ <Real Name="Cell 4 6 4">0.35388301915279685</Real>
+ <Real Name="Cell 4 6 5">0.1889207437188786</Real>
+ <Real Name="Cell 4 6 6">0.031294920070306806</Real>
+ <Real Name="Cell 4 6 7">0.00088839241932710722</Real>
+ <Real Name="Cell 4 6 8">0.0067513973570738073</Real>
+ <Real Name="Cell 4 6 9">0.25849011249778781</Real>
+ <Real Name="Cell 4 7 0">0.046113586911392966</Real>
+ <Real Name="Cell 4 7 1">0.086586623549942399</Real>
+ <Real Name="Cell 4 7 10">0.18939130215353053</Real>
+ <Real Name="Cell 4 7 2">0.29401359829336382</Real>
+ <Real Name="Cell 4 7 3">0.1226165174894152</Real>
+ <Real Name="Cell 4 7 4">0.080674623996323191</Real>
+ <Real Name="Cell 4 7 5">0.072437720000441491</Real>
+ <Real Name="Cell 4 7 6">0.012449077210919422</Real>
+ <Real Name="Cell 4 7 7">0.00039933846794491562</Real>
+ <Real Name="Cell 4 7 8">0.0022422119322471771</Real>
+ <Real Name="Cell 4 7 9">0.085552623145093917</Real>
+ <Real Name="Cell 4 8 0">0.00088190565035645976</Real>
+ <Real Name="Cell 4 8 1">0.028534428512314008</Real>
+ <Real Name="Cell 4 8 10">0.0025142438095358496</Real>
+ <Real Name="Cell 4 8 2">0.097038819412092817</Real>
+ <Real Name="Cell 4 8 3">0.036184746445648806</Real>
+ <Real Name="Cell 4 8 4">0.0025278411086193707</Real>
+ <Real Name="Cell 4 8 5">0.0018660508879273638</Real>
+ <Real Name="Cell 4 8 6">0.0014684278997884725</Real>
+ <Real Name="Cell 4 8 7">0.0023522276490109636</Real>
+ <Real Name="Cell 4 8 8">0.0014009731105222895</Real>
+ <Real Name="Cell 4 8 9">0.001343792287701223</Real>
+ <Real Name="Cell 4 9 0">3.6699944314404438e-06</Real>
+ <Real Name="Cell 4 9 1">0.00051323694881170502</Real>
+ <Real Name="Cell 4 9 10">7.6313889834793078e-06</Real>
+ <Real Name="Cell 4 9 2">0.0023579123079199684</Real>
+ <Real Name="Cell 4 9 3">0.001305385804122302</Real>
+ <Real Name="Cell 4 9 4">6.0712403742290838e-05</Real>
+ <Real Name="Cell 4 9 5">0.00011036854728014495</Real>
+ <Real Name="Cell 4 9 6">0.0024641295503743874</Real>
+ <Real Name="Cell 4 9 7">0.013803468717253149</Real>
+ <Real Name="Cell 4 9 8">0.019961719491648291</Real>
+ <Real Name="Cell 4 9 9">0.0036976669643922848</Real>
+ <Real Name="Cell 5 0 1">6.6801493069522987e-07</Real>
+ <Real Name="Cell 5 0 2">0.0011211955772253319</Real>
+ <Real Name="Cell 5 0 3">0.0073828731016401432</Real>
+ <Real Name="Cell 5 0 4">0.0049307434177830248</Real>
+ <Real Name="Cell 5 0 5">0.00025161152022929893</Real>
+ <Real Name="Cell 5 1 1">7.3481642376475287e-06</Real>
+ <Real Name="Cell 5 1 2">0.012333151349478651</Real>
+ <Real Name="Cell 5 1 3">0.081211604118041569</Real>
+ <Real Name="Cell 5 1 4">0.054238177595613266</Real>
+ <Real Name="Cell 5 1 5">0.002767726722522288</Real>
+ <Real Name="Cell 5 10 0">3.5393822397109359e-06</Real>
+ <Real Name="Cell 5 10 1">0.026840343291110891</Real>
+ <Real Name="Cell 5 10 10">6.5998975308475378e-09</Real>
+ <Real Name="Cell 5 10 2">0.21052804515636045</Real>
+ <Real Name="Cell 5 10 3">0.16204246517613069</Real>
+ <Real Name="Cell 5 10 4">0.010236060595090411</Real>
+ <Real Name="Cell 5 10 6">3.5267467117074908e-07</Real>
+ <Real Name="Cell 5 10 7">9.3607842658854868e-06</Real>
+ <Real Name="Cell 5 10 8">1.6887561330253376e-05</Real>
+ <Real Name="Cell 5 10 9">3.1977063660362546e-06</Real>
+ <Real Name="Cell 5 11 0">1.3558231785038738e-05</Real>
+ <Real Name="Cell 5 11 1">0.10281669819324503</Real>
+ <Real Name="Cell 5 11 10">9.1281045091860911e-10</Real>
+ <Real Name="Cell 5 11 2">0.80646503829271543</Real>
+ <Real Name="Cell 5 11 3">0.62073241969380488</Real>
+ <Real Name="Cell 5 11 4">0.039211046650127243</Real>
+ <Real Name="Cell 5 11 6">4.8777291482827472e-08</Real>
+ <Real Name="Cell 5 11 7">1.2946597529367214e-06</Real>
+ <Real Name="Cell 5 11 8">2.3356639100432653e-06</Real>
+ <Real Name="Cell 5 11 9">4.4226441035547786e-07</Real>
+ <Real Name="Cell 5 12 0">5.6285509124927381e-06</Real>
+ <Real Name="Cell 5 12 1">0.042683222237996747</Real>
+ <Real Name="Cell 5 12 10">2.6459444411273003e-13</Real>
+ <Real Name="Cell 5 12 2">0.33479509711472194</Real>
+ <Real Name="Cell 5 12 3">0.25769024181580685</Real>
+ <Real Name="Cell 5 12 4">0.016278035063975595</Real>
+ <Real Name="Cell 5 12 6">1.4138970815063686e-11</Real>
+ <Real Name="Cell 5 12 7">3.7528029756745265e-10</Real>
+ <Real Name="Cell 5 12 8">6.7703398146913598e-10</Real>
+ <Real Name="Cell 5 12 9">1.2819825374598627e-10</Real>
+ <Real Name="Cell 5 13 0">1.2352014641877625e-07</Real>
+ <Real Name="Cell 5 13 1">0.00093669541991005787</Real>
+ <Real Name="Cell 5 13 2">0.0073471733770965027</Real>
+ <Real Name="Cell 5 13 3">0.005655085455322225</Real>
+ <Real Name="Cell 5 13 4">0.00035722609704915478</Real>
+ <Real Name="Cell 5 2 1">7.3481642376475287e-06</Real>
+ <Real Name="Cell 5 2 2">0.013042143634651629</Real>
+ <Real Name="Cell 5 2 3">0.091426355929468628</Real>
+ <Real Name="Cell 5 2 4">0.066668728502675093</Real>
+ <Real Name="Cell 5 2 5">0.0042268127511236667</Real>
+ <Real Name="Cell 5 2 6">6.7833686770156194e-08</Real>
+ <Real Name="Cell 5 3 1">6.6801493069522987e-07</Real>
+ <Real Name="Cell 5 3 2">0.022241664194336302</Real>
+ <Real Name="Cell 5 3 3">0.31168122240742901</Real>
+ <Real Name="Cell 5 3 4">0.37524454556954639</Real>
+ <Real Name="Cell 5 3 5">0.043719801159408919</Real>
+ <Real Name="Cell 5 3 6">2.0225412078983892e-06</Real>
+ <Real Name="Cell 5 4 0">0.00010653918816651577</Real>
+ <Real Name="Cell 5 4 1">5.3623884589502417e-07</Real>
+ <Real Name="Cell 5 4 10">0.00044962719916150242</Real>
+ <Real Name="Cell 5 4 2">0.042242958063500702</Real>
+ <Real Name="Cell 5 4 3">0.61295662309693943</Real>
+ <Real Name="Cell 5 4 4">0.75088323345063446</Real>
+ <Real Name="Cell 5 4 5">0.089629650057529514</Real>
+ <Real Name="Cell 5 4 6">0.00011787241108008185</Real>
+ <Real Name="Cell 5 4 7">2.1398031419035043e-06</Real>
+ <Real Name="Cell 5 4 8">5.3563348578314463e-06</Real>
+ <Real Name="Cell 5 4 9">0.00020417116915455951</Real>
+ <Real Name="Cell 5 5 0">0.0081056073864261835</Real>
+ <Real Name="Cell 5 5 1">0.00093744906805072914</Real>
+ <Real Name="Cell 5 5 10">0.034171272140952703</Real>
+ <Real Name="Cell 5 5 2">0.01991522221554216</Real>
+ <Real Name="Cell 5 5 3">0.29241884634567228</Real>
+ <Real Name="Cell 5 5 4">0.56314919987641943</Real>
+ <Real Name="Cell 5 5 5">0.23249097234455948</Real>
+ <Real Name="Cell 5 5 6">0.018178802605955689</Real>
+ <Real Name="Cell 5 5 7">0.00021997346387257196</Real>
+ <Real Name="Cell 5 5 8">0.00040707674368090373</Real>
+ <Real Name="Cell 5 5 9">0.015516829492361151</Real>
+ <Real Name="Cell 5 6 0">0.025166538179984405</Real>
+ <Real Name="Cell 5 6 1">0.068272168746508821</Real>
+ <Real Name="Cell 5 6 10">0.10341257342264018</Real>
+ <Real Name="Cell 5 6 2">0.23676580818573023</Real>
+ <Real Name="Cell 5 6 3">0.27850507761420418</Real>
+ <Real Name="Cell 5 6 4">1.0513162219764158</Real>
+ <Real Name="Cell 5 6 5">0.81949700800476777</Real>
+ <Real Name="Cell 5 6 6">0.073395637261637017</Real>
+ <Real Name="Cell 5 6 7">0.00074816665104905969</Real>
+ <Real Name="Cell 5 6 8">0.0012319369753313802</Real>
+ <Real Name="Cell 5 6 9">0.046958604951739688</Real>
+ <Real Name="Cell 5 7 0">0.010103024267042652</Real>
+ <Real Name="Cell 5 7 1">0.20628063442319733</Real>
+ <Real Name="Cell 5 7 10">0.034170950295530973</Real>
+ <Real Name="Cell 5 7 2">0.70165841477427537</Real>
+ <Real Name="Cell 5 7 3">0.31326546464329735</Real>
+ <Real Name="Cell 5 7 4">0.44176896497145529</Real>
+ <Real Name="Cell 5 7 5">0.37059277333899682</Real>
+ <Real Name="Cell 5 7 6">0.032286502959641465</Real>
+ <Real Name="Cell 5 7 7">0.00027732188980392105</Real>
+ <Real Name="Cell 5 7 8">0.00040707290958933969</Real>
+ <Real Name="Cell 5 7 9">0.015516683345606318</Real>
+ <Real Name="Cell 5 8 0">0.00076945915687349532</Real>
+ <Real Name="Cell 5 8 1">0.068149360973100898</Real>
+ <Real Name="Cell 5 8 10">0.00044961284265584929</Real>
+ <Real Name="Cell 5 8 2">0.23178534792764141</Real>
+ <Real Name="Cell 5 8 3">0.087279207571151665</Real>
+ <Real Name="Cell 5 8 4">0.013299556590620813</Real>
+ <Real Name="Cell 5 8 5">0.010002156198763004</Real>
+ <Real Name="Cell 5 8 6">0.00081197311820122649</Real>
+ <Real Name="Cell 5 8 7">5.1619762730474361e-06</Real>
+ <Real Name="Cell 5 8 8">6.0542717291521941e-06</Real>
+ <Real Name="Cell 5 8 9">0.00020429671539371323</Real>
+ <Real Name="Cell 5 9 0">8.7470740352536622e-06</Real>
+ <Real Name="Cell 5 9 1">0.0010817207936087941</Real>
+ <Real Name="Cell 5 9 10">4.758016777469524e-09</Real>
+ <Real Name="Cell 5 9 2">0.0045010967184971225</Real>
+ <Real Name="Cell 5 9 3">0.0022475177785366597</Real>
+ <Real Name="Cell 5 9 4">9.002770289817758e-05</Real>
+ <Real Name="Cell 5 9 6">2.5425122050394683e-07</Real>
+ <Real Name="Cell 5 9 7">6.7484030440145877e-06</Real>
+ <Real Name="Cell 5 9 8">1.2174628433901255e-05</Real>
+ <Real Name="Cell 5 9 9">2.3052995092588617e-06</Real>
+ <Real Name="Cell 6 0 1">9.9569463451105728e-12</Real>
+ <Real Name="Cell 6 0 2">1.6711728573475769e-08</Real>
+ <Real Name="Cell 6 0 3">1.1004375496410728e-07</Real>
+ <Real Name="Cell 6 0 4">7.3494087327176079e-08</Real>
+ <Real Name="Cell 6 0 5">3.7503389394717347e-09</Real>
+ <Real Name="Cell 6 1 1">1.0952640979621631e-10</Real>
+ <Real Name="Cell 6 1 2">1.8382901430823346e-07</Real>
+ <Real Name="Cell 6 1 3">1.2104813046051801e-06</Real>
+ <Real Name="Cell 6 1 4">8.0843496059893693e-07</Real>
+ <Real Name="Cell 6 1 5">4.1253728334189086e-08</Real>
+ <Real Name="Cell 6 10 0">4.7005982717197042e-07</Real>
+ <Real Name="Cell 6 10 1">0.0035646240711447843</Real>
+ <Real Name="Cell 6 10 2">0.027959900858047414</Real>
+ <Real Name="Cell 6 10 3">0.021520606709444542</Real>
+ <Real Name="Cell 6 10 4">0.0013594352201538366</Real>
+ <Real Name="Cell 6 11 0">1.800647587064043e-06</Real>
+ <Real Name="Cell 6 11 1">0.013654925099883123</Real>
+ <Real Name="Cell 6 11 2">0.10710536213547556</Real>
+ <Real Name="Cell 6 11 3">0.08243850315108632</Real>
+ <Real Name="Cell 6 11 4">0.0052075578627235808</Real>
+ <Real Name="Cell 6 12 0">7.4751905557706981e-07</Real>
+ <Real Name="Cell 6 12 1">0.0056686920794330959</Real>
+ <Real Name="Cell 6 12 2">0.044463613938635266</Real>
+ <Real Name="Cell 6 12 3">0.034223438534780631</Real>
+ <Real Name="Cell 6 12 4">0.002161860412538138</Real>
+ <Real Name="Cell 6 13 0">1.6404517722451026e-08</Real>
+ <Real Name="Cell 6 13 1">0.00012440105571407794</Real>
+ <Real Name="Cell 6 13 2">0.00097576662082209684</Real>
+ <Real Name="Cell 6 13 3">0.00075104306676652944</Real>
+ <Real Name="Cell 6 13 4">4.7442640005436991e-05</Real>
+ <Real Name="Cell 6 2 1">1.0952640979621631e-10</Real>
+ <Real Name="Cell 6 2 2">7.249742613524083e-05</Real>
+ <Real Name="Cell 6 2 3">0.0010430630693079226</Real>
+ <Real Name="Cell 6 2 4">0.0012686612298118173</Real>
+ <Real Name="Cell 6 2 5">0.00014886058708866713</Real>
+ <Real Name="Cell 6 2 6">6.9186900886062962e-09</Real>
+ <Real Name="Cell 6 3 1">9.9569463451105728e-12</Real>
+ <Real Name="Cell 6 3 2">0.0021540462685153455</Real>
+ <Real Name="Cell 6 3 3">0.031034407153948909</Real>
+ <Real Name="Cell 6 3 4">0.037766649253532458</Real>
+ <Real Name="Cell 6 3 5">0.0044330538887957273</Real>
+ <Real Name="Cell 6 3 6">2.0616437515539892e-07</Real>
+ <Real Name="Cell 6 4 0">1.8605274344523832e-07</Real>
+ <Real Name="Cell 6 4 1">9.3645080404352049e-10</Real>
+ <Real Name="Cell 6 4 10">7.8519815451238663e-07</Real>
+ <Real Name="Cell 6 4 2">0.0042152434969009766</Real>
+ <Real Name="Cell 6 4 3">0.060979669263615414</Real>
+ <Real Name="Cell 6 4 4">0.074927869949635836</Real>
+ <Real Name="Cell 6 4 5">0.0092869040285360211</Real>
+ <Real Name="Cell 6 4 6">4.1863798242267894e-05</Real>
+ <Real Name="Cell 6 4 7">1.5376751949877226e-07</Real>
+ <Real Name="Cell 6 4 8">9.3539364459331444e-09</Real>
+ <Real Name="Cell 6 4 9">3.5655055015302284e-07</Real>
+ <Real Name="Cell 6 5 0">1.6396472616472288e-05</Real>
+ <Real Name="Cell 6 5 1">0.00023205348902448984</Real>
+ <Real Name="Cell 6 5 10">5.96743699501574e-05</Real>
+ <Real Name="Cell 6 5 2">0.001990997708296922</Real>
+ <Real Name="Cell 6 5 3">0.034602716321019668</Real>
+ <Real Name="Cell 6 5 4">0.16179540654780275</Real>
+ <Real Name="Cell 6 5 5">0.11863014090461818</Real>
+ <Real Name="Cell 6 5 6">0.0085135403850301623</Real>
+ <Real Name="Cell 6 5 7">1.5807423231068199e-05</Real>
+ <Real Name="Cell 6 5 8">7.1089095250295752e-07</Real>
+ <Real Name="Cell 6 5 9">2.7097528583694584e-05</Real>
+ <Real Name="Cell 6 6 0">0.00021429509529400956</Real>
+ <Real Name="Cell 6 6 1">0.017630868154979922</Real>
+ <Real Name="Cell 6 6 10">0.00018059263753674208</Real>
+ <Real Name="Cell 6 6 2">0.060174469001166922</Real>
+ <Real Name="Cell 6 6 3">0.095100125373405134</Real>
+ <Real Name="Cell 6 6 4">0.60456394409670589</Real>
+ <Real Name="Cell 6 6 5">0.50060502742307966</Real>
+ <Real Name="Cell 6 6 6">0.036445059221526251</Real>
+ <Real Name="Cell 6 6 7">5.37636980947593e-05</Real>
+ <Real Name="Cell 6 6 8">2.1513703826407522e-06</Real>
+ <Real Name="Cell 6 6 9">8.2005292418571343e-05</Real>
+ <Real Name="Cell 6 7 0">0.00053316390534166472</Real>
+ <Real Name="Cell 6 7 1">0.05335598970762679</Real>
+ <Real Name="Cell 6 7 10">5.9673807901349731e-05</Real>
+ <Real Name="Cell 6 7 2">0.18148172267598461</Real>
+ <Real Name="Cell 6 7 3">0.099598782295309621</Real>
+ <Real Name="Cell 6 7 4">0.27959541735444116</Real>
+ <Real Name="Cell 6 7 5">0.23193886550615328</Real>
+ <Real Name="Cell 6 7 6">0.016793788683833303</Real>
+ <Real Name="Cell 6 7 7">1.9928515040840058e-05</Real>
+ <Real Name="Cell 6 7 8">7.1088425690797147e-07</Real>
+ <Real Name="Cell 6 7 9">2.7097273363008653e-05</Real>
+ <Real Name="Cell 6 8 0">0.00017168967930050437</Real>
+ <Real Name="Cell 6 8 1">0.017630650848171565</Real>
+ <Real Name="Cell 6 8 10">7.8517260683931051e-07</Real>
+ <Real Name="Cell 6 8 2">0.05996475648638866</Real>
+ <Real Name="Cell 6 8 3">0.023108395611492947</Real>
+ <Real Name="Cell 6 8 4">0.0079994069118838572</Real>
+ <Real Name="Cell 6 8 5">0.006340722447411404</Real>
+ <Real Name="Cell 6 8 6">0.00045464336680280028</Real>
+ <Real Name="Cell 6 8 7">3.4313525080816315e-07</Real>
+ <Real Name="Cell 6 8 8">9.3536321007065007e-09</Real>
+ <Real Name="Cell 6 8 9">3.5653894921275306e-07</Real>
+ <Real Name="Cell 6 9 0">2.2598666876396731e-06</Real>
+ <Real Name="Cell 6 9 1">0.00025655519153948544</Real>
+ <Real Name="Cell 6 9 2">0.0009817530230581521</Real>
+ <Real Name="Cell 6 9 3">0.0004408145560120188</Real>
+ <Real Name="Cell 6 9 4">1.4407031242653609e-05</Real>
+ <Real Name="Cell 7 10 0">9.417616732444329e-11</Real>
+ <Real Name="Cell 7 10 1">7.1417001319292355e-07</Real>
+ <Real Name="Cell 7 10 2">5.6017471593440044e-06</Real>
+ <Real Name="Cell 7 10 3">4.3116389472923664e-06</Real>
+ <Real Name="Cell 7 10 4">2.7236192365171194e-07</Real>
+ <Real Name="Cell 7 11 0">3.6075852189270068e-10</Real>
+ <Real Name="Cell 7 11 1">2.7357549755871065e-06</Real>
+ <Real Name="Cell 7 11 2">2.1458486606908898e-05</Real>
+ <Real Name="Cell 7 11 3">1.6516498151825687e-05</Real>
+ <Real Name="Cell 7 11 4">1.0433306832071701e-06</Real>
+ <Real Name="Cell 7 12 0">1.4976493541210618e-10</Real>
+ <Real Name="Cell 7 12 1">1.1357186105336493e-06</Real>
+ <Real Name="Cell 7 12 2">8.9082548732725608e-06</Real>
+ <Real Name="Cell 7 12 3">6.8566426815498987e-06</Real>
+ <Real Name="Cell 7 12 4">4.3312726630603258e-07</Real>
+ <Real Name="Cell 7 13 0">3.2866339912539245e-12</Real>
+ <Real Name="Cell 7 13 1">2.492366707606405e-08</Real>
+ <Real Name="Cell 7 13 2">1.9549418018768319e-07</Real>
+ <Real Name="Cell 7 13 3">1.5047096866201918e-07</Real>
+ <Real Name="Cell 7 13 4">9.5051007237654569e-09</Real>
+ <Real Name="Cell 7 2 2">1.5824445019438774e-10</Real>
+ <Real Name="Cell 7 2 3">2.2798947436741577e-09</Real>
+ <Real Name="Cell 7 2 4">2.7744528890345081e-09</Real>
+ <Real Name="Cell 7 2 5">3.2566259353020388e-10</Real>
+ <Real Name="Cell 7 2 6">1.5140227463804852e-14</Real>
+ <Real Name="Cell 7 3 2">4.7134565129665686e-09</Real>
+ <Real Name="Cell 7 3 3">6.7908762141412058e-08</Real>
+ <Real Name="Cell 7 3 4">8.2639631428934694e-08</Real>
+ <Real Name="Cell 7 3 5">9.7001599147327556e-09</Real>
+ <Real Name="Cell 7 3 6">4.5096560201260841e-13</Real>
+ <Real Name="Cell 7 4 2">9.2204302934674245e-09</Real>
+ <Real Name="Cell 7 4 3">3.722633554063567e-06</Real>
+ <Real Name="Cell 7 4 4">3.1186802917091703e-05</Real>
+ <Real Name="Cell 7 4 5">2.5794980566283604e-05</Real>
+ <Real Name="Cell 7 4 6">1.8169870306999936e-06</Real>
+ <Real Name="Cell 7 5 0">1.5128749607123834e-08</Real>
+ <Real Name="Cell 7 5 1">1.5552422060434383e-06</Real>
+ <Real Name="Cell 7 5 2">5.3207630150312277e-06</Real>
+ <Real Name="Cell 7 5 3">0.00077902940276503442</Real>
+ <Real Name="Cell 7 5 4">0.0067126009639382738</Real>
+ <Real Name="Cell 7 5 5">0.0055764797454387303</Real>
+ <Real Name="Cell 7 5 6">0.00039308923379469585</Real>
+ <Real Name="Cell 7 6 0">1.149784740992458e-06</Real>
+ <Real Name="Cell 7 6 1">0.00011819838410268673</Real>
+ <Real Name="Cell 7 6 2">0.00040213864420885154</Real>
+ <Real Name="Cell 7 6 3">0.0035096071237953508</Real>
+ <Real Name="Cell 7 6 4">0.029033306212592931</Real>
+ <Real Name="Cell 7 6 5">0.024117450841427791</Real>
+ <Real Name="Cell 7 6 6">0.0017000540105888611</Real>
+ <Real Name="Cell 7 7 0">3.4796114336337115e-06</Real>
+ <Real Name="Cell 7 7 1">0.00035770560705626522</Real>
+ <Real Name="Cell 7 7 2">0.0012166740486485661</Real>
+ <Real Name="Cell 7 7 3">0.0020113925291494706</Real>
+ <Real Name="Cell 7 7 4">0.013487672213987152</Real>
+ <Real Name="Cell 7 7 5">0.01119850893059283</Real>
+ <Real Name="Cell 7 7 6">0.00078938981378719251</Real>
+ <Real Name="Cell 7 8 0">1.1497845542785223e-06</Real>
+ <Real Name="Cell 7 8 1">0.00011819836490841088</Real>
+ <Real Name="Cell 7 8 2">0.00040201357626689033</Real>
+ <Real Name="Cell 7 8 3">0.00019173837051812416</Real>
+ <Real Name="Cell 7 8 4">0.00037165171663785244</Real>
+ <Real Name="Cell 7 8 5">0.00030662024662803062</Real>
+ <Real Name="Cell 7 8 6">2.1613850637548296e-05</Real>
+ <Real Name="Cell 7 9 0">1.5129390330565356e-08</Real>
+ <Real Name="Cell 7 9 1">1.5601645178667451e-06</Real>
+ <Real Name="Cell 7 9 2">5.3282461478527664e-06</Real>
+ <Real Name="Cell 7 9 3">1.9904200548264883e-06</Real>
+ <Real Name="Cell 7 9 4">3.5637343175257864e-08</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>0.036090455589515444</Real>
+ <Real>0.69648414270597081</Real>
+ <Real>0.26742540170451373</Real>
+ <Real>0.18259480726201247</Real>
+ <Real>0.73911958987718629</Real>
+ <Real>0.078285602860801204</Real>
+ <Real>0.18282127502653051</Real>
+ <Real>0.73904129300301158</Real>
+ <Real>0.07813743197045793</Real>
+ <Real>0.02177213641407599</Real>
+ <Real>0.66512837230808042</Real>
+ <Real>0.31309949127784359</Real>
+ <Real>0.088180370703606098</Real>
+ <Real>0.74359251957216421</Real>
+ <Real>0.16822710972422975</Real>
+ <Real>0.1357364132155662</Real>
+ <Real>0.74955771627354661</Real>
+ <Real>0.11470587051088713</Real>
+ <Real>0.2383247396874062</Real>
+ <Real>0.71374857926586222</Real>
+ <Real>0.047926681046731583</Real>
+ <Real>0.0038522301444038455</Real>
+ <Real>0.58007059475992295</Real>
+ <Real>0.41607717509567321</Real>
+ <Real>0.025951435289900862</Real>
+ <Real>0.67591914455438529</Real>
+ <Real>0.29812942015571386</Real>
+ <Real>0.13200413949930864</Real>
+ <Real>0.74980908057442919</Real>
+ <Real>0.11818677992626223</Real>
+ <Real>0.20127801669320952</Real>
+ <Real>0.73191700259416459</Real>
+ <Real>0.066804980712625833</Real>
+ <Real>0.016581614822692537</Real>
+ <Real>0.64894451221471561</Real>
+ <Real>0.33447387296259184</Real>
+ <Real>0.052315161615281575</Real>
+ <Real>0.71883578508770118</Real>
+ <Real>0.22884905329701719</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>0.0015578001757111505</Real>
+ <Real>0.5527019627575338</Real>
+ <Real>0.44574023706675503</Real>
+ <Real>0.49203512289596113</Real>
+ <Real>0.50793290228368859</Real>
+ <Real>3.1974820350303207e-05</Real>
+ <Real>0.30128157916062442</Real>
+ <Real>0.67368625927676062</Real>
+ <Real>0.025032161562614976</Real>
+ <Real>0.007465335582521662</Real>
+ <Real>0.60726045439259824</Real>
+ <Real>0.3852742100248801</Real>
+ <Real>0.27952824743682397</Real>
+ <Real>0.68864431084589117</Real>
+ <Real>0.031827441717284875</Real>
+ <Real>0.15426655549059071</Real>
+ <Real>0.74692445803843455</Real>
+ <Real>0.098808986470974761</Real>
+ <Real>0.14169664987958924</Real>
+ <Real>0.74895367333184837</Real>
+ <Real>0.10934967678856237</Real>
+ <Real>0.083426634674385811</Real>
+ <Real>0.74162349785931769</Real>
+ <Real>0.17494986746629645</Real>
+ <Real>0.012535251765837658</Real>
+ <Real>0.63326617425232812</Real>
+ <Real>0.35419857398183424</Real>
+ <Real>0.02716938719551423</Real>
+ <Real>0.6787680131356939</Real>
+ <Real>0.29406259966879189</Real>
+ <Real>0.21968820016588803</Real>
+ <Real>0.7234783351357893</Real>
+ <Real>0.056833464698322671</Real>
+ <Real>0.021448711607312865</Real>
+ <Real>0.66421950804553398</Real>
+ <Real>0.31433178034715314</Real>
+ <Real>0.34943592393514256</Real>
+ <Real>0.63711370695125913</Real>
+ <Real>0.013450369113598334</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>0.022015595113395979</Real>
+ <Real>0.66580491302236766</Real>
+ <Real>0.31217949186423638</Real>
+ <Real>0.1526054876007322</Real>
+ <Real>0.74724805061082555</Real>
+ <Real>0.1001464617884423</Real>
+ <Real>0.23929588540952862</Real>
+ <Real>0.71321150383281751</Real>
+ <Real>0.047492610757653875</Real>
+ <Real>0.20124826514116861</Real>
+ <Real>0.73192961221364883</Real>
+ <Real>0.066822122645182544</Real>
+ <Real>0.043536694275114363</Real>
+ <Real>0.70800861454421404</Real>
+ <Real>0.24845469118067159</Real>
+ <Real>0.41241064286055051</Real>
+ <Real>0.58337543620708399</Real>
+ <Real>0.0042139209323654933</Real>
+ <Real>0.076754913733512689</Real>
+ <Real>0.73829347454436067</Real>
+ <Real>0.18495161172212665</Real>
+ <Real>0.33324912758583197</Real>
+ <Real>0.64989518868470608</Real>
+ <Real>0.016855683729461973</Real>
+ <Real>0.193013961710223</Real>
+ <Real>0.73528353102124222</Real>
+ <Real>0.07170250726853479</Real>
+ <Real>0.15170115356515579</Real>
+ <Real>0.74741736130057479</Real>
+ <Real>0.10088148513426944</Real>
+ <Real>0.024127918118492662</Real>
+ <Real>0.67141627450305674</Real>
+ <Real>0.30445580737845057</Real>
+ <Real>0.42440740434438973</Real>
+ <Real>0.57249665259278926</Real>
+ <Real>0.0030959430628210299</Real>
+ <Real>0.1590110177845997</Real>
+ <Real>0.74591238931475767</Real>
+ <Real>0.095076592900642645</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>-0.26866505388500173</Real>
+ <Real>-0.46266989222999655</Real>
+ <Real>0.73133494611499827</Real>
+ <Real>-0.60430920440121128</Real>
+ <Real>0.20861840880242255</Real>
+ <Real>0.39569079559878872</Real>
+ <Real>-0.60468384305607259</Real>
+ <Real>0.20936768611214518</Real>
+ <Real>0.39531615694392741</Real>
+ <Real>-0.2086726451362324</Real>
+ <Real>-0.58265470972753519</Real>
+ <Real>0.7913273548637676</Real>
+ <Real>-0.41995326097937635</Real>
+ <Real>-0.16009347804124729</Real>
+ <Real>0.58004673902062365</Real>
+ <Real>-0.52103054270467908</Real>
+ <Real>0.042061085409358157</Real>
+ <Real>0.47896945729532092</Real>
+ <Real>-0.69039805864067461</Real>
+ <Real>0.38079611728134921</Real>
+ <Real>0.30960194135932539</Real>
+ <Real>-0.087775055048730621</Real>
+ <Real>-0.82444988990253876</Real>
+ <Real>0.91222494495126938</Real>
+ <Real>-0.22782201513418698</Real>
+ <Real>-0.54435596973162603</Real>
+ <Real>0.77217798486581302</Real>
+ <Real>-0.51381735957304642</Real>
+ <Real>0.027634719146092834</Real>
+ <Real>0.48618264042695358</Real>
+ <Real>-0.63447303598058369</Real>
+ <Real>0.26894607196116738</Real>
+ <Real>0.36552696401941631</Real>
+ <Real>-0.1821077418601007</Real>
+ <Real>-0.63578451627979859</Real>
+ <Real>0.8178922581398993</Real>
+ <Real>-0.32346610831826439</Real>
+ <Real>-0.35306778336347122</Real>
+ <Real>0.67653389168173561</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>-0.055817563108956136</Real>
+ <Real>-0.88836487378208773</Real>
+ <Real>0.94418243689104386</Real>
+ <Real>-0.99200314807561085</Real>
+ <Real>0.9840062961512217</Real>
+ <Real>0.0079968519243891478</Real>
+ <Real>-0.77624941759800947</Real>
+ <Real>0.55249883519601894</Real>
+ <Real>0.22375058240199053</Real>
+ <Real>-0.12219112555764156</Real>
+ <Real>-0.75561774888471689</Real>
+ <Real>0.87780887444235844</Real>
+ <Real>-0.74770080571953912</Real>
+ <Real>0.49540161143907824</Real>
+ <Real>0.25229919428046088</Real>
+ <Real>-0.55545756901961596</Real>
+ <Real>0.11091513803923192</Real>
+ <Real>0.44454243098038404</Real>
+ <Real>-0.53234697309102685</Real>
+ <Real>0.064693946182053708</Real>
+ <Real>0.46765302690897315</Real>
+ <Real>-0.40847676720808934</Real>
+ <Real>-0.18304646558382132</Real>
+ <Real>0.59152323279191066</Real>
+ <Real>-0.1583366777840034</Real>
+ <Real>-0.6833266444319932</Real>
+ <Real>0.8416633222159966</Real>
+ <Real>-0.23310678752672231</Real>
+ <Real>-0.53378642494655537</Real>
+ <Real>0.76689321247327769</Real>
+ <Real>-0.66285473546756535</Real>
+ <Real>0.3257094709351307</Real>
+ <Real>0.33714526453243465</Real>
+ <Real>-0.20711693126015973</Real>
+ <Real>-0.58576613747968054</Real>
+ <Real>0.79288306873984027</Real>
+ <Real>-0.83598555482154424</Real>
+ <Real>0.67197110964308848</Real>
+ <Real>0.16401444517845576</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>-0.20983610324915958</Real>
+ <Real>-0.58032779350168084</Real>
+ <Real>0.79016389675084042</Real>
+ <Real>-0.55245902581228989</Real>
+ <Real>0.10491805162457979</Real>
+ <Real>0.44754097418771011</Real>
+ <Real>-0.69180327465187474</Real>
+ <Real>0.38360654930374949</Real>
+ <Real>0.30819672534812526</Real>
+ <Real>-0.63442614249598606</Real>
+ <Real>0.26885228499197211</Real>
+ <Real>0.36557385750401394</Real>
+ <Real>-0.29508200309444277</Real>
+ <Real>-0.40983599381111446</Real>
+ <Real>0.70491799690555723</Real>
+ <Real>-0.90819672192818501</Real>
+ <Real>0.81639344385637003</Real>
+ <Real>0.091803278071814987</Real>
+ <Real>-0.39180330201138602</Real>
+ <Real>-0.21639339597722795</Real>
+ <Real>0.60819669798861398</Real>
+ <Real>-0.81639344385637003</Real>
+ <Real>0.63278688771274005</Real>
+ <Real>0.18360655614362997</Real>
+ <Real>-0.62131145444168823</Real>
+ <Real>0.24262290888337645</Real>
+ <Real>0.37868854555831177</Real>
+ <Real>-0.55081966843088637</Real>
+ <Real>0.10163933686177273</Real>
+ <Real>0.44918033156911363</Real>
+ <Real>-0.21967211074004211</Real>
+ <Real>-0.56065577851991577</Real>
+ <Real>0.78032788925995789</Real>
+ <Real>-0.92131146128156871</Real>
+ <Real>0.84262292256313742</Real>
+ <Real>0.078688538718431289</Real>
+ <Real>-0.56393442488395706</Real>
+ <Real>0.12786884976791413</Real>
+ <Real>0.43606557511604294</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">4</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">11</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">10</Int>
+ <Int Name="Z">13</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 1 1">2.5797474023194253e-05</Real>
+ <Real Name="Cell 0 1 2">0.0007801780901102414</Real>
+ <Real Name="Cell 0 1 3">0.00036580625190737114</Real>
+ <Real Name="Cell 0 1 4">0.0035520662581957122</Real>
+ <Real Name="Cell 0 1 5">0.057764916517143869</Real>
+ <Real Name="Cell 0 1 6">0.02027088964670782</Real>
+ <Real Name="Cell 0 2 1">0.0091528520468274425</Real>
+ <Real Name="Cell 0 2 2">0.27680441203410755</Real>
+ <Real Name="Cell 0 2 3">0.12978675735858289</Real>
+ <Real Name="Cell 0 2 4">0.0087508516326493032</Real>
+ <Real Name="Cell 0 2 5">0.14230934258266517</Real>
+ <Real Name="Cell 0 2 6">0.049939256440067588</Real>
+ <Real Name="Cell 0 3 1">0.041407805893118807</Real>
+ <Real Name="Cell 0 3 2">0.26913490493268388</Real>
+ <Real Name="Cell 0 3 3">0.10491796958061207</Real>
+ <Real Name="Cell 0 3 4">0.00040444278116904555</Real>
+ <Real Name="Cell 0 3 5">0.0065771868518180567</Real>
+ <Real Name="Cell 0 3 6">0.0023080692727983467</Real>
+ <Real Name="Cell 0 4 1">1.0682172328334281</Real>
+ <Real Name="Cell 0 4 2">1.4646071359710569</Real>
+ <Real Name="Cell 0 4 3">0.010564124651040705</Real>
+ <Real Name="Cell 0 5 1">0.53107624953265142</Real>
+ <Real Name="Cell 0 5 2">0.76927967298649325</Real>
+ <Real Name="Cell 0 5 3">0.010071897180004931</Real>
+ <Real Name="Cell 0 6 1">0.001204628163136146</Real>
+ <Real Name="Cell 0 6 2">0.003590344490542938</Real>
+ <Real Name="Cell 0 6 3">0.00023908031833318956</Real>
+ <Real Name="Cell 1 0 0">0.019349343136229973</Real>
+ <Real Name="Cell 1 0 1">0.073711006282066616</Real>
+ <Real Name="Cell 1 0 2">0.0071880624830126987</Real>
+ <Real Name="Cell 1 1 0">0.010822478801160527</Real>
+ <Real Name="Cell 1 1 1">0.041237961348894979</Real>
+ <Real Name="Cell 1 1 2">0.0043199895999238456</Real>
+ <Real Name="Cell 1 1 3">0.0001404567281062272</Real>
+ <Real Name="Cell 1 1 4">0.029953263720074206</Real>
+ <Real Name="Cell 1 1 5">0.48711022048472935</Real>
+ <Real Name="Cell 1 1 6">0.17093693059002246</Real>
+ <Real Name="Cell 1 11 0">0.00038301254287360795</Real>
+ <Real Name="Cell 1 11 1">0.0014590800191560194</Real>
+ <Real Name="Cell 1 11 2">0.0001422848347134895</Real>
+ <Real Name="Cell 1 2 1">0.0035143730995152579</Real>
+ <Real Name="Cell 1 2 2">0.10628315354633035</Real>
+ <Real Name="Cell 1 2 3">0.049833547663694334</Real>
+ <Real Name="Cell 1 2 4">0.073792701958529855</Real>
+ <Real Name="Cell 1 2 5">1.2000421609179603</Real>
+ <Real Name="Cell 1 2 6">0.42111931743457376</Real>
+ <Real Name="Cell 1 3 1">0.020371801103436751</Real>
+ <Real Name="Cell 1 3 2">0.10937164714289969</Real>
+ <Real Name="Cell 1 3 3">0.040317435195201638</Real>
+ <Real Name="Cell 1 3 4">0.0034105166974532273</Real>
+ <Real Name="Cell 1 3 5">0.055462989141644582</Real>
+ <Real Name="Cell 1 3 6">0.019463096290170498</Real>
+ <Real Name="Cell 1 4 1">0.60170900531440941</Real>
+ <Real Name="Cell 1 4 2">0.90728766137964656</Real>
+ <Real Name="Cell 1 4 3">0.015593921061816004</Real>
+ <Real Name="Cell 1 5 1">0.38806872374325674</Real>
+ <Real Name="Cell 1 5 2">0.73729836237251578</Real>
+ <Real Name="Cell 1 5 3">0.027885133861340006</Real>
+ <Real Name="Cell 1 6 1">0.0048696190043679907</Real>
+ <Real Name="Cell 1 6 2">0.014513698333150976</Real>
+ <Real Name="Cell 1 6 3">0.00096646425623544768</Real>
+ <Real Name="Cell 13 3 0">0.02417998570750084</Real>
+ <Real Name="Cell 13 3 1">0.034203796516386366</Real>
+ <Real Name="Cell 13 3 2">0.00024706575759149223</Real>
+ <Real Name="Cell 13 4 0">0.11707412966158916</Real>
+ <Real Name="Cell 13 4 1">0.16560719914056177</Real>
+ <Real Name="Cell 13 4 2">0.0011962376193726339</Real>
+ <Real Name="Cell 13 5 0">0.015487477976304072</Real>
+ <Real Name="Cell 13 5 1">0.021907810519887643</Real>
+ <Real Name="Cell 13 5 2">0.00015824763197482477</Real>
+ <Real Name="Cell 14 3 0">0.1335256651997847</Real>
+ <Real Name="Cell 14 3 1">0.18887871719427107</Real>
+ <Real Name="Cell 14 3 2">0.0013643357787535453</Real>
+ <Real Name="Cell 14 4 0">0.64650166587568469</Real>
+ <Real Name="Cell 14 4 1">0.91450887087402799</Real>
+ <Real Name="Cell 14 4 2">0.0066058113431468526</Real>
+ <Real Name="Cell 14 5 0">0.085524277146760794</Real>
+ <Real Name="Cell 14 5 1">0.12097835822257741</Real>
+ <Real Name="Cell 14 5 2">0.00087386818922620174</Real>
+ <Real Name="Cell 15 1 1">1.3367750009906849e-06</Real>
+ <Real Name="Cell 15 1 2">4.0427313396743701e-05</Real>
+ <Real Name="Cell 15 1 3">1.8955369518590044e-05</Real>
+ <Real Name="Cell 15 2 1">0.00047428301673895304</Real>
+ <Real Name="Cell 15 2 2">0.014343467032409222</Real>
+ <Real Name="Cell 15 2 3">0.0067252976993254898</Real>
+ <Real Name="Cell 15 3 0">0.020433620159941126</Real>
+ <Real Name="Cell 15 3 1">0.030156300536097254</Real>
+ <Real Name="Cell 15 3 2">0.012949230487125235</Real>
+ <Real Name="Cell 15 3 3">0.0054301257607806469</Real>
+ <Real Name="Cell 15 4 0">0.09893505831637088</Real>
+ <Real Name="Cell 15 4 1">0.1668728452989488</Real>
+ <Real Name="Cell 15 4 2">0.037329898211844563</Real>
+ <Real Name="Cell 15 4 3">0.00019640562194681352</Real>
+ <Real Name="Cell 15 5 0">0.013087900300333131</Real>
+ <Real Name="Cell 15 5 1">0.031254988413792179</Real>
+ <Real Name="Cell 15 5 2">0.017321144433225886</Real>
+ <Real Name="Cell 15 5 3">9.2945973535754072e-05</Real>
+ <Real Name="Cell 2 0 0">0.58694086273196078</Real>
+ <Real Name="Cell 2 0 1">1.9310426184393541</Real>
+ <Real Name="Cell 2 0 13">0.016841557142288337</Real>
+ <Real Name="Cell 2 0 2">0.18721696855095113</Real>
+ <Real Name="Cell 2 1 0">0.29696384581386692</Real>
+ <Real Name="Cell 2 1 1">1.1445771610757201</Real>
+ <Real Name="Cell 2 1 2">0.11373484937937912</Real>
+ <Real Name="Cell 2 1 4">0.0067764949885925985</Real>
+ <Real Name="Cell 2 1 5">0.11020167948492346</Real>
+ <Real Name="Cell 2 1 6">0.038672021330763293</Real>
+ <Real Name="Cell 2 10 0">0.0076664903300319356</Real>
+ <Real Name="Cell 2 10 1">0.0010347724983472929</Real>
+ <Real Name="Cell 2 10 13">0.0015560455069416677</Real>
+ <Real Name="Cell 2 11 0">0.20150634558713815</Real>
+ <Real Name="Cell 2 11 1">0.063854065928642068</Real>
+ <Real Name="Cell 2 11 13">0.038874410729068672</Real>
+ <Real Name="Cell 2 11 2">0.003705885346543055</Real>
+ <Real Name="Cell 2 2 0">0.056417829346471646</Real>
+ <Real Name="Cell 2 2 1">0.27647027453863693</Real>
+ <Real Name="Cell 2 2 2">0.038482666424098783</Real>
+ <Real Name="Cell 2 2 4">0.016694537185994698</Real>
+ <Real Name="Cell 2 2 5">0.27149227428296563</Real>
+ <Real Name="Cell 2 2 6">0.095272187059950025</Real>
+ <Real Name="Cell 2 3 0">0.031004836149050478</Real>
+ <Real Name="Cell 2 3 1">0.17103507381595617</Real>
+ <Real Name="Cell 2 3 2">0.030399888552461542</Real>
+ <Real Name="Cell 2 3 4">0.00077158033678027241</Real>
+ <Real Name="Cell 2 3 5">0.012547703364920297</Real>
+ <Real Name="Cell 2 3 6">0.0044032455262777897</Real>
+ <Real Name="Cell 2 4 0">6.8103856373110224e-05</Real>
+ <Real Name="Cell 2 4 1">0.00804913833139362</Real>
+ <Real Name="Cell 2 4 2">0.019306059718609787</Real>
+ <Real Name="Cell 2 4 3">0.0012298452032841604</Real>
+ <Real Name="Cell 2 5 1">0.013856219323555284</Real>
+ <Real Name="Cell 2 5 2">0.041297889448778206</Real>
+ <Real Name="Cell 2 5 3">0.0027500181617418204</Real>
+ <Real Name="Cell 2 6 1">0.0005148555666351683</Real>
+ <Real Name="Cell 2 6 2">0.0015345057534447018</Real>
+ <Real Name="Cell 2 6 3">0.00010218242984315733</Real>
+ <Real Name="Cell 2 7 0">0.00054513462395007701</Real>
+ <Real Name="Cell 2 7 1">0.0010631096677045397</Real>
+ <Real Name="Cell 2 7 2">2.7572815802541165e-05</Real>
+ <Real Name="Cell 2 8 0">0.004845990110904066</Real>
+ <Real Name="Cell 2 8 1">0.0094505443429227249</Real>
+ <Real Name="Cell 2 8 2">0.0002451093488443149</Real>
+ <Real Name="Cell 2 9 0">0.0011431748455824604</Real>
+ <Real Name="Cell 2 9 1">0.0022293946794446433</Real>
+ <Real Name="Cell 2 9 2">5.7821587663876302e-05</Real>
+ <Real Name="Cell 3 0 0">0.69360889878227783</Real>
+ <Real Name="Cell 3 0 1">0.91040637793099377</Real>
+ <Real Name="Cell 3 0 13">0.095663306652342267</Real>
+ <Real Name="Cell 3 0 2">0.082576276655402028</Real>
+ <Real Name="Cell 3 1 0">0.33162478626599567</Real>
+ <Real Name="Cell 3 1 1">1.446043578060217</Real>
+ <Real Name="Cell 3 1 2">0.170134206887115</Real>
+ <Real Name="Cell 3 10 0">0.04354715001664098</Real>
+ <Real Name="Cell 3 10 1">0.0058777082183362308</Real>
+ <Real Name="Cell 3 10 13">0.0088386398738504249</Real>
+ <Real Name="Cell 3 11 0">1.0923308142069499</Real>
+ <Real Name="Cell 3 11 1">0.16360362246020402</Real>
+ <Real Name="Cell 3 11 13">0.22081418262484387</Real>
+ <Real Name="Cell 3 11 2">0.0016345645162289698</Real>
+ <Real Name="Cell 3 2 0">0.50999022695333962</Real>
+ <Real Name="Cell 3 2 1">2.5122011878832065</Real>
+ <Real Name="Cell 3 2 2">0.35027008991016406</Real>
+ <Real Name="Cell 3 3 0">0.21065780466812811</Real>
+ <Real Name="Cell 3 3 1">1.4774930885137767</Real>
+ <Real Name="Cell 3 3 2">0.31499733311583844</Real>
+ <Real Name="Cell 3 3 3">4.4856017500429612e-05</Real>
+ <Real Name="Cell 3 4 0">0.011910102317287511</Real>
+ <Real Name="Cell 3 4 1">0.12990084340822095</Real>
+ <Real Name="Cell 3 4 2">0.071111330073043141</Real>
+ <Real Name="Cell 3 4 3">0.0036487690698496721</Real>
+ <Real Name="Cell 3 5 1">0.0069719328295118951</Real>
+ <Real Name="Cell 3 5 2">0.025356561899824073</Real>
+ <Real Name="Cell 3 5 3">0.002314948406043751</Real>
+ <Real Name="Cell 3 7 0">0.082086623510362583</Real>
+ <Real Name="Cell 3 7 1">0.16008354488795243</Real>
+ <Real Name="Cell 3 7 2">0.0041519273413663212</Real>
+ <Real Name="Cell 3 8 0">0.7297114296030327</Real>
+ <Real Name="Cell 3 8 1">1.4230673330273156</Real>
+ <Real Name="Cell 3 8 2">0.036908678982195769</Real>
+ <Real Name="Cell 3 9 0">0.17213979636053725</Real>
+ <Real Name="Cell 3 9 1">0.335703280744716</Real>
+ <Real Name="Cell 3 9 2">0.008706801382277838</Real>
+ <Real Name="Cell 4 0 0">0.074291288586959311</Real>
+ <Real Name="Cell 4 0 1">0.010027350063356486</Real>
+ <Real Name="Cell 4 0 13">0.01507868931338798</Real>
+ <Real Name="Cell 4 1 0">0.065995033097346487</Real>
+ <Real Name="Cell 4 1 1">0.30957925750297188</Real>
+ <Real Name="Cell 4 1 2">0.039460051150421262</Real>
+ <Real Name="Cell 4 10 0">0.0068640105445105931</Real>
+ <Real Name="Cell 4 10 1">0.00092645904893429924</Real>
+ <Real Name="Cell 4 10 13">0.0013931684913951292</Real>
+ <Real Name="Cell 4 11 0">0.17148236601409761</Real>
+ <Real Name="Cell 4 11 1">0.023145563180039061</Real>
+ <Real Name="Cell 4 11 13">0.034805282948142918</Real>
+ <Real Name="Cell 4 2 0">0.17795321010669471</Real>
+ <Real Name="Cell 4 2 1">1.0622806245370715</Real>
+ <Real Name="Cell 4 2 2">0.19013223348046562</Real>
+ <Real Name="Cell 4 3 0">0.25471021463831761</Real>
+ <Real Name="Cell 4 3 1">2.3868328005936488</Real>
+ <Real Name="Cell 4 3 2">0.60478691865321432</Real>
+ <Real Name="Cell 4 3 3">0.0013703299180596153</Real>
+ <Real Name="Cell 4 4 0">0.03494787133213529</Real>
+ <Real Name="Cell 4 4 1">0.67226341940984968</Real>
+ <Real Name="Cell 4 4 2">1.3053903497833907</Real>
+ <Real Name="Cell 4 4 3">0.11146815297318073</Real>
+ <Real Name="Cell 4 5 1">0.21298921918091981</Real>
+ <Real Name="Cell 4 5 2">0.77463085950790644</Real>
+ <Real Name="Cell 4 5 3">0.070720568528755093</Real>
+ <Real Name="Cell 4 7 0">0.058879679011257922</Real>
+ <Real Name="Cell 4 7 1">0.11482586729611367</Real>
+ <Real Name="Cell 4 7 2">0.0029781240680079066</Real>
+ <Real Name="Cell 4 8 0">0.52341262082059925</Real>
+ <Real Name="Cell 4 8 1">1.0207478904218499</Real>
+ <Real Name="Cell 4 8 2">0.026474120609028446</Real>
+ <Real Name="Cell 4 9 0">0.12347366137543997</Real>
+ <Real Name="Cell 4 9 1">0.24079564450327059</Real>
+ <Real Name="Cell 4 9 2">0.0062452766197476578</Real>
+ <Real Name="Cell 5 2 0">0.0030388668685303035</Real>
+ <Real Name="Cell 5 2 1">0.029230383696795037</Real>
+ <Real Name="Cell 5 2 2">0.0073225712570666674</Real>
+ <Real Name="Cell 5 3 0">0.016062274626014745</Real>
+ <Real Name="Cell 5 3 1">0.15644323644182084</Real>
+ <Real Name="Cell 5 3 2">0.04576991184270697</Real>
+ <Real Name="Cell 5 3 3">0.00064506284514434086</Real>
+ <Real Name="Cell 5 4 0">0.002345144434675343</Real>
+ <Real Name="Cell 5 4 1">0.18058758771061995</Real>
+ <Real Name="Cell 5 4 2">0.58039799171281714</Real>
+ <Real Name="Cell 5 4 3">0.052472009077697473</Real>
+ <Real Name="Cell 5 5 1">0.10026157197564638</Real>
+ <Real Name="Cell 5 5 2">0.3646461918297238</Real>
+ <Real Name="Cell 5 5 3">0.03329067733555785</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>0.05089318151490263</Real>
+ <Real>0.71725338845863429</Real>
+ <Real>0.23185343002646308</Real>
+ <Real>0.012030669800701029</Real>
+ <Real>0.6310558406250385</Real>
+ <Real>0.35691348957426045</Real>
+ <Real>0.14074805168117607</Real>
+ <Real>0.74906596026673178</Real>
+ <Real>0.11018598805209209</Real>
+ <Real>0.12390180576498261</Real>
+ <Real>0.74999515456931432</Real>
+ <Real>0.12610303966570308</Real>
+ <Real>0.048421007610068734</Real>
+ <Real>0.71435248219287506</Real>
+ <Real>0.23722651019705621</Real>
+ <Real>0.4937434649966933</Real>
+ <Real>0.50623683946842246</Real>
+ <Real>1.9695534884260206e-05</Real>
+ <Real>0.0024393502229682756</Real>
+ <Real>0.56496899418986768</Real>
+ <Real>0.43259165558716406</Real>
+ <Real>0.1467372554828546</Real>
+ <Real>0.74825836690465708</Real>
+ <Real>0.10500437761248832</Real>
+ <Real>0.40099473052793144</Real>
+ <Real>0.59354918191598727</Real>
+ <Real>0.0054560875560812957</Real>
+ <Real>0.0011356479385134484</Real>
+ <Real>0.54538681861596261</Real>
+ <Real>0.45347753344552394</Real>
+ <Real>0.018228417474878484</Real>
+ <Real>0.65447989527718753</Real>
+ <Real>0.327291687247934</Real>
+ <Real>0.023382667777312426</Real>
+ <Real>0.66948760790424433</Real>
+ <Real>0.30712972431844326</Real>
+ <Real>0.33752642870877159</Real>
+ <Real>0.64656314621039446</Real>
+ <Real>0.015910425080833981</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>0.030194454142256941</Real>
+ <Real>0.68535263945317304</Real>
+ <Real>0.28445290640456999</Real>
+ <Real>0.01206491498369449</Real>
+ <Real>0.63120796313972638</Real>
+ <Real>0.35672712187657912</Real>
+ <Real>0.00013371589069704963</Real>
+ <Real>0.51608590981578717</Real>
+ <Real>0.48378037429351578</Real>
+ <Real>0.1282394341754734</Real>
+ <Real>0.74995855952237578</Real>
+ <Real>0.12180200630215082</Real>
+ <Real>0.025517545395280731</Real>
+ <Real>0.67487438397878385</Real>
+ <Real>0.29960807062593542</Real>
+ <Real>0.0072278135424509414</Real>
+ <Real>0.60577592902622013</Real>
+ <Real>0.38699625743132893</Real>
+ <Real>0.12708775130249114</Real>
+ <Real>0.74998270927396971</Real>
+ <Real>0.12292953942353911</Real>
+ <Real>0.030096369796856738</Real>
+ <Real>0.68514934728441157</Real>
+ <Real>0.28475428291873167</Real>
+ <Real>0.025157553891160367</Real>
+ <Real>0.67399518574501771</Real>
+ <Real>0.30084726036382192</Real>
+ <Real>0.27893076277274931</Real>
+ <Real>0.68903975678403295</Real>
+ <Real>0.032029480443217746</Real>
+ <Real>0.23739096068816348</Real>
+ <Real>0.71426228720272134</Real>
+ <Real>0.048346752109115224</Real>
+ <Real>0.19640714569586232</Real>
+ <Real>0.73393469456016713</Real>
+ <Real>0.069658159743970549</Real>
+ <Real>0.061593317344401516</Real>
+ <Real>0.72779290130838736</Real>
+ <Real>0.21061378134721118</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>0.17608709093451638</Real>
+ <Real>0.74126847068387636</Real>
+ <Real>0.082644438381607302</Real>
+ <Real>0.2101857747525209</Real>
+ <Real>0.72798911363318541</Real>
+ <Real>0.061825111614293639</Real>
+ <Real>0.47251948092640972</Real>
+ <Real>0.52709218251650869</Real>
+ <Real>0.00038833655708161568</Real>
+ <Real>0.42971002799396185</Real>
+ <Real>0.56762905597320845</Real>
+ <Real>0.0026609160328297157</Real>
+ <Real>0.045988990006773256</Real>
+ <Real>0.71130073670351313</Real>
+ <Real>0.24271027328971362</Real>
+ <Real>0.43047030413140991</Real>
+ <Real>0.56692824468075209</Real>
+ <Real>0.0026014511878380275</Real>
+ <Real>0.13631047718434056</Real>
+ <Real>0.74951021149740771</Real>
+ <Real>0.11417931131825178</Real>
+ <Real>0.36614351063849898</Real>
+ <Real>0.62345068461014941</Real>
+ <Real>0.010405804751351597</Real>
+ <Real>0.24672432328322841</Real>
+ <Real>0.70901035335201301</Real>
+ <Real>0.044265323364758566</Real>
+ <Real>0.093652242762162843</Real>
+ <Real>0.74548239681422868</Real>
+ <Real>0.16086536042360849</Real>
+ <Real>0.074840090544688584</Real>
+ <Real>0.73720504877779824</Real>
+ <Real>0.18795486067751316</Real>
+ <Real>0.011621874147413528</Real>
+ <Real>0.6292152569978321</Real>
+ <Real>0.3591628688547544</Real>
+ <Real>0.21607229169952644</Real>
+ <Real>0.72523246472405656</Real>
+ <Real>0.058695243576417054</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">39</Int>
+ <Real>-0.31903975148843955</Real>
+ <Real>-0.3619204970231209</Real>
+ <Real>0.68096024851156045</Real>
+ <Real>-0.15511718022644061</Real>
+ <Real>-0.68976563954711878</Real>
+ <Real>0.84488281977355939</Real>
+ <Real>-0.53056206362908398</Real>
+ <Real>0.06112412725816796</Real>
+ <Real>0.46943793637091602</Real>
+ <Real>-0.49779876609927953</Real>
+ <Real>-0.0044024678014409346</Real>
+ <Real>0.50220123390072047</Real>
+ <Real>-0.31119449741301253</Real>
+ <Real>-0.37761100517397495</Real>
+ <Real>0.68880550258698747</Real>
+ <Real>-0.99372376946180907</Real>
+ <Real>0.98744753892361814</Real>
+ <Real>0.00627623053819093</Real>
+ <Real>-0.069847694635804203</Real>
+ <Real>-0.86030461072839159</Real>
+ <Real>0.9301523053641958</Real>
+ <Real>-0.54173287787036628</Real>
+ <Real>0.083465755740732561</Real>
+ <Real>0.45826712212963372</Real>
+ <Real>-0.89553864297185015</Real>
+ <Real>0.7910772859437003</Real>
+ <Real>0.10446135702814985</Real>
+ <Real>-0.047658114492989512</Real>
+ <Real>-0.90468377101402098</Real>
+ <Real>0.95234188550701049</Real>
+ <Real>-0.19093673022694446</Real>
+ <Real>-0.61812653954611108</Real>
+ <Real>0.80906326977305554</Real>
+ <Real>-0.21625294345886914</Real>
+ <Real>-0.56749411308226172</Real>
+ <Real>0.78374705654113086</Real>
+ <Real>-0.82161600362793763</Real>
+ <Real>0.64323200725587526</Real>
+ <Real>0.17838399637206237</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">39</Int>
+ <Real>-0.24574154773768697</Real>
+ <Real>-0.50851690452462606</Real>
+ <Real>0.75425845226231303</Real>
+ <Real>-0.15533779310711537</Real>
+ <Real>-0.68932441378576925</Real>
+ <Real>0.84466220689288463</Real>
+ <Real>-0.01635334159718127</Real>
+ <Real>-0.96729331680563746</Real>
+ <Real>0.98364665840281873</Real>
+ <Real>-0.50643742787332258</Real>
+ <Real>0.012874855746645153</Real>
+ <Real>0.49356257212667742</Real>
+ <Real>-0.22590947476934531</Real>
+ <Real>-0.54818105046130938</Real>
+ <Real>0.77409052523065469</Real>
+ <Real>-0.12023155611112202</Real>
+ <Real>-0.75953688777775596</Real>
+ <Real>0.87976844388887798</Real>
+ <Real>-0.50415821187895205</Real>
+ <Real>0.0083164237579040901</Real>
+ <Real>0.49584178812104795</Real>
+ <Real>-0.24534208687812509</Real>
+ <Real>-0.50931582624374983</Real>
+ <Real>0.75465791312187491</Real>
+ <Real>-0.22431029352733844</Real>
+ <Real>-0.55137941294532311</Real>
+ <Real>0.77568970647266156</Real>
+ <Real>-0.74690128232953157</Real>
+ <Real>0.49380256465906314</Real>
+ <Real>0.25309871767046843</Real>
+ <Real>-0.68904420857904825</Real>
+ <Real>0.37808841715809649</Real>
+ <Real>0.31095579142095175</Real>
+ <Real>-0.62674898595189177</Real>
+ <Real>0.25349797190378354</Real>
+ <Real>0.37325101404810823</Real>
+ <Real>-0.35097953599719034</Real>
+ <Real>-0.29804092800561932</Real>
+ <Real>0.64902046400280966</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">39</Int>
+ <Real>-0.59344265255290907</Real>
+ <Real>0.18688530510581813</Real>
+ <Real>0.40655734744709093</Real>
+ <Real>-0.64836066313822727</Real>
+ <Real>0.29672132627645453</Real>
+ <Real>0.35163933686177273</Real>
+ <Real>-0.97213114436932813</Real>
+ <Real>0.94426228873865625</Real>
+ <Real>0.027868855630671874</Real>
+ <Real>-0.92704911196113216</Real>
+ <Real>0.85409822392226431</Real>
+ <Real>0.072950888038867845</Real>
+ <Real>-0.30327871671705964</Real>
+ <Real>-0.39344256656588072</Real>
+ <Real>0.69672128328294036</Real>
+ <Real>-0.92786885294357191</Real>
+ <Real>0.85573770588714382</Real>
+ <Real>0.072131147056428091</Real>
+ <Real>-0.52213116586608876</Real>
+ <Real>0.044262331732177529</Real>
+ <Real>0.47786883413391124</Real>
+ <Real>-0.85573770588714737</Real>
+ <Real>0.71147541177429474</Real>
+ <Real>0.14426229411285263</Real>
+ <Real>-0.70245899991846983</Real>
+ <Real>0.40491799983693966</Real>
+ <Real>0.29754100008153017</Real>
+ <Real>-0.43278688233855434</Real>
+ <Real>-0.13442623532289133</Real>
+ <Real>0.56721311766144566</Real>
+ <Real>-0.38688522986717544</Real>
+ <Real>-0.22622954026564912</Real>
+ <Real>0.61311477013282456</Real>
+ <Real>-0.1524590052926591</Real>
+ <Real>-0.6950819894146818</Real>
+ <Real>0.8475409947073409</Real>
+ <Real>-0.65737704812310938</Real>
+ <Real>0.31475409624621875</Real>
+ <Real>0.34262295187689062</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">4</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">16</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">10</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">16</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">15</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 1 3">0.00018808517987243056</Real>
+ <Real Name="Cell 0 1 4">0.0029090686050415276</Real>
+ <Real Name="Cell 0 1 5">0.0009926333542410739</Real>
+ <Real Name="Cell 0 2 1">0.0041186139190493107</Real>
+ <Real Name="Cell 0 2 2">0.017338003739560695</Real>
+ <Real Name="Cell 0 2 3">0.0069073999573910144</Real>
+ <Real Name="Cell 0 2 4">0.076937489573057044</Real>
+ <Real Name="Cell 0 2 5">0.026252635709394366</Real>
+ <Real Name="Cell 0 3 1">0.093484151328262238</Real>
+ <Real Name="Cell 0 3 2">0.39353738834865115</Real>
+ <Real Name="Cell 0 3 3">0.046084061115039682</Real>
+ <Real Name="Cell 0 3 4">0.034156123505365274</Real>
+ <Real Name="Cell 0 3 5">0.011654763790804143</Real>
+ <Real Name="Cell 0 4 1">0.038800227820390172</Real>
+ <Real Name="Cell 0 4 2">0.16333613887290838</Real>
+ <Real Name="Cell 0 4 3">0.018210437916127798</Real>
+ <Real Name="Cell 0 5 0">0.0088023472191847106</Real>
+ <Real Name="Cell 0 5 1">0.47657415536293973</Real>
+ <Real Name="Cell 0 5 2">0.27203900659924801</Real>
+ <Real Name="Cell 0 5 3">8.0394508390120395e-09</Real>
+ <Real Name="Cell 0 6 0">0.032892632265675077</Real>
+ <Real Name="Cell 0 6 1">1.8185820988028998</Real>
+ <Real Name="Cell 0 6 2">1.0586309034261097</Real>
+ <Real Name="Cell 0 6 3">3.1028827456798062e-05</Real>
+ <Real Name="Cell 0 7 0">0.0031218584565417917</Real>
+ <Real Name="Cell 0 7 1">0.20441112723321075</Real>
+ <Real Name="Cell 0 7 2">0.13595738222468978</Real>
+ <Real Name="Cell 0 7 3">2.9086509581896539e-05</Real>
+ <Real Name="Cell 1 1 3">0.002774810391959405</Real>
+ <Real Name="Cell 1 1 4">0.04291733033760034</Real>
+ <Real Name="Cell 1 1 5">0.014644265691862666</Real>
+ <Real Name="Cell 1 2 1">0.0013313492546036102</Real>
+ <Real Name="Cell 1 2 2">0.0056045404615897845</Real>
+ <Real Name="Cell 1 2 3">0.074011553572345776</Real>
+ <Real Name="Cell 1 2 4">1.1350545840102093</Real>
+ <Real Name="Cell 1 2 5">0.38730370161094119</Real>
+ <Real Name="Cell 1 3 1">0.030218917731638664</Real>
+ <Real Name="Cell 1 3 2">0.12721165880912841</Real>
+ <Real Name="Cell 1 3 3">0.046762662589622535</Real>
+ <Real Name="Cell 1 3 4">0.50390342565011836</Real>
+ <Real Name="Cell 1 3 5">0.17194209402617516</Real>
+ <Real Name="Cell 1 4 1">0.01254224246370985</Real>
+ <Real Name="Cell 1 4 2">0.052798696603364434</Real>
+ <Real Name="Cell 1 4 3">0.0058865563566196924</Real>
+ <Real Name="Cell 1 5 0">0.0040381068191034947</Real>
+ <Real Name="Cell 1 5 1">0.21867759350058125</Real>
+ <Real Name="Cell 1 5 2">0.12485189059509993</Real>
+ <Real Name="Cell 1 5 3">4.2786233207568734e-08</Real>
+ <Real Name="Cell 1 6 0">0.015089607276658711</Real>
+ <Real Name="Cell 1 6 1">1.0178948988864061</Real>
+ <Real Name="Cell 1 6 2">0.69047084849042828</Real>
+ <Real Name="Cell 1 6 3">0.00016513648435806865</Real>
+ <Real Name="Cell 1 7 0">0.0014321632182563401</Real>
+ <Real Name="Cell 1 7 1">0.26589472537246744</Real>
+ <Real Name="Cell 1 7 2">0.25437004369160016</Real>
+ <Real Name="Cell 1 7 3">0.00015479940198479322</Real>
+ <Real Name="Cell 16 4 0">0.0043013969422817924</Real>
+ <Real Name="Cell 16 4 1">0.0056649283231824119</Real>
+ <Real Name="Cell 16 4 2">2.5994532206908954e-05</Real>
+ <Real Name="Cell 16 5 0">0.36050774048298312</Real>
+ <Real Name="Cell 16 5 1">0.4747877345877265</Real>
+ <Real Name="Cell 16 5 2">0.0021786480523821776</Real>
+ <Real Name="Cell 16 6 0">0.23030817115201113</Real>
+ <Real Name="Cell 16 6 1">0.30331524835447249</Real>
+ <Real Name="Cell 16 6 2">0.0013918160199717393</Real>
+ <Real Name="Cell 17 4 0">0.0044102367883987166</Real>
+ <Real Name="Cell 17 4 1">0.0058082701107997868</Real>
+ <Real Name="Cell 17 4 2">2.6652281520270527e-05</Real>
+ <Real Name="Cell 17 5 0">0.36962980187946365</Real>
+ <Real Name="Cell 17 5 1">0.48680146516505807</Real>
+ <Real Name="Cell 17 5 2">0.0022337751940866178</Real>
+ <Real Name="Cell 17 6 0">0.23613574443669338</Real>
+ <Real Name="Cell 17 6 1">0.31099014685809795</Real>
+ <Real Name="Cell 17 6 2">0.0014270336582110122</Real>
+ <Real Name="Cell 18 2 1">0.00029223893416861806</Real>
+ <Real Name="Cell 18 2 2">0.0012302293521676579</Real>
+ <Real Name="Cell 18 2 3">0.00013715896184909214</Real>
+ <Real Name="Cell 18 3 1">0.0066332288684478819</Real>
+ <Real Name="Cell 18 3 2">0.027923701805256392</Real>
+ <Real Name="Cell 18 3 3">0.0031132292070939218</Real>
+ <Real Name="Cell 18 4 0">1.7158366547358471e-07</Real>
+ <Real Name="Cell 18 4 1">0.0027533214210761553</Real>
+ <Real Name="Cell 18 4 2">0.011589623194678714</Real>
+ <Real Name="Cell 18 4 3">0.001292133487613084</Real>
+ <Real Name="Cell 18 5 0">0.00032181339947092179</Real>
+ <Real Name="Cell 18 5 1">0.01666352889051886</Real>
+ <Real Name="Cell 18 5 2">0.0095009984797486229</Real>
+ <Real Name="Cell 18 6 0">0.0011580021722818275</Real>
+ <Real Name="Cell 18 6 1">0.062209641413896677</Real>
+ <Real Name="Cell 18 6 2">0.035503084743494354</Real>
+ <Real Name="Cell 18 7 0">0.00010903469799182714</Real>
+ <Real Name="Cell 18 7 1">0.0059032041345824576</Real>
+ <Real Name="Cell 18 7 2">0.0033696127181149838</Real>
+ <Real Name="Cell 2 0 0">0.406836631155853</Real>
+ <Real Name="Cell 2 0 1">1.1689180985182439</Real>
+ <Real Name="Cell 2 0 10">9.7426659105024389e-06</Real>
+ <Real Name="Cell 2 0 2">0.07297749122996576</Real>
+ <Real Name="Cell 2 1 0">0.18156265350916104</Real>
+ <Real Name="Cell 2 1 1">0.52175561536461634</Real>
+ <Real Name="Cell 2 1 2">0.032574532829179541</Real>
+ <Real Name="Cell 2 1 3">0.00092147588501739904</Real>
+ <Real Name="Cell 2 1 4">0.014252247674299079</Real>
+ <Real Name="Cell 2 1 5">0.0048631566783596302</Real>
+ <Real Name="Cell 2 15 0">0.00067537276197739496</Real>
+ <Real Name="Cell 2 15 1">0.0001457366173098991</Real>
+ <Real Name="Cell 2 15 10">8.4844624272759466e-05</Real>
+ <Real Name="Cell 2 16 0">0.016851061444656389</Real>
+ <Real Name="Cell 2 16 1">0.043990440575358343</Real>
+ <Real Name="Cell 2 16 10">0.00020959079124938432</Real>
+ <Real Name="Cell 2 16 2">0.0027239588758043564</Real>
+ <Real Name="Cell 2 2 0">6.3762254037022745e-05</Real>
+ <Real Name="Cell 2 2 1">0.00022084380759982648</Real>
+ <Real Name="Cell 2 2 2">1.8755353340441018e-05</Real>
+ <Real Name="Cell 2 2 3">0.024370701045855054</Real>
+ <Real Name="Cell 2 2 4">0.37693581888501343</Real>
+ <Real Name="Cell 2 2 5">0.12861816513539928</Real>
+ <Real Name="Cell 2 3 0">0.0034136157314101061</Real>
+ <Real Name="Cell 2 3 1">0.012319647322337986</Real>
+ <Real Name="Cell 2 3 2">0.0011764351123614851</Real>
+ <Real Name="Cell 2 3 3">0.010819285623351859</Real>
+ <Real Name="Cell 2 3 4">0.16733930954696927</Real>
+ <Real Name="Cell 2 3 5">0.057099574703781263</Real>
+ <Real Name="Cell 2 4 0">0.0021191365405715309</Real>
+ <Real Name="Cell 2 4 1">0.0088333535499049813</Real>
+ <Real Name="Cell 2 4 2">0.0011418609327748059</Real>
+ <Real Name="Cell 2 5 0">1.5829303519544015e-05</Real>
+ <Real Name="Cell 2 5 1">0.0001635831317127439</Real>
+ <Real Name="Cell 2 5 2">4.8296593356786407e-05</Real>
+ <Real Name="Cell 2 5 3">6.293762673883149e-09</Real>
+ <Real Name="Cell 2 6 1">0.029557029516431226</Real>
+ <Real Name="Cell 2 6 2">0.032970660100566145</Real>
+ <Real Name="Cell 2 6 3">2.4291220877215411e-05</Real>
+ <Real Name="Cell 2 7 1">0.027706842079001048</Real>
+ <Real Name="Cell 2 7 2">0.030906788929481923</Real>
+ <Real Name="Cell 2 7 3">2.2770658342949888e-05</Real>
+ <Real Name="Cell 3 0 0">0.63932566264442026</Real>
+ <Real Name="Cell 3 0 1">1.7382352159757049</Real>
+ <Real Name="Cell 3 0 10">0.0046788457809578392</Real>
+ <Real Name="Cell 3 0 2">0.10802069683259874</Real>
+ <Real Name="Cell 3 1 0">0.29206110095876386</Real>
+ <Real Name="Cell 3 1 1">0.85054876868078688</Real>
+ <Real Name="Cell 3 1 2">0.054549593611895285</Real>
+ <Real Name="Cell 3 10 0">0.0082304511774808527</Real>
+ <Real Name="Cell 3 10 1">0.014014396738324461</Real>
+ <Real Name="Cell 3 10 2">0.00023390956136037089</Real>
+ <Real Name="Cell 3 11 0">0.18736772209305352</Real>
+ <Real Name="Cell 3 11 1">0.31904029763917302</Real>
+ <Real Name="Cell 3 11 2">0.0053249938238856638</Real>
+ <Real Name="Cell 3 12 0">0.077871724695048175</Real>
+ <Real Name="Cell 3 12 1">0.13259604133974251</Real>
+ <Real Name="Cell 3 12 2">0.0022131157299895977</Real>
+ <Real Name="Cell 3 15 0">0.32434294955607429</Real>
+ <Real Name="Cell 3 15 1">0.069988970503076953</Real>
+ <Real Name="Cell 3 15 10">0.040746025365359297</Real>
+ <Real Name="Cell 3 16 0">0.82369431210280031</Real>
+ <Real Name="Cell 3 16 1">0.23747443528036877</Real>
+ <Real Name="Cell 3 16 10">0.10065448188135853</Real>
+ <Real Name="Cell 3 16 2">0.0040319820666417684</Real>
+ <Real Name="Cell 3 2 0">0.27881948439827597</Real>
+ <Real Name="Cell 3 2 1">0.9361975580964299</Real>
+ <Real Name="Cell 3 2 2">0.075815536664766078</Real>
+ <Real Name="Cell 3 3 0">0.25773644310361049</Real>
+ <Real Name="Cell 3 3 1">0.90246891412795205</Real>
+ <Real Name="Cell 3 3 2">0.08033987532708721</Real>
+ <Real Name="Cell 3 4 0">0.10874064438493782</Real>
+ <Real Name="Cell 3 4 1">0.43321472040346831</Real>
+ <Real Name="Cell 3 4 2">0.051393093435294919</Real>
+ <Real Name="Cell 3 5 0">0.00080664349445461094</Real>
+ <Real Name="Cell 3 5 1">0.0069087073888523436</Real>
+ <Real Name="Cell 3 5 2">0.0016269550683567472</Real>
+ <Real Name="Cell 4 0 0">0.036502228650249352</Real>
+ <Real Name="Cell 4 0 1">0.022586945687235831</Real>
+ <Real Name="Cell 4 0 10">0.0038903606975782099</Real>
+ <Real Name="Cell 4 0 2">0.00099295963627660006</Real>
+ <Real Name="Cell 4 1 0">0.047129615318141325</Real>
+ <Real Name="Cell 4 1 1">0.15699489479143533</Real>
+ <Real Name="Cell 4 1 2">0.012574730231023285</Real>
+ <Real Name="Cell 4 10 0">0.041969600267397121</Real>
+ <Real Name="Cell 4 10 1">0.071463716437015462</Real>
+ <Real Name="Cell 4 10 2">0.0011927767478746832</Real>
+ <Real Name="Cell 4 11 0">0.95544560433989678</Real>
+ <Real Name="Cell 4 11 1">1.6268845379635501</Real>
+ <Real Name="Cell 4 11 2">0.02715378019935526</Real>
+ <Real Name="Cell 4 12 0">0.39709185889178705</Real>
+ <Real Name="Cell 4 12 1">0.67614796954200196</Real>
+ <Real Name="Cell 4 12 2">0.011285357330991628</Real>
+ <Real Name="Cell 4 15 0">0.26968426029875026</Real>
+ <Real Name="Cell 4 15 1">0.058194339556408806</Real>
+ <Real Name="Cell 4 15 10">0.033879452985831809</Real>
+ <Real Name="Cell 4 16 0">0.66640479962494958</Real>
+ <Real Name="Cell 4 16 1">0.14435052290460143</Real>
+ <Real Name="Cell 4 16 10">0.083692059682756156</Real>
+ <Real Name="Cell 4 16 2">3.706322550918936e-05</Real>
+ <Real Name="Cell 4 2 0">0.52958933416905918</Real>
+ <Real Name="Cell 4 2 1">1.7777344644186996</Real>
+ <Real Name="Cell 4 2 2">0.143903554795795</Real>
+ <Real Name="Cell 4 3 0">0.31012941343083311</Real>
+ <Real Name="Cell 4 3 1">1.182820148258702</Real>
+ <Real Name="Cell 4 3 2">0.1218930946316889</Real>
+ <Real Name="Cell 4 4 0">0.39685309808198815</Real>
+ <Real Name="Cell 4 4 1">2.0865717815302651</Real>
+ <Real Name="Cell 4 4 2">0.30905066626026545</Real>
+ <Real Name="Cell 4 5 0">0.055476536285432781</Real>
+ <Real Name="Cell 4 5 1">0.33447588928119287</Real>
+ <Real Name="Cell 4 5 2">0.084194101614856576</Real>
+ <Real Name="Cell 4 5 3">0.0001746145636465291</Real>
+ <Real Name="Cell 4 6 1">0.16490751776386439</Real>
+ <Real Name="Cell 4 6 2">0.21783596503012673</Real>
+ <Real Name="Cell 4 6 3">0.0010211655054933554</Real>
+ <Real Name="Cell 4 7 1">0.026782901885590082</Real>
+ <Real Name="Cell 4 7 2">0.035379098282887149</Real>
+ <Real Name="Cell 4 7 3">0.00016584917360614468</Real>
+ <Real Name="Cell 5 1 0">0.0010989598324157807</Real>
+ <Real Name="Cell 5 1 1">0.0036885865449326352</Real>
+ <Real Name="Cell 5 1 2">0.00029852839777366085</Real>
+ <Real Name="Cell 5 10 0">0.0058896658555967693</Real>
+ <Real Name="Cell 5 10 1">0.010028625670283108</Real>
+ <Real Name="Cell 5 10 2">0.0001673844030095395</Real>
+ <Real Name="Cell 5 11 0">0.13407931733703174</Real>
+ <Real Name="Cell 5 11 1">0.22830349236577308</Real>
+ <Real Name="Cell 5 11 2">0.0038105364614291256</Real>
+ <Real Name="Cell 5 12 0">0.055724580361733632</Real>
+ <Real Name="Cell 5 12 1">0.094885002100821458</Real>
+ <Real Name="Cell 5 12 2">0.0015836935142835525</Real>
+ <Real Name="Cell 5 2 0">0.012985421135592702</Real>
+ <Real Name="Cell 5 2 1">0.043584713715823439</Real>
+ <Real Name="Cell 5 2 2">0.0035274419061370019</Real>
+ <Real Name="Cell 5 3 0">0.047447567779325767</Real>
+ <Real Name="Cell 5 3 1">0.25284323272175968</Real>
+ <Real Name="Cell 5 3 2">0.037617148170581045</Real>
+ <Real Name="Cell 5 4 0">0.2578262761675304</Real>
+ <Real Name="Cell 5 4 1">1.4176711194296565</Real>
+ <Real Name="Cell 5 4 2">0.21596598633241318</Real>
+ <Real Name="Cell 5 5 0">0.042260261454884658</Real>
+ <Real Name="Cell 5 5 1">0.40305926133387909</Real>
+ <Real Name="Cell 5 5 2">0.26087204666098224</Real>
+ <Real Name="Cell 5 5 3">0.0010569666506760804</Real>
+ <Real Name="Cell 5 6 1">0.99820852901488599</Real>
+ <Real Name="Cell 5 6 2">1.318591906347335</Real>
+ <Real Name="Cell 5 6 3">0.0061812592351240172</Real>
+ <Real Name="Cell 5 7 1">0.16212069320118783</Real>
+ <Real Name="Cell 5 7 2">0.21415468581246491</Real>
+ <Real Name="Cell 5 7 3">0.0010039085050129897</Real>
+ <Real Name="Cell 6 5 1">0.028699392301152461</Real>
+ <Real Name="Cell 6 5 2">0.037910702328633687</Real>
+ <Real Name="Cell 6 5 3">0.0001777167581196857</Real>
+ <Real Name="Cell 6 6 1">0.16783725729707202</Real>
+ <Real Name="Cell 6 6 2">0.22170602897358535</Real>
+ <Real Name="Cell 6 6 3">0.0010393074858709619</Real>
+ <Real Name="Cell 6 7 1">0.0272587257141956</Real>
+ <Real Name="Cell 6 7 2">0.036007641749516935</Real>
+ <Real Name="Cell 6 7 3">0.00016879564255463438</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>0.0032320813985638091</Real>
+ <Real>0.32739340500299152</Real>
+ <Real>0.60418199968332709</Real>
+ <Real>0.065192513915117434</Real>
+ <Real>0.036781240901433088</Real>
+ <Real>0.5410723534249855</Real>
+ <Real>0.41182077484694096</Real>
+ <Real>0.010325630826640411</Real>
+ <Real>0.036849690391817888</Real>
+ <Real>0.54128079204577983</Real>
+ <Real>0.41157318778905927</Real>
+ <Real>0.010296329773342997</Real>
+ <Real>0.0015144164319307073</Real>
+ <Real>0.28823187635306668</Real>
+ <Real>0.62766564313430673</Real>
+ <Real>0.082588064080695744</Real>
+ <Real>0.012343878077116547</Real>
+ <Real>0.42779203362861129</Real>
+ <Real>0.52733755949080408</Real>
+ <Real>0.032526528803468034</Real>
+ <Real>0.023574272347497677</Real>
+ <Real>0.49219553419207929</Real>
+ <Real>0.46591665727802722</Real>
+ <Real>0.018313536182395652</Real>
+ <Real>0.054846312535409794</Real>
+ <Real>0.58565149806818073</Real>
+ <Real>0.35455612489808364</Real>
+ <Real>0.0049460644983257609</Real>
+ <Real>0.00011270990432847568</Real>
+ <Real>0.21406829462245039</Real>
+ <Real>0.65930033609084437</Real>
+ <Real>0.12651865938237672</Real>
+ <Real>0.0019707694277898893</Real>
+ <Real>0.30061680124029133</Real>
+ <Real>0.62067610437023457</Real>
+ <Real>0.07673632496168413</Real>
+ <Real>0.022608672803415615</Real>
+ <Real>0.48775346754225168</Real>
+ <Real>0.47048440607829622</Real>
+ <Real>0.01915345357603648</Real>
+ <Real>0.042568491442497081</Real>
+ <Real>0.55747572702267667</Real>
+ <Real>0.39181610760773877</Real>
+ <Real>0.0081396739270872612</Real>
+ <Real>0.0010065468105848374</Real>
+ <Real>0.27128251198765502</Real>
+ <Real>0.63652307745303605</Real>
+ <Real>0.091187863748724007</Real>
+ <Real>0.0056407272445787252</Real>
+ <Real>0.36379270070734426</Real>
+ <Real>0.57895852516983959</Real>
+ <Real>0.051608046878237321</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>2.8984203206300032e-05</Real>
+ <Real>0.19604629578723692</Real>
+ <Real>0.66363801892486318</Real>
+ <Real>0.14028670108469343</Real>
+ <Real>0.16270013029218783</Real>
+ <Real>0.6666029727238697</Real>
+ <Real>0.17069681175130791</Real>
+ <Real>8.5232634550106489e-08</Real>
+ <Real>0.07795655011881443</Real>
+ <Real>0.62220330426985249</Real>
+ <Real>0.29797315870186108</Real>
+ <Real>0.0018669869094719406</Real>
+ <Real>0.00030406591916461119</Real>
+ <Real>0.23431536727051527</Real>
+ <Real>0.65264819325911705</Real>
+ <Real>0.11273237355120293</Real>
+ <Real>0.069667831943294664</Real>
+ <Real>0.61104182113337613</Real>
+ <Real>0.31661366762290266</Real>
+ <Real>0.0026766793004264337</Real>
+ <Real>0.028562841964611067</Real>
+ <Real>0.51297348077323213</Real>
+ <Real>0.44382208157931846</Real>
+ <Real>0.014641595682838331</Real>
+ <Real>0.025143927553512784</Real>
+ <Real>0.49910502043123089</Real>
+ <Real>0.45870514956802655</Real>
+ <Real>0.017045902447229689</Real>
+ <Real>0.011359280676947803</Real>
+ <Real>0.42025384291425372</Real>
+ <Real>0.53389123934873839</Real>
+ <Real>0.034495637060059994</Real>
+ <Real>0.00066159670659626552</Real>
+ <Real>0.25638546720471722</Real>
+ <Real>0.64358095325478015</Real>
+ <Real>0.099371982833906358</Real>
+ <Real>0.002111122856071995</Real>
+ <Real>0.30405607905732607</Real>
+ <Real>0.6186612608438542</Real>
+ <Real>0.075171537242747735</Real>
+ <Real>0.048540454602101754</Real>
+ <Real>0.57216087076003208</Real>
+ <Real>0.37291163014119588</Real>
+ <Real>0.006387044496670261</Real>
+ <Real>0.0014807971091969363</Real>
+ <Real>0.28723145257646854</Real>
+ <Real>0.62821163477963171</Real>
+ <Real>0.083076115534702732</Real>
+ <Real>0.097374461581833008</Real>
+ <Real>0.64197198326708227</Real>
+ <Real>0.25991820354188061</Real>
+ <Real>0.00073535160920408949</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>0.0015398888964354171</Real>
+ <Real>0.28898064671533619</Real>
+ <Real>0.62725514312918096</Real>
+ <Real>0.082224321259047425</Real>
+ <Real>0.028102759671169996</Real>
+ <Real>0.5111933881600339</Real>
+ <Real>0.44576397047871225</Real>
+ <Real>0.014939881690083917</Real>
+ <Real>0.055181892379010555</Real>
+ <Real>0.5863185122651009</Real>
+ <Real>0.35362057298464111</Real>
+ <Real>0.0048790223712473569</Real>
+ <Real>0.042559053512507009</Real>
+ <Real>0.55745084251830734</Real>
+ <Real>0.3918472969218505</Real>
+ <Real>0.0081428070473352349</Real>
+ <Real>0.0042822983182703679</Real>
+ <Real>0.34489746753419126</Real>
+ <Real>0.59244017307124897</Real>
+ <Real>0.058380061076289277</Real>
+ <Real>0.12484999797808245</Real>
+ <Real>0.65862567655706228</Real>
+ <Real>0.21639537487981303</Real>
+ <Real>0.00012895058504219708</Real>
+ <Real>0.010024276215463116</Real>
+ <Real>0.40925040275948299</Real>
+ <Real>0.54322966784603066</Real>
+ <Real>0.037495653179023217</Real>
+ <Real>0.090687467643976075</Real>
+ <Real>0.63605011324875538</Real>
+ <Real>0.27223081442693087</Real>
+ <Real>0.0010316046803375766</Real>
+ <Real>0.03997392842591032</Real>
+ <Real>0.55041457032000274</Real>
+ <Real>0.40056052852395163</Real>
+ <Real>0.0090509727301352396</Real>
+ <Real>0.027853326369114029</Real>
+ <Real>0.51021767533992357</Real>
+ <Real>0.44682433864369708</Real>
+ <Real>0.01510465964726525</Real>
+ <Real>0.0017667435669507293</Real>
+ <Real>0.29533040945432815</Real>
+ <Real>0.62371106113053343</Real>
+ <Real>0.079191785848187535</Real>
+ <Real>0.13033713529174909</Real>
+ <Real>0.66071839577659341</Real>
+ <Real>0.2088632638531345</Real>
+ <Real>8.120507852295045e-05</Real>
+ <Real>0.02989059562152363</Real>
+ <Real>0.51797311002867397</Real>
+ <Real>0.43831641796203813</Real>
+ <Real>0.013819876387764206</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>-0.036090455589515444</Real>
+ <Real>-0.66039368711645541</Real>
+ <Real>0.42905874100145708</Real>
+ <Real>0.26742540170451373</Real>
+ <Real>-0.18259480726201247</Real>
+ <Real>-0.5565247826151738</Real>
+ <Real>0.66083398701638507</Real>
+ <Real>0.078285602860801204</Real>
+ <Real>-0.18282127502653051</Real>
+ <Real>-0.55622001797648113</Real>
+ <Real>0.66090386103255361</Real>
+ <Real>0.07813743197045793</Real>
+ <Real>-0.02177213641407599</Real>
+ <Real>-0.64335623589400448</Real>
+ <Real>0.35202888103023683</Real>
+ <Real>0.31309949127784359</Real>
+ <Real>-0.088180370703606098</Real>
+ <Real>-0.65541214886855814</Real>
+ <Real>0.57536540984793449</Real>
+ <Real>0.16822710972422975</Real>
+ <Real>-0.1357364132155662</Real>
+ <Real>-0.61382130305798044</Real>
+ <Real>0.63485184576265952</Real>
+ <Real>0.11470587051088713</Real>
+ <Real>-0.2383247396874062</Real>
+ <Real>-0.47542383957845602</Real>
+ <Real>0.66582189821913063</Real>
+ <Real>0.047926681046731583</Real>
+ <Real>-0.0038522301444038455</Real>
+ <Real>-0.57621836461551912</Real>
+ <Real>0.16399341966424974</Real>
+ <Real>0.41607717509567321</Real>
+ <Real>-0.025951435289900862</Real>
+ <Real>-0.64996770926448444</Real>
+ <Real>0.37778972439867142</Real>
+ <Real>0.29812942015571386</Real>
+ <Real>-0.13200413949930864</Real>
+ <Real>-0.61780494107512052</Real>
+ <Real>0.63162230064816693</Real>
+ <Real>0.11818677992626223</Real>
+ <Real>-0.20127801669320952</Real>
+ <Real>-0.53063898590095504</Real>
+ <Real>0.66511202188153873</Real>
+ <Real>0.066804980712625833</Real>
+ <Real>-0.016581614822692537</Real>
+ <Real>-0.63236289739202312</Real>
+ <Real>0.31447063925212376</Real>
+ <Real>0.33447387296259184</Real>
+ <Real>-0.052315161615281575</Real>
+ <Real>-0.66652062347241958</Real>
+ <Real>0.48998673179068397</Real>
+ <Real>0.22884905329701719</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>-0.0015578001757111505</Real>
+ <Real>-0.55114416258182264</Real>
+ <Real>0.10696172569077878</Real>
+ <Real>0.44574023706675503</Real>
+ <Real>-0.49203512289596113</Real>
+ <Real>-0.015897779387727462</Real>
+ <Real>0.50790092746333826</Real>
+ <Real>3.1974820350303207e-05</Real>
+ <Real>-0.30128157916062442</Real>
+ <Real>-0.3724046801161362</Real>
+ <Real>0.64865409771414562</Real>
+ <Real>0.025032161562614976</Real>
+ <Real>-0.007465335582521662</Real>
+ <Real>-0.59979511881007652</Real>
+ <Real>0.22198624436771813</Real>
+ <Real>0.3852742100248801</Real>
+ <Real>-0.27952824743682397</Real>
+ <Real>-0.4091160634090672</Real>
+ <Real>0.65681686912860626</Real>
+ <Real>0.031827441717284875</Real>
+ <Real>-0.15426655549059071</Real>
+ <Real>-0.59265790254784378</Real>
+ <Real>0.64811547156745974</Real>
+ <Real>0.098808986470974761</Real>
+ <Real>-0.14169664987958924</Real>
+ <Real>-0.60725702345225918</Real>
+ <Real>0.63960399654328604</Real>
+ <Real>0.10934967678856237</Real>
+ <Real>-0.083426634674385811</Real>
+ <Real>-0.65819686318493187</Real>
+ <Real>0.56667363039302121</Real>
+ <Real>0.17494986746629645</Real>
+ <Real>-0.012535251765837658</Real>
+ <Real>-0.62073092248649042</Real>
+ <Real>0.27906760027049388</Real>
+ <Real>0.35419857398183424</Real>
+ <Real>-0.02716938719551423</Real>
+ <Real>-0.6515986259401797</Real>
+ <Real>0.38470541346690201</Real>
+ <Real>0.29406259966879189</Real>
+ <Real>-0.21968820016588803</Real>
+ <Real>-0.50379013496990122</Real>
+ <Real>0.66664487043746667</Real>
+ <Real>0.056833464698322671</Real>
+ <Real>-0.021448711607312865</Real>
+ <Real>-0.6427707964382211</Real>
+ <Real>0.34988772769838083</Real>
+ <Real>0.31433178034715314</Real>
+ <Real>-0.34943592393514256</Real>
+ <Real>-0.28767778301611657</Real>
+ <Real>0.62366333783766081</Real>
+ <Real>0.013450369113598334</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>-0.022015595113395979</Real>
+ <Real>-0.64378931790897165</Real>
+ <Real>0.35362542115813128</Real>
+ <Real>0.31217949186423638</Real>
+ <Real>-0.1526054876007322</Real>
+ <Real>-0.59464256301009333</Real>
+ <Real>0.64710158882238322</Real>
+ <Real>0.1001464617884423</Real>
+ <Real>-0.23929588540952862</Real>
+ <Real>-0.47391561842328889</Real>
+ <Real>0.66571889307516363</Real>
+ <Real>0.047492610757653875</Real>
+ <Real>-0.20124826514116861</Real>
+ <Real>-0.53068134707248027</Real>
+ <Real>0.66510748956846633</Real>
+ <Real>0.066822122645182544</Real>
+ <Real>-0.043536694275114363</Real>
+ <Real>-0.66447192026909963</Real>
+ <Real>0.45955392336354245</Real>
+ <Real>0.24845469118067159</Real>
+ <Real>-0.41241064286055051</Real>
+ <Real>-0.17096479334653347</Real>
+ <Real>0.57916151527471849</Real>
+ <Real>0.0042139209323654933</Real>
+ <Real>-0.076754913733512689</Real>
+ <Real>-0.66153856081084794</Real>
+ <Real>0.55334186282223397</Real>
+ <Real>0.18495161172212665</Real>
+ <Real>-0.33324912758583197</Real>
+ <Real>-0.31664606109887411</Real>
+ <Real>0.63303950495524408</Real>
+ <Real>0.016855683729461973</Real>
+ <Real>-0.193013961710223</Real>
+ <Real>-0.54226956931101922</Real>
+ <Real>0.66358102375270744</Real>
+ <Real>0.07170250726853479</Real>
+ <Real>-0.15170115356515579</Real>
+ <Real>-0.595716207735419</Real>
+ <Real>0.64653587616630537</Real>
+ <Real>0.10088148513426944</Real>
+ <Real>-0.024127918118492662</Real>
+ <Real>-0.64728835638456406</Real>
+ <Real>0.36696046712460617</Real>
+ <Real>0.30445580737845057</Real>
+ <Real>-0.42440740434438973</Real>
+ <Real>-0.14808924824839953</Real>
+ <Real>0.56940070952996824</Real>
+ <Real>0.0030959430628210299</Real>
+ <Real>-0.1590110177845997</Real>
+ <Real>-0.58690137153015798</Real>
+ <Real>0.65083579641411504</Real>
+ <Real>0.095076592900642645</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">4</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">7</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">1</Int>
+ <Int Name="Y">11</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">10</Int>
+ <Int Name="Z">13</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 1 1">1.578136093948518e-08</Real>
+ <Real Name="Cell 0 1 2">2.9615824238341996e-06</Real>
+ <Real Name="Cell 0 1 3">6.4283467708510775e-06</Real>
+ <Real Name="Cell 0 1 4">1.3032248079823335e-05</Real>
+ <Real Name="Cell 0 1 5">0.00098175226244482891</Real>
+ <Real Name="Cell 0 1 6">0.0016863837372718463</Real>
+ <Real Name="Cell 0 1 7">0.00016617911825528967</Real>
+ <Real Name="Cell 0 2 1">0.00010674357106339121</Real>
+ <Real Name="Cell 0 2 2">0.020031851823861083</Real>
+ <Real Name="Cell 0 2 3">0.043480704419960381</Real>
+ <Real Name="Cell 0 2 4">0.0058066206494026742</Real>
+ <Real Name="Cell 0 2 5">0.008610741480147904</Real>
+ <Real Name="Cell 0 2 6">0.014790915135568187</Real>
+ <Real Name="Cell 0 2 7">0.0014575219038781074</Real>
+ <Real Name="Cell 0 3 0">0.00018286062146263715</Real>
+ <Real Name="Cell 0 3 1">0.0016275736041690731</Real>
+ <Real Name="Cell 0 3 2">0.069655757150767592</Real>
+ <Real Name="Cell 0 3 3">0.14767038255915954</Real>
+ <Real Name="Cell 0 3 4">0.019349717312040677</Real>
+ <Real Name="Cell 0 3 5">0.0044616887857618611</Real>
+ <Real Name="Cell 0 3 6">0.0076639695133881112</Real>
+ <Real Name="Cell 0 3 7">0.00075522057519993371</Real>
+ <Real Name="Cell 0 4 0">0.0032840797006217187</Real>
+ <Real Name="Cell 0 4 1">0.076073842891386814</Real>
+ <Real Name="Cell 0 4 2">0.31842564661451356</Real>
+ <Real Name="Cell 0 4 3">0.1259776045669844</Real>
+ <Real Name="Cell 0 4 4">0.0041309267860407386</Real>
+ <Real Name="Cell 0 4 5">3.7719502469544199e-05</Real>
+ <Real Name="Cell 0 4 6">6.4791860407043583e-05</Real>
+ <Real Name="Cell 0 4 7">6.3846999912254604e-06</Real>
+ <Real Name="Cell 0 5 0">0.0028413692782037741</Real>
+ <Real Name="Cell 0 5 1">0.14432447322557718</Real>
+ <Real Name="Cell 0 5 2">0.66829686527291721</Real>
+ <Real Name="Cell 0 5 3">0.21394913146163794</Real>
+ <Real Name="Cell 0 5 4">0.00020276663663295686</Real>
+ <Real Name="Cell 0 6 0">9.373616564786184e-05</Real>
+ <Real Name="Cell 0 6 1">0.018080533852036267</Real>
+ <Real Name="Cell 0 6 2">0.093014453839735778</Real>
+ <Real Name="Cell 0 6 3">0.031384521315035774</Real>
+ <Real Name="Cell 0 6 4">6.947153745591987e-05</Real>
+ <Real Name="Cell 0 7 1">4.1760376030672574e-06</Real>
+ <Real Name="Cell 0 7 2">4.4371224853550681e-05</Real>
+ <Real Name="Cell 0 7 3">2.6761184626639464e-05</Real>
+ <Real Name="Cell 0 7 4">3.692330945918291e-07</Real>
+ <Real Name="Cell 1 0 0">0.00012320714087502198</Real>
+ <Real Name="Cell 1 0 1">0.0016964808858046813</Real>
+ <Real Name="Cell 1 0 2">0.0012346026375239822</Real>
+ <Real Name="Cell 1 0 3">2.789679463915135e-05</Real>
+ <Real Name="Cell 1 1 0">0.00030927559988737032</Real>
+ <Real Name="Cell 1 1 1">0.004258549692340464</Real>
+ <Real Name="Cell 1 1 2">0.0031045753071671936</Real>
+ <Real Name="Cell 1 1 3">8.1889839824169614e-05</Real>
+ <Real Name="Cell 1 1 4">0.00042399980815044483</Real>
+ <Real Name="Cell 1 1 5">0.034023812795862418</Real>
+ <Real Name="Cell 1 1 6">0.05844366931840763</Real>
+ <Real Name="Cell 1 1 7">0.0057591384572105286</Real>
+ <Real Name="Cell 1 11 0">3.1793314777459778e-07</Real>
+ <Real Name="Cell 1 11 1">4.3777292804029945e-06</Real>
+ <Real Name="Cell 1 11 2">3.1858632544438581e-06</Real>
+ <Real Name="Cell 1 11 3">7.1987026640312263e-08</Real>
+ <Real Name="Cell 1 2 0">4.7753634484560603e-05</Real>
+ <Real Name="Cell 1 2 1">0.00085452389504690827</Real>
+ <Real Name="Cell 1 2 2">0.037445921488349618</Real>
+ <Real Name="Cell 1 2 3">0.080251460394392293</Real>
+ <Real Name="Cell 1 2 4">0.014223592994074028</Real>
+ <Real Name="Cell 1 2 5">0.29841566692654647</Real>
+ <Real Name="Cell 1 2 6">0.51259706435394181</Real>
+ <Real Name="Cell 1 2 7">0.050512185507904046</Real>
+ <Real Name="Cell 1 3 1">0.0013744459657307258</Real>
+ <Real Name="Cell 1 3 2">0.12872582299847918</Real>
+ <Real Name="Cell 1 3 3">0.27275726530417721</Real>
+ <Real Name="Cell 1 3 4">0.03752628436599631</Real>
+ <Real Name="Cell 1 3 5">0.15462522451654762</Real>
+ <Real Name="Cell 1 3 6">0.26560413861166682</Real>
+ <Real Name="Cell 1 3 7">0.026173083020147432</Real>
+ <Real Name="Cell 1 4 1">0.13996001705531683</Real>
+ <Real Name="Cell 1 4 2">0.74946868661100219</Real>
+ <Real Name="Cell 1 4 3">0.29378563449513984</Real>
+ <Real Name="Cell 1 4 4">0.0078549772341450896</Real>
+ <Real Name="Cell 1 4 5">0.0013072150071555984</Real>
+ <Real Name="Cell 1 4 6">0.0022454403351158912</Real>
+ <Real Name="Cell 1 4 7">0.00022126950511754709</Real>
+ <Real Name="Cell 1 5 1">0.32064305884265848</Real>
+ <Real Name="Cell 1 5 2">1.7390157845254106</Real>
+ <Real Name="Cell 1 5 3">0.61207020778629195</Real>
+ <Real Name="Cell 1 5 4">0.0019945451176575663</Real>
+ <Real Name="Cell 1 6 1">0.049489274873467437</Real>
+ <Real Name="Cell 1 6 2">0.30526912304037801</Real>
+ <Real Name="Cell 1 6 3">0.12635515085077775</Real>
+ <Real Name="Cell 1 6 4">0.0008903500740208148</Real>
+ <Real Name="Cell 1 7 1">6.134132790171573e-05</Real>
+ <Real Name="Cell 1 7 2">0.00065176373199879337</Real>
+ <Real Name="Cell 1 7 3">0.0003930919108619452</Real>
+ <Real Name="Cell 1 7 4">5.4236217391545922e-06</Real>
+ <Real Name="Cell 13 3 0">0.00023538906135106544</Real>
+ <Real Name="Cell 13 3 1">0.0012417563660168706</Real>
+ <Real Name="Cell 13 3 2">0.00040798642369712474</Real>
+ <Real Name="Cell 13 3 3">2.4312020556926323e-07</Real>
+ <Real Name="Cell 13 4 0">0.0042274625993731756</Real>
+ <Real Name="Cell 13 4 1">0.022301285220049618</Real>
+ <Real Name="Cell 13 4 2">0.0073272196139109414</Real>
+ <Real Name="Cell 13 4 3">4.3663098459070614e-06</Real>
+ <Real Name="Cell 13 5 0">0.003657579428520089</Real>
+ <Real Name="Cell 13 5 1">0.019294960069547899</Real>
+ <Real Name="Cell 13 5 2">0.0063394736436138566</Real>
+ <Real Name="Cell 13 5 3">3.7777093695169178e-06</Real>
+ <Real Name="Cell 13 6 0">0.00012066276418625477</Real>
+ <Real Name="Cell 13 6 1">0.00063653661180970646</Real>
+ <Real Name="Cell 13 6 2">0.00020913788156170309</Real>
+ <Real Name="Cell 13 6 3">1.2462582528321472e-07</Real>
+ <Real Name="Cell 14 3 0">0.0049145714059317565</Real>
+ <Real Name="Cell 14 3 1">0.025926014975090592</Real>
+ <Real Name="Cell 14 3 2">0.0085181460871702145</Real>
+ <Real Name="Cell 14 3 3">5.0759861296738361e-06</Real>
+ <Real Name="Cell 14 4 0">0.08826309383824435</Real>
+ <Real Name="Cell 14 4 1">0.4656174676465622</Real>
+ <Real Name="Cell 14 4 2">0.15298138236679812</Real>
+ <Real Name="Cell 14 4 3">9.1162016599103174e-05</Real>
+ <Real Name="Cell 14 5 0">0.076364785904473306</Real>
+ <Real Name="Cell 14 5 1">0.40284989664395854</Real>
+ <Real Name="Cell 14 5 2">0.13235872439754579</Real>
+ <Real Name="Cell 14 5 3">7.8872919331025219e-05</Real>
+ <Real Name="Cell 14 6 0">0.0025192579775235591</Real>
+ <Real Name="Cell 14 6 1">0.013289932052377872</Real>
+ <Real Name="Cell 14 6 2">0.0043664860496102917</Real>
+ <Real Name="Cell 14 6 3">2.6020007635956435e-06</Real>
+ <Real Name="Cell 15 1 1">1.5579618390928022e-10</Real>
+ <Real Name="Cell 15 1 2">2.9237227494856138e-08</Real>
+ <Real Name="Cell 15 1 3">6.3461693803501172e-08</Real>
+ <Real Name="Cell 15 1 4">8.3189348961108985e-09</Real>
+ <Real Name="Cell 15 2 1">1.0537900433489441e-06</Real>
+ <Real Name="Cell 15 2 2">0.00019775772715426666</Real>
+ <Real Name="Cell 15 2 3">0.00042924864644393508</Real>
+ <Real Name="Cell 15 2 4">5.626845629219268e-05</Real>
+ <Real Name="Cell 15 3 0">0.0046521768734949787</Real>
+ <Real Name="Cell 15 3 1">0.02454648184631009</Real>
+ <Real Name="Cell 15 3 2">0.0087384564427777679</Real>
+ <Real Name="Cell 15 3 3">0.001459651435021985</Real>
+ <Real Name="Cell 15 3 4">0.00019047553736359761</Real>
+ <Real Name="Cell 15 4 0">0.083550627312443893</Real>
+ <Real Name="Cell 15 4 1">0.44097542629927661</Real>
+ <Real Name="Cell 15 4 2">0.14605532868375404</Real>
+ <Real Name="Cell 15 4 3">0.00074127306681089457</Real>
+ <Real Name="Cell 15 4 4">4.0399780738420634e-05</Real>
+ <Real Name="Cell 15 5 0">0.072287583512449072</Real>
+ <Real Name="Cell 15 5 1">0.38181599694312202</Real>
+ <Real Name="Cell 15 5 2">0.12769840335756452</Real>
+ <Real Name="Cell 15 5 3">0.00083538124283651029</Real>
+ <Real Name="Cell 15 5 4">2.9576422658338407e-07</Real>
+ <Real Name="Cell 15 6 0">0.0023847519413914848</Real>
+ <Real Name="Cell 15 6 1">0.012643144570544053</Real>
+ <Real Name="Cell 15 6 2">0.0044515902324904679</Real>
+ <Real Name="Cell 15 6 3">0.00010306232161466888</Real>
+ <Real Name="Cell 15 6 4">3.9112524662635974e-08</Real>
+ <Real Name="Cell 2 0 0">0.039204049865150054</Real>
+ <Real Name="Cell 2 0 1">0.27665180841072834</Real>
+ <Real Name="Cell 2 0 13">0.0011142203247297578</Real>
+ <Real Name="Cell 2 0 2">0.18892778412908051</Real>
+ <Real Name="Cell 2 0 3">0.0042553152342553356</Real>
+ <Real Name="Cell 2 1 0">0.049741413483468042</Real>
+ <Real Name="Cell 2 1 1">0.65323372369663812</Real>
+ <Real Name="Cell 2 1 13">0.00013538532301635305</Real>
+ <Real Name="Cell 2 1 2">0.47405486342880254</Real>
+ <Real Name="Cell 2 1 3">0.010722404053741445</Real>
+ <Real Name="Cell 2 1 4">0.00052091375150695163</Real>
+ <Real Name="Cell 2 1 5">0.041941020388234954</Real>
+ <Real Name="Cell 2 1 6">0.072043281602603954</Real>
+ <Real Name="Cell 2 1 7">0.007099267354360372</Real>
+ <Real Name="Cell 2 10 0">7.1442929248053273e-05</Real>
+ <Real Name="Cell 2 10 1">7.3581984906150396e-05</Real>
+ <Real Name="Cell 2 10 13">3.8021711445589364e-06</Real>
+ <Real Name="Cell 2 10 2">7.4493163488209558e-06</Real>
+ <Real Name="Cell 2 10 3">2.0415374459620007e-08</Real>
+ <Real Name="Cell 2 11 0">0.010079636463766932</Real>
+ <Real Name="Cell 2 11 1">0.0094525634469115501</Real>
+ <Real Name="Cell 2 11 13">0.00054761059821526121</Real>
+ <Real Name="Cell 2 11 2">0.00078292983107846941</Real>
+ <Real Name="Cell 2 11 3">1.0980741518645826e-05</Real>
+ <Real Name="Cell 2 2 0">0.0081983598974018444</Real>
+ <Real Name="Cell 2 2 1">0.11659517003468504</Real>
+ <Real Name="Cell 2 2 2">0.091103123292234203</Real>
+ <Real Name="Cell 2 2 3">0.010793304055686917</Real>
+ <Real Name="Cell 2 2 4">0.0057023123423931973</Real>
+ <Real Name="Cell 2 2 5">0.36785582044635079</Real>
+ <Real Name="Cell 2 2 6">0.63187638775253607</Real>
+ <Real Name="Cell 2 2 7">0.06226617266419187</Real>
+ <Real Name="Cell 2 3 0">0.0016778584421366038</Real>
+ <Real Name="Cell 2 3 1">0.032036430604903146</Real>
+ <Real Name="Cell 2 3 2">0.043840291535881599</Real>
+ <Real Name="Cell 2 3 3">0.030804821703040206</Real>
+ <Real Name="Cell 2 3 4">0.0062086164085601156</Real>
+ <Real Name="Cell 2 3 5">0.19060590689508433</Real>
+ <Real Name="Cell 2 3 6">0.32740917837598099</Real>
+ <Real Name="Cell 2 3 7">0.032263456631305656</Real>
+ <Real Name="Cell 2 4 0">0.00037613719788839146</Real>
+ <Real Name="Cell 2 4 1">0.029470369111757898</Real>
+ <Real Name="Cell 2 4 2">0.13146240221710898</Real>
+ <Real Name="Cell 2 4 3">0.050684445721015721</Real>
+ <Real Name="Cell 2 4 4">0.0010166091404921454</Real>
+ <Real Name="Cell 2 4 5">0.0016113988045921457</Real>
+ <Real Name="Cell 2 4 6">0.0027679454810283144</Real>
+ <Real Name="Cell 2 4 7">0.00027275804981381329</Real>
+ <Real Name="Cell 2 5 0">1.1546917062218504e-07</Real>
+ <Real Name="Cell 2 5 1">0.058569944450123292</Real>
+ <Real Name="Cell 2 5 2">0.38321377342230895</Real>
+ <Real Name="Cell 2 5 3">0.16853388911122885</Real>
+ <Real Name="Cell 2 5 4">0.0014011685649805391</Real>
+ <Real Name="Cell 2 6 1">0.013131393009735775</Real>
+ <Real Name="Cell 2 6 2">0.10792576797876144</Real>
+ <Real Name="Cell 2 6 3">0.056817724704946018</Real>
+ <Real Name="Cell 2 6 4">0.00066173103103508589</Real>
+ <Real Name="Cell 2 7 0">5.9098707380832857e-07</Real>
+ <Real Name="Cell 2 7 1">5.0787026388975193e-05</Real>
+ <Real Name="Cell 2 7 2">0.00049735505993768502</Real>
+ <Real Name="Cell 2 7 3">0.00029890166452569041</Real>
+ <Real Name="Cell 2 7 4">4.1239543714625355e-06</Real>
+ <Real Name="Cell 2 8 0">2.1864464480098968e-05</Real>
+ <Real Name="Cell 2 8 1">0.00015334969064619266</Real>
+ <Real Name="Cell 2 8 2">6.5633996924396618e-05</Real>
+ <Real Name="Cell 2 8 3">2.4871665817479734e-07</Real>
+ <Real Name="Cell 2 9 0">2.7776655075961438e-05</Real>
+ <Real Name="Cell 2 9 1">0.00019481572333782598</Real>
+ <Real Name="Cell 2 9 2">8.3381547967253339e-05</Real>
+ <Real Name="Cell 2 9 3">3.1597009074040129e-07</Real>
+ <Real Name="Cell 3 0 0">0.47912946209747515</Real>
+ <Real Name="Cell 3 0 1">0.91990835507739344</Real>
+ <Real Name="Cell 3 0 13">0.024037891640896713</Real>
+ <Real Name="Cell 3 0 2">0.40186257222397703</Real>
+ <Real Name="Cell 3 0 3">0.008785844542180966</Real>
+ <Real Name="Cell 3 1 0">0.15640164199786069</Real>
+ <Real Name="Cell 3 1 1">1.4832677885127843</Real>
+ <Real Name="Cell 3 1 13">0.0029207667928909924</Real>
+ <Real Name="Cell 3 1 2">1.0582056900769019</Real>
+ <Real Name="Cell 3 1 3">0.024595101295715377</Real>
+ <Real Name="Cell 3 1 4">3.2119954280957093e-05</Real>
+ <Real Name="Cell 3 1 5">0.0025869498258800847</Real>
+ <Real Name="Cell 3 1 6">0.0044436771702856866</Real>
+ <Real Name="Cell 3 1 7">0.00043788749716233656</Real>
+ <Real Name="Cell 3 10 0">0.0049112158978242716</Real>
+ <Real Name="Cell 3 10 1">0.025222912512218112</Real>
+ <Real Name="Cell 3 10 13">8.2027024587995315e-05</Real>
+ <Real Name="Cell 3 10 2">0.010276743373912343</Real>
+ <Real Name="Cell 3 10 3">3.8774626069356451e-05</Real>
+ <Real Name="Cell 3 11 0">0.21650925726023235</Real>
+ <Real Name="Cell 3 11 1">0.19089953249076932</Real>
+ <Real Name="Cell 3 11 13">0.011814004761129914</Real>
+ <Real Name="Cell 3 11 2">0.0074100092484539696</Real>
+ <Real Name="Cell 3 11 3">2.26716665228627e-05</Real>
+ <Real Name="Cell 3 2 0">0.056532521058634988</Real>
+ <Real Name="Cell 3 2 1">0.93418053191533734</Real>
+ <Real Name="Cell 3 2 2">0.77242019261172157</Real>
+ <Real Name="Cell 3 2 3">0.02372084682759755</Real>
+ <Real Name="Cell 3 2 4">0.00028171732650632329</Real>
+ <Real Name="Cell 3 2 5">0.022689589853650934</Real>
+ <Real Name="Cell 3 2 6">0.038974552744374745</Real>
+ <Real Name="Cell 3 2 7">0.0038406186363800403</Real>
+ <Real Name="Cell 3 3 0">0.037588244043927535</Real>
+ <Real Name="Cell 3 3 1">0.72746360502384166</Real>
+ <Real Name="Cell 3 3 2">0.68557111467741128</Real>
+ <Real Name="Cell 3 3 3">0.030091062110324043</Real>
+ <Real Name="Cell 3 3 4">0.00014598840119149094</Real>
+ <Real Name="Cell 3 3 5">0.011756698170182624</Real>
+ <Real Name="Cell 3 3 6">0.020194814268965147</Real>
+ <Real Name="Cell 3 3 7">0.001990031304485349</Real>
+ <Real Name="Cell 3 4 0">0.0070246411523578632</Real>
+ <Real Name="Cell 3 4 1">0.17426735629017845</Real>
+ <Real Name="Cell 3 4 2">0.19878554833932208</Real>
+ <Real Name="Cell 3 4 3">0.013240277078022018</Real>
+ <Real Name="Cell 3 4 4">1.7475484977519544e-05</Real>
+ <Real Name="Cell 3 4 5">9.9392142069399457e-05</Real>
+ <Real Name="Cell 3 4 6">0.00017072870459299545</Real>
+ <Real Name="Cell 3 4 7">1.6823896580045288e-05</Real>
+ <Real Name="Cell 3 5 0">5.6149750152812813e-05</Real>
+ <Real Name="Cell 3 5 1">0.0030456374401335302</Real>
+ <Real Name="Cell 3 5 2">0.0099012447635933119</Real>
+ <Real Name="Cell 3 5 3">0.004363553291023399</Real>
+ <Real Name="Cell 3 5 4">6.7621776851363994e-05</Real>
+ <Real Name="Cell 3 6 1">0.00021623759631415483</Real>
+ <Real Name="Cell 3 6 2">0.0023717795830038644</Real>
+ <Real Name="Cell 3 6 3">0.0014696976434452284</Real>
+ <Real Name="Cell 3 6 4">2.220729040611576e-05</Real>
+ <Real Name="Cell 3 7 0">0.0011224532199527251</Real>
+ <Real Name="Cell 3 7 1">0.007873660323692246</Real>
+ <Real Name="Cell 3 7 2">0.003381842069657122</Real>
+ <Real Name="Cell 3 7 3">2.0245792489656967e-05</Real>
+ <Real Name="Cell 3 7 4">1.0316899992173508e-07</Real>
+ <Real Name="Cell 3 8 0">0.041526861831479897</Real>
+ <Real Name="Cell 3 8 1">0.29125485424812941</Real>
+ <Real Name="Cell 3 8 2">0.12465770310578665</Real>
+ <Real Name="Cell 3 8 3">0.00047238395930589356</Real>
+ <Real Name="Cell 3 9 0">0.052755800103406157</Real>
+ <Real Name="Cell 3 9 1">0.37001069168711215</Real>
+ <Real Name="Cell 3 9 2">0.15836537066264197</Real>
+ <Real Name="Cell 3 9 3">0.00060011743315276556</Real>
+ <Real Name="Cell 4 0 0">0.42953393306754173</Real>
+ <Real Name="Cell 4 0 1">0.43802035858157973</Real>
+ <Real Name="Cell 4 0 13">0.02318682269759989</Real>
+ <Real Name="Cell 4 0 2">0.060646069022436661</Real>
+ <Real Name="Cell 4 0 3">0.0010862242272653689</Real>
+ <Real Name="Cell 4 1 0">0.07239641094376241</Real>
+ <Real Name="Cell 4 1 1">0.36256509394910369</Real>
+ <Real Name="Cell 4 1 13">0.0028173561466838587</Real>
+ <Real Name="Cell 4 1 2">0.25044574353069737</Real>
+ <Real Name="Cell 4 1 3">0.0067702105943121</Real>
+ <Real Name="Cell 4 10 0">0.011947517585427198</Real>
+ <Real Name="Cell 4 10 1">0.074899596623516598</Real>
+ <Real Name="Cell 4 10 13">7.9122832565633588e-05</Real>
+ <Real Name="Cell 4 10 2">0.031556836204469231</Real>
+ <Real Name="Cell 4 10 3">0.00011942041227735595</Real>
+ <Real Name="Cell 4 11 0">0.20875947484206031</Real>
+ <Real Name="Cell 4 11 1">0.1829812203328243</Real>
+ <Real Name="Cell 4 11 13">0.01139572629068984</Real>
+ <Real Name="Cell 4 11 2">0.0063038695772131776</Real>
+ <Real Name="Cell 4 11 3">2.8029762342575523e-06</Real>
+ <Real Name="Cell 4 2 0">0.064322248760643158</Real>
+ <Real Name="Cell 4 2 1">1.1328378637970524</Real>
+ <Real Name="Cell 4 2 2">0.97604860162715812</Real>
+ <Real Name="Cell 4 2 3">0.032752082412234672</Real>
+ <Real Name="Cell 4 3 0">0.05664611465083845</Real>
+ <Real Name="Cell 4 3 1">1.4111503874271834</Real>
+ <Real Name="Cell 4 3 2">1.5575693598920775</Real>
+ <Real Name="Cell 4 3 3">0.087664742935699605</Real>
+ <Real Name="Cell 4 3 4">2.9473652718122413e-06</Real>
+ <Real Name="Cell 4 4 0">0.019956660100731011</Real>
+ <Real Name="Cell 4 4 1">0.73943559381681567</Real>
+ <Real Name="Cell 4 4 2">1.094615567563646</Real>
+ <Real Name="Cell 4 4 3">0.17302479750547023</Real>
+ <Real Name="Cell 4 4 4">0.0022712607122903914</Real>
+ <Real Name="Cell 4 5 0">0.00058448254061990561</Real>
+ <Real Name="Cell 4 5 1">0.057060646568843514</Real>
+ <Real Name="Cell 4 5 2">0.46508059214329511</Real>
+ <Real Name="Cell 4 5 3">0.3066602706090148</Real>
+ <Real Name="Cell 4 5 4">0.0063262355242172229</Real>
+ <Real Name="Cell 4 6 1">0.005711269904622643</Real>
+ <Real Name="Cell 4 6 2">0.074807871825573441</Real>
+ <Real Name="Cell 4 6 3">0.052584479433026465</Real>
+ <Real Name="Cell 4 6 4">0.0010927350349774119</Real>
+ <Real Name="Cell 4 7 0">0.0034569985549063702</Real>
+ <Real Name="Cell 4 7 1">0.024246176230007868</Real>
+ <Real Name="Cell 4 7 2">0.010377415496587604</Real>
+ <Real Name="Cell 4 7 3">3.9324682691131902e-05</Real>
+ <Real Name="Cell 4 8 0">0.12789691257446686</Real>
+ <Real Name="Cell 4 8 1">0.89702411855315956</Real>
+ <Real Name="Cell 4 8 2">0.38392824915483065</Real>
+ <Real Name="Cell 4 8 3">0.0014548763687008736</Real>
+ <Real Name="Cell 4 9 0">0.16248046820880935</Real>
+ <Real Name="Cell 4 9 1">1.1395810566752411</Real>
+ <Real Name="Cell 4 9 2">0.48774313957691978</Real>
+ <Real Name="Cell 4 9 3">0.0018482775605299685</Real>
+ <Real Name="Cell 5 0 0">0.01729105660838327</Real>
+ <Real Name="Cell 5 0 1">0.015142683813029854</Real>
+ <Real Name="Cell 5 0 13">0.00094393719829337266</Real>
+ <Real Name="Cell 5 0 2">0.00051189039038528463</Real>
+ <Real Name="Cell 5 1 0">0.0028805673038345345</Real>
+ <Real Name="Cell 5 1 1">0.015349370121486038</Real>
+ <Real Name="Cell 5 1 13">0.00011469476876496123</Real>
+ <Real Name="Cell 5 1 2">0.011494076482990032</Real>
+ <Real Name="Cell 5 1 3">0.00036044085717739011</Real>
+ <Real Name="Cell 5 10 0">0.002073580858346971</Real>
+ <Real Name="Cell 5 10 1">0.014181208340325416</Real>
+ <Real Name="Cell 5 10 13">3.2210961315010522e-06</Real>
+ <Real Name="Cell 5 10 2">0.0060492182591495997</Real>
+ <Real Name="Cell 5 10 3">2.2916582378535227e-05</Real>
+ <Real Name="Cell 5 11 0">0.0084981090749598875</Real>
+ <Real Name="Cell 5 11 1">0.0074422391670597443</Real>
+ <Real Name="Cell 5 11 13">0.00046392082639530244</Real>
+ <Real Name="Cell 5 11 2">0.00025158094559755685</Real>
+ <Real Name="Cell 5 2 0">0.0057595155073241148</Real>
+ <Real Name="Cell 5 2 1">0.11215849848576423</Real>
+ <Real Name="Cell 5 2 2">0.10522642388864858</Real>
+ <Real Name="Cell 5 2 3">0.0043850876005894369</Real>
+ <Real Name="Cell 5 3 0">0.012829031413087565</Real>
+ <Real Name="Cell 5 3 1">0.46599366235353873</Real>
+ <Real Name="Cell 5 3 2">0.59850364197295436</Real>
+ <Real Name="Cell 5 3 3">0.040257965301610792</Real>
+ <Real Name="Cell 5 3 4">6.4183043953738888e-06</Real>
+ <Real Name="Cell 5 4 0">0.0096154361251026225</Real>
+ <Real Name="Cell 5 4 1">0.41609069805215393</Real>
+ <Real Name="Cell 5 4 2">0.85585704834134446</Real>
+ <Real Name="Cell 5 4 3">0.27367824045973532</Real>
+ <Real Name="Cell 5 4 4">0.0049459911712164944</Real>
+ <Real Name="Cell 5 5 0">0.00035322686967433889</Real>
+ <Real Name="Cell 5 5 1">0.086426421979336018</Real>
+ <Real Name="Cell 5 5 2">0.96226232910242926</Real>
+ <Real Name="Cell 5 5 3">0.66426243850893629</Real>
+ <Real Name="Cell 5 5 4">0.013776271865444051</Real>
+ <Real Name="Cell 5 6 1">0.012437097323015922</Real>
+ <Real Name="Cell 5 6 2">0.16290471260503855</Real>
+ <Real Name="Cell 5 6 3">0.1145101351031125</Real>
+ <Real Name="Cell 5 6 4">0.0023795849618809487</Real>
+ <Real Name="Cell 5 7 0">0.00066339238539884831</Real>
+ <Real Name="Cell 5 7 1">0.0046528016805784918</Real>
+ <Real Name="Cell 5 7 2">0.0019914091114633633</Real>
+ <Real Name="Cell 5 7 3">7.5463424821215634e-06</Real>
+ <Real Name="Cell 5 8 0">0.024543208963019512</Real>
+ <Real Name="Cell 5 8 1">0.17213746558346391</Real>
+ <Real Name="Cell 5 8 2">0.073675204945442802</Real>
+ <Real Name="Cell 5 8 3">0.00027918840270357793</Real>
+ <Real Name="Cell 5 9 0">0.031179736894244411</Real>
+ <Real Name="Cell 5 9 1">0.21868374647428904</Real>
+ <Real Name="Cell 5 9 2">0.09359711312769689</Real>
+ <Real Name="Cell 5 9 3">0.00035468144990079368</Real>
+ <Real Name="Cell 6 2 0">7.2679924277060463e-06</Real>
+ <Real Name="Cell 6 2 1">0.00029672255276678392</Real>
+ <Real Name="Cell 6 2 2">0.0003938627615148788</Real>
+ <Real Name="Cell 6 2 3">2.7185815466323189e-05</Real>
+ <Real Name="Cell 6 3 0">0.00014426908848683313</Real>
+ <Real Name="Cell 6 3 1">0.0058943337071926567</Real>
+ <Real Name="Cell 6 3 2">0.00787596055564313</Real>
+ <Real Name="Cell 6 3 3">0.00058027617419253942</Real>
+ <Real Name="Cell 6 3 4">8.4451863901227645e-07</Real>
+ <Real Name="Cell 6 4 0">0.00013259128059905746</Real>
+ <Real Name="Cell 6 4 1">0.0088145809942466007</Real>
+ <Real Name="Cell 6 4 2">0.051738077221165343</Real>
+ <Real Name="Cell 6 4 3">0.031813303597487373</Real>
+ <Real Name="Cell 6 4 4">0.00065079209011855614</Real>
+ <Real Name="Cell 6 5 0">4.9272131271541582e-06</Real>
+ <Real Name="Cell 6 5 1">0.0096752686701172558</Real>
+ <Real Name="Cell 6 5 2">0.12436166478492172</Real>
+ <Real Name="Cell 6 5 3">0.087247922527886476</Real>
+ <Real Name="Cell 6 5 4">0.001812677874058696</Real>
+ <Real Name="Cell 6 6 1">0.0016364696744621716</Real>
+ <Real Name="Cell 6 6 2">0.02143495504467717</Real>
+ <Real Name="Cell 6 6 3">0.015067210511252014</Real>
+ <Real Name="Cell 6 6 4">0.00031310510216222171</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>0.0054123159943235263</Real>
+ <Real>0.36084277594281844</Real>
+ <Real>0.58111725161983196</Real>
+ <Real>0.052627656443025993</Real>
+ <Real>0.00062205452524004593</Real>
+ <Real>0.25438976300486782</Real>
+ <Real>0.64447149064098475</Real>
+ <Real>0.10051669182890735</Real>
+ <Real>0.024891858917245911</Real>
+ <Real>0.49802017341064697</Real>
+ <Real>0.45984614005605218</Real>
+ <Real>0.01724182761605484</Real>
+ <Real>0.020559388675760314</Real>
+ <Real>0.47778968945400813</Real>
+ <Real>0.4805412211639824</Real>
+ <Real>0.021109700706249193</Real>
+ <Real>0.0050227837091489976</Real>
+ <Real>0.35561657185579465</Real>
+ <Real>0.58489300257397614</Real>
+ <Real>0.054467641861080135</Real>
+ <Real>0.16354820572788292</Real>
+ <Real>0.66662739921061565</Real>
+ <Real>0.1698243538569289</Real>
+ <Real>4.1204572502199554e-08</Real>
+ <Real>5.6794329827889662e-05</Real>
+ <Real>0.20385948121805342</Real>
+ <Real>0.66195834921021379</Real>
+ <Real>0.13412537524190493</Real>
+ <Real>0.026497465234508667</Real>
+ <Real>0.50477796538117836</Real>
+ <Real>0.45268455140448349</Real>
+ <Real>0.016040017979829454</Real>
+ <Real>0.11970209227194881</Real>
+ <Real>0.65632444186467664</Real>
+ <Real>0.22378348242665025</Real>
+ <Real>0.00018998343672421792</Real>
+ <Real>1.8040946492467145e-05</Real>
+ <Real>0.19157724901219744</Real>
+ <Real>0.66444949362911709</Real>
+ <Real>0.14395521641219289</Real>
+ <Real>0.001160158143288331</Real>
+ <Real>0.27688297482515234</Real>
+ <Real>0.63369030614677468</Real>
+ <Real>0.088266560884784587</Real>
+ <Real>0.0016855235775882218</Real>
+ <Real>0.293119235440649</Real>
+ <Real>0.62495790184480637</Real>
+ <Real>0.080237339136956284</Real>
+ <Real>0.092439038491503631</Real>
+ <Real>0.63768398171489615</Real>
+ <Real>0.26893092472363433</Real>
+ <Real>0.0009460550699658196</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>0.0024733439646709445</Real>
+ <Real>0.31231186278375422</Real>
+ <Real>0.61369779027616556</Real>
+ <Real>0.07151700297540918</Real>
+ <Real>0.00062471242253069026</Real>
+ <Real>0.25452634093632676</Real>
+ <Real>0.64441097396686975</Real>
+ <Real>0.10043797267427278</Real>
+ <Real>7.289005458467352e-07</Real>
+ <Real>0.17497486665431677</Real>
+ <Real>0.66640142158691007</Real>
+ <Real>0.15862298285822721</Real>
+ <Real>0.021648416398585668</Real>
+ <Real>0.48317956558304431</Real>
+ <Real>0.47513304751147684</Real>
+ <Real>0.020038970506893111</Real>
+ <Real>0.0019215517592169318</Real>
+ <Real>0.29937429416896921</Real>
+ <Real>0.62139623115375597</Real>
+ <Real>0.077307922918057798</Real>
+ <Real>0.00028967042316330595</Real>
+ <Real>0.23314124699518871</Real>
+ <Real>0.65308005085125465</Real>
+ <Real>0.11348903173039328</Real>
+ <Real>0.021357444482793631</Real>
+ <Real>0.4817611904602529</Real>
+ <Real>0.47656349751006521</Real>
+ <Real>0.020317867546888163</Real>
+ <Real>0.0024613020578055349</Real>
+ <Real>0.31205017372916932</Real>
+ <Real>0.61385783324636978</Real>
+ <Real>0.071630690966655336</Real>
+ <Real>0.0018810327659186724</Real>
+ <Real>0.29833626902374022</Real>
+ <Real>0.6219946571821019</Real>
+ <Real>0.077788041028239135</Real>
+ <Real>0.069444581465373606</Real>
+ <Real>0.61071432620806088</Real>
+ <Real>0.31713888551728886</Real>
+ <Real>0.0027022068092765858</Real>
+ <Real>0.054524288877065188</Real>
+ <Real>0.58500686501315868</Real>
+ <Real>0.35545761192153524</Real>
+ <Real>0.0050112341882408307</Real>
+ <Real>0.04103265979952906</Real>
+ <Real>0.55335032593988764</Real>
+ <Real>0.39695035467352918</Real>
+ <Real>0.0086666595870540392</Real>
+ <Real>0.0072059979806885803</Real>
+ <Real>0.38213175806759764</Real>
+ <Real>0.56509802591992941</Real>
+ <Real>0.045564218031784426</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>0.034832530108168232</Real>
+ <Real>0.53497749355313284</Real>
+ <Real>0.41899007512213859</Real>
+ <Real>0.011199901216560273</Real>
+ <Real>0.045425396100255505</Real>
+ <Real>0.56475658468753465</Real>
+ <Real>0.38257130546239138</Real>
+ <Real>0.0072467137498184323</Real>
+ <Real>0.15311696790993051</Real>
+ <Real>0.66590081604794882</Real>
+ <Real>0.18097860854363881</Real>
+ <Real>3.6074984818065711e-06</Real>
+ <Real>0.13278743328419851</Real>
+ <Real>0.66153895078859903</Real>
+ <Real>0.20560891053133856</Real>
+ <Real>6.4705395863929661e-05</Real>
+ <Real>0.0046491606241226236</Real>
+ <Real>0.35034753315960182</Real>
+ <Real>0.58863616852548795</Real>
+ <Real>0.056367137690787474</Real>
+ <Real>0.13313999577356062</Real>
+ <Real>0.66165140994918059</Real>
+ <Real>0.20514604572452869</Real>
+ <Real>6.2548552730021432e-05</Real>
+ <Real>0.023723982790674208</Real>
+ <Real>0.49287077841202898</Real>
+ <Real>0.46521766067000814</Real>
+ <Real>0.018187578127288623</Real>
+ <Real>0.1044409359397518</Real>
+ <Real>0.64735622242948376</Real>
+ <Real>0.24770245320892417</Real>
+ <Real>0.00050038842184013438</Real>
+ <Real>0.057771240463032621</Real>
+ <Real>0.59130676852003206</Real>
+ <Real>0.34653174148930771</Real>
+ <Real>0.0043902495276275291</Real>
+ <Real>0.013510487389683298</Real>
+ <Real>0.43618088842905678</Real>
+ <Real>0.51989364331139076</Real>
+ <Real>0.030414980869869036</Real>
+ <Real>0.0096515085445540213</Real>
+ <Real>0.40599484651128087</Real>
+ <Real>0.54594101121095151</Real>
+ <Real>0.038412633733213512</Real>
+ <Real>0.00059061979071704568</Real>
+ <Real>0.25274618408825861</Real>
+ <Real>0.6451947777439907</Real>
+ <Real>0.10146841837703359</Real>
+ <Real>0.047346988432876699</Real>
+ <Real>0.5693865171291177</Real>
+ <Real>0.37656304856624395</Real>
+ <Real>0.0067034458717617042</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">52</Int>
+ <Real>-0.05089318151490263</Real>
+ <Real>-0.66636020694373166</Real>
+ <Real>0.48539995843217121</Real>
+ <Real>0.23185343002646308</Real>
+ <Real>-0.012030669800701029</Real>
+ <Real>-0.6190251708243375</Real>
+ <Real>0.27414235105077805</Real>
+ <Real>0.35691348957426045</Real>
+ <Real>-0.14074805168117607</Real>
+ <Real>-0.60831790858555568</Real>
+ <Real>0.63887997221463966</Real>
+ <Real>0.11018598805209209</Real>
+ <Real>-0.12390180576498261</Real>
+ <Real>-0.62609334880433165</Real>
+ <Real>0.62389211490361118</Real>
+ <Real>0.12610303966570308</Real>
+ <Real>-0.048421007610068734</Real>
+ <Real>-0.66593147458280633</Real>
+ <Real>0.47712597199581885</Real>
+ <Real>0.23722651019705621</Real>
+ <Real>-0.4937434649966933</Real>
+ <Real>-0.012493374471729157</Real>
+ <Real>0.50621714393353823</Real>
+ <Real>1.9695534884260206e-05</Real>
+ <Real>-0.0024393502229682756</Real>
+ <Real>-0.56252964396689942</Real>
+ <Real>0.13237733860270362</Real>
+ <Real>0.43259165558716406</Real>
+ <Real>-0.1467372554828546</Real>
+ <Real>-0.60152111142180242</Real>
+ <Real>0.6432539892921687</Real>
+ <Real>0.10500437761248832</Real>
+ <Real>-0.40099473052793144</Real>
+ <Real>-0.19255445138805583</Real>
+ <Real>0.58809309435990598</Real>
+ <Real>0.0054560875560812957</Real>
+ <Real>-0.0011356479385134484</Real>
+ <Real>-0.54425117067744921</Real>
+ <Real>0.09190928517043867</Real>
+ <Real>0.45347753344552394</Real>
+ <Real>-0.018228417474878484</Real>
+ <Real>-0.63625147780230906</Real>
+ <Real>0.32718820802925352</Real>
+ <Real>0.327291687247934</Real>
+ <Real>-0.023382667777312426</Real>
+ <Real>-0.64610494012693187</Real>
+ <Real>0.36235788358580107</Real>
+ <Real>0.30712972431844326</Real>
+ <Real>-0.33752642870877159</Real>
+ <Real>-0.30903671750162287</Real>
+ <Real>0.6306527211295605</Real>
+ <Real>0.015910425080833981</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">52</Int>
+ <Real>-0.030194454142256941</Real>
+ <Real>-0.65515818531091607</Real>
+ <Real>0.40089973304860305</Real>
+ <Real>0.28445290640456999</Real>
+ <Real>-0.01206491498369449</Real>
+ <Real>-0.61914304815603194</Real>
+ <Real>0.27448084126314726</Real>
+ <Real>0.35672712187657912</Real>
+ <Real>-0.00013371589069704963</Real>
+ <Real>-0.51595219392509017</Real>
+ <Real>0.032305535522271389</Real>
+ <Real>0.48378037429351578</Real>
+ <Real>-0.1282394341754734</Real>
+ <Real>-0.62171912534690232</Real>
+ <Real>0.6281565532202249</Real>
+ <Real>0.12180200630215082</Real>
+ <Real>-0.025517545395280731</Real>
+ <Real>-0.64935683858350313</Real>
+ <Real>0.37526631335284844</Real>
+ <Real>0.29960807062593542</Real>
+ <Real>-0.0072278135424509414</Real>
+ <Real>-0.59854811548376918</Real>
+ <Real>0.2187796715948912</Real>
+ <Real>0.38699625743132893</Real>
+ <Real>-0.12708775130249114</Real>
+ <Real>-0.62289495797147854</Real>
+ <Real>0.62705316985043058</Real>
+ <Real>0.12292953942353911</Real>
+ <Real>-0.030096369796856738</Real>
+ <Real>-0.65505297748755487</Real>
+ <Real>0.4003950643656799</Real>
+ <Real>0.28475428291873167</Real>
+ <Real>-0.025157553891160367</Real>
+ <Real>-0.64883763185385734</Real>
+ <Real>0.37314792538119579</Real>
+ <Real>0.30084726036382192</Real>
+ <Real>-0.27893076277274931</Real>
+ <Real>-0.41010899401128365</Real>
+ <Real>0.65701027634081521</Real>
+ <Real>0.032029480443217746</Real>
+ <Real>-0.23739096068816348</Real>
+ <Real>-0.47687132651455788</Real>
+ <Real>0.66591553509360613</Real>
+ <Real>0.048346752109115224</Real>
+ <Real>-0.19640714569586232</Real>
+ <Real>-0.53752754886430476</Real>
+ <Real>0.66427653481619653</Real>
+ <Real>0.069658159743970549</Real>
+ <Real>-0.061593317344401516</Real>
+ <Real>-0.66619958396398582</Real>
+ <Real>0.51717911996117616</Real>
+ <Real>0.21061378134721118</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">52</Int>
+ <Real>-0.17608709093451638</Real>
+ <Real>-0.56518137974936</Real>
+ <Real>0.65862403230226907</Real>
+ <Real>0.082644438381607302</Real>
+ <Real>-0.2101857747525209</Real>
+ <Real>-0.51780333888066454</Real>
+ <Real>0.66616400201889181</Real>
+ <Real>0.061825111614293639</Real>
+ <Real>-0.47251948092640972</Real>
+ <Real>-0.054572701590098971</Real>
+ <Real>0.5267038459594271</Real>
+ <Real>0.00038833655708161568</Real>
+ <Real>-0.42971002799396185</Real>
+ <Real>-0.1379190279792466</Real>
+ <Real>0.56496813994037876</Real>
+ <Real>0.0026609160328297157</Real>
+ <Real>-0.045988990006773256</Real>
+ <Real>-0.66531174669673987</Real>
+ <Real>0.46859046341379951</Real>
+ <Real>0.24271027328971362</Real>
+ <Real>-0.43047030413140991</Real>
+ <Real>-0.13645794054934218</Real>
+ <Real>0.56432679349291404</Real>
+ <Real>0.0026014511878380275</Real>
+ <Real>-0.13631047718434056</Real>
+ <Real>-0.61319973431306718</Real>
+ <Real>0.63533090017915594</Real>
+ <Real>0.11417931131825178</Real>
+ <Real>-0.36614351063849898</Real>
+ <Real>-0.25730717397165043</Real>
+ <Real>0.61304487985879785</Real>
+ <Real>0.010405804751351597</Real>
+ <Real>-0.24672432328322841</Real>
+ <Real>-0.4622860300687846</Real>
+ <Real>0.66474502998725449</Real>
+ <Real>0.044265323364758566</Real>
+ <Real>-0.093652242762162843</Real>
+ <Real>-0.65183015405206579</Real>
+ <Real>0.58461703639062024</Real>
+ <Real>0.16086536042360849</Real>
+ <Real>-0.074840090544688584</Real>
+ <Real>-0.6623649582331097</Real>
+ <Real>0.54925018810028514</Real>
+ <Real>0.18795486067751316</Real>
+ <Real>-0.011621874147413528</Real>
+ <Real>-0.61759338285041854</Real>
+ <Real>0.27005238814307769</Real>
+ <Real>0.3591628688547544</Real>
+ <Real>-0.21607229169952644</Real>
+ <Real>-0.50916017302453009</Real>
+ <Real>0.66653722114763947</Real>
+ <Real>0.058695243576417054</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">4</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">3</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">16</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">10</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">16</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">15</Int>
+ <Int Name="Z">10</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">2</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">3</Int>
+ <Int Name="Y">1</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 1 3">1.4852484278813739e-07</Real>
+ <Real Name="Cell 0 1 4">1.1192410090920781e-05</Real>
+ <Real Name="Cell 0 1 5">1.8804920169037745e-05</Real>
+ <Real Name="Cell 0 1 6">1.8007380129012918e-06</Real>
+ <Real Name="Cell 0 2 1">3.3574637039544062e-05</Real>
+ <Real Name="Cell 0 2 2">0.00051565806774855677</Real>
+ <Real Name="Cell 0 2 3">0.00042699915833960749</Real>
+ <Real Name="Cell 0 2 4">0.0017545527247491788</Real>
+ <Real Name="Cell 0 2 5">0.0029297726046181032</Real>
+ <Real Name="Cell 0 2 6">0.00028055173065712658</Real>
+ <Real Name="Cell 0 3 1">0.0042395063468268837</Real>
+ <Real Name="Cell 0 3 2">0.065112711373102039</Real>
+ <Real Name="Cell 0 3 3">0.051043782790330998</Real>
+ <Real Name="Cell 0 3 4">0.0049825822205819331</Real>
+ <Real Name="Cell 0 3 5">0.0060811822862108528</Real>
+ <Real Name="Cell 0 3 6">0.00058232717861743583</Real>
+ <Real Name="Cell 0 4 0">4.4495503882781831e-12</Real>
+ <Real Name="Cell 0 4 1">0.0083306975938243367</Real>
+ <Real Name="Cell 0 4 2">0.12794751609666455</Real>
+ <Real Name="Cell 0 4 3">0.10021344216990317</Real>
+ <Real Name="Cell 0 4 4">0.0031289098483462422</Real>
+ <Real Name="Cell 0 4 5">0.00075656006242612935</Real>
+ <Real Name="Cell 0 4 6">7.2447340972860833e-05</Real>
+ <Real Name="Cell 0 5 0">4.0920647233743564e-05</Real>
+ <Real Name="Cell 0 5 1">0.018480631465922048</Real>
+ <Real Name="Cell 0 5 2">0.059608248467664236</Real>
+ <Real Name="Cell 0 5 3">0.018707184490057021</Real>
+ <Real Name="Cell 0 5 4">0.00031215139967351969</Real>
+ <Real Name="Cell 0 6 0">0.00055180150534747305</Real>
+ <Real Name="Cell 0 6 1">0.23686386639064808</Real>
+ <Real Name="Cell 0 6 2">0.60596895389480154</Real>
+ <Real Name="Cell 0 6 3">0.095664785114731615</Real>
+ <Real Name="Cell 0 6 4">1.7283506352435327e-08</Real>
+ <Real Name="Cell 0 7 0">0.00039583384252009905</Real>
+ <Real Name="Cell 0 7 1">0.17218384128729677</Real>
+ <Real Name="Cell 0 7 2">0.44455867696811047</Real>
+ <Real Name="Cell 0 7 3">0.071306187928466533</Real>
+ <Real Name="Cell 0 7 4">6.5825186345327837e-08</Real>
+ <Real Name="Cell 0 8 0">8.6422445965792202e-06</Real>
+ <Real Name="Cell 0 8 1">0.0043633360324719225</Real>
+ <Real Name="Cell 0 8 2">0.012332995580887908</Real>
+ <Real Name="Cell 0 8 3">0.002270774430897566</Real>
+ <Real Name="Cell 0 8 4">1.5668315023143775e-08</Real>
+ <Real Name="Cell 1 1 3">1.0515661928967893e-05</Real>
+ <Real Name="Cell 1 1 4">0.00079243040071335486</Real>
+ <Real Name="Cell 1 1 5">0.0013314013964714636</Real>
+ <Real Name="Cell 1 1 6">0.00012749350082344484</Real>
+ <Real Name="Cell 1 2 1">5.4070088418910366e-05</Real>
+ <Real Name="Cell 1 2 2">0.00083043868156340811</Real>
+ <Real Name="Cell 1 2 3">0.0022887140434028584</Real>
+ <Real Name="Cell 1 2 4">0.12347661093162883</Real>
+ <Real Name="Cell 1 2 5">0.20742993334025839</Real>
+ <Real Name="Cell 1 2 6">0.019863257201931415</Real>
+ <Real Name="Cell 1 3 1">0.0068274895348972679</Real>
+ <Real Name="Cell 1 3 2">0.10486040569826598</Real>
+ <Real Name="Cell 1 3 3">0.085526408479558322</Real>
+ <Real Name="Cell 1 3 4">0.2584534135331904</Real>
+ <Real Name="Cell 1 3 5">0.43055192552157256</Real>
+ <Real Name="Cell 1 3 6">0.041229168315805434</Real>
+ <Real Name="Cell 1 4 1">0.013416125802436393</Real>
+ <Real Name="Cell 1 4 2">0.20605236922763329</Real>
+ <Real Name="Cell 1 4 3">0.16180162662213007</Real>
+ <Real Name="Cell 1 4 4">0.036194844667286404</Real>
+ <Real Name="Cell 1 4 5">0.053564977387523222</Real>
+ <Real Name="Cell 1 4 6">0.0051293220112003752</Real>
+ <Real Name="Cell 1 5 0">8.7239050302150001e-05</Real>
+ <Real Name="Cell 1 5 1">0.03889604365906639</Real>
+ <Real Name="Cell 1 5 2">0.11931268078999198</Real>
+ <Real Name="Cell 1 5 3">0.033793911774638682</Real>
+ <Real Name="Cell 1 5 4">0.00050270249548867261</Real>
+ <Real Name="Cell 1 6 0">0.0011764715510822188</Real>
+ <Real Name="Cell 1 6 1">0.51812901157850511</Real>
+ <Real Name="Cell 1 6 2">1.349010945795253</Real>
+ <Real Name="Cell 1 6 3">0.21946541530760227</Real>
+ <Real Name="Cell 1 6 4">3.4579718852657778e-07</Real>
+ <Real Name="Cell 1 7 0">0.00084395143107973095</Real>
+ <Real Name="Cell 1 7 1">0.41705369514315466</Real>
+ <Real Name="Cell 1 7 2">1.165035073098555</Real>
+ <Real Name="Cell 1 7 3">0.21106053689593204</Real>
+ <Real Name="Cell 1 7 4">1.3169876475467115e-06</Real>
+ <Real Name="Cell 1 8 0">1.8426081939618633e-05</Real>
+ <Real Name="Cell 1 8 1">0.021190578196421634</Real>
+ <Real Name="Cell 1 8 2">0.077993616489624176</Real>
+ <Real Name="Cell 1 8 3">0.018892131821834048</Real>
+ <Real Name="Cell 1 8 4">3.1348148769525742e-07</Real>
+ <Real Name="Cell 16 4 0">1.7661049201756804e-05</Real>
+ <Real Name="Cell 16 4 1">8.7768202467111508e-05</Real>
+ <Real Name="Cell 16 4 2">2.7212667283306599e-05</Real>
+ <Real Name="Cell 16 4 3">8.2970790320766862e-09</Real>
+ <Real Name="Cell 16 5 0">0.014214495871467179</Real>
+ <Real Name="Cell 16 5 1">0.070640239850005684</Real>
+ <Real Name="Cell 16 5 2">0.021902115912326089</Real>
+ <Real Name="Cell 16 5 3">6.6779042569542913e-06</Real>
+ <Real Name="Cell 16 6 0">0.039817937864741325</Real>
+ <Real Name="Cell 16 6 1">0.19787889113563242</Real>
+ <Real Name="Cell 16 6 2">0.061352657061438727</Real>
+ <Real Name="Cell 16 6 3">1.8706282598726599e-05</Real>
+ <Real Name="Cell 16 7 0">0.0069193649505605234</Real>
+ <Real Name="Cell 16 7 1">0.034386418212583932</Real>
+ <Real Name="Cell 16 7 2">0.01066156229227007</Real>
+ <Real Name="Cell 16 7 3">3.2506855731352154e-06</Real>
+ <Real Name="Cell 17 4 0">7.1986967049254814e-05</Real>
+ <Real Name="Cell 17 4 1">0.00035774582963869398</Real>
+ <Real Name="Cell 17 4 2">0.00011091964926131698</Real>
+ <Real Name="Cell 17 4 3">3.3819143362544609e-08</Real>
+ <Real Name="Cell 17 5 0">0.057938712147367184</Real>
+ <Real Name="Cell 17 5 1">0.28793173952134038</Real>
+ <Real Name="Cell 17 5 2">0.089273682354768666</Real>
+ <Real Name="Cell 17 5 3">2.7219338342346502e-05</Real>
+ <Real Name="Cell 17 6 0">0.16229911078857545</Real>
+ <Real Name="Cell 17 6 1">0.80656030415831037</Real>
+ <Real Name="Cell 17 6 2">0.25007527309457284</Real>
+ <Real Name="Cell 17 6 3">7.6247369772042118e-05</Real>
+ <Real Name="Cell 17 7 0">0.028203539382485897</Real>
+ <Real Name="Cell 17 7 1">0.14016007353430293</Real>
+ <Real Name="Cell 17 7 2">0.04345684815548094</Real>
+ <Real Name="Cell 17 7 3">1.3249892040247265e-05</Real>
+ <Real Name="Cell 18 2 1">5.0358925595209205e-07</Real>
+ <Real Name="Cell 18 2 2">7.7344056573817727e-06</Real>
+ <Real Name="Cell 18 2 3">6.0575243752560386e-06</Real>
+ <Real Name="Cell 18 2 4">1.6192191330545645e-07</Real>
+ <Real Name="Cell 18 3 1">6.3588769233399731e-05</Real>
+ <Real Name="Cell 18 3 2">0.00097663190922313726</Real>
+ <Real Name="Cell 18 3 3">0.0007648902653723304</Real>
+ <Real Name="Cell 18 3 4">2.0446058086653773e-05</Real>
+ <Real Name="Cell 18 4 0">1.8338790424360122e-05</Real>
+ <Real Name="Cell 18 4 1">0.00021608924506664109</Real>
+ <Real Name="Cell 18 4 2">0.0019473542253280766</Real>
+ <Real Name="Cell 18 4 3">0.0015030301833394641</Real>
+ <Real Name="Cell 18 4 4">4.0176830158787832e-05</Real>
+ <Real Name="Cell 18 5 0">0.014760211196061928</Real>
+ <Real Name="Cell 18 5 1">0.073466300813910868</Real>
+ <Real Name="Cell 18 5 2">0.023223275326072778</Real>
+ <Real Name="Cell 18 5 3">0.00022251013668336917</Real>
+ <Real Name="Cell 18 5 4">4.6819892910410096e-06</Real>
+ <Real Name="Cell 18 6 0">0.041349120723697577</Real>
+ <Real Name="Cell 18 6 1">0.20683029603754097</Real>
+ <Real Name="Cell 18 6 2">0.067173217850274594</Real>
+ <Real Name="Cell 18 6 3">0.00056453946205176498</Real>
+ <Real Name="Cell 18 7 0">0.0071871711303569345</Real>
+ <Real Name="Cell 18 7 1">0.036680037022704497</Real>
+ <Real Name="Cell 18 7 2">0.013557175380755782</Real>
+ <Real Name="Cell 18 7 3">0.00039441834193904121</Real>
+ <Real Name="Cell 18 8 0">4.969550022508899e-08</Real>
+ <Real Name="Cell 18 8 1">2.1266385322102851e-05</Real>
+ <Real Name="Cell 18 8 2">5.4287509031277304e-05</Real>
+ <Real Name="Cell 18 8 3">8.5376817498333205e-06</Real>
+ <Real Name="Cell 2 0 0">0.012592024317158865</Real>
+ <Real Name="Cell 2 0 1">0.12881877238921938</Real>
+ <Real Name="Cell 2 0 10">2.2107816325567422e-07</Real>
+ <Real Name="Cell 2 0 2">0.075488971487600753</Real>
+ <Real Name="Cell 2 0 3">0.00095637194731275767</Real>
+ <Real Name="Cell 2 1 0">0.02623801181817411</Real>
+ <Real Name="Cell 2 1 1">0.26855373164199592</Real>
+ <Real Name="Cell 2 1 10">1.8837138724171884e-09</Real>
+ <Real Name="Cell 2 1 2">0.15738424562743988</Real>
+ <Real Name="Cell 2 1 3">0.0020112140364247442</Real>
+ <Real Name="Cell 2 1 4">0.0013033335144799743</Real>
+ <Real Name="Cell 2 1 5">0.0021897949140827987</Real>
+ <Real Name="Cell 2 1 6">0.00020969229897286986</Real>
+ <Real Name="Cell 2 15 0">1.5628969123845743e-06</Real>
+ <Real Name="Cell 2 15 1">1.8628513799083989e-06</Real>
+ <Real Name="Cell 2 15 10">4.840995923089627e-08</Real>
+ <Real Name="Cell 2 15 2">1.0898111529589788e-07</Real>
+ <Real Name="Cell 2 16 0">9.3093200561282708e-05</Real>
+ <Real Name="Cell 2 16 1">0.00082854089110981604</Real>
+ <Real Name="Cell 2 16 10">4.2573020111292651e-07</Real>
+ <Real Name="Cell 2 16 2">0.00047691895241848105</Real>
+ <Real Name="Cell 2 16 3">6.0299975433345314e-06</Real>
+ <Real Name="Cell 2 2 0">0.0032814136477268075</Real>
+ <Real Name="Cell 2 2 1">0.033591275848255837</Real>
+ <Real Name="Cell 2 2 2">0.019758342383185207</Real>
+ <Real Name="Cell 2 2 3">0.0030028660754793249</Real>
+ <Real Name="Cell 2 2 4">0.20305858248835423</Real>
+ <Real Name="Cell 2 2 5">0.34116609330653302</Real>
+ <Real Name="Cell 2 2 6">0.032669681519926365</Real>
+ <Real Name="Cell 2 3 0">1.5178159172396139e-05</Real>
+ <Real Name="Cell 2 3 1">0.00081136338598438254</Real>
+ <Real Name="Cell 2 3 2">0.0096313453891943689</Real>
+ <Real Name="Cell 2 3 3">0.013033568770678041</Real>
+ <Real Name="Cell 2 3 4">0.42167407442096549</Real>
+ <Real Name="Cell 2 3 5">0.70814137588739057</Real>
+ <Real Name="Cell 2 3 6">0.067810821987334055</Real>
+ <Real Name="Cell 2 4 0">3.9629275690581939e-05</Real>
+ <Real Name="Cell 2 4 1">0.0017542849472656223</Real>
+ <Real Name="Cell 2 4 2">0.019070141132790173</Real>
+ <Real Name="Cell 2 4 3">0.015323066368989988</Real>
+ <Real Name="Cell 2 4 4">0.05282641643694802</Real>
+ <Real Name="Cell 2 4 5">0.088099888859229175</Real>
+ <Real Name="Cell 2 4 6">0.0084363463059205796</Real>
+ <Real Name="Cell 2 5 0">1.8087312463302894e-05</Real>
+ <Real Name="Cell 2 5 1">0.0050486387709806424</Real>
+ <Real Name="Cell 2 5 2">0.01451428910116921</Real>
+ <Real Name="Cell 2 5 3">0.0036321982620402299</Real>
+ <Real Name="Cell 2 5 4">4.5526190883183145e-05</Real>
+ <Real Name="Cell 2 6 0">0.00015105875581281753</Real>
+ <Real Name="Cell 2 6 1">0.078189980353204305</Real>
+ <Real Name="Cell 2 6 2">0.22394040492032885</Real>
+ <Real Name="Cell 2 6 3">0.04196761353982939</Real>
+ <Real Name="Cell 2 6 4">3.1929128753398059e-07</Real>
+ <Real Name="Cell 2 7 0">0.00010835356588143395</Real>
+ <Real Name="Cell 2 7 1">0.097981793961272212</Real>
+ <Real Name="Cell 2 7 2">0.34283182009632313</Real>
+ <Real Name="Cell 2 7 3">0.079620548239234562</Real>
+ <Real Name="Cell 2 7 4">1.2160384630172265e-06</Real>
+ <Real Name="Cell 2 8 0">2.365695003119852e-06</Real>
+ <Real Name="Cell 2 8 1">0.013297912855161896</Real>
+ <Real Name="Cell 2 8 2">0.056013766199145658</Real>
+ <Real Name="Cell 2 8 3">0.014927495424731353</Real>
+ <Real Name="Cell 2 8 4">2.894526362425686e-07</Real>
+ <Real Name="Cell 3 0 0">0.1447951839891552</Real>
+ <Real Name="Cell 3 0 1">0.79660311578495036</Real>
+ <Real Name="Cell 3 0 10">0.0023476343855282716</Real>
+ <Real Name="Cell 3 0 2">0.41918698287268091</Real>
+ <Real Name="Cell 3 0 3">0.0052437703687671765</Real>
+ <Real Name="Cell 3 1 0">0.1446716993295708</Real>
+ <Real Name="Cell 3 1 1">1.4752131212023569</Real>
+ <Real Name="Cell 3 1 10">2.0003203365991888e-05</Real>
+ <Real Name="Cell 3 1 2">0.86428185741592523</Real>
+ <Real Name="Cell 3 1 3">0.010957405675058065</Real>
+ <Real Name="Cell 3 1 4">0.00012137177702559288</Real>
+ <Real Name="Cell 3 1 5">0.00020392270826387809</Real>
+ <Real Name="Cell 3 1 6">1.9527409271811653e-05</Real>
+ <Real Name="Cell 3 10 0">3.4670315698056223e-05</Real>
+ <Real Name="Cell 3 10 1">0.00021489700756491175</Real>
+ <Real Name="Cell 3 10 2">8.2227549711833898e-05</Real>
+ <Real Name="Cell 3 10 3">1.6610943209908981e-07</Real>
+ <Real Name="Cell 3 11 0">0.0043955913507298505</Real>
+ <Real Name="Cell 3 11 1">0.027245192572705992</Real>
+ <Real Name="Cell 3 11 2">0.010425019185080851</Real>
+ <Real Name="Cell 3 11 3">2.1059778900436783e-05</Real>
+ <Real Name="Cell 3 12 0">0.0086469049196471748</Real>
+ <Real Name="Cell 3 12 1">0.053596108212959549</Real>
+ <Real Name="Cell 3 12 2">0.020507854913292635</Real>
+ <Real Name="Cell 3 12 3">4.1428306512303993e-05</Real>
+ <Real Name="Cell 3 13 0">0.001009001988036391</Real>
+ <Real Name="Cell 3 13 1">0.0062540967248309156</Real>
+ <Real Name="Cell 3 13 2">0.0023930489082697659</Real>
+ <Real Name="Cell 3 13 3">4.8342434686562201e-06</Real>
+ <Real Name="Cell 3 15 0">0.016596440274866547</Real>
+ <Real Name="Cell 3 15 1">0.019781664051297939</Real>
+ <Real Name="Cell 3 15 10">0.00051406653293496155</Real>
+ <Real Name="Cell 3 15 2">0.0011572731104427807</Real>
+ <Real Name="Cell 3 16 0">0.14638862663064428</Real>
+ <Real Name="Cell 3 16 1">0.17841832432159288</Real>
+ <Real Name="Cell 3 16 10">0.0045208393464654878</Real>
+ <Real Name="Cell 3 16 2">0.012787054165212907</Real>
+ <Real Name="Cell 3 16 3">3.3062369228126233e-05</Real>
+ <Real Name="Cell 3 2 0">0.026686988989901881</Real>
+ <Real Name="Cell 3 2 1">0.28872478564464071</Real>
+ <Real Name="Cell 3 2 2">0.17708332784615444</Real>
+ <Real Name="Cell 3 2 3">0.002849546069958088</Real>
+ <Real Name="Cell 3 2 4">0.018909503688767565</Real>
+ <Real Name="Cell 3 2 5">0.031770789706128871</Real>
+ <Real Name="Cell 3 2 6">0.0030423351021674036</Real>
+ <Real Name="Cell 3 3 0">0.019018610348532101</Real>
+ <Real Name="Cell 3 3 1">0.23226704011615046</Real>
+ <Real Name="Cell 3 3 2">0.15584315155684203</Real>
+ <Real Name="Cell 3 3 3">0.0034581918334634859</Real>
+ <Real Name="Cell 3 3 4">0.039249509908009184</Real>
+ <Real Name="Cell 3 3 5">0.065945037261697384</Real>
+ <Real Name="Cell 3 3 6">0.0063148226257749148</Real>
+ <Real Name="Cell 3 4 0">0.016977492023025901</Real>
+ <Real Name="Cell 3 4 1">0.22180346034633217</Real>
+ <Real Name="Cell 3 4 2">0.16060458227326968</Real>
+ <Real Name="Cell 3 4 3">0.0041903671756561792</Real>
+ <Real Name="Cell 3 4 4">0.0048830326519780972</Real>
+ <Real Name="Cell 3 4 5">0.0082042239747577451</Real>
+ <Real Name="Cell 3 4 6">0.0007856272637640436</Real>
+ <Real Name="Cell 3 5 0">0.0026574508176976214</Real>
+ <Real Name="Cell 3 5 1">0.039825894173325861</Real>
+ <Real Name="Cell 3 5 2">0.033398431724949579</Real>
+ <Real Name="Cell 3 5 3">0.0012971878338948056</Real>
+ <Real Name="Cell 3 5 4">4.9871269748312929e-14</Real>
+ <Real Name="Cell 3 6 0">3.3736135172618111e-06</Real>
+ <Real Name="Cell 3 6 1">0.00064664470491959062</Real>
+ <Real Name="Cell 3 6 2">0.002394773361223148</Real>
+ <Real Name="Cell 3 6 3">0.0006135051211589985</Real>
+ <Real Name="Cell 3 6 4">1.1971755027231609e-08</Real>
+ <Real Name="Cell 3 7 1">0.0019352417670423301</Real>
+ <Real Name="Cell 3 7 2">0.0084163047996196894</Real>
+ <Real Name="Cell 3 7 3">0.0022873843896966226</Real>
+ <Real Name="Cell 3 7 4">4.5595088720935213e-08</Real>
+ <Real Name="Cell 3 8 1">0.00046064400779500169</Real>
+ <Real Name="Cell 3 8 2">0.0020033261165328712</Real>
+ <Real Name="Cell 3 8 3">0.00054446422694148528</Real>
+ <Real Name="Cell 3 8 4">1.0852961506861105e-08</Real>
+ <Real Name="Cell 4 0 0">0.28639936380806902</Real>
+ <Real Name="Cell 4 0 1">0.55413404081027673</Real>
+ <Real Name="Cell 4 0 10">0.0081423263291104473</Real>
+ <Real Name="Cell 4 0 2">0.15945607569211365</Real>
+ <Real Name="Cell 4 0 3">0.001787940718517914</Real>
+ <Real Name="Cell 4 1 0">0.052420932224019015</Real>
+ <Real Name="Cell 4 1 1">0.51831090169375649</Real>
+ <Real Name="Cell 4 1 10">6.9377331682256987e-05</Real>
+ <Real Name="Cell 4 1 2">0.30336716249047002</Real>
+ <Real Name="Cell 4 1 3">0.0038875071843456005</Real>
+ <Real Name="Cell 4 10 0">0.000660471153082068</Real>
+ <Real Name="Cell 4 10 1">0.0040937981533361286</Real>
+ <Real Name="Cell 4 10 2">0.0015664387093058056</Real>
+ <Real Name="Cell 4 10 3">3.1643925342867354e-06</Real>
+ <Real Name="Cell 4 11 0">0.08373622303234099</Real>
+ <Real Name="Cell 4 11 1">0.51902220652253772</Real>
+ <Real Name="Cell 4 11 2">0.19859710831704536</Real>
+ <Real Name="Cell 4 11 3">0.00040118978365128382</Real>
+ <Real Name="Cell 4 12 0">0.16472394750044236</Real>
+ <Real Name="Cell 4 12 1">1.0210083952050457</Real>
+ <Real Name="Cell 4 12 2">0.39067560560406223</Real>
+ <Real Name="Cell 4 12 3">0.00078921119757651402</Real>
+ <Real Name="Cell 4 13 0">0.019221535572514457</Real>
+ <Real Name="Cell 4 13 1">0.11914083826953564</Real>
+ <Real Name="Cell 4 13 2">0.045587694833575693</Real>
+ <Real Name="Cell 4 13 3">9.2092566616052958e-05</Real>
+ <Real Name="Cell 4 15 0">0.057561617538306228</Real>
+ <Real Name="Cell 4 15 1">0.068608964424525021</Real>
+ <Real Name="Cell 4 15 10">0.0017829426472167566</Real>
+ <Real Name="Cell 4 15 2">0.0040137831406867166</Real>
+ <Real Name="Cell 4 16 0">0.50636068817263258</Real>
+ <Real Name="Cell 4 16 1">0.60488401834051164</Real>
+ <Real Name="Cell 4 16 10">0.015679677153868782</Real>
+ <Real Name="Cell 4 16 2">0.036188098336917891</Real>
+ <Real Name="Cell 4 16 3">1.1273101611338928e-05</Real>
+ <Real Name="Cell 4 2 0">0.066052296032392988</Real>
+ <Real Name="Cell 4 2 1">0.78336482781740691</Real>
+ <Real Name="Cell 4 2 2">0.51335665149739507</Real>
+ <Real Name="Cell 4 2 3">0.0089501028968885944</Real>
+ <Real Name="Cell 4 3 0">0.10480564876387043</Real>
+ <Real Name="Cell 4 3 1">1.2743823695925314</Real>
+ <Real Name="Cell 4 3 2">0.85175618754233717</Real>
+ <Real Name="Cell 4 3 3">0.015801639074619279</Real>
+ <Real Name="Cell 4 4 0">0.061010906542406498</Real>
+ <Real Name="Cell 4 4 1">0.89439020566808269</Real>
+ <Real Name="Cell 4 4 2">0.70379612100417177</Real>
+ <Real Name="Cell 4 4 3">0.02113226045271871</Real>
+ <Real Name="Cell 4 5 0">0.020104281709067348</Real>
+ <Real Name="Cell 4 5 1">0.37775503800864418</Real>
+ <Real Name="Cell 4 5 2">0.34598301092016664</Real>
+ <Real Name="Cell 4 5 3">0.013736272788794244</Real>
+ <Real Name="Cell 4 5 4">1.1893971458531676e-07</Real>
+ <Real Name="Cell 4 6 0">0.00058023778672453518</Real>
+ <Real Name="Cell 4 6 1">0.01765902735533683</Real>
+ <Real Name="Cell 4 6 2">0.038790964977005835</Real>
+ <Real Name="Cell 4 6 3">0.0089039641842783984</Real>
+ <Real Name="Cell 4 6 4">2.6546625196870846e-06</Real>
+ <Real Name="Cell 4 7 1">0.005357133577463845</Real>
+ <Real Name="Cell 4 7 2">0.026688915045784911</Real>
+ <Real Name="Cell 4 7 3">0.0082950198764348507</Real>
+ <Real Name="Cell 4 7 4">2.6104537172870925e-06</Real>
+ <Real Name="Cell 4 8 1">0.00022593974955550041</Real>
+ <Real Name="Cell 4 8 2">0.0011256181489891861</Real>
+ <Real Name="Cell 4 8 3">0.00034984655251528251</Real>
+ <Real Name="Cell 4 8 4">1.1009717241161162e-07</Real>
+ <Real Name="Cell 5 0 0">0.056972048987246365</Real>
+ <Real Name="Cell 5 0 1">0.068086876618959347</Real>
+ <Real Name="Cell 5 0 10">0.0017640623704953126</Real>
+ <Real Name="Cell 5 0 2">0.0040910900563363422</Real>
+ <Real Name="Cell 5 0 3">1.5178918420600495e-06</Real>
+ <Real Name="Cell 5 1 0">0.0010031135325047212</Real>
+ <Real Name="Cell 5 1 1">0.0067313944853817295</Real>
+ <Real Name="Cell 5 1 10">1.503083212821962e-05</Real>
+ <Real Name="Cell 5 1 2">0.0040710169888644185</Real>
+ <Real Name="Cell 5 1 3">7.0586420194077576e-05</Real>
+ <Real Name="Cell 5 10 0">0.00059231010098228457</Real>
+ <Real Name="Cell 5 10 1">0.0036713155242108129</Real>
+ <Real Name="Cell 5 10 2">0.0014047812168053822</Real>
+ <Real Name="Cell 5 10 3">2.8378251688731499e-06</Real>
+ <Real Name="Cell 5 11 0">0.075094590412789972</Real>
+ <Real Name="Cell 5 11 1">0.46545877760570908</Real>
+ <Real Name="Cell 5 11 2">0.17810175771210765</Real>
+ <Real Name="Cell 5 11 3">0.00035978673732935292</Real>
+ <Real Name="Cell 5 12 0">0.14772432909884275</Real>
+ <Real Name="Cell 5 12 1">0.91563966548061526</Real>
+ <Real Name="Cell 5 12 2">0.35035762928756425</Real>
+ <Real Name="Cell 5 12 3">0.0007077640892437432</Real>
+ <Real Name="Cell 5 13 0">0.017237860613385392</Real>
+ <Real Name="Cell 5 13 1">0.10684542635547038</Real>
+ <Real Name="Cell 5 13 2">0.040883015108866695</Real>
+ <Real Name="Cell 5 13 3">8.2588553909627329e-05</Real>
+ <Real Name="Cell 5 15 0">0.012470917939156412</Real>
+ <Real Name="Cell 5 15 1">0.01486436277888396</Real>
+ <Real Name="Cell 5 15 10">0.00038628051807031871</Real>
+ <Real Name="Cell 5 15 2">0.00086959961018750846</Real>
+ <Real Name="Cell 5 16 0">0.10967273229018376</Real>
+ <Real Name="Cell 5 16 1">0.13072249298520022</Real>
+ <Real Name="Cell 5 16 10">0.0033970547642834183</Real>
+ <Real Name="Cell 5 16 2">0.0076482482606756675</Real>
+ <Real Name="Cell 5 16 3">9.5704229974411844e-09</Real>
+ <Real Name="Cell 5 2 0">0.025264205753332727</Real>
+ <Real Name="Cell 5 2 1">0.3038159746366968</Real>
+ <Real Name="Cell 5 2 2">0.20092548444720354</Real>
+ <Real Name="Cell 5 2 3">0.0035767032899450984</Real>
+ <Real Name="Cell 5 3 0">0.041739779619336732</Real>
+ <Real Name="Cell 5 3 1">0.52038674454903411</Real>
+ <Real Name="Cell 5 3 2">0.35644063738972892</Real>
+ <Real Name="Cell 5 3 3">0.0072181831762580121</Real>
+ <Real Name="Cell 5 4 0">0.053388420535682303</Real>
+ <Real Name="Cell 5 4 1">1.0340535029022566</Real>
+ <Real Name="Cell 5 4 2">0.94744786276377313</Real>
+ <Real Name="Cell 5 4 3">0.035698125343962862</Real>
+ <Real Name="Cell 5 5 0">0.044663399523051185</Real>
+ <Real Name="Cell 5 5 1">0.92711515781101317</Real>
+ <Real Name="Cell 5 5 2">0.89605359503052484</Real>
+ <Real Name="Cell 5 5 3">0.042675298794380062</Real>
+ <Real Name="Cell 5 5 4">2.7640982030982142e-06</Real>
+ <Real Name="Cell 5 6 0">0.0018612472781498015</Real>
+ <Real Name="Cell 5 6 1">0.16529506254790416</Real>
+ <Real Name="Cell 5 6 2">0.66727680980185566</Real>
+ <Real Name="Cell 5 6 3">0.19746686029335783</Real>
+ <Real Name="Cell 5 6 4">6.1693000744808424e-05</Real>
+ <Real Name="Cell 5 7 1">0.12449704749041782</Real>
+ <Real Name="Cell 5 7 2">0.62023675084387708</Real>
+ <Real Name="Cell 5 7 3">0.19277202417255557</Real>
+ <Real Name="Cell 5 7 4">6.0665610762404447e-05</Real>
+ <Real Name="Cell 5 8 1">0.0052507243516785509</Real>
+ <Real Name="Cell 5 8 2">0.026158790727246653</Real>
+ <Real Name="Cell 5 8 3">0.008130255151015604</Real>
+ <Real Name="Cell 5 8 4">2.5586020404550271e-06</Real>
+ <Real Name="Cell 6 1 0">1.6752139333715467e-06</Real>
+ <Real Name="Cell 6 1 1">2.0145826768282194e-05</Real>
+ <Real Name="Cell 6 1 2">1.3323416897895206e-05</Real>
+ <Real Name="Cell 6 1 3">2.3717888502871541e-07</Real>
+ <Real Name="Cell 6 10 0">2.0987384349463681e-05</Real>
+ <Real Name="Cell 6 10 1">0.00013008609822284559</Real>
+ <Real Name="Cell 6 10 2">4.9775756440938395e-05</Real>
+ <Real Name="Cell 6 10 3">1.0055294926922717e-07</Real>
+ <Real Name="Cell 6 11 0">0.0026608342976847379</Real>
+ <Real Name="Cell 6 11 1">0.016492648442500101</Real>
+ <Real Name="Cell 6 11 2">0.0063106977851975837</Real>
+ <Real Name="Cell 6 11 3">1.2748360238409143e-05</Real>
+ <Real Name="Cell 6 12 0">0.0052343312521979136</Real>
+ <Real Name="Cell 6 12 1">0.032443953856580915</Real>
+ <Real Name="Cell 6 12 2">0.012414257689393934</Real>
+ <Real Name="Cell 6 12 3">2.5078277316345857e-05</Real>
+ <Real Name="Cell 6 13 0">0.000610790877034902</Real>
+ <Real Name="Cell 6 13 1">0.0037858649129666648</Real>
+ <Real Name="Cell 6 13 2">0.0014486120530981437</Real>
+ <Real Name="Cell 6 13 3">2.9263686722431767e-06</Real>
+ <Real Name="Cell 6 2 0">8.8836056742474097e-05</Real>
+ <Real Name="Cell 6 2 1">0.0010683267218947118</Real>
+ <Real Name="Cell 6 2 2">0.00070653651809290767</Real>
+ <Real Name="Cell 6 2 3">1.2577520081940823e-05</Real>
+ <Real Name="Cell 6 3 0">0.00052757287491048198</Real>
+ <Real Name="Cell 6 3 1">0.0098110213634352086</Real>
+ <Real Name="Cell 6 3 2">0.0088141843515628353</Real>
+ <Real Name="Cell 6 3 3">0.000322340855692457</Real>
+ <Real Name="Cell 6 4 0">0.0089477397317942985</Real>
+ <Real Name="Cell 6 4 1">0.18579851404036285</Real>
+ <Real Name="Cell 6 4 2">0.17533806948335917</Real>
+ <Real Name="Cell 6 4 3">0.0068530079125408176</Real>
+ <Real Name="Cell 6 5 0">0.0088407248412974947</Real>
+ <Real Name="Cell 6 5 1">0.18937304256253962</Real>
+ <Real Name="Cell 6 5 2">0.20178552039832159</Real>
+ <Real Name="Cell 6 5 3">0.015611412376668892</Real>
+ <Real Name="Cell 6 5 4">2.7800163026788034e-06</Real>
+ <Real Name="Cell 6 6 0">0.00037691656470221498</Real>
+ <Real Name="Cell 6 6 1">0.13516506836567235</Real>
+ <Real Name="Cell 6 6 2">0.6417641808357567</Real>
+ <Real Name="Cell 6 6 3">0.19745458264448704</Real>
+ <Real Name="Cell 6 6 4">6.2048283103510618e-05</Real>
+ <Real Name="Cell 6 7 1">0.12521401058428347</Real>
+ <Real Name="Cell 6 7 2">0.62380861755700889</Real>
+ <Real Name="Cell 6 7 3">0.19388217441023198</Real>
+ <Real Name="Cell 6 7 4">6.1014976509305474e-05</Real>
+ <Real Name="Cell 6 8 1">0.005280962623606284</Real>
+ <Real Name="Cell 6 8 2">0.026309435966709337</Real>
+ <Real Name="Cell 6 8 3">0.008177076284564478</Real>
+ <Real Name="Cell 6 8 4">2.5733367130587029e-06</Real>
+ <Real Name="Cell 7 5 1">0.00025061972476839135</Real>
+ <Real Name="Cell 7 5 2">0.0012485722908384461</Real>
+ <Real Name="Cell 7 5 3">0.00038806118389988348</Real>
+ <Real Name="Cell 7 5 4">1.2212336741038272e-07</Real>
+ <Real Name="Cell 7 6 1">0.0055936807344506168</Real>
+ <Real Name="Cell 7 6 2">0.027867378656194021</Real>
+ <Real Name="Cell 7 6 3">0.0086612910064238005</Real>
+ <Real Name="Cell 7 6 4">2.7257197259353487e-06</Real>
+ <Real Name="Cell 7 7 1">0.0055005276784805789</Real>
+ <Real Name="Cell 7 7 2">0.027403295772859129</Real>
+ <Real Name="Cell 7 7 3">0.0085170522190856062</Real>
+ <Real Name="Cell 7 7 4">2.6803275889431705e-06</Real>
+ <Real Name="Cell 7 8 1">0.0002319874664554018</Real>
+ <Real Name="Cell 7 8 2">0.0011557475083244519</Real>
+ <Real Name="Cell 7 8 3">0.0003592108760226837</Real>
+ <Real Name="Cell 7 8 4">1.130441373946878e-07</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99759236333609846</Real>
+ <Real>0.99039264020161522</Real>
+ <Real>0.97847016786610419</Real>
+ <Real>0.96193976625564348</Real>
+ <Real>0.94096063217417747</Real>
+ <Real>0.91573480615127245</Real>
+ <Real>0.88650522668136855</Real>
+ <Real>0.85355339059327373</Real>
+ <Real>0.81719664208182263</Real>
+ <Real>0.77778511650980098</Real>
+ <Real>0.73569836841299885</Real>
+ <Real>0.69134171618254503</Real>
+ <Real>0.64514233862723136</Real>
+ <Real>0.59754516100806421</Real>
+ <Real>0.54900857016478033</Real>
+ <Real>0.5</Real>
+ <Real>0.45099142983521967</Real>
+ <Real>0.4024548389919359</Real>
+ <Real>0.35485766137276892</Real>
+ <Real>0.30865828381745519</Real>
+ <Real>0.26430163158700121</Real>
+ <Real>0.22221488349019899</Real>
+ <Real>0.18280335791817731</Real>
+ <Real>0.1464466094067263</Real>
+ <Real>0.11349477331863152</Real>
+ <Real>0.084265193848727327</Real>
+ <Real>0.059039367825822531</Real>
+ <Real>0.038060233744356645</Real>
+ <Real>0.021529832133895557</Real>
+ <Real>0.009607359798384809</Real>
+ <Real>0.0024076366639015686</Real>
+ <Real>0.002407636663901563</Real>
+ <Real>0.0024076366639015573</Real>
+ <Real>0.009607359798384783</Real>
+ <Real>0.021529832133895539</Real>
+ <Real>0.038060233744356603</Real>
+ <Real>0.059039367825822482</Real>
+ <Real>0.084265193848727285</Real>
+ <Real>0.11349477331863143</Real>
+ <Real>0.14644660940672619</Real>
+ <Real>0.18280335791817706</Real>
+ <Real>0.22221488349019888</Real>
+ <Real>0.2643016315870011</Real>
+ <Real>0.30865828381745486</Real>
+ <Real>0.35485766137276881</Real>
+ <Real>0.40245483899193568</Real>
+ <Real>0.45099142983521989</Real>
+ <Real>0.49999999999999994</Real>
+ <Real>0.54900857016478011</Real>
+ <Real>0.59754516100806421</Real>
+ <Real>0.64514233862723114</Real>
+ <Real>0.69134171618254492</Real>
+ <Real>0.73569836841299885</Real>
+ <Real>0.77778511650980087</Real>
+ <Real>0.81719664208182274</Real>
+ <Real>0.85355339059327373</Real>
+ <Real>0.88650522668136833</Real>
+ <Real>0.91573480615127245</Real>
+ <Real>0.94096063217417725</Real>
+ <Real>0.96193976625564326</Real>
+ <Real>0.97847016786610441</Real>
+ <Real>0.9903926402016151</Real>
+ <Real>0.99759236333609846</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.99039264020161522</Real>
+ <Real>0.96193976625564348</Real>
+ <Real>0.91573480615127245</Real>
+ <Real>0.85355339059327373</Real>
+ <Real>0.77778511650980098</Real>
+ <Real>0.69134171618254503</Real>
+ <Real>0.59754516100806421</Real>
+ <Real>0.5</Real>
+ <Real>0.4024548389919359</Real>
+ <Real>0.30865828381745519</Real>
+ <Real>0.22221488349019899</Real>
+ <Real>0.1464466094067263</Real>
+ <Real>0.084265193848727327</Real>
+ <Real>0.038060233744356645</Real>
+ <Real>0.009607359798384809</Real>
+ <Real>0.0096073597983847951</Real>
+ <Real>0.009607359798384783</Real>
+ <Real>0.038060233744356603</Real>
+ <Real>0.084265193848727285</Real>
+ <Real>0.14644660940672619</Real>
+ <Real>0.22221488349019888</Real>
+ <Real>0.30865828381745486</Real>
+ <Real>0.40245483899193568</Real>
+ <Real>0.49999999999999994</Real>
+ <Real>0.59754516100806421</Real>
+ <Real>0.69134171618254492</Real>
+ <Real>0.77778511650980087</Real>
+ <Real>0.85355339059327373</Real>
+ <Real>0.91573480615127245</Real>
+ <Real>0.96193976625564326</Real>
+ <Real>0.9903926402016151</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99759236333609846</Real>
+ <Real>0.99039264020161522</Real>
+ <Real>0.97847016786610419</Real>
+ <Real>0.96193976625564348</Real>
+ <Real>0.94096063217417747</Real>
+ <Real>0.91573480615127245</Real>
+ <Real>0.88650522668136855</Real>
+ <Real>0.85355339059327373</Real>
+ <Real>0.81719664208182263</Real>
+ <Real>0.77778511650980098</Real>
+ <Real>0.73569836841299885</Real>
+ <Real>0.69134171618254503</Real>
+ <Real>0.64514233862723136</Real>
+ <Real>0.59754516100806421</Real>
+ <Real>0.54900857016478033</Real>
+ <Real>0.5</Real>
+ <Real>0.45099142983521967</Real>
+ <Real>0.4024548389919359</Real>
+ <Real>0.35485766137276892</Real>
+ <Real>0.30865828381745519</Real>
+ <Real>0.26430163158700121</Real>
+ <Real>0.22221488349019899</Real>
+ <Real>0.18280335791817731</Real>
+ <Real>0.1464466094067263</Real>
+ <Real>0.11349477331863152</Real>
+ <Real>0.084265193848727327</Real>
+ <Real>0.059039367825822531</Real>
+ <Real>0.038060233744356645</Real>
+ <Real>0.021529832133895557</Real>
+ <Real>0.009607359798384809</Real>
+ <Real>0.0024076366639015686</Real>
+ <Real>0.002407636663901563</Real>
+ <Real>0.0024076366639015573</Real>
+ <Real>0.009607359798384783</Real>
+ <Real>0.021529832133895539</Real>
+ <Real>0.038060233744356603</Real>
+ <Real>0.059039367825822482</Real>
+ <Real>0.084265193848727285</Real>
+ <Real>0.11349477331863143</Real>
+ <Real>0.14644660940672619</Real>
+ <Real>0.18280335791817706</Real>
+ <Real>0.22221488349019888</Real>
+ <Real>0.2643016315870011</Real>
+ <Real>0.30865828381745486</Real>
+ <Real>0.35485766137276881</Real>
+ <Real>0.40245483899193568</Real>
+ <Real>0.45099142983521989</Real>
+ <Real>0.49999999999999994</Real>
+ <Real>0.54900857016478011</Real>
+ <Real>0.59754516100806421</Real>
+ <Real>0.64514233862723114</Real>
+ <Real>0.69134171618254492</Real>
+ <Real>0.73569836841299885</Real>
+ <Real>0.77778511650980087</Real>
+ <Real>0.81719664208182274</Real>
+ <Real>0.85355339059327373</Real>
+ <Real>0.88650522668136833</Real>
+ <Real>0.91573480615127245</Real>
+ <Real>0.94096063217417725</Real>
+ <Real>0.96193976625564326</Real>
+ <Real>0.97847016786610441</Real>
+ <Real>0.9903926402016151</Real>
+ <Real>0.99759236333609846</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99759313626102608</Real>
+ <Real>0.99040494896489739</Real>
+ <Real>0.97853199445156747</Real>
+ <Real>0.96213303679655804</Real>
+ <Real>0.94142587779030484</Real>
+ <Real>0.91668306539587419</Real>
+ <Real>0.8882266204150725</Real>
+ <Real>0.85642195165849222</Real>
+ <Real>0.82167115397292223</Real>
+ <Real>0.78440590014224809</Real>
+ <Real>0.74508014638808595</Real>
+ <Real>0.704162871796433</Real>
+ <Real>0.66213106482234474</Real>
+ <Real>0.61946315604830537</Real>
+ <Real>0.57663307743738934</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.49232964455793721</Real>
+ <Real>0.45174004290269998</Real>
+ <Real>0.41275066727856663</Real>
+ <Real>0.37575638235588521</Real>
+ <Real>0.34113384114481293</Real>
+ <Real>0.30924521810841143</Real>
+ <Real>0.28044554827137741</Real>
+ <Real>0.25509573620985398</Real>
+ <Real>0.23358484501772991</Real>
+ <Real>0.21636788858636874</Real>
+ <Real>0.20402973233710939</Real>
+ <Real>0.1973930234488693</Real>
+ <Real>0.197700265275248</Real>
+ <Real>0.20692047834147811</Real>
+ <Real>0.22826483825615454</Real>
+ <Real>0.2670525537709178</Real>
+ <Real>0.22826483825615454</Real>
+ <Real>0.20692047834147811</Real>
+ <Real>0.197700265275248</Real>
+ <Real>0.1973930234488693</Real>
+ <Real>0.20402973233710939</Real>
+ <Real>0.21636788858636874</Real>
+ <Real>0.23358484501772991</Real>
+ <Real>0.25509573620985398</Real>
+ <Real>0.28044554827137741</Real>
+ <Real>0.30924521810841143</Real>
+ <Real>0.34113384114481293</Real>
+ <Real>0.37575638235588521</Real>
+ <Real>0.41275066727856663</Real>
+ <Real>0.45174004290269998</Real>
+ <Real>0.49232964455793721</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.57663307743738934</Real>
+ <Real>0.61946315604830537</Real>
+ <Real>0.66213106482234474</Real>
+ <Real>0.704162871796433</Real>
+ <Real>0.74508014638808595</Real>
+ <Real>0.78440590014224809</Real>
+ <Real>0.82167115397292223</Real>
+ <Real>0.85642195165849222</Real>
+ <Real>0.8882266204150725</Real>
+ <Real>0.91668306539587419</Real>
+ <Real>0.94142587779030484</Real>
+ <Real>0.96213303679655804</Real>
+ <Real>0.97853199445156747</Real>
+ <Real>0.99040494896489739</Real>
+ <Real>0.99759313626102608</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.99040494896489739</Real>
+ <Real>0.96213303679655804</Real>
+ <Real>0.91668306539587419</Real>
+ <Real>0.85642195165849222</Real>
+ <Real>0.78440590014224809</Real>
+ <Real>0.704162871796433</Real>
+ <Real>0.61946315604830537</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.45174004290269998</Real>
+ <Real>0.37575638235588521</Real>
+ <Real>0.30924521810841143</Real>
+ <Real>0.25509573620985398</Real>
+ <Real>0.21636788858636874</Real>
+ <Real>0.1973930234488693</Real>
+ <Real>0.20692047834147811</Real>
+ <Real>0.2670525537709178</Real>
+ <Real>0.20692047834147811</Real>
+ <Real>0.1973930234488693</Real>
+ <Real>0.21636788858636874</Real>
+ <Real>0.25509573620985398</Real>
+ <Real>0.30924521810841143</Real>
+ <Real>0.37575638235588521</Real>
+ <Real>0.45174004290269998</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.61946315604830537</Real>
+ <Real>0.704162871796433</Real>
+ <Real>0.78440590014224809</Real>
+ <Real>0.85642195165849222</Real>
+ <Real>0.91668306539587419</Real>
+ <Real>0.96213303679655804</Real>
+ <Real>0.99040494896489739</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99759313626102608</Real>
+ <Real>0.99040494896489739</Real>
+ <Real>0.97853199445156747</Real>
+ <Real>0.96213303679655804</Real>
+ <Real>0.94142587779030484</Real>
+ <Real>0.91668306539587419</Real>
+ <Real>0.8882266204150725</Real>
+ <Real>0.85642195165849222</Real>
+ <Real>0.82167115397292223</Real>
+ <Real>0.78440590014224809</Real>
+ <Real>0.74508014638808595</Real>
+ <Real>0.704162871796433</Real>
+ <Real>0.66213106482234474</Real>
+ <Real>0.61946315604830537</Real>
+ <Real>0.57663307743738934</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.49232964455793721</Real>
+ <Real>0.45174004290269998</Real>
+ <Real>0.41275066727856663</Real>
+ <Real>0.37575638235588521</Real>
+ <Real>0.34113384114481293</Real>
+ <Real>0.30924521810841143</Real>
+ <Real>0.28044554827137741</Real>
+ <Real>0.25509573620985398</Real>
+ <Real>0.23358484501772991</Real>
+ <Real>0.21636788858636874</Real>
+ <Real>0.20402973233710939</Real>
+ <Real>0.1973930234488693</Real>
+ <Real>0.197700265275248</Real>
+ <Real>0.20692047834147811</Real>
+ <Real>0.22826483825615454</Real>
+ <Real>0.2670525537709178</Real>
+ <Real>0.22826483825615454</Real>
+ <Real>0.20692047834147811</Real>
+ <Real>0.197700265275248</Real>
+ <Real>0.1973930234488693</Real>
+ <Real>0.20402973233710939</Real>
+ <Real>0.21636788858636874</Real>
+ <Real>0.23358484501772991</Real>
+ <Real>0.25509573620985398</Real>
+ <Real>0.28044554827137741</Real>
+ <Real>0.30924521810841143</Real>
+ <Real>0.34113384114481293</Real>
+ <Real>0.37575638235588521</Real>
+ <Real>0.41275066727856663</Real>
+ <Real>0.45174004290269998</Real>
+ <Real>0.49232964455793721</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.57663307743738934</Real>
+ <Real>0.61946315604830537</Real>
+ <Real>0.66213106482234474</Real>
+ <Real>0.704162871796433</Real>
+ <Real>0.74508014638808595</Real>
+ <Real>0.78440590014224809</Real>
+ <Real>0.82167115397292223</Real>
+ <Real>0.85642195165849222</Real>
+ <Real>0.8882266204150725</Real>
+ <Real>0.91668306539587419</Real>
+ <Real>0.94142587779030484</Real>
+ <Real>0.96213303679655804</Real>
+ <Real>0.97853199445156747</Real>
+ <Real>0.99040494896489739</Real>
+ <Real>0.99759313626102608</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99359456296950732</Real>
+ <Real>0.9746173395105846</Real>
+ <Real>0.94377114413720775</Real>
+ <Real>0.90218036114469657</Real>
+ <Real>0.85132452097735178</Real>
+ <Real>0.79295295531904542</Real>
+ <Real>0.7289872415404699</Real>
+ <Real>0.66141885238450659</Real>
+ <Real>0.59220942658258502</Real>
+ <Real>0.52320040489228981</Real>
+ <Real>0.45603754023519838</Real>
+ <Real>0.39211415200068039</Real>
+ <Real>0.33253514767267173</Real>
+ <Real>0.27810198156777877</Real>
+ <Real>0.22931704539006106</Real>
+ <Real>0.18640463592844536</Real>
+ <Real>0.14934471796128809</Real>
+ <Real>0.11791523482559967</Real>
+ <Real>0.091738699755794559</Real>
+ <Real>0.070329166320450678</Real>
+ <Real>0.053136331569776436</Real>
+ <Real>0.039584359326425025</Real>
+ <Real>0.029103910644517863</Real>
+ <Real>0.021156733405364819</Real>
+ <Real>0.015252915086482025</Real>
+ <Real>0.010961491220026948</Real>
+ <Real>0.0079155044959704057</Real>
+ <Real>0.0058128284706795742</Real>
+ <Real>0.0044141270290442821</Real>
+ <Real>0.0035392492112647795</Real>
+ <Real>0.003063195698103806</Real>
+ <Real>0.0029125724363819575</Real>
+ <Real>0.0030631956981038082</Real>
+ <Real>0.0035392492112647786</Real>
+ <Real>0.0044141270290442812</Real>
+ <Real>0.0058128284706795725</Real>
+ <Real>0.0079155044959703658</Real>
+ <Real>0.010961491220026993</Real>
+ <Real>0.015252915086482015</Real>
+ <Real>0.021156733405364836</Real>
+ <Real>0.029103910644517856</Real>
+ <Real>0.039584359326424984</Real>
+ <Real>0.053136331569776346</Real>
+ <Real>0.070329166320450651</Real>
+ <Real>0.091738699755794365</Real>
+ <Real>0.11791523482559939</Real>
+ <Real>0.14934471796128818</Real>
+ <Real>0.186404635928445</Real>
+ <Real>0.22931704539006126</Real>
+ <Real>0.2781019815677791</Real>
+ <Real>0.33253514767267195</Real>
+ <Real>0.39211415200068039</Real>
+ <Real>0.45603754023519832</Real>
+ <Real>0.52320040489228958</Real>
+ <Real>0.59220942658258446</Real>
+ <Real>0.66141885238450582</Real>
+ <Real>0.72898724154046912</Real>
+ <Real>0.79295295531904642</Real>
+ <Real>0.85132452097735112</Real>
+ <Real>0.90218036114469724</Real>
+ <Real>0.94377114413720775</Real>
+ <Real>0.9746173395105846</Real>
+ <Real>0.99359456296950754</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.9746173395105846</Real>
+ <Real>0.90218036114469657</Real>
+ <Real>0.79295295531904542</Real>
+ <Real>0.66141885238450659</Real>
+ <Real>0.52320040489228981</Real>
+ <Real>0.39211415200068039</Real>
+ <Real>0.27810198156777877</Real>
+ <Real>0.18640463592844536</Real>
+ <Real>0.11791523482559967</Real>
+ <Real>0.070329166320450678</Real>
+ <Real>0.039584359326425025</Real>
+ <Real>0.021156733405364819</Real>
+ <Real>0.010961491220026948</Real>
+ <Real>0.0058128284706795742</Real>
+ <Real>0.0035392492112647795</Real>
+ <Real>0.0029125724363819575</Real>
+ <Real>0.0035392492112647786</Real>
+ <Real>0.0058128284706795725</Real>
+ <Real>0.010961491220026993</Real>
+ <Real>0.021156733405364836</Real>
+ <Real>0.039584359326424984</Real>
+ <Real>0.070329166320450651</Real>
+ <Real>0.11791523482559939</Real>
+ <Real>0.186404635928445</Real>
+ <Real>0.2781019815677791</Real>
+ <Real>0.39211415200068039</Real>
+ <Real>0.52320040489228958</Real>
+ <Real>0.66141885238450582</Real>
+ <Real>0.79295295531904642</Real>
+ <Real>0.90218036114469724</Real>
+ <Real>0.9746173395105846</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99359456296950732</Real>
+ <Real>0.9746173395105846</Real>
+ <Real>0.94377114413720775</Real>
+ <Real>0.90218036114469657</Real>
+ <Real>0.85132452097735178</Real>
+ <Real>0.79295295531904542</Real>
+ <Real>0.7289872415404699</Real>
+ <Real>0.66141885238450659</Real>
+ <Real>0.59220942658258502</Real>
+ <Real>0.52320040489228981</Real>
+ <Real>0.45603754023519838</Real>
+ <Real>0.39211415200068039</Real>
+ <Real>0.33253514767267173</Real>
+ <Real>0.27810198156777877</Real>
+ <Real>0.22931704539006106</Real>
+ <Real>0.18640463592844536</Real>
+ <Real>0.14934471796128809</Real>
+ <Real>0.11791523482559967</Real>
+ <Real>0.091738699755794559</Real>
+ <Real>0.070329166320450678</Real>
+ <Real>0.053136331569776436</Real>
+ <Real>0.039584359326425025</Real>
+ <Real>0.029103910644517863</Real>
+ <Real>0.021156733405364819</Real>
+ <Real>0.015252915086482025</Real>
+ <Real>0.010961491220026948</Real>
+ <Real>0.0079155044959704057</Real>
+ <Real>0.0058128284706795742</Real>
+ <Real>0.0044141270290442821</Real>
+ <Real>0.0035392492112647795</Real>
+ <Real>0.003063195698103806</Real>
+ <Real>0.0029125724363819575</Real>
+ <Real>0.0030631956981038082</Real>
+ <Real>0.0035392492112647786</Real>
+ <Real>0.0044141270290442812</Real>
+ <Real>0.0058128284706795725</Real>
+ <Real>0.0079155044959703658</Real>
+ <Real>0.010961491220026993</Real>
+ <Real>0.015252915086482015</Real>
+ <Real>0.021156733405364836</Real>
+ <Real>0.029103910644517856</Real>
+ <Real>0.039584359326424984</Real>
+ <Real>0.053136331569776346</Real>
+ <Real>0.070329166320450651</Real>
+ <Real>0.091738699755794365</Real>
+ <Real>0.11791523482559939</Real>
+ <Real>0.14934471796128818</Real>
+ <Real>0.186404635928445</Real>
+ <Real>0.22931704539006126</Real>
+ <Real>0.2781019815677791</Real>
+ <Real>0.33253514767267195</Real>
+ <Real>0.39211415200068039</Real>
+ <Real>0.45603754023519832</Real>
+ <Real>0.52320040489228958</Real>
+ <Real>0.59220942658258446</Real>
+ <Real>0.66141885238450582</Real>
+ <Real>0.72898724154046912</Real>
+ <Real>0.79295295531904642</Real>
+ <Real>0.85132452097735112</Real>
+ <Real>0.90218036114469724</Real>
+ <Real>0.94377114413720775</Real>
+ <Real>0.9746173395105846</Real>
+ <Real>0.99359456296950754</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99359456296949322</Real>
+ <Real>0.97461733950689855</Real>
+ <Real>0.94377114404174522</Real>
+ <Real>0.90218036017845771</Real>
+ <Real>0.85132451513286955</Real>
+ <Real>0.79295292981514398</Real>
+ <Real>0.72898715282651005</Real>
+ <Real>0.66141859145189652</Real>
+ <Real>0.59220875271982998</Real>
+ <Real>0.52319883754353402</Real>
+ <Real>0.45603419748120122</Real>
+ <Real>0.39210752851646108</Real>
+ <Real>0.33252283355373813</Real>
+ <Real>0.27808033609763227</Real>
+ <Real>0.22928085553476424</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.14925605025534092</Real>
+ <Real>0.11778437226576131</Real>
+ <Real>0.091552297002078148</Real>
+ <Real>0.070072349847468088</Real>
+ <Real>0.052793486472092074</Real>
+ <Real>0.039140255209952811</Real>
+ <Real>0.028545152841074214</Real>
+ <Real>0.020473509426959413</Real>
+ <Real>0.014441011915963002</Real>
+ <Real>0.010024605753721196</Real>
+ <Real>0.0068680064109441037</Real>
+ <Real>0.004683556831785461</Real>
+ <Real>0.0032533768155527912</Real>
+ <Real>0.0024376935527143208</Real>
+ <Real>0.0022199287318187566</Real>
+ <Real>0.0029116688417632187</Real>
+ <Real>0.0022199287318187566</Real>
+ <Real>0.0024376935527143208</Real>
+ <Real>0.0032533768155527912</Real>
+ <Real>0.004683556831785461</Real>
+ <Real>0.0068680064109441037</Real>
+ <Real>0.010024605753721196</Real>
+ <Real>0.014441011915963002</Real>
+ <Real>0.020473509426959413</Real>
+ <Real>0.028545152841074214</Real>
+ <Real>0.039140255209952811</Real>
+ <Real>0.052793486472092074</Real>
+ <Real>0.070072349847468088</Real>
+ <Real>0.091552297002078148</Real>
+ <Real>0.11778437226576131</Real>
+ <Real>0.14925605025534092</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.22928085553476424</Real>
+ <Real>0.27808033609763227</Real>
+ <Real>0.33252283355373813</Real>
+ <Real>0.39210752851646108</Real>
+ <Real>0.45603419748120122</Real>
+ <Real>0.52319883754353402</Real>
+ <Real>0.59220875271982998</Real>
+ <Real>0.66141859145189652</Real>
+ <Real>0.72898715282651005</Real>
+ <Real>0.79295292981514398</Real>
+ <Real>0.85132451513286955</Real>
+ <Real>0.90218036017845771</Real>
+ <Real>0.94377114404174522</Real>
+ <Real>0.97461733950689855</Real>
+ <Real>0.99359456296949322</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.97461733950689855</Real>
+ <Real>0.90218036017845771</Real>
+ <Real>0.79295292981514398</Real>
+ <Real>0.66141859145189652</Real>
+ <Real>0.52319883754353402</Real>
+ <Real>0.39210752851646108</Real>
+ <Real>0.27808033609763227</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.11778437226576131</Real>
+ <Real>0.070072349847468088</Real>
+ <Real>0.039140255209952811</Real>
+ <Real>0.020473509426959413</Real>
+ <Real>0.010024605753721196</Real>
+ <Real>0.004683556831785461</Real>
+ <Real>0.0024376935527143208</Real>
+ <Real>0.0029116688417632187</Real>
+ <Real>0.0024376935527143208</Real>
+ <Real>0.004683556831785461</Real>
+ <Real>0.010024605753721196</Real>
+ <Real>0.020473509426959413</Real>
+ <Real>0.039140255209952811</Real>
+ <Real>0.070072349847468088</Real>
+ <Real>0.11778437226576131</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.27808033609763227</Real>
+ <Real>0.39210752851646108</Real>
+ <Real>0.52319883754353402</Real>
+ <Real>0.66141859145189652</Real>
+ <Real>0.79295292981514398</Real>
+ <Real>0.90218036017845771</Real>
+ <Real>0.97461733950689855</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99359456296949322</Real>
+ <Real>0.97461733950689855</Real>
+ <Real>0.94377114404174522</Real>
+ <Real>0.90218036017845771</Real>
+ <Real>0.85132451513286955</Real>
+ <Real>0.79295292981514398</Real>
+ <Real>0.72898715282651005</Real>
+ <Real>0.66141859145189652</Real>
+ <Real>0.59220875271982998</Real>
+ <Real>0.52319883754353402</Real>
+ <Real>0.45603419748120122</Real>
+ <Real>0.39210752851646108</Real>
+ <Real>0.33252283355373813</Real>
+ <Real>0.27808033609763227</Real>
+ <Real>0.22928085553476424</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.14925605025534092</Real>
+ <Real>0.11778437226576131</Real>
+ <Real>0.091552297002078148</Real>
+ <Real>0.070072349847468088</Real>
+ <Real>0.052793486472092074</Real>
+ <Real>0.039140255209952811</Real>
+ <Real>0.028545152841074214</Real>
+ <Real>0.020473509426959413</Real>
+ <Real>0.014441011915963002</Real>
+ <Real>0.010024605753721196</Real>
+ <Real>0.0068680064109441037</Real>
+ <Real>0.004683556831785461</Real>
+ <Real>0.0032533768155527912</Real>
+ <Real>0.0024376935527143208</Real>
+ <Real>0.0022199287318187566</Real>
+ <Real>0.0029116688417632187</Real>
+ <Real>0.0022199287318187566</Real>
+ <Real>0.0024376935527143208</Real>
+ <Real>0.0032533768155527912</Real>
+ <Real>0.004683556831785461</Real>
+ <Real>0.0068680064109441037</Real>
+ <Real>0.010024605753721196</Real>
+ <Real>0.014441011915963002</Real>
+ <Real>0.020473509426959413</Real>
+ <Real>0.028545152841074214</Real>
+ <Real>0.039140255209952811</Real>
+ <Real>0.052793486472092074</Real>
+ <Real>0.070072349847468088</Real>
+ <Real>0.091552297002078148</Real>
+ <Real>0.11778437226576131</Real>
+ <Real>0.14925605025534092</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.22928085553476424</Real>
+ <Real>0.27808033609763227</Real>
+ <Real>0.33252283355373813</Real>
+ <Real>0.39210752851646108</Real>
+ <Real>0.45603419748120122</Real>
+ <Real>0.52319883754353402</Real>
+ <Real>0.59220875271982998</Real>
+ <Real>0.66141859145189652</Real>
+ <Real>0.72898715282651005</Real>
+ <Real>0.79295292981514398</Real>
+ <Real>0.85132451513286955</Real>
+ <Real>0.90218036017845771</Real>
+ <Real>0.94377114404174522</Real>
+ <Real>0.97461733950689855</Real>
+ <Real>0.99359456296949322</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.99696533865897474</Real>
+ <Real>0.98789819131371792</Real>
+ <Real>0.97290862085031737</Real>
+ <Real>0.95217858034878877</Real>
+ <Real>0.92595970441916342</Real>
+ <Real>0.89457025469819695</Real>
+ <Real>0.85839125658422555</Real>
+ <Real>0.8178618741049839</Real>
+ <Real>0.77347407906121335</Real>
+ <Real>0.72576667915544457</Real>
+ <Real>0.67531877759637726</Real>
+ <Real>0.6227427435703996</Real>
+ <Real>0.56867677890920409</Real>
+ <Real>0.51377717118408106</Real>
+ <Real>0.45871032726383398</Real>
+ <Real>0.40414468403813075</Real>
+ <Real>0.35074259449915274</Real>
+ <Real>0.29915228767351526</Real>
+ <Real>0.25000000000000011</Real>
+ <Real>0.20388237366751011</Real>
+ <Real>0.16135921418712934</Real>
+ <Real>0.12294669511155193</Real>
+ <Real>0.089111092387377466</Real>
+ <Real>0.060263124396755505</Real>
+ <Real>0.036752966392599146</Real>
+ <Real>0.018865999845374768</Real>
+ <Real>0.0068193482986388214</Real>
+ <Real>0.00075924178334189039</Real>
+ <Real>0.00075924178334188411</Real>
+ <Real>0.0068193482986387685</Real>
+ <Real>0.018865999845374789</Real>
+ <Real>0.036752966392599097</Real>
+ <Real>0.060263124396755435</Real>
+ <Real>0.089111092387377411</Real>
+ <Real>0.12294669511155171</Real>
+ <Real>0.16135921418712945</Real>
+ <Real>0.2038823736675098</Real>
+ <Real>0.24999999999999983</Real>
+ <Real>0.29915228767351509</Real>
+ <Real>0.35074259449915257</Real>
+ <Real>0.40414468403813064</Real>
+ <Real>0.45871032726383404</Real>
+ <Real>0.51377717118408084</Real>
+ <Real>0.56867677890920387</Real>
+ <Real>0.62274274357039938</Real>
+ <Real>0.67531877759637693</Real>
+ <Real>0.7257666791554449</Real>
+ <Real>0.77347407906121335</Real>
+ <Real>0.81786187410498368</Real>
+ <Real>0.85839125658422555</Real>
+ <Real>0.89457025469819684</Real>
+ <Real>0.92595970441916364</Real>
+ <Real>0.95217858034878877</Real>
+ <Real>0.97290862085031726</Real>
+ <Real>0.9878981913137177</Real>
+ <Real>0.99696533865897463</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.99860189859059001</Real>
+ <Real>0.99441541311256421</Real>
+ <Real>0.98746395609091187</Real>
+ <Real>0.97778640289307028</Real>
+ <Real>0.96543687432210223</Real>
+ <Real>0.95048443395120974</Real>
+ <Real>0.93301270189221941</Real>
+ <Real>0.91311938715799768</Real>
+ <Real>0.89091574123401496</Real>
+ <Real>0.86652593591491323</Real>
+ <Real>0.84008636888545962</Real>
+ <Real>0.8117449009293668</Real>
+ <Real>0.78166002903181098</Real>
+ <Real>0.74999999999999989</Real>
+ <Real>0.71694186955877914</Real>
+ <Real>0.68267051218319763</Real>
+ <Real>0.64737758720545202</Real>
+ <Real>0.61126046697815717</Real>
+ <Real>0.57452113308808728</Real>
+ <Real>0.53736504679321218</Real>
+ <Real>0.5</Real>
+ <Real>0.46263495320678805</Real>
+ <Real>0.42547886691191283</Real>
+ <Real>0.38873953302184278</Real>
+ <Real>0.35262241279454792</Real>
+ <Real>0.31732948781680242</Real>
+ <Real>0.28305813044122108</Real>
+ <Real>0.25000000000000011</Real>
+ <Real>0.21833997096818897</Real>
+ <Real>0.18825509907063326</Real>
+ <Real>0.15991363111454038</Real>
+ <Real>0.1334740640850868</Real>
+ <Real>0.10908425876598513</Real>
+ <Real>0.086880612842002519</Real>
+ <Real>0.066987298107780785</Real>
+ <Real>0.049515566048790448</Real>
+ <Real>0.034563125677897849</Real>
+ <Real>0.022213597106929692</Real>
+ <Real>0.012536043909088213</Real>
+ <Real>0.0055845868874357454</Real>
+ <Real>0.0013981014094099416</Real>
+ <Real>0.0013981014094099288</Real>
+ <Real>0.001398101409409916</Real>
+ <Real>0.0055845868874356977</Real>
+ <Real>0.01253604390908818</Real>
+ <Real>0.022213597106929585</Real>
+ <Real>0.034563125677897863</Real>
+ <Real>0.049515566048790399</Real>
+ <Real>0.066987298107780605</Real>
+ <Real>0.086880612842002575</Real>
+ <Real>0.10908425876598506</Real>
+ <Real>0.13347406408508691</Real>
+ <Real>0.15991363111454029</Real>
+ <Real>0.1882550990706332</Real>
+ <Real>0.21833997096818905</Real>
+ <Real>0.24999999999999983</Real>
+ <Real>0.2830581304412208</Real>
+ <Real>0.31732948781680248</Real>
+ <Real>0.35262241279454759</Real>
+ <Real>0.38873953302184272</Real>
+ <Real>0.42547886691191283</Real>
+ <Real>0.46263495320678771</Real>
+ <Real>0.49999999999999994</Real>
+ <Real>0.53736504679321218</Real>
+ <Real>0.57452113308808683</Real>
+ <Real>0.61126046697815706</Real>
+ <Real>0.64737758720545224</Real>
+ <Real>0.68267051218319774</Real>
+ <Real>0.71694186955877914</Real>
+ <Real>0.74999999999999956</Real>
+ <Real>0.78166002903181131</Real>
+ <Real>0.81174490092936669</Real>
+ <Real>0.8400863688854594</Real>
+ <Real>0.86652593591491334</Real>
+ <Real>0.89091574123401474</Real>
+ <Real>0.91311938715799723</Real>
+ <Real>0.93301270189221919</Real>
+ <Real>0.95048443395120952</Real>
+ <Real>0.96543687432210223</Real>
+ <Real>0.97778640289307028</Real>
+ <Real>0.98746395609091187</Real>
+ <Real>0.99441541311256409</Real>
+ <Real>0.99860189859059012</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.98831027785504322</Real>
+ <Real>0.95378770983547845</Real>
+ <Real>0.89804653285282199</Real>
+ <Real>0.82369314239091374</Real>
+ <Real>0.73420422034989519</Real>
+ <Real>0.63376416926461054</Real>
+ <Real>0.52706945429270879</Real>
+ <Real>0.41910900172361765</Real>
+ <Real>0.31493092233004294</Real>
+ <Real>0.21940646731880881</Real>
+ <Real>0.13700225403843475</Real>
+ <Real>0.071571411916205363</Real>
+ <Real>0.026173414408598751</Real>
+ <Real>0.0029310214228202036</Real>
+ <Real>0.002931021422820168</Real>
+ <Real>0.026173414408598775</Real>
+ <Real>0.071571411916205391</Real>
+ <Real>0.1370022540384345</Real>
+ <Real>0.21940646731880872</Real>
+ <Real>0.31493092233004277</Real>
+ <Real>0.41910900172361765</Real>
+ <Real>0.52706945429270846</Real>
+ <Real>0.6337641692646101</Real>
+ <Real>0.73420422034989519</Real>
+ <Real>0.82369314239091396</Real>
+ <Real>0.89804653285282199</Real>
+ <Real>0.95378770983547856</Real>
+ <Real>0.98831027785504355</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.99696656660775951</Real>
+ <Real>0.98791772233095498</Real>
+ <Real>0.97300652443155822</Real>
+ <Real>0.95248375455969336</Real>
+ <Real>0.92669163563931867</Real>
+ <Real>0.89605540132524364</Real>
+ <Real>0.86107306257852145</Real>
+ <Real>0.82230378514128921</Real>
+ <Real>0.7803553410560129</Real>
+ <Real>0.73587112468566351</Real>
+ <Real>0.68951722811810012</Real>
+ <Real>0.64197005325186551</Real>
+ <Real>0.59390490139645091</Real>
+ <Real>0.54598593224673653</Real>
+ <Real>0.49885783396168321</Real>
+ <Real>0.45313951429664129</Real>
+ <Real>0.40942014266734855</Real>
+ <Real>0.36825800204726461</Real>
+ <Real>0.3301829471406319</Real>
+ <Real>0.29570398453575975</Real>
+ <Real>0.26532489435174572</Real>
+ <Real>0.23957343194663078</Real>
+ <Real>0.2190544144461728</Real>
+ <Real>0.20454555031604094</Real>
+ <Real>0.19717010656521591</Real>
+ <Real>0.19870756117866156</Real>
+ <Real>0.21215140990095066</Real>
+ <Real>0.24270871389263426</Real>
+ <Real>0.24270871389263426</Real>
+ <Real>0.21215140990095066</Real>
+ <Real>0.19870756117866156</Real>
+ <Real>0.19717010656521591</Real>
+ <Real>0.20454555031604094</Real>
+ <Real>0.2190544144461728</Real>
+ <Real>0.23957343194663078</Real>
+ <Real>0.26532489435174572</Real>
+ <Real>0.29570398453575975</Real>
+ <Real>0.3301829471406319</Real>
+ <Real>0.36825800204726461</Real>
+ <Real>0.40942014266734855</Real>
+ <Real>0.45313951429664129</Real>
+ <Real>0.49885783396168321</Real>
+ <Real>0.54598593224673653</Real>
+ <Real>0.59390490139645091</Real>
+ <Real>0.64197005325186551</Real>
+ <Real>0.68951722811810012</Real>
+ <Real>0.73587112468566351</Real>
+ <Real>0.7803553410560129</Real>
+ <Real>0.82230378514128921</Real>
+ <Real>0.86107306257852145</Real>
+ <Real>0.89605540132524364</Real>
+ <Real>0.92669163563931867</Real>
+ <Real>0.95248375455969336</Real>
+ <Real>0.97300652443155822</Real>
+ <Real>0.98791772233095498</Real>
+ <Real>0.99696656660775951</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.99860215922139717</Real>
+ <Real>0.99441957183361773</Real>
+ <Real>0.98748491402436001</Real>
+ <Real>0.97785221971601055</Real>
+ <Real>0.96559624954959267</Real>
+ <Real>0.95081162440523803</Real>
+ <Real>0.93361173994840618</Real>
+ <Real>0.91412748276565448</Real>
+ <Real>0.89250577227050065</Real>
+ <Real>0.86890795563906131</Real>
+ <Real>0.84350808550915102</Real>
+ <Real>0.81649111199327118</Real>
+ <Real>0.78805102167992025</Real>
+ <Real>0.75838895671363937</Real>
+ <Real>0.72771134675963611</Real>
+ <Real>0.69622808570858563</Real>
+ <Real>0.66415078342968292</Real>
+ <Real>0.63169112084631851</Real>
+ <Real>0.59905933425595059</Real>
+ <Real>0.56646285238799932</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.50218454077555041</Real>
+ <Real>0.47089382125013918</Real>
+ <Real>0.4404193025196152</Real>
+ <Real>0.41094074531162983</Real>
+ <Real>0.38263134936935156</Real>
+ <Real>0.35565815943534768</Real>
+ <Real>0.33018294714063184</Real>
+ <Real>0.30636372827068858</Real>
+ <Real>0.28435716364329472</Real>
+ <Real>0.26432222633550939</Real>
+ <Real>0.24642571976242944</Real>
+ <Real>0.23085053171587089</Real>
+ <Real>0.217807955305068</Real>
+ <Real>0.20755606705812685</Real>
+ <Real>0.20042712586833097</Real>
+ <Real>0.19686839270742718</Real>
+ <Real>0.19750289044735603</Real>
+ <Real>0.20321975336085121</Real>
+ <Real>0.21530844579905295</Real>
+ <Real>0.23565799171305502</Real>
+ <Real>0.2670525537709178</Real>
+ <Real>0.23565799171305502</Real>
+ <Real>0.21530844579905295</Real>
+ <Real>0.20321975336085121</Real>
+ <Real>0.19750289044735603</Real>
+ <Real>0.19686839270742718</Real>
+ <Real>0.20042712586833097</Real>
+ <Real>0.20755606705812685</Real>
+ <Real>0.217807955305068</Real>
+ <Real>0.23085053171587089</Real>
+ <Real>0.24642571976242944</Real>
+ <Real>0.26432222633550939</Real>
+ <Real>0.28435716364329472</Real>
+ <Real>0.30636372827068858</Real>
+ <Real>0.33018294714063184</Real>
+ <Real>0.35565815943534768</Real>
+ <Real>0.38263134936935156</Real>
+ <Real>0.41094074531162983</Real>
+ <Real>0.4404193025196152</Real>
+ <Real>0.47089382125013918</Real>
+ <Real>0.50218454077555041</Real>
+ <Real>0.53410510754183604</Real>
+ <Real>0.56646285238799932</Real>
+ <Real>0.59905933425595059</Real>
+ <Real>0.63169112084631851</Real>
+ <Real>0.66415078342968292</Real>
+ <Real>0.69622808570858563</Real>
+ <Real>0.72771134675963611</Real>
+ <Real>0.75838895671363937</Real>
+ <Real>0.78805102167992025</Real>
+ <Real>0.81649111199327118</Real>
+ <Real>0.84350808550915102</Real>
+ <Real>0.86890795563906131</Real>
+ <Real>0.89250577227050065</Real>
+ <Real>0.91412748276565448</Real>
+ <Real>0.93361173994840618</Real>
+ <Real>0.95081162440523803</Real>
+ <Real>0.96559624954959267</Real>
+ <Real>0.97785221971601055</Real>
+ <Real>0.98748491402436001</Real>
+ <Real>0.99441957183361773</Real>
+ <Real>0.99860215922139717</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.98832850126686445</Real>
+ <Real>0.95407268332389905</Real>
+ <Real>0.89943524093127036</Real>
+ <Real>0.82785442132742759</Real>
+ <Real>0.74369297639299847</Real>
+ <Real>0.65187208271592423</Real>
+ <Real>0.55750420447989546</Real>
+ <Real>0.46557626648701822</Real>
+ <Real>0.38072635390533288</Real>
+ <Real>0.30715580638020212</Real>
+ <Real>0.24876055053672902</Real>
+ <Real>0.20975887354800338</Real>
+ <Real>0.19676185240721122</Real>
+ <Real>0.22536122439134543</Real>
+ <Real>0.22536122439134543</Real>
+ <Real>0.19676185240721122</Real>
+ <Real>0.20975887354800338</Real>
+ <Real>0.24876055053672902</Real>
+ <Real>0.30715580638020212</Real>
+ <Real>0.38072635390533288</Real>
+ <Real>0.46557626648701822</Real>
+ <Real>0.55750420447989546</Real>
+ <Real>0.65187208271592423</Real>
+ <Real>0.74369297639299847</Real>
+ <Real>0.82785442132742759</Real>
+ <Real>0.89943524093127036</Real>
+ <Real>0.95407268332389905</Real>
+ <Real>0.98832850126686445</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99595787784283507</Real>
+ <Real>0.98392934565094792</Real>
+ <Real>0.96420435794452586</Real>
+ <Real>0.9372545018772549</Real>
+ <Real>0.90371603494541697</Real>
+ <Real>0.86436719790621919</Real>
+ <Real>0.82010080265087626</Real>
+ <Real>0.77189329743088908</Real>
+ <Real>0.72077165779591346</Real>
+ <Real>0.66777953410122992</Real>
+ <Real>0.61394410176472991</Real>
+ <Real>0.56024500810666122</Real>
+ <Real>0.50758669234655629</Real>
+ <Real>0.45677517902844306</Real>
+ <Real>0.40850021848992346</Real>
+ <Real>0.36332338207751624</Real>
+ <Real>0.3216724275978442</Real>
+ <Real>0.28384194617502795</Real>
+ <Real>0.24999999999999994</Real>
+ <Real>0.22020017598213704</Real>
+ <Real>0.19439822675120766</Real>
+ <Real>0.1724722599779577</Real>
+ <Real>0.15424527963282181</Real>
+ <Real>0.13950878602613967</Real>
+ <Real>0.12804610974722422</Real>
+ <Real>0.11965418924246241</Real>
+ <Real>0.11416260080438093</Real>
+ <Real>0.11144880810285662</Real>
+ <Real>0.11144880810285659</Real>
+ <Real>0.11416260080438081</Real>
+ <Real>0.11965418924246238</Real>
+ <Real>0.12804610974722422</Real>
+ <Real>0.13950878602613973</Real>
+ <Real>0.15424527963282186</Real>
+ <Real>0.17247225997795768</Real>
+ <Real>0.1943982267512076</Real>
+ <Real>0.22020017598213701</Real>
+ <Real>0.25000000000000006</Real>
+ <Real>0.28384194617502811</Real>
+ <Real>0.32167242759784387</Real>
+ <Real>0.36332338207751563</Real>
+ <Real>0.40850021848992313</Real>
+ <Real>0.45677517902844317</Real>
+ <Real>0.50758669234655607</Real>
+ <Real>0.56024500810666145</Real>
+ <Real>0.6139441017647298</Real>
+ <Real>0.66777953410122959</Real>
+ <Real>0.72077165779591368</Real>
+ <Real>0.77189329743088875</Real>
+ <Real>0.82010080265087626</Real>
+ <Real>0.86436719790621874</Real>
+ <Real>0.90371603494541697</Real>
+ <Real>0.93725450187725468</Real>
+ <Real>0.96420435794452608</Real>
+ <Real>0.98392934565094803</Real>
+ <Real>0.99595787784283507</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99813673353747623</Real>
+ <Real>0.99256774531039826</Real>
+ <Real>0.98335512029761163</Real>
+ <Real>0.97060117892250686</Real>
+ <Real>0.95444677005463663</Real>
+ <Real>0.93506893028211602</Real>
+ <Real>0.91267795723752809</Real>
+ <Real>0.8875139566052419</Real>
+ <Real>0.85984293298336401</Real>
+ <Real>0.82995250379027963</Real>
+ <Real>0.79814732269894051</Real>
+ <Real>0.76474430449519737</Real>
+ <Real>0.73006774667458774</Real>
+ <Real>0.6944444444444442</Real>
+ <Real>0.65819889506009632</Real>
+ <Real>0.62164868461674083</Real>
+ <Real>0.58510014560951307</Real>
+ <Real>0.54884436687489413</Real>
+ <Real>0.51315362909018081</Real>
+ <Real>0.47827832902590361</Real>
+ <Real>0.44444444444444442</Real>
+ <Real>0.41185157917130444</Real>
+ <Real>0.38067161471135902</Real>
+ <Real>0.35104798113594815</Real>
+ <Real>0.32309554613315405</Real>
+ <Real>0.29690110740216724</Real>
+ <Real>0.2725244602889334</Real>
+ <Real>0.24999999999999994</Real>
+ <Real>0.22933880617359045</Real>
+ <Real>0.21053114728743447</Real>
+ <Real>0.19354933356923457</Real>
+ <Real>0.17835083994154516</Real>
+ <Real>0.16488161523400408</Real>
+ <Real>0.15307949054657974</Real>
+ <Real>0.14287759831802727</Real>
+ <Real>0.13420771436885445</Real>
+ <Real>0.12700343792645519</Real>
+ <Real>0.12120312933482608</Real>
+ <Real>0.11675253169154608</Real>
+ <Real>0.1136070108880618</Real>
+ <Real>0.11173335826531594</Real>
+ <Real>0.11111111111111113</Real>
+ <Real>0.1117333582653159</Real>
+ <Real>0.11360701088806179</Real>
+ <Real>0.11675253169154612</Real>
+ <Real>0.12120312933482608</Real>
+ <Real>0.1270034379264551</Real>
+ <Real>0.1342077143688544</Real>
+ <Real>0.14287759831802727</Real>
+ <Real>0.15307949054657974</Real>
+ <Real>0.16488161523400399</Real>
+ <Real>0.17835083994154527</Real>
+ <Real>0.19354933356923443</Real>
+ <Real>0.2105311472874343</Real>
+ <Real>0.22933880617359059</Real>
+ <Real>0.25000000000000006</Real>
+ <Real>0.2725244602889334</Real>
+ <Real>0.29690110740216724</Real>
+ <Real>0.32309554613315422</Real>
+ <Real>0.3510479811359476</Real>
+ <Real>0.38067161471135902</Real>
+ <Real>0.41185157917130388</Real>
+ <Real>0.44444444444444425</Real>
+ <Real>0.4782783290259035</Real>
+ <Real>0.5131536290901807</Real>
+ <Real>0.54884436687489446</Real>
+ <Real>0.58510014560951307</Real>
+ <Real>0.62164868461674094</Real>
+ <Real>0.65819889506009566</Real>
+ <Real>0.6944444444444442</Real>
+ <Real>0.73006774667458785</Real>
+ <Real>0.76474430449519715</Real>
+ <Real>0.79814732269894006</Real>
+ <Real>0.82995250379027941</Real>
+ <Real>0.85984293298336367</Real>
+ <Real>0.88751395660524168</Real>
+ <Real>0.91267795723752831</Real>
+ <Real>0.9350689302821158</Real>
+ <Real>0.95444677005463674</Real>
+ <Real>0.97060117892250664</Real>
+ <Real>0.9833551202976113</Real>
+ <Real>0.99256774531039815</Real>
+ <Real>0.99813673353747601</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.98447443696398029</Real>
+ <Real>0.93933275789719339</Real>
+ <Real>0.86868182578746489</Real>
+ <Real>0.77873934898343644</Real>
+ <Real>0.67700447001310771</Real>
+ <Real>0.57129830733700993</Real>
+ <Real>0.46883185064049882</Real>
+ <Real>0.37544949202194877</Real>
+ <Real>0.29516107029764194</Real>
+ <Real>0.23002029565339052</Real>
+ <Real>0.18034305406668735</Real>
+ <Real>0.14519727951994868</Real>
+ <Real>0.12304820534684577</Real>
+ <Real>0.11241760547084502</Real>
+ <Real>0.11241760547084489</Real>
+ <Real>0.12304820534684582</Real>
+ <Real>0.14519727951994876</Real>
+ <Real>0.1803430540666871</Real>
+ <Real>0.23002029565339013</Real>
+ <Real>0.2951610702976416</Real>
+ <Real>0.37544949202194894</Real>
+ <Real>0.46883185064049865</Real>
+ <Real>0.57129830733701015</Real>
+ <Real>0.67700447001310726</Real>
+ <Real>0.778739348983436</Real>
+ <Real>0.86868182578746533</Real>
+ <Real>0.93933275789719284</Real>
+ <Real>0.9844744369639804</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.99595746961106935</Real>
+ <Real>0.98392290411739991</Real>
+ <Real>0.96417249585689879</Real>
+ <Real>0.93715702990301086</Real>
+ <Real>0.90348786274003334</Real>
+ <Real>0.86391786113433711</Real>
+ <Real>0.81931787951960255</Real>
+ <Real>0.77064952856941005</Real>
+ <Real>0.71893516132582791</Real>
+ <Real>0.66522616885086927</Real>
+ <Real>0.61057082453529554</Real>
+ <Real>0.55598303255336479</Real>
+ <Real>0.50241340863405681</Real>
+ <Real>0.45072413946621243</Real>
+ <Real>0.40166902542472988</Real>
+ <Real>0.35588001551284348</Real>
+ <Real>0.31386141771105369</Real>
+ <Real>0.27599286746285367</Real>
+ <Real>0.24254216886929247</Real>
+ <Real>0.21368948507772698</Real>
+ <Real>0.18956541097020155</Real>
+ <Real>0.17030789936928309</Real>
+ <Real>0.15614816416805158</Real>
+ <Real>0.1475462110421403</Real>
+ <Real>0.14541798763152783</Real>
+ <Real>0.15153961053372036</Real>
+ <Real>0.16930353151461464</Real>
+ <Real>0.20518747914506352</Real>
+ <Real>0.20518747914506352</Real>
+ <Real>0.16930353151461464</Real>
+ <Real>0.15153961053372036</Real>
+ <Real>0.14541798763152783</Real>
+ <Real>0.1475462110421403</Real>
+ <Real>0.15614816416805158</Real>
+ <Real>0.17030789936928309</Real>
+ <Real>0.18956541097020155</Real>
+ <Real>0.21368948507772698</Real>
+ <Real>0.24254216886929247</Real>
+ <Real>0.27599286746285367</Real>
+ <Real>0.31386141771105369</Real>
+ <Real>0.35588001551284348</Real>
+ <Real>0.40166902542472988</Real>
+ <Real>0.45072413946621243</Real>
+ <Real>0.50241340863405681</Real>
+ <Real>0.55598303255336479</Real>
+ <Real>0.61057082453529554</Real>
+ <Real>0.66522616885086927</Real>
+ <Real>0.71893516132582791</Real>
+ <Real>0.77064952856941005</Real>
+ <Real>0.81931787951960255</Real>
+ <Real>0.86391786113433711</Real>
+ <Real>0.90348786274003334</Real>
+ <Real>0.93715702990301086</Real>
+ <Real>0.96417249585689879</Real>
+ <Real>0.98392290411739991</Real>
+ <Real>0.99595746961106935</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.99813664676658265</Real>
+ <Real>0.9925663658296221</Real>
+ <Real>0.98334821080237111</Real>
+ <Real>0.97057966570670828</Real>
+ <Real>0.95439524956616717</Real>
+ <Real>0.93496458813901551</Real>
+ <Real>0.9124899783466649</Real>
+ <Real>0.88720347856845028</Real>
+ <Real>0.85936356574592299</Real>
+ <Real>0.82925140811986475</Real>
+ <Real>0.79716681031855896</Real>
+ <Real>0.76342389528860444</Real>
+ <Real>0.72834659502631327</Real>
+ <Real>0.69226402900504336</Real>
+ <Real>0.65550585534580197</Real>
+ <Real>0.61839768487013713</Real>
+ <Real>0.58125665192995213</Real>
+ <Real>0.54438723807606892</Real>
+ <Real>0.50807744500843544</Real>
+ <Real>0.47259541174334813</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.40507140750487103</Real>
+ <Real>0.3734439706933132</Real>
+ <Real>0.34347109672106363</Real>
+ <Real>0.31529252955077341</Real>
+ <Real>0.28902193869824733</Real>
+ <Real>0.2647489338337406</Real>
+ <Real>0.24254216886929233</Real>
+ <Real>0.22245367254997173</Real>
+ <Real>0.20452461728862817</Real>
+ <Real>0.18879286598937658</Real>
+ <Real>0.1753028486476319</Real>
+ <Real>0.16411866568055694</Real>
+ <Real>0.15534187249635459</Real>
+ <Real>0.14913629897657579</Real>
+ <Real>0.14576371059594109</Real>
+ <Real>0.14563647564909091</Real>
+ <Real>0.1493972480929823</Real>
+ <Real>0.15804197939885326</Real>
+ <Real>0.17311296177291857</Real>
+ <Real>0.19700581106261494</Real>
+ <Real>0.23346292694334683</Real>
+ <Real>0.19700581106261494</Real>
+ <Real>0.17311296177291857</Real>
+ <Real>0.15804197939885326</Real>
+ <Real>0.1493972480929823</Real>
+ <Real>0.14563647564909091</Real>
+ <Real>0.14576371059594109</Real>
+ <Real>0.14913629897657579</Real>
+ <Real>0.15534187249635459</Real>
+ <Real>0.16411866568055694</Real>
+ <Real>0.1753028486476319</Real>
+ <Real>0.18879286598937658</Real>
+ <Real>0.20452461728862817</Real>
+ <Real>0.22245367254997173</Real>
+ <Real>0.24254216886929233</Real>
+ <Real>0.2647489338337406</Real>
+ <Real>0.28902193869824733</Real>
+ <Real>0.31529252955077341</Real>
+ <Real>0.34347109672106363</Real>
+ <Real>0.3734439706933132</Real>
+ <Real>0.40507140750487103</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.47259541174334813</Real>
+ <Real>0.50807744500843544</Real>
+ <Real>0.54438723807606892</Real>
+ <Real>0.58125665192995213</Real>
+ <Real>0.61839768487013713</Real>
+ <Real>0.65550585534580197</Real>
+ <Real>0.69226402900504336</Real>
+ <Real>0.72834659502631327</Real>
+ <Real>0.76342389528860444</Real>
+ <Real>0.79716681031855896</Real>
+ <Real>0.82925140811986475</Real>
+ <Real>0.85936356574592299</Real>
+ <Real>0.88720347856845028</Real>
+ <Real>0.9124899783466649</Real>
+ <Real>0.93496458813901551</Real>
+ <Real>0.95439524956616717</Real>
+ <Real>0.97057966570670828</Real>
+ <Real>0.98334821080237111</Real>
+ <Real>0.9925663658296221</Real>
+ <Real>0.99813664676658265</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.98446842450555616</Real>
+ <Real>0.93924160417612246</Real>
+ <Real>0.86826025265339679</Real>
+ <Real>0.77756700407501733</Real>
+ <Real>0.67458281427952937</Real>
+ <Real>0.56722374129711373</Real>
+ <Real>0.46298628726392016</Real>
+ <Real>0.36815395301498727</Real>
+ <Real>0.28728291393347499</Real>
+ <Real>0.22311064862270136</Real>
+ <Real>0.17702819848076223</Real>
+ <Real>0.15038677384389965</Real>
+ <Real>0.14760833414605379</Real>
+ <Real>0.18500370061649021</Real>
+ <Real>0.18500370061649021</Real>
+ <Real>0.14760833414605379</Real>
+ <Real>0.15038677384389965</Real>
+ <Real>0.17702819848076223</Real>
+ <Real>0.22311064862270136</Real>
+ <Real>0.28728291393347499</Real>
+ <Real>0.36815395301498727</Real>
+ <Real>0.46298628726392016</Real>
+ <Real>0.56722374129711373</Real>
+ <Real>0.67458281427952937</Real>
+ <Real>0.77756700407501733</Real>
+ <Real>0.86826025265339679</Real>
+ <Real>0.93924160417612246</Real>
+ <Real>0.98446842450555616</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99494939068045452</Real>
+ <Real>0.97994403041828604</Real>
+ <Real>0.95541633655567315</Real>
+ <Real>0.92206417335942237</Real>
+ <Real>0.88081815972655553</Real>
+ <Real>0.83279888241711397</Real>
+ <Real>0.77926671299848038</Real>
+ <Real>0.7215673206267248</Real>
+ <Real>0.66107613182548253</Real>
+ <Real>0.59914490755703098</Real>
+ <Real>0.53705330286897801</Real>
+ <Real>0.47596777973251997</Real>
+ <Real>0.41690960880755507</Real>
+ <Real>0.36073298004042298</Real>
+ <Real>0.30811350836714391</Real>
+ <Real>0.2595467302579938</Real>
+ <Real>0.21535559236527288</Real>
+ <Real>0.17570547548805457</Real>
+ <Real>0.14062499999999986</Real>
+ <Real>0.11003073009920575</Real>
+ <Real>0.083753924189319984</Real>
+ <Real>0.061567643166775265</Real>
+ <Real>0.043212792097817088</Real>
+ <Real>0.028421992051017742</Real>
+ <Real>0.016940514768528789</Real>
+ <Real>0.0085438242312313867</Real>
+ <Real>0.0030515249292297555</Real>
+ <Real>0.00033769704037479138</Real>
+ <Real>0.00033769704037478818</Real>
+ <Real>0.0030515249292297057</Real>
+ <Real>0.0085438242312312826</Real>
+ <Real>0.016940514768528779</Real>
+ <Real>0.028421992051017839</Real>
+ <Real>0.043212792097817386</Real>
+ <Real>0.061567643166775432</Real>
+ <Real>0.083753924189319692</Real>
+ <Real>0.11003073009920591</Real>
+ <Real>0.14062500000000014</Real>
+ <Real>0.17570547548805493</Real>
+ <Real>0.21535559236527266</Real>
+ <Real>0.25954673025799285</Real>
+ <Real>0.3081135083671433</Real>
+ <Real>0.36073298004042298</Real>
+ <Real>0.41690960880755462</Real>
+ <Real>0.47596777973252047</Real>
+ <Real>0.53705330286897823</Real>
+ <Real>0.59914490755703076</Real>
+ <Real>0.66107613182548275</Real>
+ <Real>0.72156732062672435</Real>
+ <Real>0.77926671299848038</Real>
+ <Real>0.83279888241711375</Real>
+ <Real>0.88081815972655575</Real>
+ <Real>0.92206417335942226</Real>
+ <Real>0.95541633655567315</Real>
+ <Real>0.97994403041828604</Real>
+ <Real>0.99494939068045474</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99767135099320636</Real>
+ <Real>0.9907165928659406</Real>
+ <Real>0.97922860423028468</Real>
+ <Real>0.96335990994523879</Real>
+ <Real>0.94331934366491299</Real>
+ <Real>0.91936751626699431</Real>
+ <Real>0.89181122479574559</Real>
+ <Real>0.86099696642115131</Real>
+ <Real>0.82730374583628341</Real>
+ <Real>0.79113538169690201</Real>
+ <Real>0.75291252763844485</Real>
+ <Real>0.71306462587103303</Real>
+ <Real>0.67202200644047028</Real>
+ <Real>0.63020833333333326</Real>
+ <Real>0.58803358034978093</Real>
+ <Real>0.54588769595915243</Real>
+ <Real>0.50413508827548392</Real>
+ <Real>0.4631100300695869</Real>
+ <Real>0.42311305068326482</Real>
+ <Real>0.38440834816649128</Real>
+ <Real>0.34722222222222221</Real>
+ <Real>0.31174249782689201</Real>
+ <Real>0.27811888176607463</Real>
+ <Real>0.24646417066754356</Real>
+ <Real>0.21685621009290576</Real>
+ <Real>0.18934049028906835</Real>
+ <Real>0.16393325547735715</Real>
+ <Real>0.14062499999999986</Real>
+ <Real>0.11938422594799727</Real>
+ <Real>0.10016134255230789</Real>
+ <Real>0.082892596952518285</Real>
+ <Real>0.067503938156579582</Real>
+ <Real>0.053914730184820014</Real>
+ <Real>0.04204124563482544</Real>
+ <Real>0.031799886315365442</Real>
+ <Real>0.023110092350312129</Real>
+ <Real>0.015896914531310535</Real>
+ <Real>0.01009323613081602</Real>
+ <Real>0.005641639477029229</Real>
+ <Real>0.0024959191291642081</Real>
+ <Real>0.00062224745785503723</Real>
+ <Real>0.00062224745785502671</Real>
+ <Real>0.00062224745785501609</Real>
+ <Real>0.0024959191291641634</Real>
+ <Real>0.0056416394770293365</Real>
+ <Real>0.010093236130816099</Real>
+ <Real>0.01589691453131041</Real>
+ <Real>0.023110092350312087</Real>
+ <Real>0.031799886315365573</Real>
+ <Real>0.042041245634825385</Real>
+ <Real>0.053914730184819785</Real>
+ <Real>0.067503938156579721</Real>
+ <Real>0.082892596952517966</Real>
+ <Real>0.10016134255230759</Real>
+ <Real>0.11938422594799739</Real>
+ <Real>0.14062500000000014</Real>
+ <Real>0.16393325547735713</Real>
+ <Real>0.18934049028906835</Real>
+ <Real>0.21685621009290634</Real>
+ <Real>0.24646417066754278</Real>
+ <Real>0.27811888176607447</Real>
+ <Real>0.31174249782689112</Real>
+ <Real>0.34722222222222199</Real>
+ <Real>0.38440834816649111</Real>
+ <Real>0.42311305068326494</Real>
+ <Real>0.46311003006958729</Real>
+ <Real>0.50413508827548359</Real>
+ <Real>0.54588769595915254</Real>
+ <Real>0.58803358034977982</Real>
+ <Real>0.63020833333333348</Real>
+ <Real>0.67202200644046983</Real>
+ <Real>0.71306462587103292</Real>
+ <Real>0.75291252763844418</Real>
+ <Real>0.79113538169690145</Real>
+ <Real>0.82730374583628263</Real>
+ <Real>0.86099696642115153</Real>
+ <Real>0.89181122479574582</Real>
+ <Real>0.91936751626699442</Real>
+ <Real>0.94331934366491299</Real>
+ <Real>0.96335990994523857</Real>
+ <Real>0.9792286042302849</Real>
+ <Real>0.99071659286594016</Real>
+ <Real>0.99767135099320625</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.98062323529517048</Real>
+ <Real>0.92462955422457049</Real>
+ <Real>0.83804442252850697</Real>
+ <Real>0.72972283897039203</Real>
+ <Real>0.60986858897549723</Real>
+ <Real>0.48847117722940447</Real>
+ <Real>0.37398974608946534</Real>
+ <Real>0.27251810127650261</Real>
+ <Real>0.18752054994359144</Real>
+ <Real>0.12008274580351165</Real>
+ <Real>0.069517662946712813</Real>
+ <Real>0.034126904208387411</Real>
+ <Real>0.011939086461878554</Real>
+ <Real>0.0013064971575197132</Real>
+ <Real>0.0013064971575196787</Real>
+ <Real>0.011939086461878627</Real>
+ <Real>0.034126904208387515</Real>
+ <Real>0.069517662946712799</Real>
+ <Real>0.12008274580351111</Real>
+ <Real>0.18752054994359071</Real>
+ <Real>0.27251810127650294</Real>
+ <Real>0.37398974608946534</Real>
+ <Real>0.4884711772294047</Real>
+ <Real>0.60986858897549667</Real>
+ <Real>0.72972283897039136</Real>
+ <Real>0.83804442252850708</Real>
+ <Real>0.92462955422457016</Real>
+ <Real>0.98062323529517048</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.99494939127197923</Real>
+ <Real>0.9799440679435939</Real>
+ <Real>0.95541675775135737</Real>
+ <Real>0.92206649160055121</Real>
+ <Real>0.88082677118404018</Real>
+ <Real>0.83282377210865988</Real>
+ <Real>0.77932709828961222</Real>
+ <Real>0.72169598676563462</Real>
+ <Real>0.66132403592671196</Real>
+ <Real>0.59958548922687738</Real>
+ <Real>0.53778586364542869</Real>
+ <Real>0.47711929657339158</Real>
+ <Real>0.41863443844503245</Real>
+ <Real>0.36321009172092422</Real>
+ <Real>0.31154114346152084</Real>
+ <Real>0.26413471053519755</Real>
+ <Real>0.22131585891635455</Real>
+ <Real>0.18324180764543538</Real>
+ <Real>0.14992321097434119</Real>
+ <Real>0.12125095507366032</Real>
+ <Real>0.097026960331861353</Real>
+ <Real>0.076997902013451275</Real>
+ <Real>0.060892024312349677</Real>
+ <Real>0.048462702886541115</Real>
+ <Real>0.039551969610798522</Real>
+ <Real>0.034213419233233101</Real>
+ <Real>0.033005268440282939</Real>
+ <Real>0.037756945100019701</Real>
+ <Real>0.037756945100019701</Real>
+ <Real>0.033005268440282939</Real>
+ <Real>0.034213419233233101</Real>
+ <Real>0.039551969610798522</Real>
+ <Real>0.048462702886541115</Real>
+ <Real>0.060892024312349677</Real>
+ <Real>0.076997902013451275</Real>
+ <Real>0.097026960331861353</Real>
+ <Real>0.12125095507366032</Real>
+ <Real>0.14992321097434119</Real>
+ <Real>0.18324180764543538</Real>
+ <Real>0.22131585891635455</Real>
+ <Real>0.26413471053519755</Real>
+ <Real>0.31154114346152084</Real>
+ <Real>0.36321009172092422</Real>
+ <Real>0.41863443844503245</Real>
+ <Real>0.47711929657339158</Real>
+ <Real>0.53778586364542869</Real>
+ <Real>0.59958548922687738</Real>
+ <Real>0.66132403592671196</Real>
+ <Real>0.72169598676563462</Real>
+ <Real>0.77932709828961222</Real>
+ <Real>0.83282377210865988</Real>
+ <Real>0.88082677118404018</Real>
+ <Real>0.92206649160055121</Real>
+ <Real>0.95541675775135737</Real>
+ <Real>0.9799440679435939</Real>
+ <Real>0.99494939127197923</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.99767135105104621</Real>
+ <Real>0.99071659655276323</Real>
+ <Real>0.97922864594230408</Real>
+ <Real>0.96336014209944676</Real>
+ <Real>0.94332021852360948</Real>
+ <Real>0.91937008986699287</Real>
+ <Real>0.89181760077675287</Real>
+ <Real>0.86101088605709308</Real>
+ <Real>0.82733131793012282</Real>
+ <Real>0.79118593294295625</Real>
+ <Real>0.75299954137234981</Real>
+ <Real>0.71320672561299991</Real>
+ <Real>0.67224393106003733</Real>
+ <Real>0.63054184372494826</Real>
+ <Real>0.5885182338069832</Real>
+ <Real>0.54657142443460582</Real>
+ <Real>0.50507452071616155</Real>
+ <Real>0.46437050713986255</Real>
+ <Real>0.42476829235622371</Real>
+ <Real>0.3865397505982584</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.31509536642106994</Real>
+ <Real>0.28222562811429547</Real>
+ <Real>0.25142276879144704</Real>
+ <Real>0.22276387888579641</Real>
+ <Real>0.19629148487173642</Real>
+ <Real>0.17201674873386533</Real>
+ <Real>0.14992321097434108</Real>
+ <Real>0.12997097208672034</Real>
+ <Real>0.11210121703674311</Real>
+ <Real>0.096241010481140643</Real>
+ <Real>0.082308338034130235</Real>
+ <Real>0.070217463333273111</Real>
+ <Real>0.059884857726556467</Real>
+ <Real>0.051236330892951661</Real>
+ <Real>0.044216728742829996</Real>
+ <Real>0.038805028015203503</Real>
+ <Real>0.035040546624042074</Real>
+ <Real>0.033071671888768056</Real>
+ <Real>0.033249640426096155</Real>
+ <Real>0.036311630888043747</Real>
+ <Real>0.043739722444097656</Real>
+ <Real>0.036311630888043747</Real>
+ <Real>0.033249640426096155</Real>
+ <Real>0.033071671888768056</Real>
+ <Real>0.035040546624042074</Real>
+ <Real>0.038805028015203503</Real>
+ <Real>0.044216728742829996</Real>
+ <Real>0.051236330892951661</Real>
+ <Real>0.059884857726556467</Real>
+ <Real>0.070217463333273111</Real>
+ <Real>0.082308338034130235</Real>
+ <Real>0.096241010481140643</Real>
+ <Real>0.11210121703674311</Real>
+ <Real>0.12997097208672034</Real>
+ <Real>0.14992321097434108</Real>
+ <Real>0.17201674873386533</Real>
+ <Real>0.19629148487173642</Real>
+ <Real>0.22276387888579641</Real>
+ <Real>0.25142276879144704</Real>
+ <Real>0.28222562811429547</Real>
+ <Real>0.31509536642106994</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.3865397505982584</Real>
+ <Real>0.42476829235622371</Real>
+ <Real>0.46437050713986255</Real>
+ <Real>0.50507452071616155</Real>
+ <Real>0.54657142443460582</Real>
+ <Real>0.5885182338069832</Real>
+ <Real>0.63054184372494826</Real>
+ <Real>0.67224393106003733</Real>
+ <Real>0.71320672561299991</Real>
+ <Real>0.75299954137234981</Real>
+ <Real>0.79118593294295625</Real>
+ <Real>0.82733131793012282</Real>
+ <Real>0.86101088605709308</Real>
+ <Real>0.89181760077675287</Real>
+ <Real>0.91937008986699287</Real>
+ <Real>0.94332021852360948</Real>
+ <Real>0.96336014209944676</Real>
+ <Real>0.97922864594230408</Real>
+ <Real>0.99071659655276323</Real>
+ <Real>0.99767135105104621</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.98062326911566944</Real>
+ <Real>0.92463164612174864</Real>
+ <Real>0.83806692785041004</Real>
+ <Real>0.72983951519887702</Real>
+ <Real>0.61026962025499942</Real>
+ <Real>0.48952422891097952</Real>
+ <Real>0.37626774010234398</Real>
+ <Real>0.27676472172225453</Real>
+ <Real>0.1945468549937158</Real>
+ <Real>0.13062393044503182</Real>
+ <Real>0.084118646872820113</Real>
+ <Real>0.053173105906025683</Real>
+ <Real>0.036146384873032851</Real>
+ <Real>0.034510897785185804</Real>
+ <Real>0.034510897785185804</Real>
+ <Real>0.036146384873032851</Real>
+ <Real>0.053173105906025683</Real>
+ <Real>0.084118646872820113</Real>
+ <Real>0.13062393044503182</Real>
+ <Real>0.1945468549937158</Real>
+ <Real>0.27676472172225453</Real>
+ <Real>0.37626774010234398</Real>
+ <Real>0.48952422891097952</Real>
+ <Real>0.61026962025499942</Real>
+ <Real>0.72983951519887702</Real>
+ <Real>0.83806692785041004</Real>
+ <Real>0.92463164612174864</Real>
+ <Real>0.98062326911566944</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.99394233481497718</Real>
+ <Real>0.97598141849367381</Real>
+ <Real>0.94674160991483403</Real>
+ <Real>0.9072248154338074</Real>
+ <Real>0.8587555295403756</Real>
+ <Real>0.80290974618244992</Real>
+ <Real>0.74143292517658166</Real>
+ <Real>0.67615280819988821</Real>
+ <Real>0.60889297367088469</Real>
+ <Real>0.54139261577970732</Real>
+ <Real>0.47523719723429253</Real>
+ <Real>0.41180346564684528</Real>
+ <Real>0.35222097340504771</Real>
+ <Real>0.29735084281184915</Real>
+ <Real>0.24778120691639133</Real>
+ <Real>0.20383764427828754</Real>
+ <Real>0.16560609275165325</Real>
+ <Real>0.13296521498033564</Real>
+ <Real>0.10562500000000008</Real>
+ <Real>0.083168490441534557</Real>
+ <Real>0.06509386645826154</Real>
+ <Real>0.05085462256619782</Real>
+ <Real>0.0398961632045189</Real>
+ <Real>0.031687741829208173</Real>
+ <Real>0.025749212878354629</Real>
+ <Real>0.021672508458015584</Real>
+ <Real>0.019138063289678757</Real>
+ <Real>0.017926582309016018</Real>
+ <Real>0.017926582309016028</Real>
+ <Real>0.019138063289678757</Real>
+ <Real>0.021672508458015584</Real>
+ <Real>0.025749212878354591</Real>
+ <Real>0.03168774182920818</Real>
+ <Real>0.039896163204518879</Real>
+ <Real>0.050854622566197757</Real>
+ <Real>0.065093866458261609</Real>
+ <Real>0.083168490441534362</Real>
+ <Real>0.10562499999999994</Real>
+ <Real>0.13296521498033548</Real>
+ <Real>0.16560609275165311</Real>
+ <Real>0.20383764427828743</Real>
+ <Real>0.24778120691639138</Real>
+ <Real>0.29735084281184893</Real>
+ <Real>0.35222097340504754</Real>
+ <Real>0.41180346564684495</Real>
+ <Real>0.47523719723429225</Real>
+ <Real>0.54139261577970754</Real>
+ <Real>0.60889297367088457</Real>
+ <Real>0.67615280819988799</Real>
+ <Real>0.74143292517658144</Real>
+ <Real>0.80290974618244992</Real>
+ <Real>0.85875552954037593</Real>
+ <Real>0.90722481543380695</Real>
+ <Real>0.94674160991483414</Real>
+ <Real>0.9759814184936737</Real>
+ <Real>0.99394233481497696</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.99720627239005266</Real>
+ <Real>0.98887028410399891</Real>
+ <Real>0.9751264469717813</Real>
+ <Real>0.95619491607323037</Real>
+ <Real>0.93237593572814026</Real>
+ <Real>0.9040422032368971</Real>
+ <Real>0.87162951483124795</Real>
+ <Real>0.8356260134676966</Real>
+ <Real>0.79656039947962531</Real>
+ <Real>0.75498949118750946</Real>
+ <Real>0.71148553261965164</Real>
+ <Real>0.66662363958893034</Real>
+ <Real>0.62096975434726776</Real>
+ <Real>0.57506944444444452</Real>
+ <Real>0.52943783539115363</Real>
+ <Real>0.4845509118634278</Real>
+ <Real>0.44083836138004096</Real>
+ <Real>0.39867807065886807</Real>
+ <Real>0.35839232119761033</Real>
+ <Real>0.32024566982017466</Real>
+ <Real>0.28444444444444456</Real>
+ <Real>0.25113773718423743</Real>
+ <Real>0.22041973760769953</Real>
+ <Real>0.19233321949021653</Real>
+ <Real>0.16687397511358193</Real>
+ <Real>0.14399598192965166</Real>
+ <Real>0.12361708659889853</Real>
+ <Real>0.10562500000000008</Real>
+ <Real>0.089883412441655375</Real>
+ <Real>0.076238059437568603</Real>
+ <Real>0.064522593368110989</Real>
+ <Real>0.054564143476825672</Real>
+ <Real>0.046188474345041246</Real>
+ <Real>0.03922467981458605</Real>
+ <Real>0.033509374057641109</Real>
+ <Real>0.028890363143075554</Real>
+ <Real>0.025229798308550752</Real>
+ <Real>0.022406825780016942</Real>
+ <Real>0.020319757213500347</Real>
+ <Real>0.018887789743089457</Real>
+ <Real>0.018052305497639386</Real>
+ <Real>0.017777777777777778</Real>
+ <Real>0.018052305497639393</Real>
+ <Real>0.018887789743089457</Real>
+ <Real>0.020319757213500336</Real>
+ <Real>0.022406825780016917</Real>
+ <Real>0.025229798308550766</Real>
+ <Real>0.028890363143075536</Real>
+ <Real>0.033509374057641046</Real>
+ <Real>0.039224679814586064</Real>
+ <Real>0.046188474345041239</Real>
+ <Real>0.054564143476825727</Real>
+ <Real>0.06452259336811092</Real>
+ <Real>0.076238059437568562</Real>
+ <Real>0.089883412441655416</Real>
+ <Real>0.10562499999999994</Real>
+ <Real>0.12361708659889853</Real>
+ <Real>0.14399598192965177</Real>
+ <Real>0.16687397511358176</Real>
+ <Real>0.19233321949021651</Real>
+ <Real>0.22041973760769942</Real>
+ <Real>0.25113773718423715</Real>
+ <Real>0.28444444444444444</Real>
+ <Real>0.32024566982017455</Real>
+ <Real>0.35839232119760994</Real>
+ <Real>0.39867807065886796</Real>
+ <Real>0.44083836138004107</Real>
+ <Real>0.48455091186342819</Real>
+ <Real>0.52943783539115352</Real>
+ <Real>0.57506944444444408</Real>
+ <Real>0.62096975434726787</Real>
+ <Real>0.66662363958893001</Real>
+ <Real>0.71148553261965097</Real>
+ <Real>0.75498949118750946</Real>
+ <Real>0.79656039947962509</Real>
+ <Real>0.83562601346769649</Real>
+ <Real>0.87162951483124751</Real>
+ <Real>0.90404220323689677</Real>
+ <Real>0.93237593572814004</Real>
+ <Real>0.95619491607323004</Real>
+ <Real>0.97512644697178119</Real>
+ <Real>0.98887028410399869</Real>
+ <Real>0.99720627239005233</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.97679321956799314</Real>
+ <Real>0.91025424608948602</Real>
+ <Real>0.80897876349947651</Real>
+ <Real>0.68531524119907727</Real>
+ <Real>0.55297646481359697</Real>
+ <Real>0.42464510777126263</Real>
+ <Real>0.3101278395646998</Real>
+ <Real>0.21538904078841092</Real>
+ <Real>0.14251144028518392</Real>
+ <Real>0.090390403912195938</Real>
+ <Real>0.055839707378934816</Real>
+ <Real>0.034783007569253982</Real>
+ <Real>0.023292409670689136</Real>
+ <Real>0.018355885667517561</Real>
+ <Real>0.018355885667517561</Real>
+ <Real>0.023292409670689143</Real>
+ <Real>0.034783007569254031</Real>
+ <Real>0.055839707378934726</Real>
+ <Real>0.090390403912195827</Real>
+ <Real>0.14251144028518381</Real>
+ <Real>0.21538904078841084</Real>
+ <Real>0.31012783956469941</Real>
+ <Real>0.4246451077712623</Real>
+ <Real>0.55297646481359697</Real>
+ <Real>0.6853152411990775</Real>
+ <Real>0.80897876349947662</Real>
+ <Real>0.9102542460894858</Real>
+ <Real>0.97679321956799292</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.99394233469628879</Real>
+ <Real>0.97598141089179258</Real>
+ <Real>0.94674152324479255</Real>
+ <Real>0.90722432819348298</Real>
+ <Real>0.85875367175041695</Real>
+ <Real>0.80290421150777025</Real>
+ <Real>0.74141903744684357</Real>
+ <Real>0.67612212380676495</Real>
+ <Real>0.60883155879062278</Real>
+ <Real>0.54127911188492994</Real>
+ <Real>0.47504087184025068</Real>
+ <Real>0.41148252492562132</Real>
+ <Real>0.35172147384038532</Real>
+ <Real>0.296606565620393</Real>
+ <Real>0.24671484078000847</Real>
+ <Real>0.20236355564261158</Real>
+ <Real>0.16363485481098436</Real>
+ <Real>0.13040993308132204</Real>
+ <Real>0.1024093385705175</Real>
+ <Real>0.079236208884266926</Real>
+ <Real>0.060419654754816671</Real>
+ <Real>0.045456176328449546</Real>
+ <Real>0.0338479899109973</Real>
+ <Real>0.025138955077774604</Real>
+ <Real>0.018953401231942061</Real>
+ <Real>0.015057546528290352</Real>
+ <Real>0.013511057412693969</Real>
+ <Real>0.015136223367319493</Real>
+ <Real>0.015136223367319493</Real>
+ <Real>0.013511057412693969</Real>
+ <Real>0.015057546528290352</Real>
+ <Real>0.018953401231942061</Real>
+ <Real>0.025138955077774604</Real>
+ <Real>0.0338479899109973</Real>
+ <Real>0.045456176328449546</Real>
+ <Real>0.060419654754816671</Real>
+ <Real>0.079236208884266926</Real>
+ <Real>0.1024093385705175</Real>
+ <Real>0.13040993308132204</Real>
+ <Real>0.16363485481098436</Real>
+ <Real>0.20236355564261158</Real>
+ <Real>0.24671484078000847</Real>
+ <Real>0.296606565620393</Real>
+ <Real>0.35172147384038532</Real>
+ <Real>0.41148252492562132</Real>
+ <Real>0.47504087184025068</Real>
+ <Real>0.54127911188492994</Real>
+ <Real>0.60883155879062278</Real>
+ <Real>0.67612212380676495</Real>
+ <Real>0.74141903744684357</Real>
+ <Real>0.80290421150777025</Real>
+ <Real>0.85875367175041695</Real>
+ <Real>0.90722432819348298</Real>
+ <Real>0.94674152324479255</Real>
+ <Real>0.97598141089179258</Real>
+ <Real>0.99394233469628879</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.99720627237846593</Real>
+ <Real>0.98887028336224359</Real>
+ <Real>0.97512643851789638</Real>
+ <Real>0.95619486854349123</Real>
+ <Real>0.93237575431714581</Real>
+ <Real>0.90404166140062658</Real>
+ <Real>0.87162814883418571</Real>
+ <Real>0.83562297271034502</Real>
+ <Real>0.79655424707085953</Real>
+ <Real>0.75497795158484893</Real>
+ <Real>0.711465186436539</Real>
+ <Real>0.66658956985227713</Real>
+ <Real>0.62091515345733406</Real>
+ <Real>0.57498519660083891</Real>
+ <Real>0.52931209495227383</Real>
+ <Real>0.48436870356467054</Real>
+ <Real>0.44058123306096036</Real>
+ <Real>0.39832383264886684</Real>
+ <Real>0.35791490833811923</Real>
+ <Real>0.31961516191294181</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.25009714030836877</Real>
+ <Real>0.21911640244644226</Real>
+ <Real>0.19072623636552247</Real>
+ <Real>0.16492202533715164</Real>
+ <Real>0.141658787735681</Real>
+ <Real>0.12085710459189307</Real>
+ <Real>0.10240933857051719</Real>
+ <Real>0.086185950490232893</Real>
+ <Real>0.072041745806303639</Real>
+ <Real>0.059821916711369744</Real>
+ <Real>0.049367787310129883</Real>
+ <Real>0.040522226335123285</Real>
+ <Real>0.033134782570204697</Real>
+ <Real>0.027066768383207464</Real>
+ <Real>0.02219687507318183</Real>
+ <Real>0.018428701142637595</Real>
+ <Real>0.015703384014872881</Real>
+ <Real>0.014024643029010873</Real>
+ <Real>0.013512879057637064</Real>
+ <Real>0.014526046402321378</Real>
+ <Real>0.017932325748914145</Real>
+ <Real>0.014526046402321378</Real>
+ <Real>0.013512879057637064</Real>
+ <Real>0.014024643029010873</Real>
+ <Real>0.015703384014872881</Real>
+ <Real>0.018428701142637595</Real>
+ <Real>0.02219687507318183</Real>
+ <Real>0.027066768383207464</Real>
+ <Real>0.033134782570204697</Real>
+ <Real>0.040522226335123285</Real>
+ <Real>0.049367787310129883</Real>
+ <Real>0.059821916711369744</Real>
+ <Real>0.072041745806303639</Real>
+ <Real>0.086185950490232893</Real>
+ <Real>0.10240933857051719</Real>
+ <Real>0.12085710459189307</Real>
+ <Real>0.141658787735681</Real>
+ <Real>0.16492202533715164</Real>
+ <Real>0.19072623636552247</Real>
+ <Real>0.21911640244644226</Real>
+ <Real>0.25009714030836877</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.31961516191294181</Real>
+ <Real>0.35791490833811923</Real>
+ <Real>0.39832383264886684</Real>
+ <Real>0.44058123306096036</Real>
+ <Real>0.48436870356467054</Real>
+ <Real>0.52931209495227383</Real>
+ <Real>0.57498519660083891</Real>
+ <Real>0.62091515345733406</Real>
+ <Real>0.66658956985227713</Real>
+ <Real>0.711465186436539</Real>
+ <Real>0.75497795158484893</Real>
+ <Real>0.79655424707085953</Real>
+ <Real>0.83562297271034502</Real>
+ <Real>0.87162814883418571</Real>
+ <Real>0.90404166140062658</Real>
+ <Real>0.93237575431714581</Real>
+ <Real>0.95619486854349123</Real>
+ <Real>0.97512643851789638</Real>
+ <Real>0.98887028336224359</Real>
+ <Real>0.99720627237846593</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.97679321271960218</Real>
+ <Real>0.91025380713600412</Real>
+ <Real>0.80897377554073846</Real>
+ <Real>0.68528755848646272</Real>
+ <Real>0.55287384922299132</Real>
+ <Real>0.42435396506286321</Real>
+ <Real>0.30944933832540578</Real>
+ <Real>0.21403629922390921</Real>
+ <Real>0.14014625148844487</Real>
+ <Real>0.086709898455324869</Real>
+ <Real>0.05071060594404888</Real>
+ <Real>0.028417516579249732</Real>
+ <Real>0.016526844645414884</Real>
+ <Real>0.013844502036860955</Real>
+ <Real>0.013844502036860955</Real>
+ <Real>0.016526844645414884</Real>
+ <Real>0.028417516579249732</Real>
+ <Real>0.05071060594404888</Real>
+ <Real>0.086709898455324869</Real>
+ <Real>0.14014625148844487</Real>
+ <Real>0.21403629922390921</Real>
+ <Real>0.30944933832540578</Real>
+ <Real>0.42435396506286321</Real>
+ <Real>0.55287384922299132</Real>
+ <Real>0.68528755848646272</Real>
+ <Real>0.80897377554073846</Real>
+ <Real>0.91025380713600412</Real>
+ <Real>0.97679321271960218</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99679239409893372</Real>
+ <Real>0.98723120976317369</Real>
+ <Real>0.97149957212001192</Real>
+ <Real>0.94989683562649085</Real>
+ <Real>0.92283001932258024</Real>
+ <Real>0.89080224059919155</Real>
+ <Real>0.85439855271766807</Real>
+ <Real>0.81426968052735449</Real>
+ <Real>0.77111421951627979</Real>
+ <Real>0.72565991287731824</Real>
+ <Real>0.67864464786602108</Real>
+ <Real>0.63079781542967595</Real>
+ <Real>0.58282265587406412</Real>
+ <Real>0.53538016908987429</Real>
+ <Real>0.48907510234629203</Real>
+ <Real>0.44444444444444442</Real>
+ <Real>0.4019487553866824</Real>
+ <Real>0.36196654951998258</Real>
+ <Real>0.3247918316478754</Real>
+ <Real>0.29063476443848546</Real>
+ <Real>0.25962532624291201</Real>
+ <Real>0.23181970574878294</Real>
+ <Real>0.2072090780374837</Real>
+ <Real>0.18573031947264551</Real>
+ <Real>0.16727814972856847</Real>
+ <Real>0.15171814077470705</Real>
+ <Real>0.13890000656848678</Real>
+ <Real>0.12867058450534741</Real>
+ <Real>0.12088594035804859</Real>
+ <Real>0.11542207162696907</Real>
+ <Real>0.11218374816809194</Real>
+ <Real>0.11111111111111113</Real>
+ <Real>0.112183748168092</Real>
+ <Real>0.11542207162696905</Real>
+ <Real>0.12088594035804853</Real>
+ <Real>0.12867058450534735</Real>
+ <Real>0.13890000656848675</Real>
+ <Real>0.15171814077470702</Real>
+ <Real>0.1672781497285685</Real>
+ <Real>0.18573031947264537</Real>
+ <Real>0.20720907803748359</Real>
+ <Real>0.23181970574878286</Real>
+ <Real>0.2596253262429119</Real>
+ <Real>0.29063476443848507</Real>
+ <Real>0.32479183164787534</Real>
+ <Real>0.36196654951998264</Real>
+ <Real>0.40194875538668234</Real>
+ <Real>0.44444444444444425</Real>
+ <Real>0.48907510234629159</Real>
+ <Real>0.53538016908987418</Real>
+ <Real>0.58282265587406357</Real>
+ <Real>0.63079781542967606</Real>
+ <Real>0.67864464786602086</Real>
+ <Real>0.72565991287731779</Real>
+ <Real>0.77111421951627979</Real>
+ <Real>0.81426968052735449</Real>
+ <Real>0.85439855271766763</Real>
+ <Real>0.89080224059919133</Real>
+ <Real>0.92283001932258024</Real>
+ <Real>0.94989683562649074</Real>
+ <Real>0.9714995721200117</Real>
+ <Real>0.98723120976317369</Real>
+ <Real>0.99679239409893361</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.98723120976317369</Real>
+ <Real>0.94989683562649085</Real>
+ <Real>0.89080224059919155</Real>
+ <Real>0.81426968052735449</Real>
+ <Real>0.72565991287731824</Real>
+ <Real>0.63079781542967595</Real>
+ <Real>0.53538016908987429</Real>
+ <Real>0.44444444444444442</Real>
+ <Real>0.36196654951998258</Real>
+ <Real>0.29063476443848546</Real>
+ <Real>0.23181970574878294</Real>
+ <Real>0.18573031947264551</Real>
+ <Real>0.15171814077470705</Real>
+ <Real>0.12867058450534741</Real>
+ <Real>0.11542207162696907</Real>
+ <Real>0.11111111111111113</Real>
+ <Real>0.11542207162696905</Real>
+ <Real>0.12867058450534735</Real>
+ <Real>0.15171814077470702</Real>
+ <Real>0.18573031947264537</Real>
+ <Real>0.23181970574878286</Real>
+ <Real>0.29063476443848507</Real>
+ <Real>0.36196654951998264</Real>
+ <Real>0.44444444444444425</Real>
+ <Real>0.53538016908987418</Real>
+ <Real>0.63079781542967606</Real>
+ <Real>0.72565991287731779</Real>
+ <Real>0.81426968052735449</Real>
+ <Real>0.89080224059919133</Real>
+ <Real>0.94989683562649074</Real>
+ <Real>0.98723120976317369</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99679239409893372</Real>
+ <Real>0.98723120976317369</Real>
+ <Real>0.97149957212001192</Real>
+ <Real>0.94989683562649085</Real>
+ <Real>0.92283001932258024</Real>
+ <Real>0.89080224059919155</Real>
+ <Real>0.85439855271766807</Real>
+ <Real>0.81426968052735449</Real>
+ <Real>0.77111421951627979</Real>
+ <Real>0.72565991287731824</Real>
+ <Real>0.67864464786602108</Real>
+ <Real>0.63079781542967595</Real>
+ <Real>0.58282265587406412</Real>
+ <Real>0.53538016908987429</Real>
+ <Real>0.48907510234629203</Real>
+ <Real>0.44444444444444442</Real>
+ <Real>0.4019487553866824</Real>
+ <Real>0.36196654951998258</Real>
+ <Real>0.3247918316478754</Real>
+ <Real>0.29063476443848546</Real>
+ <Real>0.25962532624291201</Real>
+ <Real>0.23181970574878294</Real>
+ <Real>0.2072090780374837</Real>
+ <Real>0.18573031947264551</Real>
+ <Real>0.16727814972856847</Real>
+ <Real>0.15171814077470705</Real>
+ <Real>0.13890000656848678</Real>
+ <Real>0.12867058450534741</Real>
+ <Real>0.12088594035804859</Real>
+ <Real>0.11542207162696907</Real>
+ <Real>0.11218374816809194</Real>
+ <Real>0.11111111111111113</Real>
+ <Real>0.112183748168092</Real>
+ <Real>0.11542207162696905</Real>
+ <Real>0.12088594035804853</Real>
+ <Real>0.12867058450534735</Real>
+ <Real>0.13890000656848675</Real>
+ <Real>0.15171814077470702</Real>
+ <Real>0.1672781497285685</Real>
+ <Real>0.18573031947264537</Real>
+ <Real>0.20720907803748359</Real>
+ <Real>0.23181970574878286</Real>
+ <Real>0.2596253262429119</Real>
+ <Real>0.29063476443848507</Real>
+ <Real>0.32479183164787534</Real>
+ <Real>0.36196654951998264</Real>
+ <Real>0.40194875538668234</Real>
+ <Real>0.44444444444444425</Real>
+ <Real>0.48907510234629159</Real>
+ <Real>0.53538016908987418</Real>
+ <Real>0.58282265587406357</Real>
+ <Real>0.63079781542967606</Real>
+ <Real>0.67864464786602086</Real>
+ <Real>0.72565991287731779</Real>
+ <Real>0.77111421951627979</Real>
+ <Real>0.81426968052735449</Real>
+ <Real>0.85439855271766763</Real>
+ <Real>0.89080224059919133</Real>
+ <Real>0.92283001932258024</Real>
+ <Real>0.94989683562649074</Real>
+ <Real>0.9714995721200117</Real>
+ <Real>0.98723120976317369</Real>
+ <Real>0.99679239409893361</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99293629743143541</Real>
+ <Real>0.97203477780395642</Real>
+ <Real>0.93814505871719378</Real>
+ <Real>0.89262105791292667</Real>
+ <Real>0.83723362292112424</Real>
+ <Real>0.77405914830226275</Real>
+ <Real>0.70535366793118959</Real>
+ <Real>0.63342276382324902</Real>
+ <Real>0.56049743155528897</Real>
+ <Real>0.48862486224864865</Real>
+ <Real>0.41958113040177153</Real>
+ <Real>0.35481028404913162</Real>
+ <Real>0.29539162793120283</Real>
+ <Real>0.24203437918365034</Real>
+ <Real>0.19509662614010267</Real>
+ <Real>0.1546238325516216</Real>
+ <Real>0.12040111394787817</Real>
+ <Real>0.092013192235849639</Real>
+ <Real>0.068906250000000127</Real>
+ <Real>0.050446735243276537</Real>
+ <Real>0.035973348788724116</Real>
+ <Real>0.024839803791898197</Real>
+ <Real>0.016447311108468962</Real>
+ <Real>0.01026697222271509</Real>
+ <Real>0.0058532460907484716</Real>
+ <Real>0.0028503316368781138</Real>
+ <Real>0.00099364786527341895</Real>
+ <Real>0.0001086077931603231</Real>
+ <Real>0.00010860779316032216</Real>
+ <Real>0.00099364786527340876</Real>
+ <Real>0.0028503316368781902</Real>
+ <Real>0.0058532460907484637</Real>
+ <Real>0.010266972222715005</Real>
+ <Real>0.016447311108468771</Real>
+ <Real>0.024839803791897968</Real>
+ <Real>0.035973348788724345</Real>
+ <Real>0.050446735243276218</Real>
+ <Real>0.068906249999999725</Real>
+ <Real>0.092013192235849153</Real>
+ <Real>0.12040111394787807</Real>
+ <Real>0.15462383255162196</Real>
+ <Real>0.19509662614010334</Real>
+ <Real>0.24203437918365009</Real>
+ <Real>0.29539162793120266</Real>
+ <Real>0.35481028404913062</Real>
+ <Real>0.41958113040177086</Real>
+ <Real>0.48862486224864954</Real>
+ <Real>0.56049743155528831</Real>
+ <Real>0.63342276382324869</Real>
+ <Real>0.70535366793118925</Real>
+ <Real>0.77405914830226319</Real>
+ <Real>0.83723362292112458</Real>
+ <Real>0.8926210579129269</Real>
+ <Real>0.93814505871719367</Real>
+ <Real>0.97203477780395642</Real>
+ <Real>0.99293629743143519</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99674141050890508</Real>
+ <Real>0.98702741098370728</Real>
+ <Real>0.97104141608284489</Real>
+ <Real>0.94908288808508878</Real>
+ <Real>0.92155826424873033</Real>
+ <Real>0.88896878196077733</Real>
+ <Real>0.85189569598331061</Real>
+ <Real>0.81098347908176738</Real>
+ <Real>0.76692166484224311</Real>
+ <Real>0.72042602682911738</Real>
+ <Real>0.67221979054407921</Real>
+ <Real>0.62301554493158862</Real>
+ <Real>0.57349846118404957</Real>
+ <Real>0.5243113425925926</Real>
+ <Real>0.4760419256162659</Real>
+ <Real>0.42921273546095995</Real>
+ <Real>0.38427367591921779</Real>
+ <Real>0.34159740964749719</Real>
+ <Real>0.30147746765616906</Real>
+ <Real>0.26412892101138158</Real>
+ <Real>0.22969135802469134</Real>
+ <Real>0.19823383975668096</Real>
+ <Real>0.1697614574053431</Real>
+ <Real>0.14422308770631728</Real>
+ <Real>0.12151993623309564</Real>
+ <Real>0.10151447176686693</Real>
+ <Real>0.084039385146186182</Real>
+ <Real>0.068906250000000127</Real>
+ <Real>0.055913616910146603</Real>
+ <Real>0.04485433308308312</Real>
+ <Real>0.035521942845509483</Real>
+ <Real>0.027716086784539334</Real>
+ <Real>0.021246876110046373</Real>
+ <Real>0.015938271321125595</Real>
+ <Real>0.011630538584590228</Real>
+ <Real>0.0081818920534518398</Real>
+ <Real>0.0054694549226529986</Real>
+ <Real>0.0033896861326249278</Real>
+ <Real>0.0018584235604375595</Real>
+ <Real>0.00081068895897857336</Real>
+ <Real>0.00020038581963129673</Real>
+ <Real>0.00020038581963129518</Real>
+ <Real>0.00020038581963129364</Real>
+ <Real>0.00081068895897857271</Real>
+ <Real>0.0018584235604375034</Real>
+ <Real>0.003389686132624822</Real>
+ <Real>0.0054694549226530897</Real>
+ <Real>0.0081818920534518346</Real>
+ <Real>0.011630538584590056</Real>
+ <Real>0.015938271321125658</Real>
+ <Real>0.021246876110046411</Real>
+ <Real>0.027716086784539323</Real>
+ <Real>0.035521942845509608</Real>
+ <Real>0.044854333083083259</Real>
+ <Real>0.055913616910146548</Real>
+ <Real>0.068906249999999725</Real>
+ <Real>0.084039385146186127</Real>
+ <Real>0.10151447176686712</Real>
+ <Real>0.12151993623309497</Real>
+ <Real>0.14422308770631762</Real>
+ <Real>0.16976145740534321</Real>
+ <Real>0.19823383975668116</Real>
+ <Real>0.22969135802469126</Real>
+ <Real>0.26412892101138163</Real>
+ <Real>0.30147746765616856</Real>
+ <Real>0.3415974096474968</Real>
+ <Real>0.38427367591921813</Real>
+ <Real>0.42921273546096006</Real>
+ <Real>0.47604192561626668</Real>
+ <Real>0.52431134259259149</Real>
+ <Real>0.5734984611840499</Real>
+ <Real>0.62301554493158839</Real>
+ <Real>0.67221979054407854</Real>
+ <Real>0.72042602682911738</Real>
+ <Real>0.76692166484224344</Real>
+ <Real>0.81098347908176716</Real>
+ <Real>0.85189569598331061</Real>
+ <Real>0.88896878196077711</Real>
+ <Real>0.92155826424873044</Real>
+ <Real>0.94908288808508867</Real>
+ <Real>0.97104141608284467</Real>
+ <Real>0.98702741098370717</Real>
+ <Real>0.99674141050890508</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.97297811546027457</Real>
+ <Real>0.89609952702199769</Real>
+ <Real>0.78089025164742498</Real>
+ <Real>0.64345222053817641</Real>
+ <Real>0.50086041897423228</Real>
+ <Real>0.36780213122533956</Real>
+ <Real>0.25433397578287836</Real>
+ <Real>0.16515116321224893</Real>
+ <Real>0.10023011466040034</Real>
+ <Real>0.056328260625575277</Real>
+ <Real>0.028709139040944638</Real>
+ <Real>0.012586618383384689</Real>
+ <Real>0.0040410309448576029</Real>
+ <Real>0.00042206334646079926</Real>
+ <Real>0.00042206334646079877</Real>
+ <Real>0.004041030944857589</Real>
+ <Real>0.012586618383384688</Real>
+ <Real>0.028709139040944513</Real>
+ <Real>0.056328260625575576</Real>
+ <Real>0.10023011466040069</Real>
+ <Real>0.16515116321224854</Real>
+ <Real>0.25433397578287764</Real>
+ <Real>0.36780213122533884</Real>
+ <Real>0.50086041897423261</Real>
+ <Real>0.6434522205381773</Real>
+ <Real>0.78089025164742532</Real>
+ <Real>0.89609952702199769</Real>
+ <Real>0.97297811546027435</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.99293629743168654</Real>
+ <Real>0.97203477786767201</Real>
+ <Real>0.93814506032243061</Real>
+ <Real>0.89262107356599829</Real>
+ <Real>0.8372337133624983</Real>
+ <Real>0.7740595225726723</Real>
+ <Real>0.70535489520651073</Real>
+ <Real>0.63342615067862673</Real>
+ <Real>0.56050560842274966</Real>
+ <Real>0.48864259492939621</Real>
+ <Real>0.41961632697852747</Real>
+ <Real>0.35487510938368044</Real>
+ <Real>0.29550357667902794</Real>
+ <Real>0.24221710707749461</Real>
+ <Real>0.19538031305624226</Real>
+ <Real>0.15504486355218705</Real>
+ <Real>0.12100092637404439</Real>
+ <Real>0.092836252208210415</Real>
+ <Real>0.069997287104629088</Real>
+ <Real>0.051847569248538034</Real>
+ <Real>0.03771987195092983</Real>
+ <Real>0.026959926212416486</Real>
+ <Real>0.018960962681762932</Real>
+ <Real>0.01318979364150431</Real>
+ <Real>0.0092074161121755982</Real>
+ <Real>0.0066936075825058403</Real>
+ <Real>0.0055105467586834996</Real>
+ <Real>0.0059466765207910549</Real>
+ <Real>0.0059466765207910549</Real>
+ <Real>0.0055105467586834996</Real>
+ <Real>0.0066936075825058403</Real>
+ <Real>0.0092074161121755982</Real>
+ <Real>0.01318979364150431</Real>
+ <Real>0.018960962681762932</Real>
+ <Real>0.026959926212416486</Real>
+ <Real>0.03771987195092983</Real>
+ <Real>0.051847569248538034</Real>
+ <Real>0.069997287104629088</Real>
+ <Real>0.092836252208210415</Real>
+ <Real>0.12100092637404439</Real>
+ <Real>0.15504486355218705</Real>
+ <Real>0.19538031305624226</Real>
+ <Real>0.24221710707749461</Real>
+ <Real>0.29550357667902794</Real>
+ <Real>0.35487510938368044</Real>
+ <Real>0.41961632697852747</Real>
+ <Real>0.48864259492939621</Real>
+ <Real>0.56050560842274966</Real>
+ <Real>0.63342615067862673</Real>
+ <Real>0.70535489520651073</Real>
+ <Real>0.7740595225726723</Real>
+ <Real>0.8372337133624983</Real>
+ <Real>0.89262107356599829</Real>
+ <Real>0.93814506032243061</Real>
+ <Real>0.97203477786767201</Real>
+ <Real>0.99293629743168654</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.99674141050891507</Real>
+ <Real>0.9870274109865933</Real>
+ <Real>0.97104141615621542</Real>
+ <Real>0.94908288880993164</Real>
+ <Real>0.9215582685081537</Real>
+ <Real>0.88896879995906597</Real>
+ <Real>0.85189575649289284</Real>
+ <Real>0.81098365101084746</Real>
+ <Real>0.76692209409240086</Real>
+ <Real>0.72042699386112352</Real>
+ <Real>0.67222179390131365</Real>
+ <Real>0.62301941503640845</Real>
+ <Real>0.57350550693962055</Real>
+ <Real>0.52432353069059301</Real>
+ <Real>0.47606208906480318</Real>
+ <Real>0.42924480390382203</Real>
+ <Real>0.38432291611213432</Real>
+ <Real>0.34167066036902483</Real>
+ <Real>0.30158334980102902</Real>
+ <Real>0.26427800111314936</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.19850917766423412</Real>
+ <Real>0.17012383379813972</Real>
+ <Real>0.1446907932352707</Real>
+ <Real>0.12211260860350447</Real>
+ <Real>0.10225261380805185</Real>
+ <Real>0.084943777029759818</Real>
+ <Real>0.069997287104629269</Real>
+ <Real>0.057210619972190936</Real>
+ <Real>0.046374893040217122</Real>
+ <Real>0.03728137891452072</Real>
+ <Real>0.029727113355527277</Real>
+ <Real>0.023519594837572814</Real>
+ <Real>0.018480638640988686</Real>
+ <Real>0.014449532808924836</Real>
+ <Real>0.011285793500657533</Real>
+ <Real>0.0088721624647573345</Real>
+ <Real>0.0071193751787466692</Real>
+ <Real>0.0059765660173935206</Real>
+ <Real>0.0054573457400799311</Real>
+ <Real>0.0057077485219992341</Real>
+ <Real>0.007184257576382103</Real>
+ <Real>0.0057077485219992341</Real>
+ <Real>0.0054573457400799311</Real>
+ <Real>0.0059765660173935206</Real>
+ <Real>0.0071193751787466692</Real>
+ <Real>0.0088721624647573345</Real>
+ <Real>0.011285793500657533</Real>
+ <Real>0.014449532808924836</Real>
+ <Real>0.018480638640988686</Real>
+ <Real>0.023519594837572814</Real>
+ <Real>0.029727113355527277</Real>
+ <Real>0.03728137891452072</Real>
+ <Real>0.046374893040217122</Real>
+ <Real>0.057210619972190936</Real>
+ <Real>0.069997287104629269</Real>
+ <Real>0.084943777029759818</Real>
+ <Real>0.10225261380805185</Real>
+ <Real>0.12211260860350447</Real>
+ <Real>0.1446907932352707</Real>
+ <Real>0.17012383379813972</Real>
+ <Real>0.19850917766423412</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.26427800111314936</Real>
+ <Real>0.30158334980102902</Real>
+ <Real>0.34167066036902483</Real>
+ <Real>0.38432291611213432</Real>
+ <Real>0.42924480390382203</Real>
+ <Real>0.47606208906480318</Real>
+ <Real>0.52432353069059301</Real>
+ <Real>0.57350550693962055</Real>
+ <Real>0.62301941503640845</Real>
+ <Real>0.67222179390131365</Real>
+ <Real>0.72042699386112352</Real>
+ <Real>0.76692209409240086</Real>
+ <Real>0.81098365101084746</Real>
+ <Real>0.85189575649289284</Real>
+ <Real>0.88896879995906597</Real>
+ <Real>0.9215582685081537</Real>
+ <Real>0.94908288880993164</Real>
+ <Real>0.97104141615621542</Real>
+ <Real>0.9870274109865933</Real>
+ <Real>0.99674141050891507</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.97297811551573965</Real>
+ <Real>0.89609954066760555</Real>
+ <Real>0.78089057870742196</Real>
+ <Real>0.64345519050916622</Real>
+ <Real>0.5008760414411888</Real>
+ <Real>0.36785958159082133</Real>
+ <Real>0.25449710346867382</Real>
+ <Real>0.16553035204390604</Real>
+ <Real>0.10097905569026178</Real>
+ <Real>0.057617856941626314</Real>
+ <Real>0.030684806374171453</Real>
+ <Real>0.015338183773234699</Real>
+ <Real>0.0076532954239202228</Real>
+ <Real>0.0054817471316373021</Real>
+ <Real>0.0054817471316373021</Real>
+ <Real>0.0076532954239202228</Real>
+ <Real>0.015338183773234699</Real>
+ <Real>0.030684806374171453</Real>
+ <Real>0.057617856941626314</Real>
+ <Real>0.10097905569026178</Real>
+ <Real>0.16553035204390604</Real>
+ <Real>0.25449710346867382</Real>
+ <Real>0.36785958159082133</Real>
+ <Real>0.5008760414411888</Real>
+ <Real>0.64345519050916622</Real>
+ <Real>0.78089057870742196</Real>
+ <Real>0.89609954066760555</Real>
+ <Real>0.97297811551573965</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99193127844649409</Real>
+ <Real>0.96810410408333403</Real>
+ <Real>0.92962665398015176</Real>
+ <Real>0.87825288461282425</Real>
+ <Real>0.8162530500090498</Real>
+ <Real>0.7462511581756055</Real>
+ <Real>0.67104521835376052</Real>
+ <Real>0.59342703817645626</Real>
+ <Real>0.5160172836875867</Real>
+ <Real>0.44112876699547454</Real>
+ <Real>0.37066694386142046</Real>
+ <Real>0.3060719875940312</Real>
+ <Real>0.24830219075902438</Real>
+ <Real>0.19785440413602559</Real>
+ <Real>0.1548141842976353</Real>
+ <Real>0.11892653039631937</Real>
+ <Real>0.089677589925257761</Real>
+ <Real>0.066378365077993856</Real>
+ <Real>0.0482429846938775</Real>
+ <Real>0.034456177152976754</Real>
+ <Real>0.024226831981760157</Real>
+ <Real>0.016826660985003003</Real>
+ <Real>0.011614733348713855</Real>
+ <Real>0.0080499320349045177</Real>
+ <Real>0.0056941260851402367</Real>
+ <Real>0.0042091187954661864</Real>
+ <Real>0.0033503095195367158</Real>
+ <Real>0.0029596118817922222</Real>
+ <Real>0.0029596118817922196</Real>
+ <Real>0.0033503095195367241</Real>
+ <Real>0.0042091187954661994</Real>
+ <Real>0.0056941260851402307</Real>
+ <Real>0.0080499320349044796</Real>
+ <Real>0.011614733348713791</Real>
+ <Real>0.016826660985002902</Real>
+ <Real>0.024226831981760174</Real>
+ <Real>0.034456177152976636</Real>
+ <Real>0.048242984693877611</Real>
+ <Real>0.06637836507799369</Real>
+ <Real>0.0896775899252579</Real>
+ <Real>0.11892653039631947</Real>
+ <Real>0.15481418429763574</Real>
+ <Real>0.19785440413602556</Real>
+ <Real>0.24830219075902377</Real>
+ <Real>0.30607198759403043</Real>
+ <Real>0.37066694386141941</Real>
+ <Real>0.44112876699547565</Real>
+ <Real>0.51601728368758537</Real>
+ <Real>0.59342703817645603</Real>
+ <Real>0.67104521835376074</Real>
+ <Real>0.74625115817560594</Real>
+ <Real>0.81625305000905002</Real>
+ <Real>0.87825288461282414</Real>
+ <Real>0.92962665398015132</Real>
+ <Real>0.96810410408333403</Real>
+ <Real>0.99193127844649376</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99627676534133136</Real>
+ <Real>0.98518797301387973</Real>
+ <Real>0.96697350687603367</Real>
+ <Real>0.94202380662007779</Real>
+ <Real>0.91086628854960949</Real>
+ <Real>0.87414724744706795</Real>
+ <Real>0.83261008676316861</Real>
+ <Real>0.78707087800851039</Real>
+ <Real>0.73839234623961181</Real>
+ <Real>0.68745741286369988</Real>
+ <Real>0.63514339972072009</Real>
+ <Real>0.58229791360658945</Real>
+ <Real>0.52971729570097492</Real>
+ <Real>0.47812834624590589</Real>
+ <Real>0.42817383377522444</Real>
+ <Real>0.38040208372436973</Real>
+ <Real>0.33526072687671404</Real>
+ <Real>0.293094486419747</Real>
+ <Real>0.25414670424212998</Real>
+ <Real>0.21856416098060585</Real>
+ <Real>0.18640463592844536</Real>
+ <Real>0.1576465850096847</Real>
+ <Real>0.13220028750107038</Real>
+ <Real>0.10991982235054854</Real>
+ <Real>0.090615277957865767</Real>
+ <Real>0.074064668731352826</Real>
+ <Real>0.060025120244528413</Real>
+ <Real>0.048242984693877652</Real>
+ <Real>0.038462652173631234</Real>
+ <Real>0.030433924359437956</Real>
+ <Real>0.023917909986791643</Real>
+ <Real>0.018691481848758126</Real>
+ <Real>0.014550400217029913</Real>
+ <Real>0.011311256343814337</Real>
+ <Real>0.0088124220551732777</Real>
+ <Real>0.0069142084873060269</Real>
+ <Real>0.0054984406117524675</Real>
+ <Real>0.0044676466805511558</Real>
+ <Real>0.0037440456080141816</Real>
+ <Real>0.0032684930126888941</Real>
+ <Real>0.0029995202968429351</Real>
+ <Real>0.0029125724363819575</Real>
+ <Real>0.0029995202968429347</Real>
+ <Real>0.0032684930126888898</Real>
+ <Real>0.0037440456080141526</Real>
+ <Real>0.0044676466805511532</Real>
+ <Real>0.0054984406117524901</Real>
+ <Real>0.0069142084873060356</Real>
+ <Real>0.0088124220551732673</Real>
+ <Real>0.011311256343814337</Real>
+ <Real>0.014550400217030076</Real>
+ <Real>0.018691481848758091</Real>
+ <Real>0.023917909986791695</Real>
+ <Real>0.030433924359437974</Real>
+ <Real>0.038462652173631193</Real>
+ <Real>0.048242984693877278</Real>
+ <Real>0.060025120244528156</Real>
+ <Real>0.074064668731353075</Real>
+ <Real>0.090615277957865462</Real>
+ <Real>0.10991982235054876</Real>
+ <Real>0.1322002875010703</Real>
+ <Real>0.15764658500968512</Real>
+ <Real>0.18640463592844567</Real>
+ <Real>0.21856416098060552</Real>
+ <Real>0.25414670424212982</Real>
+ <Real>0.29309448641974739</Real>
+ <Real>0.33526072687671399</Real>
+ <Real>0.38040208372436929</Real>
+ <Real>0.42817383377522528</Real>
+ <Real>0.47812834624590517</Real>
+ <Real>0.52971729570097448</Real>
+ <Real>0.58229791360658956</Real>
+ <Real>0.63514339972071954</Real>
+ <Real>0.6874574128636991</Real>
+ <Real>0.73839234623961159</Real>
+ <Real>0.78707087800851072</Real>
+ <Real>0.83261008676316894</Real>
+ <Real>0.87414724744706784</Real>
+ <Real>0.91086628854960949</Real>
+ <Real>0.9420238066200779</Real>
+ <Real>0.96697350687603367</Real>
+ <Real>0.98518797301387928</Real>
+ <Real>0.99627676534133158</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.96917791908558748</Real>
+ <Real>0.88216537239769921</Real>
+ <Real>0.75378233627323288</Real>
+ <Real>0.6041770102709294</Real>
+ <Real>0.45377217342940634</Real>
+ <Real>0.31890105676761415</Real>
+ <Real>0.20935022433017264</Real>
+ <Real>0.12813776789921963</Real>
+ <Real>0.073018671122717774</Real>
+ <Real>0.038769336070128772</Real>
+ <Real>0.019343447783351012</Real>
+ <Real>0.0093556684327434619</Real>
+ <Real>0.0047848541871871432</Real>
+ <Real>0.0030965032198494846</Real>
+ <Real>0.0030965032198494854</Real>
+ <Real>0.004784854187187138</Real>
+ <Real>0.0093556684327433959</Real>
+ <Real>0.019343447783350964</Real>
+ <Real>0.038769336070129043</Real>
+ <Real>0.073018671122718204</Real>
+ <Real>0.12813776789921927</Real>
+ <Real>0.20935022433017228</Real>
+ <Real>0.3189010567676136</Real>
+ <Real>0.45377217342940562</Real>
+ <Real>0.60417701027092974</Real>
+ <Real>0.75378233627323299</Real>
+ <Real>0.88216537239769943</Real>
+ <Real>0.96917791908558759</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">57</Int>
+ <Real>1</Real>
+ <Real>0.9919312784464579</Real>
+ <Real>0.96810410407400227</Real>
+ <Real>0.92962665373789177</Real>
+ <Real>0.87825288215462305</Real>
+ <Real>0.81625303510994751</Real>
+ <Real>0.74625109309937454</Real>
+ <Real>0.67104499215886504</Real>
+ <Real>0.59342637479853322</Real>
+ <Real>0.51601557976094403</Real>
+ <Real>0.44112483623292992</Real>
+ <Real>0.37065865400702902</Real>
+ <Real>0.30605579558399515</Real>
+ <Real>0.24827261141223606</Real>
+ <Real>0.1978034837607025</Real>
+ <Real>0.15473108602317279</Real>
+ <Real>0.11879736361383499</Real>
+ <Real>0.089485622848125321</Real>
+ <Real>0.066104741182465745</Real>
+ <Real>0.047868021041824929</Real>
+ <Real>0.03396126438376966</Real>
+ <Real>0.023596900712822586</Real>
+ <Real>0.016053155268528081</Real>
+ <Real>0.010699078328354525</Real>
+ <Real>0.0070076840823060605</Real>
+ <Real>0.0045606884104341452</Real>
+ <Real>0.0030508666701079268</Real>
+ <Real>0.0022996596630090486</Real>
+ <Real>0.0023683132890026382</Real>
+ <Real>0.0023683132890026382</Real>
+ <Real>0.0022996596630090486</Real>
+ <Real>0.0030508666701079268</Real>
+ <Real>0.0045606884104341452</Real>
+ <Real>0.0070076840823060605</Real>
+ <Real>0.010699078328354525</Real>
+ <Real>0.016053155268528081</Real>
+ <Real>0.023596900712822586</Real>
+ <Real>0.03396126438376966</Real>
+ <Real>0.047868021041824929</Real>
+ <Real>0.066104741182465745</Real>
+ <Real>0.089485622848125321</Real>
+ <Real>0.11879736361383499</Real>
+ <Real>0.15473108602317279</Real>
+ <Real>0.1978034837607025</Real>
+ <Real>0.24827261141223606</Real>
+ <Real>0.30605579558399515</Real>
+ <Real>0.37065865400702902</Real>
+ <Real>0.44112483623292992</Real>
+ <Real>0.51601557976094403</Real>
+ <Real>0.59342637479853322</Real>
+ <Real>0.67104499215886504</Real>
+ <Real>0.74625109309937454</Real>
+ <Real>0.81625303510994751</Real>
+ <Real>0.87825288215462305</Real>
+ <Real>0.92962665373789177</Real>
+ <Real>0.96810410407400227</Real>
+ <Real>0.9919312784464579</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">84</Int>
+ <Real>1</Real>
+ <Real>0.9962767653413287</Real>
+ <Real>0.98518797301346384</Real>
+ <Real>0.96697350686527894</Real>
+ <Real>0.94202380651173623</Real>
+ <Real>0.91086628789736601</Real>
+ <Real>0.87414724461158877</Real>
+ <Real>0.83261007691987088</Real>
+ <Real>0.787070849041003</Real>
+ <Real>0.73839227114940331</Real>
+ <Real>0.68745723689264115</Real>
+ <Real>0.63514301999540812</Real>
+ <Real>0.58229714886548378</Real>
+ <Real>0.52971584366150437</Real>
+ <Real>0.47812572651811547</Real>
+ <Real>0.42816931502090799</Real>
+ <Real>0.38039459504912959</Real>
+ <Real>0.33524875522378467</Real>
+ <Real>0.29307596393494545</Real>
+ <Real>0.25411889204827737</Real>
+ <Real>0.21852353831426113</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.1575662097981721</Real>
+ <Real>0.13209106727404829</Real>
+ <Real>0.1097745310797878</Real>
+ <Real>0.090425868886316554</Real>
+ <Real>0.073822459118630945</Real>
+ <Real>0.059721061668809007</Real>
+ <Real>0.047868021041824728</Real>
+ <Real>0.038008163362592905</Real>
+ <Real>0.029892250579570376</Real>
+ <Real>0.023282949794115493</Real>
+ <Real>0.017959358953134743</Real>
+ <Real>0.013720199916616887</Real>
+ <Real>0.01038584637701591</Real>
+ <Real>0.0077994023793495834</Real>
+ <Real>0.0058271051667861881</Real>
+ <Real>0.0043584494641990641</Real>
+ <Real>0.0033067900681457208</Real>
+ <Real>0.0026122974912873775</Real>
+ <Real>0.0022525975538414582</Real>
+ <Real>0.0022769636247049127</Real>
+ <Real>0.0029116688417632187</Real>
+ <Real>0.0022769636247049127</Real>
+ <Real>0.0022525975538414582</Real>
+ <Real>0.0026122974912873775</Real>
+ <Real>0.0033067900681457208</Real>
+ <Real>0.0043584494641990641</Real>
+ <Real>0.0058271051667861881</Real>
+ <Real>0.0077994023793495834</Real>
+ <Real>0.01038584637701591</Real>
+ <Real>0.013720199916616887</Real>
+ <Real>0.017959358953134743</Real>
+ <Real>0.023282949794115493</Real>
+ <Real>0.029892250579570376</Real>
+ <Real>0.038008163362592905</Real>
+ <Real>0.047868021041824728</Real>
+ <Real>0.059721061668809007</Real>
+ <Real>0.073822459118630945</Real>
+ <Real>0.090425868886316554</Real>
+ <Real>0.1097745310797878</Real>
+ <Real>0.13209106727404829</Real>
+ <Real>0.1575662097981721</Real>
+ <Real>0.18634680587273886</Real>
+ <Real>0.21852353831426113</Real>
+ <Real>0.25411889204827737</Real>
+ <Real>0.29307596393494545</Real>
+ <Real>0.33524875522378467</Real>
+ <Real>0.38039459504912959</Real>
+ <Real>0.42816931502090799</Real>
+ <Real>0.47812572651811547</Real>
+ <Real>0.52971584366150437</Real>
+ <Real>0.58229714886548378</Real>
+ <Real>0.63514301999540812</Real>
+ <Real>0.68745723689264115</Real>
+ <Real>0.73839227114940331</Real>
+ <Real>0.787070849041003</Real>
+ <Real>0.83261007691987088</Real>
+ <Real>0.87414724461158877</Real>
+ <Real>0.91086628789736601</Real>
+ <Real>0.94202380651173623</Real>
+ <Real>0.96697350686527894</Real>
+ <Real>0.98518797301346384</Real>
+ <Real>0.9962767653413287</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">29</Int>
+ <Real>1</Real>
+ <Real>0.96917791907747108</Real>
+ <Real>0.88216537026122621</Real>
+ <Real>0.75378227973535905</Real>
+ <Real>0.60417643346431482</Real>
+ <Real>0.45376874694186936</Real>
+ <Real>0.31888687751663913</Real>
+ <Real>0.20930533305661311</Real>
+ <Real>0.12802286870126137</Real>
+ <Real>0.072772488825568721</Real>
+ <Real>0.038317724135902481</Real>
+ <Real>0.018624855991253263</Real>
+ <Real>0.008362805329911337</Real>
+ <Real>0.0036266823497955996</Real>
+ <Real>0.0022103327659906773</Real>
+ <Real>0.0022103327659906773</Real>
+ <Real>0.0036266823497955996</Real>
+ <Real>0.008362805329911337</Real>
+ <Real>0.018624855991253263</Real>
+ <Real>0.038317724135902481</Real>
+ <Real>0.072772488825568721</Real>
+ <Real>0.12802286870126137</Real>
+ <Real>0.20930533305661311</Real>
+ <Real>0.31888687751663913</Real>
+ <Real>0.45376874694186936</Real>
+ <Real>0.60417643346431482</Real>
+ <Real>0.75378227973535905</Real>
+ <Real>0.88216537026122621</Real>
+ <Real>0.96917791907747108</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99679213699886537</Real>
+ <Real>0.98722714126407807</Real>
+ <Real>0.9714793508556292</Real>
+ <Real>0.94983455505992243</Real>
+ <Real>0.92268294451100652</Real>
+ <Real>0.8905094656677498</Real>
+ <Real>0.85388180727504404</Real>
+ <Real>0.81343631504757941</Real>
+ <Real>0.76986220016018247</Real>
+ <Real>0.72388447541602163</Real>
+ <Real>0.67624611751597763</Real>
+ <Real>0.62769001121533641</Real>
+ <Real>0.57894127734366008</Real>
+ <Real>0.53069061757903879</Real>
+ <Real>0.48357932090399453</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.39501963656238342</Real>
+ <Real>0.35450757605533195</Real>
+ <Real>0.31699884553256041</Real>
+ <Real>0.28276340257865784</Real>
+ <Real>0.25199972745538329</Real>
+ <Real>0.22484741790164994</Real>
+ <Real>0.20140635909365345</Real>
+ <Real>0.18176427632469225</Real>
+ <Real>0.16603606468681617</Real>
+ <Real>0.1544213105775194</Real>
+ <Real>0.147292091880976</Real>
+ <Real>0.14533378613132461</Real>
+ <Real>0.14978169836524</Real>
+ <Real>0.16283453532845385</Real>
+ <Real>0.18839912911864681</Real>
+ <Real>0.23346292694334683</Real>
+ <Real>0.18839912911864681</Real>
+ <Real>0.16283453532845385</Real>
+ <Real>0.14978169836524</Real>
+ <Real>0.14533378613132461</Real>
+ <Real>0.147292091880976</Real>
+ <Real>0.1544213105775194</Real>
+ <Real>0.16603606468681617</Real>
+ <Real>0.18176427632469225</Real>
+ <Real>0.20140635909365345</Real>
+ <Real>0.22484741790164994</Real>
+ <Real>0.25199972745538329</Real>
+ <Real>0.28276340257865784</Real>
+ <Real>0.31699884553256041</Real>
+ <Real>0.35450757605533195</Real>
+ <Real>0.39501963656238342</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.48357932090399453</Real>
+ <Real>0.53069061757903879</Real>
+ <Real>0.57894127734366008</Real>
+ <Real>0.62769001121533641</Real>
+ <Real>0.67624611751597763</Real>
+ <Real>0.72388447541602163</Real>
+ <Real>0.76986220016018247</Real>
+ <Real>0.81343631504757941</Real>
+ <Real>0.85388180727504404</Real>
+ <Real>0.8905094656677498</Real>
+ <Real>0.92268294451100652</Real>
+ <Real>0.94983455505992243</Real>
+ <Real>0.9714793508556292</Real>
+ <Real>0.98722714126407807</Real>
+ <Real>0.99679213699886537</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.98722714126407807</Real>
+ <Real>0.94983455505992243</Real>
+ <Real>0.8905094656677498</Real>
+ <Real>0.81343631504757941</Real>
+ <Real>0.72388447541602163</Real>
+ <Real>0.62769001121533641</Real>
+ <Real>0.53069061757903879</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.35450757605533195</Real>
+ <Real>0.28276340257865784</Real>
+ <Real>0.22484741790164994</Real>
+ <Real>0.18176427632469225</Real>
+ <Real>0.1544213105775194</Real>
+ <Real>0.14533378613132461</Real>
+ <Real>0.16283453532845385</Real>
+ <Real>0.23346292694334683</Real>
+ <Real>0.16283453532845385</Real>
+ <Real>0.14533378613132461</Real>
+ <Real>0.1544213105775194</Real>
+ <Real>0.18176427632469225</Real>
+ <Real>0.22484741790164994</Real>
+ <Real>0.28276340257865784</Real>
+ <Real>0.35450757605533195</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.53069061757903879</Real>
+ <Real>0.62769001121533641</Real>
+ <Real>0.72388447541602163</Real>
+ <Real>0.81343631504757941</Real>
+ <Real>0.8905094656677498</Real>
+ <Real>0.94983455505992243</Real>
+ <Real>0.98722714126407807</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99679213699886537</Real>
+ <Real>0.98722714126407807</Real>
+ <Real>0.9714793508556292</Real>
+ <Real>0.94983455505992243</Real>
+ <Real>0.92268294451100652</Real>
+ <Real>0.8905094656677498</Real>
+ <Real>0.85388180727504404</Real>
+ <Real>0.81343631504757941</Real>
+ <Real>0.76986220016018247</Real>
+ <Real>0.72388447541602163</Real>
+ <Real>0.67624611751597763</Real>
+ <Real>0.62769001121533641</Real>
+ <Real>0.57894127734366008</Real>
+ <Real>0.53069061757903879</Real>
+ <Real>0.48357932090399453</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.39501963656238342</Real>
+ <Real>0.35450757605533195</Real>
+ <Real>0.31699884553256041</Real>
+ <Real>0.28276340257865784</Real>
+ <Real>0.25199972745538329</Real>
+ <Real>0.22484741790164994</Real>
+ <Real>0.20140635909365345</Real>
+ <Real>0.18176427632469225</Real>
+ <Real>0.16603606468681617</Real>
+ <Real>0.1544213105775194</Real>
+ <Real>0.147292091880976</Real>
+ <Real>0.14533378613132461</Real>
+ <Real>0.14978169836524</Real>
+ <Real>0.16283453532845385</Real>
+ <Real>0.18839912911864681</Real>
+ <Real>0.23346292694334683</Real>
+ <Real>0.18839912911864681</Real>
+ <Real>0.16283453532845385</Real>
+ <Real>0.14978169836524</Real>
+ <Real>0.14533378613132461</Real>
+ <Real>0.147292091880976</Real>
+ <Real>0.1544213105775194</Real>
+ <Real>0.16603606468681617</Real>
+ <Real>0.18176427632469225</Real>
+ <Real>0.20140635909365345</Real>
+ <Real>0.22484741790164994</Real>
+ <Real>0.25199972745538329</Real>
+ <Real>0.28276340257865784</Real>
+ <Real>0.31699884553256041</Real>
+ <Real>0.35450757605533195</Real>
+ <Real>0.39501963656238342</Real>
+ <Real>0.43818656757996727</Real>
+ <Real>0.48357932090399453</Real>
+ <Real>0.53069061757903879</Real>
+ <Real>0.57894127734366008</Real>
+ <Real>0.62769001121533641</Real>
+ <Real>0.67624611751597763</Real>
+ <Real>0.72388447541602163</Real>
+ <Real>0.76986220016018247</Real>
+ <Real>0.81343631504757941</Real>
+ <Real>0.85388180727504404</Real>
+ <Real>0.8905094656677498</Real>
+ <Real>0.92268294451100652</Real>
+ <Real>0.94983455505992243</Real>
+ <Real>0.9714793508556292</Real>
+ <Real>0.98722714126407807</Real>
+ <Real>0.99679213699886537</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99599177923169246</Real>
+ <Real>0.9840594250875444</Real>
+ <Real>0.96447636376571355</Real>
+ <Real>0.93768682558188565</Real>
+ <Real>0.90428924676588729</Real>
+ <Real>0.86501423524055476</Real>
+ <Real>0.82069821242500096</Real>
+ <Real>0.77225403794614478</Real>
+ <Real>0.72064003918992392</Real>
+ <Real>0.6668288976714164</Real>
+ <Real>0.61177778997574395</Real>
+ <Real>0.55640104899164056</Real>
+ <Real>0.50154641292836599</Real>
+ <Real>0.44797568090291112</Real>
+ <Real>0.39635031326736697</Real>
+ <Real>0.34722222222222221</Real>
+ <Real>0.30102971333769502</Real>
+ <Real>0.25809827940786451</Real>
+ <Real>0.21864572963652307</Real>
+ <Real>0.18279097054930363</Real>
+ <Real>0.15056564664626138</Real>
+ <Real>0.12192780016169502</Real>
+ <Real>0.096776717168722937</Real>
+ <Real>0.074968184276077238</Real>
+ <Real>0.05632947566079672</Real>
+ <Real>0.04067351137077823</Real>
+ <Real>0.02781176105655182</Real>
+ <Real>0.017565599321614365</Real>
+ <Real>0.0097759381138420327</Real>
+ <Real>0.0043110590461244089</Real>
+ <Real>0.0010726386076899712</Real>
+ <Real>0.0010726386076899683</Real>
+ <Real>0.0010726386076899655</Real>
+ <Real>0.0043110590461243941</Real>
+ <Real>0.0097759381138420171</Real>
+ <Real>0.017565599321614323</Real>
+ <Real>0.027811761056551795</Real>
+ <Real>0.040673511370778202</Real>
+ <Real>0.056329475660796699</Real>
+ <Real>0.074968184276077002</Real>
+ <Real>0.096776717168722659</Real>
+ <Real>0.12192780016169497</Real>
+ <Real>0.15056564664626132</Real>
+ <Real>0.18279097054930318</Real>
+ <Real>0.21864572963652326</Real>
+ <Real>0.25809827940786451</Real>
+ <Real>0.30102971333769535</Real>
+ <Real>0.34722222222222199</Real>
+ <Real>0.39635031326736658</Real>
+ <Real>0.44797568090291079</Real>
+ <Real>0.50154641292836544</Real>
+ <Real>0.55640104899164067</Real>
+ <Real>0.61177778997574372</Real>
+ <Real>0.66682889767141607</Real>
+ <Real>0.72064003918992425</Real>
+ <Real>0.77225403794614522</Real>
+ <Real>0.82069821242500074</Real>
+ <Real>0.86501423524055443</Real>
+ <Real>0.90428924676588762</Real>
+ <Real>0.93768682558188543</Real>
+ <Real>0.96447636376571333</Real>
+ <Real>0.9840594250875444</Real>
+ <Real>0.99599177923169235</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.9840594250875444</Real>
+ <Real>0.93768682558188565</Real>
+ <Real>0.86501423524055476</Real>
+ <Real>0.77225403794614478</Real>
+ <Real>0.6668288976714164</Real>
+ <Real>0.55640104899164056</Real>
+ <Real>0.44797568090291112</Real>
+ <Real>0.34722222222222221</Real>
+ <Real>0.25809827940786451</Real>
+ <Real>0.18279097054930363</Real>
+ <Real>0.12192780016169502</Real>
+ <Real>0.074968184276077238</Real>
+ <Real>0.04067351137077823</Real>
+ <Real>0.017565599321614365</Real>
+ <Real>0.0043110590461244089</Real>
+ <Real>0.0043110590461244019</Real>
+ <Real>0.0043110590461243941</Real>
+ <Real>0.017565599321614323</Real>
+ <Real>0.040673511370778202</Real>
+ <Real>0.074968184276077002</Real>
+ <Real>0.12192780016169497</Real>
+ <Real>0.18279097054930318</Real>
+ <Real>0.25809827940786451</Real>
+ <Real>0.34722222222222199</Real>
+ <Real>0.44797568090291079</Real>
+ <Real>0.55640104899164067</Real>
+ <Real>0.66682889767141607</Real>
+ <Real>0.77225403794614522</Real>
+ <Real>0.86501423524055443</Real>
+ <Real>0.93768682558188543</Real>
+ <Real>0.9840594250875444</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999978</Real>
+ <Real>0.99599177923169246</Real>
+ <Real>0.9840594250875444</Real>
+ <Real>0.96447636376571355</Real>
+ <Real>0.93768682558188565</Real>
+ <Real>0.90428924676588729</Real>
+ <Real>0.86501423524055476</Real>
+ <Real>0.82069821242500096</Real>
+ <Real>0.77225403794614478</Real>
+ <Real>0.72064003918992392</Real>
+ <Real>0.6668288976714164</Real>
+ <Real>0.61177778997574395</Real>
+ <Real>0.55640104899164056</Real>
+ <Real>0.50154641292836599</Real>
+ <Real>0.44797568090291112</Real>
+ <Real>0.39635031326736697</Real>
+ <Real>0.34722222222222221</Real>
+ <Real>0.30102971333769502</Real>
+ <Real>0.25809827940786451</Real>
+ <Real>0.21864572963652307</Real>
+ <Real>0.18279097054930363</Real>
+ <Real>0.15056564664626138</Real>
+ <Real>0.12192780016169502</Real>
+ <Real>0.096776717168722937</Real>
+ <Real>0.074968184276077238</Real>
+ <Real>0.05632947566079672</Real>
+ <Real>0.04067351137077823</Real>
+ <Real>0.02781176105655182</Real>
+ <Real>0.017565599321614365</Real>
+ <Real>0.0097759381138420327</Real>
+ <Real>0.0043110590461244089</Real>
+ <Real>0.0010726386076899712</Real>
+ <Real>0.0010726386076899683</Real>
+ <Real>0.0010726386076899655</Real>
+ <Real>0.0043110590461243941</Real>
+ <Real>0.0097759381138420171</Real>
+ <Real>0.017565599321614323</Real>
+ <Real>0.027811761056551795</Real>
+ <Real>0.040673511370778202</Real>
+ <Real>0.056329475660796699</Real>
+ <Real>0.074968184276077002</Real>
+ <Real>0.096776717168722659</Real>
+ <Real>0.12192780016169497</Real>
+ <Real>0.15056564664626132</Real>
+ <Real>0.18279097054930318</Real>
+ <Real>0.21864572963652326</Real>
+ <Real>0.25809827940786451</Real>
+ <Real>0.30102971333769535</Real>
+ <Real>0.34722222222222199</Real>
+ <Real>0.39635031326736658</Real>
+ <Real>0.44797568090291079</Real>
+ <Real>0.50154641292836544</Real>
+ <Real>0.55640104899164067</Real>
+ <Real>0.61177778997574372</Real>
+ <Real>0.66682889767141607</Real>
+ <Real>0.72064003918992425</Real>
+ <Real>0.77225403794614522</Real>
+ <Real>0.82069821242500074</Real>
+ <Real>0.86501423524055443</Real>
+ <Real>0.90428924676588762</Real>
+ <Real>0.93768682558188543</Real>
+ <Real>0.96447636376571333</Real>
+ <Real>0.9840594250875444</Real>
+ <Real>0.99599177923169235</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99599177952708939</Real>
+ <Real>0.98405944386122601</Real>
+ <Real>0.96447657513014773</Real>
+ <Real>0.93768799390763358</Real>
+ <Real>0.90429361071025816</Real>
+ <Real>0.86502693413175713</Real>
+ <Real>0.82072927057868161</Real>
+ <Real>0.77232083699097831</Real>
+ <Real>0.72077012325834022</Real>
+ <Real>0.66706288046749973</Real>
+ <Real>0.61217207500421655</Real>
+ <Real>0.55703004225461283</Real>
+ <Real>0.50250390701447112</Real>
+ <Real>0.44937512408934693</Real>
+ <Real>0.39832374774258422</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.30460768763511636</Real>
+ <Real>0.26272595143111366</Real>
+ <Real>0.22449127839581315</Real>
+ <Real>0.19001697209284932</Real>
+ <Real>0.15932281325392275</Real>
+ <Real>0.13234975413966146</Real>
+ <Real>0.10897673699334089</Real>
+ <Real>0.08903906947532618</Real>
+ <Real>0.072348133312829188</Real>
+ <Real>0.058713055603409205</Real>
+ <Real>0.047967068542932936</Real>
+ <Real>0.040006441190879767</Real>
+ <Real>0.034862523812425897</Real>
+ <Real>0.032858315342583898</Real>
+ <Real>0.034975731876511651</Real>
+ <Real>0.043739722444097656</Real>
+ <Real>0.034975731876511651</Real>
+ <Real>0.032858315342583898</Real>
+ <Real>0.034862523812425897</Real>
+ <Real>0.040006441190879767</Real>
+ <Real>0.047967068542932936</Real>
+ <Real>0.058713055603409205</Real>
+ <Real>0.072348133312829188</Real>
+ <Real>0.08903906947532618</Real>
+ <Real>0.10897673699334089</Real>
+ <Real>0.13234975413966146</Real>
+ <Real>0.15932281325392275</Real>
+ <Real>0.19001697209284932</Real>
+ <Real>0.22449127839581315</Real>
+ <Real>0.26272595143111366</Real>
+ <Real>0.30460768763511636</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.39832374774258422</Real>
+ <Real>0.44937512408934693</Real>
+ <Real>0.50250390701447112</Real>
+ <Real>0.55703004225461283</Real>
+ <Real>0.61217207500421655</Real>
+ <Real>0.66706288046749973</Real>
+ <Real>0.72077012325834022</Real>
+ <Real>0.77232083699097831</Real>
+ <Real>0.82072927057868161</Real>
+ <Real>0.86502693413175713</Real>
+ <Real>0.90429361071025816</Real>
+ <Real>0.93768799390763358</Real>
+ <Real>0.96447657513014773</Real>
+ <Real>0.98405944386122601</Real>
+ <Real>0.99599177952708939</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.98405944386122601</Real>
+ <Real>0.93768799390763358</Real>
+ <Real>0.86502693413175713</Real>
+ <Real>0.77232083699097831</Real>
+ <Real>0.66706288046749973</Real>
+ <Real>0.55703004225461283</Real>
+ <Real>0.44937512408934693</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.26272595143111366</Real>
+ <Real>0.19001697209284932</Real>
+ <Real>0.13234975413966146</Real>
+ <Real>0.08903906947532618</Real>
+ <Real>0.058713055603409205</Real>
+ <Real>0.040006441190879767</Real>
+ <Real>0.032858315342583898</Real>
+ <Real>0.043739722444097656</Real>
+ <Real>0.032858315342583898</Real>
+ <Real>0.040006441190879767</Real>
+ <Real>0.058713055603409205</Real>
+ <Real>0.08903906947532618</Real>
+ <Real>0.13234975413966146</Real>
+ <Real>0.19001697209284932</Real>
+ <Real>0.26272595143111366</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.44937512408934693</Real>
+ <Real>0.55703004225461283</Real>
+ <Real>0.66706288046749973</Real>
+ <Real>0.77232083699097831</Real>
+ <Real>0.86502693413175713</Real>
+ <Real>0.93768799390763358</Real>
+ <Real>0.98405944386122601</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99599177952708939</Real>
+ <Real>0.98405944386122601</Real>
+ <Real>0.96447657513014773</Real>
+ <Real>0.93768799390763358</Real>
+ <Real>0.90429361071025816</Real>
+ <Real>0.86502693413175713</Real>
+ <Real>0.82072927057868161</Real>
+ <Real>0.77232083699097831</Real>
+ <Real>0.72077012325834022</Real>
+ <Real>0.66706288046749973</Real>
+ <Real>0.61217207500421655</Real>
+ <Real>0.55703004225461283</Real>
+ <Real>0.50250390701447112</Real>
+ <Real>0.44937512408934693</Real>
+ <Real>0.39832374774258422</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.30460768763511636</Real>
+ <Real>0.26272595143111366</Real>
+ <Real>0.22449127839581315</Real>
+ <Real>0.19001697209284932</Real>
+ <Real>0.15932281325392275</Real>
+ <Real>0.13234975413966146</Real>
+ <Real>0.10897673699334089</Real>
+ <Real>0.08903906947532618</Real>
+ <Real>0.072348133312829188</Real>
+ <Real>0.058713055603409205</Real>
+ <Real>0.047967068542932936</Real>
+ <Real>0.040006441190879767</Real>
+ <Real>0.034862523812425897</Real>
+ <Real>0.032858315342583898</Real>
+ <Real>0.034975731876511651</Real>
+ <Real>0.043739722444097656</Real>
+ <Real>0.034975731876511651</Real>
+ <Real>0.032858315342583898</Real>
+ <Real>0.034862523812425897</Real>
+ <Real>0.040006441190879767</Real>
+ <Real>0.047967068542932936</Real>
+ <Real>0.058713055603409205</Real>
+ <Real>0.072348133312829188</Real>
+ <Real>0.08903906947532618</Real>
+ <Real>0.10897673699334089</Real>
+ <Real>0.13234975413966146</Real>
+ <Real>0.15932281325392275</Real>
+ <Real>0.19001697209284932</Real>
+ <Real>0.22449127839581315</Real>
+ <Real>0.26272595143111366</Real>
+ <Real>0.30460768763511636</Real>
+ <Real>0.34991777955278341</Real>
+ <Real>0.39832374774258422</Real>
+ <Real>0.44937512408934693</Real>
+ <Real>0.50250390701447112</Real>
+ <Real>0.55703004225461283</Real>
+ <Real>0.61217207500421655</Real>
+ <Real>0.66706288046749973</Real>
+ <Real>0.72077012325834022</Real>
+ <Real>0.77232083699097831</Real>
+ <Real>0.82072927057868161</Real>
+ <Real>0.86502693413175713</Real>
+ <Real>0.90429361071025816</Real>
+ <Real>0.93768799390763358</Real>
+ <Real>0.96447657513014773</Real>
+ <Real>0.98405944386122601</Real>
+ <Real>0.99599177952708939</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99519206545587935</Real>
+ <Real>0.98090195914095746</Real>
+ <Real>0.95752482092227065</Real>
+ <Real>0.92569973735431099</Real>
+ <Real>0.88628175571309442</Real>
+ <Real>0.84030507487319939</Real>
+ <Real>0.78893956803574239</Real>
+ <Real>0.73344312125447653</Real>
+ <Real>0.67511242174423391</Real>
+ <Real>0.61523479682321514</Real>
+ <Real>0.55504349911147488</Real>
+ <Real>0.49567848103759116</Real>
+ <Real>0.43815423731549918</Real>
+ <Real>0.38333576031933869</Real>
+ <Real>0.33192309536911935</Real>
+ <Real>0.28444444444444456</Real>
+ <Real>0.24125728601051996</Real>
+ <Real>0.20255658537845778</Real>
+ <Real>0.16838888398780899</Real>
+ <Real>0.13867088585165055</Real>
+ <Real>0.11321110319069098</Real>
+ <Real>0.091733169806735446</Real>
+ <Real>0.073899561666448732</Real>
+ <Real>0.059334656523301256</Real>
+ <Real>0.047646293257735658</Real>
+ <Real>0.03844523250730239</Real>
+ <Real>0.031362151188981613</Real>
+ <Real>0.026062006867558715</Real>
+ <Real>0.022255770792402298</Real>
+ <Real>0.01970964337301654</Real>
+ <Real>0.018251930682543428</Real>
+ <Real>0.017777777777777778</Real>
+ <Real>0.018251930682543431</Real>
+ <Real>0.019709643373016533</Real>
+ <Real>0.022255770792402284</Real>
+ <Real>0.026062006867558708</Real>
+ <Real>0.031362151188981606</Real>
+ <Real>0.038445232507302342</Real>
+ <Real>0.047646293257735631</Real>
+ <Real>0.059334656523301228</Real>
+ <Real>0.073899561666448621</Real>
+ <Real>0.091733169806735404</Real>
+ <Real>0.11321110319069089</Real>
+ <Real>0.13867088585165038</Real>
+ <Real>0.16838888398780893</Real>
+ <Real>0.20255658537845753</Real>
+ <Real>0.24125728601052007</Real>
+ <Real>0.28444444444444444</Real>
+ <Real>0.33192309536911896</Real>
+ <Real>0.38333576031933875</Real>
+ <Real>0.43815423731549907</Real>
+ <Real>0.49567848103759121</Real>
+ <Real>0.55504349911147466</Real>
+ <Real>0.61523479682321447</Real>
+ <Real>0.67511242174423391</Real>
+ <Real>0.7334431212544763</Real>
+ <Real>0.78893956803574194</Real>
+ <Real>0.84030507487319928</Real>
+ <Real>0.88628175571309442</Real>
+ <Real>0.92569973735431066</Real>
+ <Real>0.9575248209222702</Real>
+ <Real>0.98090195914095757</Real>
+ <Real>0.99519206545587924</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.98090195914095746</Real>
+ <Real>0.92569973735431099</Real>
+ <Real>0.84030507487319939</Real>
+ <Real>0.73344312125447653</Real>
+ <Real>0.61523479682321514</Real>
+ <Real>0.49567848103759116</Real>
+ <Real>0.38333576031933869</Real>
+ <Real>0.28444444444444456</Real>
+ <Real>0.20255658537845778</Real>
+ <Real>0.13867088585165055</Real>
+ <Real>0.091733169806735446</Real>
+ <Real>0.059334656523301256</Real>
+ <Real>0.03844523250730239</Real>
+ <Real>0.026062006867558715</Real>
+ <Real>0.01970964337301654</Real>
+ <Real>0.017777777777777778</Real>
+ <Real>0.019709643373016533</Real>
+ <Real>0.026062006867558708</Real>
+ <Real>0.038445232507302342</Real>
+ <Real>0.059334656523301228</Real>
+ <Real>0.091733169806735404</Real>
+ <Real>0.13867088585165038</Real>
+ <Real>0.20255658537845753</Real>
+ <Real>0.28444444444444444</Real>
+ <Real>0.38333576031933875</Real>
+ <Real>0.49567848103759121</Real>
+ <Real>0.61523479682321447</Real>
+ <Real>0.7334431212544763</Real>
+ <Real>0.84030507487319928</Real>
+ <Real>0.92569973735431066</Real>
+ <Real>0.98090195914095757</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99519206545587935</Real>
+ <Real>0.98090195914095746</Real>
+ <Real>0.95752482092227065</Real>
+ <Real>0.92569973735431099</Real>
+ <Real>0.88628175571309442</Real>
+ <Real>0.84030507487319939</Real>
+ <Real>0.78893956803574239</Real>
+ <Real>0.73344312125447653</Real>
+ <Real>0.67511242174423391</Real>
+ <Real>0.61523479682321514</Real>
+ <Real>0.55504349911147488</Real>
+ <Real>0.49567848103759116</Real>
+ <Real>0.43815423731549918</Real>
+ <Real>0.38333576031933869</Real>
+ <Real>0.33192309536911935</Real>
+ <Real>0.28444444444444456</Real>
+ <Real>0.24125728601051996</Real>
+ <Real>0.20255658537845778</Real>
+ <Real>0.16838888398780899</Real>
+ <Real>0.13867088585165055</Real>
+ <Real>0.11321110319069098</Real>
+ <Real>0.091733169806735446</Real>
+ <Real>0.073899561666448732</Real>
+ <Real>0.059334656523301256</Real>
+ <Real>0.047646293257735658</Real>
+ <Real>0.03844523250730239</Real>
+ <Real>0.031362151188981613</Real>
+ <Real>0.026062006867558715</Real>
+ <Real>0.022255770792402298</Real>
+ <Real>0.01970964337301654</Real>
+ <Real>0.018251930682543428</Real>
+ <Real>0.017777777777777778</Real>
+ <Real>0.018251930682543431</Real>
+ <Real>0.019709643373016533</Real>
+ <Real>0.022255770792402284</Real>
+ <Real>0.026062006867558708</Real>
+ <Real>0.031362151188981606</Real>
+ <Real>0.038445232507302342</Real>
+ <Real>0.047646293257735631</Real>
+ <Real>0.059334656523301228</Real>
+ <Real>0.073899561666448621</Real>
+ <Real>0.091733169806735404</Real>
+ <Real>0.11321110319069089</Real>
+ <Real>0.13867088585165038</Real>
+ <Real>0.16838888398780893</Real>
+ <Real>0.20255658537845753</Real>
+ <Real>0.24125728601052007</Real>
+ <Real>0.28444444444444444</Real>
+ <Real>0.33192309536911896</Real>
+ <Real>0.38333576031933875</Real>
+ <Real>0.43815423731549907</Real>
+ <Real>0.49567848103759121</Real>
+ <Real>0.55504349911147466</Real>
+ <Real>0.61523479682321447</Real>
+ <Real>0.67511242174423391</Real>
+ <Real>0.7334431212544763</Real>
+ <Real>0.78893956803574194</Real>
+ <Real>0.84030507487319928</Real>
+ <Real>0.88628175571309442</Real>
+ <Real>0.92569973735431066</Real>
+ <Real>0.9575248209222702</Real>
+ <Real>0.98090195914095757</Real>
+ <Real>0.99519206545587924</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99519206539664795</Real>
+ <Real>0.98090195534776159</Real>
+ <Real>0.95752477767965549</Real>
+ <Real>0.92569949422153175</Real>
+ <Real>0.88628082812780185</Real>
+ <Real>0.84030230781068749</Real>
+ <Real>0.78893260887116534</Real>
+ <Real>0.7334276905744932</Real>
+ <Real>0.67508138110804994</Real>
+ <Real>0.61517704054824585</Real>
+ <Real>0.5549427315744101</Real>
+ <Real>0.4955119785320366</Real>
+ <Real>0.43789172953994737</Real>
+ <Real>0.38293859560014715</Real>
+ <Real>0.33134387031599155</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.24013890206896338</Real>
+ <Real>0.20106831932581998</Real>
+ <Real>0.16645969346411715</Real>
+ <Real>0.13623136708511188</Real>
+ <Real>0.11019846583152162</Real>
+ <Real>0.088097074458449012</Real>
+ <Real>0.069608709285530979</Real>
+ <Real>0.05438405768510373</Real>
+ <Real>0.042065295084498688</Real>
+ <Real>0.032306804602271443</Real>
+ <Real>0.024795128706184621</Real>
+ <Real>0.019271489544086841</Real>
+ <Real>0.015567297482519917</Real>
+ <Real>0.013683799764266789</Real>
+ <Real>0.014007804808888453</Real>
+ <Real>0.017932325748914145</Real>
+ <Real>0.014007804808888453</Real>
+ <Real>0.013683799764266789</Real>
+ <Real>0.015567297482519917</Real>
+ <Real>0.019271489544086841</Real>
+ <Real>0.024795128706184621</Real>
+ <Real>0.032306804602271443</Real>
+ <Real>0.042065295084498688</Real>
+ <Real>0.05438405768510373</Real>
+ <Real>0.069608709285530979</Real>
+ <Real>0.088097074458449012</Real>
+ <Real>0.11019846583152162</Real>
+ <Real>0.13623136708511188</Real>
+ <Real>0.16645969346411715</Real>
+ <Real>0.20106831932581998</Real>
+ <Real>0.24013890206896338</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.33134387031599155</Real>
+ <Real>0.38293859560014715</Real>
+ <Real>0.43789172953994737</Real>
+ <Real>0.4955119785320366</Real>
+ <Real>0.5549427315744101</Real>
+ <Real>0.61517704054824585</Real>
+ <Real>0.67508138110804994</Real>
+ <Real>0.7334276905744932</Real>
+ <Real>0.78893260887116534</Real>
+ <Real>0.84030230781068749</Real>
+ <Real>0.88628082812780185</Real>
+ <Real>0.92569949422153175</Real>
+ <Real>0.95752477767965549</Real>
+ <Real>0.98090195534776159</Real>
+ <Real>0.99519206539664795</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.98090195534776159</Real>
+ <Real>0.92569949422153175</Real>
+ <Real>0.84030230781068749</Real>
+ <Real>0.7334276905744932</Real>
+ <Real>0.61517704054824585</Real>
+ <Real>0.4955119785320366</Real>
+ <Real>0.38293859560014715</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.20106831932581998</Real>
+ <Real>0.13623136708511188</Real>
+ <Real>0.088097074458449012</Real>
+ <Real>0.05438405768510373</Real>
+ <Real>0.032306804602271443</Real>
+ <Real>0.019271489544086841</Real>
+ <Real>0.013683799764266789</Real>
+ <Real>0.017932325748914145</Real>
+ <Real>0.013683799764266789</Real>
+ <Real>0.019271489544086841</Real>
+ <Real>0.032306804602271443</Real>
+ <Real>0.05438405768510373</Real>
+ <Real>0.088097074458449012</Real>
+ <Real>0.13623136708511188</Real>
+ <Real>0.20106831932581998</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.38293859560014715</Real>
+ <Real>0.4955119785320366</Real>
+ <Real>0.61517704054824585</Real>
+ <Real>0.7334276905744932</Real>
+ <Real>0.84030230781068749</Real>
+ <Real>0.92569949422153175</Real>
+ <Real>0.98090195534776159</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.99519206539664795</Real>
+ <Real>0.98090195534776159</Real>
+ <Real>0.95752477767965549</Real>
+ <Real>0.92569949422153175</Real>
+ <Real>0.88628082812780185</Real>
+ <Real>0.84030230781068749</Real>
+ <Real>0.78893260887116534</Real>
+ <Real>0.7334276905744932</Real>
+ <Real>0.67508138110804994</Real>
+ <Real>0.61517704054824585</Real>
+ <Real>0.5549427315744101</Real>
+ <Real>0.4955119785320366</Real>
+ <Real>0.43789172953994737</Real>
+ <Real>0.38293859560014715</Real>
+ <Real>0.33134387031599155</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.24013890206896338</Real>
+ <Real>0.20106831932581998</Real>
+ <Real>0.16645969346411715</Real>
+ <Real>0.13623136708511188</Real>
+ <Real>0.11019846583152162</Real>
+ <Real>0.088097074458449012</Real>
+ <Real>0.069608709285530979</Real>
+ <Real>0.05438405768510373</Real>
+ <Real>0.042065295084498688</Real>
+ <Real>0.032306804602271443</Real>
+ <Real>0.024795128706184621</Real>
+ <Real>0.019271489544086841</Real>
+ <Real>0.015567297482519917</Real>
+ <Real>0.013683799764266789</Real>
+ <Real>0.014007804808888453</Real>
+ <Real>0.017932325748914145</Real>
+ <Real>0.014007804808888453</Real>
+ <Real>0.013683799764266789</Real>
+ <Real>0.015567297482519917</Real>
+ <Real>0.019271489544086841</Real>
+ <Real>0.024795128706184621</Real>
+ <Real>0.032306804602271443</Real>
+ <Real>0.042065295084498688</Real>
+ <Real>0.05438405768510373</Real>
+ <Real>0.069608709285530979</Real>
+ <Real>0.088097074458449012</Real>
+ <Real>0.11019846583152162</Real>
+ <Real>0.13623136708511188</Real>
+ <Real>0.16645969346411715</Real>
+ <Real>0.20106831932581998</Real>
+ <Real>0.24013890206896338</Real>
+ <Real>0.28362727851290037</Real>
+ <Real>0.33134387031599155</Real>
+ <Real>0.38293859560014715</Real>
+ <Real>0.43789172953994737</Real>
+ <Real>0.4955119785320366</Real>
+ <Real>0.5549427315744101</Real>
+ <Real>0.61517704054824585</Real>
+ <Real>0.67508138110804994</Real>
+ <Real>0.7334276905744932</Real>
+ <Real>0.78893260887116534</Real>
+ <Real>0.84030230781068749</Real>
+ <Real>0.88628082812780185</Real>
+ <Real>0.92569949422153175</Real>
+ <Real>0.95752477767965549</Real>
+ <Real>0.98090195534776159</Real>
+ <Real>0.99519206539664795</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99439299338254172</Real>
+ <Real>0.97775459804016207</Real>
+ <Real>0.95062308706588539</Real>
+ <Real>0.91386426325293835</Real>
+ <Real>0.86862680875708975</Real>
+ <Real>0.81628422030148851</Real>
+ <Real>0.75836730630936389</Real>
+ <Real>0.69649174294903782</Real>
+ <Real>0.6322853339762925</Real>
+ <Real>0.56731939718573354</Real>
+ <Real>0.50304814581753765</Real>
+ <Real>0.4407591133040894</Real>
+ <Real>0.38153667201800334</Real>
+ <Real>0.32623961953760694</Real>
+ <Real>0.27549274763416898</Real>
+ <Real>0.22969135802469134</Real>
+ <Real>0.18901691535672854</Real>
+ <Real>0.1534614791515895</Real>
+ <Real>0.12285825431769751</Real>
+ <Real>0.096915541336904859</Real>
+ <Real>0.075251527682212882</Real>
+ <Real>0.057427700224227017</Real>
+ <Real>0.042979122601058753</Real>
+ <Real>0.031440355816394101</Real>
+ <Real>0.022366350281397697</Real>
+ <Real>0.015348154926586595</Real>
+ <Real>0.010023735161529325</Real>
+ <Real>0.0060845388961903949</Real>
+ <Real>0.0032786827602900564</Real>
+ <Real>0.001411744212852303</Real>
+ <Real>0.00034614403869458372</Real>
+ <Real>0.0003461440386945796</Real>
+ <Real>0.00034614403869457548</Real>
+ <Real>0.0014117442128522993</Real>
+ <Real>0.0032786827602900586</Real>
+ <Real>0.0060845388961903845</Real>
+ <Real>0.010023735161529325</Real>
+ <Real>0.015348154926586557</Real>
+ <Real>0.022366350281397676</Real>
+ <Real>0.031440355816394171</Real>
+ <Real>0.042979122601058718</Real>
+ <Real>0.057427700224226982</Real>
+ <Real>0.075251527682212813</Real>
+ <Real>0.096915541336904776</Real>
+ <Real>0.12285825431769723</Real>
+ <Real>0.15346147915158917</Real>
+ <Real>0.18901691535672849</Real>
+ <Real>0.22969135802469109</Real>
+ <Real>0.27549274763416887</Real>
+ <Real>0.32623961953760716</Real>
+ <Real>0.38153667201800379</Real>
+ <Real>0.44075911330408957</Real>
+ <Real>0.50304814581753743</Real>
+ <Real>0.56731939718573332</Real>
+ <Real>0.63228533397629227</Real>
+ <Real>0.69649174294903737</Real>
+ <Real>0.75836730630936322</Real>
+ <Real>0.81628422030148906</Real>
+ <Real>0.86862680875708931</Real>
+ <Real>0.91386426325293857</Real>
+ <Real>0.95062308706588561</Real>
+ <Real>0.97775459804016185</Real>
+ <Real>0.99439299338254172</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.97775459804016207</Real>
+ <Real>0.91386426325293835</Real>
+ <Real>0.81628422030148851</Real>
+ <Real>0.69649174294903782</Real>
+ <Real>0.56731939718573354</Real>
+ <Real>0.4407591133040894</Real>
+ <Real>0.32623961953760694</Real>
+ <Real>0.22969135802469134</Real>
+ <Real>0.1534614791515895</Real>
+ <Real>0.096915541336904859</Real>
+ <Real>0.057427700224227017</Real>
+ <Real>0.031440355816394101</Real>
+ <Real>0.015348154926586595</Real>
+ <Real>0.0060845388961903949</Real>
+ <Real>0.001411744212852303</Real>
+ <Real>0.0014117442128523013</Real>
+ <Real>0.0014117442128522993</Real>
+ <Real>0.0060845388961903845</Real>
+ <Real>0.015348154926586557</Real>
+ <Real>0.031440355816394171</Real>
+ <Real>0.057427700224226982</Real>
+ <Real>0.096915541336904776</Real>
+ <Real>0.15346147915158917</Real>
+ <Real>0.22969135802469109</Real>
+ <Real>0.32623961953760716</Real>
+ <Real>0.44075911330408957</Real>
+ <Real>0.56731939718573332</Real>
+ <Real>0.69649174294903737</Real>
+ <Real>0.81628422030148906</Real>
+ <Real>0.91386426325293857</Real>
+ <Real>0.97775459804016185</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>0.99999999999999956</Real>
+ <Real>0.99439299338254172</Real>
+ <Real>0.97775459804016207</Real>
+ <Real>0.95062308706588539</Real>
+ <Real>0.91386426325293835</Real>
+ <Real>0.86862680875708975</Real>
+ <Real>0.81628422030148851</Real>
+ <Real>0.75836730630936389</Real>
+ <Real>0.69649174294903782</Real>
+ <Real>0.6322853339762925</Real>
+ <Real>0.56731939718573354</Real>
+ <Real>0.50304814581753765</Real>
+ <Real>0.4407591133040894</Real>
+ <Real>0.38153667201800334</Real>
+ <Real>0.32623961953760694</Real>
+ <Real>0.27549274763416898</Real>
+ <Real>0.22969135802469134</Real>
+ <Real>0.18901691535672854</Real>
+ <Real>0.1534614791515895</Real>
+ <Real>0.12285825431769751</Real>
+ <Real>0.096915541336904859</Real>
+ <Real>0.075251527682212882</Real>
+ <Real>0.057427700224227017</Real>
+ <Real>0.042979122601058753</Real>
+ <Real>0.031440355816394101</Real>
+ <Real>0.022366350281397697</Real>
+ <Real>0.015348154926586595</Real>
+ <Real>0.010023735161529325</Real>
+ <Real>0.0060845388961903949</Real>
+ <Real>0.0032786827602900564</Real>
+ <Real>0.001411744212852303</Real>
+ <Real>0.00034614403869458372</Real>
+ <Real>0.0003461440386945796</Real>
+ <Real>0.00034614403869457548</Real>
+ <Real>0.0014117442128522993</Real>
+ <Real>0.0032786827602900586</Real>
+ <Real>0.0060845388961903845</Real>
+ <Real>0.010023735161529325</Real>
+ <Real>0.015348154926586557</Real>
+ <Real>0.022366350281397676</Real>
+ <Real>0.031440355816394171</Real>
+ <Real>0.042979122601058718</Real>
+ <Real>0.057427700224226982</Real>
+ <Real>0.075251527682212813</Real>
+ <Real>0.096915541336904776</Real>
+ <Real>0.12285825431769723</Real>
+ <Real>0.15346147915158917</Real>
+ <Real>0.18901691535672849</Real>
+ <Real>0.22969135802469109</Real>
+ <Real>0.27549274763416887</Real>
+ <Real>0.32623961953760716</Real>
+ <Real>0.38153667201800379</Real>
+ <Real>0.44075911330408957</Real>
+ <Real>0.50304814581753743</Real>
+ <Real>0.56731939718573332</Real>
+ <Real>0.63228533397629227</Real>
+ <Real>0.69649174294903737</Real>
+ <Real>0.75836730630936322</Real>
+ <Real>0.81628422030148906</Real>
+ <Real>0.86862680875708931</Real>
+ <Real>0.91386426325293857</Real>
+ <Real>0.95062308706588561</Real>
+ <Real>0.97775459804016185</Real>
+ <Real>0.99439299338254172</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="X">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.9943929933826412</Real>
+ <Real>0.97775459806545628</Real>
+ <Real>0.95062308770542614</Real>
+ <Real>0.91386426952058264</Real>
+ <Real>0.86862684520717015</Real>
+ <Real>0.81628437236115869</Real>
+ <Real>0.75836780976663731</Real>
+ <Real>0.69649314812801999</Real>
+ <Real>0.63228877105049019</Real>
+ <Real>0.56732696252619141</Real>
+ <Real>0.50306341536533861</Real>
+ <Real>0.44078776809104703</Real>
+ <Real>0.38158719500517224</Real>
+ <Real>0.32632399523249089</Real>
+ <Real>0.27562707102208034</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.18931758530084425</Real>
+ <Real>0.15388744802462673</Real>
+ <Real>0.12344252180808435</Real>
+ <Real>0.097693301009772776</Real>
+ <Real>0.076258450968699501</Real>
+ <Real>0.058697954219134638</Real>
+ <Real>0.044543380510381522</Real>
+ <Real>0.033324165671369955</Real>
+ <Real>0.024589341948346485</Real>
+ <Real>0.017924720035043865</Real>
+ <Real>0.012966158129245784</Real>
+ <Real>0.0094106738097037273</Real>
+ <Real>0.0070303430050181626</Real>
+ <Real>0.0057049431829982985</Real>
+ <Real>0.0055285593395392749</Real>
+ <Real>0.007184257576382103</Real>
+ <Real>0.0055285593395392749</Real>
+ <Real>0.0057049431829982985</Real>
+ <Real>0.0070303430050181626</Real>
+ <Real>0.0094106738097037273</Real>
+ <Real>0.012966158129245784</Real>
+ <Real>0.017924720035043865</Real>
+ <Real>0.024589341948346485</Real>
+ <Real>0.033324165671369955</Real>
+ <Real>0.044543380510381522</Real>
+ <Real>0.058697954219134638</Real>
+ <Real>0.076258450968699501</Real>
+ <Real>0.097693301009772776</Real>
+ <Real>0.12344252180808435</Real>
+ <Real>0.15388744802462673</Real>
+ <Real>0.18931758530084425</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.27562707102208034</Real>
+ <Real>0.32632399523249089</Real>
+ <Real>0.38158719500517224</Real>
+ <Real>0.44078776809104703</Real>
+ <Real>0.50306341536533861</Real>
+ <Real>0.56732696252619141</Real>
+ <Real>0.63228877105049019</Real>
+ <Real>0.69649314812801999</Real>
+ <Real>0.75836780976663731</Real>
+ <Real>0.81628437236115869</Real>
+ <Real>0.86862684520717015</Real>
+ <Real>0.91386426952058264</Real>
+ <Real>0.95062308770542614</Real>
+ <Real>0.97775459806545628</Real>
+ <Real>0.9943929933826412</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">32</Int>
+ <Real>1</Real>
+ <Real>0.97775459806545628</Real>
+ <Real>0.91386426952058264</Real>
+ <Real>0.81628437236115869</Real>
+ <Real>0.69649314812801999</Real>
+ <Real>0.56732696252619141</Real>
+ <Real>0.44078776809104703</Real>
+ <Real>0.32632399523249089</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.15388744802462673</Real>
+ <Real>0.097693301009772776</Real>
+ <Real>0.058697954219134638</Real>
+ <Real>0.033324165671369955</Real>
+ <Real>0.017924720035043865</Real>
+ <Real>0.0094106738097037273</Real>
+ <Real>0.0057049431829982985</Real>
+ <Real>0.007184257576382103</Real>
+ <Real>0.0057049431829982985</Real>
+ <Real>0.0094106738097037273</Real>
+ <Real>0.017924720035043865</Real>
+ <Real>0.033324165671369955</Real>
+ <Real>0.058697954219134638</Real>
+ <Real>0.097693301009772776</Real>
+ <Real>0.15388744802462673</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.32632399523249089</Real>
+ <Real>0.44078776809104703</Real>
+ <Real>0.56732696252619141</Real>
+ <Real>0.69649314812801999</Real>
+ <Real>0.81628437236115869</Real>
+ <Real>0.91386426952058264</Real>
+ <Real>0.97775459806545628</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">64</Int>
+ <Real>1</Real>
+ <Real>0.9943929933826412</Real>
+ <Real>0.97775459806545628</Real>
+ <Real>0.95062308770542614</Real>
+ <Real>0.91386426952058264</Real>
+ <Real>0.86862684520717015</Real>
+ <Real>0.81628437236115869</Real>
+ <Real>0.75836780976663731</Real>
+ <Real>0.69649314812801999</Real>
+ <Real>0.63228877105049019</Real>
+ <Real>0.56732696252619141</Real>
+ <Real>0.50306341536533861</Real>
+ <Real>0.44078776809104703</Real>
+ <Real>0.38158719500517224</Real>
+ <Real>0.32632399523249089</Real>
+ <Real>0.27562707102208034</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.18931758530084425</Real>
+ <Real>0.15388744802462673</Real>
+ <Real>0.12344252180808435</Real>
+ <Real>0.097693301009772776</Real>
+ <Real>0.076258450968699501</Real>
+ <Real>0.058697954219134638</Real>
+ <Real>0.044543380510381522</Real>
+ <Real>0.033324165671369955</Real>
+ <Real>0.024589341948346485</Real>
+ <Real>0.017924720035043865</Real>
+ <Real>0.012966158129245784</Real>
+ <Real>0.0094106738097037273</Real>
+ <Real>0.0070303430050181626</Real>
+ <Real>0.0057049431829982985</Real>
+ <Real>0.0055285593395392749</Real>
+ <Real>0.007184257576382103</Real>
+ <Real>0.0055285593395392749</Real>
+ <Real>0.0057049431829982985</Real>
+ <Real>0.0070303430050181626</Real>
+ <Real>0.0094106738097037273</Real>
+ <Real>0.012966158129245784</Real>
+ <Real>0.017924720035043865</Real>
+ <Real>0.024589341948346485</Real>
+ <Real>0.033324165671369955</Real>
+ <Real>0.044543380510381522</Real>
+ <Real>0.058697954219134638</Real>
+ <Real>0.076258450968699501</Real>
+ <Real>0.097693301009772776</Real>
+ <Real>0.12344252180808435</Real>
+ <Real>0.15388744802462673</Real>
+ <Real>0.18931758530084425</Real>
+ <Real>0.22989624244423834</Real>
+ <Real>0.27562707102208034</Real>
+ <Real>0.32632399523249089</Real>
+ <Real>0.38158719500517224</Real>
+ <Real>0.44078776809104703</Real>
+ <Real>0.50306341536533861</Real>
+ <Real>0.56732696252619141</Real>
+ <Real>0.63228877105049019</Real>
+ <Real>0.69649314812801999</Real>
+ <Real>0.75836780976663731</Real>
+ <Real>0.81628437236115869</Real>
+ <Real>0.86862684520717015</Real>
+ <Real>0.91386426952058264</Real>
+ <Real>0.95062308770542614</Real>
+ <Real>0.97775459806545628</Real>
+ <Real>0.9943929933826412</Real>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>0.33619974975590594</Real>
+ <Real>0.64760019531240687</Real>
+ <Real>0.016200054931687191</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>0.013564033407368874</Real>
+ <Real>0.63757793433500098</Real>
+ <Real>0.34885803225763012</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>0.061250029206279422</Real>
+ <Real>0.72750002503394384</Real>
+ <Real>0.21124994575977674</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>-0.81999969482421875</Real>
+ <Real>0.6399993896484375</Real>
+ <Real>0.18000030517578125</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>-0.16470600114973877</Real>
+ <Real>-0.67058799770052246</Real>
+ <Real>0.83529399885026123</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>-0.35000008344650269</Real>
+ <Real>-0.29999983310699463</Real>
+ <Real>0.64999991655349731</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">11</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 11 4 6">0.0013826037132043639</Real>
+ <Real Name="Cell 11 4 7">0.016421938879093271</Real>
+ <Real Name="Cell 11 4 8">0.0047685684922374521</Real>
+ <Real Name="Cell 11 5 6">0.064989342992169435</Real>
+ <Real Name="Cell 11 5 7">0.77191389565730451</Real>
+ <Real Name="Cell 11 5 8">0.22414675323374061</Real>
+ <Real Name="Cell 11 6 6">0.035559659600847962</Real>
+ <Real Name="Cell 11 6 7">0.42236148431359816</Real>
+ <Real Name="Cell 11 6 8">0.12264445028452525</Real>
+ <Real Name="Cell 12 4 6">0.0026632215977581233</Real>
+ <Real Name="Cell 12 4 7">0.03163253641095963</Real>
+ <Real Name="Cell 12 4 8">0.0091853902008423947</Real>
+ <Real Name="Cell 12 5 6">0.12518483801820438</Real>
+ <Real Name="Cell 12 5 7">1.4868886427041421</Real>
+ <Real Name="Cell 12 5 8">0.43175963479509505</Real>
+ <Real Name="Cell 12 6 6">0.068496310658979945</Real>
+ <Real Name="Cell 12 6 7">0.81356806461786901</Real>
+ <Real Name="Cell 12 6 8">0.23624220427262857</Real>
+ <Real Name="Cell 13 4 6">6.6621870239128315e-05</Real>
+ <Real Name="Cell 13 4 7">0.00079130431274643503</Real>
+ <Real Name="Cell 13 4 8">0.0002297773022610718</Real>
+ <Real Name="Cell 13 5 6">0.0031315636826374821</Real>
+ <Real Name="Cell 13 5 7">0.037195290958009747</Real>
+ <Real Name="Cell 13 5 8">0.010800691308611372</Real>
+ <Real Name="Cell 13 6 6">0.0017134707545263879</Real>
+ <Real Name="Cell 13 6 7">0.020351827304681189</Real>
+ <Real Name="Cell 13 6 8">0.0059097213282235219</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>0.2619067689657868</Real>
+ <Real>0.69993609967218617</Real>
+ <Real>0.03815713136202703</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>0.011250025244333649</Real>
+ <Real>0.62750011780679593</Real>
+ <Real>0.36124985694887041</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>0.30031255081296182</Real>
+ <Real>0.67437496393918561</Real>
+ <Real>0.025312485247852567</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>-0.72374963760375977</Real>
+ <Real>0.44749927520751953</Real>
+ <Real>0.27625036239624023</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>-0.15000016829546325</Real>
+ <Real>-0.69999966340907349</Real>
+ <Real>0.84999983170453675</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>-0.77500006556510925</Real>
+ <Real>0.55000013113021851</Real>
+ <Real>0.22499993443489075</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">5</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 13 6 5">0.004380048151535948</Real>
+ <Real Name="Cell 13 6 6">0.0098357354904011641</Real>
+ <Real Name="Cell 13 6 7">0.00036918172057913309</Real>
+ <Real Name="Cell 13 7 5">0.24430885010436626</Real>
+ <Real Name="Cell 13 7 6">0.54861434040353418</Real>
+ <Real Name="Cell 13 7 7">0.02059209362860796</Real>
+ <Real Name="Cell 13 8 5">0.14064784156537652</Real>
+ <Real Name="Cell 13 8 6">0.31583556140764957</Real>
+ <Real Name="Cell 13 8 7">0.011854803953842074</Real>
+ <Real Name="Cell 14 6 5">0.011705515789715702</Real>
+ <Real Name="Cell 14 6 6">0.026285637304234787</Real>
+ <Real Name="Cell 14 6 7">0.00098662441827221674</Real>
+ <Real Name="Cell 14 7 5">0.6529063159867583</Real>
+ <Real Name="Cell 14 7 6">1.4661514216016331</Real>
+ <Real Name="Cell 14 7 7">0.055031604396506215</Real>
+ <Real Name="Cell 14 8 5">0.37587612584935198</Real>
+ <Real Name="Cell 14 8 6">0.8440587918455954</Real>
+ <Real Name="Cell 14 8 7">0.031681522683037484</Real>
+ <Real Name="Cell 15 6 5">0.00063812811463453717</Real>
+ <Real Name="Cell 15 6 6">0.0014329658321981548</Real>
+ <Real Name="Cell 15 6 7">5.3785992107891378e-05</Real>
+ <Real Name="Cell 15 7 5">0.035593294984887676</Real>
+ <Real Name="Cell 15 7 6">0.079927485404564111</Real>
+ <Real Name="Cell 15 7 7">0.0030000569466327744</Real>
+ <Real Name="Cell 15 8 5">0.02049094869746073</Real>
+ <Real Name="Cell 15 8 6">0.046014003582341645</Real>
+ <Real Name="Cell 15 8 7">0.0017271234093110433</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>0.021324316667810716</Real>
+ <Real>0.37703209201365662</Real>
+ <Real>0.52779403433509819</Real>
+ <Real>0.073826004296754302</Real>
+ <Real>2.3552686680204097e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>0.0016495581997036655</Real>
+ <Real>0.17394692978238177</Real>
+ <Real>0.59714209698097642</Real>
+ <Real>0.22333826404637869</Real>
+ <Real>0.0039231509905593431</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>0.028552316185848529</Real>
+ <Real>0.41157446110166374</Real>
+ <Real>0.50103294517195562</Real>
+ <Real>0.058837523817601385</Real>
+ <Real>2.7537229307044074e-06</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>-0.10084712538648778</Real>
+ <Real>-0.54387723433073287</Real>
+ <Real>0.39090683963196193</Real>
+ <Real>0.25320652527422582</Real>
+ <Real>0.00061099481103286458</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>-0.014792204869455098</Real>
+ <Real>-0.4300140093047109</Real>
+ <Real>-0.067266223023428329</Real>
+ <Real>0.48374329343880984</Real>
+ <Real>0.028329143758784502</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>-0.12552730045233818</Real>
+ <Real>-0.53337632601106966</Real>
+ <Real>0.44345671853734003</Real>
+ <Real>0.21532474276788161</Real>
+ <Real>0.00012216515818619025</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">12</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 3 1">5.4910402122506737e-09</Real>
+ <Real Name="Cell 0 3 2">7.9151964468814374e-08</Real>
+ <Real Name="Cell 0 3 3">9.6356177610738879e-08</Real>
+ <Real Name="Cell 0 3 4">1.1315341535473563e-08</Real>
+ <Real Name="Cell 0 3 5">5.2958237249379593e-13</Real>
+ <Real Name="Cell 0 4 1">5.790335778417459e-07</Real>
+ <Real Name="Cell 0 4 2">8.3466234826196632e-06</Real>
+ <Real Name="Cell 0 4 3">1.016081837183126e-05</Real>
+ <Real Name="Cell 0 4 4">1.1932097454265494e-06</Real>
+ <Real Name="Cell 0 4 5">5.5844787882424654e-11</Real>
+ <Real Name="Cell 0 5 1">1.9877633099209692e-06</Real>
+ <Real Name="Cell 0 5 2">2.8653108481751327e-05</Real>
+ <Real Name="Cell 0 5 3">3.4881054797511526e-05</Real>
+ <Real Name="Cell 0 5 4">4.096167551870835e-06</Real>
+ <Real Name="Cell 0 5 5">1.9170947014292434e-10</Real>
+ <Real Name="Cell 0 6 1">7.4344717817972915e-07</Real>
+ <Real Name="Cell 0 6 2">1.0716604205599626e-05</Real>
+ <Real Name="Cell 0 6 3">1.3045930384022172e-05</Real>
+ <Real Name="Cell 0 6 4">1.5320155033502546e-06</Real>
+ <Real Name="Cell 0 6 5">7.1701627601605536e-11</Real>
+ <Real Name="Cell 0 7 1">1.3059363320289248e-08</Real>
+ <Real Name="Cell 0 7 2">1.8824743974861345e-07</Real>
+ <Real Name="Cell 0 7 3">2.2916428999473404e-07</Real>
+ <Real Name="Cell 0 7 4">2.6911322899298214e-08</Real>
+ <Real Name="Cell 0 7 5">1.2595079152739433e-12</Real>
+ <Real Name="Cell 12 3 1">4.9715211649349404e-06</Real>
+ <Real Name="Cell 12 3 2">7.1663227984556779e-05</Real>
+ <Real Name="Cell 12 3 3">8.7239713760477178e-05</Real>
+ <Real Name="Cell 12 3 4">1.0244772895046167e-05</Real>
+ <Real Name="Cell 12 3 5">4.7947745266105399e-10</Real>
+ <Real Name="Cell 12 4 1">0.00052424997380748155</Real>
+ <Real Name="Cell 12 4 2">0.0075569316005024223</Real>
+ <Real Name="Cell 12 4 3">0.0091994816348128436</Real>
+ <Real Name="Cell 12 4 4">0.0010803176218524323</Real>
+ <Real Name="Cell 12 4 5">5.0561193175997469e-08</Real>
+ <Real Name="Cell 12 5 1">0.0017996967758687563</Real>
+ <Real Name="Cell 12 5 2">0.025942176664522407</Real>
+ <Real Name="Cell 12 5 3">0.031580883671949243</Real>
+ <Real Name="Cell 12 5 4">0.0037086203874108401</Real>
+ <Real Name="Cell 12 5 5">1.7357142754257098e-07</Real>
+ <Real Name="Cell 12 6 1">0.00067310805211108352</Real>
+ <Real Name="Cell 12 6 2">0.0097026833832877281</Real>
+ <Real Name="Cell 12 6 3">0.011811627034843718</Real>
+ <Real Name="Cell 12 6 4">0.0013870682430847487</Real>
+ <Real Name="Cell 12 6 5">6.4917783407664483e-08</Real>
+ <Real Name="Cell 12 7 1">1.1823789052308096e-05</Real>
+ <Real Name="Cell 12 7 2">0.00017043694724126757</Real>
+ <Real Name="Cell 12 7 3">0.00020748256685760699</Real>
+ <Real Name="Cell 12 7 4">2.4365185137739379e-05</Real>
+ <Real Name="Cell 12 7 5">1.1403431801897063e-09</Real>
+ <Real Name="Cell 13 3 1">8.7900731099864658e-05</Real>
+ <Real Name="Cell 13 3 2">0.0012670669446704962</Real>
+ <Real Name="Cell 13 3 3">0.001542472488013479</Real>
+ <Real Name="Cell 13 3 4">0.0001811363157373624</Real>
+ <Real Name="Cell 13 3 5">8.4775699904636615e-09</Real>
+ <Real Name="Cell 13 4 1">0.0092691863210373308</Real>
+ <Real Name="Cell 13 4 2">0.13361299097768722</Real>
+ <Real Name="Cell 13 4 3">0.1626546754227505</Real>
+ <Real Name="Cell 13 4 4">0.019100936238725361</Real>
+ <Real Name="Cell 13 4 5">8.9396498536476137e-07</Real>
+ <Real Name="Cell 13 5 1">0.031820172761751316</Real>
+ <Real Name="Cell 13 5 2">0.45867979225694588</Real>
+ <Real Name="Cell 13 5 3">0.55837693765112328</Real>
+ <Real Name="Cell 13 5 4">0.06557156906512783</Real>
+ <Real Name="Cell 13 5 5">3.0688907625798746e-06</Real>
+ <Real Name="Cell 13 6 1">0.011901124007493654</Real>
+ <Real Name="Cell 13 6 2">0.1715517111818754</Real>
+ <Real Name="Cell 13 6 3">0.20883963225675545</Real>
+ <Real Name="Cell 13 6 4">0.024524548645696</Real>
+ <Real Name="Cell 13 6 5">1.1478017358477941e-06</Real>
+ <Real Name="Cell 13 7 1">0.00020905466709042131</Real>
+ <Real Name="Cell 13 7 2">0.0030134704795393413</Real>
+ <Real Name="Cell 13 7 3">0.0036684686059259434</Real>
+ <Real Name="Cell 13 7 4">0.00043079723809621464</Real>
+ <Real Name="Cell 13 7 5">2.0162239266003734e-08</Real>
+ <Real Name="Cell 14 3 1">0.00012304915807146138</Real>
+ <Real Name="Cell 14 3 2">0.0017737226847948657</Real>
+ <Real Name="Cell 14 3 3">0.002159253269268236</Real>
+ <Real Name="Cell 14 3 4">0.00025356639095898442</Real>
+ <Real Name="Cell 14 3 5">1.1867453623716749e-08</Real>
+ <Real Name="Cell 14 4 1">0.012975609628494957</Real>
+ <Real Name="Cell 14 4 2">0.18704015133316099</Real>
+ <Real Name="Cell 14 4 3">0.22769458930230768</Real>
+ <Real Name="Cell 14 4 4">0.026738732353449569</Real>
+ <Real Name="Cell 14 4 5">1.2514303057334815e-06</Real>
+ <Real Name="Cell 14 5 1">0.044543946552316853</Real>
+ <Real Name="Cell 14 5 2">0.64208979328610949</Real>
+ <Real Name="Cell 14 5 3">0.78165233900537368</Real>
+ <Real Name="Cell 14 5 4">0.091791345372565211</Real>
+ <Real Name="Cell 14 5 5">4.2960328068229237e-06</Real>
+ <Real Name="Cell 14 6 1">0.016659967111791241</Real>
+ <Real Name="Cell 14 6 2">0.24014923837966554</Real>
+ <Real Name="Cell 14 6 3">0.29234729449465219</Real>
+ <Real Name="Cell 14 6 4">0.034331057605277847</Real>
+ <Real Name="Cell 14 6 5">1.6067674917125967e-06</Real>
+ <Real Name="Cell 14 7 1">0.00029264831423484708</Real>
+ <Real Name="Cell 14 7 2">0.0042184518915917169</Real>
+ <Real Name="Cell 14 7 3">0.00513536085220877</Real>
+ <Real Name="Cell 14 7 4">0.00060305798124734504</Real>
+ <Real Name="Cell 14 7 5">2.8224413329378312e-08</Real>
+ <Real Name="Cell 15 3 1">1.721169070040701e-05</Real>
+ <Real Name="Cell 15 3 2">0.00024810219523204715</Real>
+ <Real Name="Cell 15 3 3">0.00030202888013995292</Real>
+ <Real Name="Cell 15 3 4">3.5467989879865154e-05</Real>
+ <Real Name="Cell 15 3 5">1.6599783726615397e-09</Real>
+ <Real Name="Cell 15 4 1">0.0018149834023665329</Real>
+ <Real Name="Cell 15 4 2">0.026162529543144672</Real>
+ <Real Name="Cell 15 4 3">0.031849131734420645</Real>
+ <Real Name="Cell 15 4 4">0.0037401214132750569</Real>
+ <Real Name="Cell 15 4 5">1.7504574344906493e-07</Real>
+ <Real Name="Cell 15 5 1">0.0062306532011270465</Real>
+ <Real Name="Cell 15 5 2">0.08981329979934205</Real>
+ <Real Name="Cell 15 5 3">0.10933482605705404</Real>
+ <Real Name="Cell 15 5 4">0.012839455956369107</Real>
+ <Real Name="Cell 15 5 5">6.0091421240684457e-07</Real>
+ <Real Name="Cell 15 6 1">0.0023303385858241682</Real>
+ <Real Name="Cell 15 6 2">0.033591244976488487</Real>
+ <Real Name="Cell 15 6 3">0.040892528553673785</Real>
+ <Real Name="Cell 15 6 4">0.0048021096135963202</Real>
+ <Real Name="Cell 15 6 5">2.2474908019090314e-07</Real>
+ <Real Name="Cell 15 7 1">4.0934634153940817e-05</Real>
+ <Real Name="Cell 15 7 2">0.00059006246227590465</Real>
+ <Real Name="Cell 15 7 3">0.00071831651681731961</Real>
+ <Real Name="Cell 15 7 4">8.4353664911816168e-05</Real>
+ <Real Name="Cell 15 7 5">3.9479333303815013e-09</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>0.0043033234951522009</Real>
+ <Real>0.22964313623763247</Real>
+ <Real>0.59616637285212148</Real>
+ <Real>0.16842109522125989</Real>
+ <Real>0.0014660721938338738</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>0.036170521700431418</Real>
+ <Real>0.44067912152529032</Real>
+ <Real>0.47538401613235459</Real>
+ <Real>0.047766279909607884</Real>
+ <Real>6.0732315723613201e-08</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>1.7640122565251958e-05</Real>
+ <Real>0.071139063318108806</Real>
+ <Real>0.5235408156117729</Real>
+ <Real>0.38287323863964373</Real>
+ <Real>0.022429242307909311</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>-0.030364083489944928</Real>
+ <Real>-0.48934445009998118</Real>
+ <Real>0.083321307620603857</Real>
+ <Real>0.42284706901851549</Real>
+ <Real>0.013540156950806738</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>-0.14989020738891354</Real>
+ <Real>-0.5155901329125363</Real>
+ <Real>0.48085787951917658</Real>
+ <Real>0.18461546925491013</Real>
+ <Real>6.9915273631839181e-06</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>-0.00049190742688337704</Real>
+ <Real>-0.24670823977340217</Real>
+ <Real>-0.40036645642627017</Real>
+ <Real>0.54282526188028035</Real>
+ <Real>0.10474134174627532</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">14</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 14 5 0">1.3591442370183604e-08</Real>
+ <Real Name="Cell 14 5 1">5.4811551097808827e-05</Real>
+ <Real Name="Cell 14 5 2">0.00040338012377776793</Real>
+ <Real Name="Cell 14 5 3">0.00029499792525857345</Real>
+ <Real Name="Cell 14 5 4">1.7281385268565402e-05</Real>
+ <Real Name="Cell 14 6 0">1.6558967364528452e-07</Real>
+ <Real Name="Cell 14 6 1">0.00066778982032025423</Real>
+ <Real Name="Cell 14 6 2">0.0049145323382225204</Real>
+ <Real Name="Cell 14 6 3">0.0035940710955568228</Real>
+ <Real Name="Cell 14 6 4">0.00021054564105998669</Real>
+ <Real Name="Cell 14 7 0">1.7863039168971306e-07</Real>
+ <Real Name="Cell 14 7 1">0.00072038041107406374</Real>
+ <Real Name="Cell 14 7 2">0.0053015675266623102</Real>
+ <Real Name="Cell 14 7 3">0.0038771157248323612</Real>
+ <Real Name="Cell 14 7 4">0.00022712678576607709</Real>
+ <Real Name="Cell 14 8 0">1.7948666762573985e-08</Real>
+ <Real Name="Cell 14 8 1">7.2383359955421496e-05</Real>
+ <Real Name="Cell 14 8 2">0.00053269809216247282</Real>
+ <Real Name="Cell 14 8 3">0.00038957009211416867</Real>
+ <Real Name="Cell 14 8 4">2.2821553219516418e-05</Real>
+ <Real Name="Cell 14 9 0">2.2820786938094924e-14</Real>
+ <Real Name="Cell 14 9 1">9.203163985697721e-11</Real>
+ <Real Name="Cell 14 9 2">6.7729764134448123e-10</Real>
+ <Real Name="Cell 14 9 3">4.9531790785314671e-10</Real>
+ <Real Name="Cell 14 9 4">2.9016406093456866e-11</Real>
+ <Real Name="Cell 15 5 0">7.2529556641467702e-07</Real>
+ <Real Name="Cell 15 5 1">0.0029249710160832052</Real>
+ <Real Name="Cell 15 5 2">0.021526031409120152</Real>
+ <Real Name="Cell 15 5 3">0.015742309128349063</Real>
+ <Real Name="Cell 15 5 4">0.00092220617763801591</Real>
+ <Real Name="Cell 15 6 0">8.836549710312734e-06</Real>
+ <Real Name="Cell 15 6 1">0.035636026168765732</Real>
+ <Real Name="Cell 15 6 2">0.26225976749413965</Real>
+ <Real Name="Cell 15 6 3">0.19179449538815141</Real>
+ <Real Name="Cell 15 6 4">0.011235586027554296</Real>
+ <Real Name="Cell 15 7 0">9.5324563494224515e-06</Real>
+ <Real Name="Cell 15 7 1">0.038442477557070545</Real>
+ <Real Name="Cell 15 7 2">0.28291356556620223</Real>
+ <Real Name="Cell 15 7 3">0.2068989272151511</Real>
+ <Real Name="Cell 15 7 4">0.012120424473236134</Real>
+ <Real Name="Cell 15 8 0">9.5781507741282704e-07</Real>
+ <Real Name="Cell 15 8 1">0.003862675397354143</Real>
+ <Real Name="Cell 15 8 2">0.028426972940751926</Real>
+ <Real Name="Cell 15 8 3">0.020789071014127174</Real>
+ <Real Name="Cell 15 8 4">0.0012178524484733003</Real>
+ <Real Name="Cell 15 9 0">1.2178115565280235e-12</Real>
+ <Real Name="Cell 15 9 1">4.9111888598793464e-09</Real>
+ <Real Name="Cell 15 9 2">3.6143402814107232e-08</Real>
+ <Real Name="Cell 15 9 3">2.6432211736393347e-08</Real>
+ <Real Name="Cell 15 9 4">1.5484354139661328e-09</Real>
+ <Real Name="Cell 16 5 0">1.8829076895541218e-06</Real>
+ <Real Name="Cell 16 5 1">0.0075933876793577385</Real>
+ <Real Name="Cell 16 5 2">0.055882776543325213</Real>
+ <Real Name="Cell 16 5 3">0.040867911347688447</Real>
+ <Real Name="Cell 16 5 4">0.0023940986042594353</Real>
+ <Real Name="Cell 16 6 0">2.2940175245966322e-05</Real>
+ <Real Name="Cell 16 6 1">0.092513108869547195</Real>
+ <Real Name="Cell 16 6 2">0.68084096434840546</Real>
+ <Real Name="Cell 16 6 3">0.49790919302825487</Real>
+ <Real Name="Cell 16 6 4">0.029168207152438941</Real>
+ <Real Name="Cell 16 7 0">2.4746787643266283e-05</Real>
+ <Real Name="Cell 16 7 1">0.099798812993619784</Real>
+ <Real Name="Cell 16 7 2">0.73445937456511778</Real>
+ <Real Name="Cell 16 7 3">0.53712113937171768</Real>
+ <Real Name="Cell 16 7 4">0.031465297043148266</Real>
+ <Real Name="Cell 16 8 0">2.4865412914993295e-06</Real>
+ <Real Name="Cell 16 8 1">0.010027720483501996</Real>
+ <Real Name="Cell 16 8 2">0.073798005143583645</Real>
+ <Real Name="Cell 16 8 3">0.053969586309047995</Real>
+ <Real Name="Cell 16 8 4">0.0031616127909179083</Real>
+ <Real Name="Cell 16 9 0">3.161506633150278e-12</Real>
+ <Real Name="Cell 16 9 1">1.2749719834675436e-08</Real>
+ <Real Name="Cell 16 9 2">9.3830286901857782e-08</Real>
+ <Real Name="Cell 16 9 3">6.8619493948378575e-08</Real>
+ <Real Name="Cell 16 9 4">4.01982458288987e-09</Real>
+ <Real Name="Cell 17 5 0">5.3193435543520483e-07</Real>
+ <Real Name="Cell 17 5 1">0.0021451841761532531</Real>
+ <Real Name="Cell 17 5 2">0.015787268215757554</Real>
+ <Real Name="Cell 17 5 3">0.011545465665320862</Real>
+ <Real Name="Cell 17 5 4">0.00067634930005869569</Real>
+ <Real Name="Cell 17 6 0">6.4807570762661043e-06</Real>
+ <Real Name="Cell 17 6 1">0.026135588700836845</Real>
+ <Real Name="Cell 17 6 2">0.19234224892369181</Real>
+ <Real Name="Cell 17 6 3">0.14066276702150288</Real>
+ <Real Name="Cell 17 6 4">0.0082402188683542276</Real>
+ <Real Name="Cell 17 7 0">6.991137487589706e-06</Real>
+ <Real Name="Cell 17 7 1">0.028193850159234684</Real>
+ <Real Name="Cell 17 7 2">0.20748981809891848</Real>
+ <Real Name="Cell 17 7 3">0.15174041119879605</Real>
+ <Real Name="Cell 17 7 4">0.0088891625405108487</Real>
+ <Real Name="Cell 17 8 0">7.0246499416545011e-07</Real>
+ <Real Name="Cell 17 8 1">0.0028328999140362333</Real>
+ <Real Name="Cell 17 8 2">0.020848443349738489</Real>
+ <Real Name="Cell 17 8 3">0.015246778833436227</Real>
+ <Real Name="Cell 17 8 4">0.00089317732961771733</Real>
+ <Real Name="Cell 17 9 0">8.931473393191955e-13</Real>
+ <Real Name="Cell 17 9 1">3.6018834273514096e-09</Real>
+ <Real Name="Cell 17 9 2">2.6507700542271014e-08</Real>
+ <Real Name="Cell 17 9 3">1.9385478367430883e-08</Real>
+ <Real Name="Cell 17 9 4">1.1356280556528323e-09</Real>
+ <Real Name="Cell 18 5 0">4.6303829483116718e-09</Real>
+ <Real Name="Cell 18 5 1">1.8673402326347753e-05</Real>
+ <Real Name="Cell 18 5 2">0.00013742503525055938</Real>
+ <Real Name="Cell 18 5 3">0.00010050098626038372</Real>
+ <Real Name="Cell 18 5 4">5.8874863676215402e-06</Real>
+ <Real Name="Cell 18 6 0">5.6413703592318757e-08</Real>
+ <Real Name="Cell 18 6 1">0.00022750511041053328</Real>
+ <Real Name="Cell 18 6 2">0.0016743010872601334</Real>
+ <Real Name="Cell 18 6 3">0.0012244414582807338</Real>
+ <Real Name="Cell 18 6 4">7.1729469150693423e-05</Real>
+ <Real Name="Cell 18 7 0">6.0856463736682049e-08</Real>
+ <Real Name="Cell 18 7 1">0.0002454218677373561</Real>
+ <Real Name="Cell 18 7 2">0.0018061576693753387</Real>
+ <Real Name="Cell 18 7 3">0.0013208701513739559</Real>
+ <Real Name="Cell 18 7 4">7.7378394968824387e-05</Real>
+ <Real Name="Cell 18 8 0">6.1148182995406646e-09</Real>
+ <Real Name="Cell 18 8 1">2.4659831278419495e-05</Real>
+ <Real Name="Cell 18 8 2">0.00018148155989377549</Real>
+ <Real Name="Cell 18 8 3">0.00013272018249180763</Real>
+ <Real Name="Cell 18 8 4">7.7749313136519353e-06</Real>
+ <Real Name="Cell 18 9 0">7.7746702540578876e-15</Real>
+ <Real Name="Cell 18 9 1">3.1353680079883351e-11</Real>
+ <Real Name="Cell 18 9 2">2.3074427010728188e-10</Real>
+ <Real Name="Cell 18 9 3">1.6874674019499523e-10</Real>
+ <Real Name="Cell 18 9 4">9.8854167451114012e-12</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>0.091894564066607176</Real>
+ <Real>0.63718257163486036</Real>
+ <Real>0.26995085935467633</Real>
+ <Real>0.00097200494385603809</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>0.00074469256732973097</Real>
+ <Real>0.26034962294691572</Real>
+ <Real>0.64177267755391809</Real>
+ <Real>0.097133006931836421</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>0.0071458384444328411</Real>
+ <Real>0.38147922226289888</Real>
+ <Real>0.5656041235874063</Real>
+ <Real>0.045770815705261904</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>-0.33619974975590594</Real>
+ <Real>-0.31140044555650093</Real>
+ <Real>0.63140014038071968</Real>
+ <Real>0.016200054931687191</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>-0.013564033407368874</Real>
+ <Real>-0.62401390092763209</Real>
+ <Real>0.28871990207737086</Real>
+ <Real>0.34885803225763012</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>-0.061250029206279422</Real>
+ <Real>-0.66624999582766442</Real>
+ <Real>0.51625007927416711</Real>
+ <Real>0.21124994575977674</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">11</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 11 4 6">2.4206121932465698e-06</Real>
+ <Real Name="Cell 11 4 7">0.00012922392019640487</Real>
+ <Real Name="Cell 11 4 8">0.00019159518491113612</Real>
+ <Real Name="Cell 11 4 9">1.5504603896735891e-05</Real>
+ <Real Name="Cell 11 5 6">0.00084626260481180846</Real>
+ <Real Name="Cell 11 5 7">0.045177567730389195</Real>
+ <Real Name="Cell 11 5 8">0.066982989139963478</Real>
+ <Real Name="Cell 11 5 9">0.0054205157343394797</Real>
+ <Real Name="Cell 11 6 6">0.0020860726113460328</Real>
+ <Real Name="Cell 11 6 7">0.1113645884312153</Real>
+ <Real Name="Cell 11 6 8">0.16511586152626936</Real>
+ <Real Name="Cell 11 6 9">0.013361797329199482</Real>
+ <Real Name="Cell 11 7 6">0.00031572940467096281</Real>
+ <Real Name="Cell 11 7 7">0.01685515404189445</Real>
+ <Real Name="Cell 11 7 8">0.024990468873364941</Real>
+ <Real Name="Cell 11 7 9">0.0020223228535463586</Real>
+ <Real Name="Cell 12 4 6">1.6784147331126181e-05</Real>
+ <Real Name="Cell 12 4 7">0.00089601850363860429</Real>
+ <Real Name="Cell 12 4 8">0.0013284911232186406</Real>
+ <Real Name="Cell 12 4 9">0.00010750650469315406</Real>
+ <Real Name="Cell 12 5 6">0.0058678528843290716</Real>
+ <Real Name="Cell 12 5 7">0.31325420691688016</Real>
+ <Real Name="Cell 12 5 8">0.46444959731302682</Real>
+ <Real Name="Cell 12 5 9">0.037585010498447133</Real>
+ <Real Name="Cell 12 6 6">0.014464502058588301</Real>
+ <Real Name="Cell 12 6 7">0.77218468324444689</Real>
+ <Real Name="Cell 12 6 8">1.1448876256571181</Real>
+ <Real Name="Cell 12 6 9">0.092648618232870364</Real>
+ <Real Name="Cell 12 7 6">0.0021892184380261047</Real>
+ <Real Name="Cell 12 7 7">0.11687100871311136</Real>
+ <Real Name="Cell 12 7 8">0.17328001264089909</Real>
+ <Real Name="Cell 12 7 9">0.014022471183002953</Real>
+ <Real Name="Cell 13 4 6">7.1108269392048839e-06</Real>
+ <Real Name="Cell 13 4 7">0.00037961013973486886</Real>
+ <Real Name="Cell 13 4 8">0.00056283290900091337</Real>
+ <Real Name="Cell 13 4 9">4.5546558584727484e-05</Real>
+ <Real Name="Cell 13 5 6">0.002485993809634806</Real>
+ <Real Name="Cell 13 5 7">0.13271430531552367</Real>
+ <Real Name="Cell 13 5 8">0.19677024059194384</Real>
+ <Real Name="Cell 13 5 9">0.015923388891315431</Real>
+ <Real Name="Cell 13 6 6">0.0061280784106113326</Real>
+ <Real Name="Cell 13 6 7">0.32714629699854858</Real>
+ <Real Name="Cell 13 6 8">0.48504684868842246</Real>
+ <Real Name="Cell 13 6 9">0.039251817647515765</Real>
+ <Real Name="Cell 13 7 6">0.00092749146785972201</Real>
+ <Real Name="Cell 13 7 7">0.049513955089518336</Real>
+ <Real Name="Cell 13 7 8">0.073412378812215309</Real>
+ <Real Name="Cell 13 7 9">0.0059408061592385415</Real>
+ <Real Name="Cell 14 4 6">2.5603767131301463e-08</Real>
+ <Real Name="Cell 14 4 7">1.3668522242982891e-06</Real>
+ <Real Name="Cell 14 4 8">2.0265776201696924e-06</Real>
+ <Real Name="Cell 14 4 9">1.6399829297011971e-07</Real>
+ <Real Name="Cell 14 5 6">8.9512523839968256e-06</Real>
+ <Real Name="Cell 14 5 7">0.00047786090103763202</Real>
+ <Real Name="Cell 14 5 8">0.00070850541878742976</Real>
+ <Real Name="Cell 14 5 9">5.7334926668877825e-05</Real>
+ <Real Name="Cell 14 6 6">2.2065210407890048e-05</Real>
+ <Real Name="Cell 14 6 7">0.0011779470486107807</Real>
+ <Real Name="Cell 14 6 8">0.0017464954031040799</Real>
+ <Real Name="Cell 14 6 9">0.00014133298519562604</Real>
+ <Real Name="Cell 14 7 6">3.3395940813045107e-06</Real>
+ <Real Name="Cell 14 7 7">0.00017828359299143661</Real>
+ <Real Name="Cell 14 7 8">0.00026433401737000037</Real>
+ <Real Name="Cell 14 7 9">2.1390904148534e-05</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>0.063184976374986601</Real>
+ <Real>0.60089332530937345</Real>
+ <Real>0.3324080578600529</Real>
+ <Real>0.0035136404555869702</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>0.00056250189332608582</Real>
+ <Real>0.25122927037875364</Real>
+ <Real>0.64585412185797764</Real>
+ <Real>0.1023541058699426</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>0.07758074885669021</Real>
+ <Real>0.62173700369211249</Real>
+ <Real>0.29878381161081358</Real>
+ <Real>0.0018984358403836554</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>-0.2619067689657868</Real>
+ <Real>-0.43802933070639938</Real>
+ <Real>0.66177896831015914</Real>
+ <Real>0.03815713136202703</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>-0.011250025244333649</Real>
+ <Real>-0.61625009256246233</Real>
+ <Real>0.26625026085792552</Real>
+ <Real>0.36124985694887041</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>-0.30031255081296182</Real>
+ <Real>-0.37406241312622379</Real>
+ <Real>0.64906247869133304</Real>
+ <Real>0.025312485247852567</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">5</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 13 6 5">1.3648878431251139e-05</Real>
+ <Real Name="Cell 13 6 6">0.00010938297070681329</Real>
+ <Real Name="Cell 13 6 7">5.2565410646331537e-05</Real>
+ <Real Name="Cell 13 6 8">3.339941980038275e-07</Real>
+ <Real Name="Cell 13 7 5">0.0060959755166258966</Real>
+ <Real Name="Cell 13 7 6">0.048853531425542843</Real>
+ <Real Name="Cell 13 7 7">0.023477200557939917</Real>
+ <Real Name="Cell 13 7 8">0.00014917126443625306</Real>
+ <Real Name="Cell 13 8 5">0.015671386173364891</Real>
+ <Real Name="Cell 13 8 6">0.12559147503368878</Real>
+ <Real Name="Cell 13 8 7">0.060354618421541308</Real>
+ <Real Name="Cell 13 8 8">0.00038348587269976031</Real>
+ <Real Name="Cell 13 9 5">0.0024835805257430389</Real>
+ <Real Name="Cell 13 9 6">0.019903570631368037</Real>
+ <Real Name="Cell 13 9 7">0.0095649199944517187</Real>
+ <Real Name="Cell 13 9 8">6.077433322097759e-05</Real>
+ <Real Name="Cell 14 6 5">0.00012980174113896896</Real>
+ <Real Name="Cell 14 6 6">0.0010402393222426643</Real>
+ <Real Name="Cell 14 6 7">0.00049990054933424189</Real>
+ <Real Name="Cell 14 6 8">3.1763070240223655e-06</Real>
+ <Real Name="Cell 14 7 5">0.057973132370117746</Real>
+ <Real Name="Cell 14 7 6">0.46460033121135497</Real>
+ <Real Name="Cell 14 7 7">0.22326973786446375</Real>
+ <Real Name="Cell 14 7 8">0.0014186286403865571</Real>
+ <Real Name="Cell 14 8 5">0.14903592420505299</Real>
+ <Real Name="Cell 14 8 6">1.1943832757905088</Real>
+ <Real Name="Cell 14 8 7">0.57397643303472723</Real>
+ <Real Name="Cell 14 8 8">0.0036469761401532992</Real>
+ <Real Name="Cell 14 9 5">0.023619015886474689</Real>
+ <Real Name="Cell 14 9 6">0.18928427971917966</Real>
+ <Real Name="Cell 14 9 7">0.090963024939255982</Real>
+ <Real Name="Cell 14 9 8">0.00057796794867632627</Real>
+ <Real Name="Cell 15 6 5">7.1804999093047747e-05</Real>
+ <Real Name="Cell 15 6 6">0.00057544978160360314</Real>
+ <Real Name="Cell 15 6 7">0.00027653988441594821</Real>
+ <Real Name="Cell 15 6 8">1.7571006442431672e-06</Real>
+ <Real Name="Cell 15 7 5">0.032070145444356456</Real>
+ <Real Name="Cell 15 7 6">0.25701216384720382</Real>
+ <Real Name="Cell 15 7 7">0.12351054141637972</Real>
+ <Real Name="Cell 15 7 8">0.00078477089245874976</Real>
+ <Real Name="Cell 15 8 5">0.082445152957679083</Real>
+ <Real Name="Cell 15 8 6">0.66072064428680677</Real>
+ <Real Name="Cell 15 8 7">0.31751790763241178</Real>
+ <Real Name="Cell 15 8 8">0.0020174699980003248</Real>
+ <Real Name="Cell 15 9 5">0.013065798651277376</Real>
+ <Real Name="Cell 15 9 6">0.10471013265540433</Real>
+ <Real Name="Cell 15 9 7">0.050319817484353033</Real>
+ <Real Name="Cell 15 9 8">0.00031972597336797116</Real>
+ <Real Name="Cell 16 6 5">7.5899769503463048e-07</Real>
+ <Real Name="Cell 16 6 6">6.0826552936702764e-06</Real>
+ <Real Name="Cell 16 6 7">2.9230991923676517e-06</Real>
+ <Real Name="Cell 16 6 8">1.8573015190714658e-08</Real>
+ <Real Name="Cell 16 7 5">0.0003389898583544255</Real>
+ <Real Name="Cell 16 7 6">0.0027166860583496279</Real>
+ <Real Name="Cell 16 7 7">0.0013055388542799651</Real>
+ <Real Name="Cell 16 7 8">8.295234399134357e-06</Real>
+ <Real Name="Cell 16 8 5">0.00087146691528493649</Real>
+ <Real Name="Cell 16 8 6">0.0069839907027314041</Real>
+ <Real Name="Cell 16 8 7">0.0033562476578117909</Real>
+ <Real Name="Cell 16 8 8">2.1325187627946444e-05</Real>
+ <Real Name="Cell 16 9 5">0.00013810892257313989</Real>
+ <Real Name="Cell 16 9 6">0.0011068135970482469</Real>
+ <Real Name="Cell 16 9 7">0.00053189368383245483</Real>
+ <Real Name="Cell 16 9 8">3.3795874924325363e-06</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>0.018838378622655624</Real>
+ <Real>0.36297420692464072</Real>
+ <Real>0.53757988540360191</Real>
+ <Real>0.080563788752470042</Real>
+ <Real>4.3740296631613747e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>3.0663833712703144e-05</Real>
+ <Real>0.076521720794453157</Real>
+ <Real>0.5318542225048053</Real>
+ <Real>0.37130973842191789</Real>
+ <Real>0.020283654445110946</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>0.00062526101296168034</Real>
+ <Real>0.13526982290347628</Real>
+ <Real>0.58502241119791654</Real>
+ <Real>0.27164474828839408</Real>
+ <Real>0.0074377565972514352</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>-0.091894564066607176</Real>
+ <Real>-0.54528800756825313</Real>
+ <Real>0.36723171228018403</Real>
+ <Real>0.26897885441082031</Real>
+ <Real>0.00097200494385603809</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>-0.00074469256732973097</Real>
+ <Real>-0.25960493037958599</Real>
+ <Real>-0.38142305460700238</Real>
+ <Real>0.54463967062208163</Real>
+ <Real>0.097133006931836421</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>-0.0071458384444328411</Real>
+ <Real>-0.37433338381846604</Real>
+ <Real>-0.18412490132450743</Real>
+ <Real>0.51983330788214444</Real>
+ <Real>0.045770815705261904</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">11</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">6</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 11 4 10">2.1267533054017136e-08</Real>
+ <Real Name="Cell 11 4 6">1.7878723357880327e-09</Real>
+ <Real Name="Cell 11 4 7">3.8679074694025961e-07</Real>
+ <Real Name="Cell 11 4 8">1.6728140138506729e-06</Real>
+ <Real Name="Cell 11 4 9">7.7674142567511696e-07</Real>
+ <Real Name="Cell 11 5 10">5.3073214575648657e-05</Real>
+ <Real Name="Cell 11 5 6">4.4616426301131996e-06</Real>
+ <Real Name="Cell 11 5 7">0.0009652378701420813</Real>
+ <Real Name="Cell 11 5 8">0.004174514123323733</Real>
+ <Real Name="Cell 11 5 9">0.0019383613628315987</Real>
+ <Real Name="Cell 11 6 10">0.00036887844367462823</Real>
+ <Real Name="Cell 11 6 6">3.1010064168671417e-05</Real>
+ <Real Name="Cell 11 6 7">0.0067087597041312654</Real>
+ <Real Name="Cell 11 6 8">0.029014414996749671</Real>
+ <Real Name="Cell 11 6 9">0.01347232739748952</Real>
+ <Real Name="Cell 11 7 10">0.0002575295121006073</Real>
+ <Real Name="Cell 11 7 6">2.1649426342219628e-05</Real>
+ <Real Name="Cell 11 7 7">0.0046836665113699962</Real>
+ <Real Name="Cell 11 7 8">0.020256179958805826</Real>
+ <Real Name="Cell 11 7 9">0.0094055967786381058</Real>
+ <Real Name="Cell 11 8 10">1.4068146057971513e-05</Real>
+ <Real Name="Cell 11 8 6">1.1826500557911143e-06</Real>
+ <Real Name="Cell 11 8 7">0.00025585613093943968</Real>
+ <Real Name="Cell 11 8 8">0.0011065407452242196</Real>
+ <Real Name="Cell 11 8 9">0.00051380250816681131</Real>
+ <Real Name="Cell 12 4 10">4.0977868096576318e-07</Real>
+ <Real Name="Cell 12 4 6">3.4448375635932738e-08</Real>
+ <Real Name="Cell 12 4 7">7.4526087105812087e-06</Real>
+ <Real Name="Cell 12 4 8">3.2231454318454416e-05</Real>
+ <Real Name="Cell 12 4 9">1.4966102370979737e-05</Real>
+ <Real Name="Cell 12 5 10">0.0010226043522859028</Real>
+ <Real Name="Cell 12 5 6">8.5966060438921849e-05</Real>
+ <Real Name="Cell 12 5 7">0.018598015117240595</Real>
+ <Real Name="Cell 12 5 8">0.080433724343286508</Real>
+ <Real Name="Cell 12 5 9">0.037347968872492233</Real>
+ <Real Name="Cell 12 6 10">0.0071074779431054419</Real>
+ <Real Name="Cell 12 6 6">0.00059749587126192933</Real>
+ <Real Name="Cell 12 6 7">0.12926307416533703</Real>
+ <Real Name="Cell 12 6 8">0.55904409205164396</Real>
+ <Real Name="Cell 12 6 9">0.25958217798276284</Real>
+ <Real Name="Cell 12 7 10">0.004962028436034817</Real>
+ <Real Name="Cell 12 7 6">0.00041713692639610173</Real>
+ <Real Name="Cell 12 7 7">0.090243973301369448</Real>
+ <Real Name="Cell 12 7 8">0.39029212668164731</Real>
+ <Real Name="Cell 12 7 9">0.18122520519220012</Real>
+ <Real Name="Cell 12 8 10">0.00027106229578330771</Real>
+ <Real Name="Cell 12 8 6">2.278707072772741e-05</Real>
+ <Real Name="Cell 12 8 7">0.0049297860540324185</Real>
+ <Real Name="Cell 12 8 8">0.021320611368567048</Real>
+ <Real Name="Cell 12 8 9">0.0098998465660655281</Real>
+ <Real Name="Cell 13 4 10">6.0689925661894107e-07</Real>
+ <Real Name="Cell 13 4 6">5.1019475966648357e-08</Real>
+ <Real Name="Cell 13 4 7">1.103762322545392e-05</Real>
+ <Real Name="Cell 13 4 8">4.7736123361799961e-05</Real>
+ <Real Name="Cell 13 4 9">2.2165419591922221e-05</Real>
+ <Real Name="Cell 13 5 10">0.0015145195444402838</Real>
+ <Real Name="Cell 13 5 6">0.00012731930819797732</Real>
+ <Real Name="Cell 13 5 7">0.027544433308828421</Real>
+ <Real Name="Cell 13 5 8">0.11912568852041348</Real>
+ <Real Name="Cell 13 5 9">0.055313894055012233</Real>
+ <Real Name="Cell 13 6 10">0.010526470215434671</Real>
+ <Real Name="Cell 13 6 6">0.0008849162168396166</Real>
+ <Real Name="Cell 13 6 7">0.191443984919695</Real>
+ <Real Name="Cell 13 6 8">0.82796753380076538</Real>
+ <Real Name="Cell 13 6 9">0.38445199364196991</Real>
+ <Real Name="Cell 13 7 10">0.007348970332117356</Real>
+ <Real Name="Cell 13 7 6">0.00061779712390468524</Real>
+ <Real Name="Cell 13 7 7">0.13365507493425849</Real>
+ <Real Name="Cell 13 7 8">0.57803885987691861</Real>
+ <Real Name="Cell 13 7 9">0.26840206047944826</Real>
+ <Real Name="Cell 13 8 10">0.00040145452521005479</Real>
+ <Real Name="Cell 13 8 6">3.3748598762111889e-05</Real>
+ <Real Name="Cell 13 8 7">0.0073012180244014895</Real>
+ <Real Name="Cell 13 8 8">0.031576711506194177</Real>
+ <Real Name="Cell 13 8 9">0.014662084194879646</Real>
+ <Real Name="Cell 14 4 10">9.095225627270441e-08</Real>
+ <Real Name="Cell 14 4 6">7.6459748507012131e-09</Real>
+ <Real Name="Cell 14 4 7">1.6541406589221847e-06</Real>
+ <Real Name="Cell 14 4 8">7.1539190040463777e-06</Real>
+ <Real Name="Cell 14 4 9">3.321795011494524e-06</Real>
+ <Real Name="Cell 14 5 10">0.00022697172262717378</Real>
+ <Real Name="Cell 14 5 6">1.9080561100368405e-05</Real>
+ <Real Name="Cell 14 5 7">0.0041279146907308821</Real>
+ <Real Name="Cell 14 5 8">0.017852633749020911</Real>
+ <Real Name="Cell 14 5 9">0.008289552858509271</Real>
+ <Real Name="Cell 14 6 10">0.0015775373033326005</Real>
+ <Real Name="Cell 14 6 6">0.00013261694697445272</Real>
+ <Real Name="Cell 14 6 7">0.028690531728920277</Real>
+ <Real Name="Cell 14 6 8">0.12408239835266263</Real>
+ <Real Name="Cell 14 6 9">0.05761545407894849</Real>
+ <Real Name="Cell 14 7 10">0.0011013449525559672</Real>
+ <Real Name="Cell 14 7 6">9.2585452569105993e-05</Real>
+ <Real Name="Cell 14 7 7">0.020030063466037206</Real>
+ <Real Name="Cell 14 7 8">0.086627126241674443</Real>
+ <Real Name="Cell 14 7 9">0.040223764854891417</Real>
+ <Real Name="Cell 14 8 10">6.0163518838626006e-05</Real>
+ <Real Name="Cell 14 8 6">5.0576947820905883e-06</Real>
+ <Real Name="Cell 14 8 7">0.0010941886081023875</Real>
+ <Real Name="Cell 14 8 8">0.0047322074064820889</Real>
+ <Real Name="Cell 14 8 9">0.0021973163167375068</Real>
+ <Real Name="Cell 15 4 10">4.9380481358762696e-11</Real>
+ <Real Name="Cell 15 4 6">4.1512100310361337e-12</Real>
+ <Real Name="Cell 15 4 7">8.9807845698482103e-10</Real>
+ <Real Name="Cell 15 4 8">3.8840593790461917e-09</Real>
+ <Real Name="Cell 15 4 9">1.8034938699147332e-09</Real>
+ <Real Name="Cell 15 5 10">1.2322919053874011e-07</Real>
+ <Real Name="Cell 15 5 6">1.0359361387434206e-08</Real>
+ <Real Name="Cell 15 5 7">2.2411584142016798e-06</Real>
+ <Real Name="Cell 15 5 8">9.6926858571282351e-06</Real>
+ <Real Name="Cell 15 5 9">4.5006262315775254e-06</Real>
+ <Real Name="Cell 15 6 10">8.5648838843975567e-07</Real>
+ <Real Name="Cell 15 6 6">7.2001387830257749e-08</Real>
+ <Real Name="Cell 15 6 7">1.5576878741359136e-05</Real>
+ <Real Name="Cell 15 6 8">6.7367746660761682e-05</Real>
+ <Real Name="Cell 15 6 9">3.1281014597281609e-05</Real>
+ <Real Name="Cell 15 7 10">5.9795046465030628e-07</Real>
+ <Real Name="Cell 15 7 6">5.0267188545309557e-08</Real>
+ <Real Name="Cell 15 7 7">1.0874872335589548e-05</Real>
+ <Real Name="Cell 15 7 8">4.7032249312367646e-05</Real>
+ <Real Name="Cell 15 7 9">2.1838588199953398e-05</Real>
+ <Real Name="Cell 15 8 10">3.2664429033850529e-08</Real>
+ <Real Name="Cell 15 8 6">2.7459615972197525e-09</Real>
+ <Real Name="Cell 15 8 7">5.9406508842800209e-07</Real>
+ <Real Name="Cell 15 8 8">2.5692455492356669e-06</Real>
+ <Real Name="Cell 15 8 9">1.192983460384201e-06</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>0.011432525938349669</Real>
+ <Real>0.31069986337177463</Real>
+ <Real>0.56829499415745799</Real>
+ <Real>0.10932995542012119</Real>
+ <Real>0.00024266111229649778</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>2.1093844666357399e-05</Real>
+ <Real>0.072769833852738011</Real>
+ <Real>0.526147462246918</Real>
+ <Real>0.3793113668647477</Real>
+ <Real>0.021750243190929889</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>0.015031271362631297</Real>
+ <Real>0.33844528307349747</Real>
+ <Real>0.55312247231512424</Real>
+ <Real>0.093294186263843212</Real>
+ <Real>0.0001067869849037923</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">5</Int>
+ <Real>-0.063184976374986601</Real>
+ <Real>-0.53770834893438679</Real>
+ <Real>0.26848526744932055</Real>
+ <Real>0.3288944174044659</Real>
+ <Real>0.0035136404555869702</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">5</Int>
+ <Real>-0.00056250189332608582</Real>
+ <Real>-0.25066676848542757</Real>
+ <Real>-0.39462485147922399</Real>
+ <Real>0.54350001598803499</Real>
+ <Real>0.1023541058699426</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">5</Int>
+ <Real>-0.07758074885669021</Real>
+ <Real>-0.54415625483542229</Real>
+ <Real>0.32295319208129891</Real>
+ <Real>0.29688537577042995</Real>
+ <Real>0.0018984358403836554</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">13</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">5</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 13 10 5">1.8501511503215527e-05</Real>
+ <Real Name="Cell 13 10 6">0.00041658148182730962</Real>
+ <Real Name="Cell 13 10 7">0.00068082077273028758</Real>
+ <Real Name="Cell 13 10 8">0.00011483283208064365</Real>
+ <Real Name="Cell 13 10 9">1.3144068668090074e-07</Real>
+ <Real Name="Cell 13 6 5">1.7943156143854031e-08</Real>
+ <Real Name="Cell 13 6 6">4.0400950883209747e-07</Real>
+ <Real Name="Cell 13 6 7">6.6027434725837286e-07</Real>
+ <Real Name="Cell 13 6 8">1.1136730294202473e-07</Real>
+ <Real Name="Cell 13 6 9">1.2747395067483544e-10</Real>
+ <Real Name="Cell 13 7 5">6.190054549251936e-05</Real>
+ <Real Name="Cell 13 7 6">0.0013937575296326917</Real>
+ <Real Name="Cell 13 7 7">0.0022778234744398559</Real>
+ <Real Name="Cell 13 7 8">0.00038419644497733732</Real>
+ <Real Name="Cell 13 7 9">4.3976137863357888e-07</Real>
+ <Real Name="Cell 13 8 5">0.00044755928656505428</Real>
+ <Real Name="Cell 13 8 6">0.010077279943881344</Real>
+ <Real Name="Cell 13 8 7">0.016469338695321131</Real>
+ <Real Name="Cell 13 8 8">0.0027778541440425168</Real>
+ <Real Name="Cell 13 8 9">3.1796050796336644e-06</Real>
+ <Real Name="Cell 13 9 5">0.00032265540921744978</Real>
+ <Real Name="Cell 13 9 6">0.0072649344605191643</Real>
+ <Real Name="Cell 13 9 7">0.011873111285575399</Real>
+ <Real Name="Cell 13 9 8">0.0020026166197361387</Real>
+ <Real Name="Cell 13 9 9">2.292247773457744e-06</Real>
+ <Real Name="Cell 14 10 5">0.00050281251293186988</Real>
+ <Real Name="Cell 14 10 6">0.011321365915539791</Real>
+ <Real Name="Cell 14 10 7">0.018502553347235329</Real>
+ <Real Name="Cell 14 10 8">0.0031207928528172888</Real>
+ <Real Name="Cell 14 10 9">3.5721417658242645e-06</Real>
+ <Real Name="Cell 14 6 5">4.8763818183461111e-07</Real>
+ <Real Name="Cell 14 6 6">1.0979699488278664e-05</Real>
+ <Real Name="Cell 14 6 7">1.7944166546162054e-05</Real>
+ <Real Name="Cell 14 6 8">3.0266107415597976e-06</Real>
+ <Real Name="Cell 14 6 9">3.4643384385663596e-09</Real>
+ <Real Name="Cell 14 7 5">0.0016822608696342367</Real>
+ <Real Name="Cell 14 7 6">0.037877917475582001</Real>
+ <Real Name="Cell 14 7 7">0.061904031192221924</Real>
+ <Real Name="Cell 14 7 8">0.010441243134376979</Real>
+ <Real Name="Cell 14 7 9">1.1951322130773126e-05</Real>
+ <Real Name="Cell 14 8 5">0.012163244582728204</Real>
+ <Real Name="Cell 14 8 6">0.27386856750705363</Real>
+ <Real Name="Cell 14 8 7">0.44758448920680238</Real>
+ <Real Name="Cell 14 8 8">0.075493281858699787</Real>
+ <Real Name="Cell 14 8 9">8.6411600476192556e-05</Real>
+ <Real Name="Cell 14 9 5">0.0087687526011856164</Real>
+ <Real Name="Cell 14 9 6">0.19743792023392859</Real>
+ <Real Name="Cell 14 9 7">0.32267357836046773</Real>
+ <Real Name="Cell 14 9 8">0.054424780096137042</Real>
+ <Real Name="Cell 14 9 9">6.2296037976921901e-05</Real>
+ <Real Name="Cell 15 10 5">0.00091968445366517068</Real>
+ <Real Name="Cell 15 10 6">0.020707687177601158</Real>
+ <Real Name="Cell 15 10 7">0.033842655520525011</Real>
+ <Real Name="Cell 15 10 8">0.005708180675754855</Real>
+ <Real Name="Cell 15 10 9">6.5337340734831138e-06</Real>
+ <Real Name="Cell 15 6 5">8.9192938384094845e-07</Real>
+ <Real Name="Cell 15 6 6">2.008275185198814e-05</Real>
+ <Real Name="Cell 15 6 7">3.2821321232154791e-05</Real>
+ <Real Name="Cell 15 6 8">5.5359140330020441e-06</Real>
+ <Real Name="Cell 15 6 9">6.3365531331076159e-09</Real>
+ <Real Name="Cell 15 7 5">0.0030769901882324352</Real>
+ <Real Name="Cell 15 7 6">0.069281752031945226</Real>
+ <Real Name="Cell 15 7 7">0.11322744291847905</Real>
+ <Real Name="Cell 15 7 8">0.019097871951579394</Real>
+ <Real Name="Cell 15 7 9">2.1859927670308133e-05</Real>
+ <Real Name="Cell 15 8 5">0.022247550848795136</Real>
+ <Real Name="Cell 15 8 6">0.5009275970781496</Real>
+ <Real Name="Cell 15 8 7">0.81866796437689004</Real>
+ <Real Name="Cell 15 8 8">0.13808327337911078</Real>
+ <Real Name="Cell 15 8 9">0.00015805375469056472</Real>
+ <Real Name="Cell 15 9 5">0.016038752493097084</Real>
+ <Real Name="Cell 15 9 6">0.36112980710114506</Real>
+ <Real Name="Cell 15 9 7">0.5901958801626771</Real>
+ <Real Name="Cell 15 9 8">0.099547292203813989</Real>
+ <Real Name="Cell 15 9 9">0.00011394445479934425</Real>
+ <Real Name="Cell 16 10 5">0.00017693110330641487</Real>
+ <Real Name="Cell 16 10 6">0.0039837945772115482</Real>
+ <Real Name="Cell 16 10 7">0.0065107313233386515</Real>
+ <Real Name="Cell 16 10 8">0.0010981535034203778</Real>
+ <Real Name="Cell 16 10 9">1.2569754481823129e-06</Real>
+ <Real Name="Cell 16 6 5">1.7159151633527958e-07</Real>
+ <Real Name="Cell 16 6 6">3.863568018835778e-06</Real>
+ <Real Name="Cell 16 6 7">6.3142445807761812e-06</Real>
+ <Real Name="Cell 16 6 8">1.0650124330851349e-06</Real>
+ <Real Name="Cell 16 6 9">1.2190413054525996e-09</Real>
+ <Real Name="Cell 16 7 5">0.00059195876009140753</Real>
+ <Real Name="Cell 16 7 6">0.013328589797470166</Real>
+ <Real Name="Cell 16 7 7">0.021782967321337571</Real>
+ <Real Name="Cell 16 7 8">0.0036740944589542567</Real>
+ <Real Name="Cell 16 7 9">4.2054653696627108e-06</Real>
+ <Real Name="Cell 16 8 5">0.0042800372474013481</Real>
+ <Real Name="Cell 16 8 6">0.096369653824697157</Real>
+ <Real Name="Cell 16 8 7">0.15749730856226324</Real>
+ <Real Name="Cell 16 8 8">0.026564791662795732</Real>
+ <Real Name="Cell 16 8 9">3.0406760805488328e-05</Real>
+ <Real Name="Cell 16 9 5">0.0030855737127587889</Real>
+ <Real Name="Cell 16 9 6">0.069475019342341349</Real>
+ <Real Name="Cell 16 9 7">0.11354330045259273</Real>
+ <Real Name="Cell 16 9 8">0.019151147081582883</Real>
+ <Real Name="Cell 16 9 9">2.1920907788483351e-05</Real>
+ <Real Name="Cell 17 10 5">3.9270388580328203e-07</Real>
+ <Real Name="Cell 17 10 6">8.8421514446990794e-06</Real>
+ <Real Name="Cell 17 10 7">1.4450763276303683e-05</Real>
+ <Real Name="Cell 17 10 8">2.4373846087130266e-06</Real>
+ <Real Name="Cell 17 10 9">2.7898946744578373e-09</Real>
+ <Real Name="Cell 17 6 5">3.8085251251184906e-10</Real>
+ <Real Name="Cell 17 6 6">8.5753049956089219e-09</Real>
+ <Real Name="Cell 17 6 7">1.4014655063156549e-08</Real>
+ <Real Name="Cell 17 6 8">2.363827009980425e-09</Real>
+ <Real Name="Cell 17 6 9">2.7056987079138661e-12</Real>
+ <Real Name="Cell 17 7 5">1.3138702069844619e-06</Real>
+ <Real Name="Cell 17 7 6">2.9583204467333142e-05</Real>
+ <Real Name="Cell 17 7 7">4.8347948730080787e-05</Real>
+ <Real Name="Cell 17 7 8">8.1547627515830453e-06</Real>
+ <Real Name="Cell 17 7 9">9.3341564112532426e-09</Real>
+ <Real Name="Cell 17 8 5">9.4996709285560274e-06</Real>
+ <Real Name="Cell 17 8 6">0.00021389533452993275</Real>
+ <Real Name="Cell 17 8 7">0.00034956999600486218</Real>
+ <Real Name="Cell 17 8 8">5.8961351150723794e-05</Real>
+ <Real Name="Cell 17 8 9">6.7488716793489128e-08</Real>
+ <Real Name="Cell 17 9 5">6.848523319466036e-06</Real>
+ <Real Name="Cell 17 9 6">0.0001542018873569441</Real>
+ <Real Name="Cell 17 9 7">0.00025201275785548152</Real>
+ <Real Name="Cell 17 9 8">4.2506544841373341e-05</Real>
+ <Real Name="Cell 17 9 9">4.8654111730510713e-08</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>0.35769526137043567</Real>
+ <Real>0.63041709293829207</Real>
+ <Real>0.011887645691272288</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>0.099485422038718782</Real>
+ <Real>0.74709063607685411</Real>
+ <Real>0.1534239418844271</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>0.41390083004880668</Real>
+ <Real>0.58203440211228463</Real>
+ <Real>0.0040647678389086929</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>-0.8458076156791634</Real>
+ <Real>0.69161523135832681</Real>
+ <Real>0.1541923843208366</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>-0.4460614801542917</Real>
+ <Real>-0.1078770396914166</Real>
+ <Real>0.5539385198457083</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>-0.90983606220989799</Real>
+ <Real>0.81967212441979598</Real>
+ <Real>0.090163937790102011</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">12</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 12 3 1">0.072907820051953801</Real>
+ <Real Name="Cell 12 3 2">0.1025242192634528</Real>
+ <Real Name="Cell 12 3 3">0.0007160008887084824</Real>
+ <Real Name="Cell 12 4 1">0.54750483579787468</Real>
+ <Real Name="Cell 12 4 2">0.76991063226334622</Real>
+ <Real Name="Cell 12 4 3">0.0053768436461839415</Real>
+ <Real Name="Cell 12 5 1">0.1124366255612588</Real>
+ <Real Name="Cell 12 5 2">0.15811029933511669</Real>
+ <Real Name="Cell 12 5 3">0.0011041987508044659</Real>
+ <Real Name="Cell 13 3 1">0.12849579218222132</Real>
+ <Real Name="Cell 13 3 2">0.18069297316437982</Real>
+ <Real Name="Cell 13 3 3">0.0012619099203927632</Real>
+ <Real Name="Cell 13 4 1">0.96494542765525437</Real>
+ <Real Name="Cell 13 4 2">1.3569227077657271</Real>
+ <Real Name="Cell 13 4 3">0.009476374184058927</Real>
+ <Real Name="Cell 13 5 1">0.1981630127124144</Real>
+ <Real Name="Cell 13 5 2">0.27866020614464265</Real>
+ <Real Name="Cell 13 5 3">0.0019460860729361054</Real>
+ <Real Name="Cell 14 3 1">0.0024230187718452647</Real>
+ <Real Name="Cell 14 3 2">0.0034072902970779312</Real>
+ <Real Name="Cell 14 3 3">2.379557628745825e-05</Real>
+ <Real Name="Cell 14 4 1">0.01819577781737226</Real>
+ <Real Name="Cell 14 4 2">0.025587212911975576</Real>
+ <Real Name="Cell 14 4 3">0.00017869404240446077</Real>
+ <Real Name="Cell 14 5 1">0.0037367192460799189</Real>
+ <Real Name="Cell 14 5 2">0.0052546382958379937</Real>
+ <Real Name="Cell 14 5 3">3.6696945528487431e-05</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>0.16068584558358961</Real>
+ <Real>0.74552485245182998</Real>
+ <Real>0.093789301964580393</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>0.46585741402556702</Real>
+ <Real>0.5335389355007798</Real>
+ <Real>0.00060365047365315571</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>0.010287892660380538</Real>
+ <Real>0.62286683498701589</Real>
+ <Real>0.36684527235260356</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">3</Int>
+ <Real>-0.56689654361900921</Real>
+ <Real>0.13379308723801842</Real>
+ <Real>0.43310345638099079</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">3</Int>
+ <Real>-0.96525376355191383</Real>
+ <Real>0.93050752710382767</Real>
+ <Real>0.034746236448086165</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">3</Int>
+ <Real>-0.14344262030777699</Real>
+ <Real>-0.71311475938444602</Real>
+ <Real>0.85655737969222301</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">14</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 14 5 0">0.0038120820586983882</Real>
+ <Real Name="Cell 14 5 1">0.23079745920720227</Real>
+ <Real Name="Cell 14 5 2">0.13593107230202739</Real>
+ <Real Name="Cell 14 6 0">0.0043659157124156783</Real>
+ <Real Name="Cell 14 6 1">0.26432858422842925</Real>
+ <Real Name="Cell 14 6 2">0.15567965097046402</Real>
+ <Real Name="Cell 14 7 0">4.9396340404956768e-06</Real>
+ <Real Name="Cell 14 7 1">0.0002990636005220395</Real>
+ <Real Name="Cell 14 7 2">0.00017613727657621198</Real>
+ <Real Name="Cell 15 5 0">0.017686697319378761</Real>
+ <Real Name="Cell 15 5 1">1.0708176634773812</Real>
+ <Real Name="Cell 15 5 2">0.63067155824170218</Real>
+ <Real Name="Cell 15 6 0">0.020256287387943012</Real>
+ <Real Name="Cell 15 6 1">1.226390090801043</Real>
+ <Real Name="Cell 15 6 2">0.72229789996736815</Real>
+ <Real Name="Cell 15 7 0">2.2918135233578232e-05</Real>
+ <Real Name="Cell 15 7 1">0.0013875481430436379</Real>
+ <Real Name="Cell 15 7 2">0.00081721396588374062</Real>
+ <Real Name="Cell 16 5 0">0.0022250405069501418</Real>
+ <Real Name="Cell 16 5 1">0.13471213046566496</Real>
+ <Real Name="Cell 16 5 2">0.07934040699230116</Real>
+ <Real Name="Cell 16 6 0">0.0025483027805996055</Real>
+ <Real Name="Cell 16 6 1">0.15428361666848664</Real>
+ <Real Name="Cell 16 6 2">0.090867280447634521</Real>
+ <Real Name="Cell 16 7 0">2.8831713641981376e-06</Real>
+ <Real Name="Cell 16 7 1">0.00017455779153481807</Real>
+ <Real Name="Cell 16 7 2">0.00010280801124721018</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>0.10084712538648778</Real>
+ <Real>0.64472435971722064</Real>
+ <Real>0.25381752008525871</Real>
+ <Real>0.00061099481103286458</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>0.014792204869455098</Real>
+ <Real>0.44480621417416599</Real>
+ <Real>0.51207243719759432</Real>
+ <Real>0.028329143758784502</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>0.12552730045233818</Real>
+ <Real>0.65890362646340783</Real>
+ <Real>0.2154469079260678</Real>
+ <Real>0.00012216515818619025</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>-0.35769526137043567</Real>
+ <Real>-0.2727218315678564</Real>
+ <Real>0.61852944724701975</Real>
+ <Real>0.011887645691272288</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>-0.099485422038718782</Real>
+ <Real>-0.64760521403813531</Real>
+ <Real>0.59366669419242701</Real>
+ <Real>0.1534239418844271</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>-0.41390083004880668</Real>
+ <Real>-0.16813357206347795</Real>
+ <Real>0.57796963427337589</Real>
+ <Real>0.0040647678389086929</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">12</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 12 3 1">0.0009269147811435288</Real>
+ <Real Name="Cell 12 3 2">0.0048654556301073616</Real>
+ <Real Name="Cell 12 3 3">0.00159089634516729</Real>
+ <Real Name="Cell 12 3 4">9.0208815497081667e-07</Real>
+ <Real Name="Cell 12 4 1">0.027872616577525572</Real>
+ <Real Name="Cell 12 4 2">0.14630576835298786</Real>
+ <Real Name="Cell 12 4 3">0.047838749306305883</Real>
+ <Real Name="Cell 12 4 4">2.7126072184985119e-05</Real>
+ <Real Name="Cell 12 5 1">0.032087678290256549</Real>
+ <Real Name="Cell 12 5 2">0.16843099082074922</Real>
+ <Real Name="Cell 12 5 3">0.05507320754330311</Real>
+ <Real Name="Cell 12 5 4">3.1228237045097364e-05</Real>
+ <Real Name="Cell 12 6 1">0.0017751716068630003</Real>
+ <Real Name="Cell 12 6 2">0.0093180288681586048</Real>
+ <Real Name="Cell 12 6 3">0.0030467892829575999</Real>
+ <Real Name="Cell 12 6 4">1.7276251411332925e-06</Real>
+ <Real Name="Cell 13 3 1">0.0059258460416687364</Real>
+ <Real Name="Cell 13 3 2">0.031105276960862349</Real>
+ <Real Name="Cell 13 3 3">0.010170737376832328</Real>
+ <Real Name="Cell 13 3 4">5.7671272819440762e-06</Real>
+ <Real Name="Cell 13 4 1">0.17819203876877718</Real>
+ <Real Name="Cell 13 4 2">0.93534538007718659</Real>
+ <Real Name="Cell 13 4 3">0.30583724521624522</Real>
+ <Real Name="Cell 13 4 4">0.0001734193161588215</Real>
+ <Real Name="Cell 13 5 1">0.20513929138995271</Real>
+ <Real Name="Cell 13 5 2">1.0767938332131626</Real>
+ <Real Name="Cell 13 5 3">0.35208775991236324</Real>
+ <Real Name="Cell 13 5 4">0.00019964480947610265</Real>
+ <Real Name="Cell 13 6 1">0.011348824998598179</Real>
+ <Real Name="Cell 13 6 2">0.059570961223006459</Real>
+ <Real Name="Cell 13 6 3">0.019478386340909273</Real>
+ <Real Name="Cell 13 6 4">1.1044856347464868e-05</Real>
+ <Real Name="Cell 14 3 1">0.0023329094426695835</Real>
+ <Real Name="Cell 14 3 2">0.012245642871682449</Real>
+ <Real Name="Cell 14 3 3">0.0040040542900508591</Real>
+ <Real Name="Cell 14 3 4">2.2704244420997422e-06</Real>
+ <Real Name="Cell 14 4 1">0.070151314585142469</Real>
+ <Real Name="Cell 14 4 2">0.36823030061796208</Real>
+ <Real Name="Cell 14 4 3">0.12040316138286143</Real>
+ <Real Name="Cell 14 4 4">6.827237112867819e-05</Real>
+ <Real Name="Cell 14 5 1">0.080760010736188589</Real>
+ <Real Name="Cell 14 5 2">0.42391626168606278</Real>
+ <Real Name="Cell 14 5 3">0.13861123862688607</Real>
+ <Real Name="Cell 14 5 4">7.8596922351970562e-05</Real>
+ <Real Name="Cell 14 6 1">0.0044678482728482518</Real>
+ <Real Name="Cell 14 6 2">0.023452120923971892</Real>
+ <Real Name="Cell 14 6 3">0.0076683246751846198</Real>
+ <Real Name="Cell 14 6 4">4.3481807466388225e-06</Real>
+ <Real Name="Cell 15 3 1">5.6158281099030878e-06</Real>
+ <Real Name="Cell 15 3 2">2.9477966098818985e-05</Real>
+ <Real Name="Cell 15 3 3">9.6386427284183423e-06</Real>
+ <Real Name="Cell 15 3 4">5.4654129175131595e-09</Real>
+ <Real Name="Cell 15 4 1">0.00016886970286471379</Real>
+ <Real Name="Cell 15 4 2">0.00088641163489057938</Real>
+ <Real Name="Cell 15 4 3">0.00028983699317592336</Real>
+ <Real Name="Cell 15 4 4">1.6434667111443035e-07</Real>
+ <Real Name="Cell 15 5 1">0.00019440717678667242</Real>
+ <Real Name="Cell 15 5 2">0.001020460038044778</Real>
+ <Real Name="Cell 15 5 3">0.00033366785525056536</Real>
+ <Real Name="Cell 15 5 4">1.8920014545913153e-07</Real>
+ <Real Name="Cell 15 6 1">1.0755097245751444e-05</Real>
+ <Real Name="Cell 15 6 2">5.6454433040906165e-05</Real>
+ <Real Name="Cell 15 6 3">1.8459350577057324e-05</Real>
+ <Real Name="Cell 15 6 4">1.0467031088858332e-08</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>0.030364083489944928</Real>
+ <Real>0.51970853358992608</Real>
+ <Real>0.43638722596932222</Real>
+ <Real>0.013540156950806738</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>0.14989020738891354</Real>
+ <Real>0.66548034030144987</Real>
+ <Real>0.18462246078227332</Real>
+ <Real>6.9915273631839181e-06</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>0.00049190742688337704</Real>
+ <Real>0.24720014720028555</Real>
+ <Real>0.64756660362655571</Real>
+ <Real>0.10474134174627532</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">4</Int>
+ <Real>-0.16068584558358961</Real>
+ <Real>-0.58483900686824031</Real>
+ <Real>0.65173555048724963</Real>
+ <Real>0.093789301964580393</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">4</Int>
+ <Real>-0.46585741402556702</Real>
+ <Real>-0.06768152147521278</Real>
+ <Real>0.53293528502712662</Real>
+ <Real>0.00060365047365315571</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">4</Int>
+ <Real>-0.010287892660380538</Real>
+ <Real>-0.61257894232663535</Real>
+ <Real>0.25602156263441234</Real>
+ <Real>0.36684527235260356</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Int Name="X">14</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 14 5 0">1.1082098329049421e-05</Real>
+ <Real Name="Cell 14 5 1">0.0055691298575952257</Real>
+ <Real Name="Cell 14 5 2">0.014588917312076819</Real>
+ <Real Name="Cell 14 5 3">0.002359699782747918</Real>
+ <Real Name="Cell 14 6 0">4.9202137322650837e-05</Real>
+ <Real Name="Cell 14 6 1">0.024725740909806469</Real>
+ <Real Name="Cell 14 6 2">0.064771660714832549</Real>
+ <Real Name="Cell 14 6 3">0.010476560422375462</Real>
+ <Real Name="Cell 14 7 0">1.3650019569534291e-05</Real>
+ <Real Name="Cell 14 7 1">0.0068595972788100265</Real>
+ <Real Name="Cell 14 7 2">0.017969431500726232</Real>
+ <Real Name="Cell 14 7 3">0.0029064846075497453</Real>
+ <Real Name="Cell 14 8 0">5.1691698249511246e-10</Real>
+ <Real Name="Cell 14 8 1">2.5976829618678269e-07</Real>
+ <Real Name="Cell 14 8 2">6.8049018253714748e-07</Real>
+ <Real Name="Cell 14 8 3">1.1006660066307617e-07</Real>
+ <Real Name="Cell 15 5 0">0.00018968005649164056</Real>
+ <Real Name="Cell 15 5 1">0.095320654503573091</Real>
+ <Real Name="Cell 15 5 2">0.24970240993557094</Real>
+ <Real Name="Cell 15 5 3">0.040388379060098935</Real>
+ <Real Name="Cell 15 6 0">0.00084213872768176281</Real>
+ <Real Name="Cell 15 6 1">0.4232032412378034</Real>
+ <Real Name="Cell 15 6 2">1.108625090542817</Real>
+ <Real Name="Cell 15 6 3">0.17931573189034475</Real>
+ <Real Name="Cell 15 7 0">0.00023363233263094045</Real>
+ <Real Name="Cell 15 7 1">0.11740816231019631</Real>
+ <Real Name="Cell 15 7 2">0.30756294349472535</Real>
+ <Real Name="Cell 15 7 3">0.049747091948010899</Real>
+ <Real Name="Cell 15 8 0">8.8474979674333547e-09</Real>
+ <Real Name="Cell 15 8 1">4.4461674704949669e-06</Real>
+ <Real Name="Cell 15 8 2">1.1647200054822518e-05</Real>
+ <Real Name="Cell 15 8 3">1.8838886293662687e-06</Real>
+ <Real Name="Cell 16 5 0">0.00015926995291442304</Real>
+ <Real Name="Cell 16 5 1">0.080038547200797311</Real>
+ <Real Name="Cell 16 5 2">0.20966933376471794</Real>
+ <Real Name="Cell 16 5 3">0.033913187027521378</Real>
+ <Real Name="Cell 16 6 0">0.0007071243966610566</Real>
+ <Real Name="Cell 16 6 1">0.35535396578789352</Real>
+ <Real Name="Cell 16 6 2">0.93088682719937987</Real>
+ <Real Name="Cell 16 6 3">0.15056726944959112</Real>
+ <Real Name="Cell 16 7 0">0.00019617566182587374</Real>
+ <Real Name="Cell 16 7 1">0.098584916246785378</Real>
+ <Real Name="Cell 16 7 2">0.25825348449738106</Real>
+ <Real Name="Cell 16 7 3">0.041771481613505086</Real>
+ <Real Name="Cell 16 8 0">7.4290392503424114e-09</Real>
+ <Real Name="Cell 16 8 1">3.7333439095985362e-06</Real>
+ <Real Name="Cell 16 8 2">9.7798842884581363e-06</Real>
+ <Real Name="Cell 16 8 3">1.5818576757351712e-06</Real>
+ <Real Name="Cell 17 5 0">4.9418040485000138e-06</Real>
+ <Real Name="Cell 17 5 1">0.0024834239563408639</Real>
+ <Real Name="Cell 17 5 2">0.0065055884269741224</Real>
+ <Real Name="Cell 17 5 3">0.0010522532460356282</Real>
+ <Real Name="Cell 17 6 0">2.1940549000415319e-05</Real>
+ <Real Name="Cell 17 6 1">0.011025869190309286</Real>
+ <Real Name="Cell 17 6 2">0.02888341590595549</Real>
+ <Real Name="Cell 17 6 3">0.0046717785001002578</Real>
+ <Real Name="Cell 17 7 0">6.0869088116650081e-06</Real>
+ <Real Name="Cell 17 7 1">0.0030588778945088799</Real>
+ <Real Name="Cell 17 7 2">0.008013050119466826</Real>
+ <Real Name="Cell 17 7 3">0.0012960792238092631</Real>
+ <Real Name="Cell 17 8 0">2.3050710803897667e-10</Real>
+ <Real Name="Cell 17 8 1">1.158376310741421e-07</Real>
+ <Real Name="Cell 17 8 2">3.0344877289272717e-07</Real>
+ <Real Name="Cell 17 8 3">4.9081641094595856e-08</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>0.5</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>0.43431199655580521</Real>
+ <Real>0.5633760031929016</Real>
+ <Real>0.0023120002512931892</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>0.080000067318198045</Real>
+ <Real>0.74000003365906364</Real>
+ <Real>0.17999989902273833</Real>
+ <Real>0.015570977931379222</Real>
+ <Real>0.64532887986586396</Real>
+ <Real>0.3391001422027568</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>0.10580000383853916</Real>
+ <Real>0.74840000066757195</Real>
+ <Real>0.14579999549388889</Real>
+ <Real>0.10580000383853916</Real>
+ <Real>0.74840000066757195</Real>
+ <Real>0.14579999549388889</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>-1</Real>
+ <Real>1</Real>
+ <Real>0</Real>
+ <Real>-0.93199999630451202</Real>
+ <Real>0.86399999260902405</Real>
+ <Real>0.068000003695487976</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>-0.4000001682954597</Real>
+ <Real>-0.1999996634090806</Real>
+ <Real>0.5999998317045403</Real>
+ <Real>-0.17647083572862243</Real>
+ <Real>-0.64705832854275513</Real>
+ <Real>0.82352916427137757</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>-0.46000000834465027</Real>
+ <Real>-0.079999983310699463</Real>
+ <Real>0.53999999165534973</Real>
+ <Real>-0.46000000834465027</Real>
+ <Real>-0.079999983310699463</Real>
+ <Real>0.53999999165534973</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 3 1">0.01316153110868244</Real>
+ <Real Name="Cell 0 3 2">0.093101035284992792</Real>
+ <Real Name="Cell 0 3 3">0.018137534089952206</Real>
+ <Real Name="Cell 0 4 1">0.12174406584798354</Real>
+ <Real Name="Cell 0 4 2">0.86118389089050773</Real>
+ <Real Name="Cell 0 4 3">0.16777205678680626</Real>
+ <Real Name="Cell 0 5 1">0.032453897671338813</Real>
+ <Real Name="Cell 0 5 2">0.22956990697242161</Real>
+ <Real Name="Cell 0 5 3">0.044723799268112249</Real>
+ <Real Name="Cell 0 6 1">0.11772240343026551</Real>
+ <Real Name="Cell 0 6 2">0.83273576190274157</Real>
+ <Real Name="Cell 0 6 3">0.1622299174568676</Real>
+ <Real Name="Cell 0 7 1">0.061859440959702472</Real>
+ <Real Name="Cell 0 7 2">0.43757659712553931</Real>
+ <Real Name="Cell 0 7 3">0.085246747504311229</Real>
+ <Real Name="Cell 1 3 1">0.01316153110868244</Real>
+ <Real Name="Cell 1 3 2">0.093101035284992792</Real>
+ <Real Name="Cell 1 3 3">0.018137534089952206</Real>
+ <Real Name="Cell 1 4 1">0.12174406584798354</Real>
+ <Real Name="Cell 1 4 2">0.86118389089050773</Real>
+ <Real Name="Cell 1 4 3">0.16777205678680626</Real>
+ <Real Name="Cell 1 5 1">0.033298004134634109</Real>
+ <Real Name="Cell 1 5 2">0.23554088291546391</Real>
+ <Real Name="Cell 1 5 3">0.045887038531625263</Real>
+ <Real Name="Cell 1 6 1">0.15270583740894556</Real>
+ <Real Name="Cell 1 6 2">1.0801989099471756</Real>
+ <Real Name="Cell 1 6 3">0.21043959922811106</Real>
+ <Real Name="Cell 1 7 1">0.080242141326958519</Real>
+ <Real Name="Cell 1 7 2">0.5676107414354169</Real>
+ <Real Name="Cell 1 7 3">0.11057942740479287</Real>
+ <Real Name="Cell 2 5 1">1.51209807142001e-05</Real>
+ <Real Name="Cell 2 5 2">0.00010696164051063565</Real>
+ <Real Name="Cell 2 5 3">2.0837796219346491e-05</Real>
+ <Real Name="Cell 2 6 1">0.00062667904288165363</Real>
+ <Real Name="Cell 2 6 2">0.0044329544337893545</Real>
+ <Real Name="Cell 2 6 3">0.0008636086797094893</Real>
+ <Real Name="Cell 2 7 1">0.00032930023618473001</Real>
+ <Real Name="Cell 2 7 2">0.0023293789039609777</Real>
+ <Real Name="Cell 2 7 3">0.00045379934981043112</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>0.5</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>0.42251027721597068</Real>
+ <Real>0.57422944117966668</Real>
+ <Real>0.0032602816043626613</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>0.40500021457674196</Real>
+ <Real>0.58999980926508666</Real>
+ <Real>0.0049999761581713646</Real>
+ <Real>0.28125026296171923</Real>
+ <Real>0.68749982469210524</Real>
+ <Real>0.031249912346175537</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>0.31205000517964365</Real>
+ <Real>0.66589999619722362</Real>
+ <Real>0.022049998623132727</Real>
+ <Real>0.31205000517964365</Real>
+ <Real>0.66589999619722362</Real>
+ <Real>0.022049998623132727</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>-1</Real>
+ <Real>1</Real>
+ <Real>0</Real>
+ <Real>-0.91924999561160803</Real>
+ <Real>0.83849999122321606</Real>
+ <Real>0.080750004388391972</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>-0.90000023841857058</Real>
+ <Real>0.80000047683714115</Real>
+ <Real>0.099999761581429425</Real>
+ <Real>-0.75000035061554371</Real>
+ <Real>0.50000070123108742</Real>
+ <Real>0.24999964938445629</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>-0.79000000655651093</Real>
+ <Real>0.58000001311302185</Real>
+ <Real>0.20999999344348907</Real>
+ <Real>-0.79000000655651093</Real>
+ <Real>0.58000001311302185</Real>
+ <Real>0.20999999344348907</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">8</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 10 1">0.016356891948842441</Real>
+ <Real Name="Cell 0 10 2">0.034904836102348874</Real>
+ <Real Name="Cell 0 10 3">0.0011558065661401713</Real>
+ <Real Name="Cell 0 5 1">0.19652138950383574</Real>
+ <Real Name="Cell 0 5 2">0.41936737814806518</Real>
+ <Real Name="Cell 0 5 3">0.013886544771826166</Real>
+ <Real Name="Cell 0 6 1">0.28629017504335769</Real>
+ <Real Name="Cell 0 6 2">0.61092973340258316</Real>
+ <Real Name="Cell 0 6 3">0.020229764014547336</Real>
+ <Real Name="Cell 0 7 1">0.0024261771394782738</Real>
+ <Real Name="Cell 0 7 2">0.0051773476081895782</Real>
+ <Real Name="Cell 0 7 3">0.00017143791602943349</Real>
+ <Real Name="Cell 0 8 1">0.14721257809900301</Real>
+ <Real Name="Cell 0 8 2">0.31414469978898246</Real>
+ <Real Name="Cell 0 8 3">0.010402297998752245</Real>
+ <Real Name="Cell 0 9 1">0.35985254047322562</Real>
+ <Real Name="Cell 0 9 2">0.76790835236401411</Real>
+ <Real Name="Cell 0 9 3">0.025427809294210697</Real>
+ <Real Name="Cell 1 10 1">0.022230486285707198</Real>
+ <Real Name="Cell 1 10 2">0.047438809445277126</Real>
+ <Real Name="Cell 1 10 3">0.001570845005143398</Real>
+ <Real Name="Cell 1 5 1">0.19652138950383574</Real>
+ <Real Name="Cell 1 5 2">0.41936737814806518</Real>
+ <Real Name="Cell 1 5 3">0.013886544771826166</Real>
+ <Real Name="Cell 1 6 1">0.28629017504335769</Real>
+ <Real Name="Cell 1 6 2">0.61092973340258316</Real>
+ <Real Name="Cell 1 6 3">0.020229764014547336</Real>
+ <Real Name="Cell 1 7 1">0.0024261771394782738</Real>
+ <Real Name="Cell 1 7 2">0.0051773476081895782</Real>
+ <Real Name="Cell 1 7 3">0.00017143791602943349</Real>
+ <Real Name="Cell 1 8 1">0.20007512483110124</Real>
+ <Real Name="Cell 1 8 2">0.42695088175848722</Real>
+ <Real Name="Cell 1 8 3">0.014137657919631024</Real>
+ <Real Name="Cell 1 9 1">0.48907194538465282</Real>
+ <Real Name="Cell 1 9 2">1.0436564690467567</Real>
+ <Real Name="Cell 1 9 3">0.034558678235355876</Real>
+ <Real Name="Cell 2 10 1">0.00012621722310934347</Real>
+ <Real Name="Cell 2 10 2">0.00026934160228630805</Real>
+ <Real Name="Cell 2 10 3">8.9187295291806413e-06</Real>
+ <Real Name="Cell 2 8 1">0.0011359592563511709</Real>
+ <Real Name="Cell 2 8 2">0.0024240834863917867</Real>
+ <Real Name="Cell 2 8 3">8.0268865959666954e-05</Real>
+ <Real Name="Cell 2 9 1">0.0027767859890147082</Real>
+ <Real Name="Cell 2 9 2">0.0059255303599848172</Real>
+ <Real Name="Cell 2 9 3">0.00019621254997018896</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>0.0044864524938991648</Real>
+ <Real>0.23255589436182172</Real>
+ <Real>0.59564989873306362</Real>
+ <Real>0.16592043459990793</Real>
+ <Real>0.0013873198113074732</Real>
+ <Real>8.1720113811712452e-07</Real>
+ <Real>0.053911011090761712</Real>
+ <Real>0.49035772206459577</Real>
+ <Real>0.42409626041193482</Real>
+ <Real>0.031634189231569541</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>8.6954037185588164e-06</Real>
+ <Real>0.065564778558807185</Real>
+ <Real>0.51400178637626759</Real>
+ <Real>0.39545922310468573</Real>
+ <Real>0.024965516556520795</Real>
+ <Real>0.00024279846432818689</Real>
+ <Real>0.1093428100092559</Real>
+ <Real>0.56830548647196055</Real>
+ <Real>0.31067884836151949</Real>
+ <Real>0.011430056692935849</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>0.013011542449021224</Real>
+ <Real>0.32353820593028937</Real>
+ <Real>0.56159920103377459</Real>
+ <Real>0.10168179137308819</Real>
+ <Real>0.00016925921382653379</Real>
+ <Real>0.013011542449021224</Real>
+ <Real>0.32353820593028937</Real>
+ <Real>0.56159920103377459</Real>
+ <Real>0.10168179137308819</Real>
+ <Real>0.00016925921382653379</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>-0.03132813098882218</Real>
+ <Real>-0.49184024359641992</Real>
+ <Real>0.090655791595095681</Real>
+ <Real>0.41952167155435716</Real>
+ <Real>0.012990911435789263</Real>
+ <Real>-4.9119496114044609e-05</Real>
+ <Real>-0.20195851058360476</Real>
+ <Real>-0.46037775789046542</Real>
+ <Real>0.52682752551620138</Real>
+ <Real>0.13555786245398288</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>-0.00028938398568676441</Real>
+ <Real>-0.23282813529132843</Real>
+ <Real>-0.41997120336041105</Real>
+ <Real>0.53958434853755444</Real>
+ <Real>0.11350437409987174</Real>
+ <Real>-0.0035151319538936445</Real>
+ <Real>-0.32891879020819559</Real>
+ <Real>-0.26844228284257243</Real>
+ <Real>0.53770146412530617</Real>
+ <Real>0.063174740879355443</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>-0.069623165976186063</Real>
+ <Real>-0.54135325243356403</Real>
+ <Real>0.29425777213021775</Real>
+ <Real>0.31403687694500071</Real>
+ <Real>0.0026817693345315848</Real>
+ <Real>-0.069623165976186063</Real>
+ <Real>-0.54135325243356403</Real>
+ <Real>0.29425777213021775</Real>
+ <Real>0.31403687694500071</Real>
+ <Real>0.0026817693345315848</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">4</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 4 0">6.7614945975548057e-07</Real>
+ <Real Name="Cell 0 4 1">1.6812778654576693e-05</Real>
+ <Real Name="Cell 0 4 2">2.9183703459128362e-05</Real>
+ <Real Name="Cell 0 4 3">5.283930677185383e-06</Real>
+ <Real Name="Cell 0 4 4">8.7956156186584266e-09</Real>
+ <Real Name="Cell 0 5 0">0.00030449979212377425</Real>
+ <Real Name="Cell 0 5 1">0.0075715324940036468</Real>
+ <Real Name="Cell 0 5 2">0.013142703153116627</Real>
+ <Real Name="Cell 0 5 3">0.0023795860065927402</Real>
+ <Real Name="Cell 0 5 4">3.961051937319697e-06</Real>
+ <Real Name="Cell 0 6 0">0.0015826271748353986</Real>
+ <Real Name="Cell 0 6 1">0.039352779181171159</Real>
+ <Real Name="Cell 0 6 2">0.068308746668905393</Real>
+ <Real Name="Cell 0 6 3">0.012367816255719805</Real>
+ <Real Name="Cell 0 6 4">2.0587430924709335e-05</Real>
+ <Real Name="Cell 0 7 0">0.00086518395434805658</Real>
+ <Real Name="Cell 0 7 1">0.021513211480203888</Real>
+ <Real Name="Cell 0 7 2">0.037342737758632179</Real>
+ <Real Name="Cell 0 7 3">0.006761185669572959</Real>
+ <Real Name="Cell 0 7 4">1.125464997728225e-05</Real>
+ <Real Name="Cell 0 8 0">3.1830624132188476e-05</Real>
+ <Real Name="Cell 0 8 1">0.00079148364352024376</Real>
+ <Real Name="Cell 0 8 2">0.001373861181414978</Real>
+ <Real Name="Cell 0 8 3">0.00024874797857096824</Real>
+ <Real Name="Cell 0 8 4">4.1406516078556029e-07</Real>
+ <Real Name="Cell 1 4 0">6.1500443444237396e-06</Real>
+ <Real Name="Cell 1 4 1">0.00015292378450767436</Real>
+ <Real Name="Cell 1 4 2">0.00026544585345532714</Real>
+ <Real Name="Cell 1 4 3">4.8060983424142505e-05</Real>
+ <Real Name="Cell 1 4 4">8.0002173056261036e-08</Real>
+ <Real Name="Cell 1 5 0">0.0027696350228635126</Real>
+ <Real Name="Cell 1 5 1">0.068868295199418381</Real>
+ <Real Name="Cell 1 5 2">0.11954192380260908</Real>
+ <Real Name="Cell 1 5 3">0.021643971241518001</Real>
+ <Real Name="Cell 1 5 4">3.6028491502295021e-05</Real>
+ <Real Name="Cell 1 6 0">0.014395082574565158</Real>
+ <Real Name="Cell 1 6 1">0.35794059072093531</Real>
+ <Real Name="Cell 1 6 2">0.62131502889568113</Real>
+ <Real Name="Cell 1 6 3">0.11249379455818613</Real>
+ <Real Name="Cell 1 6 4">0.00018725684284434833</Real>
+ <Real Name="Cell 1 7 0">0.0078694430773466328</Real>
+ <Real Name="Cell 1 7 1">0.19567745368319411</Real>
+ <Real Name="Cell 1 7 2">0.33965788161810795</Real>
+ <Real Name="Cell 1 7 3">0.061497633531783606</Real>
+ <Real Name="Cell 1 7 4">0.00010236878169847925</Real>
+ <Real Name="Cell 1 8 0">0.00028952141734230941</Real>
+ <Real Name="Cell 1 8 1">0.0071990880644878241</Real>
+ <Real Name="Cell 1 8 2">0.012496212289868676</Real>
+ <Real Name="Cell 1 8 3">0.0022625339364324188</Real>
+ <Real Name="Cell 1 8 4">3.766207402181542e-06</Real>
+ <Real Name="Cell 15 4 0">1.0249299667543124e-11</Real>
+ <Real Name="Cell 15 4 1">2.5485372233698999e-10</Real>
+ <Real Name="Cell 15 4 2">4.423763383165181e-10</Real>
+ <Real Name="Cell 15 4 3">8.009558855904725e-11</Real>
+ <Real Name="Cell 15 4 4">1.3332688348039785e-13</Real>
+ <Real Name="Cell 15 5 0">4.6157096972461982e-09</Real>
+ <Real Name="Cell 15 5 1">1.1477182204900004e-07</Real>
+ <Real Name="Cell 15 5 2">1.9922149032932706e-07</Real>
+ <Real Name="Cell 15 5 3">3.6070560605167372e-08</Real>
+ <Real Name="Cell 15 5 4">6.0042950147403033e-11</Real>
+ <Real Name="Cell 15 6 0">2.3989992068841083e-08</Real>
+ <Real Name="Cell 15 6 1">5.9652258943508866e-07</Real>
+ <Real Name="Cell 15 6 2">1.0354468297247273e-06</Real>
+ <Real Name="Cell 15 6 3">1.8747549555659604e-07</Real>
+ <Real Name="Cell 15 6 4">3.120711639827352e-10</Real>
+ <Real Name="Cell 15 7 0">1.311474776430346e-08</Real>
+ <Real Name="Cell 15 7 1">3.2610445529539798e-07</Real>
+ <Real Name="Cell 15 7 2">5.6605370923924125e-07</Real>
+ <Real Name="Cell 15 7 3">1.0248831384175304e-07</Real>
+ <Real Name="Cell 15 7 4">1.7060174877931372e-10</Real>
+ <Real Name="Cell 15 8 0">4.8249924721334526e-10</Real>
+ <Real Name="Cell 15 8 1">1.1997573801702798e-08</Real>
+ <Real Name="Cell 15 8 2">2.0825447313112048e-08</Real>
+ <Real Name="Cell 15 8 3">3.770605059702976e-09</Real>
+ <Real Name="Cell 15 8 4">6.2765382025378959e-12</Real>
+ <Real Name="Cell 2 4 0">5.3189960930075703e-06</Real>
+ <Real Name="Cell 2 4 1">0.00013225937355423531</Real>
+ <Real Name="Cell 2 4 2">0.00022957646780451645</Real>
+ <Real Name="Cell 2 4 3">4.1566559319348901e-05</Real>
+ <Real Name="Cell 2 4 4">6.9191573602912018e-08</Real>
+ <Real Name="Cell 2 5 0">0.0023953775030947878</Real>
+ <Real Name="Cell 2 5 1">0.059562203552228493</Real>
+ <Real Name="Cell 2 5 2">0.10338836438361731</Real>
+ <Real Name="Cell 2 5 3">0.01871924689050183</Real>
+ <Real Name="Cell 2 5 4">3.1160003864268063e-05</Real>
+ <Real Name="Cell 2 6 0">0.012449892014527874</Real>
+ <Real Name="Cell 2 6 1">0.30957250012347204</Real>
+ <Real Name="Cell 2 6 2">0.53735746055546063</Real>
+ <Real Name="Cell 2 6 3">0.097292640545773856</Real>
+ <Real Name="Cell 2 6 4">0.00016195304614040934</Real>
+ <Real Name="Cell 2 7 0">0.0068060544995101604</Real>
+ <Real Name="Cell 2 7 1">0.16923578975073281</Real>
+ <Real Name="Cell 2 7 2">0.29376031197629132</Real>
+ <Real Name="Cell 2 7 3">0.053187530717783496</Real>
+ <Real Name="Cell 2 7 4">8.8535808752965279e-05</Real>
+ <Real Name="Cell 2 8 0">0.00025039872908917264</Real>
+ <Real Name="Cell 2 8 1">0.0062262837702865594</Real>
+ <Real Name="Cell 2 8 2">0.010807613835739371</Real>
+ <Real Name="Cell 2 8 3">0.0019568003894301516</Real>
+ <Real Name="Cell 2 8 4">3.257284230124825e-06</Real>
+ <Real Name="Cell 3 4 0">3.9675456879705457e-07</Real>
+ <Real Name="Cell 3 4 1">9.8654914961984932e-06</Real>
+ <Real Name="Cell 3 4 2">1.7124568414230297e-05</Real>
+ <Real Name="Cell 3 4 3">3.1005328883030617e-06</Real>
+ <Real Name="Cell 3 4 4">5.1611380172476373e-09</Real>
+ <Real Name="Cell 3 5 0">0.00017867600421739681</Real>
+ <Real Name="Cell 3 5 1">0.0044428640242908284</Real>
+ <Real Name="Cell 3 5 2">0.0077119451137743975</Real>
+ <Real Name="Cell 3 5 3">0.0013963061070885595</Real>
+ <Real Name="Cell 3 5 4">2.3242870798748365e-06</Real>
+ <Real Name="Cell 3 6 0">0.00092866237376776914</Real>
+ <Real Name="Cell 3 6 1">0.023091632640862603</Real>
+ <Real Name="Cell 3 6 2">0.040082568933042947</Real>
+ <Real Name="Cell 3 6 3">0.0072572528672489841</Real>
+ <Real Name="Cell 3 6 4">1.2080401990006903e-05</Real>
+ <Real Name="Cell 3 7 0">0.00050767723287338073</Real>
+ <Real Name="Cell 3 7 1">0.012623636418129892</Real>
+ <Real Name="Cell 3 7 2">0.02191216986623867</Real>
+ <Real Name="Cell 3 7 3">0.0039673644135696587</Real>
+ <Real Name="Cell 3 7 4">6.6040632500293949e-06</Real>
+ <Real Name="Cell 3 8 0">1.8677742575842075e-05</Real>
+ <Real Name="Cell 3 8 1">0.00046443097330634318</Real>
+ <Real Name="Cell 3 8 2">0.00080616155608026908</Real>
+ <Real Name="Cell 3 8 3">0.00014596165914671283</Real>
+ <Real Name="Cell 3 8 4">2.4296735278139286e-07</Real>
+ <Real Name="Cell 4 2 0">1.5786359234655713e-09</Real>
+ <Real Name="Cell 4 2 1">3.9253534813128706e-08</Real>
+ <Real Name="Cell 4 2 2">6.8136477809221614e-08</Real>
+ <Real Name="Cell 4 2 3">1.2336625673150951e-08</Real>
+ <Real Name="Cell 4 2 4">2.053551117179089e-11</Real>
+ <Real Name="Cell 4 3 0">1.1903175297782832e-05</Real>
+ <Real Name="Cell 4 3 1">0.00029597812832775193</Real>
+ <Real Name="Cell 4 3 2">0.00051376028347067005</Real>
+ <Real Name="Cell 4 3 3">9.3020192805619046e-05</Real>
+ <Real Name="Cell 4 3 4">1.5484114207333613e-07</Real>
+ <Real Name="Cell 4 4 0">9.3316160003843764e-05</Real>
+ <Real Name="Cell 4 4 1">0.0023203508046979121</Real>
+ <Real Name="Cell 4 4 2">0.0040276762810423543</Real>
+ <Real Name="Cell 4 4 3">0.00072924131404284993</Real>
+ <Real Name="Cell 4 4 4">1.2138929678356282e-06</Real>
+ <Real Name="Cell 4 5 0">7.1794956975535651e-05</Real>
+ <Real Name="Cell 4 5 1">0.0017852158316906115</Real>
+ <Real Name="Cell 4 5 2">0.0030987863763029927</Real>
+ <Real Name="Cell 4 5 3">0.0005610587572863362</Real>
+ <Real Name="Cell 4 5 4">9.3393677359928201e-07</Real>
+ <Real Name="Cell 4 6 0">4.5324475504088847e-06</Real>
+ <Real Name="Cell 4 6 1">0.00011270146907469336</Real>
+ <Real Name="Cell 4 6 2">0.00019562776150560031</Real>
+ <Real Name="Cell 4 6 3">3.5419888766900883e-05</Real>
+ <Real Name="Cell 4 6 4">5.8959843700153721e-08</Real>
+ <Real Name="Cell 5 2 0">8.1828814537200707e-08</Real>
+ <Real Name="Cell 5 2 1">2.0347124833581762e-06</Real>
+ <Real Name="Cell 5 2 2">3.5318638851375948e-06</Real>
+ <Real Name="Cell 5 2 3">6.3947072229739122e-07</Real>
+ <Real Name="Cell 5 2 4">1.0644611022243331e-09</Real>
+ <Real Name="Cell 5 3 0">0.00061700276128760138</Real>
+ <Real Name="Cell 5 3 1">0.015342067800427581</Real>
+ <Real Name="Cell 5 3 2">0.026630836361819295</Real>
+ <Real Name="Cell 5 3 3">0.0048217147425580276</Real>
+ <Real Name="Cell 5 3 4">8.026212319831134e-06</Real>
+ <Real Name="Cell 5 4 0">0.0048370562437950312</Real>
+ <Real Name="Cell 5 4 1">0.12027570945050192</Real>
+ <Real Name="Cell 5 4 2">0.20877516501320445</Real>
+ <Real Name="Cell 5 4 3">0.037800325808294781</Real>
+ <Real Name="Cell 5 4 4">6.2922312267525238e-05</Real>
+ <Real Name="Cell 5 5 0">0.0037215016659194488</Real>
+ <Real Name="Cell 5 5 1">0.092536913058200457</Real>
+ <Real Name="Cell 5 5 2">0.16062602650029709</Real>
+ <Real Name="Cell 5 5 3">0.029082559386883981</Real>
+ <Real Name="Cell 5 5 4">4.8410743668214756e-05</Real>
+ <Real Name="Cell 5 6 0">0.00023494005456799487</Real>
+ <Real Name="Cell 5 6 1">0.0058418964587715928</Real>
+ <Real Name="Cell 5 6 2">0.010140392459476816</Real>
+ <Real Name="Cell 5 6 3">0.0018359949027843226</Real>
+ <Real Name="Cell 5 6 4">3.0561917688346847e-06</Real>
+ <Real Name="Cell 6 2 0">2.0958972132822456e-07</Real>
+ <Real Name="Cell 6 2 1">5.2115483376118884e-06</Real>
+ <Real Name="Cell 6 2 2">9.0462311062649314e-06</Real>
+ <Real Name="Cell 6 2 3">1.6378886977879666e-06</Real>
+ <Real Name="Cell 6 2 4">2.7264247568747047e-09</Real>
+ <Real Name="Cell 6 3 0">0.0015803410757982278</Real>
+ <Real Name="Cell 6 3 1">0.039295934238769981</Real>
+ <Real Name="Cell 6 3 2">0.068210074939724225</Real>
+ <Real Name="Cell 6 3 3">0.012349950991377274</Real>
+ <Real Name="Cell 6 3 4">2.0557692457707663e-05</Real>
+ <Real Name="Cell 6 4 0">0.012389245474466216</Real>
+ <Real Name="Cell 6 4 1">0.30806449499308075</Real>
+ <Real Name="Cell 6 4 2">0.53473985787095712</Real>
+ <Real Name="Cell 6 4 3">0.096818703742492476</Real>
+ <Real Name="Cell 6 4 4">0.00016116413231775123</Real>
+ <Real Name="Cell 6 5 0">0.0095319540127027664</Real>
+ <Real Name="Cell 6 5 1">0.23701658065234701</Real>
+ <Real Name="Cell 6 5 2">0.41141454049725196</Real>
+ <Real Name="Cell 6 5 3">0.074489720422840591</Real>
+ <Real Name="Cell 6 5 4">0.00012399537170492097</Real>
+ <Real Name="Cell 6 6 0">0.00060175649426472068</Real>
+ <Real Name="Cell 6 6 1">0.014962962102617864</Real>
+ <Real Name="Cell 6 6 2">0.025972782836471003</Real>
+ <Real Name="Cell 6 6 3">0.004702569164797909</Real>
+ <Real Name="Cell 6 6 4">7.827882938038561e-06</Real>
+ <Real Name="Cell 7 2 0">5.8381975258316781e-08</Real>
+ <Real Name="Cell 7 2 1">1.4516956469802116e-06</Real>
+ <Real Name="Cell 7 2 2">2.5198604076575621e-06</Real>
+ <Real Name="Cell 7 2 3">4.5623982332790372e-07</Real>
+ <Real Name="Cell 7 2 4">7.5945548136041175e-10</Real>
+ <Real Name="Cell 7 3 0">0.00044020972499155241</Real>
+ <Real Name="Cell 7 3 1">0.010946024671160078</Real>
+ <Real Name="Cell 7 3 2">0.019000163186736588</Real>
+ <Real Name="Cell 7 3 3">0.0034401235358812263</Real>
+ <Real Name="Cell 7 3 4">5.726419620332537e-06</Real>
+ <Real Name="Cell 7 4 0">0.0034510691563293511</Real>
+ <Real Name="Cell 7 4 1">0.085812479785142365</Real>
+ <Real Name="Cell 7 4 2">0.14895372232003581</Real>
+ <Real Name="Cell 7 4 3">0.026969200257604922</Real>
+ <Real Name="Cell 7 4 4">4.4892852215629916e-05</Real>
+ <Real Name="Cell 7 5 0">0.0026551602807922885</Real>
+ <Real Name="Cell 7 5 1">0.066021826164777322</Real>
+ <Real Name="Cell 7 5 2">0.11460100892356005</Real>
+ <Real Name="Cell 7 5 3">0.020749381158414522</Real>
+ <Real Name="Cell 7 5 4">3.4539359454969746e-05</Real>
+ <Real Name="Cell 7 6 0">0.00016762144888144058</Real>
+ <Real Name="Cell 7 6 1">0.0041679872358727551</Real>
+ <Real Name="Cell 7 6 2">0.0072348126393748172</Real>
+ <Real Name="Cell 7 6 3">0.0013099176566956151</Real>
+ <Real Name="Cell 7 6 4">2.1804851169102829e-06</Real>
+ <Real Name="Cell 8 2 0">4.8815247557922276e-10</Real>
+ <Real Name="Cell 8 2 1">1.2138144020059024e-08</Real>
+ <Real Name="Cell 8 2 2">2.1069449785991587e-08</Real>
+ <Real Name="Cell 8 2 3">3.8147835565672601e-09</Real>
+ <Real Name="Cell 8 2 4">6.3500775997722537e-12</Real>
+ <Real Name="Cell 8 3 0">3.6807501986336657e-06</Real>
+ <Real Name="Cell 8 3 1">9.1523608396871779e-05</Real>
+ <Real Name="Cell 8 3 2">0.00015886712731072626</Real>
+ <Real Name="Cell 8 3 3">2.8764097358962612e-05</Real>
+ <Real Name="Cell 8 3 4">4.7880632703884907e-08</Real>
+ <Real Name="Cell 8 4 0">2.8855617587506811e-05</Real>
+ <Real Name="Cell 8 4 1">0.0007175086875249551</Real>
+ <Real Name="Cell 8 4 2">0.0012454550908143085</Real>
+ <Real Name="Cell 8 4 3">0.00022549908275441971</Real>
+ <Real Name="Cell 8 4 4">3.7536511650914242e-07</Real>
+ <Real Name="Cell 8 5 0">2.2200740183824827e-05</Real>
+ <Real Name="Cell 8 5 1">0.0005520319883319816</Real>
+ <Real Name="Cell 8 5 2">0.00095821982662265526</Real>
+ <Real Name="Cell 8 5 3">0.00017349296138749657</Real>
+ <Real Name="Cell 8 5 4">2.8879587832140487e-07</Real>
+ <Real Name="Cell 8 6 0">1.4015425971733469e-06</Real>
+ <Real Name="Cell 8 6 1">3.4850024829950365e-05</Real>
+ <Real Name="Cell 8 6 2">6.0492843632582693e-05</Real>
+ <Real Name="Cell 8 6 3">1.0952687778918683e-05</Real>
+ <Real Name="Cell 8 6 4">1.8231812183020921e-08</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>0.012680492607976912</Real>
+ <Real>0.32094073925313427</Real>
+ <Real>0.56299959840307168</Real>
+ <Real>0.10319666359097672</Real>
+ <Real>0.00018250614484040877</Real>
+ <Real>1.6250376818931188e-06</Real>
+ <Real>0.056474647330642905</Real>
+ <Real>0.49604793417672399</Real>
+ <Real>0.41749944736272515</Real>
+ <Real>0.029976346092225929</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>0.029885006865026001</Real>
+ <Real>0.41712679291586424</Real>
+ <Real>0.49636495411809156</Real>
+ <Real>0.056621562516519237</Real>
+ <Real>1.6835844989861392e-06</Real>
+ <Real>0.00037533948339706124</Real>
+ <Real>0.12011256810581823</Real>
+ <Real>0.5762759369960514</Real>
+ <Real>0.29368577777675831</Real>
+ <Real>0.0095503776379748471</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>0.017206987782729517</Real>
+ <Real>0.352960679890503</Real>
+ <Real>0.54416152671166218</Real>
+ <Real>0.085606298010210635</Real>
+ <Real>6.4507604894689253e-05</Real>
+ <Real>0.017206987782729517</Real>
+ <Real>0.352960679890503</Real>
+ <Real>0.54416152671166218</Real>
+ <Real>0.085606298010210635</Real>
+ <Real>6.4507604894689253e-05</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>-0.068290339976017453</Real>
+ <Real>-0.5407067209453843</Real>
+ <Real>0.28912215410382691</Real>
+ <Real>0.31703721453256878</Real>
+ <Real>0.0028376922850060237</Real>
+ <Real>-8.2253570274950675e-05</Real>
+ <Real>-0.20897306651756287</Real>
+ <Real>-0.45161303688449128</Real>
+ <Real>0.53047428760277104</Real>
+ <Real>0.13019406936955807</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>-0.12989642566818113</Real>
+ <Real>-0.5306670662362496</Real>
+ <Real>0.45110787575743655</Real>
+ <Real>0.20937114986660027</Real>
+ <Real>8.4466280393928373e-05</Real>
+ <Real>-0.0048733249390969704</Real>
+ <Real>-0.34866735478088184</Real>
+ <Real>-0.23283470004267681</Real>
+ <Real>0.53116476418438718</Real>
+ <Real>0.055210615578268486</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>-0.08585899856030095</Real>
+ <Real>-0.54536316105369675</Real>
+ <Real>0.3496041322869341</Real>
+ <Real>0.28031721282842603</Real>
+ <Real>0.001300814498637627</Real>
+ <Real>-0.08585899856030095</Real>
+ <Real>-0.54536316105369675</Real>
+ <Real>0.3496041322869341</Real>
+ <Real>0.28031721282842603</Real>
+ <Real>0.001300814498637627</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">5</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 10 0">3.6844225564855471e-05</Real>
+ <Real Name="Cell 0 10 1">0.0007557721938097143</Real>
+ <Real Name="Cell 0 10 2">0.0011651783732887751</Real>
+ <Real Name="Cell 0 10 3">0.00018330330639428798</Real>
+ <Real Name="Cell 0 10 4">1.3812602039352923e-07</Real>
+ <Real Name="Cell 0 6 0">1.4480152632592761e-06</Real>
+ <Real Name="Cell 0 6 1">2.9702610257258285e-05</Real>
+ <Real Name="Cell 0 6 2">4.5792686454268243e-05</Real>
+ <Real Name="Cell 0 6 3">7.2040050074495806e-06</Real>
+ <Real Name="Cell 0 6 4">5.4284920558589289e-09</Real>
+ <Real Name="Cell 0 7 0">0.00046338005890657612</Real>
+ <Real Name="Cell 0 7 1">0.0095051465546761721</Real>
+ <Real Name="Cell 0 7 2">0.014654139555758068</Real>
+ <Real Name="Cell 0 7 3">0.0023053570976879489</Real>
+ <Real Name="Cell 0 7 4">1.7371743464608655e-06</Real>
+ <Real Name="Cell 0 8 0">0.0022232042977918605</Real>
+ <Real Name="Cell 0 8 1">0.045603780882072967</Real>
+ <Real Name="Cell 0 8 2">0.070307613404165609</Real>
+ <Real Name="Cell 0 8 3">0.01106063955280852</Real>
+ <Real Name="Cell 0 8 4">8.3346130219302644e-06</Real>
+ <Real Name="Cell 0 9 0">0.0011330049398854357</Real>
+ <Real Name="Cell 0 9 1">0.023240918105529414</Real>
+ <Real Name="Cell 0 9 2">0.035830658197986663</Real>
+ <Real Name="Cell 0 9 3">0.0056368005693723843</Real>
+ <Real Name="Cell 0 9 4">4.2475438425787674e-06</Real>
+ <Real Name="Cell 1 10 0">0.0003236231272199738</Real>
+ <Real Name="Cell 1 10 1">0.0066383634633890099</Real>
+ <Real Name="Cell 1 10 2">0.010234403441837537</Real>
+ <Real Name="Cell 1 10 3">0.0016100539049371438</Real>
+ <Real Name="Cell 1 10 4">1.2132369179946192e-06</Real>
+ <Real Name="Cell 1 6 0">1.2718715635190705e-05</Real>
+ <Real Name="Cell 1 6 1">0.00026089438631650885</Real>
+ <Real Name="Cell 1 6 2">0.0004022223880930187</Real>
+ <Real Name="Cell 1 6 3">6.3276744001996738e-05</Real>
+ <Real Name="Cell 1 6 4">4.7681435781936809e-08</Real>
+ <Real Name="Cell 1 7 0">0.0040701222906898158</Real>
+ <Real Name="Cell 1 7 1">0.083488937697815027</Real>
+ <Real Name="Cell 1 7 2">0.12871537933140828</Real>
+ <Real Name="Cell 1 7 3">0.020249221197478118</Real>
+ <Real Name="Cell 1 7 4">1.5258559134005365e-05</Real>
+ <Real Name="Cell 1 8 0">0.019527627905594439</Real>
+ <Real Name="Cell 1 8 1">0.40056312640178027</Real>
+ <Real Name="Cell 1 8 2">0.61755049450496635</Real>
+ <Real Name="Cell 1 8 3">0.097151689477961933</Real>
+ <Real Name="Cell 1 8 4">7.3207496940802329e-05</Real>
+ <Real Name="Cell 1 9 0">0.0099518064548805348</Real>
+ <Real Name="Cell 1 9 1">0.20413778499795809</Real>
+ <Real Name="Cell 1 9 2">0.31472040675603546</Real>
+ <Real Name="Cell 1 9 3">0.049511124194062714</Real>
+ <Real Name="Cell 1 9 4">3.7308517149305342e-05</Real>
+ <Real Name="Cell 18 10 0">1.0601793500810928e-09</Real>
+ <Real Name="Cell 18 10 1">2.17470732783385e-08</Real>
+ <Real Name="Cell 18 10 2">3.3527588966346738e-08</Real>
+ <Real Name="Cell 18 10 3">5.2744867685909788e-09</Real>
+ <Real Name="Cell 18 10 4">3.974526599082122e-12</Real>
+ <Real Name="Cell 18 6 0">4.1666118833396182e-11</Real>
+ <Real Name="Cell 18 6 1">8.5468193605593061e-10</Real>
+ <Real Name="Cell 18 6 2">1.3176680964048322e-09</Real>
+ <Real Name="Cell 18 6 3">2.0729265521770218e-10</Real>
+ <Real Name="Cell 18 6 4">1.5620290809397745e-13</Real>
+ <Real Name="Cell 18 7 0">1.3333594672178843e-08</Real>
+ <Real Name="Cell 18 7 1">2.7350717628800978e-07</Real>
+ <Real Name="Cell 18 7 2">4.2166759952312672e-07</Real>
+ <Real Name="Cell 18 7 3">6.6335822019909293e-08</Real>
+ <Real Name="Cell 18 7 4">4.9986567538691379e-11</Real>
+ <Real Name="Cell 18 8 0">6.3971904725790459e-08</Real>
+ <Real Name="Cell 18 8 1">1.3122324064510797e-06</Real>
+ <Real Name="Cell 18 8 2">2.023076309566433e-06</Real>
+ <Real Name="Cell 18 8 3">3.1826592831857682e-07</Real>
+ <Real Name="Cell 18 8 4">2.3982549453274426e-10</Real>
+ <Real Name="Cell 18 9 0">3.2601809982191194e-08</Real>
+ <Real Name="Cell 18 9 1">6.687490664998792e-07</Real>
+ <Real Name="Cell 18 9 2">1.0310143133406988e-06</Real>
+ <Real Name="Cell 18 9 3">1.6219691071141098e-07</Real>
+ <Real Name="Cell 18 9 4">1.222215476490168e-10</Real>
+ <Real Name="Cell 2 10 0">0.00027237786403118099</Real>
+ <Real Name="Cell 2 10 1">0.005587188024394488</Real>
+ <Real Name="Cell 2 10 2">0.0086138001726504074</Real>
+ <Real Name="Cell 2 10 3">0.0013551041526885497</Real>
+ <Real Name="Cell 2 10 4">1.0211225728083619e-06</Real>
+ <Real Name="Cell 2 6 0">1.0704725053776737e-05</Real>
+ <Real Name="Cell 2 6 1">0.00021958213027931757</Real>
+ <Real Name="Cell 2 6 2">0.00033853104342517891</Real>
+ <Real Name="Cell 2 6 3">5.3256961336995475e-05</Real>
+ <Real Name="Cell 2 6 4">4.0131148054187336e-08</Real>
+ <Real Name="Cell 2 7 0">0.0034256241987620432</Real>
+ <Real Name="Cell 2 7 1">0.070268582828772783</Real>
+ <Real Name="Cell 2 7 2">0.10833348157599899</Real>
+ <Real Name="Cell 2 7 3">0.017042785741066758</Real>
+ <Real Name="Cell 2 7 4">1.2842387936906806e-05</Real>
+ <Real Name="Cell 2 8 0">0.016435455723490762</Real>
+ <Real Name="Cell 2 8 1">0.33713452346935668</Real>
+ <Real Name="Cell 2 8 2">0.51976224959450512</Real>
+ <Real Name="Cell 2 8 3">0.081767857242912828</Real>
+ <Real Name="Cell 2 8 4">6.1615193633090463e-05</Real>
+ <Real Name="Cell 2 9 0">0.0083759520177604276</Real>
+ <Real Name="Cell 2 9 1">0.17181285627960069</Real>
+ <Real Name="Cell 2 9 2">0.26488487672565397</Real>
+ <Real Name="Cell 2 9 3">0.041671107901366938</Real>
+ <Real Name="Cell 2 9 4">3.1400766374744065e-05</Real>
+ <Real Name="Cell 3 10 0">1.9556656114484016e-05</Real>
+ <Real Name="Cell 3 10 1">0.00040115857148926686</Real>
+ <Real Name="Cell 3 10 2">0.00061846849564883366</Real>
+ <Real Name="Cell 3 10 3">9.7296107404695053e-05</Real>
+ <Real Name="Cell 3 10 4">7.3316321347112943e-08</Real>
+ <Real Name="Cell 3 6 0">7.6859633003380748e-07</Real>
+ <Real Name="Cell 3 6 1">1.5765936876084927e-05</Real>
+ <Real Name="Cell 3 6 2">2.4306436295373043e-05</Real>
+ <Real Name="Cell 3 6 3">3.8238352528190793e-06</Real>
+ <Real Name="Cell 3 6 4">2.8814054503538555e-09</Real>
+ <Real Name="Cell 3 7 0">0.00024595888021566571</Real>
+ <Real Name="Cell 3 7 1">0.0050452650215258672</Real>
+ <Real Name="Cell 3 7 2">0.0077783143369685405</Real>
+ <Real Name="Cell 3 7 3">0.0012236673532791899</Real>
+ <Real Name="Cell 3 7 4">9.2207994017506848e-07</Real>
+ <Real Name="Cell 3 8 0">0.0011800612241835537</Real>
+ <Real Name="Cell 3 8 1">0.024206166544634769</Real>
+ <Real Name="Cell 3 8 2">0.037318787313225688</Real>
+ <Real Name="Cell 3 8 3">0.0058709097782439724</Real>
+ <Real Name="Cell 3 8 4">4.4239540448549536e-06</Real>
+ <Real Name="Cell 3 9 0">0.00060139106320331254</Real>
+ <Real Name="Cell 3 9 1">0.012336116072643717</Real>
+ <Real Name="Cell 3 9 2">0.019018661676038717</Real>
+ <Real Name="Cell 3 9 3">0.0029919741460462381</Real>
+ <Real Name="Cell 3 9 4">2.2545664344141529e-06</Real>
+ <Real Name="Cell 5 4 0">2.0279381712035925e-05</Real>
+ <Real Name="Cell 5 4 1">0.00041598357871930786</Real>
+ <Real Name="Cell 5 4 2">0.00064132429525323492</Real>
+ <Real Name="Cell 5 4 3">0.00010089173167460559</Real>
+ <Real Name="Cell 5 4 4">7.6025761133020743e-08</Real>
+ <Real Name="Cell 5 5 0">0.00028305409110538661</Real>
+ <Real Name="Cell 5 5 1">0.0058061855859874133</Real>
+ <Real Name="Cell 5 5 2">0.0089514299831423508</Real>
+ <Real Name="Cell 5 5 3">0.0014082193340369351</Real>
+ <Real Name="Cell 5 5 4">1.0611468842430501e-06</Real>
+ <Real Name="Cell 5 6 0">0.00033682355900068551</Real>
+ <Real Name="Cell 5 6 1">0.0069091391177336153</Real>
+ <Real Name="Cell 5 6 2">0.010651859838142701</Real>
+ <Real Name="Cell 5 6 3">0.0016757272297021719</Real>
+ <Real Name="Cell 5 6 4">1.2627242686280706e-06</Real>
+ <Real Name="Cell 5 7 0">3.8422285950624296e-05</Real>
+ <Real Name="Cell 5 7 1">0.0007881423723501026</Real>
+ <Real Name="Cell 5 7 2">0.0012150836652321476</Real>
+ <Real Name="Cell 5 7 3">0.0001911542974781443</Real>
+ <Real Name="Cell 5 7 4">1.4404204109108032e-07</Real>
+ <Real Name="Cell 5 8 0">1.1424475441350034e-09</Real>
+ <Real Name="Cell 5 8 1">2.3434610810955146e-08</Real>
+ <Real Name="Cell 5 8 2">3.6129275365003898e-08</Real>
+ <Real Name="Cell 5 8 3">5.6837783672059079e-09</Real>
+ <Real Name="Cell 5 8 4">4.2829434018624326e-12</Real>
+ <Real Name="Cell 6 4 0">0.00051326710715978135</Real>
+ <Real Name="Cell 6 4 1">0.010528461424862504</Real>
+ <Real Name="Cell 6 4 2">0.016231790024473419</Real>
+ <Real Name="Cell 6 4 3">0.0025535496095638538</Real>
+ <Real Name="Cell 6 4 4">1.9241968537535151e-06</Real>
+ <Real Name="Cell 6 5 0">0.0071640426012188089</Real>
+ <Real Name="Cell 6 5 1">0.1469533993525976</Real>
+ <Real Name="Cell 6 5 2">0.22655890784204524</Real>
+ <Real Name="Cell 6 5 3">0.035641750527267313</Real>
+ <Real Name="Cell 6 5 4">2.6857416033734e-05</Real>
+ <Real Name="Cell 6 6 0">0.0085249371113192418</Real>
+ <Real Name="Cell 6 6 1">0.17486893329784842</Real>
+ <Real Name="Cell 6 6 2">0.26959644838432717</Real>
+ <Real Name="Cell 6 6 3">0.042412322022009022</Real>
+ <Real Name="Cell 6 6 4">3.1959299435372863e-05</Real>
+ <Real Name="Cell 6 7 0">0.00097246039550793507</Real>
+ <Real Name="Cell 6 7 1">0.019947726278365531</Real>
+ <Real Name="Cell 6 7 2">0.030753525263576525</Real>
+ <Real Name="Cell 6 7 3">0.0048380771505245985</Real>
+ <Real Name="Cell 6 7 4">3.6456753361632359e-06</Real>
+ <Real Name="Cell 6 8 0">2.8915119523192849e-08</Real>
+ <Real Name="Cell 6 8 1">5.9312532645980406e-07</Real>
+ <Real Name="Cell 6 8 2">9.1442475484194672e-07</Real>
+ <Real Name="Cell 6 8 3">1.4385529705482543e-07</Real>
+ <Real Name="Cell 6 8 4">1.0840044342665065e-10</Real>
+ <Real Name="Cell 7 4 0">0.00090038172117671168</Real>
+ <Real Name="Cell 7 4 1">0.018469202656521064</Real>
+ <Real Name="Cell 7 4 2">0.028474076823054098</Real>
+ <Real Name="Cell 7 4 3">0.0044794793208002819</Real>
+ <Real Name="Cell 7 4 4">3.3754582183386785e-06</Real>
+ <Real Name="Cell 7 5 0">0.012567283034290878</Real>
+ <Real Name="Cell 7 5 1">0.25778810447066258</Real>
+ <Real Name="Cell 7 5 2">0.397433415360541</Real>
+ <Real Name="Cell 7 5 3">0.062523353314167959</Real>
+ <Real Name="Cell 7 5 4">4.7113727214326512e-05</Real>
+ <Real Name="Cell 7 6 0">0.014954586884959644</Real>
+ <Real Name="Cell 7 6 1">0.30675799977581286</Real>
+ <Real Name="Cell 7 6 2">0.47293058688805373</Real>
+ <Real Name="Cell 7 6 3">0.074400402769994045</Real>
+ <Real Name="Cell 7 6 4">5.6063536181883203e-05</Real>
+ <Real Name="Cell 7 7 0">0.0017059062473899157</Real>
+ <Real Name="Cell 7 7 1">0.034992634185080376</Real>
+ <Real Name="Cell 7 7 2">0.05394834701622634</Real>
+ <Real Name="Cell 7 7 3">0.0084870356413059376</Real>
+ <Real Name="Cell 7 7 4">6.3953044881254987e-06</Real>
+ <Real Name="Cell 7 8 0">5.0723385000040655e-08</Real>
+ <Real Name="Cell 7 8 1">1.0404703415859642e-06</Real>
+ <Real Name="Cell 7 8 2">1.6040991584424275e-06</Real>
+ <Real Name="Cell 7 8 3">2.5235336174053621e-07</Real>
+ <Real Name="Cell 7 8 4">1.9015786608437929e-10</Real>
+ <Real Name="Cell 8 4 0">0.00016503810988016999</Real>
+ <Real Name="Cell 8 4 1">0.0033853667014057658</Real>
+ <Real Name="Cell 8 4 2">0.0052192394724740344</Real>
+ <Real Name="Cell 8 4 3">0.00082107930776961183</Real>
+ <Real Name="Cell 8 4 4">6.1871451988835687e-07</Real>
+ <Real Name="Cell 8 5 0">0.0023035570242339785</Real>
+ <Real Name="Cell 8 5 1">0.047252027124482197</Real>
+ <Real Name="Cell 8 5 2">0.072848724192892594</Real>
+ <Real Name="Cell 8 5 3">0.011460401529314424</Real>
+ <Real Name="Cell 8 5 4">8.6358488916239541e-06</Real>
+ <Real Name="Cell 8 6 0">0.0027411448894219905</Real>
+ <Real Name="Cell 8 6 1">0.056228107793500619</Real>
+ <Real Name="Cell 8 6 2">0.086687199805120491</Real>
+ <Real Name="Cell 8 6 3">0.013637440164195965</Real>
+ <Real Name="Cell 8 6 4">1.0276330390808299e-05</Real>
+ <Real Name="Cell 8 7 0">0.00031268909183769354</Real>
+ <Real Name="Cell 8 7 1">0.0064140775737721199</Real>
+ <Real Name="Cell 8 7 2">0.0098886205853684454</Real>
+ <Real Name="Cell 8 7 3">0.0015556561042756505</Real>
+ <Real Name="Cell 8 7 4">1.1722461040735086e-06</Real>
+ <Real Name="Cell 8 8 0">9.2974917085060422e-09</Real>
+ <Real Name="Cell 8 8 1">1.9071606466788833e-07</Real>
+ <Real Name="Cell 8 8 2">2.9402806270180973e-07</Real>
+ <Real Name="Cell 8 8 3">4.6255850006745022e-08</Real>
+ <Real Name="Cell 8 8 4">3.4855544109000254e-11</Real>
+ <Real Name="Cell 9 4 0">2.9187444766006241e-07</Real>
+ <Real Name="Cell 9 4 1">5.9871143508430354e-06</Real>
+ <Real Name="Cell 9 4 2">9.2303689089752043e-06</Real>
+ <Real Name="Cell 9 4 3">1.4521013941226495e-06</Real>
+ <Real Name="Cell 9 4 4">1.0942136872677136e-09</Real>
+ <Real Name="Cell 9 5 0">4.0739041097230541e-06</Real>
+ <Real Name="Cell 9 5 1">8.3566512775687409e-05</Real>
+ <Real Name="Cell 9 5 2">0.0001288349772787573</Real>
+ <Real Name="Cell 9 5 3">2.0268036084271086e-05</Real>
+ <Real Name="Cell 9 5 4">1.5272736867555231e-08</Real>
+ <Real Name="Cell 9 6 0">4.8477903142320106e-06</Real>
+ <Real Name="Cell 9 6 1">9.9440958922241982e-05</Real>
+ <Real Name="Cell 9 6 2">0.00015330870294556813</Real>
+ <Real Name="Cell 9 6 3">2.411818893413122e-05</Real>
+ <Real Name="Cell 9 6 4">1.8173973629286428e-08</Real>
+ <Real Name="Cell 9 7 0">5.5299928020091375e-07</Real>
+ <Real Name="Cell 9 7 1">1.1343473034518021e-05</Real>
+ <Real Name="Cell 9 7 2">1.748829814865161e-05</Real>
+ <Real Name="Cell 9 7 3">2.7512207120775846e-06</Real>
+ <Real Name="Cell 9 7 4">2.0731495555574459e-09</Real>
+ <Real Name="Cell 9 8 0">1.644287043165097e-11</Real>
+ <Real Name="Cell 9 8 1">3.3728661868012003e-10</Real>
+ <Real Name="Cell 9 8 2">5.1999673566281217e-10</Real>
+ <Real Name="Cell 9 8 3">8.1804746076939808e-11</Real>
+ <Real Name="Cell 9 8 4">6.1642990774022262e-14</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>0.16666666666666666</Real>
+ <Real>0.66666666666666663</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>0.13492625972833858</Real>
+ <Real>0.66219988218971215</Real>
+ <Real>0.20282145274007193</Real>
+ <Real>5.2405341877301998e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>0.010666680130309107</Real>
+ <Real>0.41466677774166727</Real>
+ <Real>0.53866657242119786</Real>
+ <Real>0.03599996970682575</Real>
+ <Real>0.00091594116288747595</Real>
+ <Real>0.26772523897369466</Real>
+ <Real>0.63827253429257058</Real>
+ <Real>0.093086285570847194</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>0.016222667549530681</Real>
+ <Real>0.45379867202893892</Real>
+ <Real>0.50373466163818037</Real>
+ <Real>0.026243998783350007</Real>
+ <Real>0.016222667549530681</Real>
+ <Real>0.45379867202893892</Real>
+ <Real>0.50373466163818037</Real>
+ <Real>0.026243998783350007</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>-0.5</Real>
+ <Real>0</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>-0.43431199655580521</Real>
+ <Real>-0.12906400663709638</Real>
+ <Real>0.56106400294160841</Real>
+ <Real>0.0023120002512931892</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>-0.080000067318198045</Real>
+ <Real>-0.65999996634086555</Real>
+ <Real>0.56000013463632525</Real>
+ <Real>0.17999989902273833</Real>
+ <Real>-0.015570977931379222</Real>
+ <Real>-0.62975790193448478</Real>
+ <Real>0.30622873766310715</Real>
+ <Real>0.3391001422027568</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>-0.10580000383853916</Real>
+ <Real>-0.64259999682903279</Real>
+ <Real>0.60260000517368306</Real>
+ <Real>0.14579999549388889</Real>
+ <Real>-0.10580000383853916</Real>
+ <Real>-0.64259999682903279</Real>
+ <Real>0.60260000517368306</Real>
+ <Real>0.14579999549388889</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 3 1">8.9693436549661624e-05</Real>
+ <Real Name="Cell 0 3 2">0.0025090055178456677</Real>
+ <Real Name="Cell 0 3 3">0.0027850963951250112</Real>
+ <Real Name="Cell 0 3 4">0.00014510033152666677</Real>
+ <Real Name="Cell 0 4 1">0.0034868288787382124</Real>
+ <Real Name="Cell 0 4 2">0.097537492519800234</Real>
+ <Real Name="Cell 0 4 3">0.10827051470164921</Real>
+ <Real Name="Cell 0 4 4">0.0056407697791971724</Real>
+ <Real Name="Cell 0 5 1">0.0045374713720079014</Real>
+ <Real Name="Cell 0 5 2">0.12692724403676031</Real>
+ <Real Name="Cell 0 5 3">0.14089431342242198</Real>
+ <Real Name="Cell 0 5 4">0.007340432318105777</Real>
+ <Real Name="Cell 0 6 1">0.0026291907002765156</Real>
+ <Real Name="Cell 0 6 2">0.073546674408108401</Real>
+ <Real Name="Cell 0 6 3">0.081639747824602149</Real>
+ <Real Name="Cell 0 6 4">0.0042533373336155313</Real>
+ <Real Name="Cell 0 7 1">0.0055464540100770522</Real>
+ <Real Name="Cell 0 7 2">0.15515163930702414</Real>
+ <Real Name="Cell 0 7 3">0.17222452013686987</Real>
+ <Real Name="Cell 0 7 4">0.0089727001954484336</Real>
+ <Real Name="Cell 0 8 1">0.00080890023328333068</Real>
+ <Real Name="Cell 0 8 2">0.022627465584628456</Real>
+ <Real Name="Cell 0 8 3">0.025117391086758218</Real>
+ <Real Name="Cell 0 8 4">0.0013085873006596508</Real>
+ <Real Name="Cell 1 3 1">0.00035877374619864649</Real>
+ <Real Name="Cell 1 3 2">0.010036022071382671</Real>
+ <Real Name="Cell 1 3 3">0.011140385580500045</Real>
+ <Real Name="Cell 1 3 4">0.00058040132610666709</Real>
+ <Real Name="Cell 1 4 1">0.01394731551495285</Real>
+ <Real Name="Cell 1 4 2">0.39014997007920094</Real>
+ <Real Name="Cell 1 4 3">0.43308205880659684</Real>
+ <Real Name="Cell 1 4 4">0.02256307911678869</Real>
+ <Real Name="Cell 1 5 1">0.018157111491429602</Real>
+ <Real Name="Cell 1 5 2">0.5079111100276793</Real>
+ <Real Name="Cell 1 5 3">0.56380163037530839</Real>
+ <Real Name="Cell 1 5 4">0.029373419040693738</Real>
+ <Real Name="Cell 1 6 1">0.012628889174436301</Real>
+ <Real Name="Cell 1 6 2">0.35326946811072585</Real>
+ <Real Name="Cell 1 6 3">0.39214322772303806</Real>
+ <Real Name="Cell 1 6 4">0.020430212917637993</Real>
+ <Real Name="Cell 1 7 1">0.027221248105733033</Real>
+ <Real Name="Cell 1 7 2">0.76146331690741509</Real>
+ <Real Name="Cell 1 7 3">0.84525471301463506</Real>
+ <Real Name="Cell 1 7 4">0.044036802208203656</Real>
+ <Real Name="Cell 1 8 1">0.0039699732302810493</Real>
+ <Real Name="Cell 1 8 2">0.11105254881119081</Real>
+ <Real Name="Cell 1 8 3">0.12327276730306372</Real>
+ <Real Name="Cell 1 8 4">0.0064223699528652492</Real>
+ <Real Name="Cell 2 3 1">8.9693436549661624e-05</Real>
+ <Real Name="Cell 2 3 2">0.0025090055178456677</Real>
+ <Real Name="Cell 2 3 3">0.0027850963951250112</Real>
+ <Real Name="Cell 2 3 4">0.00014510033152666677</Real>
+ <Real Name="Cell 2 4 1">0.0034868288787382124</Real>
+ <Real Name="Cell 2 4 2">0.097537492519800234</Real>
+ <Real Name="Cell 2 4 3">0.10827051470164921</Real>
+ <Real Name="Cell 2 4 4">0.0056407697791971724</Real>
+ <Real Name="Cell 2 5 1">0.0045414765275090477</Real>
+ <Real Name="Cell 2 5 2">0.12703928074355594</Real>
+ <Real Name="Cell 2 5 3">0.14101867864441883</Real>
+ <Real Name="Cell 2 5 4">0.0073469116036966519</Real>
+ <Real Name="Cell 2 6 1">0.0037998785753481233</Real>
+ <Real Name="Cell 2 6 2">0.10629447013565169</Real>
+ <Real Name="Cell 2 6 3">0.11799110982056298</Real>
+ <Real Name="Cell 2 6 4">0.0061472016487941232</Real>
+ <Real Name="Cell 2 7 1">0.0083374419638162847</Real>
+ <Real Name="Cell 2 7 2">0.23322428816015744</Real>
+ <Real Name="Cell 2 7 3">0.25888828047224965</Real>
+ <Real Name="Cell 2 7 4">0.013487782825271294</Real>
+ <Real Name="Cell 2 8 1">0.0012159406239128868</Real>
+ <Real Name="Cell 2 8 2">0.034013656429375004</Real>
+ <Real Name="Cell 2 8 3">0.037756517964062937</Real>
+ <Real Name="Cell 2 8 4">0.0019670713313433359</Real>
+ <Real Name="Cell 3 5 1">3.0914050612255641e-09</Real>
+ <Real Name="Cell 3 5 2">8.6476253501742167e-08</Real>
+ <Real Name="Cell 3 5 3">9.5992097338397879e-08</Real>
+ <Real Name="Cell 3 5 4">5.0010783009599958e-09</Real>
+ <Real Name="Cell 3 6 1">9.0360297398576509e-07</Real>
+ <Real Name="Cell 3 6 2">2.5276596982843479e-05</Real>
+ <Real Name="Cell 3 6 3">2.8058032809107341e-05</Real>
+ <Real Name="Cell 3 6 4">1.4617913655390116e-06</Real>
+ <Real Name="Cell 3 7 1">2.154242022198236e-06</Real>
+ <Real Name="Cell 3 7 2">6.0260876697234485e-05</Real>
+ <Real Name="Cell 3 7 3">6.6891981409689403e-05</Real>
+ <Real Name="Cell 3 7 4">3.4849955987199861e-06</Real>
+ <Real Name="Cell 3 8 1">3.1417674628491136e-07</Real>
+ <Real Name="Cell 3 8 2">8.7885047148482228e-06</Real>
+ <Real Name="Cell 3 8 3">9.7555914587544357e-06</Real>
+ <Real Name="Cell 3 8 4">5.0825513881017745e-07</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>0.16666666666666666</Real>
+ <Real>0.66666666666666663</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>0.12946419015888011</Real>
+ <Real>0.66040937121180099</Real>
+ <Real>0.21003868271136564</Real>
+ <Real>8.775591795322617e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>0.12150009655954666</Real>
+ <Real>0.65716671077405386</Real>
+ <Real>0.22116652719182275</Real>
+ <Real>0.00016666547457665597</Real>
+ <Real>0.070312598610667756</Real>
+ <Real>0.61197930910415455</Real>
+ <Real>0.3151039365752315</Real>
+ <Real>0.0026041557099462918</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>0.082173168712625921</Real>
+ <Real>0.62719716898668798</Real>
+ <Real>0.28908616244525709</Real>
+ <Real>0.0015434998554289384</Real>
+ <Real>0.082173168712625921</Real>
+ <Real>0.62719716898668798</Real>
+ <Real>0.28908616244525709</Real>
+ <Real>0.0015434998554289384</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>-0.5</Real>
+ <Real>0</Real>
+ <Real>0.5</Real>
+ <Real>0</Real>
+ <Real>-0.42251027721597068</Real>
+ <Real>-0.151719163963696</Real>
+ <Real>0.57096915957530403</Real>
+ <Real>0.0032602816043626613</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>-0.40500021457674196</Real>
+ <Real>-0.1849995946883447</Real>
+ <Real>0.58499983310691528</Real>
+ <Real>0.0049999761581713646</Real>
+ <Real>-0.28125026296171923</Real>
+ <Real>-0.40624956173038601</Real>
+ <Real>0.65624991234592966</Real>
+ <Real>0.031249912346175537</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>-0.31205000517964365</Real>
+ <Real>-0.35384999101757997</Real>
+ <Real>0.64384999757409089</Real>
+ <Real>0.022049998623132727</Real>
+ <Real>-0.31205000517964365</Real>
+ <Real>-0.35384999101757997</Real>
+ <Real>0.64384999757409089</Real>
+ <Real>0.022049998623132727</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">8</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 10 1">0.013308344424649362</Real>
+ <Real Name="Cell 0 10 2">0.10157763267266268</Real>
+ <Real Name="Cell 0 10 3">0.046818910338922895</Real>
+ <Real Name="Cell 0 10 4">0.00024997731032232439</Real>
+ <Real Name="Cell 0 11 1">0.00010998593511734224</Real>
+ <Real Name="Cell 0 11 2">0.00083948164850738407</Real>
+ <Real Name="Cell 0 11 3">0.00038693179786238589</Real>
+ <Real Name="Cell 0 11 4">2.0659210008868769e-06</Real>
+ <Real Name="Cell 0 5 1">0.0051750646708077115</Real>
+ <Real Name="Cell 0 5 2">0.039499339768735334</Real>
+ <Real Name="Cell 0 5 3">0.018205937650058786</Real>
+ <Real Name="Cell 0 5 4">9.7205836118618557e-05</Real>
+ <Real Name="Cell 0 6 1">0.027990761522489485</Real>
+ <Real Name="Cell 0 6 2">0.21364304991185623</Real>
+ <Real Name="Cell 0 6 3">0.098471824309892403</Real>
+ <Real Name="Cell 0 6 4">0.0005257645170578673</Real>
+ <Real Name="Cell 0 7 1">0.0094201660216351821</Real>
+ <Real Name="Cell 0 7 2">0.07190061613440453</Real>
+ <Real Name="Cell 0 7 3">0.033140253533551434</Real>
+ <Real Name="Cell 0 7 4">0.00017694370462163306</Real>
+ <Real Name="Cell 0 8 1">0.0029767357050703548</Real>
+ <Real Name="Cell 0 8 2">0.022720314140141636</Real>
+ <Real Name="Cell 0 8 3">0.010472190802353036</Real>
+ <Real Name="Cell 0 8 4">5.5913520220868544e-05</Real>
+ <Real Name="Cell 0 9 1">0.025846809515731168</Real>
+ <Real Name="Cell 0 9 2">0.19727906334362821</Real>
+ <Real Name="Cell 0 9 3">0.090929376235776224</Real>
+ <Real Name="Cell 0 9 4">0.00048549359086234878</Real>
+ <Real Name="Cell 1 10 1">0.067887153679846504</Real>
+ <Real Name="Cell 1 10 2">0.51815734096209587</Real>
+ <Real Name="Cell 1 10 3">0.2388277955456623</Real>
+ <Real Name="Cell 1 10 4">0.0012751584675622365</Real>
+ <Real Name="Cell 1 11 1">0.00056104890598586703</Real>
+ <Real Name="Cell 1 11 2">0.0042822771837852536</Real>
+ <Real Name="Cell 1 11 3">0.001973776571070009</Real>
+ <Real Name="Cell 1 11 4">1.0538463087704832e-05</Real>
+ <Real Name="Cell 1 5 1">0.020700258683230846</Real>
+ <Real Name="Cell 1 5 2">0.15799735907494133</Real>
+ <Real Name="Cell 1 5 3">0.072823750600235146</Real>
+ <Real Name="Cell 1 5 4">0.00038882334447447423</Real>
+ <Real Name="Cell 1 6 1">0.11196304608995794</Real>
+ <Real Name="Cell 1 6 2">0.85457219964742492</Real>
+ <Real Name="Cell 1 6 3">0.39388729723956961</Real>
+ <Real Name="Cell 1 6 4">0.0021030580682314692</Real>
+ <Real Name="Cell 1 7 1">0.037680664086540729</Real>
+ <Real Name="Cell 1 7 2">0.28760246453761812</Real>
+ <Real Name="Cell 1 7 3">0.13256101413420573</Real>
+ <Real Name="Cell 1 7 4">0.00070777481848653223</Real>
+ <Real Name="Cell 1 8 1">0.015176800632591584</Real>
+ <Real Name="Cell 1 8 2">0.11583886249203681</Real>
+ <Real Name="Cell 1 8 3">0.053392160991334946</Real>
+ <Real Name="Cell 1 8 4">0.00028507346070834452</Real>
+ <Real Name="Cell 1 9 1">0.13184707832464976</Real>
+ <Real Name="Cell 1 9 2">1.0063396064667087</Real>
+ <Real Name="Cell 1 9 3">0.46383955370867708</Real>
+ <Real Name="Cell 1 9 4">0.0024765498218100976</Real>
+ <Real Name="Cell 2 10 1">0.021591044817814965</Real>
+ <Real Name="Cell 2 10 2">0.16479639762410112</Real>
+ <Real Name="Cell 2 10 3">0.075957546573309276</Real>
+ <Real Name="Cell 2 10 4">0.00040555542736100698</Real>
+ <Real Name="Cell 2 11 1">0.00017843776646247957</Real>
+ <Real Name="Cell 2 11 2">0.0013619489636205195</Real>
+ <Real Name="Cell 2 11 3">0.00062774613599652198</Real>
+ <Real Name="Cell 2 11 4">3.3516860923434464e-06</Real>
+ <Real Name="Cell 2 5 1">0.0051750646708077115</Real>
+ <Real Name="Cell 2 5 2">0.039499339768735334</Real>
+ <Real Name="Cell 2 5 3">0.018205937650058786</Real>
+ <Real Name="Cell 2 5 4">9.7205836118618557e-05</Real>
+ <Real Name="Cell 2 6 1">0.027990761522489485</Real>
+ <Real Name="Cell 2 6 2">0.21364304991185623</Real>
+ <Real Name="Cell 2 6 3">0.098471824309892403</Real>
+ <Real Name="Cell 2 6 4">0.0005257645170578673</Real>
+ <Real Name="Cell 2 7 1">0.0094201660216351821</Real>
+ <Real Name="Cell 2 7 2">0.07190061613440453</Real>
+ <Real Name="Cell 2 7 3">0.033140253533551434</Real>
+ <Real Name="Cell 2 7 4">0.00017694370462163306</Real>
+ <Real Name="Cell 2 8 1">0.0048249455195422519</Real>
+ <Real Name="Cell 2 8 2">0.036827010784445141</Real>
+ <Real Name="Cell 2 8 3">0.016974214407258117</Real>
+ <Real Name="Cell 2 8 4">9.0629372440419111e-05</Real>
+ <Real Name="Cell 2 9 1">0.041933061306863598</Real>
+ <Real Name="Cell 2 9 2">0.32005942755581029</Real>
+ <Real Name="Cell 2 9 3">0.1475209969713667</Real>
+ <Real Name="Cell 2 9 4">0.00078764972896672506</Real>
+ <Real Name="Cell 3 10 1">9.0209190664195251e-06</Real>
+ <Real Name="Cell 3 10 2">6.8853312933605122e-05</Real>
+ <Real Name="Cell 3 10 3">3.1735698105551808e-05</Real>
+ <Real Name="Cell 3 10 4">1.6944444875368788e-07</Real>
+ <Real Name="Cell 3 11 1">7.4552790901649246e-08</Real>
+ <Real Name="Cell 3 11 2">5.6903366544250517e-07</Real>
+ <Real Name="Cell 3 11 3">2.6227758475169961e-07</Real>
+ <Real Name="Cell 3 11 4">1.4003624757485909e-09</Real>
+ <Real Name="Cell 3 8 1">2.0129366465881636e-06</Real>
+ <Real Name="Cell 3 8 2">1.5363995156434422e-05</Real>
+ <Real Name="Cell 3 8 3">7.0815345145402185e-06</Real>
+ <Real Name="Cell 3 8 4">3.7809998953089617e-08</Real>
+ <Real Name="Cell 3 9 1">1.7519983652866431e-05</Real>
+ <Real Name="Cell 3 9 2">0.00013372350512853588</Real>
+ <Real Name="Cell 3 9 3">6.163550608621703e-05</Real>
+ <Real Name="Cell 3 9 4">3.2908664298790362e-07</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>0.041666666666666664</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0</Real>
+ <Real>0.031437818392048296</Real>
+ <Real>0.4233309838221333</Real>
+ <Real>0.49102546437496075</Real>
+ <Real>0.054204842519997236</Real>
+ <Real>8.9089086032996169e-07</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>0.0010666684618193696</Real>
+ <Real>0.15473340132470725</Real>
+ <Real>0.59273335420195306</Real>
+ <Real>0.24606658207015428</Real>
+ <Real>0.0053999939413659995</Real>
+ <Real>4.0409225623249791e-05</Real>
+ <Real>0.079618265847521158</Real>
+ <Real>0.53627789409703197</Real>
+ <Real>0.36489861308950189</Real>
+ <Real>0.019164817740321645</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>0.0018656068020391501</Real>
+ <Real>0.17999357698475202</Real>
+ <Real>0.59795897375003171</Real>
+ <Real>0.21663890268217406</Real>
+ <Real>0.0035429397810030033</Real>
+ <Real>0.0018656068020391501</Real>
+ <Real>0.17999357698475202</Real>
+ <Real>0.59795897375003171</Real>
+ <Real>0.21663890268217406</Real>
+ <Real>0.0035429397810030033</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>-0.16666666666666666</Real>
+ <Real>-0.5</Real>
+ <Real>0.5</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>-0.13492625972833858</Real>
+ <Real>-0.52727362246137355</Real>
+ <Real>0.45937842944964025</Real>
+ <Real>0.20276904739819462</Real>
+ <Real>5.2405341877301998e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>-0.010666680130309107</Real>
+ <Real>-0.40400009761135819</Real>
+ <Real>-0.12399979467953059</Real>
+ <Real>0.50266660271437213</Real>
+ <Real>0.03599996970682575</Real>
+ <Real>-0.00091594116288747595</Real>
+ <Real>-0.2668092978108072</Real>
+ <Real>-0.37054729531887592</Real>
+ <Real>0.54518624872172339</Real>
+ <Real>0.093086285570847194</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>-0.016222667549530681</Real>
+ <Real>-0.43757600447940825</Real>
+ <Real>-0.049935989609241449</Real>
+ <Real>0.47749066285483038</Real>
+ <Real>0.026243998783350007</Real>
+ <Real>-0.016222667549530681</Real>
+ <Real>-0.43757600447940825</Real>
+ <Real>-0.049935989609241449</Real>
+ <Real>0.47749066285483038</Real>
+ <Real>0.026243998783350007</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">3</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 3 1">2.5786874325345551e-07</Real>
+ <Real Name="Cell 0 3 2">2.4879153227796859e-05</Real>
+ <Real Name="Cell 0 3 3">8.2651354459850881e-05</Real>
+ <Real Name="Cell 0 3 4">2.9944359933400128e-05</Real>
+ <Real Name="Cell 0 3 5">4.8971381737637177e-07</Real>
+ <Real Name="Cell 0 4 1">3.740703805086502e-05</Real>
+ <Real Name="Cell 0 4 2">0.0036090276771185504</Real>
+ <Real Name="Cell 0 4 3">0.011989597196727115</Real>
+ <Real Name="Cell 0 4 4">0.0043437983111296935</Real>
+ <Real Name="Cell 0 4 5">7.1039022292930911e-05</Real>
+ <Real Name="Cell 0 5 1">0.00014330361015577525</Real>
+ <Real Name="Cell 0 5 2">0.013825919458791263</Real>
+ <Real Name="Cell 0 5 3">0.045931264599679444</Real>
+ <Real Name="Cell 0 5 4">0.01664077168919419</Real>
+ <Real Name="Cell 0 5 5">0.00027214526695941346</Real>
+ <Real Name="Cell 0 6 1">7.8025524233388239e-05</Real>
+ <Real Name="Cell 0 6 2">0.0075278955820312684</Real>
+ <Real Name="Cell 0 6 3">0.025008518593472612</Real>
+ <Real Name="Cell 0 6 4">0.0090605179680127955</Real>
+ <Real Name="Cell 0 6 5">0.0001481768470386848</Real>
+ <Real Name="Cell 0 7 1">0.00012617396484298417</Real>
+ <Real Name="Cell 0 7 2">0.012173252814909323</Real>
+ <Real Name="Cell 0 7 3">0.040440919516919797</Real>
+ <Real Name="Cell 0 7 4">0.014651634664263882</Real>
+ <Real Name="Cell 0 7 5">0.00023961467061573354</Real>
+ <Real Name="Cell 0 8 1">8.4964056669811633e-05</Real>
+ <Real Name="Cell 0 8 2">0.0081973245693674566</Real>
+ <Real Name="Cell 0 8 3">0.027232437229746949</Real>
+ <Real Name="Cell 0 8 4">0.0098662376146223876</Real>
+ <Real Name="Cell 0 8 5">0.00016135368717665739</Real>
+ <Real Name="Cell 0 9 1">4.4623920238247299e-06</Real>
+ <Real Name="Cell 0 9 2">0.0004305311823469566</Real>
+ <Real Name="Cell 0 9 3">0.0014302731701664149</Real>
+ <Real Name="Cell 0 9 4">0.00051818406232354019</Real>
+ <Real Name="Cell 0 9 5">8.474447135569224e-06</Real>
+ <Real Name="Cell 1 3 1">2.83655617578801e-06</Real>
+ <Real Name="Cell 1 3 2">0.00027367068550576538</Real>
+ <Real Name="Cell 1 3 3">0.00090916489905835962</Real>
+ <Real Name="Cell 1 3 4">0.0003293879592674014</Real>
+ <Real Name="Cell 1 3 5">5.3868519911400891e-06</Real>
+ <Real Name="Cell 1 4 1">0.00041147741855951522</Real>
+ <Real Name="Cell 1 4 2">0.039699304448304058</Real>
+ <Real Name="Cell 1 4 3">0.13188556916399827</Real>
+ <Real Name="Cell 1 4 4">0.047781781422426631</Real>
+ <Real Name="Cell 1 4 5">0.00078142924522224002</Real>
+ <Real Name="Cell 1 5 1">0.0015763629111161547</Real>
+ <Real Name="Cell 1 5 2">0.1520873523229892</Real>
+ <Real Name="Cell 1 5 3">0.5052513464028674</Real>
+ <Real Name="Cell 1 5 4">0.18305118255347932</Real>
+ <Real Name="Cell 1 5 5">0.0029936419941150733</Real>
+ <Real Name="Cell 1 6 1">0.00090399053153762546</Real>
+ <Real Name="Cell 1 6 2">0.087216925428207095</Real>
+ <Real Name="Cell 1 6 3">0.28974446808789062</Real>
+ <Real Name="Cell 1 6 4">0.10497362926278433</Real>
+ <Real Name="Cell 1 6 5">0.0017167518966665367</Real>
+ <Real Name="Cell 1 7 1">0.0016957969392537985</Real>
+ <Real Name="Cell 1 7 2">0.16361033664889055</Real>
+ <Real Name="Cell 1 7 3">0.54353200062108642</Real>
+ <Real Name="Cell 1 7 4">0.19692015900144796</Real>
+ <Real Name="Cell 1 7 5">0.0032204569741161007</Real>
+ <Real Name="Cell 1 8 1">0.0011440971269383109</Real>
+ <Real Name="Cell 1 8 2">0.11038238822377695</Real>
+ <Real Name="Cell 1 8 3">0.36670274955399507</Real>
+ <Real Name="Cell 1 8 4">0.13285540440291682</Real>
+ <Real Name="Cell 1 8 5">0.0021727339436854827</Real>
+ <Real Name="Cell 1 9 1">6.0089055229213171e-05</Real>
+ <Real Name="Cell 1 9 2">0.0057973866607468711</Real>
+ <Real Name="Cell 1 9 3">0.019259572681229575</Real>
+ <Real Name="Cell 1 9 4">0.0069776905690077549</Real>
+ <Real Name="Cell 1 9 5">0.00011411402656860506</Real>
+ <Real Name="Cell 2 3 1">2.83655617578801e-06</Real>
+ <Real Name="Cell 2 3 2">0.00027367068550576538</Real>
+ <Real Name="Cell 2 3 3">0.00090916489905835962</Real>
+ <Real Name="Cell 2 3 4">0.0003293879592674014</Real>
+ <Real Name="Cell 2 3 5">5.3868519911400891e-06</Real>
+ <Real Name="Cell 2 4 1">0.00041147741855951522</Real>
+ <Real Name="Cell 2 4 2">0.039699304448304058</Real>
+ <Real Name="Cell 2 4 3">0.13188556916399827</Real>
+ <Real Name="Cell 2 4 4">0.047781781422426631</Real>
+ <Real Name="Cell 2 4 5">0.00078142924522224002</Real>
+ <Real Name="Cell 2 5 1">0.0015763831713481692</Real>
+ <Real Name="Cell 2 5 2">0.15208930702835738</Real>
+ <Real Name="Cell 2 5 3">0.50525784015467523</Real>
+ <Real Name="Cell 2 5 4">0.18305353522201961</Real>
+ <Real Name="Cell 2 5 5">0.0029936804699514058</Real>
+ <Real Name="Cell 2 6 1">0.00094390925093352292</Real>
+ <Real Name="Cell 2 6 2">0.091068279896289378</Real>
+ <Real Name="Cell 2 6 3">0.30253910222906988</Real>
+ <Real Name="Cell 2 6 4">0.10960909025968489</Real>
+ <Real Name="Cell 2 6 5">0.0017925608070970924</Real>
+ <Real Name="Cell 2 7 1">0.0019646740184617322</Real>
+ <Real Name="Cell 2 7 2">0.18955157314253454</Real>
+ <Real Name="Cell 2 7 3">0.6297117155386931</Real>
+ <Real Name="Cell 2 7 4">0.22814283428989943</Real>
+ <Real Name="Cell 2 7 5">0.0037310765211098474</Real>
+ <Real Name="Cell 2 8 1">0.0013270486794346719</Real>
+ <Real Name="Cell 2 8 2">0.12803353760463274</Real>
+ <Real Name="Cell 2 8 3">0.42534185960501181</Real>
+ <Real Name="Cell 2 8 4">0.15410019378377163</Real>
+ <Real Name="Cell 2 8 5">0.0025201738933185646</Real>
+ <Real Name="Cell 2 9 1">6.9697842528280385e-05</Real>
+ <Real Name="Cell 2 9 2">0.0067244415978077558</Real>
+ <Real Name="Cell 2 9 3">0.022339353793762201</Real>
+ <Real Name="Cell 2 9 4">0.0080934868527161204</Real>
+ <Real Name="Cell 2 9 5">0.00013236189891333038</Real>
+ <Real Name="Cell 3 3 1">2.5786874325345551e-07</Real>
+ <Real Name="Cell 3 3 2">2.4879153227796859e-05</Real>
+ <Real Name="Cell 3 3 3">8.2651354459850881e-05</Real>
+ <Real Name="Cell 3 3 4">2.9944359933400128e-05</Real>
+ <Real Name="Cell 3 3 5">4.8971381737637177e-07</Real>
+ <Real Name="Cell 3 4 1">3.740703805086502e-05</Real>
+ <Real Name="Cell 3 4 2">0.0036090276771185504</Real>
+ <Real Name="Cell 3 4 3">0.011989597196727115</Real>
+ <Real Name="Cell 3 4 4">0.0043437983111296935</Real>
+ <Real Name="Cell 3 4 5">7.1039022292930911e-05</Real>
+ <Real Name="Cell 3 5 1">0.00014331042408192321</Real>
+ <Real Name="Cell 3 5 2">0.013826576865775059</Real>
+ <Real Name="Cell 3 5 3">0.04593344857986336</Real>
+ <Real Name="Cell 3 5 4">0.016641562939248615</Real>
+ <Real Name="Cell 3 5 5">0.00027215820716202635</Real>
+ <Real Name="Cell 3 6 1">9.1450997628283247e-05</Real>
+ <Real Name="Cell 3 6 2">0.0088231840514019239</Real>
+ <Real Name="Cell 3 6 3">0.029311613052897353</Real>
+ <Real Name="Cell 3 6 4">0.010619517335446353</Real>
+ <Real Name="Cell 3 6 5">0.00017367291819236018</Real>
+ <Real Name="Cell 3 7 1">0.00021660276937457876</Real>
+ <Real Name="Cell 3 7 2">0.020897815767995674</Real>
+ <Real Name="Cell 3 7 3">0.069424902152516871</Real>
+ <Real Name="Cell 3 7 4">0.02515245239454484</Real>
+ <Real Name="Cell 3 7 5">0.00041134636058027727</Real>
+ <Real Name="Cell 3 8 1">0.0001464943672049502</Real>
+ <Real Name="Cell 3 8 2">0.014133763412802673</Real>
+ <Real Name="Cell 3 8 3">0.046953956952926076</Real>
+ <Real Name="Cell 3 8 4">0.017011290334979112</Real>
+ <Real Name="Cell 3 8 5">0.00027820477535565294</Real>
+ <Real Name="Cell 3 9 1">7.6940217001537177e-06</Real>
+ <Real Name="Cell 3 9 2">0.00074231852376142285</Real>
+ <Real Name="Cell 3 9 3">0.0024660659013494768</Real>
+ <Real Name="Cell 3 9 4">0.00089344893924714482</Real>
+ <Real Name="Cell 3 9 5">1.4611575991028642e-05</Real>
+ <Real Name="Cell 4 5 1">2.6663407980159471e-13</Real>
+ <Real Name="Cell 4 5 2">2.572483211203457e-11</Real>
+ <Real Name="Cell 4 5 3">8.5460795142190869e-11</Real>
+ <Real Name="Cell 4 5 4">3.0962212617767103e-11</Real>
+ <Real Name="Cell 4 5 5">5.0635990781533139e-13</Real>
+ <Real Name="Cell 4 6 1">5.2534892025840471e-10</Real>
+ <Real Name="Cell 4 6 2">5.068561672214742e-08</Real>
+ <Real Name="Cell 4 6 3">1.6838333826562169e-07</Real>
+ <Real Name="Cell 4 6 4">6.1004823463147626e-08</Real>
+ <Real Name="Cell 4 6 5">9.9768053292690404e-10</Real>
+ <Real Name="Cell 4 7 1">3.538547462988964e-09</Real>
+ <Real Name="Cell 4 7 2">3.4139874195223763e-07</Real>
+ <Real Name="Cell 4 7 3">1.1341651452074072e-06</Real>
+ <Real Name="Cell 4 7 4">4.1090493379034813e-07</Real>
+ <Real Name="Cell 4 7 5">6.7199908147246159e-09</Real>
+ <Real Name="Cell 4 8 1">2.407727552839278e-09</Real>
+ <Real Name="Cell 4 8 2">2.3229733841375152e-07</Real>
+ <Real Name="Cell 4 8 3">7.7171797132804255e-07</Real>
+ <Real Name="Cell 4 8 4">2.7959131282894596e-07</Real>
+ <Real Name="Cell 4 8 5">4.5724713907814518e-09</Real>
+ <Real Name="Cell 4 9 1">1.2645611154240632e-10</Real>
+ <Real Name="Cell 4 9 2">1.2200474303171441e-08</Real>
+ <Real Name="Cell 4 9 3">4.0531352372679661e-08</Real>
+ <Real Name="Cell 4 9 4">1.4684398240860733e-08</Real>
+ <Real Name="Cell 4 9 5">2.4015049025595398e-10</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>0.041666666666666664</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.45833333333333331</Real>
+ <Real>0.041666666666666664</Real>
+ <Real>0</Real>
+ <Real>0.029752489058852732</Real>
+ <Real>0.41658437180005581</Real>
+ <Real>0.49682555640762804</Real>
+ <Real>0.056835811160773388</Real>
+ <Real>1.7715726899575947e-06</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>0.027337528967867834</Real>
+ <Real>0.40631679437954138</Real>
+ <Real>0.50535822938281461</Real>
+ <Real>0.060983280642845715</Real>
+ <Real>4.1666269303803459e-06</Real>
+ <Real>0.013183618402672702</Real>
+ <Real>0.32486998158342723</Real>
+ <Real>0.56087229174427855</Real>
+ <Real>0.10091134876601435</Real>
+ <Real>0.00016275950360727571</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>0.016229200955435938</Real>
+ <Real>0.34661470190678911</Real>
+ <Real>0.54816403361650479</Real>
+ <Real>0.088911029781390039</Real>
+ <Real>8.1033739880025853e-05</Real>
+ <Real>0.016229200955435938</Real>
+ <Real>0.34661470190678911</Real>
+ <Real>0.54816403361650479</Real>
+ <Real>0.088911029781390039</Real>
+ <Real>8.1033739880025853e-05</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">10</Int>
+ <Real>-0.16666666666666666</Real>
+ <Real>-0.5</Real>
+ <Real>0.5</Real>
+ <Real>0.16666666666666666</Real>
+ <Real>0</Real>
+ <Real>-0.12946419015888011</Real>
+ <Real>-0.53094518105292088</Real>
+ <Real>0.45037068850043538</Real>
+ <Real>0.2099509267934124</Real>
+ <Real>8.775591795322617e-05</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">10</Int>
+ <Real>-0.12150009655954666</Real>
+ <Real>-0.53566661421450723</Real>
+ <Real>0.43600018358223114</Real>
+ <Real>0.22099986171724609</Real>
+ <Real>0.00016666547457665597</Real>
+ <Real>-0.070312598610667756</Real>
+ <Real>-0.5416667104934868</Real>
+ <Real>0.29687537252892304</Real>
+ <Real>0.31249978086528524</Real>
+ <Real>0.0026041557099462918</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">10</Int>
+ <Real>-0.082173168712625921</Real>
+ <Real>-0.54502400027406206</Real>
+ <Real>0.33811100654143089</Real>
+ <Real>0.28754266258982814</Real>
+ <Real>0.0015434998554289384</Real>
+ <Real>-0.082173168712625921</Real>
+ <Real>-0.54502400027406206</Real>
+ <Real>0.33811100654143089</Real>
+ <Real>0.28754266258982814</Real>
+ <Real>0.0015434998554289384</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">5</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">0</Int>
+ <Int Name="Y">8</Int>
+ <Int Name="Z">1</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 10 1">0.0010751645522037692</Real>
+ <Real Name="Cell 0 10 2">0.022962796614951739</Real>
+ <Real Name="Cell 0 10 3">0.036315191324320512</Real>
+ <Real Name="Cell 0 10 4">0.0058902460930379454</Real>
+ <Real Name="Cell 0 10 5">5.3683853500084065e-06</Real>
+ <Real Name="Cell 0 11 1">0.00019344208424144707</Real>
+ <Real Name="Cell 0 11 2">0.0041314338610810618</Real>
+ <Real Name="Cell 0 11 3">0.0065337778156883391</Real>
+ <Real Name="Cell 0 11 4">0.0010597647388921291</Real>
+ <Real Name="Cell 0 11 5">9.6587229274655367e-07</Real>
+ <Real Name="Cell 0 12 1">3.1200195015625759e-07</Real>
+ <Real Name="Cell 0 12 2">6.6635728551703785e-06</Real>
+ <Real Name="Cell 0 12 3">1.0538303639439763e-05</Real>
+ <Real Name="Cell 0 12 4">1.7092902329799047e-06</Real>
+ <Real Name="Cell 0 12 5">1.5578514888346727e-09</Real>
+ <Real Name="Cell 0 5 1">5.7491749784508192e-05</Real>
+ <Real Name="Cell 0 5 2">0.001227878425338146</Real>
+ <Real Name="Cell 0 5 3">0.0019418645161942477</Real>
+ <Real Name="Cell 0 5 4">0.00031496625689156278</Real>
+ <Real Name="Cell 0 5 5">2.8706105187051263e-07</Real>
+ <Real Name="Cell 0 6 1">0.00085449798711393883</Real>
+ <Real Name="Cell 0 6 2">0.018249916671605682</Real>
+ <Real Name="Cell 0 6 3">0.028861868469049271</Real>
+ <Real Name="Cell 0 6 4">0.0046813331222556476</Real>
+ <Real Name="Cell 0 6 5">4.2665789773589398e-06</Real>
+ <Real Name="Cell 0 7 1">0.0010627854810640884</Real>
+ <Real Name="Cell 0 7 2">0.022698410952050312</Real>
+ <Real Name="Cell 0 7 3">0.035897070827384997</Real>
+ <Real Name="Cell 0 7 4">0.0058224278458064039</Real>
+ <Real Name="Cell 0 7 5">5.3065756260766044e-06</Real>
+ <Real Name="Cell 0 8 1">0.00015352225267788552</Real>
+ <Real Name="Cell 0 8 2">0.0032788471837968359</Real>
+ <Real Name="Cell 0 8 3">0.005185429492732623</Real>
+ <Real Name="Cell 0 8 4">0.00084106553473771526</Real>
+ <Real Name="Cell 0 8 5">7.6654927888661482e-07</Real>
+ <Real Name="Cell 0 9 1">0.00062276851270917242</Real>
+ <Real Name="Cell 0 9 2">0.013300760954427771</Real>
+ <Real Name="Cell 0 9 3">0.021034880329192499</Real>
+ <Real Name="Cell 0 9 4">0.0034118124442750713</Real>
+ <Real Name="Cell 0 9 5">3.1095345854006703e-06</Real>
+ <Real Name="Cell 1 10 1">0.015054093413008941</Real>
+ <Real Name="Cell 1 10 2">0.32151737569552391</Real>
+ <Real Name="Cell 1 10 3">0.50847312756643193</Real>
+ <Real Name="Cell 1 10 4">0.0824732500048036</Real>
+ <Real Name="Cell 1 10 5">7.5166330930838442e-05</Real>
+ <Real Name="Cell 1 11 1">0.0027085111764603431</Real>
+ <Real Name="Cell 1 11 2">0.057846951098695719</Real>
+ <Real Name="Cell 1 11 3">0.09148376532281377</Real>
+ <Real Name="Cell 1 11 4">0.014838470392643226</Real>
+ <Real Name="Cell 1 11 5">1.3523819856449285e-05</Real>
+ <Real Name="Cell 1 12 1">4.3685466499672006e-06</Real>
+ <Real Name="Cell 1 12 2">9.3301111927947657e-05</Real>
+ <Real Name="Cell 1 12 3">0.0001475537926521143</Real>
+ <Real Name="Cell 1 12 4">2.3932908487803748e-05</Real>
+ <Real Name="Cell 1 12 5">2.1812513990014341e-08</Real>
+ <Real Name="Cell 1 5 1">0.00063240924762959002</Real>
+ <Real Name="Cell 1 5 2">0.013506662678719604</Real>
+ <Real Name="Cell 1 5 3">0.021360509678136724</Real>
+ <Real Name="Cell 1 5 4">0.0034646288258071904</Real>
+ <Real Name="Cell 1 5 5">3.1576715705756388e-06</Real>
+ <Real Name="Cell 1 6 1">0.0093994778582533259</Real>
+ <Real Name="Cell 1 6 2">0.20074908338766254</Real>
+ <Real Name="Cell 1 6 3">0.31748055315954199</Real>
+ <Real Name="Cell 1 6 4">0.051494664344812119</Real>
+ <Real Name="Cell 1 6 5">4.6932368750948339e-05</Real>
+ <Real Name="Cell 1 7 1">0.011690640291704973</Real>
+ <Real Name="Cell 1 7 2">0.24968252047255343</Real>
+ <Real Name="Cell 1 7 3">0.39486777910123499</Real>
+ <Real Name="Cell 1 7 4">0.064046706303870451</Real>
+ <Real Name="Cell 1 7 5">5.837233188684265e-05</Real>
+ <Real Name="Cell 1 8 1">0.0017646038879238295</Real>
+ <Real Name="Cell 1 8 2">0.037687477792393252</Real>
+ <Real Name="Cell 1 8 3">0.059601972247173424</Real>
+ <Real Name="Cell 1 8 4">0.0096673119805692799</Real>
+ <Real Name="Cell 1 8 5">8.8108128575120559e-06</Real>
+ <Real Name="Cell 1 9 1">0.0087197695148449033</Real>
+ <Real Name="Cell 1 9 2">0.18623223160420144</Real>
+ <Real Name="Cell 1 9 3">0.2945224501556627</Real>
+ <Real Name="Cell 1 9 4">0.047770909310328825</Real>
+ <Real Name="Cell 1 9 5">4.3538528891223591e-05</Real>
+ <Real Name="Cell 2 10 1">0.017953766013383547</Real>
+ <Real Name="Cell 2 10 2">0.38344705151665431</Real>
+ <Real Name="Cell 2 10 3">0.60641363820236704</Real>
+ <Real Name="Cell 2 10 4">0.098358990629749982</Real>
+ <Real Name="Cell 2 10 5">8.9644635554781787e-05</Real>
+ <Real Name="Cell 2 11 1">0.0032302161659752619</Real>
+ <Real Name="Cell 2 11 2">0.068989250705468977</Real>
+ <Real Name="Cell 2 11 3">0.10910508335292701</Real>
+ <Real Name="Cell 2 11 4">0.017696610358204752</Real>
+ <Real Name="Cell 2 11 5">1.6128735929061189e-05</Real>
+ <Real Name="Cell 2 12 1">5.2100025036569159e-06</Real>
+ <Real Name="Cell 2 12 2">0.00011127248160260143</Real>
+ <Real Name="Cell 2 12 3">0.00017597514476521862</Real>
+ <Real Name="Cell 2 12 4">2.8542790802562579e-05</Real>
+ <Real Name="Cell 2 12 5">2.6013972518727584e-08</Real>
+ <Real Name="Cell 2 5 1">0.00063240924762959002</Real>
+ <Real Name="Cell 2 5 2">0.013506662678719604</Real>
+ <Real Name="Cell 2 5 3">0.021360509678136724</Real>
+ <Real Name="Cell 2 5 4">0.0034646288258071904</Real>
+ <Real Name="Cell 2 5 5">3.1576715705756388e-06</Real>
+ <Real Name="Cell 2 6 1">0.0093994778582533259</Real>
+ <Real Name="Cell 2 6 2">0.20074908338766254</Real>
+ <Real Name="Cell 2 6 3">0.31748055315954199</Real>
+ <Real Name="Cell 2 6 4">0.051494664344812119</Real>
+ <Real Name="Cell 2 6 5">4.6932368750948339e-05</Real>
+ <Real Name="Cell 2 7 1">0.011690640291704973</Real>
+ <Real Name="Cell 2 7 2">0.24968252047255343</Real>
+ <Real Name="Cell 2 7 3">0.39486777910123499</Real>
+ <Real Name="Cell 2 7 4">0.064046706303870451</Real>
+ <Real Name="Cell 2 7 5">5.837233188684265e-05</Real>
+ <Real Name="Cell 2 8 1">0.0018327623218823642</Real>
+ <Real Name="Cell 2 8 2">0.039143169624285816</Real>
+ <Real Name="Cell 2 8 3">0.061904118987871723</Real>
+ <Real Name="Cell 2 8 4">0.010040715241036667</Real>
+ <Real Name="Cell 2 8 5">9.1511335438595772e-06</Real>
+ <Real Name="Cell 2 9 1">0.010399325802697977</Real>
+ <Real Name="Cell 2 9 2">0.2221033076755636</Real>
+ <Real Name="Cell 2 9 3">0.35125182037934749</Real>
+ <Real Name="Cell 2 9 4">0.056972291407874874</Real>
+ <Real Name="Cell 2 9 5">5.192469206200872e-05</Real>
+ <Real Name="Cell 3 10 1">0.0020538735207980365</Real>
+ <Real Name="Cell 3 10 2">0.043865545822033121</Real>
+ <Real Name="Cell 3 10 3">0.069372459974480716</Real>
+ <Real Name="Cell 3 10 4">0.011252064120489992</Real>
+ <Real Name="Cell 3 10 5">1.0255160009900213e-05</Real>
+ <Real Name="Cell 3 11 1">0.00036953001642133035</Real>
+ <Real Name="Cell 3 11 2">0.0078922269087184273</Real>
+ <Real Name="Cell 3 11 3">0.012481394795721081</Real>
+ <Real Name="Cell 3 11 4">0.0020244554482609718</Real>
+ <Real Name="Cell 3 11 5">1.8450938718900976e-06</Real>
+ <Real Name="Cell 3 12 1">5.9601345910243233e-07</Real>
+ <Real Name="Cell 3 12 2">1.2729340651243087e-05</Real>
+ <Real Name="Cell 3 12 3">2.0131190853353941e-05</Real>
+ <Real Name="Cell 3 12 4">3.2652359507949797e-06</Real>
+ <Real Name="Cell 3 12 5">2.9759443944603989e-09</Real>
+ <Real Name="Cell 3 5 1">5.7491749784508192e-05</Real>
+ <Real Name="Cell 3 5 2">0.001227878425338146</Real>
+ <Real Name="Cell 3 5 3">0.0019418645161942477</Real>
+ <Real Name="Cell 3 5 4">0.00031496625689156278</Real>
+ <Real Name="Cell 3 5 5">2.8706105187051263e-07</Real>
+ <Real Name="Cell 3 6 1">0.00085449798711393883</Real>
+ <Real Name="Cell 3 6 2">0.018249916671605682</Real>
+ <Real Name="Cell 3 6 3">0.028861868469049271</Real>
+ <Real Name="Cell 3 6 4">0.0046813331222556476</Real>
+ <Real Name="Cell 3 6 5">4.2665789773589398e-06</Real>
+ <Real Name="Cell 3 7 1">0.0010627854810640884</Real>
+ <Real Name="Cell 3 7 2">0.022698410952050312</Real>
+ <Real Name="Cell 3 7 3">0.035897070827384997</Real>
+ <Real Name="Cell 3 7 4">0.0058224278458064039</Real>
+ <Real Name="Cell 3 7 5">5.3065756260766044e-06</Real>
+ <Real Name="Cell 3 8 1">0.00017652735697550178</Real>
+ <Real Name="Cell 3 8 2">0.0037701780503224622</Real>
+ <Real Name="Cell 3 8 3">0.0059624591690658774</Real>
+ <Real Name="Cell 3 8 4">0.00096709808057566919</Real>
+ <Real Name="Cell 3 8 5">8.8141566341687076e-07</Real>
+ <Real Name="Cell 3 9 1">0.0011896589961273134</Real>
+ <Real Name="Cell 3 9 2">0.025408108473466265</Real>
+ <Real Name="Cell 3 9 3">0.040182401816084533</Real>
+ <Real Name="Cell 3 9 4">0.0065174993349839203</Real>
+ <Real Name="Cell 3 9 5">5.9400655585464031e-06</Real>
+ <Real Name="Cell 4 10 1">6.401925412448607e-08</Real>
+ <Real Name="Cell 4 10 2">1.3672894152697775e-06</Real>
+ <Real Name="Cell 4 10 3">2.1623401340806e-06</Real>
+ <Real Name="Cell 4 10 4">3.5072692892733134e-07</Real>
+ <Real Name="Cell 4 10 5">3.196534198006378e-10</Real>
+ <Real Name="Cell 4 11 1">1.1518253577129072e-08</Real>
+ <Real Name="Cell 4 11 2">2.4600077607555631e-07</Real>
+ <Real Name="Cell 4 11 3">3.8904517593899047e-07</Real>
+ <Real Name="Cell 4 11 4">6.3102292567441842e-08</Real>
+ <Real Name="Cell 4 11 5">5.7511590792683178e-11</Real>
+ <Real Name="Cell 4 12 1">1.8577744302904731e-11</Real>
+ <Real Name="Cell 4 12 2">3.9677365024524121e-10</Real>
+ <Real Name="Cell 4 12 3">6.2748938044083474e-10</Real>
+ <Real Name="Cell 4 12 4">1.0177743078801153e-10</Real>
+ <Real Name="Cell 4 12 5">9.2760210655656188e-14</Real>
+ <Real Name="Cell 4 8 1">1.5048085441627889e-09</Real>
+ <Real Name="Cell 4 8 2">3.2138906061611698e-08</Real>
+ <Real Name="Cell 4 8 3">5.0827019990319494e-08</Real>
+ <Real Name="Cell 4 8 4">8.2440335573350497e-09</Real>
+ <Real Name="Cell 4 8 5">7.5136332633852933e-12</Real>
+ <Real Name="Cell 4 9 1">3.7081407326659395e-08</Real>
+ <Real Name="Cell 4 9 2">7.9196511165937594e-07</Real>
+ <Real Name="Cell 4 9 3">1.2524765617342267e-06</Real>
+ <Real Name="Cell 4 9 4">2.0314901024453476e-07</Real>
+ <Real Name="Cell 4 9 5">1.8515052737006967e-10</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>0.16406923832149337</Real>
+ <Real>0.74469524848411051</Real>
+ <Real>0.091235513194396184</Real>
+ <Real>0.0022143185924122905</Real>
+ <Real>0.56211936943313945</Real>
+ <Real>0.43566631197444827</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>0.0072230479931503222</Real>
+ <Real>0.60574581716221632</Real>
+ <Real>0.38703113484463336</Real>
+ <Real>0.038167928761842988</Real>
+ <Real>0.69995358766683513</Real>
+ <Real>0.26187848357132187</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>0.2794087591578463</Real>
+ <Real>0.68872346271189799</Real>
+ <Real>0.031867778130255688</Real>
+ <Real>0.2794087591578463</Real>
+ <Real>0.68872346271189799</Real>
+ <Real>0.031867778130255688</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>-0.57283372512709718</Real>
+ <Real>0.14566745025419436</Real>
+ <Real>0.42716627487290282</Real>
+ <Real>-0.066548006617964006</Real>
+ <Real>-0.86690398676407199</Real>
+ <Real>0.93345199338203599</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>-0.12019191314851696</Real>
+ <Real>-0.75961617370296608</Real>
+ <Real>0.87980808685148304</Real>
+ <Real>-0.27628944519052112</Real>
+ <Real>-0.44742110961895776</Real>
+ <Real>0.72371055480947888</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>-0.74754098102759059</Real>
+ <Real>0.49508196205518118</Real>
+ <Real>0.25245901897240941</Real>
+ <Real>-0.74754098102759059</Real>
+ <Real>0.49508196205518118</Real>
+ <Real>0.25245901897240941</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">4</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 4 0">0.023798943058854972</Real>
+ <Real Name="Cell 0 4 1">0.058662765339858897</Real>
+ <Real Name="Cell 0 4 2">0.0027143724463760469</Real>
+ <Real Name="Cell 0 5 0">0.43644379239613479</Real>
+ <Real Name="Cell 0 5 1">1.0758040688637358</Real>
+ <Real Name="Cell 0 5 2">0.049778303244065715</Real>
+ <Real Name="Cell 0 6 0">0.16328973882082448</Real>
+ <Real Name="Cell 0 6 1">0.40249802720918582</Real>
+ <Real Name="Cell 0 6 2">0.018623901352891086</Real>
+ <Real Name="Cell 1 4 0">0.018445188540286542</Real>
+ <Real Name="Cell 1 4 1">0.045466126975150789</Real>
+ <Real Name="Cell 1 4 2">0.002103753575028464</Real>
+ <Real Name="Cell 1 5 0">0.33826241854841871</Real>
+ <Real Name="Cell 1 5 1">0.83379370392735974</Real>
+ <Real Name="Cell 1 5 2">0.038580292674414464</Real>
+ <Real Name="Cell 1 6 0">0.12655646142754229</Real>
+ <Real Name="Cell 1 6 1">0.31195301323284946</Real>
+ <Real Name="Cell 1 6 2">0.014434312102022459</Real>
+ <Real Name="Cell 15 4 0">9.3749557408290193e-05</Real>
+ <Real Name="Cell 15 4 1">0.00023108624081992141</Real>
+ <Real Name="Cell 15 4 2">1.0692542725939677e-05</Real>
+ <Real Name="Cell 15 5 0">0.001719253341190267</Real>
+ <Real Name="Cell 15 5 1">0.004237841784174824</Real>
+ <Real Name="Cell 15 5 2">0.00019608828367402901</Real>
+ <Real Name="Cell 15 6 0">0.00064323615993827751</Real>
+ <Real Name="Cell 15 6 1">0.0015855330976360846</Real>
+ <Real Name="Cell 15 6 2">7.3363867661322939e-05</Real>
+ <Real Name="Cell 4 2 0">0.0010297885376019896</Real>
+ <Real Name="Cell 4 2 1">0.0025383582448021734</Real>
+ <Real Name="Cell 4 2 2">0.00011745183914882688</Real>
+ <Real Name="Cell 4 3 0">0.086361062505128913</Real>
+ <Real Name="Cell 4 3 1">0.21287410670761991</Real>
+ <Real Name="Cell 4 3 2">0.0098498529083400309</Real>
+ <Real Name="Cell 4 4 0">0.055178953086848032</Real>
+ <Real Name="Cell 4 4 1">0.1360123417509696</Real>
+ <Real Name="Cell 4 4 2">0.0062933983878367631</Real>
+ <Real Name="Cell 5 2 0">0.0046741158716962243</Real>
+ <Real Name="Cell 5 2 1">0.011521375628931728</Real>
+ <Real Name="Cell 5 2 2">0.00053310314251878404</Real>
+ <Real Name="Cell 5 3 0">0.39198495439826581</Real>
+ <Real Name="Cell 5 3 1">0.96621607689695022</Real>
+ <Real Name="Cell 5 3 2">0.044707580373689722</Real>
+ <Real Name="Cell 5 4 0">0.25045221517750116</Real>
+ <Real Name="Cell 5 4 1">0.61734756419525116</Real>
+ <Real Name="Cell 5 4 2">0.028565158979138368</Real>
+ <Real Name="Cell 6 2 0">0.00057264412677849458</Real>
+ <Real Name="Cell 6 2 1">0.0014115285687007091</Real>
+ <Real Name="Cell 6 2 2">6.5312540790683421e-05</Real>
+ <Real Name="Cell 6 3 0">0.048023602341771679</Real>
+ <Real Name="Cell 6 3 1">0.11837489202705763</Real>
+ <Real Name="Cell 6 3 2">0.0054772996704038042</Real>
+ <Real Name="Cell 6 4 0">0.030683875624164414</Real>
+ <Real Name="Cell 6 4 1">0.075633652763753279</Real>
+ <Real Name="Cell 6 4 2">0.0034996288001652408</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>0.27583138988857209</Real>
+ <Real>0.69107726881128639</Real>
+ <Real>0.033091341300141533</Real>
+ <Real>0.0031225352025811837</Real>
+ <Real>0.57278068745366728</Real>
+ <Real>0.42409677734375156</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>0.42345016376210792</Real>
+ <Real>0.57337154943618318</Real>
+ <Real>0.0031782868017088757</Real>
+ <Real>0.047455630860650959</Real>
+ <Real>0.7131654522986024</Real>
+ <Real>0.23937891684074664</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>0.32131281751025292</Real>
+ <Real>0.65901370721545616</Real>
+ <Real>0.019673475274290902</Real>
+ <Real>0.32131281751025292</Real>
+ <Real>0.65901370721545616</Real>
+ <Real>0.019673475274290902</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">6</Int>
+ <Real>-0.74274004858843057</Real>
+ <Real>0.48548009717686114</Real>
+ <Real>0.25725995141156943</Real>
+ <Real>-0.079025757858829593</Real>
+ <Real>-0.84194848428234081</Real>
+ <Real>0.92097424214117041</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">6</Int>
+ <Real>-0.92027187696039903</Real>
+ <Real>0.84054375392079805</Real>
+ <Real>0.079728123039600973</Real>
+ <Real>-0.30807671401990433</Real>
+ <Real>-0.38384657196019134</Real>
+ <Real>0.69192328598009567</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">6</Int>
+ <Real>-0.801639342235962</Real>
+ <Real>0.60327868447192401</Real>
+ <Real>0.198360657764038</Real>
+ <Real>-0.801639342235962</Real>
+ <Real>0.60327868447192401</Real>
+ <Real>0.198360657764038</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">5</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 6 0">0.034673260125936183</Real>
+ <Real Name="Cell 0 6 1">0.07111497721720958</Real>
+ <Real Name="Cell 0 6 2">0.0021229888401351907</Real>
+ <Real Name="Cell 0 7 0">0.52107138377300621</Real>
+ <Real Name="Cell 0 7 1">1.0687192219873987</Real>
+ <Real Name="Cell 0 7 2">0.03190437612863567</Real>
+ <Real Name="Cell 0 8 0">0.17490121407628884</Real>
+ <Real Name="Cell 0 8 1">0.35872299890813186</Real>
+ <Real Name="Cell 0 8 2">0.010708924521703933</Real>
+ <Real Name="Cell 1 6 0">0.02567268450474881</Real>
+ <Real Name="Cell 1 6 1">0.052654765286814134</Real>
+ <Real Name="Cell 1 6 2">0.0015718978400627616</Real>
+ <Real Name="Cell 1 7 0">0.38581031006227273</Real>
+ <Real Name="Cell 1 7 1">0.79129828895783105</Real>
+ <Real Name="Cell 1 7 2">0.02362255466305644</Real>
+ <Real Name="Cell 1 8 0">0.12949989912022614</Real>
+ <Real Name="Cell 1 8 1">0.26560474388957295</Real>
+ <Real Name="Cell 1 8 2">0.0079290738636146659</Real>
+ <Real Name="Cell 18 6 0">0.00018902256605893007</Real>
+ <Real Name="Cell 18 6 1">0.00038768594098148308</Real>
+ <Real Name="Cell 18 6 2">1.1573552553734388e-05</Real>
+ <Real Name="Cell 18 7 0">0.0028406400120124793</Real>
+ <Real Name="Cell 18 7 1">0.0058261625530116505</Real>
+ <Real Name="Cell 18 7 2">0.00017392789205399704</Real>
+ <Real Name="Cell 18 8 0">0.00095348046798728145</Real>
+ <Real Name="Cell 18 8 1">0.0019555917589430616</Real>
+ <Real Name="Cell 18 8 2">5.8380099981129861e-05</Real>
+ <Real Name="Cell 5 4 0">0.11671708100942477</Real>
+ <Real Name="Cell 5 4 1">0.23938713944685172</Real>
+ <Real Name="Cell 5 4 2">0.0071464021420591314</Real>
+ <Real Name="Cell 5 5 0">0.15804044799387293</Real>
+ <Real Name="Cell 5 5 1">0.32414150898013988</Real>
+ <Real Name="Cell 5 5 2">0.0096765665000155283</Real>
+ <Real Name="Cell 5 6 0">0.00087604254255205336</Real>
+ <Real Name="Cell 5 6 1">0.0017967663043110956</Real>
+ <Real Name="Cell 5 6 2">5.3638698367751239e-05</Real>
+ <Real Name="Cell 6 4 0">0.29242691196315057</Real>
+ <Real Name="Cell 6 4 1">0.59976861438543239</Real>
+ <Real Name="Cell 6 4 2">0.017904836995370432</Real>
+ <Real Name="Cell 6 5 0">0.3959598695617596</Real>
+ <Real Name="Cell 6 5 1">0.81211507082227463</Real>
+ <Real Name="Cell 6 5 2">0.024243996127500132</Real>
+ <Real Name="Cell 6 6 0">0.0021948665375392468</Real>
+ <Real Name="Cell 6 6 1">0.0045016789089054494</Real>
+ <Real Name="Cell 6 6 2">0.00013438820427781094</Real>
+ <Real Name="Cell 7 4 0">0.014002484506202902</Real>
+ <Real Name="Cell 7 4 1">0.028719144465394086</Real>
+ <Real Name="Cell 7 4 2">0.00085734996457971643</Real>
+ <Real Name="Cell 7 5 0">0.018960026289630026</Real>
+ <Real Name="Cell 7 5 1">0.038887079920591365</Real>
+ <Real Name="Cell 7 5 2">0.0011608924016765663</Real>
+ <Real Name="Cell 7 6 0">0.00010509834569859741</Real>
+ <Real Name="Cell 7 6 1">0.00021555707287909291</Real>
+ <Real Name="Cell 7 6 2">6.4350053679519218e-06</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>0.03132813098882218</Real>
+ <Real>0.52316837458524212</Real>
+ <Real>0.43251258299014644</Real>
+ <Real>0.012990911435789263</Real>
+ <Real>4.9119496114044609e-05</Real>
+ <Real>0.20200763007971881</Real>
+ <Real>0.6623853879701842</Real>
+ <Real>0.13555786245398288</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>0.00028938398568676441</Real>
+ <Real>0.23311751927701518</Real>
+ <Real>0.65308872263742623</Real>
+ <Real>0.11350437409987174</Real>
+ <Real>0.0035151319538936445</Real>
+ <Real>0.33243392216208922</Real>
+ <Real>0.60087620500466166</Real>
+ <Real>0.063174740879355443</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>0.069623165976186063</Real>
+ <Real>0.61097641840975003</Real>
+ <Real>0.31671864627953228</Real>
+ <Real>0.0026817693345315848</Real>
+ <Real>0.069623165976186063</Real>
+ <Real>0.61097641840975003</Real>
+ <Real>0.31671864627953228</Real>
+ <Real>0.0026817693345315848</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>-0.16406923832149337</Real>
+ <Real>-0.58062601016261717</Real>
+ <Real>0.65345973528971435</Real>
+ <Real>0.091235513194396184</Real>
+ <Real>-0.0022143185924122905</Real>
+ <Real>-0.55990505084072717</Real>
+ <Real>0.12645305745869118</Real>
+ <Real>0.43566631197444827</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>-0.0072230479931503222</Real>
+ <Real>-0.59852276916906599</Real>
+ <Real>0.21871468231758295</Real>
+ <Real>0.38703113484463336</Real>
+ <Real>-0.038167928761842988</Real>
+ <Real>-0.66178565890499219</Real>
+ <Real>0.43807510409551326</Real>
+ <Real>0.26187848357132187</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>-0.2794087591578463</Real>
+ <Real>-0.4093147035540517</Real>
+ <Real>0.65685568458164234</Real>
+ <Real>0.031867778130255688</Real>
+ <Real>-0.2794087591578463</Real>
+ <Real>-0.4093147035540517</Real>
+ <Real>0.65685568458164234</Real>
+ <Real>0.031867778130255688</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">4</Int>
+ <Int Name="Y">2</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">15</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 4 0">0.00019626989228989163</Real>
+ <Real Name="Cell 0 4 1">0.0017223617189997022</Real>
+ <Real Name="Cell 0 4 2">0.00089283981444834208</Real>
+ <Real Name="Cell 0 4 3">7.5599920091953543e-06</Real>
+ <Real Name="Cell 0 5 0">0.018561684440889015</Real>
+ <Real Name="Cell 0 5 1">0.16288761535528778</Real>
+ <Real Name="Cell 0 5 2">0.084437866137788448</Real>
+ <Real Name="Cell 0 5 3">0.00071496542038686304</Real>
+ <Real Name="Cell 0 6 0">0.033550350195300817</Real>
+ <Real Name="Cell 0 6 1">0.29442029116758434</Real>
+ <Real Name="Cell 0 6 2">0.15262192327901958</Real>
+ <Real Name="Cell 0 6 3">0.0012923040636693877</Real>
+ <Real Name="Cell 0 7 0">0.0035274065811664443</Real>
+ <Real Name="Cell 0 7 1">0.030954671609923743</Real>
+ <Real Name="Cell 0 7 2">0.0160463176530449</Real>
+ <Real Name="Cell 0 7 3">0.00013586987415988328</Real>
+ <Real Name="Cell 1 4 0">0.00064357127847102305</Real>
+ <Real Name="Cell 1 4 1">0.0056476442746958991</Real>
+ <Real Name="Cell 1 4 2">0.0029276322218878808</Real>
+ <Real Name="Cell 1 4 3">2.4789302454002272e-05</Real>
+ <Real Name="Cell 1 5 0">0.060863980954117408</Real>
+ <Real Name="Cell 1 5 1">0.53411040092927065</Real>
+ <Real Name="Cell 1 5 2">0.27687275326670341</Real>
+ <Real Name="Cell 1 5 3">0.0023443799978314032</Real>
+ <Real Name="Cell 1 6 0">0.1100119917345689</Real>
+ <Real Name="Cell 1 6 1">0.96540758739842547</Real>
+ <Real Name="Cell 1 6 2">0.50044907622565482</Real>
+ <Real Name="Cell 1 6 3">0.0042374801795916619</Real>
+ <Real Name="Cell 1 7 0">0.011566407545459824</Real>
+ <Real Name="Cell 1 7 1">0.10150073121365499</Real>
+ <Real Name="Cell 1 7 2">0.05261606375912866</Real>
+ <Real Name="Cell 1 7 3">0.00044551891071311598</Real>
+ <Real Name="Cell 15 4 0">4.772432708523316e-08</Real>
+ <Real Name="Cell 15 4 1">4.1880368444498123e-07</Real>
+ <Real Name="Cell 15 4 2">2.1709992725993912e-07</Real>
+ <Real Name="Cell 15 4 3">1.8382622377745602e-09</Real>
+ <Real Name="Cell 15 5 0">4.5133967781542098e-06</Real>
+ <Real Name="Cell 15 5 1">3.9607204868017172e-05</Real>
+ <Real Name="Cell 15 5 2">2.0531627622167349e-05</Real>
+ <Real Name="Cell 15 5 3">1.7384858767220717e-07</Real>
+ <Real Name="Cell 15 6 0">8.1579903461694447e-06</Real>
+ <Real Name="Cell 15 6 1">7.1590248062387306e-05</Real>
+ <Real Name="Cell 15 6 2">3.711103369938734e-05</Real>
+ <Real Name="Cell 15 6 3">3.1423231097024563e-07</Real>
+ <Real Name="Cell 15 7 0">8.577123239745189e-07</Real>
+ <Real Name="Cell 15 7 1">7.5268338688748844e-06</Real>
+ <Real Name="Cell 15 7 2">3.9017686475130664e-06</Real>
+ <Real Name="Cell 15 7 3">3.3037661761480961e-08</Real>
+ <Real Name="Cell 2 4 0">0.00013170753526681934</Real>
+ <Real Name="Cell 2 4 1">0.0011557963078326714</Real>
+ <Real Name="Cell 2 4 2">0.00059914299629506543</Real>
+ <Real Name="Cell 2 4 3">5.0731566749794913e-06</Real>
+ <Real Name="Cell 2 5 0">0.012455877361460551</Real>
+ <Real Name="Cell 2 5 1">0.1093062521899574</Real>
+ <Real Name="Cell 2 5 2">0.056662298544352473</Real>
+ <Real Name="Cell 2 5 3">0.0004797798186034307</Real>
+ <Real Name="Cell 2 6 0">0.022514069172846346</Real>
+ <Real Name="Cell 2 6 1">0.19757167250567123</Real>
+ <Real Name="Cell 2 6 2">0.10241742688211861</Real>
+ <Real Name="Cell 2 6 3">0.00086720475084275505</Real>
+ <Real Name="Cell 2 7 0">0.0023670774017809835</Real>
+ <Real Name="Cell 2 7 1">0.020772230805095403</Real>
+ <Real Name="Cell 2 7 2">0.010767932480797734</Real>
+ <Real Name="Cell 2 7 3">9.1175911057107028e-05</Real>
+ <Real Name="Cell 4 2 0">1.963012758755738e-06</Real>
+ <Real Name="Cell 4 2 1">1.722637124901001e-05</Real>
+ <Real Name="Cell 4 2 2">8.9298257967071154e-06</Real>
+ <Real Name="Cell 4 2 3">7.561200853069517e-08</Real>
+ <Real Name="Cell 4 3 0">0.0015813337546798376</Real>
+ <Real Name="Cell 4 3 1">0.013876956329093026</Real>
+ <Real Name="Cell 4 3 2">0.0071935523051283668</Real>
+ <Real Name="Cell 4 3 3">6.0910363835086094e-05</Real>
+ <Real Name="Cell 4 4 0">0.0044301742962530189</Real>
+ <Real Name="Cell 4 4 1">0.038876887979805687</Real>
+ <Real Name="Cell 4 4 2">0.020153045128277546</Real>
+ <Real Name="Cell 4 4 3">0.00017064299515458792</Real>
+ <Real Name="Cell 4 5 0">0.00076994770116203869</Real>
+ <Real Name="Cell 4 5 1">0.0067566575323464257</Real>
+ <Real Name="Cell 4 5 2">0.0035025237677569509</Real>
+ <Real Name="Cell 4 5 3">2.965711347966705e-05</Real>
+ <Real Name="Cell 5 2 0">3.2781597940035372e-05</Real>
+ <Real Name="Cell 5 2 1">0.00028767412424194992</Real>
+ <Real Name="Cell 5 2 2">0.00014912483764382615</Real>
+ <Real Name="Cell 5 2 3">1.2626929967907567e-06</Real>
+ <Real Name="Cell 5 3 0">0.026407697618725138</Real>
+ <Real Name="Cell 5 3 1">0.23174011528081062</Real>
+ <Real Name="Cell 5 3 2">0.12012970286388032</Real>
+ <Real Name="Cell 5 3 3">0.0010171808862254686</Real>
+ <Real Name="Cell 5 4 0">0.07398229682220657</Real>
+ <Real Name="Cell 5 4 1">0.64922986630081603</Real>
+ <Real Name="Cell 5 4 2">0.33654851183001866</Real>
+ <Real Name="Cell 5 4 3">0.0028496758533484256</Real>
+ <Real Name="Cell 5 5 0">0.012857846115247354</Real>
+ <Real Name="Cell 5 5 1">0.1128337193204423</Real>
+ <Real Name="Cell 5 5 2">0.058490870942073829</Real>
+ <Real Name="Cell 5 5 3">0.00049526299093882893</Real>
+ <Real Name="Cell 6 2 0">2.710112898324477e-05</Real>
+ <Real Name="Cell 6 2 1">0.00023782530554136415</Real>
+ <Real Name="Cell 6 2 2">0.00012328415066841634</Real>
+ <Real Name="Cell 6 2 3">1.0438907168241979e-06</Real>
+ <Real Name="Cell 6 3 0">0.02183171243283278</Real>
+ <Real Name="Cell 6 3 1">0.19158366734609777</Real>
+ <Real Name="Cell 6 3 2">0.09931335800006387</Real>
+ <Real Name="Cell 6 3 3">0.00084092149648449686</Real>
+ <Real Name="Cell 6 4 0">0.061162478178242115</Real>
+ <Real Name="Cell 6 4 1">0.53672985613995938</Real>
+ <Real Name="Cell 6 4 2">0.27823062941923732</Real>
+ <Real Name="Cell 6 4 3">0.0023558776177812664</Real>
+ <Real Name="Cell 6 5 0">0.010629809646663468</Real>
+ <Real Name="Cell 6 5 1">0.093281638880329837</Real>
+ <Real Name="Cell 6 5 2">0.048355441386447436</Real>
+ <Real Name="Cell 6 5 3">0.00040944270693005474</Real>
+ <Real Name="Cell 7 2 0">8.1400722262745183e-07</Real>
+ <Real Name="Cell 7 2 1">7.1433008032225752e-06</Real>
+ <Real Name="Cell 7 2 2">3.7029523434844986e-06</Real>
+ <Real Name="Cell 7 2 3">3.1354213459298767e-08</Real>
+ <Real Name="Cell 7 3 0">0.00065573547189264395</Real>
+ <Real Name="Cell 7 3 1">0.0057543908614875348</Real>
+ <Real Name="Cell 7 3 2">0.0029829676381902064</Real>
+ <Real Name="Cell 7 3 3">2.525784708911082e-05</Real>
+ <Real Name="Cell 7 4 0">0.0018370710320468029</Real>
+ <Real Name="Cell 7 4 1">0.016121172655494686</Real>
+ <Real Name="Cell 7 4 2">0.0083569117007436522</Real>
+ <Real Name="Cell 7 4 3">7.0760941276133623e-05</Real>
+ <Real Name="Cell 7 5 0">0.00031927606532143246</Real>
+ <Real Name="Cell 7 5 1">0.002801799431826586</Real>
+ <Real Name="Cell 7 5 2">0.0014523999559664807</Real>
+ <Real Name="Cell 7 5 3">1.2297986585697413e-05</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Splines Name="Values">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>0.068290339976017453</Real>
+ <Real>0.60899706092140171</Real>
+ <Real>0.3198749068175748</Real>
+ <Real>0.0028376922850060237</Real>
+ <Real>8.2253570274950675e-05</Real>
+ <Real>0.20905532008783781</Real>
+ <Real>0.66066835697232906</Real>
+ <Real>0.13019406936955807</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>0.12989642566818113</Real>
+ <Real>0.66056349190443076</Real>
+ <Real>0.20945561614699421</Real>
+ <Real>8.4466280393928373e-05</Real>
+ <Real>0.0048733249390969704</Real>
+ <Real>0.35354067971997882</Real>
+ <Real>0.58637537976265564</Real>
+ <Real>0.055210615578268486</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>0.08585899856030095</Real>
+ <Real>0.63122215961399775</Real>
+ <Real>0.28161802732706365</Real>
+ <Real>0.001300814498637627</Real>
+ <Real>0.08585899856030095</Real>
+ <Real>0.63122215961399775</Real>
+ <Real>0.28161802732706365</Real>
+ <Real>0.001300814498637627</Real>
+ </Sequence>
+ </Splines>
+ <Splines Name="Derivatives">
+ <Sequence Name="X">
+ <Int Name="Length">8</Int>
+ <Real>-0.27583138988857209</Real>
+ <Real>-0.41524587892271431</Real>
+ <Real>0.65798592751114482</Real>
+ <Real>0.033091341300141533</Real>
+ <Real>-0.0031225352025811837</Real>
+ <Real>-0.56965815225108607</Real>
+ <Real>0.14868391010991572</Real>
+ <Real>0.42409677734375156</Real>
+ </Sequence>
+ <Sequence Name="Y">
+ <Int Name="Length">8</Int>
+ <Real>-0.42345016376210792</Real>
+ <Real>-0.14992138567407526</Real>
+ <Real>0.57019326263447434</Real>
+ <Real>0.0031782868017088757</Real>
+ <Real>-0.047455630860650959</Real>
+ <Real>-0.66570982143795143</Real>
+ <Real>0.47378653545785576</Real>
+ <Real>0.23937891684074664</Real>
+ </Sequence>
+ <Sequence Name="Z">
+ <Int Name="Length">8</Int>
+ <Real>-0.32131281751025292</Real>
+ <Real>-0.33770088970520323</Real>
+ <Real>0.63934023194116529</Real>
+ <Real>0.019673475274290902</Real>
+ <Real>-0.32131281751025292</Real>
+ <Real>-0.33770088970520323</Real>
+ <Real>0.63934023194116529</Real>
+ <Real>0.019673475274290902</Real>
+ </Sequence>
+ </Splines>
+ <Sequence Name="Gridline indices">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Int Name="X">5</Int>
+ <Int Name="Y">4</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ <Vector>
+ <Int Name="X">18</Int>
+ <Int Name="Y">6</Int>
+ <Int Name="Z">0</Int>
+ </Vector>
+ </Sequence>
+ <NonZeroGridValues Name="RealSpaceGrid">
+ <Real Name="Cell 0 6 0">0.00034726652598853863</Real>
+ <Real Name="Cell 0 6 1">0.002553050119052862</Real>
+ <Real Name="Cell 0 6 2">0.0011390362762841891</Real>
+ <Real Name="Cell 0 6 3">5.2612928111448962e-06</Real>
+ <Real Name="Cell 0 7 0">0.025192829367280716</Real>
+ <Real Name="Cell 0 7 1">0.18521380899677403</Real>
+ <Real Name="Cell 0 7 2">0.082632630570668553</Real>
+ <Real Name="Cell 0 7 3">0.000381686232685867</Real>
+ <Real Name="Cell 0 8 0">0.0417843143234196</Real>
+ <Real Name="Cell 0 8 1">0.30719185603702398</Real>
+ <Real Name="Cell 0 8 2">0.13705280017575541</Real>
+ <Real Name="Cell 0 8 3">0.00063305702138328741</Real>
+ <Real Name="Cell 0 9 0">0.0039342335898305027</Real>
+ <Real Name="Cell 0 9 1">0.02892388060238792</Real>
+ <Real Name="Cell 0 9 2">0.012904309637781252</Real>
+ <Real Name="Cell 0 9 3">5.9605960708758805e-05</Real>
+ <Real Name="Cell 1 6 0">0.0010974511677576001</Real>
+ <Real Name="Cell 1 6 1">0.0080682922908346111</Real>
+ <Real Name="Cell 1 6 2">0.0035996463752674176</Real>
+ <Real Name="Cell 1 6 3">1.6627032862062269e-05</Real>
+ <Real Name="Cell 1 7 0">0.079615793458747253</Real>
+ <Real Name="Cell 1 7 1">0.58532307538058348</Real>
+ <Real Name="Cell 1 7 2">0.26114027736049511</Real>
+ <Real Name="Cell 1 7 3">0.0012062262568662571</Real>
+ <Real Name="Cell 1 8 0">0.13204913550953917</Real>
+ <Real Name="Cell 1 8 1">0.97080494635576609</Real>
+ <Real Name="Cell 1 8 2">0.43312195199112263</Real>
+ <Real Name="Cell 1 8 3">0.0020006223329373431</Real>
+ <Real Name="Cell 1 9 0">0.012433185822042524</Real>
+ <Real Name="Cell 1 9 1">0.091406870998616385</Real>
+ <Real Name="Cell 1 9 2">0.04078092364582267</Real>
+ <Real Name="Cell 1 9 3">0.00018837010275876676</Real>
+ <Real Name="Cell 18 6 0">1.366332681107311e-07</Real>
+ <Real Name="Cell 18 6 1">1.0045067845905672e-06</Real>
+ <Real Name="Cell 18 6 2">4.481579342620626e-07</Real>
+ <Real Name="Cell 18 6 3">2.0700746472118896e-09</Real>
+ <Real Name="Cell 18 7 0">9.9122096482203785e-06</Real>
+ <Real Name="Cell 18 7 1">7.2873041680099007e-05</Real>
+ <Real Name="Cell 18 7 2">3.2512106760989057e-05</Real>
+ <Real Name="Cell 18 7 3">1.5017582594892596e-07</Real>
+ <Real Name="Cell 18 8 0">1.6440189291274443e-05</Real>
+ <Real Name="Cell 18 8 1">0.00012086574456855391</Real>
+ <Real Name="Cell 18 8 2">5.3923918922028441e-05</Real>
+ <Real Name="Cell 18 8 3">2.4907857008624638e-07</Real>
+ <Real Name="Cell 18 9 0">1.547938406557782e-06</Real>
+ <Real Name="Cell 18 9 1">1.1380205223924392e-05</Real>
+ <Real Name="Cell 18 9 2">5.0772472051655487e-06</Real>
+ <Real Name="Cell 18 9 3">2.3452180388922191e-08</Real>
+ <Real Name="Cell 2 6 0">0.00021626831670813599</Real>
+ <Real Name="Cell 2 6 1">0.0015899714207907613</Real>
+ <Real Name="Cell 2 6 2">0.00070936136859218936</Real>
+ <Real Name="Cell 2 6 3">3.2765926307924009e-06</Real>
+ <Real Name="Cell 2 7 0">0.015689421215786623</Real>
+ <Real Name="Cell 2 7 1">0.11534621308175426</Real>
+ <Real Name="Cell 2 7 2">0.051461395156968175</Real>
+ <Real Name="Cell 2 7 3">0.00023770399067017125</Real>
+ <Real Name="Cell 2 8 0">0.026022154878895126</Real>
+ <Real Name="Cell 2 8 1">0.19131088267853347</Real>
+ <Real Name="Cell 2 8 2">0.085352823194727964</Real>
+ <Real Name="Cell 2 8 3">0.00039425100362062732</Real>
+ <Real Name="Cell 2 9 0">0.0024501355942303862</Real>
+ <Real Name="Cell 2 9 1">0.018013020266606391</Real>
+ <Real Name="Cell 2 9 2">0.0080364593612908038</Real>
+ <Real Name="Cell 2 9 3">3.7121000221829661e-05</Real>
+ <Real Name="Cell 5 4 0">0.0023686596869420852</Real>
+ <Real Name="Cell 5 4 1">0.017414021920278012</Real>
+ <Real Name="Cell 5 4 2">0.0077692178994759522</Real>
+ <Real Name="Cell 5 4 3">3.5886592142682999e-05</Real>
+ <Real Name="Cell 5 5 0">0.012045366959800725</Real>
+ <Real Name="Cell 5 5 1">0.088555686336925024</Real>
+ <Real Name="Cell 5 5 2">0.039508875464780172</Real>
+ <Real Name="Cell 5 5 3">0.00018249441812106428</Real>
+ <Real Name="Cell 5 6 0">0.0038194205238437948</Real>
+ <Real Name="Cell 5 6 1">0.028079792589724518</Real>
+ <Real Name="Cell 5 6 2">0.012527722096618166</Real>
+ <Real Name="Cell 5 6 3">5.7866475001111562e-05</Real>
+ <Real Name="Cell 5 7 0">1.5402415597341067e-06</Real>
+ <Real Name="Cell 5 7 1">1.1323619189196228e-05</Real>
+ <Real Name="Cell 5 7 2">5.0520015016811351e-06</Real>
+ <Real Name="Cell 5 7 3">2.333556861718113e-08</Real>
+ <Real Name="Cell 6 4 0">0.021123145501652566</Real>
+ <Real Name="Cell 6 4 1">0.15529411878743787</Real>
+ <Real Name="Cell 6 4 2">0.069284043220467328</Real>
+ <Real Name="Cell 6 4 3">0.00032002812036159296</Real>
+ <Real Name="Cell 6 5 0">0.10741772670650858</Real>
+ <Real Name="Cell 6 5 1">0.78971861504869245</Real>
+ <Real Name="Cell 6 5 2">0.35233078421941649</Real>
+ <Real Name="Cell 6 5 3">0.0016274419531271879</Real>
+ <Real Name="Cell 6 6 0">0.034060686683659989</Real>
+ <Real Name="Cell 6 6 1">0.25040893286561805</Real>
+ <Real Name="Cell 6 6 2">0.11171925545486924</Real>
+ <Real Name="Cell 6 6 3">0.0005160395044736144</Real>
+ <Real Name="Cell 6 7 0">1.3735509053205462e-05</Real>
+ <Real Name="Cell 6 7 1">0.00010098135120773274</Real>
+ <Real Name="Cell 6 7 2">4.5052551610883681e-05</Real>
+ <Real Name="Cell 6 7 3">2.0810106828848415e-07</Real>
+ <Real Name="Cell 7 4 0">0.011094904446356973</Real>
+ <Real Name="Cell 7 4 1">0.081568032038269872</Real>
+ <Real Name="Cell 7 4 2">0.036391352752278901</Real>
+ <Real Name="Cell 7 4 3">0.00016809435011851408</Real>
+ <Real Name="Cell 7 5 0">0.056421019945176287</Real>
+ <Real Name="Cell 7 5 1">0.41479866588946834</Real>
+ <Real Name="Cell 7 5 2">0.18506128190607871</Real>
+ <Real Name="Cell 7 5 3">0.00085481174953446599</Real>
+ <Real Name="Cell 7 6 0">0.017890330969075892</Real>
+ <Real Name="Cell 7 6 1">0.13152696327546923</Real>
+ <Real Name="Cell 7 6 2">0.058680392273629235</Real>
+ <Real Name="Cell 7 6 3">0.00027104907231890378</Real>
+ <Real Name="Cell 7 7 0">7.2145580995720175e-06</Real>
+ <Real Name="Cell 7 7 1">5.3040322163484428e-05</Real>
+ <Real Name="Cell 7 7 2">2.3663793593061901e-05</Real>
+ <Real Name="Cell 7 7 3">1.0930481294392947e-07</Real>
+ <Real Name="Cell 8 4 0">9.8425741060900274e-05</Real>
+ <Real Name="Cell 8 4 1">0.0007236109187837216</Real>
+ <Real Name="Cell 8 4 2">0.00032283701767506321</Real>
+ <Real Name="Cell 8 4 3">1.491208063896187e-06</Real>
+ <Real Name="Cell 8 5 0">0.00050052532911531642</Real>
+ <Real Name="Cell 8 5 1">0.0036797852814901217</Real>
+ <Real Name="Cell 8 5 2">0.001641726064550905</Real>
+ <Real Name="Cell 8 5 3">7.5832541255567533e-06</Real>
+ <Real Name="Cell 8 6 0">0.00015870971146887634</Real>
+ <Real Name="Cell 8 6 1">0.0011668094026829217</Real>
+ <Real Name="Cell 8 6 2">0.00052056880013714123</Real>
+ <Real Name="Cell 8 6 3">2.4045457926965272e-06</Real>
+ <Real Name="Cell 8 7 0">6.4002194053186081e-08</Real>
+ <Real Name="Cell 8 7 1">4.7053429259267009e-07</Real>
+ <Real Name="Cell 8 7 2">2.0992757819325552e-07</Real>
+ <Real Name="Cell 8 7 3">9.6967101136791496e-10</Real>
+ </NonZeroGridValues>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.68483443256321219</Real>
+ <Real Name="Y">0.29786650520930358</Real>
+ <Real Name="Z">2.0753823516238281</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54211842890838613</Real>
+ <Real Name="Y">0.30968912522684905</Real>
+ <Real Name="Z">2.9554195699926327</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-4.2362713136143704</Real>
+ <Real Name="Y">-2.3275379753649541</Real>
+ <Real Name="Z">-11.746263473883745</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.57636324498554081</Real>
+ <Real Name="Y">-0.013594713514657464</Real>
+ <Real Name="Z">-6.1436686744664879</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.6940571045158022</Real>
+ <Real Name="Y">2.1019189996213141</Real>
+ <Real Name="Z">-0.21251856629141863</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.19104463336113997</Real>
+ <Real Name="Y">-16.083563532509753</Real>
+ <Real Name="Z">2.8065205292802267</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.6398356036393578</Real>
+ <Real Name="Y">-0.91018032292522766</Real>
+ <Real Name="Z">0.93368498675769429</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-8.0544456082501288</Real>
+ <Real Name="Y">-11.923968234039531</Real>
+ <Real Name="Z">1.9257328983388657</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.59903073971265186</Real>
+ <Real Name="Y">-1.6350310136998707</Real>
+ <Real Name="Z">-2.6446765062295143</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-7.7106240328717144</Real>
+ <Real Name="Y">-1.2779139061856373</Real>
+ <Real Name="Z">2.2200763403785335</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.060088412760632121</Real>
+ <Real Name="Y">-1.4519790167692483</Real>
+ <Real Name="Z">0.24378158880830342</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.3603736897226484</Real>
+ <Real Name="Y">-1.4452674741283262</Real>
+ <Real Name="Z">-0.088156767496452001</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-8.0344456086971636</Real>
+ <Real Name="Y">-11.05396822927116</Real>
+ <Real Name="Z">2.8757328864179366</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.5790307401596867</Real>
+ <Real Name="Y">-0.76503100893149911</Real>
+ <Real Name="Z">-1.6946765181504433</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-7.0506240066456707</Real>
+ <Real Name="Y">-0.60791388949633673</Real>
+ <Real Name="Z">2.6000763356101619</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.76991157055006731</Real>
+ <Real Name="Y">-1.1419790143850626</Real>
+ <Real Name="Z">0.9737816078817898</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.0903736789938123</Real>
+ <Real Name="Y">-0.46526745505483991</Real>
+ <Real Name="Z">0.7418432158142475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-9.4063956103865909</Real>
+ <Real Name="Y">1.0613765111849376</Real>
+ <Real Name="Z">1.4765278904032615</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.6526713761104288</Real>
+ <Real Name="Y">1.789898728665017</Real>
+ <Real Name="Z">-0.59016766968693601</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.82999998331069946</Real>
+ <Real Name="Y">0.31000000238418579</Real>
+ <Real Name="Z">0.73000001907348633</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-3.3126533138132714</Real>
+ <Real Name="Y">-8.6003366303629782</Real>
+ <Real Name="Z">-22.745529254386152</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.82959875104586944</Real>
+ <Real Name="Y">-20.491954418617421</Real>
+ <Real Name="Z">2.8871516559459058</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.7217414105226196</Real>
+ <Real Name="Y">-1.2127254019801541</Real>
+ <Real Name="Z">0.55819396762823659</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-9.3863956108336257</Real>
+ <Real Name="Y">1.9313765159533092</Real>
+ <Real Name="Z">2.4265278784823323</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.3126714023364725</Real>
+ <Real Name="Y">2.4598987453543177</Real>
+ <Real Name="Z">-0.2101676744553076</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.00040123226483002039</Real>
+ <Real Name="Y">-20.181954416233236</Real>
+ <Real Name="Z">3.6171516750193922</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.0117414319802918</Real>
+ <Real Name="Y">-1.1527254033212586</Real>
+ <Real Name="Z">0.90819396166777211</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-6.5442370567032295</Real>
+ <Real Name="Y">-14.904960292549413</Real>
+ <Real Name="Z">2.4825316419739121</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.48671247601652962</Real>
+ <Real Name="Y">-2.0437887671248385</Real>
+ <Real Name="Z">-1.9489107480528729</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.2648820267082685</Real>
+ <Real Name="Y">-1.5973923827320464</Real>
+ <Real Name="Z">1.9008625299783468</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.0488218353680136</Real>
+ <Real Name="Y">-1.8149737709615605</Real>
+ <Real Name="Z">0.30251804902903451</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.1053036228996518</Real>
+ <Real Name="Y">-1.8065843426604078</Real>
+ <Real Name="Z">0.051190455240391619</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-6.5242370571502644</Real>
+ <Real Name="Y">-14.034960287781042</Real>
+ <Real Name="Z">3.4325316300529831</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.46671247646356445</Real>
+ <Real Name="Y">-1.1737887623564669</Real>
+ <Real Name="Z">-0.99891075997380185</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.6048820004822248</Real>
+ <Real Name="Y">-0.92739236604274589</Real>
+ <Real Name="Z">2.280862525209975</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.78117814794268581</Real>
+ <Real Name="Y">-1.5049737685773747</Real>
+ <Real Name="Z">1.0325180681025208</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.83530361217081572</Real>
+ <Real Name="Y">-0.82658432358692147</Real>
+ <Real Name="Z">0.88119043855109114</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.55642797645760989</Real>
+ <Real Name="Y">0.3723331315116295</Real>
+ <Real Name="Z">1.6306575619901507</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">3.4320122274828666</Real>
+ <Real Name="Y">-0.81224418229071649</Real>
+ <Real Name="Z">-0.764761636476889</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">12.870589400646217</Real>
+ <Real Name="Y">2.4002360860135794</Real>
+ <Real Name="Z">-2.7526346195710181</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-3.9130491664545959</Real>
+ <Real Name="Y">-0.62204635074971815</Real>
+ <Real Name="Z">1.1633583220151211</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">4.1305407769409488</Real>
+ <Real Name="Y">-0.46469970389626269</Real>
+ <Real Name="Z">-3.6193285397896875</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.1597567999404905</Real>
+ <Real Name="Y">-0.73800016335319685</Real>
+ <Real Name="Z">-0.54897393926970917</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.2124223213639174</Real>
+ <Real Name="Y">-16.220145737822616</Real>
+ <Real Name="Z">2.8258755564357965</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">3.4520122270358318</Real>
+ <Real Name="Y">0.057755822477655094</Real>
+ <Real Name="Z">0.18523835160218205</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">13.530589426872261</Real>
+ <Real Name="Y">3.0702361027028799</Real>
+ <Real Name="Z">-2.3726346243393897</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-3.8930491669016307</Real>
+ <Real Name="Y">0.24795365401865344</Real>
+ <Real Name="Z">2.1133583100941919</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">4.9605407602516483</Real>
+ <Real Name="Y">-0.1546997015120769</Real>
+ <Real Name="Z">-2.8893285207162012</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.55024317860183736</Real>
+ <Real Name="Y">-0.67800016469430135</Real>
+ <Real Name="Z">-0.19897394523017364</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.4824223320927534</Real>
+ <Real Name="Y">-15.24014571874913</Real>
+ <Real Name="Z">3.6558755397464959</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-16.500695458472016</Real>
+ <Real Name="Y">-15.572010667113076</Real>
+ <Real Name="Z">6.0618364657657224</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.56750283571532234</Real>
+ <Real Name="Y">-0.70603611451836135</Real>
+ <Real Name="Z">-0.73298662849655538</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-7.5662986143550031</Real>
+ <Real Name="Y">-4.9570092424793035</Real>
+ <Real Name="Z">0.22987632186540616</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-8.3516260207559565</Real>
+ <Real Name="Y">-0.89155680381272195</Real>
+ <Real Name="Z">1.9626024243687374</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-10.991689448063681</Real>
+ <Real Name="Y">-17.399473852314976</Real>
+ <Real Name="Z">1.9943402280115583</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.5304702532285459</Real>
+ <Real Name="Y">-2.0431421404374799</Real>
+ <Real Name="Z">-2.0385186389652117</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-7.0292328592073234</Real>
+ <Real Name="Y">-14.608255429729208</Real>
+ <Real Name="Z">3.679921612389506</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.67546778632879001</Real>
+ <Real Name="Y">-0.07424836221296291</Real>
+ <Real Name="Z">0.089381774901316297</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-16.480695458919051</Real>
+ <Real Name="Y">-14.702010662344705</Real>
+ <Real Name="Z">7.0118364538447935</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44047122348806367</Real>
+ <Real Name="Y">0.3871114065335613</Real>
+ <Real Name="Z">2.3221153764227829</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.54750283616235718</Real>
+ <Real Name="Y">0.16396389025001024</Real>
+ <Real Name="Z">0.21701335958251566</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.9062985881289594</Real>
+ <Real Name="Y">-4.287009225790003</Real>
+ <Real Name="Z">0.6098763170970346</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-8.3316260212029913</Real>
+ <Real Name="Y">-0.021556799044350372</Real>
+ <Real Name="Z">2.9126024124478085</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-10.161689464752982</Real>
+ <Real Name="Y">-17.089473849930791</Real>
+ <Real Name="Z">2.7243402470850446</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.82047027468621803</Real>
+ <Real Name="Y">-1.9831421417785844</Real>
+ <Real Name="Z">-1.6885186449256762</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.7592328484784874</Real>
+ <Real Name="Y">-13.628255410655722</Real>
+ <Real Name="Z">4.5099215957002059</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.38546779467344028</Real>
+ <Real Name="Y">0.02575163927715321</Real>
+ <Real Name="Z">0.76938178205387364</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">2.788509934829829</Real>
+ <Real Name="Y">-1.0153052278633954</Real>
+ <Real Name="Z">-0.5654353231810999</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">10.457353888025052</Real>
+ <Real Name="Y">3.0002951075169739</Real>
+ <Real Name="Z">-2.4443752014337479</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-3.1793524477443595</Real>
+ <Real Name="Y">-0.77755793843714771</Real>
+ <Real Name="Z">0.99148224011632069</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">3.3560643812645212</Real>
+ <Real Name="Y">-0.58087462987032856</Real>
+ <Real Name="Z">-2.8401295588358915</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.12980239995164852</Real>
+ <Real Name="Y">-0.92250020419149636</Real>
+ <Real Name="Z">-0.37393805370732247</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.7975931361081829</Real>
+ <Real Name="Y">-20.275182172278267</Real>
+ <Real Name="Z">3.4378840352447644</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">2.8085099343827942</Real>
+ <Real Name="Y">-0.14530522309502381</Real>
+ <Real Name="Z">0.38456466489797114</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">11.117353914251096</Real>
+ <Real Name="Y">3.6702951242062745</Real>
+ <Real Name="Z">-2.0643752062021195</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-3.1593524481913944</Real>
+ <Real Name="Y">0.092442066331223871</Real>
+ <Real Name="Z">1.9414822281953916</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">4.1860643645752207</Real>
+ <Real Name="Y">-0.27087462748614277</Real>
+ <Real Name="Z">-2.1101295397624051</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.58019757859067933</Real>
+ <Real Name="Y">-0.86250020553260087</Real>
+ <Real Name="Z">-0.023938059667786948</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.067593146837019</Real>
+ <Real Name="Y">-19.295182153204781</Real>
+ <Real Name="Z">4.2678840185554634</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-13.406815060008514</Real>
+ <Real Name="Y">-19.465013333891342</Real>
+ <Real Name="Z">6.0748932006495915</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.4931516109310436</Real>
+ <Real Name="Y">-1.1695586621622649</Real>
+ <Real Name="Z">0.37948711624127879</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.1476176241634404</Real>
+ <Real Name="Y">-6.196261553099129</Real>
+ <Real Name="Z">0.61604971101077255</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-8.1581138200755436</Real>
+ <Real Name="Y">-14.70340061881376</Real>
+ <Real Name="Z">-8.9453847792568535</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-8.4309497156824804</Real>
+ <Real Name="Y">-11.184451168201075</Real>
+ <Real Name="Z">-7.7012318674352152</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-6.7856961418642161</Real>
+ <Real Name="Y">-1.1144460047659024</Real>
+ <Real Name="Z">1.6740807570530818</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-8.9307476765517411</Real>
+ <Real Name="Y">-21.749342315393726</Real>
+ <Real Name="Z">2.9757623819770487</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.2435070807481936</Real>
+ <Real Name="Y">-2.5539276755468499</Real>
+ <Real Name="Z">-1.4344239512261392</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.7112516981059507</Real>
+ <Real Name="Y">-18.260319287161511</Real>
+ <Real Name="Z">4.0572521792161034</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.5488175763921419</Real>
+ <Real Name="Y">-0.092810452766203616</Real>
+ <Real Name="Z">0.081070341914709868</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-13.386815060455548</Real>
+ <Real Name="Y">-18.59501332912297</Real>
+ <Real Name="Z">7.0248931887286625</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.4731516113780785</Real>
+ <Real Name="Y">-0.29955865739389331</Real>
+ <Real Name="Z">1.3294871043203498</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.4876175979373967</Real>
+ <Real Name="Y">-5.5262615364098284</Real>
+ <Real Name="Z">0.99604970624240097</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-6.7656961423112509</Real>
+ <Real Name="Y">-0.24444599999753081</Real>
+ <Real Name="Z">2.6240807451321526</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-8.1007476932410416</Real>
+ <Real Name="Y">-21.43934231300954</Real>
+ <Real Name="Z">3.705762401050535</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.53350710220586572</Real>
+ <Real Name="Y">-2.4939276768879544</Real>
+ <Real Name="Z">-1.0844239571866037</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.4412516873771146</Real>
+ <Real Name="Y">-17.280319268088025</Real>
+ <Real Name="Z">4.8872521625268028</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.25881758473679217</Real>
+ <Real Name="Y">0.0071895487239125033</Real>
+ <Real Name="Z">0.76107034906726723</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.57642797601057505</Real>
+ <Real Name="Y">1.242333136280001</Real>
+ <Real Name="Z">2.5806575500692217</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.1004712497141074</Real>
+ <Real Name="Y">1.0571114232228618</Real>
+ <Real Name="Z">2.7021153716544113</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-7.3281138367648442</Real>
+ <Real Name="Y">-14.393400616429574</Real>
+ <Real Name="Z">-8.2153847601833672</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-7.7209497371401525</Real>
+ <Real Name="Y">-11.12445116954218</Real>
+ <Real Name="Z">-7.3512318733956796</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-16.205517527929572</Real>
+ <Real Name="Y">-7.3188043172213684</Real>
+ <Real Name="Z">-7.9336359387100472</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.4582204419484599</Real>
+ <Real Name="Y">-3.9969224751666577</Real>
+ <Real Name="Z">-9.9756355772564991</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.067954884757908562</Real>
+ <Real Name="Y">-0.85449341275494772</Real>
+ <Real Name="Z">-5.12573966904852</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-10.040755470862207</Real>
+ <Real Name="Y">-11.762720495051008</Real>
+ <Real Name="Z">-11.385035173599631</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-10.376553496224592</Real>
+ <Real Name="Y">-8.94756093456086</Real>
+ <Real Name="Z">-9.8015678312811829</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.9109058261904628</Real>
+ <Real Name="Y">-11.975420811795583</Real>
+ <Real Name="Z">-18.523630115333241</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-16.185517528376607</Real>
+ <Real Name="Y">-6.4488043124529968</Real>
+ <Real Name="Z">-6.9836359506309762</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.4382204423954947</Real>
+ <Real Name="Y">-3.1269224703982861</Real>
+ <Real Name="Z">-9.025635589177428</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.59204514146813514</Real>
+ <Real Name="Y">-0.18449339606564719</Real>
+ <Real Name="Z">-4.7457396738168915</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.82999998331069946</Real>
+ <Real Name="Y">0.31000000238418579</Real>
+ <Real Name="Z">0.73000001907348633</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.6409058154616267</Real>
+ <Real Name="Y">-10.995420792722097</Real>
+ <Real Name="Z">-17.693630132022541</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-10.129964503493252</Real>
+ <Real Name="Y">1.0239161111946307</Real>
+ <Real Name="Z">-8.1365401298928379</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.7797999435035388</Real>
+ <Real Name="Y">1.7267257437615944</Real>
+ <Real Name="Z">1.3771557011554771</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.89341403958785948</Real>
+ <Real Name="Y">-19.76870795422418</Real>
+ <Real Name="Z">-5.5136166998409726</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.9311061344089753</Real>
+ <Real Name="Y">-1.1699232689408006</Real>
+ <Real Name="Z">-3.2719141904858438</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-10.109964503940287</Real>
+ <Real Name="Y">1.8939161159630022</Real>
+ <Real Name="Z">-7.1865401418137669</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.4397999697295827</Real>
+ <Real Name="Y">2.3967257604508951</Real>
+ <Real Name="Z">1.7571556963871056</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.063414056277160014</Real>
+ <Real Name="Y">-19.458707951839994</Real>
+ <Real Name="Z">-4.7836166807674863</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.2211061558666474</Real>
+ <Real Name="Y">-1.1099232702819051</Real>
+ <Real Name="Z">-2.9219141964463082</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.70483443211617736</Real>
+ <Real Name="Y">1.1678665099776753</Real>
+ <Real Name="Z">3.0253823397028992</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-7.0476399072188638</Real>
+ <Real Name="Y">-14.378902132683789</Real>
+ <Real Name="Z">-14.272277552262375</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.52415189724857048</Real>
+ <Real Name="Y">-1.9716549447673803</Real>
+ <Real Name="Z">-18.815861243981043</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.7467960287627502</Real>
+ <Real Name="Y">-1.5410137489785949</Real>
+ <Real Name="Z">-1.2290404991250639</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.052577361165553116</Real>
+ <Real Name="Y">-1.7509157833241376</Real>
+ <Real Name="Z">-0.070066070618527432</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.1903269785073174</Real>
+ <Real Name="Y">-1.7428224529077028</Real>
+ <Real Name="Z">-4.3636777044640338</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-7.0276399076658986</Real>
+ <Real Name="Y">-13.508902127915418</Real>
+ <Real Name="Z">-13.322277564183304</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.50415189769560531</Real>
+ <Real Name="Y">-1.1016549399990088</Real>
+ <Real Name="Z">-17.865861255901972</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.0867960025367065</Real>
+ <Real Name="Y">-0.87101373228929435</Real>
+ <Real Name="Z">-0.84904050389343544</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.77742262214514635</Real>
+ <Real Name="Y">-1.4409157809399518</Real>
+ <Real Name="Z">0.6599339484549589</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.92032696777848133</Real>
+ <Real Name="Y">-0.76282243383421644</Real>
+ <Real Name="Z">-3.5336777211533343</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-8.2305961590882664</Real>
+ <Real Name="Y">1.2798951389932887</Real>
+ <Real Name="Z">-6.3929958163443734</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.4460874540966253</Real>
+ <Real Name="Y">2.1584071797019928</Real>
+ <Real Name="Z">1.0820509080507321</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.72589890716513583</Real>
+ <Real Name="Y">-24.710884942780222</Real>
+ <Real Name="Z">-4.3321274070179072</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-2.3815237342072924</Real>
+ <Real Name="Y">-1.4624040861760008</Real>
+ <Real Name="Z">-2.5707897210960202</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-8.2105961595353012</Real>
+ <Real Name="Y">2.1498951437616602</Real>
+ <Real Name="Z">-5.4429958282653024</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.2021184551344297</Real>
+ <Real Name="Y">0.97968914191614953</Real>
+ <Real Name="Z">3.3354195652242611</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.1060874803226692</Real>
+ <Real Name="Y">2.8284071963912933</Real>
+ <Real Name="Z">1.4620509032823605</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10410107614556363</Real>
+ <Real Name="Y">-24.400884940396036</Real>
+ <Real Name="Z">-3.6021273879444209</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.6715237556649645</Real>
+ <Real Name="Y">-1.4024040875171053</Real>
+ <Real Name="Z">-2.2207897270564847</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-5.7262074246153265</Real>
+ <Real Name="Y">-17.973627665854735</Real>
+ <Real Name="Z">-11.213932362491866</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.42587341651446342</Real>
+ <Real Name="Y">-2.4645686809592258</Real>
+ <Real Name="Z">-14.783890977413678</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.4817717733697346</Real>
+ <Real Name="Y">-1.9262671862232437</Real>
+ <Real Name="Z">-0.96567467788397876</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.0427191059470119</Real>
+ <Real Name="Y">-2.1886447291551718</Real>
+ <Real Name="Z">-0.055051912628842979</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.96714067003719539</Real>
+ <Real Name="Y">-2.1785280661346289</Real>
+ <Real Name="Z">-3.4286039106503119</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-5.7062074250623613</Real>
+ <Real Name="Y">-17.103627661086364</Real>
+ <Real Name="Z">-10.263932374412795</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.40587341696149826</Real>
+ <Real Name="Y">-1.5945686761908542</Real>
+ <Real Name="Z">-13.833890989334607</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-4.8217717471436909</Real>
+ <Real Name="Y">-1.2562671695339431</Real>
+ <Real Name="Z">-0.58567468265235034</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.78728087736368757</Real>
+ <Real Name="Y">-1.878644726770986</Real>
+ <Real Name="Z">0.67494810644464331</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.69714065930835933</Real>
+ <Real Name="Y">-1.1985280470611426</Real>
+ <Real Name="Z">-2.5986039273396124</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">3.0030106990475081</Real>
+ <Real Name="Y">-0.97947087544725719</Real>
+ <Real Name="Z">0.52873130622863018</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">11.261765725565441</Real>
+ <Real Name="Y">2.8944021905057711</Real>
+ <Real Name="Z">8.1326966202729416</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-9.2107554875515074</Real>
+ <Real Name="Y">-11.452720492666822</Real>
+ <Real Name="Z">-10.655035154526145</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-9.6665535176822637</Real>
+ <Real Name="Y">-8.8875609359019645</Real>
+ <Real Name="Z">-9.4515678372416474</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-3.423918020647772</Real>
+ <Real Name="Y">-0.75011467859246217</Real>
+ <Real Name="Z">-0.37339673869951695</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">3.6142231798233309</Real>
+ <Real Name="Y">-0.5603731435929743</Real>
+ <Real Name="Z">-15.314157091800631</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.13978719994792918</Real>
+ <Real Name="Y">-0.88994132779279667</Real>
+ <Real Name="Z">-4.3663155404400467</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.935869531193428</Real>
+ <Real Name="Y">-19.559586503779869</Real>
+ <Real Name="Z">4.8894339493261105</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">3.0230106986004732</Real>
+ <Real Name="Y">-0.10947087067888561</Real>
+ <Real Name="Z">1.4787312943077011</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">11.921765751791485</Real>
+ <Real Name="Y">3.5644022071950716</Real>
+ <Real Name="Z">8.51269661550457</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-3.4039180210948068</Real>
+ <Real Name="Y">0.11988532617590941</Real>
+ <Real Name="Z">0.57660324937955409</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">4.4442231631340299</Real>
+ <Real Name="Y">-0.25037314120878851</Real>
+ <Real Name="Z">-14.584157072727145</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.57021277859439867</Real>
+ <Real Name="Y">-0.82994132913390117</Real>
+ <Real Name="Z">-4.0163155464005111</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.2058695419222643</Real>
+ <Real Name="Y">-18.579586484706383</Real>
+ <Real Name="Z">5.71943393263681</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-14.438108526163015</Real>
+ <Real Name="Y">-18.778011899791231</Real>
+ <Real Name="Z">-7.4710258563699679</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.49656498125090714</Real>
+ <Real Name="Y">-0.85139644735204068</Real>
+ <Real Name="Z">-6.170384440946111</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.6205112875606282</Real>
+ <Real Name="Y">-5.9775696621654237</Real>
+ <Real Name="Z">-16.795786276144295</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-7.3076727681614635</Real>
+ <Real Name="Y">-1.0751125611988102</Real>
+ <Real Name="Z">-3.5350277386547013</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-9.6177282670557229</Real>
+ <Real Name="Y">-20.98171739240464</Real>
+ <Real Name="Z">-24.469455185751023</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.3391614715749778</Real>
+ <Real Name="Y">-2.4637889252880081</Real>
+ <Real Name="Z">-17.156428586866937</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.1505787518064086</Real>
+ <Real Name="Y">-17.61583652610614</Real>
+ <Real Name="Z">-4.4618914487107055</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.59103431303769127</Real>
+ <Real Name="Y">-0.089534785133402892</Real>
+ <Real Name="Z">-0.71108816991442636</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-14.41810852661005</Real>
+ <Real Name="Y">-17.90801189502286</Real>
+ <Real Name="Z">-6.5210258682908968</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-0.47656498169794198</Real>
+ <Real Name="Y">0.018603557416330907</Real>
+ <Real Name="Z">-5.22038445286704</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.9605112613345845</Real>
+ <Real Name="Y">-5.3075696454761232</Real>
+ <Real Name="Z">-16.415786280912666</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-7.2876727686084983</Real>
+ <Real Name="Y">-0.20511255643043858</Real>
+ <Real Name="Z">-2.5850277505756303</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-8.7877282837450235</Real>
+ <Real Name="Y">-20.671717390020454</Real>
+ <Real Name="Z">-23.739455166677537</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.6291614930326499</Real>
+ <Real Name="Y">-2.4037889266291126</Real>
+ <Real Name="Z">-16.806428592827402</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.8805787410775725</Real>
+ <Real Name="Y">-16.635836507032653</Real>
+ <Real Name="Z">-3.6318914654000061</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.30103432138234154</Real>
+ <Real Name="Y">0.010465216356713228</Real>
+ <Real Name="Z">-0.031088162761868987</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-19.945252342067167</Real>
+ <Real Name="Y">-5.8550434537770943</Real>
+ <Real Name="Z">-10.097354831085514</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">2.4399461929761004</Real>
+ <Real Name="Y">-1.2243385943090714</Real>
+ <Real Name="Z">0.41543174060820942</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">9.1501846520219203</Real>
+ <Real Name="Y">3.6180027381322137</Real>
+ <Real Name="Z">6.3899759159287406</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-2.7819333917763145</Real>
+ <Real Name="Y">-0.93764334824057782</Real>
+ <Real Name="Z">-0.29338315183533475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.9365563336064566</Real>
+ <Real Name="Y">-0.70046642949121796</Real>
+ <Real Name="Z">-12.032552000700495</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.11357709995769247</Real>
+ <Real Name="Y">-1.112426659740996</Real>
+ <Real Name="Z">-3.4306764960600371</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.5728939940946602</Real>
+ <Real Name="Y">-24.449483129724836</Real>
+ <Real Name="Z">3.8416981030419435</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">2.4599461925290655</Real>
+ <Real Name="Y">-0.35433858954069986</Real>
+ <Real Name="Z">1.3654317286872804</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">9.810184678247964</Real>
+ <Real Name="Y">4.2880027548215143</Real>
+ <Real Name="Z">6.769975911160369</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-2.7619333922233493</Real>
+ <Real Name="Y">-0.067643343472206241</Real>
+ <Real Name="Z">0.65661683624373635</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">3.7665563169171561</Real>
+ <Real Name="Y">-0.39046642710703217</Real>
+ <Real Name="Z">-11.302551981627008</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.59642287858463539</Real>
+ <Real Name="Y">-1.0524266610821005</Real>
+ <Real Name="Z">-3.0806765020205016</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.8428940048234963</Real>
+ <Real Name="Y">-23.46948311065135</Real>
+ <Real Name="Z">4.6716980863526434</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-11.73096317750745</Real>
+ <Real Name="Y">-23.472514874739037</Real>
+ <Real Name="Z">-5.870091744290689</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.0565076595646632</Real>
+ <Real Name="Y">-1.4103500790664754</Real>
+ <Real Name="Z">-4.9677026084105016</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-5.3791654211430107</Real>
+ <Real Name="Y">-7.4719620777067792</Real>
+ <Real Name="Z">-13.196689216970519</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-5.9374841241311893</Real>
+ <Real Name="Y">-1.3438907014985126</Real>
+ <Real Name="Z">-2.7775217946572655</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-7.8144042169827745</Real>
+ <Real Name="Y">-26.227146740505805</Real>
+ <Real Name="Z">-19.226000503090088</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.0880686956546695</Real>
+ <Real Name="Y">-3.0797361566100099</Real>
+ <Real Name="Z">-13.480051032538309</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-4.9973452358427064</Real>
+ <Real Name="Y">-22.019795657632674</Real>
+ <Real Name="Z">-3.5057718525584116</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.48021537934312419</Real>
+ <Real Name="Y">-0.1119184814167536</Real>
+ <Real Name="Z">-0.55871213350419213</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-11.710963177954484</Real>
+ <Real Name="Y">-22.602514869970666</Real>
+ <Real Name="Z">-4.920091756211618</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-4.2562713131673355</Real>
+ <Real Name="Y">-3.1975379801333257</Real>
+ <Real Name="Z">-12.696263461962817</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.083636781240502847</Real>
+ <Real Name="Y">-0.683594730203958</Real>
+ <Real Name="Z">-6.5236686696981163</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.036507660011698</Real>
+ <Real Name="Y">-0.54035007429810378</Real>
+ <Real Name="Z">-4.0177026203314306</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-4.719165394916967</Real>
+ <Real Name="Y">-6.8019620610174787</Real>
+ <Real Name="Z">-12.816689221738891</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">-5.9174841245782241</Real>
+ <Real Name="Y">-0.47389069673014106</Real>
+ <Real Name="Z">-1.8275218065781944</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-6.9844042336720751</Real>
+ <Real Name="Y">-25.91714673812162</Real>
+ <Real Name="Z">-18.496000484016601</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.37806871711234158</Real>
+ <Real Name="Y">-3.0197361579511144</Real>
+ <Real Name="Z">-13.130051038498774</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-4.7273452251138703</Real>
+ <Real Name="Y">-21.039795638559188</Real>
+ <Real Name="Z">-2.6757718692477122</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.19021538768777446</Real>
+ <Real Name="Y">-0.011918479926637485</Real>
+ <Real Name="Z">0.12128787364836524</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.78266792292938536</Real>
+ <Real Name="Y">0.24701126089639641</Real>
+ <Real Name="Z">0.075197087339731225</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.61956391875244121</Real>
+ <Real Name="Y">0.25681538531643089</Real>
+ <Real Name="Z">0.264650385589911</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-11.475149109556806</Real>
+ <Real Name="Y">-9.7544516427343577</Real>
+ <Real Name="Z">3.0247422457903341</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-11.858918281399532</Real>
+ <Real Name="Y">-7.4199289605932677</Real>
+ <Real Name="Z">3.011716132619819</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.80266792248235053</Real>
+ <Real Name="Y">1.1170112656647679</Real>
+ <Real Name="Z">1.0251970754188022</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.2795639449784848</Real>
+ <Real Name="Y">0.92681540200573143</Real>
+ <Real Name="Z">0.64465038082153936</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-10.645149126246107</Real>
+ <Real Name="Y">-9.4444516403501719</Real>
+ <Real Name="Z">3.7547422648638205</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-11.148918302857204</Real>
+ <Real Name="Y">-7.3599289619343722</Real>
+ <Real Name="Z">3.3617161266593545</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-22.79457410521962</Real>
+ <Real Name="Y">-4.8554021376267826</Real>
+ <Real Name="Z">5.6800905790772545</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-4.8643100721912402</Real>
+ <Real Name="Y">-2.6516169976273649</Real>
+ <Real Name="Z">-0.25116456753339361</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.09558489284628896</Real>
+ <Real Name="Y">-0.56688346388984168</Real>
+ <Real Name="Z">-0.94910028423615156</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-3.5826533245421075</Real>
+ <Real Name="Y">-9.5803366494364646</Real>
+ <Real Name="Z">-23.575529237696852</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-4.0944609423338374</Real>
+ <Real Name="Y">-7.9446698242436193</Real>
+ <Real Name="Z">-1.3877955568392644</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-22.774574105666655</Real>
+ <Real Name="Y">-3.9854021328584111</Real>
+ <Real Name="Z">6.6300905671563255</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-4.8443100726382751</Real>
+ <Real Name="Y">-1.7816169928589933</Real>
+ <Real Name="Z">0.69883542054567749</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.56441513337975469</Real>
+ <Real Name="Y">0.10311655279945886</Real>
+ <Real Name="Z">-0.56910028900452314</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.82999998331069946</Real>
+ <Real Name="Y">0.31000000238418579</Real>
+ <Real Name="Z">0.73000001907348633</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-3.8244609316050013</Real>
+ <Real Name="Y">-6.964669805170133</Real>
+ <Real Name="Z">-0.5577955735285649</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.63591768738012566</Real>
+ <Real Name="Y">0.3087640761204955</Real>
+ <Real Name="Z">0.03426844856107035</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.50339568398635848</Real>
+ <Real Name="Y">0.32101923164553864</Real>
+ <Real Name="Z">0.18363175660878781</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-9.3235586515149063</Real>
+ <Real Name="Y">-12.193064553417946</Real>
+ <Real Name="Z">3.2071979869138385</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-9.6353711036371195</Real>
+ <Real Name="Y">-9.2749112007415846</Real>
+ <Real Name="Z">3.0222260742447977</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">0.65591768693309083</Real>
+ <Real Name="Y">1.1787640808888671</Real>
+ <Real Name="Z">0.98426843664014141</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">1.1633957102124022</Real>
+ <Real Name="Y">0.99101924833483923</Real>
+ <Real Name="Z">0.56363175184041625</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-8.4935586682042068</Real>
+ <Real Name="Y">-11.88306455103376</Real>
+ <Real Name="Z">3.9371980059873248</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-8.9253711250947916</Real>
+ <Real Name="Y">-9.2149112020826891</Real>
+ <Real Name="Z">3.3722260682843332</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.27000001072883606</Real>
+ <Real Name="Y">0.98000001907348633</Real>
+ <Real Name="Z">0.82999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-19.925252342514202</Real>
+ <Real Name="Y">-4.9850434490087228</Real>
+ <Real Name="Z">-9.1473548430064433</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-18.520591460490941</Real>
+ <Real Name="Y">-6.0692526720334774</Real>
+ <Real Name="Z">5.0076479125818185</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.9522519336553823</Real>
+ <Real Name="Y">-3.3145212470342056</Real>
+ <Real Name="Z">0.041856812732197594</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-0.077662725437609784</Real>
+ <Real Name="Y">-0.70860432986230215</Real>
+ <Real Name="Z">-0.70184026829559087</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-3.326749515646243</Real>
+ <Real Name="Y">-9.9308372803045231</Real>
+ <Real Name="Z">-0.45425921737202102</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-18.500591460937976</Real>
+ <Real Name="Y">-5.1992526672651058</Real>
+ <Real Name="Z">5.9576479006608896</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">-3.9322519341024171</Real>
+ <Real Name="Y">-2.444521242265834</Real>
+ <Real Name="Z">0.99185680081126859</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.58233730078843393</Real>
+ <Real Name="Y">-0.038604313173001614</Real>
+ <Real Name="Z">-0.32184027306396246</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0.019999999552965164</Real>
+ <Real Name="Y">0.87000000476837158</Real>
+ <Real Name="Z">0.94999998807907104</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.6600000262260437</Real>
+ <Real Name="Y">0.67000001668930054</Real>
+ <Real Name="Z">0.37999999523162842</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.44999998807907104</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.93999999761581421</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.54000002145767212</Real>
+ <Real Name="Y">0.75999999046325684</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.82999998331069946</Real>
+ <Real Name="Y">0.31000000238418579</Real>
+ <Real Name="Z">0.73000001907348633</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.70999997854232788</Real>
+ <Real Name="Y">0.059999998658895493</Real>
+ <Real Name="Z">0.34999999403953552</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.31999999284744263</Real>
+ <Real Name="Y">0.34999999403953552</Real>
+ <Real Name="Z">0.61000001430511475</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-3.0567495049174069</Real>
+ <Real Name="Y">-8.9508372612310367</Real>
+ <Real Name="Z">0.37574076593867844</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.10999999940395355</Real>
+ <Real Name="Y">0.30000001192092896</Real>
+ <Real Name="Z">0.41999998688697815</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.94999998807907104</Real>
+ <Real Name="Y">0.68999999761581421</Real>
+ <Real Name="Z">0.57999998331069946</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.28999999165534973</Real>
+ <Real Name="Y">0.10000000149011612</Real>
+ <Real Name="Z">0.68000000715255737</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.93999999761581421</Real>
+ <Real Name="Y">0.62000000476837158</Real>
+ <Real Name="Z">0.50999999046325684</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0.4699999988079071</Real>
+ <Real Name="Y">0.039999999105930328</Real>
+ <Real Name="Z">0.4699999988079071</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-11.577102289706572</Real>
+ <Real Name="Y">0.84910120894795005</Real>
+ <Real Name="Z">1.8482439089193421</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">2</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">2.0340570782897585</Real>
+ <Real Name="Y">1.4319189829320136</Real>
+ <Real Name="Z">-0.59251856152304705</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">13</Int>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-1.0210446166718394</Real>
+ <Real Name="Y">-16.393563534893939</Real>
+ <Real Name="Z">2.0765205102067403</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">-3.3498355821816856</Real>
+ <Real Name="Y">-0.97018032158412315</Real>
+ <Real Name="Z">0.58368499271815877</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ <Vector>
+ <Real Name="X">0</Real>
+ <Real Name="Y">0</Real>
+ <Real Name="Z">0</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="Forces">
+ <Int Name="Length">1</Int>
+ <Vector>
+ <Real Name="X">-11.557102290153606</Real>
+ <Real Name="Y">1.7191012137163217</Real>
+ <Real Name="Z">2.7982438969984131</Real>
+ </Vector>
+ </Sequence>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.029793791749999521</Real>
+ <Real Name="Cell 3 1 2 im">0.39228491385592074</Real>
+ <Real Name="Cell 3 5 7 re">-1.7719234621492696e-18</Real>
+ <Real Name="Cell 3 5 7 im">2.9532057266304802e-24</Real>
+ <Real Name="Cell 6 2 4 re">0.00023152408798567255</Real>
+ <Real Name="Cell 6 2 4 im">1.8844984033755337e-05</Real>
+ <Real Name="Cell 7 0 0 re">-2.5995625152404473</Real>
+ <Real Name="Cell 7 0 0 im">-0.72787749187164519</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">6.6281524398489351</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">8.2591871252955169</Real>
+ <Real Name="Cell 1 0">1.1366553211135979</Real>
+ <Real Name="Cell 1 1">-2.4225818754293491</Real>
+ <Real Name="Cell 2 0">3.8646282001861314</Real>
+ <Real Name="Cell 2 1">3.0310808563029275</Real>
+ <Real Name="Cell 2 2">6.9915989805718821</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.040960646891504318</Real>
+ <Real Name="Cell 0 0 0 im">-0.078410378960130159</Real>
+ <Real Name="Cell 3 1 2 re">-1.3292554554983258e-14</Real>
+ <Real Name="Cell 3 1 2 im">-1.7501863013212537e-13</Real>
+ <Real Name="Cell 7 0 0 re">3.8478547590276771e-09</Real>
+ <Real Name="Cell 7 0 0 im">1.0773993141797484e-09</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.33435589928707093</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.16717786512572544</Real>
+ <Real Name="Cell 1 0">-3.2035473334097224e-12</Real>
+ <Real Name="Cell 1 1">0.16717794964102289</Real>
+ <Real Name="Cell 2 0">-1.0892061239107136e-11</Real>
+ <Real Name="Cell 2 1">-8.5427928890925915e-12</Real>
+ <Real Name="Cell 2 2">0.16717794961448998</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.011587702199350205</Real>
+ <Real Name="Cell 0 6 7 re">0.0027096545878538447</Real>
+ <Real Name="Cell 2 5 10 re">0.084992949919242208</Real>
+ <Real Name="Cell 2 5 10 im">0.25143747449906617</Real>
+ <Real Name="Cell 4 2 7 re">2.9777523498154599</Real>
+ <Real Name="Cell 4 2 7 im">-8.6562566868719806</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">390.21941702065322</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">305.39495784936184</Real>
+ <Real Name="Cell 1 0">429.75989722709977</Real>
+ <Real Name="Cell 1 1">182.49318143618873</Real>
+ <Real Name="Cell 2 0">289.88123362603045</Real>
+ <Real Name="Cell 2 1">252.13109902072929</Real>
+ <Real Name="Cell 2 2">-25.953619706197543</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-4.178818756469648e-13</Real>
+ <Real Name="Cell 0 6 7 re">-1.0069137884249014e-27</Real>
+ <Real Name="Cell 2 5 10 re">-5.6094174367698197e-19</Real>
+ <Real Name="Cell 2 5 10 im">-1.6594526428986948e-18</Real>
+ <Real Name="Cell 4 2 7 re">-2.2152312932810136e-08</Real>
+ <Real Name="Cell 4 2 7 im">6.4396257454452892e-08</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-2.8806661919058218e-06</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-1.8705530331608101e-05</Real>
+ <Real Name="Cell 1 0">-1.7197688691957962e-05</Real>
+ <Real Name="Cell 1 1">-1.3240622263816033e-05</Real>
+ <Real Name="Cell 2 0">-1.1629584411980756e-05</Real>
+ <Real Name="Cell 2 1">-9.9276940353995703e-06</Real>
+ <Real Name="Cell 2 2">-5.2730666430580063e-06</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.8235250283388903</Real>
+ <Real Name="Cell 3 1 2 im">10.84307923982591</Real>
+ <Real Name="Cell 3 5 7 re">-0.0058552916207897637</Real>
+ <Real Name="Cell 3 5 7 im">9.7588192238469836e-09</Real>
+ <Real Name="Cell 6 2 4 re">24.162018358378187</Real>
+ <Real Name="Cell 6 2 4 im">1.9666759262436562</Real>
+ <Real Name="Cell 7 0 0 re">-4.5620086539352958</Real>
+ <Real Name="Cell 7 0 0 im">-1.2773624013485305</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">824.39918276470382</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">271.10568117726308</Real>
+ <Real Name="Cell 1 0">-592.09989563985494</Real>
+ <Real Name="Cell 1 1">362.90453530924833</Real>
+ <Real Name="Cell 2 0">-496.93337251229889</Real>
+ <Real Name="Cell 2 1">563.77003662042625</Real>
+ <Real Name="Cell 2 2">16.869408855207137</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.0063639096934527042</Real>
+ <Real Name="Cell 0 0 0 im">-0.012182341066375335</Real>
+ <Real Name="Cell 3 1 2 re">-9.9228430546493259e-06</Real>
+ <Real Name="Cell 3 1 2 im">-0.00013065076327181465</Real>
+ <Real Name="Cell 3 5 7 re">2.5759085022798612e-11</Real>
+ <Real Name="Cell 3 5 7 im">-4.2931807737236158e-17</Real>
+ <Real Name="Cell 6 2 4 re">-1.3138496192640048e-06</Real>
+ <Real Name="Cell 6 2 4 im">-1.0694124880568754e-07</Real>
+ <Real Name="Cell 7 0 0 re">0.00057663643475955946</Real>
+ <Real Name="Cell 7 0 0 im">0.00016145819898305986</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.053802892914868977</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.020691662312509726</Real>
+ <Real Name="Cell 1 0">-0.0023237899154683532</Real>
+ <Real Name="Cell 1 1">0.02527149273778484</Real>
+ <Real Name="Cell 2 0">0.000600553079798094</Real>
+ <Real Name="Cell 2 1">-0.00016167607048479874</Real>
+ <Real Name="Cell 2 2">0.026646993387493604</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.11021861306916146</Real>
+ <Real Name="Cell 0 6 7 re">1.2569112094750723</Real>
+ <Real Name="Cell 2 5 10 re">1.3946131972852089</Real>
+ <Real Name="Cell 2 5 10 im">4.125730670151416</Real>
+ <Real Name="Cell 4 2 7 re">30.236028240191384</Real>
+ <Real Name="Cell 4 2 7 im">-87.895429468749143</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">3985.3659847228328</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">3095.9021918163417</Real>
+ <Real Name="Cell 1 0">4308.3013422597896</Real>
+ <Real Name="Cell 1 1">1747.2571266026378</Real>
+ <Real Name="Cell 2 0">2969.2524472571986</Real>
+ <Real Name="Cell 2 1">2429.5782224871705</Real>
+ <Real Name="Cell 2 2">-179.5912331149944</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-7.0537221329547844e-09</Real>
+ <Real Name="Cell 0 6 7 re">-5.7463804790685012e-07</Real>
+ <Real Name="Cell 2 5 10 re">-4.1614840083045064e-11</Real>
+ <Real Name="Cell 2 5 10 im">-1.2311056743065747e-10</Real>
+ <Real Name="Cell 4 2 7 re">-2.2493407131842702e-07</Real>
+ <Real Name="Cell 4 2 7 im">6.5387810342123984e-07</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-3.1321432926615869e-05</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-0.00018890242348857845</Real>
+ <Real Name="Cell 1 0">-0.00017462064584253123</Real>
+ <Real Name="Cell 1 1">-0.00013613472585420061</Real>
+ <Real Name="Cell 2 0">-0.00011809371439078819</Real>
+ <Real Name="Cell 2 1">-9.3982474514113124e-05</Real>
+ <Real Name="Cell 2 2">-6.9661560924232365e-05</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.01930849403987768</Real>
+ <Real Name="Cell 0 6 7 re">1.1045009433799435e-16</Real>
+ <Real Name="Cell 2 5 10 re">2.4507459280840924e-29</Real>
+ <Real Name="Cell 2 5 10 im">7.2501233029544003e-29</Real>
+ <Real Name="Cell 4 2 7 re">9.076918472281522e-14</Real>
+ <Real Name="Cell 4 2 7 im">-2.6386390468887747e-13</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">0.0028962742328731829</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-0.0014481371089258624</Real>
+ <Real Name="Cell 1 0">8.8361515258819677e-12</Real>
+ <Real Name="Cell 1 1">0.011339167978507696</Real>
+ <Real Name="Cell 2 0">5.257510305368959e-11</Real>
+ <Real Name="Cell 2 1">6.1846841169878849e-11</Real>
+ <Real Name="Cell 2 2">-0.0014481367483985346</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-5.4292848213686879e-16</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-8.1439275556636247e-17</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">4.0719637778318123e-17</Real>
+ <Real Name="Cell 1 0">-2.215406351573413e-112</Real>
+ <Real Name="Cell 1 1">-2.3047772408403365e-15</Real>
+ <Real Name="Cell 2 0">-1.3181668161597632e-111</Real>
+ <Real Name="Cell 2 1">-1.5507844461013891e-111</Real>
+ <Real Name="Cell 2 2">4.0719637778318123e-17</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.092667581018586076</Real>
+ <Real Name="Cell 3 1 2 im">1.2201231163238289</Real>
+ <Real Name="Cell 3 5 7 re">-2.6528086898508655e-16</Real>
+ <Real Name="Cell 3 5 7 im">4.4213477511156205e-22</Real>
+ <Real Name="Cell 6 2 4 re">0.0011988827121831131</Real>
+ <Real Name="Cell 6 2 4 im">9.7583477235570334e-05</Real>
+ <Real Name="Cell 7 0 0 re">-44.241861946428088</Real>
+ <Real Name="Cell 7 0 0 im">-12.387721134038228</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">69.36892849186863</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">38.63901388333057</Real>
+ <Real Name="Cell 1 0">3.4880677727366778</Real>
+ <Real Name="Cell 1 1">-31.8980021606294</Real>
+ <Real Name="Cell 2 0">11.859430759952769</Real>
+ <Real Name="Cell 2 1">9.4739713557744256</Real>
+ <Real Name="Cell 2 2">-2.4729607327929468</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.040960646891504318</Real>
+ <Real Name="Cell 0 0 0 im">-0.078410378960130159</Real>
+ <Real Name="Cell 3 1 2 re">-4.1343810365053865e-14</Real>
+ <Real Name="Cell 3 1 2 im">-5.4436015474703515e-13</Real>
+ <Real Name="Cell 7 0 0 re">0.0073924880067034026</Real>
+ <Real Name="Cell 7 0 0 im">0.0020698966066268229</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.3443209679114585</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.15510734808993293</Real>
+ <Real Name="Cell 1 0">-9.9639879528132092e-12</Real>
+ <Real Name="Cell 1 1">0.17216048394791436</Real>
+ <Real Name="Cell 2 0">-3.3877559989804848e-11</Real>
+ <Real Name="Cell 2 1">-2.6570634540835225e-11</Real>
+ <Real Name="Cell 2 2">0.1721604838653891</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">0.28488408806756871</Real>
+ <Real Name="Cell 0 6 7 re">5.061653570583762e-14</Real>
+ <Real Name="Cell 2 5 10 re">2.3693520814969476e-27</Real>
+ <Real Name="Cell 2 5 10 im">7.0093331757134742e-27</Real>
+ <Real Name="Cell 4 2 7 re">9.2166819473361329e-13</Real>
+ <Real Name="Cell 4 2 7 im">-2.6792679633799972e-12</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">0.042732615028211886</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">-0.021366307437842177</Real>
+ <Real Name="Cell 1 0">8.9722077488322564e-11</Real>
+ <Real Name="Cell 1 1">0.10345510128367014</Real>
+ <Real Name="Cell 2 0">5.3384637602950688e-10</Real>
+ <Real Name="Cell 2 1">6.2757650480313056e-10</Real>
+ <Real Name="Cell 2 2">-0.021366303771492665</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 4 0 im">-3.36295522544755e-10</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-5.0444330386190764e-11</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">2.5222165193095382e-11</Real>
+ <Real Name="Cell 1 0">-2.2495184669680253e-111</Real>
+ <Real Name="Cell 1 1">-8.0991543667196338e-10</Real>
+ <Real Name="Cell 2 0">-1.3384635253888647e-110</Real>
+ <Real Name="Cell 2 1">8.1762240348126863e-110</Real>
+ <Real Name="Cell 2 2">2.5222165193095382e-11</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">3.5</Real>
+ <Real Name="Cell 0 0 0 im">6.6999998092651367</Real>
+ <Real Name="Cell 3 1 2 re">0.26477364495270733</Real>
+ <Real Name="Cell 3 1 2 im">3.4861862287666896</Real>
+ <Real Name="Cell 3 5 7 re">-0.00012611665265524979</Real>
+ <Real Name="Cell 3 5 7 im">2.1019441798755029e-10</Real>
+ <Real Name="Cell 6 2 4 re">2.9959899577437761</Real>
+ <Real Name="Cell 6 2 4 im">0.24385964937897381</Real>
+ <Real Name="Cell 7 0 0 re">-0.13079137357120588</Real>
+ <Real Name="Cell 7 0 0 im">-0.036621583976275775</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">118.65279828442088</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">207.87503560992724</Real>
+ <Real Name="Cell 1 0">151.72558248247225</Real>
+ <Real Name="Cell 1 1">27.021498076618471</Real>
+ <Real Name="Cell 2 0">0.45029163473062073</Real>
+ <Real Name="Cell 2 1">0.35388518348693898</Real>
+ <Real Name="Cell 2 2">-59.275738025458466</Real>
+ </Matrix>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <NonZeroGridValues Name="ComplexSpaceGrid">
+ <Real Name="Cell 0 0 0 re">-0.0063639096934527042</Real>
+ <Real Name="Cell 0 0 0 im">-0.012182341066375335</Real>
+ <Real Name="Cell 3 1 2 re">-3.1903187316269281e-06</Real>
+ <Real Name="Cell 3 1 2 im">-4.2005862137679066e-05</Real>
+ <Real Name="Cell 3 5 7 re">7.4468604604379845e-21</Real>
+ <Real Name="Cell 3 5 7 im">-1.2411433917415391e-26</Real>
+ <Real Name="Cell 6 2 4 re">-1.1742988941980482e-10</Real>
+ <Real Name="Cell 6 2 4 im">-9.5582468781340022e-12</Real>
+ <Real Name="Cell 7 0 0 re">7.4608679756532561e-13</Real>
+ <Real Name="Cell 7 0 0 im">2.089042997606721e-13</Real>
+ </NonZeroGridValues>
+ <Real Name="Energy">-0.052281447439372866</Real>
+ <Matrix Name="Virial">
+ <Real Name="Cell 0 0">0.02472611767566462</Real>
+ <Real Name="Cell 1 0">-0.00080506035697563581</Real>
+ <Real Name="Cell 1 1">0.025682559278230224</Real>
+ <Real Name="Cell 2 0">-3.29941854498715e-06</Real>
+ <Real Name="Cell 2 1">-1.8777213593421415e-06</Real>
+ <Real Name="Cell 2 2">0.026140716022377927</Real>
+ </Matrix>
+</ReferenceData>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define g_baseNR 14
const int grid_base[g_baseNR] = { 45, 48, 50, 52, 54, 56, 60, 64, 70, 72, 75, 80, 81, 84 };
-real calc_grid(FILE *fp, const matrix box, real gr_sp,
- int *nx, int *ny, int *nz)
+real calcFftGrid(FILE *fp,
+ const matrix box, real gridSpacing, int minGridPointsPerDim,
+ int *nx, int *ny, int *nz)
{
int d, n[DIM];
int i;
rvec spacing;
real max_spacing;
- if ((*nx <= 0 || *ny <= 0 || *nz <= 0) && gr_sp <= 0)
+ if ((*nx <= 0 || *ny <= 0 || *nz <= 0) && gridSpacing <= 0)
{
- gmx_fatal(FARGS, "invalid fourier grid spacing: %g", gr_sp);
+ gmx_fatal(FARGS, "invalid fourier grid spacing: %g", gridSpacing);
}
if (grid_base[g_baseNR-1] % 4 != 0)
if ((*nx <= 0) || (*ny <= 0) || (*nz <= 0))
{
- if (NULL != fp)
+ if (nullptr != fp)
{
fprintf(fp, "Calculating fourier grid dimensions for%s%s%s\n",
*nx > 0 ? "" : " X", *ny > 0 ? "" : " Y", *nz > 0 ? "" : " Z");
{
if (n[d] <= 0)
{
- nmin = static_cast<int>(box_size[d]/gr_sp + 0.999);
+ nmin = static_cast<int>(box_size[d]/gridSpacing + 0.999);
+ nmin = std::max(nmin, minGridPointsPerDim);
i = g_initNR - 1;
if (grid_init[i] >= nmin)
*nx = n[XX];
*ny = n[YY];
*nz = n[ZZ];
- if (NULL != fp)
+ if (nullptr != fp)
{
fprintf(fp, "Using a fourier grid of %dx%dx%d, spacing %.3f %.3f %.3f\n",
*nx, *ny, *nz, spacing[XX], spacing[YY], spacing[ZZ]);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/real.h"
-real calc_grid(FILE *fp,
- const matrix box, real gr_sp,
- int *nx, int *ny, int *nz);
+real calcFftGrid(FILE *fp,
+ const matrix box, real gridSpacing, int minGridPointsPerDim,
+ int *nx, int *ny, int *nz);
/* Sets the number of grid points for each zero n* to the first reasonable
- * number which gives a spacing equal to or smaller than gr_sp.
+ * number which gives a spacing equal to or smaller than gridSpacing
+ * and is >= minGridPointsPerDim.
* Returns the maximum grid spacing.
*/
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 Erik Lindahl, David van der Spoel, University of Groningen.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_fft_flag flags)
{
gmx_many_fft_t fft;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid opaque FFT datatype pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
- if ( (fft = (gmx_many_fft_t)malloc(sizeof(struct gmx_many_fft))) == NULL)
+ if ( (fft = (gmx_many_fft_t)malloc(sizeof(struct gmx_many_fft))) == nullptr)
{
return ENOMEM;
}
gmx_fft_flag flags)
{
gmx_many_fft_t fft;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid opaque FFT datatype pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
- if ( (fft = (gmx_many_fft_t)malloc(sizeof(struct gmx_many_fft))) == NULL)
+ if ( (fft = (gmx_many_fft_t)malloc(sizeof(struct gmx_many_fft))) == nullptr)
{
return ENOMEM;
}
gmx_many_fft_destroy(gmx_fft_t fft)
{
gmx_many_fft_t mfft = (gmx_many_fft_t)fft;
- if (mfft != NULL)
+ if (mfft != nullptr)
{
- if (mfft->fft != NULL)
+ if (mfft->fft != nullptr)
{
gmx_fft_destroy(mfft->fft);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
#endif
-/* largest factor */
-static int l2factor(int z)
-{
- int i;
- if (z == 1)
- {
- i = 1;
- }
- else
- {
- i = z/2;
- while (z%i != 0)
- {
- i--;
- }
- }
- return i;
-}
-
-/* largest prime factor: WARNING: slow recursion, only use for small numbers */
-static int lpfactor(int z)
-{
- int f = l2factor(z);
- if (f == 1)
- {
- return z;
- }
- return std::max(lpfactor(f), lpfactor(z/f));
-}
-
#if !GMX_MPI
#if HAVE_GETTIMEOFDAY
#include <sys/time.h>
int P[2], bMaster, prank[2], i, t;
int rNG, rMG, rKG;
- int *N0 = 0, *N1 = 0, *M0 = 0, *M1 = 0, *K0 = 0, *K1 = 0, *oN0 = 0, *oN1 = 0, *oM0 = 0, *oM1 = 0, *oK0 = 0, *oK1 = 0;
- int N[3], M[3], K[3], pN[3], pM[3], pK[3], oM[3], oK[3], *iNin[3] = {0}, *oNin[3] = {0}, *iNout[3] = {0}, *oNout[3] = {0};
+ int *N0 = nullptr, *N1 = nullptr, *M0 = nullptr, *M1 = nullptr, *K0 = nullptr, *K1 = nullptr, *oN0 = nullptr, *oN1 = nullptr, *oM0 = nullptr, *oM1 = nullptr, *oK0 = nullptr, *oK1 = nullptr;
+ int N[3], M[3], K[3], pN[3], pM[3], pK[3], oM[3], oK[3], *iNin[3] = {nullptr}, *oNin[3] = {nullptr}, *iNout[3] = {nullptr}, *oNout[3] = {nullptr};
int C[3], rC[3], nP[2];
int lsize;
- t_complex *lin = 0, *lout = 0, *lout2 = 0, *lout3 = 0;
+ t_complex *lin = nullptr, *lout = nullptr, *lout2 = nullptr, *lout3 = nullptr;
fft5d_plan plan;
int s;
{
printf("FFT5D: FATAL: Datasize cannot be zero in any dimension\n");
}
- return 0;
+ return nullptr;
}
rNG = NG; rMG = MG; rKG = KG;
if ((flags&FFT5D_REALCOMPLEX) && !(flags&FFT5D_BACKWARD))
{
plan->p3d = FFTW(plan_guru_dft_r2c)(/*rank*/ 3, dims,
- /*howmany*/ 0, /*howmany_dims*/ 0,
+ /*howmany*/ 0, /*howmany_dims*/ nullptr,
(real*)lin, (FFTW(complex) *) lout,
/*flags*/ fftwflags);
}
else if ((flags&FFT5D_REALCOMPLEX) && (flags&FFT5D_BACKWARD))
{
plan->p3d = FFTW(plan_guru_dft_c2r)(/*rank*/ 3, dims,
- /*howmany*/ 0, /*howmany_dims*/ 0,
+ /*howmany*/ 0, /*howmany_dims*/ nullptr,
(FFTW(complex) *) lin, (real*)lout,
/*flags*/ fftwflags);
}
else
{
plan->p3d = FFTW(plan_guru_dft)(/*rank*/ 3, dims,
- /*howmany*/ 0, /*howmany_dims*/ 0,
+ /*howmany*/ 0, /*howmany_dims*/ nullptr,
(FFTW(complex) *) lin, (FFTW(complex) *) lout,
/*sign*/ (flags&FFT5D_BACKWARD) ? 1 : -1, /*flags*/ fftwflags);
}
if (plan->iNin[s])
{
free(plan->iNin[s]);
- plan->iNin[s] = 0;
+ plan->iNin[s] = nullptr;
}
if (plan->oNin[s])
{
free(plan->oNin[s]);
- plan->oNin[s] = 0;
+ plan->oNin[s] = nullptr;
}
if (plan->iNout[s])
{
free(plan->iNout[s]);
- plan->iNout[s] = 0;
+ plan->iNout[s] = nullptr;
}
if (plan->oNout[s])
{
free(plan->oNout[s]);
- plan->oNout[s] = 0;
+ plan->oNout[s] = nullptr;
}
}
#if GMX_FFT_FFTW3
of processor dimensions*/
fft5d_plan fft5d_plan_3d_cart(int NG, int MG, int KG, MPI_Comm comm, int P0, int flags, t_complex** rlin, t_complex** rlout, t_complex** rlout2, t_complex** rlout3, int nthreads)
{
- MPI_Comm cart[2] = {0};
+ MPI_Comm cart[2] = {MPI_COMM_NULL, MPI_COMM_NULL};
#if GMX_MPI
int size = 1, prank = 0;
int P[2];
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
gmx_fft_t fft;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid FFT opaque type pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
- if ( (fft = (struct gmx_fft *)malloc(sizeof(struct gmx_fft))) == NULL)
+ if ( (fft = (struct gmx_fft *)malloc(sizeof(struct gmx_fft))) == nullptr)
{
return ENOMEM;
}
- fft->next = NULL;
+ fft->next = nullptr;
fft->n = nx;
/* Need 4*n storage for 1D complex FFT */
- if ( (fft->work = (real *)malloc(sizeof(real)*(4*nx))) == NULL)
+ if ( (fft->work = (real *)malloc(sizeof(real)*(4*nx))) == nullptr)
{
free(fft);
return ENOMEM;
{
gmx_fft_t fft;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid FFT opaque type pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
- if ( (fft = (struct gmx_fft *)malloc(sizeof(struct gmx_fft))) == NULL)
+ if ( (fft = (struct gmx_fft *)malloc(sizeof(struct gmx_fft))) == nullptr)
{
return ENOMEM;
}
- fft->next = NULL;
+ fft->next = nullptr;
fft->n = nx;
/* Need 2*n storage for 1D real FFT */
- if ((fft->work = (real *)malloc(sizeof(real)*(2*nx))) == NULL)
+ if ((fft->work = (real *)malloc(sizeof(real)*(2*nx))) == nullptr)
{
free(fft);
return ENOMEM;
int nyc = (ny/2 + 1);
int rc;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid FFT opaque type pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
/* Create the X transform */
- if ( (fft = (struct gmx_fft *)malloc(sizeof(struct gmx_fft))) == NULL)
+ if ( (fft = (struct gmx_fft *)malloc(sizeof(struct gmx_fft))) == nullptr)
{
return ENOMEM;
}
/* Need 4*nx storage for 1D complex FFT, and another
* 2*nx*nyc elements for complex-to-real storage in our high-level routine.
*/
- if ( (fft->work = (real *)malloc(sizeof(real)*(4*nx+2*nx*nyc))) == NULL)
+ if ( (fft->work = (real *)malloc(sizeof(real)*(4*nx+2*nx*nyc))) == nullptr)
{
free(fft);
return ENOMEM;
}
}
}
- data = (t_complex *)out_data;
+ data = static_cast<t_complex *>(out_data);
/* y real-to-complex FFTs */
for (i = 0; i < nx; i++)
if (in_data != out_data)
{
memcpy(work, in_data, sizeof(t_complex)*nx*nyc);
- data = (t_complex *)work;
+ data = reinterpret_cast<t_complex *>(work);
}
else
{
/* in-place */
- data = (t_complex *)out_data;
+ data = reinterpret_cast<t_complex *>(out_data);
}
/* Transpose to get X arrays */
void
gmx_fft_destroy(gmx_fft_t fft)
{
- if (fft != NULL)
+ if (fft != nullptr)
{
free(fft->work);
- if (fft->next != NULL)
+ if (fft->next != nullptr)
{
gmx_fft_destroy(fft->next);
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fftw_flags = (flags & GMX_FFT_FLAG_CONSERVATIVE) ? FFTW_ESTIMATE : FFTW_MEASURE;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid opaque FFT datatype pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
FFTW_LOCK;
- if ( (fft = (gmx_fft_t)FFTWPREFIX(malloc)(sizeof(struct gmx_fft))) == NULL)
+ if ( (fft = (gmx_fft_t)FFTWPREFIX(malloc)(sizeof(struct gmx_fft))) == nullptr)
{
FFTW_UNLOCK;
return ENOMEM;
/* allocate aligned, and extra memory to make it unaligned */
p1 = (FFTWPREFIX(complex) *) FFTWPREFIX(malloc)(sizeof(FFTWPREFIX(complex))*(nx+2)*howmany);
- if (p1 == NULL)
+ if (p1 == nullptr)
{
FFTWPREFIX(free)(fft);
FFTW_UNLOCK;
}
p2 = (FFTWPREFIX(complex) *) FFTWPREFIX(malloc)(sizeof(FFTWPREFIX(complex))*(nx+2)*howmany);
- if (p2 == NULL)
+ if (p2 == nullptr)
{
FFTWPREFIX(free)(p1);
FFTWPREFIX(free)(fft);
{
for (k = 0; k < 2; k++)
{
- if (fft->plan[i][j][k] == NULL)
+ if (fft->plan[i][j][k] == nullptr)
{
gmx_fatal(FARGS, "Error initializing FFTW3 plan.");
FFTW_UNLOCK;
fftw_flags = (flags & GMX_FFT_FLAG_CONSERVATIVE) ? FFTW_ESTIMATE : FFTW_MEASURE;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid opaque FFT datatype pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
FFTW_LOCK;
- if ( (fft = (gmx_fft_t) FFTWPREFIX(malloc)(sizeof(struct gmx_fft))) == NULL)
+ if ( (fft = (gmx_fft_t) FFTWPREFIX(malloc)(sizeof(struct gmx_fft))) == nullptr)
{
FFTW_UNLOCK;
return ENOMEM;
/* allocate aligned, and extra memory to make it unaligned */
p1 = (real *) FFTWPREFIX(malloc)(sizeof(real)*(nx/2+1)*2*howmany + 8);
- if (p1 == NULL)
+ if (p1 == nullptr)
{
FFTWPREFIX(free)(fft);
FFTW_UNLOCK;
}
p2 = (real *) FFTWPREFIX(malloc)(sizeof(real)*(nx/2+1)*2*howmany + 8);
- if (p2 == NULL)
+ if (p2 == nullptr)
{
FFTWPREFIX(free)(p1);
FFTWPREFIX(free)(fft);
fftw_complex *out, const int *onembed,
int ostride, int odist,
unsigned flag */
- fft->plan[0][0][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, up1, 0, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) up2, 0, 1, (nx/2+1), fftw_flags);
- fft->plan[0][1][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, up1, 0, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) up1, 0, 1, (nx/2+1), fftw_flags);
- fft->plan[1][0][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, p1, 0, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) p2, 0, 1, (nx/2+1), fftw_flags);
- fft->plan[1][1][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, p1, 0, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) p1, 0, 1, (nx/2+1), fftw_flags);
+ fft->plan[0][0][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, up1, nullptr, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) up2, nullptr, 1, (nx/2+1), fftw_flags);
+ fft->plan[0][1][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, up1, nullptr, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) up1, nullptr, 1, (nx/2+1), fftw_flags);
+ fft->plan[1][0][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, p1, nullptr, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) p2, nullptr, 1, (nx/2+1), fftw_flags);
+ fft->plan[1][1][1] = FFTWPREFIX(plan_many_dft_r2c)(1, &nx, howmany, p1, nullptr, 1, (nx/2+1) *2, (FFTWPREFIX(complex) *) p1, nullptr, 1, (nx/2+1), fftw_flags);
- fft->plan[0][0][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) up1, 0, 1, (nx/2+1), up2, 0, 1, (nx/2+1) *2, fftw_flags);
- fft->plan[0][1][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) up1, 0, 1, (nx/2+1), up1, 0, 1, (nx/2+1) *2, fftw_flags);
- fft->plan[1][0][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) p1, 0, 1, (nx/2+1), p2, 0, 1, (nx/2+1) *2, fftw_flags);
- fft->plan[1][1][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) p1, 0, 1, (nx/2+1), p1, 0, 1, (nx/2+1) *2, fftw_flags);
+ fft->plan[0][0][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) up1, nullptr, 1, (nx/2+1), up2, nullptr, 1, (nx/2+1) *2, fftw_flags);
+ fft->plan[0][1][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) up1, nullptr, 1, (nx/2+1), up1, nullptr, 1, (nx/2+1) *2, fftw_flags);
+ fft->plan[1][0][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) p1, nullptr, 1, (nx/2+1), p2, nullptr, 1, (nx/2+1) *2, fftw_flags);
+ fft->plan[1][1][0] = FFTWPREFIX(plan_many_dft_c2r)(1, &nx, howmany, (FFTWPREFIX(complex) *) p1, nullptr, 1, (nx/2+1), p1, nullptr, 1, (nx/2+1) *2, fftw_flags);
for (i = 0; i < 2; i++)
{
{
for (k = 0; k < 2; k++)
{
- if (fft->plan[i][j][k] == NULL)
+ if (fft->plan[i][j][k] == nullptr)
{
gmx_fatal(FARGS, "Error initializing FFTW3 plan.");
FFTW_UNLOCK;
fftw_flags = (flags & GMX_FFT_FLAG_CONSERVATIVE) ? FFTW_ESTIMATE : FFTW_MEASURE;
- if (pfft == NULL)
+ if (pfft == nullptr)
{
gmx_fatal(FARGS, "Invalid opaque FFT datatype pointer.");
return EINVAL;
}
- *pfft = NULL;
+ *pfft = nullptr;
FFTW_LOCK;
- if ( (fft = (gmx_fft_t) FFTWPREFIX(malloc)(sizeof(struct gmx_fft))) == NULL)
+ if ( (fft = (gmx_fft_t) FFTWPREFIX(malloc)(sizeof(struct gmx_fft))) == nullptr)
{
FFTW_UNLOCK;
return ENOMEM;
/* allocate aligned, and extra memory to make it unaligned */
p1 = (real *) FFTWPREFIX(malloc)(sizeof(real) *( nx*(ny/2+1)*2 + 2) );
- if (p1 == NULL)
+ if (p1 == nullptr)
{
FFTWPREFIX(free)(fft);
FFTW_UNLOCK;
}
p2 = (real *) FFTWPREFIX(malloc)(sizeof(real) *( nx*(ny/2+1)*2 + 2) );
- if (p2 == NULL)
+ if (p2 == nullptr)
{
FFTWPREFIX(free)(p1);
FFTWPREFIX(free)(fft);
{
for (k = 0; k < 2; k++)
{
- if (fft->plan[i][j][k] == NULL)
+ if (fft->plan[i][j][k] == nullptr)
{
gmx_fatal(FARGS, "Error initializing FFTW3 plan.");
FFTW_UNLOCK;
{
int i, j, k;
- if (fft != NULL)
+ if (fft != nullptr)
{
for (i = 0; i < 2; i++)
{
{
for (k = 0; k < 2; k++)
{
- if (fft->plan[i][j][k] != NULL)
+ if (fft->plan[i][j][k] != nullptr)
{
FFTW_LOCK;
FFTWPREFIX(destroy_plan)(fft->plan[i][j][k]);
FFTW_UNLOCK;
- fft->plan[i][j][k] = NULL;
+ fft->plan[i][j][k] = nullptr;
}
}
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int
-gmx_fft_init_1d(gmx_fft_t * pfft,
- int nx,
- gmx_fft_flag flags)
+gmx_fft_init_1d(gmx_fft_t * pfft,
+ int nx,
+ gmx_fft_flag gmx_unused flags)
{
gmx_fft_t fft;
int d;
int
-gmx_fft_init_1d_real(gmx_fft_t * pfft,
- int nx,
- gmx_fft_flag flags)
+gmx_fft_init_1d_real(gmx_fft_t * pfft,
+ int nx,
+ gmx_fft_flag gmx_unused flags)
{
gmx_fft_t fft;
int d;
int
-gmx_fft_init_2d_real(gmx_fft_t * pfft,
- int nx,
- int ny,
- gmx_fft_flag flags)
+gmx_fft_init_2d_real(gmx_fft_t * pfft,
+ int nx,
+ int ny,
+ gmx_fft_flag gmx_unused flags)
{
gmx_fft_t fft;
int d;
if (status == 0)
{
- if ((fft->work = (t_complex *)malloc(sizeof(t_complex)*(nx*(ny/2+1)))) == NULL)
+ void *memory = malloc(sizeof(t_complex)*(nx*(ny/2+1)));
+ if (nullptr == memory)
{
status = ENOMEM;
}
+ fft->work = static_cast<t_complex *>(memory);
}
if (status != 0)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2005 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(*pfft_setup)->p2 = fft5d_plan_3d(Nb, Mb, Kb, rcomm,
(flags|FFT5D_BACKWARD|FFT5D_NOMALLOC)^FFT5D_ORDER_YZ, complex_data, (t_complex**)real_data, &buf1, &buf2, nthreads);
- return (*pfft_setup)->p1 != 0 && (*pfft_setup)->p2 != 0;
+ return (*pfft_setup)->p1 != nullptr && (*pfft_setup)->p2 != nullptr;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class FFTTest : public BaseFFTTest
{
public:
- FFTTest() : fft_(NULL)
+ FFTTest() : fft_(nullptr)
{
}
~FFTTest()
class ManyFFTTest : public BaseFFTTest
{
public:
- ManyFFTTest() : fft_(NULL)
+ ManyFFTTest() : fft_(nullptr)
{
}
~ManyFFTTest()
class FFFTest3D : public BaseFFTTest
{
public:
- FFFTest3D() : fft_(NULL)
+ FFFTest3D() : fft_(nullptr)
{
}
~FFFTest3D()
std::copy(inputdata, inputdata+sizeInReals, in_.begin());
// Use memcpy to convert to t_complex easily
memcpy(rdata, in_.data(), sizeInBytes);
- gmx_parallel_3dfft_execute(fft_, GMX_FFT_REAL_TO_COMPLEX, 0, NULL);
+ gmx_parallel_3dfft_execute(fft_, GMX_FFT_REAL_TO_COMPLEX, 0, nullptr);
//TODO use std::complex and add checkComplex for it
checker_.checkSequenceArray(size*2,
reinterpret_cast<real*>(cdata), "forward");
std::copy(inputdata, inputdata+sizeInReals, in_.begin());
// Use memcpy to convert to t_complex easily
memcpy(cdata, in_.data(), sizeInBytes);
- gmx_parallel_3dfft_execute(fft_, GMX_FFT_COMPLEX_TO_REAL, 0, NULL);
+ gmx_parallel_3dfft_execute(fft_, GMX_FFT_COMPLEX_TO_REAL, 0, nullptr);
for (int i = 0; i < ndata[0]*ndata[1]; i++) //check sequence but skip unused data
{
checker_.checkSequenceArray(ndata[2], rdata+i*rsize[2],
xvgr.h
)
-if (GMX_USE_TNG AND TNG_IO_DEFINITIONS)
- set_property(SOURCE tngio.cpp
- APPEND PROPERTY COMPILE_DEFINITIONS ${TNG_IO_DEFINITIONS})
- set_property(SOURCE tngio_for_tools.cpp
- APPEND PROPERTY COMPILE_DEFINITIONS ${TNG_IO_DEFINITIONS})
-endif()
-
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
+#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/df_history.h"
+#include "gromacs/mdtypes/edsamhistory.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/mdtypes/state.h"
+#include "gromacs/mdtypes/swaphistory.h"
#include "gromacs/trajectory/trajectoryframe.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/int64_to_int.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#define CPTSTRLEN 1024
/* cpt_version should normally only be changed
- * when the header of footer format changes.
+ * when the header or footer format changes.
* The state data format itself is backward and forward compatible.
* But old code can not read a new entry that is present in the file
* (but can read a new format when new entries are not present).
"FE-lambda",
"box", "box-rel", "box-v", "pres_prev",
"nosehoover-xi", "thermostat-integral",
- "x", "v", "sdx-unsupported", "CGp", "LD-rng", "LD-rng-i",
+ "x", "v", "sdx-unsupported", "CGp", "LD-rng-unsupported", "LD-rng-i-unsupported",
"disre_initf", "disre_rm3tav",
"orire_initf", "orire_Dtav",
- "svir_prev", "nosehoover-vxi", "v_eta", "vol0", "nhpres_xi", "nhpres_vxi", "fvir_prev", "fep_state", "MC-rng", "MC-rng-i"
+ "svir_prev", "nosehoover-vxi", "v_eta", "vol0", "nhpres_xi", "nhpres_vxi", "fvir_prev", "fep_state", "MC-rng-unsupported", "MC-rng-i-unsupported"
+ "barostat-integral"
};
enum {
"accumulated_plus", "accumulated_minus", "accumulated_plus_2", "accumulated_minus_2", "Tij", "Tij_empirical"
};
-enum {
- ecprREAL, ecprRVEC, ecprMATRIX
+//! Higher level vector element type, only used for formatting checkpoint dumps
+enum class CptElementType
+{
+ integer, //!< integer
+ real, //!< float or double, not linked to precision of type real
+ real3, //!< float[3] or double[3], not linked to precision of type real
+ matrix3x3 //!< float[3][3] or double[3][3], not linked to precision of type real
};
-enum {
- cptpEST, cptpEEKS, cptpEENH, cptpEDFH
+//! \brief Parts of the checkpoint state, only used for reporting
+enum class StatePart
+{
+ microState, //!< The microstate of the simulated system
+ kineticEnergy, //!< Kinetic energy, needed for T/P-coupling state
+ energyHistory, //!< Energy observable statistics
+ freeEnergyHistory //!< Free-energy state and observable statistics
};
-/* enums for the different components of checkpoint variables, replacing the hard coded ones.
- cptpEST - state variables.
- cptpEEKS - Kinetic energy state variables.
- cptpEENH - Energy history state variables.
- cptpEDFH - free energy history variables.
- */
-
-static const char *st_names(int cptp, int ecpt)
+//! \brief Return the name of a checkpoint entry based on part and part entry
+static const char *entryName(StatePart part, int ecpt)
{
- switch (cptp)
+ switch (part)
{
- case cptpEST: return est_names [ecpt];
- case cptpEEKS: return eeks_names[ecpt];
- case cptpEENH: return eenh_names[ecpt];
- case cptpEDFH: return edfh_names[ecpt];
+ case StatePart::microState: return est_names [ecpt];
+ case StatePart::kineticEnergy: return eeks_names[ecpt];
+ case StatePart::energyHistory: return eenh_names[ecpt];
+ case StatePart::freeEnergyHistory: return edfh_names[ecpt];
}
- return NULL;
+ return nullptr;
}
static void cp_warning(FILE *fp)
}
}
-/* If nval >= 0, nval is used; on read this should match the passed value.
- * If nval n<0, *nptr is used; on read the value is stored in nptr
+template <typename T>
+struct xdr_type
+{
+};
+
+template <>
+struct xdr_type<int>
+{
+ // cppcheck-suppress unusedStructMember
+ static const int value = xdr_datatype_int;
+};
+
+template <>
+struct xdr_type<float>
+{
+ // cppcheck-suppress unusedStructMember
+ static const int value = xdr_datatype_float;
+};
+
+template <>
+struct xdr_type<double>
+{
+ // cppcheck-suppress unusedStructMember
+ static const int value = xdr_datatype_double;
+};
+
+//! \brief Returns size in byte of an xdr_datatype
+static inline unsigned int sizeOfXdrType(int xdrType)
+{
+ switch (xdrType)
+ {
+ case xdr_datatype_int:
+ return sizeof(int);
+ break;
+ case xdr_datatype_float:
+ return sizeof(float);
+ break;
+ case xdr_datatype_double:
+ return sizeof(double);
+ break;
+ default: GMX_RELEASE_ASSERT(false, "XDR data type not implemented");
+ }
+
+ return 0;
+}
+
+//! \brief Returns the XDR process function for i/o of an XDR type
+static inline xdrproc_t xdrProc(int xdrType)
+{
+ switch (xdrType)
+ {
+ case xdr_datatype_int:
+ return reinterpret_cast<xdrproc_t>(xdr_int);
+ break;
+ case xdr_datatype_float:
+ return reinterpret_cast<xdrproc_t>(xdr_float);
+ break;
+ case xdr_datatype_double:
+ return reinterpret_cast<xdrproc_t>(xdr_double);
+ break;
+ default: GMX_RELEASE_ASSERT(false, "XDR data type not implemented");
+ }
+
+ return nullptr;
+}
+
+/*! \brief Lists or only reads an xdr vector from checkpoint file
+ *
+ * When list!=NULL reads and lists the \p nf vector elements of type \p xdrType.
+ * The header for the print is set by \p part and \p ecpt.
+ * The formatting of the printing is set by \p cptElementType.
+ * When list==NULL only reads the elements.
*/
-static int do_cpte_reals_low(XDR *xd, int cptp, int ecpt, int sflags,
- int nval, int *nptr, real **v,
- FILE *list, int erealtype)
+static bool_t listXdrVector(XDR *xd, StatePart part, int ecpt, int nf, int xdrType,
+ FILE *list, CptElementType cptElementType)
{
- bool_t res = 0;
- const bool useDouble = GMX_DOUBLE;
- int dtc = useDouble ? xdr_datatype_double : xdr_datatype_float;
- real *vp, *va = NULL;
- float *vf;
- double *vd;
- int nf, dt, i;
+ bool_t res = 0;
+
+ const unsigned int elemSize = sizeOfXdrType(xdrType);
+ std::vector<char> data(nf*elemSize);
+ res = xdr_vector(xd, data.data(), nf, elemSize, xdrProc(xdrType));
- if (list == NULL)
+ if (list != nullptr)
{
- if (nval >= 0)
+ switch (xdrType)
{
- nf = nval;
- }
- else
- {
- if (nptr == NULL)
- {
- gmx_incons("*ntpr=NULL in do_cpte_reals_low");
- }
- nf = *nptr;
+ case xdr_datatype_int:
+ pr_ivec(list, 0, entryName(part, ecpt), reinterpret_cast<const int *>(data.data()), nf, TRUE);
+ break;
+ case xdr_datatype_float:
+#if !GMX_DOUBLE
+ if (cptElementType == CptElementType::real3)
+ {
+ // cppcheck-suppress invalidPointerCast
+ pr_rvecs(list, 0, entryName(part, ecpt), reinterpret_cast<const rvec *>(data.data()), nf/3);
+ }
+ else
+#endif
+ {
+ /* Note: With double precision code dumping a single precision rvec will produce float iso rvec print, but that's a minor annoyance */
+ // cppcheck-suppress invalidPointerCast
+ pr_fvec(list, 0, entryName(part, ecpt), reinterpret_cast<const float *>(data.data()), nf, TRUE);
+ }
+ break;
+ case xdr_datatype_double:
+#if GMX_DOUBLE
+ if (cptElementType == CptElementType::real3)
+ {
+ // cppcheck-suppress invalidPointerCast
+ pr_rvecs(list, 0, entryName(part, ecpt), reinterpret_cast<const rvec *>(data.data()), nf/3);
+ }
+ else
+#endif
+ {
+ /* Note: With single precision code dumping a double precision rvec will produce float iso rvec print, but that's a minor annoyance */
+ // cppcheck-suppress invalidPointerCast
+ pr_dvec(list, 0, entryName(part, ecpt), reinterpret_cast<const double *>(data.data()), nf, TRUE);
+ }
+ break;
+ default: GMX_RELEASE_ASSERT(false, "Data type not implemented for listing");
}
}
- res = xdr_int(xd, &nf);
- if (res == 0)
+
+ return res;
+}
+
+//! \brief Convert a double array, typed char*, to float
+gmx_unused static void convertArrayRealPrecision(const char *c, float *v, int n)
+{
+ // cppcheck-suppress invalidPointerCast
+ const double *d = reinterpret_cast<const double *>(c);
+ for (int i = 0; i < n; i++)
{
- return -1;
+ v[i] = static_cast<float>(d[i]);
}
- if (list == NULL)
+}
+
+//! \brief Convert a float array, typed char*, to double
+static void convertArrayRealPrecision(const char *c, double *v, int n)
+{
+ // cppcheck-suppress invalidPointerCast
+ const float *f = reinterpret_cast<const float *>(c);
+ for (int i = 0; i < n; i++)
+ {
+ v[i] = static_cast<double>(f[i]);
+ }
+}
+
+//! \brief Generate an error for trying to convert to integer
+static void convertArrayRealPrecision(const char gmx_unused *c, int gmx_unused *v, int gmx_unused n)
+{
+ GMX_RELEASE_ASSERT(false, "We only expect type mismatches between float and double, not integer");
+}
+
+/*! \brief Low-level routine for reading/writing a vector of reals from/to file.
+ *
+ * This is the only routine that does the actually i/o of real vector,
+ * all other routines are intermediate level routines for specific real
+ * data types, calling this routine.
+ * Currently this routine is (too) complex, since it handles both real *
+ * and std::vector<real>. Using real * is deprecated and this routine
+ * will simplify a lot when only std::vector needs to be supported.
+ *
+ * When not listing, we use either v or vector, depending on which is !=NULL.
+ * If nval >= 0, nval is used; on read this should match the passed value.
+ * If nval n<0, *nptr (with v) or vector->size() is used. On read using v,
+ * the value is stored in nptr
+ */
+template<typename T>
+static int doVectorLow(XDR *xd, StatePart part, int ecpt, int sflags,
+ int nval, int *nptr,
+ T **v, std::vector<T> *vector,
+ FILE *list, CptElementType cptElementType)
+{
+ GMX_RELEASE_ASSERT(list != nullptr || (v != nullptr && vector == nullptr) || (v == nullptr && vector != nullptr), "Without list, we should have exactly one of v and vector != NULL");
+
+ bool_t res = 0;
+
+ int numElemInTheFile;
+ if (list == nullptr)
{
if (nval >= 0)
{
- if (nf != nval)
- {
- gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), nval, nf);
- }
+ GMX_RELEASE_ASSERT(nptr == nullptr, "With nval>=0 we should have nptr==NULL");
+ numElemInTheFile = nval;
}
else
{
- *nptr = nf;
+ if (v != nullptr)
+ {
+ GMX_RELEASE_ASSERT(nptr != nullptr, "With nval<0 we should have nptr!=NULL");
+ // cppcheck-suppress nullPointer
+ numElemInTheFile = *nptr;
+ }
+ else
+ {
+ numElemInTheFile = vector->size();
+ }
}
}
- dt = dtc;
- res = xdr_int(xd, &dt);
+ /* Read/write the vector element count */
+ res = xdr_int(xd, &numElemInTheFile);
if (res == 0)
{
return -1;
}
- if (dt != dtc)
- {
- fprintf(stderr, "Precision mismatch for state entry %s, code precision is %s, file precision is %s\n",
- st_names(cptp, ecpt), xdr_datatype_names[dtc],
- xdr_datatype_names[dt]);
- }
- if (list || !(sflags & (1<<ecpt)))
+ /* Read/write the element data type */
+ constexpr int xdrTypeInTheCode = xdr_type<T>::value;
+ int xdrTypeInTheFile = xdrTypeInTheCode;
+ res = xdr_int(xd, &xdrTypeInTheFile);
+ if (res == 0)
{
- snew(va, nf);
- vp = va;
+ return -1;
}
- else
+
+ if (list == nullptr && (sflags & (1 << ecpt)))
{
- if (*v == NULL)
+ if (nval >= 0)
{
- snew(*v, nf);
+ if (numElemInTheFile != nval)
+ {
+ gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", entryName(part, ecpt), nval, numElemInTheFile);
+ }
}
- vp = *v;
- }
- if (dt == xdr_datatype_float)
- {
- if (!useDouble)
+ else if (nptr != nullptr)
{
- // This branch is not reached unless vp is already float *.
- vf = reinterpret_cast<float *>(vp);
+ *nptr = numElemInTheFile;
}
- else
+
+ bool typesMatch = (xdrTypeInTheFile == xdrTypeInTheCode);
+ if (!typesMatch)
{
- snew(vf, nf);
+ char buf[STRLEN];
+ sprintf(buf, "mismatch for state entry %s, code precision is %s, file precision is %s",
+ entryName(part, ecpt),
+ xdr_datatype_names[xdrTypeInTheCode],
+ xdr_datatype_names[xdrTypeInTheFile]);
+
+ /* Matching int and real should never occur, but check anyhow */
+ if (xdrTypeInTheFile == xdr_datatype_int ||
+ xdrTypeInTheCode == xdr_datatype_int)
+ {
+ gmx_fatal(FARGS, "Type %s: incompatible checkpoint formats or corrupted checkpoint file.", buf);
+ }
+ fprintf(stderr, "Precision %s\n", buf);
}
- res = xdr_vector(xd, reinterpret_cast<char *>(vf), nf,
- static_cast<unsigned int>(sizeof(float)), (xdrproc_t)xdr_float);
- if (res == 0)
+
+ T *vp;
+ if (v != nullptr)
{
- return -1;
+ if (*v == nullptr)
+ {
+ snew(*v, numElemInTheFile);
+ }
+ vp = *v;
}
- if (useDouble)
+ else
{
- for (i = 0; i < nf; i++)
+ /* This conditional ensures that we don't resize on write.
+ * In particular in the state where this code was written
+ * PaddedRVecVector has a size of numElemInThefile and we
+ * don't want to lose that padding here.
+ */
+ if (vector->size() < static_cast<unsigned int>(numElemInTheFile))
{
- vp[i] = vf[i];
+ vector->resize(numElemInTheFile);
}
- sfree(vf);
+ vp = vector->data();
}
- }
- else
- {
- if (useDouble)
+
+ char *vChar;
+ if (typesMatch)
{
- // This branch is not reached unless vp is already double *.
- // cppcheck-suppress invalidPointerCast
- vd = reinterpret_cast<double *>(vp);
+ vChar = reinterpret_cast<char *>(vp);
}
else
{
- snew(vd, nf);
+ snew(vChar, numElemInTheFile*sizeOfXdrType(xdrTypeInTheFile));
}
- res = xdr_vector(xd, reinterpret_cast<char *>(vd), nf,
- static_cast<unsigned int>(sizeof(double)), (xdrproc_t)xdr_double);
+ res = xdr_vector(xd, vChar,
+ numElemInTheFile, sizeOfXdrType(xdrTypeInTheFile),
+ xdrProc(xdrTypeInTheFile));
if (res == 0)
{
return -1;
}
- if (!useDouble)
- {
- for (i = 0; i < nf; i++)
- {
- vp[i] = vd[i];
- }
- sfree(vd);
- }
- }
- if (list)
- {
- switch (erealtype)
+ if (!typesMatch)
{
- case ecprREAL:
- pr_reals(list, 0, st_names(cptp, ecpt), vp, nf);
- break;
- case ecprRVEC:
- pr_rvecs(list, 0, st_names(cptp, ecpt), (rvec *)vp, nf/3);
- break;
- default:
- gmx_incons("Unknown checkpoint real type");
+ /* In the old code float-double conversion came for free.
+ * In the new code we still support it, mainly because
+ * the tip4p_continue regression test makes use of this.
+ * It's an open question if we do or don't want to allow this.
+ */
+ convertArrayRealPrecision(vChar, vp, numElemInTheFile);
+ sfree(vChar);
}
}
- if (va)
+ else
{
- sfree(va);
+ res = listXdrVector(xd, part, ecpt, numElemInTheFile, xdrTypeInTheFile,
+ list, cptElementType);
}
return 0;
}
+//! \brief Read/Write a std::vector.
+template <typename T>
+static int doVector(XDR *xd, StatePart part, int ecpt, int sflags,
+ std::vector<T> *vector, FILE *list)
+{
+ return doVectorLow<T>(xd, part, ecpt, sflags, -1, nullptr, nullptr, vector, list, CptElementType::real);
+}
+
+//! \brief Read/Write an ArrayRef<real>.
+static int doRealArrayRef(XDR *xd, StatePart part, int ecpt, int sflags,
+ gmx::ArrayRef<real> vector, FILE *list)
+{
+ real *v_real = vector.data();
+ return doVectorLow<real>(xd, part, ecpt, sflags, vector.size(), nullptr, &v_real, nullptr, list, CptElementType::real);
+}
+
+//! \brief Read/Write a PaddedRVecVector.
+static int doPaddedRvecVector(XDR *xd, StatePart part, int ecpt, int sflags,
+ gmx::PaddedRVecVector *vector, FILE *list)
+{
+ real *v_real;
+
+ if (list == nullptr && (sflags & (1 << ecpt)))
+ {
+ v_real = vector->data()->as_vec();
+ }
+ else
+ {
+ v_real = nullptr;
+ }
+ // The current invariant of a PaddedRVecVector is that its size is
+ // one larger than necessary to store the data. Make sure that we
+ // read/write only the valid data, and don't leak to the outside
+ // world that currently we find it convenient internally to
+ // allocate one extra element.
+ gmx::ArrayRef<real> ref(v_real, v_real + (vector->size()-1) * DIM);
+
+ return doRealArrayRef(xd, part, ecpt, sflags, ref, list);
+}
/* This function stores n along with the reals for reading,
* but on reading it assumes that n matches the value in the checkpoint file,
* a fatal error is generated when this is not the case.
*/
-static int do_cpte_reals(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_reals(XDR *xd, StatePart part, int ecpt, int sflags,
int n, real **v, FILE *list)
{
- return do_cpte_reals_low(xd, cptp, ecpt, sflags, n, NULL, v, list, ecprREAL);
+ return doVectorLow<real>(xd, part, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::real);
}
/* This function does the same as do_cpte_reals,
* except that on reading it ignores the passed value of *n
- * and stored the value read from the checkpoint file in *n.
+ * and stores the value read from the checkpoint file in *n.
*/
-static int do_cpte_n_reals(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_n_reals(XDR *xd, StatePart part, int ecpt, int sflags,
int *n, real **v, FILE *list)
{
- return do_cpte_reals_low(xd, cptp, ecpt, sflags, -1, n, v, list, ecprREAL);
+ return doVectorLow<real>(xd, part, ecpt, sflags, -1, n, v, nullptr, list, CptElementType::real);
}
-static int do_cpte_real(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_real(XDR *xd, StatePart part, int ecpt, int sflags,
real *r, FILE *list)
{
- return do_cpte_reals_low(xd, cptp, ecpt, sflags, 1, NULL, &r, list, ecprREAL);
+ return doVectorLow<real>(xd, part, ecpt, sflags, 1, nullptr, &r, nullptr, list, CptElementType::real);
}
-static int do_cpte_ints(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_ints(XDR *xd, StatePart part, int ecpt, int sflags,
int n, int **v, FILE *list)
{
- bool_t res = 0;
- int dtc = xdr_datatype_int;
- int *vp, *va = NULL;
- int nf, dt;
-
- nf = n;
- res = xdr_int(xd, &nf);
- if (res == 0)
- {
- return -1;
- }
- if (list == NULL && v != NULL && nf != n)
- {
- gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), n, nf);
- }
- dt = dtc;
- res = xdr_int(xd, &dt);
- if (res == 0)
- {
- return -1;
- }
- if (dt != dtc)
- {
- gmx_fatal(FARGS, "Type mismatch for state entry %s, code type is %s, file type is %s\n",
- st_names(cptp, ecpt), xdr_datatype_names[dtc],
- xdr_datatype_names[dt]);
- }
- if (list || !(sflags & (1<<ecpt)) || v == NULL)
- {
- snew(va, nf);
- vp = va;
- }
- else
- {
- if (*v == NULL)
- {
- snew(*v, nf);
- }
- vp = *v;
- }
- res = xdr_vector(xd, reinterpret_cast<char *>(vp), nf,
- static_cast<unsigned int>(sizeof(int)), (xdrproc_t)xdr_int);
- if (res == 0)
- {
- return -1;
- }
- if (list)
- {
- pr_ivec(list, 0, st_names(cptp, ecpt), vp, nf, TRUE);
- }
- if (va)
- {
- sfree(va);
- }
-
- return 0;
+ return doVectorLow<int>(xd, part, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::integer);
}
-static int do_cpte_int(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_int(XDR *xd, StatePart part, int ecpt, int sflags,
int *i, FILE *list)
{
- return do_cpte_ints(xd, cptp, ecpt, sflags, 1, &i, list);
+ return do_cpte_ints(xd, part, ecpt, sflags, 1, &i, list);
}
-static int do_cpte_doubles(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_doubles(XDR *xd, StatePart part, int ecpt, int sflags,
int n, double **v, FILE *list)
{
- bool_t res = 0;
- int dtc = xdr_datatype_double;
- double *vp, *va = NULL;
- int nf, dt;
-
- nf = n;
- res = xdr_int(xd, &nf);
- if (res == 0)
- {
- return -1;
- }
- if (list == NULL && nf != n)
- {
- gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), n, nf);
- }
- dt = dtc;
- res = xdr_int(xd, &dt);
- if (res == 0)
- {
- return -1;
- }
- if (dt != dtc)
- {
- gmx_fatal(FARGS, "Precision mismatch for state entry %s, code precision is %s, file precision is %s\n",
- st_names(cptp, ecpt), xdr_datatype_names[dtc],
- xdr_datatype_names[dt]);
- }
- if (list || !(sflags & (1<<ecpt)))
- {
- snew(va, nf);
- vp = va;
- }
- else
- {
- if (*v == NULL)
- {
- snew(*v, nf);
- }
- vp = *v;
- }
- res = xdr_vector(xd, reinterpret_cast<char *>(vp), nf,
- static_cast<unsigned int>(sizeof(double)), (xdrproc_t)xdr_double);
- if (res == 0)
- {
- return -1;
- }
- if (list)
- {
- pr_doubles(list, 0, st_names(cptp, ecpt), vp, nf);
- }
- if (va)
- {
- sfree(va);
- }
-
- return 0;
+ return doVectorLow<double>(xd, part, ecpt, sflags, n, nullptr, v, nullptr, list, CptElementType::real);
}
-static int do_cpte_double(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_double(XDR *xd, StatePart part, int ecpt, int sflags,
double *r, FILE *list)
{
- return do_cpte_doubles(xd, cptp, ecpt, sflags, 1, &r, list);
-}
-
-
-static int do_cpte_rvecs(XDR *xd, int cptp, int ecpt, int sflags,
- int n, rvec **v, FILE *list)
-{
- return do_cpte_reals_low(xd, cptp, ecpt, sflags,
- n*DIM, NULL, (real **)v, list, ecprRVEC);
+ return do_cpte_doubles(xd, part, ecpt, sflags, 1, &r, list);
}
-static int do_cpte_matrix(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_matrix(XDR *xd, StatePart part, int ecpt, int sflags,
matrix v, FILE *list)
{
real *vr;
int ret;
vr = &(v[0][0]);
- ret = do_cpte_reals_low(xd, cptp, ecpt, sflags,
- DIM*DIM, NULL, &vr, NULL, ecprMATRIX);
+ ret = doVectorLow<real>(xd, part, ecpt, sflags,
+ DIM*DIM, nullptr, &vr, nullptr, nullptr, CptElementType::matrix3x3);
if (list && ret == 0)
{
- pr_rvecs(list, 0, st_names(cptp, ecpt), v, DIM);
+ pr_rvecs(list, 0, entryName(part, ecpt), v, DIM);
}
return ret;
}
-static int do_cpte_nmatrix(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_nmatrix(XDR *xd, StatePart part, int ecpt, int sflags,
int n, real **v, FILE *list)
{
int i;
char name[CPTSTRLEN];
ret = 0;
- if (v == NULL)
+ if (v == nullptr)
{
snew(v, n);
}
for (i = 0; i < n; i++)
{
- reti = do_cpte_reals_low(xd, cptp, ecpt, sflags, n, NULL, &(v[i]), NULL, ecprREAL);
+ reti = doVectorLow<real>(xd, part, ecpt, sflags, n, nullptr, &(v[i]), nullptr, nullptr, CptElementType::matrix3x3);
if (list && reti == 0)
{
- sprintf(name, "%s[%d]", st_names(cptp, ecpt), i);
+ sprintf(name, "%s[%d]", entryName(part, ecpt), i);
pr_reals(list, 0, name, v[i], n);
}
if (reti != 0)
return ret;
}
-static int do_cpte_matrices(XDR *xd, int cptp, int ecpt, int sflags,
+static int do_cpte_matrices(XDR *xd, StatePart part, int ecpt, int sflags,
int n, matrix **v, FILE *list)
{
bool_t res = 0;
- matrix *vp, *va = NULL;
+ matrix *vp, *va = nullptr;
real *vr;
int nf, i, j, k;
int ret;
{
return -1;
}
- if (list == NULL && nf != n)
+ if (list == nullptr && nf != n)
{
- gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", st_names(cptp, ecpt), n, nf);
+ gmx_fatal(FARGS, "Count mismatch for state entry %s, code count is %d, file count is %d\n", entryName(part, ecpt), n, nf);
}
if (list || !(sflags & (1<<ecpt)))
{
}
else
{
- if (*v == NULL)
+ if (*v == nullptr)
{
snew(*v, nf);
}
}
}
}
- ret = do_cpte_reals_low(xd, cptp, ecpt, sflags,
- nf*DIM*DIM, NULL, &vr, NULL, ecprMATRIX);
+ ret = doVectorLow<real>(xd, part, ecpt, sflags,
+ nf*DIM*DIM, nullptr, &vr, nullptr, nullptr,
+ CptElementType::matrix3x3);
for (i = 0; i < nf; i++)
{
for (j = 0; j < DIM; j++)
{
for (i = 0; i < nf; i++)
{
- pr_rvecs(list, 0, st_names(cptp, ecpt), vp[i], DIM);
+ pr_rvecs(list, 0, entryName(part, ecpt), vp[i], DIM);
}
}
if (va)
if (*file_version >= 12)
{
do_cpt_string_err(xd, bRead, "generating host", &fhost, list);
- if (list == NULL)
+ if (list == nullptr)
{
sfree(fhost);
}
{
do_cpt_int_err(xd, "swap", eSwapCoords, list);
}
+ else
+ {
+ *eSwapCoords = eswapNO;
+ }
}
static int do_cpt_footer(XDR *xd, int file_version)
return 0;
}
-static int do_cpt_state(XDR *xd, gmx_bool bRead,
+static int do_cpt_state(XDR *xd,
int fflags, t_state *state,
FILE *list)
{
- int sflags;
- int i;
- int ret;
- int nnht, nnhtp;
-
- ret = 0;
-
- nnht = state->nhchainlength*state->ngtc;
- nnhtp = state->nhchainlength*state->nnhpres;
-
- if (bRead) /* we need to allocate space for dfhist if we are reading */
- {
- init_df_history(&state->dfhist, state->dfhist.nlambda);
- }
-
- sflags = state->flags;
- for (i = 0; (i < estNR && ret == 0); i++)
+ int ret = 0;
+ const StatePart part = StatePart::microState;
+ const int sflags = state->flags;
+ // If reading, state->natoms was probably just read, so
+ // allocations need to be managed. If writing, this won't change
+ // anything that matters.
+ state_change_natoms(state, state->natoms);
+ for (int i = 0; (i < estNR && ret == 0); i++)
{
if (fflags & (1<<i))
{
switch (i)
{
- case estLAMBDA: ret = do_cpte_reals(xd, cptpEST, i, sflags, efptNR, &(state->lambda), list); break;
- case estFEPSTATE: ret = do_cpte_int (xd, cptpEST, i, sflags, &state->fep_state, list); break;
- case estBOX: ret = do_cpte_matrix(xd, cptpEST, i, sflags, state->box, list); break;
- case estBOX_REL: ret = do_cpte_matrix(xd, cptpEST, i, sflags, state->box_rel, list); break;
- case estBOXV: ret = do_cpte_matrix(xd, cptpEST, i, sflags, state->boxv, list); break;
- case estPRES_PREV: ret = do_cpte_matrix(xd, cptpEST, i, sflags, state->pres_prev, list); break;
- case estSVIR_PREV: ret = do_cpte_matrix(xd, cptpEST, i, sflags, state->svir_prev, list); break;
- case estFVIR_PREV: ret = do_cpte_matrix(xd, cptpEST, i, sflags, state->fvir_prev, list); break;
- case estNH_XI: ret = do_cpte_doubles(xd, cptpEST, i, sflags, nnht, &state->nosehoover_xi, list); break;
- case estNH_VXI: ret = do_cpte_doubles(xd, cptpEST, i, sflags, nnht, &state->nosehoover_vxi, list); break;
- case estNHPRES_XI: ret = do_cpte_doubles(xd, cptpEST, i, sflags, nnhtp, &state->nhpres_xi, list); break;
- case estNHPRES_VXI: ret = do_cpte_doubles(xd, cptpEST, i, sflags, nnhtp, &state->nhpres_vxi, list); break;
- case estTC_INT: ret = do_cpte_doubles(xd, cptpEST, i, sflags, state->ngtc, &state->therm_integral, list); break;
- case estVETA: ret = do_cpte_real(xd, cptpEST, i, sflags, &state->veta, list); break;
- case estVOL0: ret = do_cpte_real(xd, cptpEST, i, sflags, &state->vol0, list); break;
- case estX: ret = do_cpte_rvecs(xd, cptpEST, i, sflags, state->natoms, &state->x, list); break;
- case estV: ret = do_cpte_rvecs(xd, cptpEST, i, sflags, state->natoms, &state->v, list); break;
+ case estLAMBDA: ret = doRealArrayRef(xd, part, i, sflags, gmx::arrayRefFromArray<real>(state->lambda.data(), state->lambda.size()), list); break;
+ case estFEPSTATE: ret = do_cpte_int (xd, part, i, sflags, &state->fep_state, list); break;
+ case estBOX: ret = do_cpte_matrix(xd, part, i, sflags, state->box, list); break;
+ case estBOX_REL: ret = do_cpte_matrix(xd, part, i, sflags, state->box_rel, list); break;
+ case estBOXV: ret = do_cpte_matrix(xd, part, i, sflags, state->boxv, list); break;
+ case estPRES_PREV: ret = do_cpte_matrix(xd, part, i, sflags, state->pres_prev, list); break;
+ case estSVIR_PREV: ret = do_cpte_matrix(xd, part, i, sflags, state->svir_prev, list); break;
+ case estFVIR_PREV: ret = do_cpte_matrix(xd, part, i, sflags, state->fvir_prev, list); break;
+ case estNH_XI: ret = doVector<double>(xd, part, i, sflags, &state->nosehoover_xi, list); break;
+ case estNH_VXI: ret = doVector<double>(xd, part, i, sflags, &state->nosehoover_vxi, list); break;
+ case estNHPRES_XI: ret = doVector<double>(xd, part, i, sflags, &state->nhpres_xi, list); break;
+ case estNHPRES_VXI: ret = doVector<double>(xd, part, i, sflags, &state->nhpres_vxi, list); break;
+ case estTHERM_INT: ret = doVector<double>(xd, part, i, sflags, &state->therm_integral, list); break;
+ case estBAROS_INT: ret = do_cpte_double(xd, part, i, sflags, &state->baros_integral, list); break;
+ case estVETA: ret = do_cpte_real(xd, part, i, sflags, &state->veta, list); break;
+ case estVOL0: ret = do_cpte_real(xd, part, i, sflags, &state->vol0, list); break;
+ case estX: ret = doPaddedRvecVector(xd, part, i, sflags, &state->x, list); break;
+ case estV: ret = doPaddedRvecVector(xd, part, i, sflags, &state->v, list); break;
/* The RNG entries are no longer written,
* the next 4 lines are only for reading old files.
*/
- case estLD_RNG: ret = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
- case estLD_RNGI: ret = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
- case estMC_RNG: ret = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
- case estMC_RNGI: ret = do_cpte_ints(xd, cptpEST, i, sflags, 0, NULL, list); break;
- case estDISRE_INITF: ret = do_cpte_real (xd, cptpEST, i, sflags, &state->hist.disre_initf, list); break;
- case estDISRE_RM3TAV: ret = do_cpte_n_reals(xd, cptpEST, i, sflags, &state->hist.ndisrepairs, &state->hist.disre_rm3tav, list); break;
- case estORIRE_INITF: ret = do_cpte_real (xd, cptpEST, i, sflags, &state->hist.orire_initf, list); break;
- case estORIRE_DTAV: ret = do_cpte_n_reals(xd, cptpEST, i, sflags, &state->hist.norire_Dtav, &state->hist.orire_Dtav, list); break;
+ case estLD_RNG_NOTSUPPORTED: ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list); break;
+ case estLD_RNGI_NOTSUPPORTED: ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list); break;
+ case estMC_RNG_NOTSUPPORTED: ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list); break;
+ case estMC_RNGI_NOTSUPPORTED: ret = do_cpte_ints(xd, part, i, sflags, 0, nullptr, list); break;
+ case estDISRE_INITF: ret = do_cpte_real (xd, part, i, sflags, &state->hist.disre_initf, list); break;
+ case estDISRE_RM3TAV: ret = do_cpte_n_reals(xd, part, i, sflags, &state->hist.ndisrepairs, &state->hist.disre_rm3tav, list); break;
+ case estORIRE_INITF: ret = do_cpte_real (xd, part, i, sflags, &state->hist.orire_initf, list); break;
+ case estORIRE_DTAV: ret = do_cpte_n_reals(xd, part, i, sflags, &state->hist.norire_Dtav, &state->hist.orire_Dtav, list); break;
default:
gmx_fatal(FARGS, "Unknown state entry %d\n"
"You are reading a checkpoint file written by different code, which is not supported", i);
static int do_cpt_ekinstate(XDR *xd, int fflags, ekinstate_t *ekins,
FILE *list)
{
- int i;
- int ret;
-
- ret = 0;
+ int ret = 0;
- for (i = 0; (i < eeksNR && ret == 0); i++)
+ const StatePart part = StatePart::kineticEnergy;
+ for (int i = 0; (i < eeksNR && ret == 0); i++)
{
if (fflags & (1<<i))
{
switch (i)
{
- case eeksEKIN_N: ret = do_cpte_int(xd, cptpEEKS, i, fflags, &ekins->ekin_n, list); break;
- case eeksEKINH: ret = do_cpte_matrices(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinh, list); break;
- case eeksEKINF: ret = do_cpte_matrices(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinf, list); break;
- case eeksEKINO: ret = do_cpte_matrices(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinh_old, list); break;
- case eeksEKINTOTAL: ret = do_cpte_matrix(xd, cptpEEKS, i, fflags, ekins->ekin_total, list); break;
- case eeksEKINSCALEF: ret = do_cpte_doubles(xd, cptpEEKS, i, fflags, ekins->ekin_n, &ekins->ekinscalef_nhc, list); break;
- case eeksVSCALE: ret = do_cpte_doubles(xd, 1, cptpEEKS, fflags, ekins->ekin_n, &ekins->vscale_nhc, list); break;
- case eeksEKINSCALEH: ret = do_cpte_doubles(xd, 1, cptpEEKS, fflags, ekins->ekin_n, &ekins->ekinscaleh_nhc, list); break;
- case eeksDEKINDL: ret = do_cpte_real(xd, 1, cptpEEKS, fflags, &ekins->dekindl, list); break;
- case eeksMVCOS: ret = do_cpte_real(xd, 1, cptpEEKS, fflags, &ekins->mvcos, list); break;
+ case eeksEKIN_N: ret = do_cpte_int(xd, part, i, fflags, &ekins->ekin_n, list); break;
+ case eeksEKINH: ret = do_cpte_matrices(xd, part, i, fflags, ekins->ekin_n, &ekins->ekinh, list); break;
+ case eeksEKINF: ret = do_cpte_matrices(xd, part, i, fflags, ekins->ekin_n, &ekins->ekinf, list); break;
+ case eeksEKINO: ret = do_cpte_matrices(xd, part, i, fflags, ekins->ekin_n, &ekins->ekinh_old, list); break;
+ case eeksEKINTOTAL: ret = do_cpte_matrix(xd, part, i, fflags, ekins->ekin_total, list); break;
+ case eeksEKINSCALEF: ret = doVector<double>(xd, part, i, fflags, &ekins->ekinscalef_nhc, list); break;
+ case eeksVSCALE: ret = doVector<double>(xd, part, i, fflags, &ekins->vscale_nhc, list); break;
+ case eeksEKINSCALEH: ret = doVector<double>(xd, part, i, fflags, &ekins->ekinscaleh_nhc, list); break;
+ case eeksDEKINDL: ret = do_cpte_real(xd, part, i, fflags, &ekins->dekindl, list); break;
+ case eeksMVCOS: ret = do_cpte_real(xd, part, i, fflags, &ekins->mvcos, list); break;
default:
gmx_fatal(FARGS, "Unknown ekin data state entry %d\n"
"You are probably reading a new checkpoint file with old code", i);
}
-static int do_cpt_swapstate(XDR *xd, gmx_bool bRead, swapstate_t *swapstate, FILE *list)
+static int do_cpt_swapstate(XDR *xd, gmx_bool bRead,
+ int eSwapCoords, swaphistory_t *swapstate, FILE *list)
{
- int ret = 0;
int swap_cpt_version = 2;
-
- if (eswapNO == swapstate->eSwapCoords)
+ if (eSwapCoords == eswapNO)
{
- return ret;
+ return 0;
}
- swapstate->bFromCpt = bRead;
+ swapstate->bFromCpt = bRead;
+ swapstate->eSwapCoords = eSwapCoords;
do_cpt_int_err(xd, "swap checkpoint version", &swap_cpt_version, list);
if (bRead && swap_cpt_version < 2)
do_cpt_int_err(xd, "swap influx net p", gs->inflow_net_p[ic], list);
}
- if (bRead && (NULL == gs->nMolPast[ic]) )
+ if (bRead && (nullptr == gs->nMolPast[ic]) )
{
snew(gs->nMolPast[ic], swapstate->nAverage);
}
do_cpt_n_rvecs_err(xd, "Ch1 whole x", swapstate->nat[eChan1], *swapstate->xc_old_whole_p[eChan1], list);
}
- return ret;
+ return 0;
}
int fflags, energyhistory_t *enerhist,
FILE *list)
{
- int i;
- int j;
- int ret;
+ int ret = 0;
- ret = 0;
+ if (fflags == 0)
+ {
+ return ret;
+ }
+
+ GMX_RELEASE_ASSERT(enerhist != nullptr, "With energy history, we need a valid enerhist pointer");
+ /* This is stored/read for backward compatibility */
+ int energyHistoryNumEnergies = 0;
if (bRead)
{
enerhist->nsteps = 0;
enerhist->nsum = 0;
enerhist->nsteps_sim = 0;
enerhist->nsum_sim = 0;
- enerhist->dht = NULL;
-
- if (fflags & (1<< eenhENERGY_DELTA_H_NN) )
- {
- snew(enerhist->dht, 1);
- enerhist->dht->ndh = NULL;
- enerhist->dht->dh = NULL;
- enerhist->dht->start_lambda_set = FALSE;
- }
+ }
+ else if (enerhist != nullptr)
+ {
+ energyHistoryNumEnergies = enerhist->ener_sum_sim.size();
}
- for (i = 0; (i < eenhNR && ret == 0); i++)
+ delta_h_history_t *deltaH = enerhist->deltaHForeignLambdas.get();
+ const StatePart part = StatePart::energyHistory;
+ for (int i = 0; (i < eenhNR && ret == 0); i++)
{
if (fflags & (1<<i))
{
switch (i)
{
- case eenhENERGY_N: ret = do_cpte_int(xd, cptpEENH, i, fflags, &enerhist->nener, list); break;
- case eenhENERGY_AVER: ret = do_cpte_doubles(xd, cptpEENH, i, fflags, enerhist->nener, &enerhist->ener_ave, list); break;
- case eenhENERGY_SUM: ret = do_cpte_doubles(xd, cptpEENH, i, fflags, enerhist->nener, &enerhist->ener_sum, list); break;
+ case eenhENERGY_N: ret = do_cpte_int(xd, part, i, fflags, &energyHistoryNumEnergies, list); break;
+ case eenhENERGY_AVER: ret = doVector<double>(xd, part, i, fflags, &enerhist->ener_ave, list); break;
+ case eenhENERGY_SUM: ret = doVector<double>(xd, part, i, fflags, &enerhist->ener_sum, list); break;
case eenhENERGY_NSUM: do_cpt_step_err(xd, eenh_names[i], &enerhist->nsum, list); break;
- case eenhENERGY_SUM_SIM: ret = do_cpte_doubles(xd, cptpEENH, i, fflags, enerhist->nener, &enerhist->ener_sum_sim, list); break;
+ case eenhENERGY_SUM_SIM: ret = doVector<double>(xd, part, i, fflags, &enerhist->ener_sum_sim, list); break;
case eenhENERGY_NSUM_SIM: do_cpt_step_err(xd, eenh_names[i], &enerhist->nsum_sim, list); break;
case eenhENERGY_NSTEPS: do_cpt_step_err(xd, eenh_names[i], &enerhist->nsteps, list); break;
case eenhENERGY_NSTEPS_SIM: do_cpt_step_err(xd, eenh_names[i], &enerhist->nsteps_sim, list); break;
- case eenhENERGY_DELTA_H_NN: do_cpt_int_err(xd, eenh_names[i], &(enerhist->dht->nndh), list);
- if (bRead) /* now allocate memory for it */
+ case eenhENERGY_DELTA_H_NN:
+ {
+ int numDeltaH = 0;
+ if (!bRead && deltaH != nullptr)
+ {
+ numDeltaH = deltaH->dh.size();
+ }
+ do_cpt_int_err(xd, eenh_names[i], &numDeltaH, list);
+ if (bRead)
{
- snew(enerhist->dht->dh, enerhist->dht->nndh);
- snew(enerhist->dht->ndh, enerhist->dht->nndh);
- for (j = 0; j < enerhist->dht->nndh; j++)
+ if (deltaH == nullptr)
{
- enerhist->dht->ndh[j] = 0;
- enerhist->dht->dh[j] = NULL;
+ enerhist->deltaHForeignLambdas.reset(new delta_h_history_t);
+ deltaH = enerhist->deltaHForeignLambdas.get();
}
+ deltaH->dh.resize(numDeltaH);
+ deltaH->start_lambda_set = FALSE;
}
break;
+ }
case eenhENERGY_DELTA_H_LIST:
- for (j = 0; j < enerhist->dht->nndh; j++)
+ for (auto dh : deltaH->dh)
{
- ret = do_cpte_n_reals(xd, cptpEENH, i, fflags, &enerhist->dht->ndh[j], &(enerhist->dht->dh[j]), list);
+ ret = doVector<real>(xd, part, i, fflags, &dh, list);
}
break;
case eenhENERGY_DELTA_H_STARTTIME:
- ret = do_cpte_double(xd, cptpEENH, i, fflags, &(enerhist->dht->start_time), list); break;
+ ret = do_cpte_double(xd, part, i, fflags, &(deltaH->start_time), list); break;
case eenhENERGY_DELTA_H_STARTLAMBDA:
- ret = do_cpte_double(xd, cptpEENH, i, fflags, &(enerhist->dht->start_lambda), list); break;
+ ret = do_cpte_double(xd, part, i, fflags, &(deltaH->start_lambda), list); break;
default:
gmx_fatal(FARGS, "Unknown energy history entry %d\n"
"You are probably reading a new checkpoint file with old code", i);
if ((fflags & (1<<eenhENERGY_SUM)) && !(fflags & (1<<eenhENERGY_SUM_SIM)))
{
/* Assume we have an old file format and copy sum to sum_sim */
- srenew(enerhist->ener_sum_sim, enerhist->nener);
- for (i = 0; i < enerhist->nener; i++)
- {
- enerhist->ener_sum_sim[i] = enerhist->ener_sum[i];
- }
+ enerhist->ener_sum_sim = enerhist->ener_sum;
}
if ( (fflags & (1<<eenhENERGY_NSUM)) &&
return ret;
}
-static int do_cpt_df_hist(XDR *xd, int fflags, df_history_t *dfhist, FILE *list)
+static int do_cpt_df_hist(XDR *xd, int fflags, int nlambda, df_history_t **dfhistPtr, FILE *list)
{
- int i, nlambda;
- int ret;
+ int ret = 0;
- nlambda = dfhist->nlambda;
- ret = 0;
+ if (fflags == 0)
+ {
+ return 0;
+ }
- for (i = 0; (i < edfhNR && ret == 0); i++)
+ if (*dfhistPtr == nullptr)
+ {
+ snew(*dfhistPtr, 1);
+ (*dfhistPtr)->nlambda = nlambda;
+ init_df_history(*dfhistPtr, nlambda);
+ }
+ df_history_t *dfhist = *dfhistPtr;
+
+ const StatePart part = StatePart::freeEnergyHistory;
+ for (int i = 0; (i < edfhNR && ret == 0); i++)
{
if (fflags & (1<<i))
{
switch (i)
{
- case edfhBEQUIL: ret = do_cpte_int(xd, cptpEDFH, i, fflags, &dfhist->bEquil, list); break;
- case edfhNATLAMBDA: ret = do_cpte_ints(xd, cptpEDFH, i, fflags, nlambda, &dfhist->n_at_lam, list); break;
- case edfhWLHISTO: ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->wl_histo, list); break;
- case edfhWLDELTA: ret = do_cpte_real(xd, cptpEDFH, i, fflags, &dfhist->wl_delta, list); break;
- case edfhSUMWEIGHTS: ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_weights, list); break;
- case edfhSUMDG: ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_dg, list); break;
- case edfhSUMMINVAR: ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_minvar, list); break;
- case edfhSUMVAR: ret = do_cpte_reals(xd, cptpEDFH, i, fflags, nlambda, &dfhist->sum_variance, list); break;
- case edfhACCUMP: ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_p, list); break;
- case edfhACCUMM: ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_m, list); break;
- case edfhACCUMP2: ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_p2, list); break;
- case edfhACCUMM2: ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->accum_m2, list); break;
- case edfhTIJ: ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->Tij, list); break;
- case edfhTIJEMP: ret = do_cpte_nmatrix(xd, cptpEDFH, i, fflags, nlambda, dfhist->Tij_empirical, list); break;
+ case edfhBEQUIL: ret = do_cpte_int(xd, part, i, fflags, &dfhist->bEquil, list); break;
+ case edfhNATLAMBDA: ret = do_cpte_ints(xd, part, i, fflags, nlambda, &dfhist->n_at_lam, list); break;
+ case edfhWLHISTO: ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->wl_histo, list); break;
+ case edfhWLDELTA: ret = do_cpte_real(xd, part, i, fflags, &dfhist->wl_delta, list); break;
+ case edfhSUMWEIGHTS: ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_weights, list); break;
+ case edfhSUMDG: ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_dg, list); break;
+ case edfhSUMMINVAR: ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_minvar, list); break;
+ case edfhSUMVAR: ret = do_cpte_reals(xd, part, i, fflags, nlambda, &dfhist->sum_variance, list); break;
+ case edfhACCUMP: ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_p, list); break;
+ case edfhACCUMM: ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_m, list); break;
+ case edfhACCUMP2: ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_p2, list); break;
+ case edfhACCUMM2: ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->accum_m2, list); break;
+ case edfhTIJ: ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->Tij, list); break;
+ case edfhTIJEMP: ret = do_cpte_nmatrix(xd, part, i, fflags, nlambda, dfhist->Tij_empirical, list); break;
default:
gmx_fatal(FARGS, "Unknown df history entry %d\n"
* average structure in the .cpt file
*/
static int do_cpt_EDstate(XDR *xd, gmx_bool bRead,
- edsamstate_t *EDstate, FILE *list)
+ int nED, edsamhistory_t *EDstate, FILE *list)
{
- int i;
- int ret = 0;
- char buf[STRLEN];
-
-
- EDstate->bFromCpt = bRead;
-
- if (EDstate->nED <= 0)
+ if (nED == 0)
{
- return ret;
+ return 0;
}
+ EDstate->bFromCpt = bRead;
+ EDstate->nED = nED;
+
/* When reading, init_edsam has not been called yet,
* so we have to allocate memory first. */
if (bRead)
}
/* Read/write the last whole conformation of SREF and SAV for each ED dataset (usually only one) */
- for (i = 0; i < EDstate->nED; i++)
+ for (int i = 0; i < EDstate->nED; i++)
{
+ char buf[STRLEN];
+
/* Reference structure SREF */
sprintf(buf, "ED%d # of atoms in reference structure", i+1);
do_cpt_int_err(xd, buf, &EDstate->nref[i], list);
}
}
- return ret;
+ return 0;
}
{
do_cpt_string_err(xd, bRead, "output filename", &buf, list);
std::strncpy(outputfiles[i].filename, buf, CPTSTRLEN-1);
- if (list == NULL)
+ if (list == nullptr)
{
sfree(buf);
}
ivec domdecCells, int nppnodes,
int eIntegrator, int simulation_part,
gmx_bool bExpanded, int elamstats,
- gmx_int64_t step, double t, t_state *state)
+ gmx_int64_t step, double t,
+ t_state *state, ObservablesHistory *observablesHistory)
{
t_fileio *fp;
int file_version;
gmx_file_position_t *outputfiles;
int noutputfiles;
char *ftime;
- int flags_eks, flags_enh, flags_dfh;
t_fileio *ret;
if (DOMAINDECOMP(cr))
fp = gmx_fio_open(fntemp, "w");
+ int flags_eks;
if (state->ekinstate.bUpToDate)
{
flags_eks =
flags_eks = 0;
}
- flags_enh = 0;
- if (state->enerhist->nsum > 0 || state->enerhist->nsum_sim > 0)
+ energyhistory_t *enerhist = observablesHistory->energyHistory.get();
+ int flags_enh = 0;
+ if (enerhist != nullptr && (enerhist->nsum > 0 || enerhist->nsum_sim > 0))
{
flags_enh |= (1<<eenhENERGY_N) | (1<<eenhENERGY_NSTEPS) | (1<<eenhENERGY_NSTEPS_SIM);
- if (state->enerhist->nsum > 0)
+ if (enerhist->nsum > 0)
{
flags_enh |= ((1<<eenhENERGY_AVER) | (1<<eenhENERGY_SUM) |
(1<<eenhENERGY_NSUM));
}
- if (state->enerhist->nsum_sim > 0)
+ if (enerhist->nsum_sim > 0)
{
flags_enh |= ((1<<eenhENERGY_SUM_SIM) | (1<<eenhENERGY_NSUM_SIM));
}
- if (state->enerhist->dht)
+ if (enerhist->deltaHForeignLambdas != nullptr)
{
flags_enh |= ( (1<< eenhENERGY_DELTA_H_NN) |
(1<< eenhENERGY_DELTA_H_LIST) |
}
}
+ int flags_dfh;
if (bExpanded)
{
flags_dfh = ((1<<edfhBEQUIL) | (1<<edfhNATLAMBDA) | (1<<edfhSUMWEIGHTS) | (1<<edfhSUMDG) |
ftime = &(timebuf[0]);
+ int nlambda = (state->dfhist ? state->dfhist->nlambda : 0);
+
+ edsamhistory_t *edsamhist = observablesHistory->edsamHistory.get();
+ int nED = (edsamhist ? edsamhist->nED : 0);
+
+ swaphistory_t *swaphist = observablesHistory->swapHistory.get();
+ int eSwapCoords = (swaphist ? swaphist->eSwapCoords : eswapNO);
+
do_cpt_header(gmx_fio_getxdr(fp), FALSE, &file_version,
&version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
&eIntegrator, &simulation_part, &step, &t, &nppnodes,
- DOMAINDECOMP(cr) ? domdecCells : NULL, &npmenodes,
+ DOMAINDECOMP(cr) ? domdecCells : nullptr, &npmenodes,
&state->natoms, &state->ngtc, &state->nnhpres,
- &state->nhchainlength, &(state->dfhist.nlambda), &state->flags, &flags_eks, &flags_enh, &flags_dfh,
- &state->edsamstate.nED, &state->swapstate.eSwapCoords,
- NULL);
+ &state->nhchainlength, &nlambda, &state->flags, &flags_eks, &flags_enh, &flags_dfh,
+ &nED, &eSwapCoords,
+ nullptr);
sfree(version);
sfree(btime);
sfree(bhost);
sfree(fprog);
- if ((do_cpt_state(gmx_fio_getxdr(fp), FALSE, state->flags, state, NULL) < 0) ||
- (do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, NULL) < 0) ||
- (do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, flags_enh, state->enerhist, NULL) < 0) ||
- (do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, &state->dfhist, NULL) < 0) ||
- (do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, &state->edsamstate, NULL) < 0) ||
- (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, &state->swapstate, NULL) < 0) ||
- (do_cpt_files(gmx_fio_getxdr(fp), FALSE, &outputfiles, &noutputfiles, NULL,
+ if ((do_cpt_state(gmx_fio_getxdr(fp), state->flags, state, nullptr) < 0) ||
+ (do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, nullptr) < 0) ||
+ (do_cpt_enerhist(gmx_fio_getxdr(fp), FALSE, flags_enh, enerhist, nullptr) < 0) ||
+ (do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, nlambda, &state->dfhist, nullptr) < 0) ||
+ (do_cpt_EDstate(gmx_fio_getxdr(fp), FALSE, nED, edsamhist, nullptr) < 0) ||
+ (do_cpt_swapstate(gmx_fio_getxdr(fp), FALSE, eSwapCoords, swaphist, nullptr) < 0) ||
+ (do_cpt_files(gmx_fio_getxdr(fp), FALSE, &outputfiles, &noutputfiles, nullptr,
file_version) < 0))
{
gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
"Cannot fsync '%s'; maybe you are out of disk space?",
gmx_fio_getname(ret));
- if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV) == NULL)
+ if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV) == nullptr)
{
gmx_file(buf);
}
char *btime, char *buser, char *bhost, int double_prec,
char *fprog,
const t_commrec *cr, int npp_f, int npme_f,
- ivec dd_nc, ivec dd_nc_f,
+ const ivec dd_nc, const ivec dd_nc_f,
gmx_bool reproducibilityRequested)
{
/* Note that this check_string on the version will also print a message
static void read_checkpoint(const char *fn, FILE **pfplog,
const t_commrec *cr,
- ivec dd_nc, int *npme,
+ const ivec dd_nc,
int eIntegrator, int *init_fep_state, gmx_int64_t *step, double *t,
t_state *state, gmx_bool *bReadEkin,
+ ObservablesHistory *observablesHistory,
int *simulation_part,
gmx_bool bAppendOutputFiles, gmx_bool bForceAppend,
gmx_bool reproducibilityRequested)
int eIntegrator_f, nppnodes_f, npmenodes_f;
ivec dd_nc_f;
int natoms, ngtc, nnhpres, nhchainlength, nlambda, fflags, flags_eks, flags_enh, flags_dfh;
- int d;
+ int nED, eSwapCoords;
int ret;
gmx_file_position_t *outputfiles;
int nfiles;
&nppnodes_f, dd_nc_f, &npmenodes_f,
&natoms, &ngtc, &nnhpres, &nhchainlength, &nlambda,
&fflags, &flags_eks, &flags_enh, &flags_dfh,
- &state->edsamstate.nED, &state->swapstate.eSwapCoords, NULL);
+ &nED, &eSwapCoords, nullptr);
if (bAppendOutputFiles &&
file_version >= 13 && double_prec != GMX_DOUBLE)
gmx_fatal(FARGS, "Output file appending requested, but the code and checkpoint file precision (single/double) don't match");
}
- if (cr == NULL || MASTER(cr))
+ if (cr == nullptr || MASTER(cr))
{
fprintf(stderr, "\nReading checkpoint file %s generated: %s\n\n",
fn, ftime);
gmx_fatal(FARGS, "Checkpoint file is for a system of %d NH-pressure-coupling variables, while the current system consists of %d NH-pressure-coupling variables", nnhpres, state->nnhpres);
}
- if (nlambda != state->dfhist.nlambda)
+ int nlambdaHistory = (state->dfhist ? state->dfhist->nlambda : 0);
+ if (nlambda != nlambdaHistory)
{
- gmx_fatal(FARGS, "Checkpoint file is for a system with %d lambda states, while the current system consists of %d lambda states", nlambda, state->dfhist.nlambda);
+ gmx_fatal(FARGS, "Checkpoint file is for a system with %d lambda states, while the current system consists of %d lambda states", nlambda, nlambdaHistory);
}
init_gtc_state(state, state->ngtc, state->nnhpres, nhchainlength); /* need to keep this here to keep the tpr format working */
}
}
- if (!PAR(cr))
- {
- *npme = 0;
- }
- else if (cr->nnodes == nppnodes_f + npmenodes_f)
- {
- if (*npme < 0)
- {
- *npme = npmenodes_f;
- }
- int nppnodes = cr->nnodes - *npme;
- if (nppnodes == nppnodes_f)
- {
- for (d = 0; d < DIM; d++)
- {
- if (dd_nc[d] == 0)
- {
- dd_nc[d] = dd_nc_f[d];
- }
- }
- }
- }
-
if (fflags != state->flags)
{
"You can try with the -noappend option, and get more info in the log file.\n");
}
- if (getenv("GMX_ALLOW_CPT_MISMATCH") == NULL)
+ if (getenv("GMX_ALLOW_CPT_MISMATCH") == nullptr)
{
- gmx_fatal(FARGS, "You seem to have switched ensemble, integrator, T and/or P-coupling algorithm between the cpt and tpr file. The recommended way of doing this is passing the cpt file to grompp (with option -t) instead of to mdrun. If you know what you are doing, you can override this error by setting the env.var. GMX_ALLOW_CPT_MISMATCH");
+ gmx_fatal(FARGS, "You seem to have switched ensemble, integrator, T and/or P-coupling algorithm between the cpt and tpr file, or switched GROMACS version. The recommended way of doing this is passing the cpt file to grompp (with option -t) instead of to mdrun. If you know what you are doing, you can override this error by setting the env.var. GMX_ALLOW_CPT_MISMATCH");
}
else
{
reproducibilityRequested);
}
}
- ret = do_cpt_state(gmx_fio_getxdr(fp), TRUE, fflags, state, NULL);
+ ret = do_cpt_state(gmx_fio_getxdr(fp), fflags, state, nullptr);
*init_fep_state = state->fep_state; /* there should be a better way to do this than setting it here.
Investigate for 5.0. */
if (ret)
{
cp_error();
}
- ret = do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, NULL);
+ ret = do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, nullptr);
if (ret)
{
cp_error();
*bReadEkin = ((flags_eks & (1<<eeksEKINH)) || (flags_eks & (1<<eeksEKINF)) || (flags_eks & (1<<eeksEKINO)) ||
((flags_eks & (1<<eeksEKINSCALEF)) | (flags_eks & (1<<eeksEKINSCALEH)) | (flags_eks & (1<<eeksVSCALE))));
+ if (flags_enh && observablesHistory->energyHistory == nullptr)
+ {
+ observablesHistory->energyHistory = std::unique_ptr<energyhistory_t>(new energyhistory_t {});
+ }
ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE,
- flags_enh, state->enerhist, NULL);
+ flags_enh, observablesHistory->energyHistory.get(), nullptr);
if (ret)
{
cp_error();
{
fprintf(fplog, "\nWARNING: %s\n\n", warn);
}
- state->enerhist->nsum = *step;
- state->enerhist->nsum_sim = *step;
+ observablesHistory->energyHistory->nsum = *step;
+ observablesHistory->energyHistory->nsum_sim = *step;
}
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, &state->dfhist, NULL);
+ ret = do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, nlambda, &state->dfhist, nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state->edsamstate, NULL);
+ if (nED > 0 && observablesHistory->edsamHistory == nullptr)
+ {
+ observablesHistory->edsamHistory = std::unique_ptr<edsamhistory_t>(new edsamhistory_t {});
+ }
+ ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, nED, observablesHistory->edsamHistory.get(), nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state->swapstate, NULL);
+ if (eSwapCoords != eswapNO && observablesHistory->swapHistory == nullptr)
+ {
+ observablesHistory->swapHistory = std::unique_ptr<swaphistory_t>(new swaphistory_t {});
+ }
+ ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, eSwapCoords, observablesHistory->swapHistory.get(), nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE, &outputfiles, &nfiles, NULL, file_version);
+ ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE, &outputfiles, &nfiles, nullptr, file_version);
if (ret)
{
cp_error();
void load_checkpoint(const char *fn, FILE **fplog,
- const t_commrec *cr, ivec dd_nc, int *npme,
+ const t_commrec *cr, const ivec dd_nc,
t_inputrec *ir, t_state *state,
gmx_bool *bReadEkin,
+ ObservablesHistory *observablesHistory,
gmx_bool bAppend, gmx_bool bForceAppend,
gmx_bool reproducibilityRequested)
{
{
/* Read the state from the checkpoint file */
read_checkpoint(fn, fplog,
- cr, dd_nc, npme,
- ir->eI, &(ir->fepvals->init_fep_state), &step, &t, state, bReadEkin,
+ cr, dd_nc,
+ ir->eI, &(ir->fepvals->init_fep_state), &step, &t,
+ state, bReadEkin, observablesHistory,
&ir->simulation_part, bAppend, bForceAppend,
reproducibilityRequested);
}
if (PAR(cr))
{
- gmx_bcast(sizeof(*npme), npme, cr);
- gmx_bcast(DIM*sizeof(dd_nc[0]), dd_nc, cr);
gmx_bcast(sizeof(step), &step, cr);
gmx_bcast(sizeof(*bReadEkin), bReadEkin, cr);
}
int eIntegrator;
int nppnodes, npme;
ivec dd_nc;
+ int nlambda;
int flags_eks, flags_enh, flags_dfh;
double t;
t_state state;
+ int nED, eSwapCoords;
t_fileio *fp;
- if (filename == NULL ||
+ if (filename == nullptr ||
!gmx_fexist(filename) ||
(!(fp = gmx_fio_open(filename, "r"))))
{
&version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
&eIntegrator, simulation_part, step, &t, &nppnodes, dd_nc, &npme,
&state.natoms, &state.ngtc, &state.nnhpres, &state.nhchainlength,
- &(state.dfhist.nlambda), &state.flags, &flags_eks, &flags_enh, &flags_dfh,
- &state.edsamstate.nED, &state.swapstate.eSwapCoords, NULL);
+ &nlambda, &state.flags, &flags_eks, &flags_enh, &flags_dfh,
+ &nED, &eSwapCoords, nullptr);
gmx_fio_close(fp);
}
int eIntegrator;
int nppnodes, npme;
ivec dd_nc;
+ int nlambda;
int flags_eks, flags_enh, flags_dfh;
+ int nED, eSwapCoords;
int nfiles_loc;
- gmx_file_position_t *files_loc = NULL;
+ gmx_file_position_t *files_loc = nullptr;
int ret;
do_cpt_header(gmx_fio_getxdr(fp), TRUE, &file_version,
&version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
&eIntegrator, simulation_part, step, t, &nppnodes, dd_nc, &npme,
&state->natoms, &state->ngtc, &state->nnhpres, &state->nhchainlength,
- &(state->dfhist.nlambda), &state->flags, &flags_eks, &flags_enh, &flags_dfh,
- &state->edsamstate.nED, &state->swapstate.eSwapCoords, NULL);
+ &nlambda, &state->flags, &flags_eks, &flags_enh, &flags_dfh,
+ &nED, &eSwapCoords, nullptr);
ret =
- do_cpt_state(gmx_fio_getxdr(fp), TRUE, state->flags, state, NULL);
+ do_cpt_state(gmx_fio_getxdr(fp), state->flags, state, nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, NULL);
+ ret = do_cpt_ekinstate(gmx_fio_getxdr(fp), flags_eks, &state->ekinstate, nullptr);
if (ret)
{
cp_error();
}
+
+ energyhistory_t enerhist;
ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE,
- flags_enh, state->enerhist, NULL);
+ flags_enh, &enerhist, nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, &state->dfhist, NULL);
+ ret = do_cpt_df_hist(gmx_fio_getxdr(fp), flags_dfh, nlambda, &state->dfhist, nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state->edsamstate, NULL);
+ edsamhistory_t edsamhist = {};
+ ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, nED, &edsamhist, nullptr);
if (ret)
{
cp_error();
}
- ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state->swapstate, NULL);
+ swaphistory_t swaphist = {};
+ ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, eSwapCoords, &swaphist, nullptr);
if (ret)
{
cp_error();
ret = do_cpt_files(gmx_fio_getxdr(fp), TRUE,
&files_loc,
&nfiles_loc,
- NULL, file_version);
+ nullptr, file_version);
if (outputfiles != nullptr)
{
*outputfiles = files_loc;
t_fileio *fp;
fp = gmx_fio_open(fn, "r");
- read_checkpoint_data(fp, simulation_part, step, t, state, NULL, NULL);
+ read_checkpoint_data(fp, simulation_part, step, t, state, nullptr, nullptr);
if (gmx_fio_close(fp) != 0)
{
gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
void read_checkpoint_trxframe(t_fileio *fp, t_trxframe *fr)
{
- /* This next line is nasty because the sub-structures of t_state
- * cannot be assumed to be zeroed (or even initialized in ways the
- * rest of the code might assume). Using snew would be better, but
- * this will all go away for 5.0. */
t_state state;
int simulation_part;
gmx_int64_t step;
double t;
- init_state(&state, 0, 0, 0, 0, 0);
-
- read_checkpoint_data(fp, &simulation_part, &step, &t, &state, NULL, NULL);
+ read_checkpoint_data(fp, &simulation_part, &step, &t, &state, nullptr, nullptr);
fr->natoms = state.natoms;
- fr->bTitle = FALSE;
fr->bStep = TRUE;
fr->step = gmx_int64_to_int(step,
"conversion of checkpoint to trajectory");
fr->bX = (state.flags & (1<<estX));
if (fr->bX)
{
- fr->x = state.x;
- state.x = NULL;
+ fr->x = getRvecArrayFromPaddedRVecVector(&state.x, state.natoms);
}
fr->bV = (state.flags & (1<<estV));
if (fr->bV)
{
- fr->v = state.v;
- state.v = NULL;
+ fr->v = getRvecArrayFromPaddedRVecVector(&state.v, state.natoms);
}
fr->bF = FALSE;
fr->bBox = (state.flags & (1<<estBOX));
{
copy_mat(state.box, fr->box);
}
- done_state(&state);
}
void list_checkpoint(const char *fn, FILE *out)
gmx_int64_t step;
double t;
ivec dd_nc;
- t_state state;
+ int nlambda;
int flags_eks, flags_enh, flags_dfh;
+ int nED, eSwapCoords;
int ret;
gmx_file_position_t *outputfiles;
int nfiles;
- init_state(&state, -1, -1, -1, -1, 0);
+ t_state state;
fp = gmx_fio_open(fn, "r");
do_cpt_header(gmx_fio_getxdr(fp), TRUE, &file_version,
&version, &btime, &buser, &bhost, &double_prec, &fprog, &ftime,
&eIntegrator, &simulation_part, &step, &t, &nppnodes, dd_nc, &npme,
&state.natoms, &state.ngtc, &state.nnhpres, &state.nhchainlength,
- &(state.dfhist.nlambda), &state.flags,
- &flags_eks, &flags_enh, &flags_dfh, &state.edsamstate.nED,
- &state.swapstate.eSwapCoords, out);
- ret = do_cpt_state(gmx_fio_getxdr(fp), TRUE, state.flags, &state, out);
+ &nlambda, &state.flags,
+ &flags_eks, &flags_enh, &flags_dfh, &nED, &eSwapCoords,
+ out);
+ ret = do_cpt_state(gmx_fio_getxdr(fp), state.flags, &state, out);
if (ret)
{
cp_error();
{
cp_error();
}
+
+ energyhistory_t enerhist;
ret = do_cpt_enerhist(gmx_fio_getxdr(fp), TRUE,
- flags_enh, state.enerhist, out);
+ flags_enh, &enerhist, out);
if (ret == 0)
{
ret = do_cpt_df_hist(gmx_fio_getxdr(fp),
- flags_dfh, &state.dfhist, out);
+ flags_dfh, nlambda, &state.dfhist, out);
}
if (ret == 0)
{
- ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, &state.edsamstate, out);
+ edsamhistory_t edsamhist = {};
+ ret = do_cpt_EDstate(gmx_fio_getxdr(fp), TRUE, nED, &edsamhist, out);
}
if (ret == 0)
{
- ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, &state.swapstate, out);
+ swaphistory_t swaphist = {};
+ ret = do_cpt_swapstate(gmx_fio_getxdr(fp), TRUE, eSwapCoords, &swaphist, out);
}
if (ret == 0)
{
gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
-
- done_state(&state);
}
/* This routine cannot print tons of data, since it is called before the log file is opened. */
double t;
t_state state;
- init_state(&state, 0, 0, 0, 0, 0);
-
read_checkpoint_data(fp, simulation_part, &step, &t, &state,
nfiles, outputfiles);
if (gmx_fio_close(fp) != 0)
{
gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
}
- done_state(&state);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
extern "C" {
#endif
+class energyhistory_t;
struct gmx_file_position_t;
+struct ObservablesHistory;
struct t_commrec;
struct t_fileio;
struct t_inputrec;
-struct t_state;
+class t_state;
struct t_trxframe;
/* the name of the environment variable to disable fsync failure checks with */
int eIntegrator, int simulation_part,
gmx_bool bExpanded, int elamstats,
gmx_int64_t step, double t,
- t_state *state);
+ t_state *state, ObservablesHistory *observablesHistory);
/* Loads a checkpoint from fn for run continuation.
* Generates a fatal error on system size mismatch.
* The master node reads the file
- * and communicates all the modified number of steps and the parallel setup,
+ * and communicates all the modified number of steps,
* but not the state itself.
* When bAppend is set, lock the log file and truncate the existing output
* files so they can be appended.
* With reproducibilityRequested warns about version, build, #ranks differences.
*/
void load_checkpoint(const char *fn, FILE **fplog,
- const t_commrec *cr, ivec dd_nc, int *npme,
+ const t_commrec *cr, const ivec dd_nc,
t_inputrec *ir, t_state *state,
gmx_bool *bReadEkin,
+ ObservablesHistory *observablesHistory,
gmx_bool bAppend, gmx_bool bForceAppend,
gmx_bool reproducibilityRequested);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/vec.h"
-#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
void write_sto_conf_indexed(const char *outfile, const char *title,
break;
case efG96:
clear_trxframe(&fr, TRUE);
- fr.bTitle = TRUE;
- fr.title = title;
fr.natoms = atoms->nr;
fr.bAtoms = TRUE;
fr.atoms = const_cast<t_atoms *>(atoms);
fr.bBox = TRUE;
copy_mat(box, fr.box);
out = gmx_fio_fopen(outfile, "w");
- write_g96_conf(out, &fr, nindex, index);
+ write_g96_conf(out, title, &fr, nindex, index);
gmx_fio_fclose(out);
break;
case efPDB:
case efENT:
case efPQR:
out = gmx_fio_fopen(outfile, "w");
- write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, NULL, TRUE);
+ write_pdbfile_indexed(out, title, atoms, x, ePBC, box, ' ', -1, nindex, index, nullptr, TRUE);
gmx_fio_fclose(out);
break;
case efESP:
break;
case efG96:
clear_trxframe(&fr, TRUE);
- fr.bTitle = TRUE;
- fr.title = title;
fr.natoms = atoms->nr;
fr.bAtoms = TRUE;
fr.atoms = const_cast<t_atoms *>(atoms); // TODO check
fr.bBox = TRUE;
copy_mat(box, fr.box);
out = gmx_fio_fopen(outfile, "w");
- write_g96_conf(out, &fr, -1, NULL);
+ write_g96_conf(out, title, &fr, -1, nullptr);
gmx_fio_fclose(out);
break;
case efPDB:
case efBRK:
case efENT:
out = gmx_fio_fopen(outfile, "w");
- write_pdbfile(out, title, atoms, x, ePBC, box, ' ', -1, NULL, TRUE);
+ write_pdbfile(out, title, atoms, x, ePBC, box, ' ', -1, nullptr, TRUE);
gmx_fio_fclose(out);
break;
case efESP:
out = gmx_fio_fopen(outfile, "w");
- write_espresso_conf_indexed(out, title, atoms, atoms->nr, NULL, x, v, box);
+ write_espresso_conf_indexed(out, title, atoms, atoms->nr, nullptr, x, v, box);
gmx_fio_fclose(out);
break;
case efTPR:
case efG96:
{
in = gmx_fio_fopen(infile, "r");
- fr.title = NULL;
fr.natoms = -1;
- fr.atoms = NULL;
- fr.x = NULL;
- fr.v = NULL;
- fr.f = NULL;
- *natoms = read_g96_conf(in, infile, &fr, NULL, g96_line);
- sfree(const_cast<char *>(fr.title));
+ fr.atoms = nullptr;
+ fr.x = nullptr;
+ fr.v = nullptr;
+ fr.f = nullptr;
+ *natoms = read_g96_conf(in, infile, nullptr, &fr, nullptr, g96_line);
gmx_fio_fclose(in);
break;
}
}
}
-static void read_stx_conf(const char *infile, t_topology *top,
+static void read_stx_conf(const char *infile,
+ t_symtab *symtab, char **name, t_atoms *atoms,
rvec x[], rvec *v, int *ePBC, matrix box)
{
FILE *in;
int ftp;
char g96_line[STRLEN+1];
- if (top->atoms.nr == 0)
+ if (atoms->nr == 0)
{
fprintf(stderr, "Warning: Number of atoms in %s is 0\n", infile);
}
- else if (top->atoms.atom == NULL)
+ else if (atoms->atom == nullptr)
{
gmx_mem("Uninitialized array atom");
}
switch (ftp)
{
case efGRO:
- gmx_gro_read_conf(infile, top, x, v, box);
+ gmx_gro_read_conf(infile, symtab, name, atoms, x, v, box);
break;
case efG96:
- fr.title = NULL;
- fr.natoms = top->atoms.nr;
- fr.atoms = &top->atoms;
+ fr.natoms = atoms->nr;
+ fr.atoms = atoms;
fr.x = x;
fr.v = v;
- fr.f = NULL;
+ fr.f = nullptr;
in = gmx_fio_fopen(infile, "r");
- read_g96_conf(in, infile, &fr, &top->symtab, g96_line);
+ read_g96_conf(in, infile, name, &fr, symtab, g96_line);
gmx_fio_fclose(in);
copy_mat(fr.box, box);
- top->name = put_symtab(&top->symtab, fr.title);
- sfree(const_cast<char *>(fr.title));
break;
case efPDB:
case efBRK:
case efENT:
- gmx_pdb_read_conf(infile, top, x, ePBC, box);
+ gmx_pdb_read_conf(infile, symtab, name, atoms, x, ePBC, box);
break;
case efESP:
- gmx_espresso_read_conf(infile, top, x, v, box);
+ gmx_espresso_read_conf(infile, symtab, name, atoms, x, v, box);
break;
default:
gmx_incons("Not supported in read_stx_conf");
}
}
-static void done_gmx_groups_t(gmx_groups_t *g)
+static void readConfAndAtoms(const char *infile,
+ t_symtab *symtab, char **name, t_atoms *atoms,
+ int *ePBC,
+ rvec **x, rvec **v, matrix box)
{
- int i;
+ int natoms;
+ get_stx_coordnum(infile, &natoms);
+
+ init_t_atoms(atoms, natoms, (fn2ftp(infile) == efPDB));
- for (i = 0; (i < egcNR); i++)
+ bool xIsNull = false;
+ if (x == nullptr)
{
- if (NULL != g->grps[i].nm_ind)
- {
- sfree(g->grps[i].nm_ind);
- g->grps[i].nm_ind = NULL;
- }
- if (NULL != g->grpnr[i])
- {
- sfree(g->grpnr[i]);
- g->grpnr[i] = NULL;
- }
+ snew(x, 1);
+ xIsNull = true;
+ }
+ snew(*x, natoms);
+ if (v)
+ {
+ snew(*v, natoms);
+ }
+ read_stx_conf(infile,
+ symtab, name, atoms,
+ *x, (v == nullptr) ? nullptr : *v, ePBC, box);
+ if (xIsNull)
+ {
+ sfree(*x);
+ sfree(x);
}
- /* The contents of this array is in symtab, don't free it here */
- sfree(g->grpname);
}
-gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
- rvec **x, rvec **v, matrix box, gmx_bool bMass)
+void readConfAndTopology(const char *infile,
+ bool *haveTopology, gmx_mtop_t *mtop,
+ int *ePBC,
+ rvec **x, rvec **v, matrix box)
{
- t_tpxheader header;
- int natoms, i;
- gmx_bool bTop, bXNULL = FALSE;
- gmx_mtop_t *mtop;
- gmx_atomprop_t aps;
-
- bTop = fn2bTPX(infile);
- if (ePBC != NULL)
+ GMX_RELEASE_ASSERT(mtop != nullptr, "readConfAndTopology requires mtop!=NULL");
+
+ if (ePBC != nullptr)
{
*ePBC = -1;
}
- if (bTop)
+
+ *haveTopology = fn2bTPX(infile);
+ if (*haveTopology)
{
+ t_tpxheader header;
read_tpxheader(infile, &header, TRUE);
if (x)
{
{
snew(*v, header.natoms);
}
- snew(mtop, 1);
+ int natoms;
int ePBC_tmp
- = read_tpx(infile, NULL, box, &natoms,
- (x == NULL) ? NULL : *x, (v == NULL) ? NULL : *v, mtop);
- if (ePBC != NULL)
+ = read_tpx(infile, nullptr, box, &natoms,
+ (x == nullptr) ? nullptr : *x, (v == nullptr) ? nullptr : *v, mtop);
+ if (ePBC != nullptr)
{
*ePBC = ePBC_tmp;
}
- *top = gmx_mtop_t_to_t_topology(mtop);
- /* In this case we need to throw away the group data too */
- done_gmx_groups_t(&mtop->groups);
- sfree(mtop);
- tpx_make_chain_identifiers(&top->atoms, &top->mols);
}
else
{
- open_symtab(&top->symtab);
- get_stx_coordnum(infile, &natoms);
- init_t_atoms(&top->atoms, natoms, (fn2ftp(infile) == efPDB));
- if (x == NULL)
- {
- snew(x, 1);
- bXNULL = TRUE;
- }
- snew(*x, natoms);
- if (v)
- {
- snew(*v, natoms);
- }
- read_stx_conf(infile, top, *x, (v == NULL) ? NULL : *v, ePBC, box);
- if (bXNULL)
- {
- sfree(*x);
- sfree(x);
- }
- if (bMass)
+ t_symtab symtab;
+ char *name;
+ t_atoms atoms;
+
+ open_symtab(&symtab);
+
+ readConfAndAtoms(infile, &symtab, &name, &atoms, ePBC, x, v, box);
+
+ init_mtop(mtop);
+ convertAtomsToMtop(&symtab, put_symtab(&symtab, name), &atoms, mtop);
+ sfree(name);
+ }
+}
+
+gmx_bool read_tps_conf(const char *infile, t_topology *top, int *ePBC,
+ rvec **x, rvec **v, matrix box, gmx_bool requireMasses)
+{
+ bool haveTopology;
+ gmx_mtop_t *mtop;
+
+ // Note: We should have an initializer instead of relying on snew
+ snew(mtop, 1);
+ readConfAndTopology(infile, &haveTopology, mtop, ePBC, x, v, box);
+
+ *top = gmx_mtop_t_to_t_topology(mtop, true);
+ sfree(mtop);
+
+ tpx_make_chain_identifiers(&top->atoms, &top->mols);
+
+ if (requireMasses && !top->atoms.haveMass)
+ {
+ atomsSetMassesBasedOnNames(&top->atoms, TRUE);
+
+ if (!top->atoms.haveMass)
{
- aps = gmx_atomprop_init();
- for (i = 0; (i < natoms); i++)
- {
- if (!gmx_atomprop_query(aps, epropMass,
- *top->atoms.resinfo[top->atoms.atom[i].resind].name,
- *top->atoms.atomname[i],
- &(top->atoms.atom[i].m)))
- {
- if (debug)
- {
- fprintf(debug, "Can not find mass for atom %s %d %s, setting to 1\n",
- *top->atoms.resinfo[top->atoms.atom[i].resind].name,
- top->atoms.resinfo[top->atoms.atom[i].resind].nr,
- *top->atoms.atomname[i]);
- }
- }
- }
- gmx_atomprop_destroy(aps);
+ gmx_fatal(FARGS, "Masses were requested, but for some atom(s) masses could not be found in the database. Use a tpr file as input, if possible, or add these atoms to the mass database.");
}
- top->idef.ntypes = -1;
}
- return bTop;
+ return haveTopology;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const rvec x[], const rvec *v, int ePBC, const matrix box);
/* As write_sto_conf, but uses a gmx_mtop_t struct */
-gmx_bool read_tps_conf(const char *infile, struct t_topology *top,
- int *ePBC, rvec **x, rvec **v, matrix box, gmx_bool bMass);
-/* Read title, top.atoms, x, v (if not NULL) and box from an STX file,
- * memory for atoms, x and v will be allocated.
- * Return TRUE if a complete topology was read.
- * If infile is a TPX file read the whole top,
- * else if bMass=TRUE, read the masses into top.atoms from the mass database.
+/*! \brief Read a configuration and, when available, a topology from a tpr or structure file.
+ *
+ * When reading from a tpr file, the complete topology is returned in \p mtop.
+ * When reading from a structure file, only the atoms struct in \p mtop contains data.
+ *
+ * \param[in] infile Input file name
+ * \param[out] haveTopology true when a topology was read and stored in mtop
+ * \param[out] mtop The topology, either complete or only atom data
+ * \param[out] ePBC Enum reporting the type of PBC
+ * \param[in,out] x Coordinates will be stored when *x!=NULL
+ * \param[in,out] v Velocities will be stored when *v!=NULL
+ * \param[out] box Box dimensions
+ */
+void readConfAndTopology(const char *infile,
+ bool *haveTopology, gmx_mtop_t *mtop,
+ int *ePBC,
+ rvec **x, rvec **v, matrix box);
+
+/*! \brief Read a configuration and, when available, a topology from a tpr or structure file.
+ *
+ * Deprecated, superseded by readConfAndTopology().
+ * When \p requireMasses = TRUE, this routine must return a topology with
+ * mass data. Masses are either read from a tpr input file, or otherwise
+ * looked up from the mass database, and when such lookup fails a fatal error
+ * results.
+ * When \p requireMasses = FALSE, masses will still be read from tpr input and
+ * their presence is signaled with the \p haveMass flag in t_atoms of \p top.
+ *
+ * \param[in] infile Input file name
+ * \param[out] top The topology, either complete or only atom data. Caller is responsible for calling done_top().
+ * \param[out] ePBC Enum reporting the type of PBC
+ * \param[in,out] x Coordinates will be stored when *x!=NULL
+ * \param[in,out] v Velocities will be stored when *v!=NULL
+ * \param[out] box Box dimensions
+ * \param[in] requireMasses Require masses to be present, either from tpr or from the mass database
+ * \returns if a topology is available
*/
+gmx_bool read_tps_conf(const char *infile, struct t_topology *top,
+ int *ePBC, rvec **x, rvec **v, matrix box,
+ gmx_bool requireMasses);
#ifdef __cplusplus
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/compare.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#else
sb->type = xdr_datatype_float;
#endif
- sb->fval = NULL;
- sb->dval = NULL;
- sb->ival = NULL;
- sb->lval = NULL;
- sb->cval = NULL;
- sb->sval = NULL;
+ sb->fval = nullptr;
+ sb->dval = nullptr;
+ sb->ival = nullptr;
+ sb->lval = nullptr;
+ sb->cval = nullptr;
+ sb->sval = nullptr;
sb->fval_alloc = 0;
sb->dval_alloc = 0;
sb->ival_alloc = 0;
{
sfree(sb->fval);
sb->fval_alloc = 0;
- sb->fval = NULL;
+ sb->fval = nullptr;
}
if (sb->dval_alloc)
{
sfree(sb->dval);
sb->dval_alloc = 0;
- sb->dval = NULL;
+ sb->dval = nullptr;
}
if (sb->ival_alloc)
{
sfree(sb->ival);
sb->ival_alloc = 0;
- sb->ival = NULL;
+ sb->ival = nullptr;
}
if (sb->lval_alloc)
{
sfree(sb->lval);
sb->lval_alloc = 0;
- sb->lval = NULL;
+ sb->lval = nullptr;
}
if (sb->cval_alloc)
{
sfree(sb->cval);
sb->cval_alloc = 0;
- sb->cval = NULL;
+ sb->cval = nullptr;
}
if (sb->sval_alloc)
{
}
sfree(sb->sval);
sb->sval_alloc = 0;
- sb->sval = NULL;
+ sb->sval = nullptr;
}
}
srenew(sb->sval, sb->nr);
for (i = sb->sval_alloc; i < sb->nr; i++)
{
- sb->sval[i] = NULL;
+ sb->sval[i] = nullptr;
}
sb->sval_alloc = sb->nr;
}
{
eb->id = enxOR;
eb->nsub = 0;
- eb->sub = NULL;
+ eb->sub = nullptr;
eb->nsub_alloc = 0;
}
}
sfree(eb->sub);
eb->nsub_alloc = 0;
- eb->sub = NULL;
+ eb->sub = nullptr;
}
}
void init_enxframe(t_enxframe *fr)
{
fr->e_alloc = 0;
- fr->ener = NULL;
+ fr->ener = nullptr;
/*fr->d_alloc=0;*/
- fr->ener = NULL;
-
/*fr->ndisre=0;*/
fr->nblock = 0;
fr->nblock_alloc = 0;
- fr->block = NULL;
+ fr->block = nullptr;
}
return &(ef->block[i]);
}
}
- return NULL;
+ return nullptr;
}
void add_subblocks_enxblock(t_enxblock *eb, int n)
static void enx_warning(const char *msg)
{
- if (getenv("GMX_ENX_NO_FATAL") != NULL)
+ if (getenv("GMX_ENX_NO_FATAL") != nullptr)
{
gmx_warning(msg);
}
int i;
gmx_enxnm_t *nm;
- if (*nms == NULL)
+ if (*nms == nullptr)
{
snew(*nms, n);
}
if (nm->name)
{
sfree(nm->name);
- nm->name = NULL;
+ nm->name = nullptr;
}
if (nm->unit)
{
sfree(nm->unit);
- nm->unit = NULL;
+ nm->unit = nullptr;
}
}
if (!xdr_string(xdr, &(nm->name), STRLEN))
return FALSE;
}
*file_version = enx_version;
+ // cppcheck-suppress redundantPointerOp
if (!gmx_fio_do_int(ef->fio, *file_version))
{
*bOK = FALSE;
void close_enx(ener_file_t ef)
{
- if (ef == NULL)
+ if (ef == nullptr)
{
// Nothing to do
return;
ener_file_t open_enx(const char *fn, const char *mode)
{
int nre;
- gmx_enxnm_t *nms = NULL;
+ gmx_enxnm_t *nms = nullptr;
int file_version = -1;
t_enxframe *fr;
gmx_bool bWrongPrecision, bOK = TRUE;
/*d_size = fr->ndisre*(sizeof(real)*2);*/
}
- if (!do_eheader(ef, &file_version, fr, -1, NULL, &bOK))
+ if (!do_eheader(ef, &file_version, fr, -1, nullptr, &bOK))
{
if (bRead)
{
int nre, nfr, i, j, ni, npcoupl;
char buf[STRLEN];
const char *bufi;
- gmx_enxnm_t *enm = NULL;
+ gmx_enxnm_t *enm = nullptr;
t_enxframe *fr;
ener_file_t in;
free_enxframe(fr);
sfree(fr);
}
+
+static real ener_tensor_diag(int n, int *ind1, int *ind2,
+ gmx_enxnm_t *enm1,
+ int *tensi, int i,
+ t_energy e1[], t_energy e2[])
+{
+ int d1, d2;
+ int j;
+ real prod1, prod2;
+ int nfound;
+ size_t len;
+
+ d1 = tensi[i]/DIM;
+ d2 = tensi[i] - d1*DIM;
+
+ /* Find the diagonal elements d1 and d2 */
+ len = std::strlen(enm1[ind1[i]].name);
+ prod1 = 1;
+ prod2 = 1;
+ nfound = 0;
+ for (j = 0; j < n; j++)
+ {
+ if (tensi[j] >= 0 &&
+ std::strlen(enm1[ind1[j]].name) == len &&
+ std::strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 &&
+ (tensi[j] == d1*DIM+d1 || tensi[j] == d2*DIM+d2))
+ {
+ prod1 *= fabs(e1[ind1[j]].e);
+ prod2 *= fabs(e2[ind2[j]].e);
+ nfound++;
+ }
+ }
+
+ if (nfound == 2)
+ {
+ return 0.5*(std::sqrt(prod1) + std::sqrt(prod2));
+ }
+ else
+ {
+ return 0;
+ }
+}
+
+static gmx_bool enernm_equal(const char *nm1, const char *nm2)
+{
+ int len1, len2;
+
+ len1 = std::strlen(nm1);
+ len2 = std::strlen(nm2);
+
+ /* Remove " (bar)" at the end of a name */
+ if (len1 > 6 && std::strcmp(nm1+len1-6, " (bar)") == 0)
+ {
+ len1 -= 6;
+ }
+ if (len2 > 6 && std::strcmp(nm2+len2-6, " (bar)") == 0)
+ {
+ len2 -= 6;
+ }
+
+ return (len1 == len2 && gmx_strncasecmp(nm1, nm2, len1) == 0);
+}
+
+static void cmp_energies(FILE *fp, int step1, int step2,
+ t_energy e1[], t_energy e2[],
+ gmx_enxnm_t *enm1,
+ real ftol, real abstol,
+ int nre, int *ind1, int *ind2, int maxener)
+{
+ int i, ii;
+ int *tensi, len, d1, d2;
+ real ftol_i, abstol_i;
+
+ snew(tensi, maxener);
+ /* Check for tensor elements ending on "-XX", "-XY", ... , "-ZZ" */
+ for (i = 0; (i < maxener); i++)
+ {
+ ii = ind1[i];
+ tensi[i] = -1;
+ len = std::strlen(enm1[ii].name);
+ if (len > 3 && enm1[ii].name[len-3] == '-')
+ {
+ d1 = enm1[ii].name[len-2] - 'X';
+ d2 = enm1[ii].name[len-1] - 'X';
+ if (d1 >= 0 && d1 < DIM &&
+ d2 >= 0 && d2 < DIM)
+ {
+ tensi[i] = d1*DIM + d2;
+ }
+ }
+ }
+
+ for (i = 0; (i < maxener); i++)
+ {
+ /* Check if this is an off-diagonal tensor element */
+ if (tensi[i] >= 0 && tensi[i] != 0 && tensi[i] != 4 && tensi[i] != 8)
+ {
+ /* Turn on the relative tolerance check (4 is maximum relative diff.) */
+ ftol_i = 5;
+ /* Do the relative tolerance through an absolute tolerance times
+ * the size of diagonal components of the tensor.
+ */
+ abstol_i = ftol*ener_tensor_diag(nre, ind1, ind2, enm1, tensi, i, e1, e2);
+ if (debug)
+ {
+ fprintf(debug, "tensor '%s' val %f diag %f\n",
+ enm1[i].name, e1[i].e, abstol_i/ftol);
+ }
+ if (abstol_i > 0)
+ {
+ /* We found a diagonal, we need to check with the minimum tolerance */
+ abstol_i = std::min(abstol_i, abstol);
+ }
+ else
+ {
+ /* We did not find a diagonal, ignore the relative tolerance check */
+ abstol_i = abstol;
+ }
+ }
+ else
+ {
+ ftol_i = ftol;
+ abstol_i = abstol;
+ }
+ if (!equal_real(e1[ind1[i]].e, e2[ind2[i]].e, ftol_i, abstol_i))
+ {
+ fprintf(fp, "%-15s step %3d: %12g, step %3d: %12g\n",
+ enm1[ind1[i]].name,
+ step1, e1[ind1[i]].e,
+ step2, e2[ind2[i]].e);
+ }
+ }
+
+ sfree(tensi);
+}
+
+#if 0
+static void cmp_disres(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol)
+{
+ int i;
+ char bav[64], bt[64], bs[22];
+
+ cmp_int(stdout, "ndisre", -1, fr1->ndisre, fr2->ndisre);
+ if ((fr1->ndisre == fr2->ndisre) && (fr1->ndisre > 0))
+ {
+ sprintf(bav, "step %s: disre rav", gmx_step_str(fr1->step, bs));
+ sprintf(bt, "step %s: disre rt", gmx_step_str(fr1->step, bs));
+ for (i = 0; (i < fr1->ndisre); i++)
+ {
+ cmp_real(stdout, bav, i, fr1->disre_rm3tav[i], fr2->disre_rm3tav[i], ftol, abstol);
+ cmp_real(stdout, bt, i, fr1->disre_rt[i], fr2->disre_rt[i], ftol, abstol);
+ }
+ }
+}
+#endif
+
+static void cmp_eblocks(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol)
+{
+ int i, j, k;
+ char buf[64], bs[22];
+
+ cmp_int(stdout, "nblock", -1, fr1->nblock, fr2->nblock);
+ if ((fr1->nblock == fr2->nblock) && (fr1->nblock > 0))
+ {
+ for (j = 0; (j < fr1->nblock); j++)
+ {
+ t_enxblock *b1, *b2; /* convenience vars */
+
+ b1 = &(fr1->block[j]);
+ b2 = &(fr2->block[j]);
+
+ sprintf(buf, "step %s: block[%d]", gmx_step_str(fr1->step, bs), j);
+ cmp_int(stdout, buf, -1, b1->nsub, b2->nsub);
+ cmp_int(stdout, buf, -1, b1->id, b2->id);
+
+ if ( (b1->nsub == b2->nsub) && (b1->id == b2->id) )
+ {
+ for (i = 0; i < b1->nsub; i++)
+ {
+ t_enxsubblock *s1, *s2;
+
+ s1 = &(b1->sub[i]);
+ s2 = &(b2->sub[i]);
+
+ cmp_int(stdout, buf, -1, (int)s1->type, (int)s2->type);
+ cmp_int64(stdout, buf, s1->nr, s2->nr);
+
+ if ((s1->type == s2->type) && (s1->nr == s2->nr))
+ {
+ switch (s1->type)
+ {
+ case xdr_datatype_float:
+ for (k = 0; k < s1->nr; k++)
+ {
+ cmp_float(stdout, buf, i,
+ s1->fval[k], s2->fval[k],
+ ftol, abstol);
+ }
+ break;
+ case xdr_datatype_double:
+ for (k = 0; k < s1->nr; k++)
+ {
+ cmp_double(stdout, buf, i,
+ s1->dval[k], s2->dval[k],
+ ftol, abstol);
+ }
+ break;
+ case xdr_datatype_int:
+ for (k = 0; k < s1->nr; k++)
+ {
+ cmp_int(stdout, buf, i,
+ s1->ival[k], s2->ival[k]);
+ }
+ break;
+ case xdr_datatype_int64:
+ for (k = 0; k < s1->nr; k++)
+ {
+ cmp_int64(stdout, buf,
+ s1->lval[k], s2->lval[k]);
+ }
+ break;
+ case xdr_datatype_char:
+ for (k = 0; k < s1->nr; k++)
+ {
+ cmp_uc(stdout, buf, i,
+ s1->cval[k], s2->cval[k]);
+ }
+ break;
+ case xdr_datatype_string:
+ for (k = 0; k < s1->nr; k++)
+ {
+ cmp_str(stdout, buf, i,
+ s1->sval[k], s2->sval[k]);
+ }
+ break;
+ default:
+ gmx_incons("Unknown data type!!");
+ }
+ }
+ }
+ }
+ }
+ }
+}
+
+void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const char *lastener)
+{
+ int nre, nre1, nre2;
+ ener_file_t in1, in2;
+ int i, j, maxener, *ind1, *ind2, *have;
+ gmx_enxnm_t *enm1 = nullptr, *enm2 = nullptr;
+ t_enxframe *fr1, *fr2;
+ gmx_bool b1, b2;
+
+ fprintf(stdout, "comparing energy file %s and %s\n\n", fn1, fn2);
+
+ in1 = open_enx(fn1, "r");
+ in2 = open_enx(fn2, "r");
+ do_enxnms(in1, &nre1, &enm1);
+ do_enxnms(in2, &nre2, &enm2);
+ if (nre1 != nre2)
+ {
+ fprintf(stdout, "There are %d and %d terms in the energy files\n\n",
+ nre1, nre2);
+ }
+ else
+ {
+ fprintf(stdout, "There are %d terms in the energy files\n\n", nre1);
+ }
+
+ snew(ind1, nre1);
+ snew(ind2, nre2);
+ snew(have, nre2);
+ nre = 0;
+ for (i = 0; i < nre1; i++)
+ {
+ for (j = 0; j < nre2; j++)
+ {
+ if (enernm_equal(enm1[i].name, enm2[j].name))
+ {
+ ind1[nre] = i;
+ ind2[nre] = j;
+ have[j] = 1;
+ nre++;
+ break;
+ }
+ }
+ if (nre == 0 || ind1[nre-1] != i)
+ {
+ cmp_str(stdout, "enm", i, enm1[i].name, "-");
+ }
+ }
+ for (i = 0; i < nre2; i++)
+ {
+ if (have[i] == 0)
+ {
+ cmp_str(stdout, "enm", i, "-", enm2[i].name);
+ }
+ }
+
+ maxener = nre;
+ for (i = 0; i < nre; i++)
+ {
+ if ((lastener != nullptr) && (std::strstr(enm1[i].name, lastener) != nullptr))
+ {
+ maxener = i+1;
+ break;
+ }
+ }
+
+ fprintf(stdout, "There are %d terms to compare in the energy files\n\n",
+ maxener);
+
+ for (i = 0; i < maxener; i++)
+ {
+ cmp_str(stdout, "unit", i, enm1[ind1[i]].unit, enm2[ind2[i]].unit);
+ }
+
+ snew(fr1, 1);
+ snew(fr2, 1);
+ do
+ {
+ b1 = do_enx(in1, fr1);
+ b2 = do_enx(in2, fr2);
+ if (b1 && !b2)
+ {
+ fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn2, fn1);
+ }
+ else if (!b1 && b2)
+ {
+ fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn1, fn2);
+ }
+ else if (!b1 && !b2)
+ {
+ fprintf(stdout, "\nFiles read successfully\n");
+ }
+ else
+ {
+ cmp_real(stdout, "t", -1, fr1->t, fr2->t, ftol, abstol);
+ cmp_int(stdout, "step", -1, fr1->step, fr2->step);
+ /* We don't want to print the nre mismatch for every frame */
+ /* cmp_int(stdout,"nre",-1,fr1->nre,fr2->nre); */
+ if ((fr1->nre >= nre) && (fr2->nre >= nre))
+ {
+ cmp_energies(stdout, fr1->step, fr1->step, fr1->ener, fr2->ener,
+ enm1, ftol, abstol, nre, ind1, ind2, maxener);
+ }
+ /*cmp_disres(fr1,fr2,ftol,abstol);*/
+ cmp_eblocks(fr1, fr2, ftol, abstol);
+ }
+ }
+ while (b1 && b2);
+
+ close_enx(in1);
+ close_enx(in2);
+
+ free_enxframe(fr2);
+ sfree(fr2);
+ free_enxframe(fr1);
+ sfree(fr1);
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_FILEIO_ENXIO_H
#include "gromacs/fileio/xdr_datatype.h"
-#include "gromacs/mdtypes/state.h"
#include "gromacs/trajectory/energy.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
+#include "gromacs/utility/basedefinitions.h"
struct gmx_groups_t;
struct t_fileio;
struct t_inputrec;
+class t_state;
/**************************************************************
* These are the base datatypes + functions for reading and
subbblocks. */
void add_subblocks_enxblock(t_enxblock *eb, int n);
-
-
-#ifdef __cplusplus
-}
-#endif
+void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol,
+ const char *lastener);
+/* Compare two binary energy files */
#endif
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2005, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
void gmx_espresso_read_conf(const char *infile,
- t_topology *top, rvec x[], rvec *v, matrix box)
+ t_symtab *symtab, char **name, t_atoms *atoms,
+ rvec x[], rvec *v, matrix box)
{
- t_atoms *atoms = &top->atoms;
FILE *fp;
char word[STRLEN], buf[STRLEN];
int level, r, nprop, p, i, m, molnr;
double d;
gmx_bool bFoundParticles, bFoundProp, bFoundVariable, bMol;
- // TODO: The code does not understand titles it writes...
- top->name = put_symtab(&top->symtab, "");
+ if (name != nullptr)
+ {
+ // No title reading implemented for espresso files
+ *name = gmx_strdup("");
+ }
clear_mat(box);
+ atoms->haveMass = FALSE;
+ atoms->haveCharge = FALSE;
+ atoms->haveType = FALSE;
+ atoms->haveBState = FALSE;
+ atoms->havePdbInfo = FALSE;
+
fp = gmx_fio_fopen(infile, "r");
bFoundParticles = FALSE;
{
bFoundProp = TRUE;
prop[nprop++] = p;
- /* printf(" prop[%d] = %s\n",nprop-1,esp_prop[prop[nprop-1]]); */
+ if (p == espQ)
+ {
+ atoms->haveCharge = TRUE;
+ }
+
+ if (debug)
+ {
+ fprintf(debug, " prop[%d] = %s\n", nprop-1, esp_prop[prop[nprop-1]]);
+ }
}
}
if (!bFoundProp && word[0] != '}')
break;
case espTYPE:
r = get_espresso_word(fp, word);
- atoms->atom[i].type = std::strtol(word, NULL, 10);
+ atoms->atom[i].type = std::strtol(word, nullptr, 10);
break;
case espQ:
r = get_espresso_word(fp, word);
break;
case espMOLECULE:
r = get_espresso_word(fp, word);
- molnr = std::strtol(word, NULL, 10);
+ molnr = std::strtol(word, nullptr, 10);
if (i == 0 ||
atoms->resinfo[atoms->atom[i-1].resind].nr != molnr)
{
}
/* Generate an atom name from the particle type */
sprintf(buf, "T%hu", atoms->atom[i].type);
- atoms->atomname[i] = put_symtab(&top->symtab, buf);
+ atoms->atomname[i] = put_symtab(symtab, buf);
if (bMol)
{
if (i == 0 || atoms->atom[i].resind != atoms->atom[i-1].resind)
{
atoms->resinfo[atoms->atom[i].resind].name =
- put_symtab(&top->symtab, "MOL");
+ put_symtab(symtab, "MOL");
}
}
else
sprintf(buf, "T%c%c",
'A'+atoms->atom[i].type/26, 'A'+atoms->atom[i].type%26);
}
- t_atoms_set_resinfo(atoms, i, &top->symtab, buf, i, ' ', 0, ' ');
+ t_atoms_set_resinfo(atoms, i, symtab, buf, i, ' ', 0, ' ');
}
if (r == 3)
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2005, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
struct t_atoms;
-struct t_topology;
+struct t_symtab;
void gmx_espresso_read_conf(const char *infile,
- t_topology *top, rvec x[], rvec *v, matrix box);
+ t_symtab *symtab, char **name, t_atoms *atoms,
+ rvec x[], rvec *v, matrix box);
+/* If name is not nullptr, gmx_strdup the title string into
+ * it. Reading a title from espresso format is not , so this will
+ * always be an empty string. */
int get_espresso_coordnum(const char *infile);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ eftASC, ".mdp", "grompp", "-f", "grompp input file with MD parameters" },
{ eftGEN, ".???", "traj", "-f", "Trajectory", NTRXS, trxs },
{ eftGEN, ".???", "trajout", "-f", "Trajectory", NTROS, tros },
- { eftGEN, ".???", "traj", NULL,
+ { eftGEN, ".???", "traj", nullptr,
"Full precision trajectory", NTRNS, trns },
- { eftXDR, ".trr", "traj", NULL, "Trajectory in portable xdr format" },
- { eftGEN, ".???", "traj_comp", NULL,
+ { eftXDR, ".trr", "traj", nullptr, "Trajectory in portable xdr format" },
+ { eftGEN, ".???", "traj_comp", nullptr,
"Compressed trajectory (tng format or portable xdr format)", NTRCOMPRESSED, trcompressed},
- { eftXDR, ".xtc", "traj", NULL,
+ { eftXDR, ".xtc", "traj", nullptr,
"Compressed trajectory (portable xdr format): xtc" },
- { eftTNG, ".tng", "traj", NULL,
+ { eftTNG, ".tng", "traj", nullptr,
"Trajectory file (tng format)" },
- { eftXDR, ".edr", "ener", NULL, "Energy file"},
+ { eftXDR, ".edr", "ener", nullptr, "Energy file"},
{ eftGEN, ".???", "conf", "-c", "Structure file", NSTXS, stxs },
{ eftGEN, ".???", "out", "-o", "Structure file", NSTOS, stos },
{ eftASC, ".gro", "conf", "-c", "Coordinate file in Gromos-87 format" },
{ eftASC, ".out", "hello", "-o", "Generic output file"},
{ eftASC, ".ndx", "index", "-n", "Index file", },
{ eftASC, ".top", "topol", "-p", "Topology file"},
- { eftASC, ".itp", "topinc", NULL, "Include file for topology"},
+ { eftASC, ".itp", "topinc", nullptr, "Include file for topology"},
{ eftGEN, ".???", "topol", "-s", "Structure+mass(db)", NTPSS, tpss },
{ eftXDR, ".tpr", "topol", "-s", "Portable xdr run input file"},
{ eftASC, ".tex", "doc", "-o", "LaTeX file"},
- { eftASC, ".rtp", "residue", NULL, "Residue Type file used by pdb2gmx" },
- { eftASC, ".atp", "atomtp", NULL, "Atomtype file used by pdb2gmx" },
- { eftASC, ".hdb", "polar", NULL, "Hydrogen data base"},
- { eftASC, ".dat", "nnnice", NULL, "Generic data file"},
- { eftASC, ".dlg", "user", NULL, "Dialog Box data for ngmx"},
- { eftASC, ".map", "ss", NULL, "File that maps matrix data to colors" },
- { eftASC, ".eps", "plot", NULL, "Encapsulated PostScript (tm) file" },
- { eftASC, ".mat", "ss", NULL, "Matrix Data file"},
- { eftASC, ".m2p", "ps", NULL, "Input file for mat2ps"},
+ { eftASC, ".rtp", "residue", nullptr, "Residue Type file used by pdb2gmx" },
+ { eftASC, ".atp", "atomtp", nullptr, "Atomtype file used by pdb2gmx" },
+ { eftASC, ".hdb", "polar", nullptr, "Hydrogen data base"},
+ { eftASC, ".dat", "nnnice", nullptr, "Generic data file"},
+ { eftASC, ".dlg", "user", nullptr, "Dialog Box data for ngmx"},
+ { eftASC, ".map", "ss", nullptr, "File that maps matrix data to colors" },
+ { eftASC, ".eps", "plot", nullptr, "Encapsulated PostScript (tm) file" },
+ { eftASC, ".mat", "ss", nullptr, "Matrix Data file"},
+ { eftASC, ".m2p", "ps", nullptr, "Input file for mat2ps"},
{ eftXDR, ".mtx", "hessian", "-m", "Hessian matrix"},
- { eftASC, ".edi", "sam", NULL, "ED sampling input"},
- { eftASC, ".cub", "pot", NULL, "Gaussian cube file" },
- { eftASC, ".xpm", "root", NULL, "X PixMap compatible matrix file" },
- { eftASC, "", "rundir", NULL, "Run directory" }
+ { eftASC, ".edi", "sam", nullptr, "ED sampling input"},
+ { eftASC, ".cub", "pot", nullptr, "Gaussian cube file" },
+ { eftASC, ".xpm", "root", nullptr, "X PixMap compatible matrix file" },
+ { eftASC, "", "rundir", nullptr, "Run directory" }
};
const char *ftp2ext(int ftp)
}
else
{
- return 0;
+ return nullptr;
}
}
}
else
{
- return NULL;
+ return nullptr;
}
}
}
else
{
- return NULL;
+ return nullptr;
}
}
for (i = 0; (i < efNR); i++)
{
- if ((eptr = deffile[i].ext) != NULL)
+ if ((eptr = deffile[i].ext) != nullptr)
{
if (gmx_strcasecmp(feptr, eptr) == 0)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#define CHAR_SHIFT 24
nwanted = fr->natoms;
+ if (fr->atoms != nullptr)
+ {
+ GMX_RELEASE_ASSERT(symtab != nullptr, "Reading a conformation from a g96 format with atom data requires a valid symbol table");
+ }
atoms = fr->atoms;
+ if (atoms != nullptr)
+ {
+ atoms->haveMass = FALSE;
+ atoms->haveCharge = FALSE;
+ atoms->haveType = FALSE;
+ atoms->haveBState = FALSE;
+ atoms->havePdbInfo = FALSE;
+ }
natoms = 0;
return natoms;
}
-int read_g96_conf(FILE *fp, const char *infile, t_trxframe *fr,
+int read_g96_conf(FILE *fp, const char *infile, char **name, t_trxframe *fr,
t_symtab *symtab, char *line)
{
gmx_bool bAtStart, bTime, bAtoms, bPos, bVel, bBox, bEnd, bFinished;
if (bAtStart)
{
- while (!fr->bTitle && fgets2(line, STRLEN, fp))
+ bool foundTitle = false;
+ while (!foundTitle && fgets2(line, STRLEN, fp))
{
- fr->bTitle = (std::strcmp(line, "TITLE") == 0);
+ foundTitle = (std::strcmp(line, "TITLE") == 0);
}
- if (fr->title == NULL)
+ fgets2(line, STRLEN, fp);
+ if (name != nullptr)
{
- fgets2(line, STRLEN, fp);
- fr->title = gmx_strdup(line);
+ *name = gmx_strdup(line);
}
bEnd = FALSE;
while (!bEnd && fgets2(line, STRLEN, fp))
fr->bTime = bTime;
do
{
- bFinished = (fgets2(line, STRLEN, fp) == NULL);
+ bFinished = (fgets2(line, STRLEN, fp) == nullptr);
}
while (!bFinished && (line[0] == '#'));
sscanf(line, "%15" GMX_SCNd64 "%15lf", &(fr->step), &db1);
return natoms;
}
-void write_g96_conf(FILE *out, const t_trxframe *fr,
+void write_g96_conf(FILE *out, const char *title, const t_trxframe *fr,
int nindex, const int *index)
{
t_atoms *atoms;
nout = fr->natoms;
}
- if (fr->bTitle)
- {
- fprintf(out, "TITLE\n%s\nEND\n", fr->title);
- }
+ fprintf(out, "TITLE\n%s\nEND\n", title);
if (fr->bStep || fr->bTime)
{
/* Officially the time format is %15.9, which is not enough for 10 ns */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_symtab;
struct t_trxframe;
-int read_g96_conf(FILE *fp, const char *infile, struct t_trxframe *fr,
+int read_g96_conf(FILE *fp, const char *infile, char **name, struct t_trxframe *fr,
struct t_symtab *symtab, char *line);
/* read a Gromos96 coordinate or trajectory file, *
* returns the number of atoms *
* nwanted is the number of wanted coordinates, *
* set this to -1 if you want to know the number of atoms in the file *
* title, atoms, x, v can all be NULL, in which case they won't be read *
- * line holds the previous line for trajectory reading */
+ * line holds the previous line for trajectory reading *
+ *
+ * symtab only needs to be valid if fr->atoms is valid
+ *
+ * If name is not nullptr, gmx_strdup the first g96 title string into it. */
-void write_g96_conf(FILE *out, const t_trxframe *fr, int nindex, const int *index);
+void write_g96_conf(FILE *out, const char *title, const t_trxframe *fr, int nindex, const int *index);
/* write a Gromos96 coordinate file or trajectory frame *
* index can be NULL */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
XDR *gmx_fio_getxdr(t_fileio *fio)
{
- XDR *ret = NULL;
+ XDR *ret = nullptr;
gmx_fio_lock(fio);
- GMX_RELEASE_ASSERT( fio->xdr != NULL, "Implementation error: NULL XDR pointers");
+ GMX_RELEASE_ASSERT( fio->xdr != nullptr, "Implementation error: NULL XDR pointers");
ret = fio->xdr;
gmx_fio_unlock(fio);
return ret;
double d = 0;
float f = 0;
- GMX_RELEASE_ASSERT( fio->xdr != NULL, "Implementation error: NULL XDR pointers");
+ GMX_RELEASE_ASSERT( fio->xdr != nullptr, "Implementation error: NULL XDR pointers");
gmx_fio_check_nitem(eio, nitem, srcfile, line);
switch (eio)
{
}
break;
case eioNRVEC:
- ptr = NULL;
+ ptr = nullptr;
res = 1;
for (j = 0; (j < nitem) && res; j++)
{
gmx_fio_unlock(fio);
return ret;
}
+
+namespace gmx
+{
+
+bool FileIOXdrSerializer::reading() const
+{
+ return fio_->bRead;
+}
+
+void FileIOXdrSerializer::doBool(bool *value)
+{
+ gmx_bool v = *value;
+ gmx_fio_do_gmx_bool(fio_, v);
+ *value = v;
+}
+
+void FileIOXdrSerializer::doUChar(unsigned char *value)
+{
+ gmx_fio_do_uchar(fio_, *value);
+}
+
+void FileIOXdrSerializer::doInt(int *value)
+{
+ gmx_fio_do_int(fio_, *value);
+}
+
+void FileIOXdrSerializer::doInt64(gmx_int64_t *value)
+{
+ gmx_fio_do_int64(fio_, *value);
+}
+
+void FileIOXdrSerializer::doFloat(float *value)
+{
+ gmx_fio_do_float(fio_, *value);
+}
+
+void FileIOXdrSerializer::doDouble(double *value)
+{
+ gmx_fio_do_double(fio_, *value);
+}
+
+void FileIOXdrSerializer::doString(std::string *value)
+{
+ // TODO: Use an arbitrary length buffer (but that is not supported in
+ // gmx_fio, either).
+ char buf[STRLEN];
+ if (!fio_->bRead)
+ {
+ std::strncpy(buf, value->c_str(), STRLEN);
+ buf[STRLEN-1] = 0;
+ }
+ gmx_fio_do_string(fio_, buf);
+ if (fio_->bRead)
+ {
+ *value = buf;
+ }
+}
+
+} // namespace gmx
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_GMXFIO_XDR_H
#define GMX_FILEIO_GMXFIO_XDR_H
+#include <string>
+
#include "gromacs/fileio/xdrf.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/iserializer.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
struct t_fileio;
void gmx_fio_setprecision(struct t_fileio *fio, gmx_bool bDouble);
#define gmx_fio_ndo_ivec(fio, item, n) gmx_fio_ndoe_ivec(fio, item, n, (#item), __FILE__, __LINE__)
#define gmx_fio_ndo_string(fio, item, n) gmx_fio_ndoe_string(fio, item, n, (#item), __FILE__, __LINE__)
-#ifdef __cplusplus
-}
-#endif
+namespace gmx
+{
+
+class FileIOXdrSerializer : public ISerializer
+{
+ public:
+ explicit FileIOXdrSerializer(t_fileio *fio) : fio_(fio) {}
+
+ virtual bool reading() const;
+
+ virtual void doBool(bool *value);
+ virtual void doUChar(unsigned char *value);
+ virtual void doInt(int *value);
+ virtual void doInt64(gmx_int64_t *value);
+ virtual void doFloat(float *value);
+ virtual void doDouble(double *value);
+ virtual void doString(std::string *value);
+
+ private:
+ t_fileio *fio_;
+};
+
+} // namespace gmx
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/md5.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/mutex.h"
#include "gromacs/utility/smalloc.h"
#include "gmxfio-impl.h"
/* the list of open files is a linked list, with a dummy element at its head;
it is initialized when the first file is opened. */
-static t_fileio *open_files = NULL;
+static t_fileio *open_files = nullptr;
/* this mutex locks the open_files structure so that no two threads can
opening and closing of files, or during global operations like
iterating along all open files. All these cases should be rare
during the simulation. */
-static tMPI_Thread_mutex_t open_file_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+static gmx::Mutex open_file_mutex;
+
+using Lock = gmx::lock_guard<gmx::Mutex>;
/******************************************************************
*
if (!open_files)
{
snew(open_files, 1);
- open_files->fp = NULL;
- open_files->fn = NULL;
+ open_files->fp = nullptr;
+ open_files->fn = nullptr;
open_files->next = open_files;
open_files->prev = open_files;
tMPI_Lock_init(&(open_files->mtx));
static void gmx_fio_insert(t_fileio *fio)
{
t_fileio *prev;
- /* first lock the big open_files mutex. */
- tMPI_Thread_mutex_lock(&open_file_mutex);
- /* now check whether the dummy element has been allocated,
- and allocate it if it hasn't */
+ Lock openFilesLock(open_file_mutex);
gmx_fio_make_dummy();
/* and lock the fio we got and the list's head **/
}
gmx_fio_unlock(open_files);
gmx_fio_unlock(fio);
-
- /* now unlock the big open_files mutex. */
- tMPI_Thread_mutex_unlock(&open_file_mutex);
}
/* remove a t_fileio into the list. We assume the fio is locked, and we leave
/* get the first open file, or NULL if there is none.
- Returns a locked fio. */
+ Returns a locked fio. Assumes open_files_mutex is locked. */
static t_fileio *gmx_fio_get_first(void)
{
t_fileio *ret;
- /* first lock the big open_files mutex and the dummy's mutex */
- /* first lock the big open_files mutex. */
- tMPI_Thread_mutex_lock(&open_file_mutex);
gmx_fio_make_dummy();
gmx_fio_lock(open_files);
if (ret == open_files)
{
/* after this, the open_file pointer should never change */
- ret = NULL;
+ ret = nullptr;
}
else
{
}
/* get the next open file, or NULL if there is none.
- Unlocks the previous fio and locks the next one. */
+ Unlocks the previous fio and locks the next one.
+ Assumes open_file_mutex is locked. */
static t_fileio *gmx_fio_get_next(t_fileio *fio)
{
t_fileio *ret;
/* check if that was the last one */
if (fio->next == open_files)
{
- ret = NULL;
- tMPI_Thread_mutex_unlock(&open_file_mutex);
+ ret = nullptr;
}
else
{
return ret;
}
-/* Stop looping through the open_files. Unlocks the global lock. */
+/* Stop looping through the open_files. Assumes open_file_mutex is locked. */
static void gmx_fio_stop_getting_next(t_fileio *fio)
{
gmx_fio_unlock(fio);
- tMPI_Thread_mutex_unlock(&open_file_mutex);
}
*****************************************************************/
t_fileio *gmx_fio_open(const char *fn, const char *mode)
{
- t_fileio *fio = NULL;
+ t_fileio *fio = nullptr;
char newmode[5];
gmx_bool bRead, bReadWrite;
tMPI_Lock_init(&(fio->mtx));
bRead = (newmode[0] == 'r' && newmode[1] != '+');
bReadWrite = (newmode[1] == '+');
- fio->fp = NULL;
- fio->xdr = NULL;
+ fio->fp = nullptr;
+ fio->xdr = nullptr;
if (fn)
{
if (fn2ftp(fn) == efTNG)
{
int rc = 0;
- if (fio->xdr != NULL)
+ if (fio->xdr != nullptr)
{
xdr_destroy(fio->xdr);
sfree(fio->xdr);
}
- if (fio->fp != NULL)
+ if (fio->fp != nullptr)
{
rc = gmx_ffclose(fio->fp); /* fclose returns 0 if happy */
int gmx_fio_close(t_fileio *fio)
{
- int rc = 0;
+ int rc = 0;
- /* first lock the big open_files mutex. */
- /* We don't want two processes operating on the list at the same time */
- tMPI_Thread_mutex_lock(&open_file_mutex);
+ Lock openFilesLock(open_file_mutex);
gmx_fio_lock(fio);
/* first remove it from the list */
sfree(fio->fn);
sfree(fio);
- tMPI_Thread_mutex_unlock(&open_file_mutex);
-
return rc;
}
{
int rc = 0;
gmx_fio_lock(fio);
- if (fio->xdr == NULL)
+ if (fio->xdr == nullptr)
{
rc = gmx_ffclose(fio->fp); /* fclose returns 0 if happy */
- fio->fp = NULL;
+ fio->fp = nullptr;
}
gmx_fio_unlock(fio);
t_fileio *cur;
int rc = -1;
+ Lock openFilesLock(open_file_mutex);
cur = gmx_fio_get_first();
while (cur)
{
nalloc = 100;
snew(outputfiles, nalloc);
+ Lock openFilesLock(open_file_mutex);
cur = gmx_fio_get_first();
while (cur)
{
t_fileio *gmx_fio_all_output_fsync(void)
{
- t_fileio *ret = NULL;
+ t_fileio *ret = nullptr;
t_fileio *cur;
+ Lock openFilesLock(open_file_mutex);
cur = gmx_fio_get_first();
while (cur)
{
FILE *gmx_fio_getfp(t_fileio *fio)
{
- FILE *ret = NULL;
+ FILE *ret = nullptr;
gmx_fio_lock(fio);
if (fio->fp)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
" (%d)\n", natoms, atoms->nr);
}
+ atoms->haveMass = FALSE;
+ atoms->haveCharge = FALSE;
+ atoms->haveType = FALSE;
+ atoms->haveBState = FALSE;
+ atoms->havePdbInfo = FALSE;
+
bFirst = TRUE;
bVel = FALSE;
/* just pray the arrays are big enough */
for (i = 0; (i < natoms); i++)
{
- if ((fgets2(line, STRLEN, in)) == NULL)
+ if ((fgets2(line, STRLEN, in)) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of file in file %s at line %d",
infile, i+2);
{
bFirst = FALSE;
p1 = strchr(line, '.');
- if (p1 == NULL)
+ if (p1 == nullptr)
{
gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
}
p2 = strchr(&p1[1], '.');
- if (p2 == NULL)
+ if (p2 == nullptr)
{
gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
}
*ndec = ddist - 5;
p3 = strchr(&p2[1], '.');
- if (p3 == NULL)
+ if (p3 == nullptr)
{
gmx_fatal(FARGS, "A coordinate in file %s does not contain a '.'", infile);
}
}
void gmx_gro_read_conf(const char *infile,
- t_topology *top, rvec x[], rvec *v, matrix box)
+ t_symtab *symtab, char **name, t_atoms *atoms,
+ rvec x[], rvec *v, matrix box)
{
FILE *in = gmx_fio_fopen(infile, "r");
int ndec;
char title[STRLEN];
- get_w_conf(in, infile, title, &top->symtab, &top->atoms, &ndec, x, v, box);
- top->name = put_symtab(&top->symtab, title);
+ get_w_conf(in, infile, title, symtab, atoms, &ndec, x, v, box);
+ if (name != nullptr)
+ {
+ *name = gmx_strdup(title);
+ }
gmx_fio_fclose(in);
}
{
fr->prec *= 10;
}
- fr->title = title;
- fr->bTitle = TRUE;
fr->bX = TRUE;
fr->bBox = TRUE;
sfree(atoms.atomname);
done_symtab(&symtab);
- if ((p = strstr(title, "t=")) != NULL)
+ if ((p = strstr(title, "t=")) != nullptr)
{
p += 2;
if (sscanf(p, "%lf", &tt) == 1)
get_coordnum_fp(status, title, &fr->natoms);
frewind(status);
fprintf(stderr, " '%s', %d atoms.\n", title, fr->natoms);
- fr->bTitle = TRUE;
- fr->title = title;
if (fr->natoms == 0)
{
gmx_file("No coordinates in gro file");
fprintf(out, "%s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
fprintf(out, "%5d\n", nx);
- const char *format = get_hconf_format(v != NULL);
+ const char *format = get_hconf_format(v != nullptr);
for (i = 0; (i < nx); i++)
{
{
int i, resnr;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
+ const t_atom *atom;
char *atomname, *resname;
fprintf(out, "%s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
fprintf(out, "%5d\n", mtop->natoms);
- const char *format = get_hconf_format(v != NULL);
+ const char *format = get_hconf_format(v != nullptr);
aloop = gmx_mtop_atomloop_all_init(mtop);
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_mtop_t;
struct t_atoms;
-struct t_topology;
+struct t_symtab;
struct t_trxframe;
void get_coordnum(const char *infile, int *natoms);
void gmx_gro_read_conf(const char *infile,
- struct t_topology *top, rvec x[], rvec *v, matrix box);
+ t_symtab *symtab, char **name, t_atoms *atoms,
+ rvec x[], rvec *v, matrix box);
+/* If name is not nullptr, gmx_strdup the title string into it. */
gmx_bool gro_next_x_or_v(FILE *status, struct t_trxframe *fr);
int gro_first_x_or_v(FILE *status, struct t_trxframe *fr);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int xdr3dfcoord(XDR *xdrs, float *fp, int *size, float *precision)
{
- int *ip = NULL;
- int *buf = NULL;
+ int *ip = nullptr;
+ int *buf = nullptr;
gmx_bool bRead;
/* preallocate a small buffer and ip on the stack - if we need more
bufsize = static_cast<int>(size3 * 1.2);
ip = reinterpret_cast<int *>(malloc(size3 * sizeof(*ip)));
buf = reinterpret_cast<int *>(malloc(bufsize * sizeof(*buf)));
- if (ip == NULL || buf == NULL)
+ if (ip == nullptr || buf == nullptr)
{
fprintf(stderr, "malloc failed\n");
exit(1);
bufsize = static_cast<int>(size3 * 1.2);
ip = reinterpret_cast<int *>(malloc(size3 * sizeof(*ip)));
buf = reinterpret_cast<int *>(malloc(bufsize * sizeof(*buf)));
- if (ip == NULL || buf == NULL)
+ if (ip == nullptr || buf == nullptr)
{
fprintf(stderr, "malloc failed\n");
exit(1);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <string>
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/math/utilities.h"
sfree((*m)[i]);
}
sfree(*m);
- *m = NULL;
+ *m = nullptr;
}
gmx_bool matelmt_cmp(t_xpmelmt e1, t_xpmelmt e2)
double r, g, b;
t_mapping *m;
- if (fgets2(line, STRLEN-1, in) == NULL)
+ if (fgets2(line, STRLEN-1, in) == nullptr)
{
gmx_fatal(FARGS, "Not enough lines in colormap file %s"
"(just wanted to read number of entries)", fn);
snew(m, n);
for (i = 0; (i < n); i++)
{
- if (fgets2(line, STRLEN-1, in) == NULL)
+ if (fgets2(line, STRLEN-1, in) == nullptr)
{
gmx_fatal(FARGS, "Not enough lines in colormap file %s"
"(should be %d, found only %d)", fn, n+1, i);
{
int i;
- if (*line != NULL)
+ if (*line != nullptr)
{
while (((*line)[0] != '\"' ) && ( (*line)[0] != '\0' ))
{
if ((*line)[0] != '\"')
{
- return NULL;
+ return nullptr;
}
(*line)++;
if ((*line)[i] != '\"')
{
- *line = NULL;
+ *line = nullptr;
}
else
{
static void read_xpm_entry(FILE *in, t_matrix *mm)
{
t_mapping *map;
- char *line_buf = NULL, *line = NULL, *str, buf[256] = {0};
+ char *line_buf = nullptr, *line = nullptr, *str, buf[256] = {0};
int i, m, col_len, nch = 0, n_axis_x, n_axis_y, llmax;
int llalloc = 0;
unsigned int r, g, b;
mm->legend[0] = 0;
mm->label_x[0] = 0;
mm->label_y[0] = 0;
- mm->matrix = NULL;
- mm->axis_x = NULL;
- mm->axis_y = NULL;
+ mm->matrix = nullptr;
+ mm->axis_x = nullptr;
+ mm->axis_y = nullptr;
mm->bDiscrete = FALSE;
llmax = STRLEN;
- while ((NULL != fgetline(&line_buf, llmax, &llalloc, in)) &&
+ while ((nullptr != fgetline(&line_buf, llmax, &llalloc, in)) &&
(std::strncmp(line_buf, "static", 6) != 0))
{
line = line_buf;
/* Read sizes */
bGetOnWithIt = FALSE;
- while (!bGetOnWithIt && (NULL != fgetline(&line_buf, llmax, &llalloc, in)))
+ while (!bGetOnWithIt && (nullptr != fgetline(&line_buf, llmax, &llalloc, in)))
{
line = line_buf;
while (( line[0] != '\"' ) && ( line[0] != '\0' ))
/* Read color map */
snew(map, mm->nmap);
m = 0;
- while ((m < mm->nmap) && (NULL != fgetline(&line_buf, llmax, &llalloc, in)))
+ while ((m < mm->nmap) && (nullptr != fgetline(&line_buf, llmax, &llalloc, in)))
{
line = std::strchr(line_buf, '\"');
if (line)
{
line = std::strstr(line, "x-axis");
skipstr(line);
- if (mm->axis_x == NULL)
+ if (mm->axis_x == nullptr)
{
snew(mm->axis_x, mm->nx + 1);
}
{
line = std::strstr(line, "y-axis");
skipstr(line);
- if (mm->axis_y == NULL)
+ if (mm->axis_y == nullptr)
{
snew(mm->axis_y, mm->ny + 1);
}
}
}
}
- while ((line[0] != '\"') && (NULL != fgetline(&line_buf, llmax, &llalloc, in)));
+ while ((line[0] != '\"') && (nullptr != fgetline(&line_buf, llmax, &llalloc, in)));
/* Read matrix */
snew(mm->matrix, mm->nx);
m--;
}
}
- while ((m >= 0) && (NULL != fgetline(&line_buf, llmax, &llalloc, in)));
+ while ((m >= 0) && (nullptr != fgetline(&line_buf, llmax, &llalloc, in)));
if (m >= 0)
{
gmx_incons("Not enough rows in the matrix");
int read_xpm_matrix(const char *fnm, t_matrix **mat)
{
FILE *in;
- char *line = NULL;
+ char *line = nullptr;
int nmat;
int llalloc = 0;
in = gmx_fio_fopen(fnm, "r");
nmat = 0;
- while (NULL != fgetline(&line, STRLEN, &llalloc, in))
+ while (nullptr != fgetline(&line, STRLEN, &llalloc, in))
{
if (std::strstr(line, "/* XPM */"))
{
for (i = 0; i < nmap; i++)
{
- if ((map[i].desc == NULL) || (sscanf(map[i].desc, "%lf", &tmp) != 1))
+ if ((map[i].desc == nullptr) || (sscanf(map[i].desc, "%lf", &tmp) != 1))
{
fprintf(stderr, "Could not convert matrix to reals,\n"
"color map entry %d has a non-real description: \"%s\"\n",
i, map[i].desc);
sfree(rmap);
- return NULL;
+ return nullptr;
}
rmap[i] = tmp;
}
- if (out == NULL)
+ if (out == nullptr)
{
snew(out, in->nx);
for (i = 0; i < in->nx; i++)
gmx_bool bDiscrete)
{
fprintf(out, "/* XPM */\n");
- try
- {
- gmx::BinaryInformationSettings settings;
- settings.generatedByHeader(true);
- settings.linePrefix("/* ");
- settings.lineSuffix(" */");
- gmx::printBinaryInformation(out, gmx::getProgramContext(),
- settings);
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
fprintf(out, "/* This file can be converted to EPS by the GROMACS program xpm2ps */\n");
fprintf(out, "/* title: \"%s\" */\n", title);
fprintf(out, "/* legend: \"%s\" */\n", legend);
t_rgb rlo, t_rgb rmid, t_rgb rhi)
{
int i, nmid;
- real r, g, b, clev_lo, clev_hi;
+ double r, g, b, clev_lo, clev_hi;
if (*nlevels > NMAP*NMAP)
{
fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
mapper[i % NMAP],
(*nlevels <= NMAP) ? ' ' : mapper[i/NMAP],
- static_cast<unsigned int>(round(255*r)),
- static_cast<unsigned int>(round(255*g)),
- static_cast<unsigned int>(round(255*b)),
+ static_cast<unsigned int>(std::round(255*r)),
+ static_cast<unsigned int>(std::round(255*g)),
+ static_cast<unsigned int>(std::round(255*b)),
((nmid - i)*lo + i*mid)/clev_lo);
}
for (i = 0; (i < (*nlevels-nmid)); i++)
fprintf(out, "\"%c%c c #%02X%02X%02X \" /* \"%.3g\" */,\n",
mapper[(i+nmid) % NMAP],
(*nlevels <= NMAP) ? ' ' : mapper[(i+nmid)/NMAP],
- static_cast<unsigned int>(round(255*r)),
- static_cast<unsigned int>(round(255*g)),
- static_cast<unsigned int>(round(255*b)),
+ static_cast<unsigned int>(std::round(255*r)),
+ static_cast<unsigned int>(std::round(255*g)),
+ static_cast<unsigned int>(std::round(255*b)),
((*nlevels - 1 - nmid - i)*mid + i*hi)/clev_hi);
}
}
}
void write_xpm3(FILE *out, unsigned int flags,
- const char *title, const char *legend,
- const char *label_x, const char *label_y,
+ const std::string &title, const std::string &legend,
+ const std::string &label_x, const std::string &label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
real *mat[], real lo, real mid, real hi,
t_rgb rlo, t_rgb rmid, t_rgb rhi, int *nlevels)
gmx_fatal(FARGS, "hi (%g) <= lo (%g)", hi, lo);
}
- write_xpm_header(out, title, legend, label_x, label_y, FALSE);
+ write_xpm_header(out, title.c_str(), legend.c_str(), label_x.c_str(), label_y.c_str(), FALSE);
write_xpm_map3(out, n_x, n_y, nlevels, lo, mid, hi, rlo, rmid, rhi);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
}
void write_xpm_split(FILE *out, unsigned int flags,
- const char *title, const char *legend,
- const char *label_x, const char *label_y,
+ const std::string &title, const std::string &legend,
+ const std::string &label_x, const std::string &label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
real *mat[],
real lo_top, real hi_top, int *nlevel_top,
gmx_impl("Can not plot more than 16 discrete colors");
}
- write_xpm_header(out, title, legend, label_x, label_y, FALSE);
+ write_xpm_header(out, title.c_str(), legend.c_str(), label_x.c_str(), label_y.c_str(), FALSE);
write_xpm_map_split(out, n_x, n_y, nlevel_top, lo_top, hi_top, rlo_top, rhi_top,
bDiscreteColor, nlevel_bot, lo_bot, hi_bot, rlo_bot, rhi_bot);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
}
void write_xpm(FILE *out, unsigned int flags,
- const char *title, const char *legend,
- const char *label_x, const char *label_y,
+ const std::string &title, const std::string &legend,
+ const std::string &label_x, const std::string &label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
real *mat[], real lo, real hi,
t_rgb rlo, t_rgb rhi, int *nlevels)
gmx_fatal(FARGS, "hi (%f) <= lo (%f)", hi, lo);
}
- write_xpm_header(out, title, legend, label_x, label_y, FALSE);
+ write_xpm_header(out, title.c_str(), legend.c_str(), label_x.c_str(), label_y.c_str(), FALSE);
write_xpm_map(out, n_x, n_y, nlevels, lo, hi, rlo, rhi);
write_xpm_axis(out, "x", flags & MAT_SPATIAL_X, n_x, axis_x);
write_xpm_axis(out, "y", flags & MAT_SPATIAL_Y, n_y, axis_y);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
+#include <string>
+
#include "gromacs/fileio/rgb.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
/* Writes a t_matrix struct to .xpm file */
void write_xpm3(FILE *out, unsigned int flags,
- const char *title, const char *legend,
- const char *label_x, const char *label_y,
+ const std::string &title, const std::string &legend,
+ const std::string &label_x, const std::string &label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
real *mat[], real lo, real mid, real hi,
t_rgb rlo, t_rgb rmid, t_rgb rhi, int *nlevels);
* Writes a colormap varying as rlo -> rmid -> rhi.
*/
void write_xpm_split(FILE *out, unsigned int flags,
- const char *title, const char *legend,
- const char *label_x, const char *label_y,
+ const std::string &title, const std::string &legend,
+ const std::string &label_x, const std::string &label_y,
int n_x, int n_y, real axis_x[], real axis_y[],
real *mat[],
real lo_top, real hi_top, int *nlevel_top,
*/
void write_xpm(FILE *out, unsigned int flags,
- const char *title, const char *legend,
- const char *label_x, const char *label_y,
+ const std::string &title, const std::string &legend,
+ const std::string &label_x, const std::string &label_y,
int n_x, int n_y, real t_x[], real t_y[],
real *mat[], real lo, real hi,
t_rgb rlo, t_rgb rhi, int *nlevels);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int i, j, prec;
size_t sz;
- if (full_matrix != NULL && sparse_matrix != NULL)
+ if (full_matrix != nullptr && sparse_matrix != nullptr)
{
gmx_fatal(FARGS, "Both full AND sparse matrix specified to gmx_mtxio_write().\n");
}
gmx_fio_do_int(fio, nrow);
gmx_fio_do_int(fio, ncol);
- if (full_matrix != NULL)
+ if (full_matrix != nullptr)
{
/* Full matrix storage format */
i = GMX_MTXIO_FULL_MATRIX;
gmx_fio_do_int(fio, i);
- if (i == GMX_MTXIO_FULL_MATRIX && NULL != full_matrix)
+ if (i == GMX_MTXIO_FULL_MATRIX && nullptr != full_matrix)
{
printf("Full matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
snew((*full_matrix), sz);
gmx_fio_ndo_real(fio, (*full_matrix), sz);
}
- else if (NULL != sparse_matrix)
+ else if (nullptr != sparse_matrix)
{
/* Sparse storage */
printf("Sparse matrix storage format, nrow=%d, ncols=%d\n", *nrow, *ncol);
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
struct gmx_output_env_t
{
explicit gmx_output_env_t(const gmx::IProgramContext &context)
- : programContext(context)
- {
- time_unit = time_ps;
- view = FALSE;
- xvg_format = exvgNONE;
- verbosity = 0;
- trajectory_io_verbosity = 1;
- }
+ : programContext(context),
+ time_unit(time_ps),
+ view(FALSE),
+ xvg_format(exvgNONE),
+ verbosity(0),
+ trajectory_io_verbosity(0) {}
+
const gmx::IProgramContext &programContext;
static const real timefactors[] = { real(0), real(1e3), real(1), real(1e-3), real(1e-6), real(1e-9), real(1e-12), real(0) };
static const real timeinvfactors[] = { real(0), real(1e-3), real(1), real(1e3), real(1e6), real(1e9), real(1e12), real(0) };
static const char *time_units_str[] = {
- NULL, "fs", "ps", "ns", "us",
+ nullptr, "fs", "ps", "ns", "us",
"\\mus", "ms", "s"
};
static const char *time_units_xvgr[] = {
- NULL, "fs", "ps", "ns",
- "ms", "s", NULL
+ nullptr, "fs", "ps", "ns",
+ "ms", "s", nullptr
};
return oenv->trajectory_io_verbosity;
}
-const char *output_env_get_time_unit(const gmx_output_env_t *oenv)
+std::string output_env_get_time_unit(const gmx_output_env_t *oenv)
{
return time_units_str[oenv->time_unit];
}
-const char *output_env_get_time_label(const gmx_output_env_t *oenv)
+std::string output_env_get_time_label(const gmx_output_env_t *oenv)
{
- char *label;
- snew(label, 20);
-
- sprintf(label, "Time (%s)", time_units_str[oenv->time_unit] ?
- time_units_str[oenv->time_unit] : "ps");
-
- return label;
+ return gmx::formatString("Time (%s)", time_units_str[oenv->time_unit] ?
+ time_units_str[oenv->time_unit] : "ps");
}
-const char *output_env_get_xvgr_tlabel(const gmx_output_env_t *oenv)
+std::string output_env_get_xvgr_tlabel(const gmx_output_env_t *oenv)
{
- char *label;
- snew(label, 20);
-
- sprintf(label, "Time (%s)", time_units_xvgr[oenv->time_unit] ?
- time_units_xvgr[oenv->time_unit] : "ps");
-
- return label;
+ return gmx::formatString("Time (%s)", time_units_xvgr[oenv->time_unit] ?
+ time_units_xvgr[oenv->time_unit] : "ps");
}
real output_env_get_time_factor(const gmx_output_env_t *oenv)
const char *output_env_get_program_display_name(const gmx_output_env_t *oenv)
{
- const char *displayName = NULL;
+ const char *displayName = nullptr;
try
{
#ifndef GMX_FILEIO_OENV_H
#define GMX_FILEIO_OENV_H
+#include <string>
+
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
struct gmx_output_env_t;
/* output_env member functions */
int output_env_get_trajectory_io_verbosity(const gmx_output_env_t *oenv);
/* return the verbosity for trajectory IO handling */
-const char *output_env_get_time_unit(const gmx_output_env_t *oenv);
+std::string output_env_get_time_unit(const gmx_output_env_t *oenv);
/* return time unit (e.g. ps or ns) */
-const char *output_env_get_time_label(const gmx_output_env_t *oenv);
+std::string output_env_get_time_label(const gmx_output_env_t *oenv);
/* return time unit label (e.g. "Time (ps)") */
-const char *output_env_get_xvgr_tlabel(const gmx_output_env_t *oenv);
-/* retrun x-axis time label for xmgr */
+std::string output_env_get_xvgr_tlabel(const gmx_output_env_t *oenv);
+/* return x-axis time label for xmgr */
real output_env_get_time_factor(const gmx_output_env_t *oenv);
/* return time conversion factor from ps (i.e. 1e-3 for ps->ns) */
*/
const char *output_env_get_program_display_name(const gmx_output_env_t *oenv);
-#ifdef __cplusplus
-}
-
namespace gmx
{
class IProgramContext;
output_env_get_program_context(const gmx_output_env_t *oenv);
#endif
-
-#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
sscanf(sg, "%c %d %d %d", &ident, &syma, &symb, &symc);
if (ident == 'P' && syma == 1 && symb <= 1 && symc <= 1)
{
- fc = strtod(sc, NULL)*0.1;
+ fc = strtod(sc, nullptr)*0.1;
ePBC_file = (fc > 0 ? epbcXYZ : epbcXY);
}
if (ident == 'P' && syma == 21 && symb == 1 && symc == 1)
if (box)
{
- fa = strtod(sa, NULL)*0.1;
- fb = strtod(sb, NULL)*0.1;
- fc = strtod(sc, NULL)*0.1;
+ fa = strtod(sa, nullptr)*0.1;
+ fb = strtod(sb, nullptr)*0.1;
+ fc = strtod(sc, nullptr)*0.1;
if (ePBC_file == epbcSCREW)
{
fa *= 0.5;
{
gmx_write_pdb_box(out, ePBC, box);
}
- if (atoms->pdbinfo)
+ if (atoms->havePdbInfo)
{
/* Check whether any occupancies are set, in that case leave it as is,
* otherwise set them all to one
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
lastchainnum = -1;
- p_restype = NULL;
+ p_restype = nullptr;
for (ii = 0; ii < nindex; ii++)
{
fprintf(out, "TER\n");
fprintf(out, "ENDMDL\n");
- if (NULL != gc)
+ if (nullptr != gc)
{
/* Write conect records */
for (i = 0; (i < gc->nconect); i++)
sfree(index);
}
-int line2type(char *line)
+static int line2type(char *line)
{
int k;
char type[8];
trim(anm);
/* Search backwards for number and name only */
- atomnr = std::strtol(anr, NULL, 10);
+ atomnr = std::strtol(anr, nullptr, 10);
for (i = natom-1; (i >= 0); i--)
{
if ((std::strcmp(anm, *(atoms->atomname[i])) == 0) &&
}
else
{
- ptr = NULL;
+ ptr = nullptr;
}
- std::strncpy(atoms->atom[i].elem, ptr == NULL ? "" : ptr, 4);
+ std::strncpy(atoms->atom[i].elem, ptr == nullptr ? "" : ptr, 4);
}
}
}
rnr[k] = nc;
trim(rnr);
- resnr = std::strtol(rnr, NULL, 10);
+ resnr = std::strtol(rnr, nullptr, 10);
resic = line[j];
j += 4;
atomn->atomnumber = atomnumber;
strncpy(atomn->elem, elem, 4);
}
- x[natom][XX] = strtod(xc, NULL)*0.1;
- x[natom][YY] = strtod(yc, NULL)*0.1;
- x[natom][ZZ] = strtod(zc, NULL)*0.1;
+ x[natom][XX] = strtod(xc, nullptr)*0.1;
+ x[natom][YY] = strtod(yc, nullptr)*0.1;
+ x[natom][ZZ] = strtod(zc, nullptr)*0.1;
if (atoms->pdbinfo)
{
atoms->pdbinfo[natom].type = type;
- atoms->pdbinfo[natom].atomnr = strtol(anr, NULL, 10);
+ atoms->pdbinfo[natom].atomnr = strtol(anr, nullptr, 10);
atoms->pdbinfo[natom].altloc = altloc;
strcpy(atoms->pdbinfo[natom].atomnm, anm_copy);
- atoms->pdbinfo[natom].bfac = strtod(bfac, NULL);
- atoms->pdbinfo[natom].occup = strtod(occup, NULL);
+ atoms->pdbinfo[natom].bfac = strtod(bfac, nullptr);
+ atoms->pdbinfo[natom].occup = strtod(occup, nullptr);
}
natom++;
/* Only assume pbc when there is a CRYST1 entry */
*ePBC = epbcNONE;
}
- if (box != NULL)
+ if (box != nullptr)
{
clear_mat(box);
}
+ atoms->haveMass = FALSE;
+ atoms->haveCharge = FALSE;
+ atoms->haveType = FALSE;
+ atoms->haveBState = FALSE;
+ atoms->havePdbInfo = (atoms->pdbinfo != nullptr);
+
bCOMPND = FALSE;
title[0] = '\0';
natom = 0;
chainnum = 0;
- while (!bStop && (fgets2(line, STRLEN, in) != NULL))
+ while (!bStop && (fgets2(line, STRLEN, in) != nullptr))
{
line_type = line2type(line);
break;
case epdbANISOU:
- if (atoms->pdbinfo)
+ if (atoms->havePdbInfo)
{
read_anisou(line, natom, atoms);
}
}
void gmx_pdb_read_conf(const char *infile,
- t_topology *top, rvec x[], int *ePBC, matrix box)
+ t_symtab *symtab, char **name, t_atoms *atoms,
+ rvec x[], int *ePBC, matrix box)
{
FILE *in = gmx_fio_fopen(infile, "r");
char title[STRLEN];
- read_pdbfile(in, title, NULL, &top->atoms, &top->symtab, x, ePBC, box, TRUE, NULL);
- top->name = put_symtab(&top->symtab, title);
+ read_pdbfile(in, title, nullptr, atoms, symtab, x, ePBC, box, TRUE, nullptr);
+ if (name != nullptr)
+ {
+ *name = gmx_strdup(title);
+ }
gmx_fio_fclose(in);
}
}
/* Format atom name */
- if (atom_name != NULL)
+ if (atom_name != nullptr)
{
/* If the atom name is an element name with two chars, it should start already in column 13.
* Otherwise it should start in column 14, unless the name length is 4 chars.
*/
- if ( (element != NULL) && (std::strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
+ if ( (element != nullptr) && (std::strlen(element) >= 2) && (gmx_strncasecmp(atom_name, element, 2) == 0) )
{
start_name_in_col13 = TRUE;
}
}
/* Format residue name */
- std::strncpy(tmp_resname, (res_name != NULL) ? res_name : "", 4);
+ std::strncpy(tmp_resname, (res_name != nullptr) ? res_name : "", 4);
/* Make sure the string is terminated if strlen was > 4 */
tmp_resname[4] = '\0';
/* String is properly terminated, so now we can use strcat. By adding a
x, y, z,
occupancy,
b_factor,
- (element != NULL) ? element : "");
+ (element != nullptr) ? element : "");
return n;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
void gmx_pdb_read_conf(const char *infile,
- struct t_topology *top, rvec x[], int *ePBC, matrix box);
+ t_symtab *symtab, char **name, t_atoms *atoms,
+ rvec x[], int *ePBC, matrix box);
/* Read a pdb file and extract ATOM and HETATM fields.
* Read a box from the CRYST1 line, return 0 box when no CRYST1 is found.
* ePBC may be NULL.
- */
+ *
+ * If name is not nullptr, gmx_strdup the title string into it. */
void get_pdb_coordnum(FILE *in, int *natoms);
/* Read a pdb file and count the ATOM and HETATM fields. */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "readinp.h"
-#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <algorithm>
-#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/warninp.h"
-#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/binaryinformation.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/niceheader.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/qsort_threadsafe.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textreader.h"
+#include "gromacs/utility/textwriter.h"
-t_inpfile *read_inpfile(const char *fn, int *ninp,
+t_inpfile *read_inpfile(gmx::TextInputStream *stream, const char *fn, int *ninp,
warninp_t wi)
{
- FILE *in;
- char buf[STRLEN], lbuf[STRLEN], rbuf[STRLEN], warn_buf[STRLEN];
- char *ptr, *cptr;
- t_inpfile *inp = NULL;
- int nin, lc, i, j, k;
- /* setting cppopts from command-line options would be cooler */
- gmx_bool allow_override = FALSE;
-
+ t_inpfile *inp = nullptr;
if (debug)
{
fprintf(debug, "Reading MDP file %s\n", fn);
}
- in = gmx_ffopen(fn, "r");
-
- nin = lc = 0;
- do
+ int indexOfLineReadFromFile = 0;
+ int countOfUniqueKeysFound = 0;
+ std::string line;
+ gmx::TextReader reader(stream);
+ reader.setTrimTrailingWhiteSpace(true);
+ reader.setTrimTrailingComment(true, ';');
+ while (reader.readLine(&line))
{
- ptr = fgets2(buf, STRLEN-1, in);
- lc++;
- set_warning_line(wi, fn, lc);
- if (ptr)
+ indexOfLineReadFromFile++;
+ set_warning_line(wi, fn, indexOfLineReadFromFile);
+
+ if (line.empty())
{
- // TODO This parsing should be using strip_comment, trim,
- // strchr, etc. rather than re-inventing wheels.
+ continue;
+ }
- /* Strip comment */
- if ((cptr = std::strchr(buf, COMMENTSIGN)) != NULL)
+ auto tokens = gmx::splitAndTrimDelimitedString(line, '=');
+ if (tokens.size() < 2)
+ {
+ // TODO this seems like it silently ignores the user accidentally deleting an equals sign...
+ if (debug)
{
- *cptr = '\0';
+ fprintf(debug, "No = on line %d in file %s, ignored\n", indexOfLineReadFromFile, fn);
}
- /* Strip spaces */
- trim(buf);
-
- for (j = 0; (buf[j] != '=') && (buf[j] != '\0'); j++)
+ continue;
+ }
+ if (tokens.size() > 2)
+ {
+ // TODO ignoring such lines does not seem like good behaviour
+ if (debug)
{
- ;
+ fprintf(debug, "Multiple equals signs on line %d in file %s, ignored\n", indexOfLineReadFromFile, fn);
}
- if (buf[j] == '\0')
+ continue;
+ }
+ if (tokens[0].empty())
+ {
+ // TODO ignoring such lines does not seem like good behaviour
+ if (debug)
{
- if (j > 0)
- {
- if (debug)
- {
- fprintf(debug, "No = on line %d in file %s, ignored\n", lc, fn);
- }
- }
+ fprintf(debug, "Empty left hand side on line %d in file %s, ignored\n", indexOfLineReadFromFile, fn);
}
- else
+ continue;
+ }
+ if (tokens[1].empty())
+ {
+ // TODO ignoring such lines does not seem like good behaviour
+ if (debug)
{
- for (i = 0; (i < j); i++)
- {
- lbuf[i] = buf[i];
- }
- lbuf[i] = '\0';
- trim(lbuf);
- if (lbuf[0] == '\0')
- {
- if (debug)
- {
- fprintf(debug, "Empty left hand side on line %d in file %s, ignored\n", lc, fn);
- }
- }
- else
- {
- for (i = j+1, k = 0; (buf[i] != '\0'); i++, k++)
- {
- rbuf[k] = buf[i];
- }
- rbuf[k] = '\0';
- trim(rbuf);
- if (rbuf[0] == '\0')
- {
- if (debug)
- {
- fprintf(debug, "Empty right hand side on line %d in file %s, ignored\n", lc, fn);
- }
- }
- else
- {
- /* Now finally something sensible */
- int found_index;
-
- /* first check whether we hit the 'multiple_entries' option */
- if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptName], lbuf) == 0)
- {
- /* we now check whether to allow overrides from here or not */
- if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptNo], rbuf) == 0)
- {
- allow_override = FALSE;
- }
- else if (gmx_strcasecmp_min(eMultentOpt_names[eMultentOptLast], rbuf) == 0)
- {
- allow_override = TRUE;
- }
- else
- {
- sprintf(warn_buf,
- "Parameter \"%s\" should either be %s or %s\n",
- lbuf,
- eMultentOpt_names[eMultentOptNo],
- eMultentOpt_names[eMultentOptLast]);
- warning_error(wi, warn_buf);
- }
- }
- else
- {
- /* it is a regular option; check for duplicates */
- found_index = search_einp(nin, inp, lbuf);
-
- if (found_index == -1)
- {
- /* add a new item */
- srenew(inp, ++nin);
- inp[nin-1].inp_count = 1;
- inp[nin-1].count = 0;
- inp[nin-1].bObsolete = FALSE;
- inp[nin-1].bSet = FALSE;
- inp[nin-1].name = gmx_strdup(lbuf);
- inp[nin-1].value = gmx_strdup(rbuf);
- }
- else
- {
- if (!allow_override)
- {
- sprintf(warn_buf,
- "Parameter \"%s\" doubly defined (and multiple assignments not allowed)\n",
- lbuf);
- warning_error(wi, warn_buf);
- }
- else
- {
- /* override */
- if (!inp)
- {
- gmx_fatal(FARGS, "Internal inconsistency; inp[] base pointer is NULL");
- }
- sfree(inp[found_index].value);
- inp[found_index].value = gmx_strdup(rbuf);
- sprintf(warn_buf,
- "Overriding existing parameter \"%s\" with value \"%s\"\n",
- lbuf, rbuf);
- warning_note(wi, warn_buf);
- }
- }
- }
- }
- }
+ fprintf(debug, "Empty right hand side on line %d in file %s, ignored\n", indexOfLineReadFromFile, fn);
}
+ continue;
}
- }
- while (ptr);
- gmx_ffclose(in);
+ /* Now finally something sensible; check for duplicates */
+ int found_index = search_einp(countOfUniqueKeysFound, inp, tokens[0].c_str());
+
+ if (found_index == -1)
+ {
+ /* add a new item */
+ srenew(inp, ++countOfUniqueKeysFound);
+ inp[countOfUniqueKeysFound-1].inp_count = 1;
+ inp[countOfUniqueKeysFound-1].count = 0;
+ inp[countOfUniqueKeysFound-1].bObsolete = FALSE;
+ inp[countOfUniqueKeysFound-1].bHandledAsKeyValueTree = FALSE;
+ inp[countOfUniqueKeysFound-1].bSet = FALSE;
+ inp[countOfUniqueKeysFound-1].name = gmx_strdup(tokens[0].c_str());
+ inp[countOfUniqueKeysFound-1].value = gmx_strdup(tokens[1].c_str());
+ }
+ else
+ {
+ auto message = gmx::formatString("Parameter \"%s\" doubly defined\n",
+ tokens[0].c_str());
+ warning_error(wi, message.c_str());
+ }
+ }
+ /* This preserves the behaviour of the old code, which issues some
+ warnings after completing parsing. Regenerating regressiontest
+ warning files is not worth the effort. */
+ indexOfLineReadFromFile++;
+ set_warning_line(wi, fn, indexOfLineReadFromFile);
if (debug)
{
fprintf(debug, "Done reading MDP file, there were %d entries in there\n",
- nin);
+ countOfUniqueKeysFound);
}
- *ninp = nin;
+ *ninp = countOfUniqueKeysFound;
return inp;
}
-
+gmx::KeyValueTreeObject flatKeyValueTreeFromInpFile(int ninp, t_inpfile inp[])
+{
+ gmx::KeyValueTreeBuilder builder;
+ auto root = builder.rootObject();
+ for (int i = 0; i < ninp; ++i)
+ {
+ const char *value = inp[i].value;
+ root.addValue<std::string>(inp[i].name, value != nullptr ? value : "");
+ }
+ return builder.build();
+}
static int inp_comp(const void *a, const void *b)
gmx_qsort(inp, ninp, static_cast<size_t>(sizeof(inp[0])), inp_comp);
}
-void write_inpfile(const char *fn, int ninp, t_inpfile inp[], gmx_bool bHaltOnUnknown,
+void write_inpfile(gmx::TextOutputStream *stream, const char *fn, int ninp, t_inpfile inp[],
+ gmx_bool bHaltOnUnknown,
+ WriteMdpHeader writeHeader,
warninp_t wi)
{
- FILE *out;
- int i;
- char warn_buf[STRLEN];
+ using gmx::formatString;
sort_inp(ninp, inp);
- out = gmx_fio_fopen(fn, "w");
- nice_header(out, fn);
- try
+
+ gmx::TextWriter writer(stream);
+ if (writeHeader == WriteMdpHeader::yes)
{
+ gmx::niceHeader(&writer, fn, ';');
+
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix(";\t");
- gmx::printBinaryInformation(out, gmx::getProgramContext(), settings);
+ gmx::printBinaryInformation(&writer, gmx::getProgramContext(), settings);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- for (i = 0; (i < ninp); i++)
+ for (int i = 0; (i < ninp); i++)
{
- if (inp[i].bSet)
+ if (inp[i].bHandledAsKeyValueTree)
+ {
+ }
+ else if (inp[i].bSet)
{
if (inp[i].name[0] == ';' || (strlen(inp[i].name) > 2 && inp[i].name[1] == ';'))
{
- fprintf(out, "%-24s\n", inp[i].name);
+ writer.writeLine(formatString("%-24s", inp[i].name));
}
else
{
- fprintf(out, "%-24s = %s\n", inp[i].name, inp[i].value ? inp[i].value : "");
+ writer.writeLine(formatString("%-24s = %s", inp[i].name, inp[i].value ? inp[i].value : ""));
}
}
else if (!inp[i].bObsolete)
{
- sprintf(warn_buf, "Unknown left-hand '%s' in parameter file\n",
- inp[i].name);
+ auto message = formatString("Unknown left-hand '%s' in parameter file\n",
+ inp[i].name);
if (bHaltOnUnknown)
{
- warning_error(wi, warn_buf);
+ warning_error(wi, message.c_str());
}
else
{
- warning(wi, warn_buf);
+ warning(wi, message.c_str());
}
}
}
- gmx_fio_fclose(out);
check_warning_error(wi, FARGS);
}
{
int i;
- if (inp == NULL)
+ if (inp == nullptr)
{
return -1;
}
return -1;
}
+void mark_einp_set(int ninp, t_inpfile *inp, const char *name)
+{
+ int i = search_einp(ninp, inp, name);
+ if (i != -1)
+ {
+ inp[i].count = inp[0].inp_count++;
+ inp[i].bSet = TRUE;
+ /* Prevent mdp lines being written twice for
+ options that are handled via key-value trees. */
+ inp[i].bHandledAsKeyValueTree = TRUE;
+
+ }
+}
+
static int get_einp(int *ninp, t_inpfile **inp, const char *name)
{
int i;
notfound = TRUE;
i = (*ninp)++;
srenew(*inp, (*ninp));
- (*inp)[i].name = gmx_strdup(name);
- (*inp)[i].bSet = TRUE;
+ (*inp)[i].name = gmx_strdup(name);
+ (*inp)[i].bSet = TRUE;
+ (*inp)[i].bHandledAsKeyValueTree = FALSE;
+ if (i == 0)
+ {
+ (*inp)[i].inp_count = 1;
+ }
}
(*inp)[i].count = (*inp)[0].inp_count++;
(*inp)[i].bSet = TRUE;
}
else
{
- (*inp)[(*ninp)-1].value = NULL;
+ (*inp)[(*ninp)-1].value = nullptr;
}
return def;
return 0;
}
- for (i = 0; (defs[i] != NULL); i++)
+ for (i = 0; (defs[i] != nullptr); i++)
{
if (gmx_strcasecmp_min(defs[i], (*inp)[ii].value) == 0)
{
}
}
- if (defs[i] == NULL)
+ if (defs[i] == nullptr)
{
n += sprintf(buf, "Invalid enum '%s' for variable %s, using '%s'\n",
(*inp)[ii].value, name, defs[0]);
n += sprintf(buf+n, " '%s'", defs[j]);
j++;
}
- if (wi != NULL)
+ if (wi != nullptr)
{
warning_error(wi, buf);
}
int get_eenum(int *ninp, t_inpfile **inp, const char *name, const char **defs)
{
- return get_eeenum(ninp, inp, name, defs, NULL);
+ return get_eeenum(ninp, inp, name, defs, nullptr);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
-#include "gromacs/fileio/warninp.h"
#include "gromacs/utility/basedefinitions.h"
-typedef struct {
- int count; /* sort order for output */
- gmx_bool bObsolete; /* whether it is an obsolete param value */
- gmx_bool bSet; /* whether it it has been read out */
- char *name; /* name of the parameter */
- char *value; /* parameter value string */
- int inp_count; /* number of einps read. Only valid for the first item
- in the inpfile list. */
+struct warninp;
+typedef warninp *warninp_t;
+
+namespace gmx
+{
+class KeyValueTreeObject;
+class TextInputStream;
+class TextOutputStream;
+}
+
+typedef struct t_inpfile {
+ int count; /* sort order for output */
+ gmx_bool bObsolete; /* whether it is an obsolete param value */
+ gmx_bool bSet; /* whether it it has been read out */
+ gmx_bool bHandledAsKeyValueTree; /* whether it it has been handled with key-value machinery */
+ char *name; /* name of the parameter */
+ char *value; /* parameter value string */
+ int inp_count; /* number of einps read. Only valid for the first item
+ in the inpfile list. */
} t_inpfile;
/* entry in input files (like .mdp files).
Initally read in with read_inpfile, then filled in with missing values
through get_eint, get_ereal, etc. */
-t_inpfile *read_inpfile(const char *fn, int *ninp,
+/*! \brief Create and return an array of \c ninp t_inpfile structs
+ * from "key = value" lines in \c stream corresponding to file \c fn.
+ *
+ * \param[in] stream Text stream to read.
+ * \param[in] fn Filename corresponding to \c reader.
+ * \param[out] ninp Length of returned array.
+ * \param[out] wi Handler for context-sensitive warnings.
+ * \throws std::bad_alloc If out of memory.
+ * \throws Anything the stream underlying \c reader can throw. */
+t_inpfile *read_inpfile(gmx::TextInputStream *stream, const char *fn, int *ninp,
warninp_t wi);
-/* Create & populate a t_inpfile struct from values in file fn.
- fn = the file name
- ninp = the number of read parameters
- cppopts = the cpp-style options for #include paths and #defines */
-void write_inpfile(const char *fn, int ninp, t_inpfile inp[],
+gmx::KeyValueTreeObject flatKeyValueTreeFromInpFile(int ninp, t_inpfile inp[]);
+
+enum class WriteMdpHeader
+{
+ no, yes
+};
+
+/*! \brief Write "key = value" lines from \c inp to \c stream.
+ *
+ * \param[in] stream Text stream to write.
+ * \param[in] fn Filename corresponding to \c stream.
+ * \param[in] ninp Length of \c inp.
+ * \param[in] inp Array of key-value pairs.
+ * \param[in] bHaltOnUnknown Whether to issue a fatal error if an unknown key is found.
+ * \param[in] writeHeader Whether to write a header recording some context a user might like.
+ * \param[out] wi Handler for context-sensitive warnings.
+ * \throws std::bad_alloc If out of memory.
+ * \throws Anything the stream underlying \c writer can throw. */
+void write_inpfile(gmx::TextOutputStream *stream, const char *fn, int ninp, t_inpfile inp[],
gmx_bool bHaltOnUnknown,
+ WriteMdpHeader writeHeader,
warninp_t wi);
+/* Write inp to fn, warning (and perhaps halting) if any fields are
+ * unknown. The helpful header contains irreproducible content, so
+ * its writing can be suppressed to make testing more useful. */
void replace_inp_entry(int ninp, t_inpfile *inp,
const char *old_entry, const char *new_entry);
/* Return the index of an .mdp field with the given name within the
* inp array, if it exists. Return -1 if it does not exist. */
+void mark_einp_set(int ninp, t_inpfile *inp, const char *name);
+
int get_eint(int *ninp, t_inpfile **inp, const char *name, int def,
warninp_t wi);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \brief
* Google Test formatter for GromacsFileType values.
*/
-void PrintTo(const GromacsFileType &ftp, std::ostream *os)
+static void PrintTo(const GromacsFileType &ftp, std::ostream *os)
{
*os << "'" << ftp2ext(ftp) << "'";
}
{
generateReferenceTopology();
generateReferenceCoordinates();
- testTop_ = NULL;
- testX_ = NULL;
+ testTop_ = nullptr;
+ testX_ = nullptr;
clear_mat(testBox_);
referenceFilename_ =
fileManager_.getTemporaryFilePath(getFileSuffix("ref"));
}
~StructureIORoundtripTest()
{
- if (testTop_ != NULL)
+ if (testTop_ != nullptr)
{
done_top(testTop_);
sfree(testTop_);
void writeReferenceFile()
{
write_sto_conf(referenceFilename_.c_str(), *refTop_->name,
- &refTop_->atoms, as_rvec_array(refX_.data()), NULL, -1,
+ &refTop_->atoms, as_rvec_array(refX_.data()), nullptr, -1,
refBox_);
}
snew(testTop_, 1);
int ePBC = -2;
read_tps_conf(referenceFilename_.c_str(), testTop_,
- &ePBC, &testX_, NULL, testBox_, FALSE);
+ &ePBC, &testX_, nullptr, testBox_, FALSE);
}
void testTopologies()
void writeTestFileAndTest()
{
write_sto_conf(testFilename_.c_str(), *testTop_->name,
- &testTop_->atoms, testX_, NULL, -1, testBox_);
+ &testTop_->atoms, testX_, nullptr, -1, testBox_);
testFilesEqual(referenceFilename_, testFilename_);
}
refX_.reserve(atomCount);
for (int i = 0; i < atomCount; ++i)
{
- refX_.push_back(gmx::RVec(i%4, i/4, (i/2)%3));
+ refX_.emplace_back(i%4, i/4, (i/2)%3);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
#include "gromacs/fileio/warninp.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/unique_cptr.h"
namespace gmx
{
{
public:
ReadTest() : numInputs_(1),
- inputField_(0),
+ inputField_(nullptr),
inpGuard_(),
wi_(),
wiGuard_()
int numInputs_;
t_inpfile *inputField_;
- gmx::scoped_cptr<t_inpfile> inpGuard_;
+ gmx::unique_cptr<t_inpfile> inpGuard_;
warninp_t wi_;
- gmx::scoped_cptr<struct warninp, free_warning> wiGuard_;
+ gmx::unique_cptr<struct warninp, free_warning> wiGuard_;
};
TEST_F(ReadTest, get_eint_ReadsInteger)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
-#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/utility/path.h"
#include "testutils/testfilemanager.h"
TEST_F(TngTest, CloseBeforeOpenIsNotFatal)
{
- tng_trajectory_t tng = NULL;
+ tng_trajectory_t tng = nullptr;
gmx_tng_close(&tng);
}
#include "config.h"
+#include <cmath>
+
+#include <memory>
+
#if GMX_USE_TNG
#include "tng/tng_io.h"
#endif
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/sysinfo.h"
+#include "gromacs/utility/unique_cptr.h"
static const char *modeToVerb(char mode)
{
gmx_int64_t numMolecules,
tng_molecule_t *tngMol)
{
- tng_chain_t tngChain = NULL;
- tng_residue_t tngRes = NULL;
+ tng_chain_t tngChain = nullptr;
+ tng_residue_t tngRes = nullptr;
if (tng_molecule_add(tng, moleculeName, tngMol) != TNG_SUCCESS)
{
{
const t_resinfo *resInfo = &atoms->resinfo[at->resind];
char chainName[2] = {resInfo->chainid, 0};
- tng_atom_t tngAtom = NULL;
+ tng_atom_t tngAtom = nullptr;
t_atom *prevAtom;
if (atomIndex > 0)
}
else
{
- prevAtom = 0;
+ prevAtom = nullptr;
}
/* If this is the first atom or if the residue changed add the
for (int molIndex = 0; molIndex < mtop->nmolblock; molIndex++)
{
- tng_molecule_t tngMol = NULL;
+ tng_molecule_t tngMol = nullptr;
const gmx_moltype_t *molType =
&mtop->moltype[mtop->molblock[molIndex].type];
return -1.0;
#endif
}
+
+void gmx_prepare_tng_writing(const char *filename,
+ char mode,
+ tng_trajectory_t *input,
+ tng_trajectory_t *output,
+ int nAtoms,
+ const gmx_mtop_t *mtop,
+ const int *index,
+ const char *indexGroupName)
+{
+#if GMX_USE_TNG
+ /* FIXME after 5.0: Currently only standard block types are read */
+ const int defaultNumIds = 5;
+ static gmx_int64_t fallbackIds[defaultNumIds] =
+ {
+ TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS,
+ TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES,
+ TNG_GMX_LAMBDA
+ };
+ static char fallbackNames[defaultNumIds][32] =
+ {
+ "BOX SHAPE", "POSITIONS", "VELOCITIES",
+ "FORCES", "LAMBDAS"
+ };
+
+ typedef tng_function_status (*set_writing_interval_func_pointer)(tng_trajectory_t,
+ const gmx_int64_t,
+ const gmx_int64_t,
+ const gmx_int64_t,
+ const char*,
+ const char,
+ const char);
+#if GMX_DOUBLE
+ set_writing_interval_func_pointer set_writing_interval = tng_util_generic_write_interval_double_set;
+#else
+ set_writing_interval_func_pointer set_writing_interval = tng_util_generic_write_interval_set;
+#endif
+
+ gmx_tng_open(filename, mode, output);
+
+ /* Do we have an input file in TNG format? If so, then there's
+ more data we can copy over, rather than having to improvise. */
+ if (*input)
+ {
+ /* Set parameters (compression, time per frame, molecule
+ * information, number of frames per frame set and writing
+ * intervals of positions, box shape and lambdas) of the
+ * output tng container based on their respective values int
+ * the input tng container */
+ double time, compression_precision;
+ gmx_int64_t n_frames_per_frame_set, interval = -1;
+
+ tng_compression_precision_get(*input, &compression_precision);
+ tng_compression_precision_set(*output, compression_precision);
+ // TODO make this configurable in a future version
+ char compression_type = TNG_TNG_COMPRESSION;
+
+ tng_molecule_system_copy(*input, *output);
+
+ tng_time_per_frame_get(*input, &time);
+ tng_time_per_frame_set(*output, time);
+
+ tng_num_frames_per_frame_set_get(*input, &n_frames_per_frame_set);
+ tng_num_frames_per_frame_set_set(*output, n_frames_per_frame_set);
+
+ for (int i = 0; i < defaultNumIds; i++)
+ {
+ if (tng_data_get_stride_length(*input, fallbackIds[i], -1, &interval)
+ == TNG_SUCCESS)
+ {
+ switch (fallbackIds[i])
+ {
+ case TNG_TRAJ_POSITIONS:
+ case TNG_TRAJ_VELOCITIES:
+ set_writing_interval(*output, interval, 3, fallbackIds[i],
+ fallbackNames[i], TNG_PARTICLE_BLOCK_DATA,
+ compression_type);
+ break;
+ case TNG_TRAJ_FORCES:
+ set_writing_interval(*output, interval, 3, fallbackIds[i],
+ fallbackNames[i], TNG_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
+ break;
+ case TNG_TRAJ_BOX_SHAPE:
+ set_writing_interval(*output, interval, 9, fallbackIds[i],
+ fallbackNames[i], TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
+ break;
+ case TNG_GMX_LAMBDA:
+ set_writing_interval(*output, interval, 1, fallbackIds[i],
+ fallbackNames[i], TNG_NON_PARTICLE_BLOCK_DATA,
+ TNG_GZIP_COMPRESSION);
+ break;
+ default:
+ continue;
+ }
+ }
+ }
+
+ }
+ else
+ {
+ /* TODO after trjconv is modularized: fix this so the user can
+ change precision when they are doing an operation where
+ this makes sense, and not otherwise.
+
+ char compression = bUseLossyCompression ? TNG_TNG_COMPRESSION : TNG_GZIP_COMPRESSION;
+ gmx_tng_set_compression_precision(*output, ndec2prec(nDecimalsOfPrecision));
+ */
+ gmx_tng_add_mtop(*output, mtop);
+ tng_num_frames_per_frame_set_set(*output, 1);
+ }
+
+ if (index && nAtoms > 0)
+ {
+ gmx_tng_setup_atom_subgroup(*output, nAtoms, index, indexGroupName);
+ }
+
+ /* If for some reason there are more requested atoms than there are atoms in the
+ * molecular system create a number of implicit atoms (without atom data) to
+ * compensate for that. */
+ if (nAtoms >= 0)
+ {
+ tng_implicit_num_particles_set(*output, nAtoms);
+ }
+#else
+ GMX_UNUSED_VALUE(filename);
+ GMX_UNUSED_VALUE(mode);
+ GMX_UNUSED_VALUE(input);
+ GMX_UNUSED_VALUE(output);
+ GMX_UNUSED_VALUE(nAtoms);
+ GMX_UNUSED_VALUE(mtop);
+ GMX_UNUSED_VALUE(index);
+ GMX_UNUSED_VALUE(indexGroupName);
+#endif
+}
+
+void gmx_write_tng_from_trxframe(tng_trajectory_t output,
+ const t_trxframe *frame,
+ int natoms)
+{
+#if GMX_USE_TNG
+ if (frame->step > 0)
+ {
+ double timePerFrame = frame->time * PICO / frame->step;
+ tng_time_per_frame_set(output, timePerFrame);
+ }
+ if (natoms < 0)
+ {
+ natoms = frame->natoms;
+ }
+ gmx_fwrite_tng(output,
+ TRUE,
+ frame->step,
+ frame->time,
+ 0,
+ frame->box,
+ natoms,
+ frame->x,
+ frame->v,
+ frame->f);
+#else
+ GMX_UNUSED_VALUE(output);
+ GMX_UNUSED_VALUE(frame);
+ GMX_UNUSED_VALUE(natoms);
+#endif
+}
+
+namespace
+{
+
+#if GMX_USE_TNG
+void
+convert_array_to_real_array(void *from,
+ real *to,
+ const float fact,
+ const int nAtoms,
+ const int nValues,
+ const char datatype)
+{
+ int i, j;
+
+ const bool useDouble = GMX_DOUBLE;
+ switch (datatype)
+ {
+ case TNG_FLOAT_DATA:
+ if (!useDouble)
+ {
+ if (fact == 1)
+ {
+ memcpy(to, from, nValues * sizeof(real) * nAtoms);
+ }
+ else
+ {
+ for (i = 0; i < nAtoms; i++)
+ {
+ for (j = 0; j < nValues; j++)
+ {
+ to[i*nValues+j] = reinterpret_cast<float *>(from)[i*nValues+j] * fact;
+ }
+ }
+ }
+ }
+ else
+ {
+ for (i = 0; i < nAtoms; i++)
+ {
+ for (j = 0; j < nValues; j++)
+ {
+ to[i*nValues+j] = reinterpret_cast<float *>(from)[i*nValues+j] * fact;
+ }
+ }
+ }
+ break;
+ case TNG_INT_DATA:
+ for (i = 0; i < nAtoms; i++)
+ {
+ for (j = 0; j < nValues; j++)
+ {
+ to[i*nValues+j] = reinterpret_cast<gmx_int64_t *>(from)[i*nValues+j] * fact;
+ }
+ }
+ break;
+ case TNG_DOUBLE_DATA:
+ if (sizeof(real) == sizeof(double))
+ {
+ if (fact == 1)
+ {
+ memcpy(to, from, nValues * sizeof(real) * nAtoms);
+ }
+ else
+ {
+ for (i = 0; i < nAtoms; i++)
+ {
+ for (j = 0; j < nValues; j++)
+ {
+ to[i*nValues+j] = reinterpret_cast<double *>(from)[i*nValues+j] * fact;
+ }
+ }
+ }
+ }
+ else
+ {
+ for (i = 0; i < nAtoms; i++)
+ {
+ for (j = 0; j < nValues; j++)
+ {
+ to[i*nValues+j] = reinterpret_cast<double *>(from)[i*nValues+j] * fact;
+ }
+ }
+ }
+ break;
+ default:
+ gmx_incons("Illegal datatype when converting values to a real array!");
+ return;
+ }
+ return;
+}
+
+real getDistanceScaleFactor(tng_trajectory_t in)
+{
+ gmx_int64_t exp = -1;
+ real distanceScaleFactor;
+
+ // TODO Hopefully, TNG 2.0 will do this kind of thing for us
+ tng_distance_unit_exponential_get(in, &exp);
+
+ // GROMACS expects distances in nm
+ switch (exp)
+ {
+ case 9:
+ distanceScaleFactor = NANO/NANO;
+ break;
+ case 10:
+ distanceScaleFactor = NANO/ANGSTROM;
+ break;
+ default:
+ distanceScaleFactor = pow(10.0, exp + 9.0);
+ }
+
+ return distanceScaleFactor;
+}
+#endif
+
+} // namespace
+
+void gmx_tng_setup_atom_subgroup(tng_trajectory_t tng,
+ const int nind,
+ const int *ind,
+ const char *name)
+{
+#if GMX_USE_TNG
+ gmx_int64_t nAtoms, cnt, nMols;
+ tng_molecule_t mol, iterMol;
+ tng_chain_t chain;
+ tng_residue_t res;
+ tng_atom_t atom;
+ tng_function_status stat;
+
+ tng_num_particles_get(tng, &nAtoms);
+
+ if (nAtoms == nind)
+ {
+ return;
+ }
+
+ stat = tng_molecule_find(tng, name, -1, &mol);
+ if (stat == TNG_SUCCESS)
+ {
+ tng_molecule_num_atoms_get(tng, mol, &nAtoms);
+ tng_molecule_cnt_get(tng, mol, &cnt);
+ if (nAtoms == nind)
+ {
+ stat = TNG_SUCCESS;
+ }
+ else
+ {
+ stat = TNG_FAILURE;
+ }
+ }
+ if (stat == TNG_FAILURE)
+ {
+ /* The indexed atoms are added to one separate molecule. */
+ tng_molecule_alloc(tng, &mol);
+ tng_molecule_name_set(tng, mol, name);
+ tng_molecule_chain_add(tng, mol, "", &chain);
+
+ for (int i = 0; i < nind; i++)
+ {
+ char temp_name[256], temp_type[256];
+
+ /* Try to retrieve the residue name of the atom */
+ stat = tng_residue_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
+ if (stat != TNG_SUCCESS)
+ {
+ temp_name[0] = '\0';
+ }
+ /* Check if the molecule of the selection already contains this residue */
+ if (tng_chain_residue_find(tng, chain, temp_name, -1, &res)
+ != TNG_SUCCESS)
+ {
+ tng_chain_residue_add(tng, chain, temp_name, &res);
+ }
+ /* Try to find the original name and type of the atom */
+ stat = tng_atom_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
+ if (stat != TNG_SUCCESS)
+ {
+ temp_name[0] = '\0';
+ }
+ stat = tng_atom_type_of_particle_nr_get(tng, ind[i], temp_type, 256);
+ if (stat != TNG_SUCCESS)
+ {
+ temp_type[0] = '\0';
+ }
+ tng_residue_atom_w_id_add(tng, res, temp_name, temp_type, ind[i], &atom);
+ }
+ tng_molecule_existing_add(tng, &mol);
+ }
+ /* Set the count of the molecule containing the selected atoms to 1 and all
+ * other molecules to 0 */
+ tng_molecule_cnt_set(tng, mol, 1);
+ tng_num_molecule_types_get(tng, &nMols);
+ for (gmx_int64_t k = 0; k < nMols; k++)
+ {
+ tng_molecule_of_index_get(tng, k, &iterMol);
+ if (iterMol == mol)
+ {
+ continue;
+ }
+ tng_molecule_cnt_set(tng, iterMol, 0);
+ }
+#else
+ GMX_UNUSED_VALUE(tng);
+ GMX_UNUSED_VALUE(nind);
+ GMX_UNUSED_VALUE(ind);
+ GMX_UNUSED_VALUE(name);
+#endif
+}
+
+/* TODO: If/when TNG acquires the ability to copy data blocks without
+ * uncompressing them, then this implemenation should be reconsidered.
+ * Ideally, gmx trjconv -f a.tng -o b.tng -b 10 -e 20 would be fast
+ * and lose no information. */
+gmx_bool gmx_read_next_tng_frame(tng_trajectory_t input,
+ t_trxframe *fr,
+ gmx_int64_t *requestedIds,
+ int numRequestedIds)
+{
+#if GMX_USE_TNG
+ gmx_bool bOK = TRUE;
+ tng_function_status stat;
+ gmx_int64_t numberOfAtoms = -1, frameNumber = -1;
+ gmx_int64_t nBlocks, blockId, *blockIds = nullptr, codecId;
+ char datatype = -1;
+ void *values = nullptr;
+ double frameTime = -1.0;
+ int size, blockDependency;
+ double prec;
+ const int defaultNumIds = 5;
+ static gmx_int64_t fallbackRequestedIds[defaultNumIds] =
+ {
+ TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS,
+ TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES,
+ TNG_GMX_LAMBDA
+ };
+
+
+ fr->bStep = FALSE;
+ fr->bTime = FALSE;
+ fr->bLambda = FALSE;
+ fr->bAtoms = FALSE;
+ fr->bPrec = FALSE;
+ fr->bX = FALSE;
+ fr->bV = FALSE;
+ fr->bF = FALSE;
+ fr->bBox = FALSE;
+
+ /* If no specific IDs were requested read all block types that can
+ * currently be interpreted */
+ if (!requestedIds || numRequestedIds == 0)
+ {
+ numRequestedIds = defaultNumIds;
+ requestedIds = fallbackRequestedIds;
+ }
+
+ stat = tng_num_particles_get(input, &numberOfAtoms);
+ if (stat != TNG_SUCCESS)
+ {
+ gmx_file("Cannot determine number of atoms from TNG file.");
+ }
+ fr->natoms = numberOfAtoms;
+
+ bool nextFrameExists = gmx_get_tng_data_block_types_of_next_frame(input,
+ fr->step,
+ numRequestedIds,
+ requestedIds,
+ &frameNumber,
+ &nBlocks,
+ &blockIds);
+ gmx::unique_cptr<gmx_int64_t, gmx::free_wrapper> blockIdsGuard(blockIds);
+ if (!nextFrameExists)
+ {
+ return FALSE;
+ }
+
+ if (nBlocks == 0)
+ {
+ return FALSE;
+ }
+
+ for (gmx_int64_t i = 0; i < nBlocks; i++)
+ {
+ blockId = blockIds[i];
+ tng_data_block_dependency_get(input, blockId, &blockDependency);
+ if (blockDependency & TNG_PARTICLE_DEPENDENT)
+ {
+ stat = tng_util_particle_data_next_frame_read(input,
+ blockId,
+ &values,
+ &datatype,
+ &frameNumber,
+ &frameTime);
+ }
+ else
+ {
+ stat = tng_util_non_particle_data_next_frame_read(input,
+ blockId,
+ &values,
+ &datatype,
+ &frameNumber,
+ &frameTime);
+ }
+ if (stat == TNG_CRITICAL)
+ {
+ gmx_file("Cannot read positions from TNG file.");
+ return FALSE;
+ }
+ else if (stat == TNG_FAILURE)
+ {
+ continue;
+ }
+ switch (blockId)
+ {
+ case TNG_TRAJ_BOX_SHAPE:
+ switch (datatype)
+ {
+ case TNG_INT_DATA:
+ size = sizeof(gmx_int64_t);
+ break;
+ case TNG_FLOAT_DATA:
+ size = sizeof(float);
+ break;
+ case TNG_DOUBLE_DATA:
+ size = sizeof(double);
+ break;
+ default:
+ gmx_incons("Illegal datatype of box shape values!");
+ }
+ for (int i = 0; i < DIM; i++)
+ {
+ convert_array_to_real_array(reinterpret_cast<char *>(values) + size * i * DIM,
+ reinterpret_cast<real *>(fr->box[i]),
+ getDistanceScaleFactor(input),
+ 1,
+ DIM,
+ datatype);
+ }
+ fr->bBox = TRUE;
+ break;
+ case TNG_TRAJ_POSITIONS:
+ srenew(fr->x, fr->natoms);
+ convert_array_to_real_array(values,
+ reinterpret_cast<real *>(fr->x),
+ getDistanceScaleFactor(input),
+ fr->natoms,
+ DIM,
+ datatype);
+ fr->bX = TRUE;
+ tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
+ /* This must be updated if/when more lossy compression methods are added */
+ if (codecId == TNG_TNG_COMPRESSION)
+ {
+ fr->prec = prec;
+ fr->bPrec = TRUE;
+ }
+ break;
+ case TNG_TRAJ_VELOCITIES:
+ srenew(fr->v, fr->natoms);
+ convert_array_to_real_array(values,
+ (real *) fr->v,
+ getDistanceScaleFactor(input),
+ fr->natoms,
+ DIM,
+ datatype);
+ fr->bV = TRUE;
+ tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
+ /* This must be updated if/when more lossy compression methods are added */
+ if (codecId == TNG_TNG_COMPRESSION)
+ {
+ fr->prec = prec;
+ fr->bPrec = TRUE;
+ }
+ break;
+ case TNG_TRAJ_FORCES:
+ srenew(fr->f, fr->natoms);
+ convert_array_to_real_array(values,
+ reinterpret_cast<real *>(fr->f),
+ getDistanceScaleFactor(input),
+ fr->natoms,
+ DIM,
+ datatype);
+ fr->bF = TRUE;
+ break;
+ case TNG_GMX_LAMBDA:
+ switch (datatype)
+ {
+ case TNG_FLOAT_DATA:
+ fr->lambda = *(reinterpret_cast<float *>(values));
+ break;
+ case TNG_DOUBLE_DATA:
+ fr->lambda = *(reinterpret_cast<double *>(values));
+ break;
+ default:
+ gmx_incons("Illegal datatype lambda value!");
+ }
+ fr->bLambda = TRUE;
+ break;
+ default:
+ gmx_warning("Illegal block type! Currently GROMACS tools can only handle certain data types. Skipping block.");
+ }
+ /* values does not have to be freed before reading next frame. It will
+ * be reallocated if it is not NULL. */
+ }
+
+ fr->step = frameNumber;
+ fr->bStep = TRUE;
+ // Convert the time to ps
+ fr->time = frameTime / PICO;
+ fr->bTime = TRUE;
+
+ // TODO This does not leak, but is not exception safe.
+ /* values must be freed before leaving this function */
+ sfree(values);
+
+ return bOK;
+#else
+ GMX_UNUSED_VALUE(input);
+ GMX_UNUSED_VALUE(fr);
+ GMX_UNUSED_VALUE(requestedIds);
+ GMX_UNUSED_VALUE(numRequestedIds);
+ return FALSE;
+#endif
+}
+
+void gmx_print_tng_molecule_system(tng_trajectory_t input,
+ FILE *stream)
+{
+#if GMX_USE_TNG
+ gmx_int64_t nMolecules, nChains, nResidues, nAtoms, *molCntList;
+ tng_molecule_t molecule;
+ tng_chain_t chain;
+ tng_residue_t residue;
+ tng_atom_t atom;
+ char str[256], varNAtoms;
+
+ tng_num_molecule_types_get(input, &nMolecules);
+ tng_molecule_cnt_list_get(input, &molCntList);
+ /* Can the number of particles change in the trajectory or is it constant? */
+ tng_num_particles_variable_get(input, &varNAtoms);
+
+ for (gmx_int64_t i = 0; i < nMolecules; i++)
+ {
+ tng_molecule_of_index_get(input, i, &molecule);
+ tng_molecule_name_get(input, molecule, str, 256);
+ if (varNAtoms == TNG_CONSTANT_N_ATOMS)
+ {
+ if ((int)molCntList[i] == 0)
+ {
+ continue;
+ }
+ fprintf(stream, "Molecule: %s, count: %d\n", str, (int)molCntList[i]);
+ }
+ else
+ {
+ fprintf(stream, "Molecule: %s\n", str);
+ }
+ tng_molecule_num_chains_get(input, molecule, &nChains);
+ if (nChains > 0)
+ {
+ for (gmx_int64_t j = 0; j < nChains; j++)
+ {
+ tng_molecule_chain_of_index_get(input, molecule, j, &chain);
+ tng_chain_name_get(input, chain, str, 256);
+ fprintf(stream, "\tChain: %s\n", str);
+ tng_chain_num_residues_get(input, chain, &nResidues);
+ for (gmx_int64_t k = 0; k < nResidues; k++)
+ {
+ tng_chain_residue_of_index_get(input, chain, k, &residue);
+ tng_residue_name_get(input, residue, str, 256);
+ fprintf(stream, "\t\tResidue: %s\n", str);
+ tng_residue_num_atoms_get(input, residue, &nAtoms);
+ for (gmx_int64_t l = 0; l < nAtoms; l++)
+ {
+ tng_residue_atom_of_index_get(input, residue, l, &atom);
+ tng_atom_name_get(input, atom, str, 256);
+ fprintf(stream, "\t\t\tAtom: %s", str);
+ tng_atom_type_get(input, atom, str, 256);
+ fprintf(stream, " (%s)\n", str);
+ }
+ }
+ }
+ }
+ /* It is possible to have a molecule without chains, in which case
+ * residues in the molecule can be iterated through without going
+ * through chains. */
+ else
+ {
+ tng_molecule_num_residues_get(input, molecule, &nResidues);
+ if (nResidues > 0)
+ {
+ for (gmx_int64_t k = 0; k < nResidues; k++)
+ {
+ tng_molecule_residue_of_index_get(input, molecule, k, &residue);
+ tng_residue_name_get(input, residue, str, 256);
+ fprintf(stream, "\t\tResidue: %s\n", str);
+ tng_residue_num_atoms_get(input, residue, &nAtoms);
+ for (gmx_int64_t l = 0; l < nAtoms; l++)
+ {
+ tng_residue_atom_of_index_get(input, residue, l, &atom);
+ tng_atom_name_get(input, atom, str, 256);
+ fprintf(stream, "\t\t\tAtom: %s", str);
+ tng_atom_type_get(input, atom, str, 256);
+ fprintf(stream, " (%s)\n", str);
+ }
+ }
+ }
+ else
+ {
+ tng_molecule_num_atoms_get(input, molecule, &nAtoms);
+ for (gmx_int64_t l = 0; l < nAtoms; l++)
+ {
+ tng_molecule_atom_of_index_get(input, molecule, l, &atom);
+ tng_atom_name_get(input, atom, str, 256);
+ fprintf(stream, "\t\t\tAtom: %s", str);
+ tng_atom_type_get(input, atom, str, 256);
+ fprintf(stream, " (%s)\n", str);
+ }
+ }
+ }
+ }
+#else
+ GMX_UNUSED_VALUE(input);
+ GMX_UNUSED_VALUE(stream);
+#endif
+}
+
+gmx_bool gmx_get_tng_data_block_types_of_next_frame(tng_trajectory_t input,
+ int frame,
+ int nRequestedIds,
+ gmx_int64_t *requestedIds,
+ gmx_int64_t *nextFrame,
+ gmx_int64_t *nBlocks,
+ gmx_int64_t **blockIds)
+{
+#if GMX_USE_TNG
+ tng_function_status stat;
+
+ stat = tng_util_trajectory_next_frame_present_data_blocks_find(input, frame,
+ nRequestedIds, requestedIds,
+ nextFrame,
+ nBlocks, blockIds);
+
+ if (stat == TNG_CRITICAL)
+ {
+ gmx_file("Cannot read TNG file. Cannot find data blocks of next frame.");
+ }
+ else if (stat == TNG_FAILURE)
+ {
+ return FALSE;
+ }
+ return TRUE;
+#else
+ GMX_UNUSED_VALUE(input);
+ GMX_UNUSED_VALUE(frame);
+ GMX_UNUSED_VALUE(nRequestedIds);
+ GMX_UNUSED_VALUE(requestedIds);
+ GMX_UNUSED_VALUE(nextFrame);
+ GMX_UNUSED_VALUE(nBlocks);
+ GMX_UNUSED_VALUE(blockIds);
+ return FALSE;
+#endif
+}
+
+gmx_bool gmx_get_tng_data_next_frame_of_block_type(tng_trajectory_t input,
+ gmx_int64_t blockId,
+ real **values,
+ gmx_int64_t *frameNumber,
+ double *frameTime,
+ gmx_int64_t *nValuesPerFrame,
+ gmx_int64_t *nAtoms,
+ real *prec,
+ char *name,
+ int maxLen,
+ gmx_bool *bOK)
+{
+#if GMX_USE_TNG
+ tng_function_status stat;
+ char datatype = -1;
+ gmx_int64_t codecId;
+ int blockDependency;
+ void *data = nullptr;
+ double localPrec;
+
+ stat = tng_data_block_name_get(input, blockId, name, maxLen);
+ if (stat != TNG_SUCCESS)
+ {
+ gmx_file("Cannot read next frame of TNG file");
+ }
+ stat = tng_data_block_dependency_get(input, blockId, &blockDependency);
+ if (stat != TNG_SUCCESS)
+ {
+ gmx_file("Cannot read next frame of TNG file");
+ }
+ if (blockDependency & TNG_PARTICLE_DEPENDENT)
+ {
+ tng_num_particles_get(input, nAtoms);
+ stat = tng_util_particle_data_next_frame_read(input,
+ blockId,
+ &data,
+ &datatype,
+ frameNumber,
+ frameTime);
+ }
+ else
+ {
+ *nAtoms = 1; /* There are not actually any atoms, but it is used for
+ allocating memory */
+ stat = tng_util_non_particle_data_next_frame_read(input,
+ blockId,
+ &data,
+ &datatype,
+ frameNumber,
+ frameTime);
+ }
+ if (stat == TNG_CRITICAL)
+ {
+ gmx_file("Cannot read next frame of TNG file");
+ }
+ if (stat == TNG_FAILURE)
+ {
+ *bOK = TRUE;
+ return FALSE;
+ }
+
+ stat = tng_data_block_num_values_per_frame_get(input, blockId, nValuesPerFrame);
+ if (stat != TNG_SUCCESS)
+ {
+ gmx_file("Cannot read next frame of TNG file");
+ }
+ srenew(*values, sizeof(real) * *nValuesPerFrame * *nAtoms);
+ convert_array_to_real_array(data,
+ *values,
+ getDistanceScaleFactor(input),
+ *nAtoms,
+ *nValuesPerFrame,
+ datatype);
+
+ tng_util_frame_current_compression_get(input, blockId, &codecId, &localPrec);
+
+ /* This must be updated if/when more lossy compression methods are added */
+ if (codecId != TNG_TNG_COMPRESSION)
+ {
+ *prec = -1.0;
+ }
+ else
+ {
+ *prec = localPrec;
+ }
+
+ *bOK = TRUE;
+ return TRUE;
+#else
+ GMX_UNUSED_VALUE(input);
+ GMX_UNUSED_VALUE(blockId);
+ GMX_UNUSED_VALUE(values);
+ GMX_UNUSED_VALUE(frameNumber);
+ GMX_UNUSED_VALUE(frameTime);
+ GMX_UNUSED_VALUE(nValuesPerFrame);
+ GMX_UNUSED_VALUE(nAtoms);
+ GMX_UNUSED_VALUE(prec);
+ GMX_UNUSED_VALUE(name);
+ GMX_UNUSED_VALUE(maxLen);
+ GMX_UNUSED_VALUE(bOK);
+ return FALSE;
+#endif
+}
#ifndef GMX_FILEIO_TNGIO_H
#define GMX_FILEIO_TNGIO_H
-#include "tng/tng_io_fwd.h"
+#include <cstdio>
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
struct gmx_mtop_t;
struct t_inputrec;
+struct tng_trajectory;
+typedef struct tng_trajectory *tng_trajectory_t;
+struct t_trxframe;
/*! \brief Open a TNG trajectory file
*
*/
float gmx_tng_get_time_of_final_frame(tng_trajectory_t tng);
+/*! \brief Prepare to write TNG output from trajectory conversion tools */
+void gmx_prepare_tng_writing(const char *filename,
+ char mode,
+ tng_trajectory_t *in,
+ tng_trajectory_t *out,
+ int nAtoms,
+ const struct gmx_mtop_t *mtop,
+ const int *index,
+ const char *indexGroupName);
+
+/*! \brief Write a trxframe to a TNG file
+ *
+ * \param output Trajectory to write to
+ * \param frame Frame data to write
+ * \param natoms Number of atoms to actually write
+ *
+ * The natoms field in frame is the number of atoms in the system. The
+ * parameter natoms supports writing an index-group subset of the
+ * atoms.
+ */
+void gmx_write_tng_from_trxframe(tng_trajectory_t output,
+ const t_trxframe *frame,
+ int natoms);
+
+/*! \brief Creates a molecule containing only the indexed atoms and sets
+ * the number of all other molecules to 0. Works similar to a
+ * selection group. */
+void gmx_tng_setup_atom_subgroup(tng_trajectory_t tng,
+ const int nind,
+ const int *ind,
+ const char *name);
+
+/*! \brief Read the first/next TNG frame. */
+gmx_bool gmx_read_next_tng_frame(tng_trajectory_t input,
+ struct t_trxframe *fr,
+ gmx_int64_t *requestedIds,
+ int numRequestedIds);
+
+/*! \brief Print the molecule system to stream */
+void gmx_print_tng_molecule_system(tng_trajectory_t input,
+ FILE *stream);
+
+/*! \brief Get a list of block IDs present in the next frame with data. */
+gmx_bool gmx_get_tng_data_block_types_of_next_frame(tng_trajectory_t input,
+ int frame,
+ int nRequestedIds,
+ gmx_int64_t *requestedIds,
+ gmx_int64_t *nextFrame,
+ gmx_int64_t *nBlocks,
+ gmx_int64_t **blockIds);
+
+/*! \brief Get data of the next frame with data from the data block
+ * with the specified block ID. */
+gmx_bool gmx_get_tng_data_next_frame_of_block_type(tng_trajectory_t input,
+ gmx_int64_t blockId,
+ real **values,
+ gmx_int64_t *frameNumber,
+ double *frameTime,
+ gmx_int64_t *nValuesPerFrame,
+ gmx_int64_t *nAtoms,
+ real *prec,
+ char *name,
+ int maxLen,
+ gmx_bool *bOK);
+
#endif /* GMX_FILEIO_TNGIO_H */
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "tngio_for_tools.h"
-
-#include "config.h"
-
-#include <cmath>
-
-#if GMX_USE_TNG
-#include "tng/tng_io.h"
-#endif
-
-#include "gromacs/fileio/tngio.h"
-#include "gromacs/math/units.h"
-#include "gromacs/trajectory/trajectoryframe.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-void gmx_prepare_tng_writing(const char *filename,
- char mode,
- tng_trajectory_t *input,
- tng_trajectory_t *output,
- int nAtoms,
- const gmx_mtop_t *mtop,
- const int *index,
- const char *indexGroupName)
-{
-#if GMX_USE_TNG
- /* FIXME after 5.0: Currently only standard block types are read */
- const int defaultNumIds = 5;
- static gmx_int64_t fallbackIds[defaultNumIds] =
- {
- TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS,
- TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES,
- TNG_GMX_LAMBDA
- };
- static char fallbackNames[defaultNumIds][32] =
- {
- "BOX SHAPE", "POSITIONS", "VELOCITIES",
- "FORCES", "LAMBDAS"
- };
-
- typedef tng_function_status (*set_writing_interval_func_pointer)(tng_trajectory_t,
- const gmx_int64_t,
- const gmx_int64_t,
- const gmx_int64_t,
- const char*,
- const char,
- const char);
-#if GMX_DOUBLE
- set_writing_interval_func_pointer set_writing_interval = tng_util_generic_write_interval_double_set;
-#else
- set_writing_interval_func_pointer set_writing_interval = tng_util_generic_write_interval_set;
-#endif
-
- gmx_tng_open(filename, mode, output);
-
- /* Do we have an input file in TNG format? If so, then there's
- more data we can copy over, rather than having to improvise. */
- if (*input)
- {
- /* Set parameters (compression, time per frame, molecule
- * information, number of frames per frame set and writing
- * intervals of positions, box shape and lambdas) of the
- * output tng container based on their respective values int
- * the input tng container */
- double time, compression_precision;
- gmx_int64_t n_frames_per_frame_set, interval = -1;
-
- tng_compression_precision_get(*input, &compression_precision);
- tng_compression_precision_set(*output, compression_precision);
- // TODO make this configurable in a future version
- char compression_type = TNG_TNG_COMPRESSION;
-
- tng_molecule_system_copy(*input, *output);
-
- tng_time_per_frame_get(*input, &time);
- tng_time_per_frame_set(*output, time);
-
- tng_num_frames_per_frame_set_get(*input, &n_frames_per_frame_set);
- tng_num_frames_per_frame_set_set(*output, n_frames_per_frame_set);
-
- for (int i = 0; i < defaultNumIds; i++)
- {
- if (tng_data_get_stride_length(*input, fallbackIds[i], -1, &interval)
- == TNG_SUCCESS)
- {
- switch (fallbackIds[i])
- {
- case TNG_TRAJ_POSITIONS:
- case TNG_TRAJ_VELOCITIES:
- set_writing_interval(*output, interval, 3, fallbackIds[i],
- fallbackNames[i], TNG_PARTICLE_BLOCK_DATA,
- compression_type);
- break;
- case TNG_TRAJ_FORCES:
- set_writing_interval(*output, interval, 3, fallbackIds[i],
- fallbackNames[i], TNG_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION);
- break;
- case TNG_TRAJ_BOX_SHAPE:
- set_writing_interval(*output, interval, 9, fallbackIds[i],
- fallbackNames[i], TNG_NON_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION);
- break;
- case TNG_GMX_LAMBDA:
- set_writing_interval(*output, interval, 1, fallbackIds[i],
- fallbackNames[i], TNG_NON_PARTICLE_BLOCK_DATA,
- TNG_GZIP_COMPRESSION);
- default:
- continue;
- }
- }
- }
-
- }
- else
- {
- /* TODO after trjconv is modularized: fix this so the user can
- change precision when they are doing an operation where
- this makes sense, and not otherwise.
-
- char compression = bUseLossyCompression ? TNG_TNG_COMPRESSION : TNG_GZIP_COMPRESSION;
- gmx_tng_set_compression_precision(*output, ndec2prec(nDecimalsOfPrecision));
- */
- gmx_tng_add_mtop(*output, mtop);
- tng_num_frames_per_frame_set_set(*output, 1);
- }
-
- if (index && nAtoms > 0)
- {
- gmx_tng_setup_atom_subgroup(*output, nAtoms, index, indexGroupName);
- }
-
- /* If for some reason there are more requested atoms than there are atoms in the
- * molecular system create a number of implicit atoms (without atom data) to
- * compensate for that. */
- if (nAtoms >= 0)
- {
- tng_implicit_num_particles_set(*output, nAtoms);
- }
-#else
- GMX_UNUSED_VALUE(filename);
- GMX_UNUSED_VALUE(mode);
- GMX_UNUSED_VALUE(input);
- GMX_UNUSED_VALUE(output);
- GMX_UNUSED_VALUE(nAtoms);
- GMX_UNUSED_VALUE(mtop);
- GMX_UNUSED_VALUE(index);
- GMX_UNUSED_VALUE(indexGroupName);
-#endif
-}
-
-void gmx_write_tng_from_trxframe(tng_trajectory_t output,
- const t_trxframe *frame,
- int natoms)
-{
-#if GMX_USE_TNG
- if (frame->step > 0)
- {
- double timePerFrame = frame->time * PICO / frame->step;
- tng_time_per_frame_set(output, timePerFrame);
- }
- if (natoms < 0)
- {
- natoms = frame->natoms;
- }
- gmx_fwrite_tng(output,
- TRUE,
- frame->step,
- frame->time,
- 0,
- frame->box,
- natoms,
- frame->x,
- frame->v,
- frame->f);
-#else
- GMX_UNUSED_VALUE(output);
- GMX_UNUSED_VALUE(frame);
- GMX_UNUSED_VALUE(natoms);
-#endif
-}
-
-#if GMX_USE_TNG
-static void
-convert_array_to_real_array(void *from,
- real *to,
- const float fact,
- const int nAtoms,
- const int nValues,
- const char datatype)
-{
- int i, j;
-
- const bool useDouble = GMX_DOUBLE;
- switch (datatype)
- {
- case TNG_FLOAT_DATA:
- if (!useDouble)
- {
- if (fact == 1)
- {
- memcpy(to, from, nValues * sizeof(real) * nAtoms);
- }
- else
- {
- for (i = 0; i < nAtoms; i++)
- {
- for (j = 0; j < nValues; j++)
- {
- to[i*nValues+j] = reinterpret_cast<float *>(from)[i*nValues+j] * fact;
- }
- }
- }
- }
- else
- {
- for (i = 0; i < nAtoms; i++)
- {
- for (j = 0; j < nValues; j++)
- {
- to[i*nValues+j] = reinterpret_cast<float *>(from)[i*nValues+j] * fact;
- }
- }
- }
- break;
- case TNG_INT_DATA:
- for (i = 0; i < nAtoms; i++)
- {
- for (j = 0; j < nValues; j++)
- {
- to[i*nValues+j] = reinterpret_cast<gmx_int64_t *>(from)[i*nValues+j] * fact;
- }
- }
- break;
- case TNG_DOUBLE_DATA:
- if (sizeof(real) == sizeof(double))
- {
- if (fact == 1)
- {
- memcpy(to, from, nValues * sizeof(real) * nAtoms);
- }
- else
- {
- for (i = 0; i < nAtoms; i++)
- {
- for (j = 0; j < nValues; j++)
- {
- to[i*nValues+j] = reinterpret_cast<double *>(from)[i*nValues+j] * fact;
- }
- }
- }
- }
- else
- {
- for (i = 0; i < nAtoms; i++)
- {
- for (j = 0; j < nValues; j++)
- {
- to[i*nValues+j] = reinterpret_cast<double *>(from)[i*nValues+j] * fact;
- }
- }
- }
- break;
- default:
- gmx_incons("Illegal datatype when converting values to a real array!");
- return;
- }
- return;
-}
-
-static real getDistanceScaleFactor(tng_trajectory_t in)
-{
- gmx_int64_t exp = -1;
- real distanceScaleFactor;
-
- // TODO Hopefully, TNG 2.0 will do this kind of thing for us
- tng_distance_unit_exponential_get(in, &exp);
-
- // GROMACS expects distances in nm
- switch (exp)
- {
- case 9:
- distanceScaleFactor = NANO/NANO;
- break;
- case 10:
- distanceScaleFactor = NANO/ANGSTROM;
- break;
- default:
- distanceScaleFactor = pow(10.0, exp + 9.0);
- }
-
- return distanceScaleFactor;
-}
-#endif
-
-void gmx_tng_setup_atom_subgroup(tng_trajectory_t tng,
- const int nind,
- const int *ind,
- const char *name)
-{
-#if GMX_USE_TNG
- gmx_int64_t nAtoms, cnt, nMols;
- tng_molecule_t mol, iterMol;
- tng_chain_t chain;
- tng_residue_t res;
- tng_atom_t atom;
- tng_function_status stat;
-
- tng_num_particles_get(tng, &nAtoms);
-
- if (nAtoms == nind)
- {
- return;
- }
-
- stat = tng_molecule_find(tng, name, -1, &mol);
- if (stat == TNG_SUCCESS)
- {
- tng_molecule_num_atoms_get(tng, mol, &nAtoms);
- tng_molecule_cnt_get(tng, mol, &cnt);
- if (nAtoms == nind)
- {
- stat = TNG_SUCCESS;
- }
- else
- {
- stat = TNG_FAILURE;
- }
- }
- if (stat == TNG_FAILURE)
- {
- /* The indexed atoms are added to one separate molecule. */
- tng_molecule_alloc(tng, &mol);
- tng_molecule_name_set(tng, mol, name);
- tng_molecule_chain_add(tng, mol, "", &chain);
-
- for (int i = 0; i < nind; i++)
- {
- char temp_name[256], temp_type[256];
-
- /* Try to retrieve the residue name of the atom */
- stat = tng_residue_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
- if (stat != TNG_SUCCESS)
- {
- temp_name[0] = '\0';
- }
- /* Check if the molecule of the selection already contains this residue */
- if (tng_chain_residue_find(tng, chain, temp_name, -1, &res)
- != TNG_SUCCESS)
- {
- tng_chain_residue_add(tng, chain, temp_name, &res);
- }
- /* Try to find the original name and type of the atom */
- stat = tng_atom_name_of_particle_nr_get(tng, ind[i], temp_name, 256);
- if (stat != TNG_SUCCESS)
- {
- temp_name[0] = '\0';
- }
- stat = tng_atom_type_of_particle_nr_get(tng, ind[i], temp_type, 256);
- if (stat != TNG_SUCCESS)
- {
- temp_type[0] = '\0';
- }
- tng_residue_atom_w_id_add(tng, res, temp_name, temp_type, ind[i], &atom);
- }
- tng_molecule_existing_add(tng, &mol);
- }
- /* Set the count of the molecule containing the selected atoms to 1 and all
- * other molecules to 0 */
- tng_molecule_cnt_set(tng, mol, 1);
- tng_num_molecule_types_get(tng, &nMols);
- for (gmx_int64_t k = 0; k < nMols; k++)
- {
- tng_molecule_of_index_get(tng, k, &iterMol);
- if (iterMol == mol)
- {
- continue;
- }
- tng_molecule_cnt_set(tng, iterMol, 0);
- }
-#else
- GMX_UNUSED_VALUE(tng);
- GMX_UNUSED_VALUE(nind);
- GMX_UNUSED_VALUE(ind);
- GMX_UNUSED_VALUE(name);
-#endif
-}
-
-/* TODO: If/when TNG acquires the ability to copy data blocks without
- * uncompressing them, then this implemenation should be reconsidered.
- * Ideally, gmx trjconv -f a.tng -o b.tng -b 10 -e 20 would be fast
- * and lose no information. */
-gmx_bool gmx_read_next_tng_frame(tng_trajectory_t input,
- t_trxframe *fr,
- gmx_int64_t *requestedIds,
- int numRequestedIds)
-{
-#if GMX_USE_TNG
- gmx_bool bOK = TRUE;
- tng_function_status stat;
- gmx_int64_t numberOfAtoms = -1, frameNumber = -1;
- gmx_int64_t nBlocks, blockId, *blockIds = NULL, codecId;
- char datatype = -1;
- void *values = NULL;
- double frameTime = -1.0;
- int size, blockDependency;
- double prec;
- const int defaultNumIds = 5;
- static gmx_int64_t fallbackRequestedIds[defaultNumIds] =
- {
- TNG_TRAJ_BOX_SHAPE, TNG_TRAJ_POSITIONS,
- TNG_TRAJ_VELOCITIES, TNG_TRAJ_FORCES,
- TNG_GMX_LAMBDA
- };
-
-
- fr->bStep = FALSE;
- fr->bTime = FALSE;
- fr->bLambda = FALSE;
- fr->bAtoms = FALSE;
- fr->bPrec = FALSE;
- fr->bX = FALSE;
- fr->bV = FALSE;
- fr->bF = FALSE;
- fr->bBox = FALSE;
-
- /* If no specific IDs were requested read all block types that can
- * currently be interpreted */
- if (!requestedIds || numRequestedIds == 0)
- {
- numRequestedIds = defaultNumIds;
- requestedIds = fallbackRequestedIds;
- }
-
- stat = tng_num_particles_get(input, &numberOfAtoms);
- if (stat != TNG_SUCCESS)
- {
- gmx_file("Cannot determine number of atoms from TNG file.");
- }
- fr->natoms = numberOfAtoms;
-
- if (!gmx_get_tng_data_block_types_of_next_frame(input,
- fr->step,
- numRequestedIds,
- requestedIds,
- &frameNumber,
- &nBlocks,
- &blockIds))
- {
- return FALSE;
- }
-
- if (nBlocks == 0)
- {
- return FALSE;
- }
-
- for (gmx_int64_t i = 0; i < nBlocks; i++)
- {
- blockId = blockIds[i];
- tng_data_block_dependency_get(input, blockId, &blockDependency);
- if (blockDependency & TNG_PARTICLE_DEPENDENT)
- {
- stat = tng_util_particle_data_next_frame_read(input,
- blockId,
- &values,
- &datatype,
- &frameNumber,
- &frameTime);
- }
- else
- {
- stat = tng_util_non_particle_data_next_frame_read(input,
- blockId,
- &values,
- &datatype,
- &frameNumber,
- &frameTime);
- }
- if (stat == TNG_CRITICAL)
- {
- gmx_file("Cannot read positions from TNG file.");
- return FALSE;
- }
- else if (stat == TNG_FAILURE)
- {
- continue;
- }
- switch (blockId)
- {
- case TNG_TRAJ_BOX_SHAPE:
- switch (datatype)
- {
- case TNG_INT_DATA:
- size = sizeof(gmx_int64_t);
- break;
- case TNG_FLOAT_DATA:
- size = sizeof(float);
- break;
- case TNG_DOUBLE_DATA:
- size = sizeof(double);
- break;
- default:
- gmx_incons("Illegal datatype of box shape values!");
- }
- for (int i = 0; i < DIM; i++)
- {
- convert_array_to_real_array(reinterpret_cast<char *>(values) + size * i * DIM,
- reinterpret_cast<real *>(fr->box[i]),
- getDistanceScaleFactor(input),
- 1,
- DIM,
- datatype);
- }
- fr->bBox = TRUE;
- break;
- case TNG_TRAJ_POSITIONS:
- srenew(fr->x, fr->natoms);
- convert_array_to_real_array(values,
- reinterpret_cast<real *>(fr->x),
- getDistanceScaleFactor(input),
- fr->natoms,
- DIM,
- datatype);
- fr->bX = TRUE;
- tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
- /* This must be updated if/when more lossy compression methods are added */
- if (codecId == TNG_TNG_COMPRESSION)
- {
- fr->prec = prec;
- fr->bPrec = TRUE;
- }
- break;
- case TNG_TRAJ_VELOCITIES:
- srenew(fr->v, fr->natoms);
- convert_array_to_real_array(values,
- (real *) fr->v,
- getDistanceScaleFactor(input),
- fr->natoms,
- DIM,
- datatype);
- fr->bV = TRUE;
- tng_util_frame_current_compression_get(input, blockId, &codecId, &prec);
- /* This must be updated if/when more lossy compression methods are added */
- if (codecId == TNG_TNG_COMPRESSION)
- {
- fr->prec = prec;
- fr->bPrec = TRUE;
- }
- break;
- case TNG_TRAJ_FORCES:
- srenew(fr->f, fr->natoms);
- convert_array_to_real_array(values,
- reinterpret_cast<real *>(fr->f),
- getDistanceScaleFactor(input),
- fr->natoms,
- DIM,
- datatype);
- fr->bF = TRUE;
- break;
- case TNG_GMX_LAMBDA:
- switch (datatype)
- {
- case TNG_FLOAT_DATA:
- fr->lambda = *(reinterpret_cast<float *>(values));
- break;
- case TNG_DOUBLE_DATA:
- fr->lambda = *(reinterpret_cast<double *>(values));
- break;
- default:
- gmx_incons("Illegal datatype lambda value!");
- }
- fr->bLambda = TRUE;
- break;
- default:
- gmx_warning("Illegal block type! Currently GROMACS tools can only handle certain data types. Skipping block.");
- }
- /* values does not have to be freed before reading next frame. It will
- * be reallocated if it is not NULL. */
- }
-
- fr->step = frameNumber;
- fr->bStep = TRUE;
- // Convert the time to ps
- fr->time = frameTime / PICO;
- fr->bTime = TRUE;
-
- /* values must be freed before leaving this function */
- sfree(values);
-
- return bOK;
-#else
- GMX_UNUSED_VALUE(input);
- GMX_UNUSED_VALUE(fr);
- GMX_UNUSED_VALUE(requestedIds);
- GMX_UNUSED_VALUE(numRequestedIds);
- return FALSE;
-#endif
-}
-
-void gmx_print_tng_molecule_system(tng_trajectory_t input,
- FILE *stream)
-{
-#if GMX_USE_TNG
- gmx_int64_t nMolecules, nChains, nResidues, nAtoms, *molCntList;
- tng_molecule_t molecule;
- tng_chain_t chain;
- tng_residue_t residue;
- tng_atom_t atom;
- char str[256], varNAtoms;
-
- tng_num_molecule_types_get(input, &nMolecules);
- tng_molecule_cnt_list_get(input, &molCntList);
- /* Can the number of particles change in the trajectory or is it constant? */
- tng_num_particles_variable_get(input, &varNAtoms);
-
- for (gmx_int64_t i = 0; i < nMolecules; i++)
- {
- tng_molecule_of_index_get(input, i, &molecule);
- tng_molecule_name_get(input, molecule, str, 256);
- if (varNAtoms == TNG_CONSTANT_N_ATOMS)
- {
- if ((int)molCntList[i] == 0)
- {
- continue;
- }
- fprintf(stream, "Molecule: %s, count: %d\n", str, (int)molCntList[i]);
- }
- else
- {
- fprintf(stream, "Molecule: %s\n", str);
- }
- tng_molecule_num_chains_get(input, molecule, &nChains);
- if (nChains > 0)
- {
- for (gmx_int64_t j = 0; j < nChains; j++)
- {
- tng_molecule_chain_of_index_get(input, molecule, j, &chain);
- tng_chain_name_get(input, chain, str, 256);
- fprintf(stream, "\tChain: %s\n", str);
- tng_chain_num_residues_get(input, chain, &nResidues);
- for (gmx_int64_t k = 0; k < nResidues; k++)
- {
- tng_chain_residue_of_index_get(input, chain, k, &residue);
- tng_residue_name_get(input, residue, str, 256);
- fprintf(stream, "\t\tResidue: %s\n", str);
- tng_residue_num_atoms_get(input, residue, &nAtoms);
- for (gmx_int64_t l = 0; l < nAtoms; l++)
- {
- tng_residue_atom_of_index_get(input, residue, l, &atom);
- tng_atom_name_get(input, atom, str, 256);
- fprintf(stream, "\t\t\tAtom: %s", str);
- tng_atom_type_get(input, atom, str, 256);
- fprintf(stream, " (%s)\n", str);
- }
- }
- }
- }
- /* It is possible to have a molecule without chains, in which case
- * residues in the molecule can be iterated through without going
- * through chains. */
- else
- {
- tng_molecule_num_residues_get(input, molecule, &nResidues);
- if (nResidues > 0)
- {
- for (gmx_int64_t k = 0; k < nResidues; k++)
- {
- tng_molecule_residue_of_index_get(input, molecule, k, &residue);
- tng_residue_name_get(input, residue, str, 256);
- fprintf(stream, "\t\tResidue: %s\n", str);
- tng_residue_num_atoms_get(input, residue, &nAtoms);
- for (gmx_int64_t l = 0; l < nAtoms; l++)
- {
- tng_residue_atom_of_index_get(input, residue, l, &atom);
- tng_atom_name_get(input, atom, str, 256);
- fprintf(stream, "\t\t\tAtom: %s", str);
- tng_atom_type_get(input, atom, str, 256);
- fprintf(stream, " (%s)\n", str);
- }
- }
- }
- else
- {
- tng_molecule_num_atoms_get(input, molecule, &nAtoms);
- for (gmx_int64_t l = 0; l < nAtoms; l++)
- {
- tng_molecule_atom_of_index_get(input, molecule, l, &atom);
- tng_atom_name_get(input, atom, str, 256);
- fprintf(stream, "\t\t\tAtom: %s", str);
- tng_atom_type_get(input, atom, str, 256);
- fprintf(stream, " (%s)\n", str);
- }
- }
- }
- }
-#else
- GMX_UNUSED_VALUE(input);
- GMX_UNUSED_VALUE(stream);
-#endif
-}
-
-gmx_bool gmx_get_tng_data_block_types_of_next_frame(tng_trajectory_t input,
- int frame,
- int nRequestedIds,
- gmx_int64_t *requestedIds,
- gmx_int64_t *nextFrame,
- gmx_int64_t *nBlocks,
- gmx_int64_t **blockIds)
-{
-#if GMX_USE_TNG
- tng_function_status stat;
-
- stat = tng_util_trajectory_next_frame_present_data_blocks_find(input, frame,
- nRequestedIds, requestedIds,
- nextFrame,
- nBlocks, blockIds);
-
- if (stat == TNG_CRITICAL)
- {
- gmx_file("Cannot read TNG file. Cannot find data blocks of next frame.");
- }
- else if (stat == TNG_FAILURE)
- {
- return FALSE;
- }
- return TRUE;
-#else
- GMX_UNUSED_VALUE(input);
- GMX_UNUSED_VALUE(frame);
- GMX_UNUSED_VALUE(nRequestedIds);
- GMX_UNUSED_VALUE(requestedIds);
- GMX_UNUSED_VALUE(nextFrame);
- GMX_UNUSED_VALUE(nBlocks);
- GMX_UNUSED_VALUE(blockIds);
- return FALSE;
-#endif
-}
-
-gmx_bool gmx_get_tng_data_next_frame_of_block_type(tng_trajectory_t input,
- gmx_int64_t blockId,
- real **values,
- gmx_int64_t *frameNumber,
- double *frameTime,
- gmx_int64_t *nValuesPerFrame,
- gmx_int64_t *nAtoms,
- real *prec,
- char *name,
- int maxLen,
- gmx_bool *bOK)
-{
-#if GMX_USE_TNG
- tng_function_status stat;
- char datatype = -1;
- gmx_int64_t codecId;
- int blockDependency;
- void *data = 0;
- double localPrec;
-
- stat = tng_data_block_name_get(input, blockId, name, maxLen);
- if (stat != TNG_SUCCESS)
- {
- gmx_file("Cannot read next frame of TNG file");
- }
- stat = tng_data_block_dependency_get(input, blockId, &blockDependency);
- if (stat != TNG_SUCCESS)
- {
- gmx_file("Cannot read next frame of TNG file");
- }
- if (blockDependency & TNG_PARTICLE_DEPENDENT)
- {
- tng_num_particles_get(input, nAtoms);
- stat = tng_util_particle_data_next_frame_read(input,
- blockId,
- &data,
- &datatype,
- frameNumber,
- frameTime);
- }
- else
- {
- *nAtoms = 1; /* There are not actually any atoms, but it is used for
- allocating memory */
- stat = tng_util_non_particle_data_next_frame_read(input,
- blockId,
- &data,
- &datatype,
- frameNumber,
- frameTime);
- }
- if (stat == TNG_CRITICAL)
- {
- gmx_file("Cannot read next frame of TNG file");
- }
- if (stat == TNG_FAILURE)
- {
- *bOK = TRUE;
- return FALSE;
- }
-
- stat = tng_data_block_num_values_per_frame_get(input, blockId, nValuesPerFrame);
- if (stat != TNG_SUCCESS)
- {
- gmx_file("Cannot read next frame of TNG file");
- }
- srenew(*values, sizeof(real) * *nValuesPerFrame * *nAtoms);
- convert_array_to_real_array(data,
- *values,
- getDistanceScaleFactor(input),
- *nAtoms,
- *nValuesPerFrame,
- datatype);
-
- tng_util_frame_current_compression_get(input, blockId, &codecId, &localPrec);
-
- /* This must be updated if/when more lossy compression methods are added */
- if (codecId != TNG_TNG_COMPRESSION)
- {
- *prec = -1.0;
- }
- else
- {
- *prec = localPrec;
- }
-
- *bOK = TRUE;
- return TRUE;
-#else
- GMX_UNUSED_VALUE(input);
- GMX_UNUSED_VALUE(blockId);
- GMX_UNUSED_VALUE(values);
- GMX_UNUSED_VALUE(frameNumber);
- GMX_UNUSED_VALUE(frameTime);
- GMX_UNUSED_VALUE(nValuesPerFrame);
- GMX_UNUSED_VALUE(nAtoms);
- GMX_UNUSED_VALUE(prec);
- GMX_UNUSED_VALUE(name);
- GMX_UNUSED_VALUE(maxLen);
- GMX_UNUSED_VALUE(bOK);
- return FALSE;
-#endif
-}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#ifndef GMX_FILEIO_TNGIO_FOR_TOOLS_H
-#define GMX_FILEIO_TNGIO_FOR_TOOLS_H
-
-#include <stdio.h>
-
-#include "tng/tng_io_fwd.h"
-
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/real.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-struct gmx_mtop_t;
-struct t_trxframe;
-
-/*! \brief Prepare to write TNG output from trajectory conversion tools */
-void gmx_prepare_tng_writing(const char *filename,
- char mode,
- tng_trajectory_t *in,
- tng_trajectory_t *out,
- int nAtoms,
- const struct gmx_mtop_t *mtop,
- const int *index,
- const char *indexGroupName);
-
-/*! \brief Write a trxframe to a TNG file
- *
- * \param output Trajectory to write to
- * \param frame Frame data to write
- * \param natoms Number of atoms to actually write
- *
- * The natoms field in frame is the number of atoms in the system. The
- * parameter natoms supports writing an index-group subset of the
- * atoms.
- */
-void gmx_write_tng_from_trxframe(tng_trajectory_t output,
- const t_trxframe *frame,
- int natoms);
-
-/*! \brief Creates a molecule containing only the indexed atoms and sets
- * the number of all other molecules to 0. Works similar to a
- * selection group. */
-void gmx_tng_setup_atom_subgroup(tng_trajectory_t tng,
- const int nind,
- const int *ind,
- const char *name);
-
-/*! \brief Read the first/next TNG frame. */
-gmx_bool gmx_read_next_tng_frame(tng_trajectory_t input,
- struct t_trxframe *fr,
- gmx_int64_t *requestedIds,
- int numRequestedIds);
-
-/*! \brief Print the molecule system to stream */
-void gmx_print_tng_molecule_system(tng_trajectory_t input,
- FILE *stream);
-
-/*! \brief Get a list of block IDs present in the next frame with data. */
-gmx_bool gmx_get_tng_data_block_types_of_next_frame(tng_trajectory_t input,
- int frame,
- int nRequestedIds,
- gmx_int64_t *requestedIds,
- gmx_int64_t *nextFrame,
- gmx_int64_t *nBlocks,
- gmx_int64_t **blockIds);
-
-/*! \brief Get data of the next frame with data from the data block
- * with the specified block ID. */
-gmx_bool gmx_get_tng_data_next_frame_of_block_type(tng_trajectory_t input,
- gmx_int64_t blockId,
- real **values,
- gmx_int64_t *frameNumber,
- double *frameTime,
- gmx_int64_t *nValuesPerFrame,
- gmx_int64_t *nAtoms,
- real *prec,
- char *name,
- int maxLen,
- gmx_bool *bOK);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/keyvaluetreeserializer.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
#include "gromacs/utility/txtdump.h"
tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
tpxv_PullExternalPotential, /**< Added pull type external potential */
+ tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
tpxv_Count /**< the total number of tpxv versions */
};
/* This number should be the most recent backwards incompatible version
* I.e., if this number is 9, we cannot read tpx version 9 with this code.
*/
-static const int tpx_incompatible_version = 9;
+static const int tpx_incompatible_version = 30; // GMX3.2 has version 31
* 2. ascending file version number
*/
static const t_ftupd ftupd[] = {
- { 20, F_CUBICBONDS },
- { 20, F_CONNBONDS },
- { 20, F_HARMONIC },
{ 34, F_FENEBONDS },
{ 43, F_TABBONDS },
{ 43, F_TABBONDSNC },
{ 70, F_RESTRBONDS },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
{ 76, F_LINEAR_ANGLES },
- { 30, F_CROSS_BOND_BONDS },
- { 30, F_CROSS_BOND_ANGLES },
- { 30, F_UREY_BRADLEY },
{ 34, F_QUARTIC_ANGLES },
{ 43, F_TABANGLES },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
- { 26, F_FOURDIHS },
- { 26, F_PIDIHS },
{ 43, F_TABDIHS },
{ 65, F_CMAP },
{ 60, F_GB12 },
{ 32, F_COUL_RECIP },
{ 93, F_LJ_RECIP },
{ 46, F_DPD },
- { 30, F_POLARIZATION },
{ 36, F_THOLE_POL },
{ 90, F_FBPOSRES },
- { 22, F_DISRESVIOL },
- { 22, F_ORIRES },
- { 22, F_ORIRESDEV },
- { 26, F_DIHRES },
- { 26, F_DIHRESVIOL },
{ 49, F_VSITE4FDN },
{ 50, F_VSITEN },
{ 46, F_COM_PULL },
- { 20, F_EQM },
{ 46, F_ECONSERVED },
{ 69, F_VTEMP_NOLONGERUSED},
{ 66, F_PDISPCORR },
}
else
{
- pcrd->externalPotentialProvider = NULL;
+ pcrd->externalPotentialProvider = nullptr;
}
}
else
{
if (bRead)
{
- pcrd->externalPotentialProvider = NULL;
+ pcrd->externalPotentialProvider = nullptr;
}
}
/* Note that we try to support adding new geometries without
else
{
fepvals->n_lambda = 0;
- fepvals->all_lambda = NULL;
+ fepvals->all_lambda = nullptr;
if (fepvals->init_lambda >= 0)
{
fepvals->separate_dvdl[efptFEP] = TRUE;
}
}
- if (file_version >= 13)
- {
- gmx_fio_do_real(fio, fepvals->sc_alpha);
- }
- else
- {
- fepvals->sc_alpha = 0;
- }
+ gmx_fio_do_real(fio, fepvals->sc_alpha);
if (file_version >= 38)
{
gmx_fio_do_int(fio, fepvals->sc_power);
{
fepvals->sc_r_power = 6.0;
}
- if (file_version >= 15)
- {
- gmx_fio_do_real(fio, fepvals->sc_sigma);
- }
- else
- {
- fepvals->sc_sigma = 0.3;
- }
+ gmx_fio_do_real(fio, fepvals->sc_sigma);
if (bRead)
{
if (file_version >= 71)
}
+static void do_legacy_efield(t_fileio *fio, gmx::KeyValueTreeObjectBuilder *root)
+{
+ const char *const dimName[] = { "x", "y", "z" };
+
+ auto appliedForcesObj = root->addObject("applied-forces");
+ auto efieldObj = appliedForcesObj.addObject("electric-field");
+ // The content of the tpr file for this feature has
+ // been the same since gromacs 4.0 that was used for
+ // developing.
+ for (int j = 0; j < DIM; ++j)
+ {
+ int n, nt;
+ gmx_fio_do_int(fio, n);
+ gmx_fio_do_int(fio, nt);
+ std::vector<real> aa(n+1), phi(nt+1), at(nt+1), phit(nt+1);
+ gmx_fio_ndo_real(fio, aa.data(), n);
+ gmx_fio_ndo_real(fio, phi.data(), n);
+ gmx_fio_ndo_real(fio, at.data(), nt);
+ gmx_fio_ndo_real(fio, phit.data(), nt);
+ if (n > 0)
+ {
+ if (n > 1 || nt > 1)
+ {
+ gmx_fatal(FARGS, "Can not handle tpr files with more than one electric field term per direction.");
+ }
+ auto dimObj = efieldObj.addObject(dimName[j]);
+ dimObj.addValue<real>("E0", aa[0]);
+ dimObj.addValue<real>("omega", at[0]);
+ dimObj.addValue<real>("t0", phi[0]);
+ dimObj.addValue<real>("sigma", phit[0]);
+ }
+ }
+}
+
static void do_inputrec(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
int file_version, real *fudgeQQ)
{
- int i, j, k, *tmp, idum = 0;
+ int i, j, k, idum = 0;
real rdum, bd_temp;
- rvec vdum;
- gmx_bool bSimAnn, bdum = 0;
- real zerotemptime, finish_t, init_temp, finish_temp;
+ gmx_bool bdum = 0;
if (file_version != tpx_version)
{
file_version, tpx_version);
}
- if (bRead)
- {
- init_inputrec(ir);
- }
-
if (file_version == 0)
{
return;
}
+ gmx::KeyValueTreeBuilder paramsBuilder;
+ gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
+
/* Basic inputrec stuff */
gmx_fio_do_int(fio, ir->eI);
if (file_version >= 62)
ir->nsteps = idum;
}
- if (file_version > 25)
+ if (file_version >= 62)
{
- if (file_version >= 62)
- {
- gmx_fio_do_int64(fio, ir->init_step);
- }
- else
- {
- gmx_fio_do_int(fio, idum);
- ir->init_step = idum;
- }
+ gmx_fio_do_int64(fio, ir->init_step);
}
else
{
- ir->init_step = 0;
+ gmx_fio_do_int(fio, idum);
+ ir->init_step = idum;
}
if (file_version >= 58)
* since we always want it, also without reading the inputrec.
*/
gmx_fio_do_int(fio, ir->ePBC);
- if ((file_version <= 15) && (ir->ePBC == 2))
- {
- ir->ePBC = epbcNONE;
- }
if (file_version >= 45)
{
gmx_fio_do_int(fio, ir->bPeriodicMols);
ir->nstcomm = abs(ir->nstcomm);
/* ignore nstcheckpoint */
- if (file_version > 25 && file_version < tpxv_RemoveObsoleteParameters1)
+ if (file_version < tpxv_RemoveObsoleteParameters1)
{
gmx_fio_do_int(fio, idum);
}
gmx_fio_do_int(fio, ir->nstcgsteep);
- if (file_version >= 30)
- {
- gmx_fio_do_int(fio, ir->nbfgscorr);
- }
- else if (bRead)
- {
- ir->nbfgscorr = 10;
- }
+ gmx_fio_do_int(fio, ir->nbfgscorr);
gmx_fio_do_int(fio, ir->nstlog);
gmx_fio_do_int(fio, ir->nstxout);
ir->delta_t = rdum;
}
gmx_fio_do_real(fio, ir->x_compression_precision);
- if (file_version < 19)
- {
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_int(fio, idum);
- }
- if (file_version < 18)
- {
- gmx_fio_do_int(fio, idum);
- }
if (file_version >= 81)
{
gmx_fio_do_real(fio, ir->verletbuf_tol);
ir->epsilon_rf = 1.0;
}
}
- if (file_version >= 29)
- {
- gmx_fio_do_real(fio, ir->tabext);
- }
- else
- {
- ir->tabext = 1.0;
- }
+ gmx_fio_do_real(fio, ir->tabext);
- if (file_version > 25)
- {
- gmx_fio_do_int(fio, ir->gb_algorithm);
- gmx_fio_do_int(fio, ir->nstgbradii);
- gmx_fio_do_real(fio, ir->rgbradii);
- gmx_fio_do_real(fio, ir->gb_saltconc);
- gmx_fio_do_int(fio, ir->implicit_solvent);
- }
- else
- {
- ir->gb_algorithm = egbSTILL;
- ir->nstgbradii = 1;
- ir->rgbradii = 1.0;
- ir->gb_saltconc = 0;
- ir->implicit_solvent = eisNO;
- }
+ gmx_fio_do_int(fio, ir->gb_algorithm);
+ gmx_fio_do_int(fio, ir->nstgbradii);
+ gmx_fio_do_real(fio, ir->rgbradii);
+ gmx_fio_do_real(fio, ir->gb_saltconc);
+ gmx_fio_do_int(fio, ir->implicit_solvent);
if (file_version >= 55)
{
gmx_fio_do_real(fio, ir->gb_epsilon_solvent);
{
ir->ewald_rtol_lj = ir->ewald_rtol;
}
-
- if (file_version >= 24)
- {
- gmx_fio_do_int(fio, ir->ewald_geometry);
- }
- else
- {
- ir->ewald_geometry = eewg3D;
- }
-
- if (file_version <= 17)
- {
- ir->epsilon_surface = 0;
- if (file_version == 17)
- {
- gmx_fio_do_int(fio, idum);
- }
- }
- else
- {
- gmx_fio_do_real(fio, ir->epsilon_surface);
- }
+ gmx_fio_do_int(fio, ir->ewald_geometry);
+ gmx_fio_do_real(fio, ir->epsilon_surface);
/* ignore bOptFFT */
if (file_version < tpxv_RemoveObsoleteParameters1)
{
ir->nsttcouple = ir->nstcalcenergy;
}
- if (file_version <= 15)
- {
- gmx_fio_do_int(fio, idum);
- }
- if (file_version <= 17)
- {
- gmx_fio_do_int(fio, ir->epct);
- if (file_version <= 15)
- {
- if (ir->epct == 5)
- {
- ir->epct = epctSURFACETENSION;
- }
- gmx_fio_do_int(fio, idum);
- }
- ir->epct -= 1;
- /* we have removed the NO alternative at the beginning */
- if (ir->epct == -1)
- {
- ir->epc = epcNO;
- ir->epct = epctISOTROPIC;
- }
- else
- {
- ir->epc = epcBERENDSEN;
- }
- }
- else
- {
- gmx_fio_do_int(fio, ir->epc);
- gmx_fio_do_int(fio, ir->epct);
- }
+ gmx_fio_do_int(fio, ir->epc);
+ gmx_fio_do_int(fio, ir->epct);
if (file_version >= 71)
{
gmx_fio_do_int(fio, ir->nstpcouple);
ir->nstpcouple = ir->nstcalcenergy;
}
gmx_fio_do_real(fio, ir->tau_p);
- if (file_version <= 15)
- {
- gmx_fio_do_rvec(fio, vdum);
- clear_mat(ir->ref_p);
- for (i = 0; i < DIM; i++)
- {
- ir->ref_p[i][i] = vdum[i];
- }
- }
- else
- {
- gmx_fio_do_rvec(fio, ir->ref_p[XX]);
- gmx_fio_do_rvec(fio, ir->ref_p[YY]);
- gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
- }
- if (file_version <= 15)
- {
- gmx_fio_do_rvec(fio, vdum);
- clear_mat(ir->compress);
- for (i = 0; i < DIM; i++)
- {
- ir->compress[i][i] = vdum[i];
- }
- }
- else
- {
- gmx_fio_do_rvec(fio, ir->compress[XX]);
- gmx_fio_do_rvec(fio, ir->compress[YY]);
- gmx_fio_do_rvec(fio, ir->compress[ZZ]);
- }
+ gmx_fio_do_rvec(fio, ir->ref_p[XX]);
+ gmx_fio_do_rvec(fio, ir->ref_p[YY]);
+ gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
+ gmx_fio_do_rvec(fio, ir->compress[XX]);
+ gmx_fio_do_rvec(fio, ir->compress[YY]);
+ gmx_fio_do_rvec(fio, ir->compress[ZZ]);
if (file_version >= 47)
{
gmx_fio_do_int(fio, ir->refcoord_scaling);
clear_rvec(ir->posres_com);
clear_rvec(ir->posres_comB);
}
- if ((file_version > 25) && (file_version < 79))
+ if (file_version < 79)
{
gmx_fio_do_int(fio, ir->andersen_seed);
}
{
ir->andersen_seed = 0;
}
- if (file_version < 26)
- {
- gmx_fio_do_gmx_bool(fio, bSimAnn);
- gmx_fio_do_real(fio, zerotemptime);
- }
if (file_version < 37)
{
gmx_fio_do_real(fio, ir->shake_tol);
if (file_version < 54)
{
+ // cppcheck-suppress redundantPointerOp
gmx_fio_do_real(fio, *fudgeQQ);
}
gmx_fio_do_int(fio, ir->efep);
- if (file_version <= 14 && ir->efep != efepNO)
- {
- ir->efep = efepYES;
- }
do_fepvals(fio, ir->fepvals, bRead, file_version);
if (file_version >= 79)
gmx_fio_do_int(fio, ir->eDisre);
}
gmx_fio_do_int(fio, ir->eDisreWeighting);
- if (file_version < 22)
- {
- if (ir->eDisreWeighting == 0)
- {
- ir->eDisreWeighting = edrwEqual;
- }
- else
- {
- ir->eDisreWeighting = edrwConservative;
- }
- }
gmx_fio_do_gmx_bool(fio, ir->bDisreMixed);
gmx_fio_do_real(fio, ir->dr_fc);
gmx_fio_do_real(fio, ir->dr_tau);
gmx_fio_do_int(fio, ir->nstdisreout);
- if (file_version >= 22)
- {
- gmx_fio_do_real(fio, ir->orires_fc);
- gmx_fio_do_real(fio, ir->orires_tau);
- gmx_fio_do_int(fio, ir->nstorireout);
- }
- else
- {
- ir->orires_fc = 0;
- ir->orires_tau = 0;
- ir->nstorireout = 0;
- }
+ gmx_fio_do_real(fio, ir->orires_fc);
+ gmx_fio_do_real(fio, ir->orires_tau);
+ gmx_fio_do_int(fio, ir->nstorireout);
/* ignore dihre_fc */
- if (file_version >= 26 && file_version < 79)
+ if (file_version < 79)
{
gmx_fio_do_real(fio, rdum);
if (file_version < 56)
gmx_fio_do_real(fio, ir->em_stepsize);
gmx_fio_do_real(fio, ir->em_tol);
- if (file_version >= 22)
- {
- gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
- }
- else if (bRead)
- {
- ir->bShakeSOR = TRUE;
- }
- if (file_version >= 11)
- {
- gmx_fio_do_int(fio, ir->niter);
- }
- else if (bRead)
- {
- ir->niter = 25;
- fprintf(stderr, "Note: niter not in run input file, setting it to %d\n",
- ir->niter);
- }
- if (file_version >= 21)
- {
- gmx_fio_do_real(fio, ir->fc_stepsize);
- }
- else
- {
- ir->fc_stepsize = 0;
- }
+ gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
+ gmx_fio_do_int(fio, ir->niter);
+ gmx_fio_do_real(fio, ir->fc_stepsize);
gmx_fio_do_int(fio, ir->eConstrAlg);
gmx_fio_do_int(fio, ir->nProjOrder);
gmx_fio_do_real(fio, ir->LincsWarnAngle);
- if (file_version <= 14)
- {
- gmx_fio_do_int(fio, idum);
- }
- if (file_version >= 26)
- {
- gmx_fio_do_int(fio, ir->nLincsIter);
- }
- else if (bRead)
- {
- ir->nLincsIter = 1;
- fprintf(stderr, "Note: nLincsIter not in run input file, setting it to %d\n",
- ir->nLincsIter);
- }
+ gmx_fio_do_int(fio, ir->nLincsIter);
if (file_version < 33)
{
gmx_fio_do_real(fio, bd_temp);
clear_rvec(ir->deform[i]);
}
}
- if (file_version >= 14)
- {
- gmx_fio_do_real(fio, ir->cos_accel);
- }
- else if (bRead)
- {
- ir->cos_accel = 0;
- }
+ gmx_fio_do_real(fio, ir->cos_accel);
+
gmx_fio_do_int(fio, ir->userint1);
gmx_fio_do_int(fio, ir->userint2);
gmx_fio_do_int(fio, ir->userint3);
}
if (ir->opts.ngtc > 0)
{
- if (bRead && file_version < 13)
- {
- snew(tmp, ir->opts.ngtc);
- gmx_fio_ndo_int(fio, tmp, ir->opts.ngtc);
- for (i = 0; i < ir->opts.ngtc; i++)
- {
- ir->opts.nrdf[i] = tmp[i];
- }
- sfree(tmp);
- }
- else
- {
- gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
- }
+ gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc);
gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc);
if (file_version < 33 && ir->eI == eiBD)
{
gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc);
}
- if (file_version >= 12)
- {
- gmx_fio_ndo_int(fio, ir->opts.egp_flags,
- ir->opts.ngener*ir->opts.ngener);
- }
+ gmx_fio_ndo_int(fio, ir->opts.egp_flags,
+ ir->opts.ngener*ir->opts.ngener);
- if (bRead && file_version < 26)
+ /* First read the lists with annealing and npoints for each group */
+ gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
+ gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc);
+ for (j = 0; j < (ir->opts.ngtc); j++)
{
- for (i = 0; i < ir->opts.ngtc; i++)
- {
- if (bSimAnn)
- {
- ir->opts.annealing[i] = eannSINGLE;
- ir->opts.anneal_npoints[i] = 2;
- snew(ir->opts.anneal_time[i], 2);
- snew(ir->opts.anneal_temp[i], 2);
- /* calculate the starting/ending temperatures from reft, zerotemptime, and nsteps */
- finish_t = ir->init_t + ir->nsteps * ir->delta_t;
- init_temp = ir->opts.ref_t[i]*(1-ir->init_t/zerotemptime);
- finish_temp = ir->opts.ref_t[i]*(1-finish_t/zerotemptime);
- ir->opts.anneal_time[i][0] = ir->init_t;
- ir->opts.anneal_time[i][1] = finish_t;
- ir->opts.anneal_temp[i][0] = init_temp;
- ir->opts.anneal_temp[i][1] = finish_temp;
- }
- else
- {
- ir->opts.annealing[i] = eannNO;
- ir->opts.anneal_npoints[i] = 0;
- }
- }
- }
- else
- {
- /* file version 26 or later */
- /* First read the lists with annealing and npoints for each group */
- gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
- gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, ir->opts.ngtc);
- for (j = 0; j < (ir->opts.ngtc); j++)
+ k = ir->opts.anneal_npoints[j];
+ if (bRead)
{
- k = ir->opts.anneal_npoints[j];
- if (bRead)
- {
- snew(ir->opts.anneal_time[j], k);
- snew(ir->opts.anneal_temp[j], k);
- }
- gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
- gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
+ snew(ir->opts.anneal_time[j], k);
+ snew(ir->opts.anneal_temp[j], k);
}
+ gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
+ gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
}
/* Walls */
if (file_version >= 45)
ir->wall_ewald_zfac = 3;
}
/* Cosine stuff for electric fields */
- for (j = 0; (j < DIM); j++)
+ if (file_version < tpxv_GenericParamsForElectricField)
{
- gmx_fio_do_int(fio, ir->ex[j].n);
- gmx_fio_do_int(fio, ir->et[j].n);
- if (bRead)
- {
- snew(ir->ex[j].a, ir->ex[j].n);
- snew(ir->ex[j].phi, ir->ex[j].n);
- snew(ir->et[j].a, ir->et[j].n);
- snew(ir->et[j].phi, ir->et[j].n);
- }
- gmx_fio_ndo_real(fio, ir->ex[j].a, ir->ex[j].n);
- gmx_fio_ndo_real(fio, ir->ex[j].phi, ir->ex[j].n);
- gmx_fio_ndo_real(fio, ir->et[j].a, ir->et[j].n);
- gmx_fio_ndo_real(fio, ir->et[j].phi, ir->et[j].n);
+ do_legacy_efield(fio, ¶msObj);
}
/* Swap ions */
}
/* end of QMMM stuff */
}
+
+ if (file_version >= tpxv_GenericParamsForElectricField)
+ {
+ gmx::FileIOXdrSerializer serializer(fio);
+ if (bRead)
+ {
+ paramsObj.mergeObject(
+ gmx::deserializeKeyValueTree(&serializer));
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(ir->params != nullptr,
+ "Parameters should be present when writing inputrec");
+ gmx::serializeKeyValueTree(*ir->params, &serializer);
+ }
+ }
+ if (bRead)
+ {
+ ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
+ }
}
gmx_fio_do_real(fio, iparams->harmonic.krB);
}
-void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
- gmx_bool bRead, int file_version)
+static void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
+ gmx_bool bRead, int file_version)
{
int idum;
real rdum;
gmx_fio_do_real(fio, iparams->anharm_polarize.khyp);
break;
case F_WATER_POL:
- if (file_version < 31)
- {
- gmx_fatal(FARGS, "Old tpr files with water_polarization not supported. Make a new.");
- }
gmx_fio_do_real(fio, iparams->wpol.al_x);
gmx_fio_do_real(fio, iparams->wpol.al_y);
gmx_fio_do_real(fio, iparams->wpol.al_z);
case F_POSRES:
gmx_fio_do_rvec(fio, iparams->posres.pos0A);
gmx_fio_do_rvec(fio, iparams->posres.fcA);
- if (bRead && file_version < 27)
- {
- copy_rvec(iparams->posres.pos0A, iparams->posres.pos0B);
- copy_rvec(iparams->posres.fcA, iparams->posres.fcB);
- }
- else
- {
- gmx_fio_do_rvec(fio, iparams->posres.pos0B);
- gmx_fio_do_rvec(fio, iparams->posres.fcB);
- }
+ gmx_fio_do_rvec(fio, iparams->posres.pos0B);
+ gmx_fio_do_rvec(fio, iparams->posres.fcB);
break;
case F_FBPOSRES:
gmx_fio_do_int(fio, iparams->fbposres.geom);
break;
case F_RBDIHS:
gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
- if (file_version >= 25)
- {
- gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
- }
+ gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
break;
case F_FOURDIHS:
/* Fourier dihedrals are internally represented
if (bClear)
{
ilist[j].nr = 0;
- ilist[j].iatoms = NULL;
+ ilist[j].iatoms = nullptr;
}
else
{
}
if (bRead)
{
- if ((block->nalloc_index > 0) && (NULL != block->index))
+ if ((block->nalloc_index > 0) && (nullptr != block->index))
{
sfree(block->index);
}
{
atom->atomnumber = 0;
}
- if (file_version < 23)
- {
- myngrp = 8;
- }
- else if (file_version < 39)
+ if (file_version < 39)
{
myngrp = 9;
}
{
int j, myngrp;
- if (file_version < 23)
- {
- myngrp = 8;
- }
- else if (file_version < 39)
+ if (file_version < 39)
{
myngrp = 9;
}
}
if (bRead)
{
+ /* Since we have always written all t_atom properties in the tpr file
+ * (at least for all backward compatible versions), we don't store
+ * but simple set the booleans here.
+ */
+ atoms->haveMass = TRUE;
+ atoms->haveCharge = TRUE;
+ atoms->haveType = TRUE;
+ atoms->haveBState = TRUE;
+ atoms->havePdbInfo = FALSE;
+
snew(atoms->atom, atoms->nr);
snew(atoms->atomname, atoms->nr);
snew(atoms->atomtype, atoms->nr);
{
snew(groups->grpname, groups->ngrpname);
}
- atoms->pdbinfo = NULL;
+ atoms->pdbinfo = nullptr;
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState, "Mass, charge, atomtype and B-state parameters should be present in t_atoms when writing a tpr file");
}
for (i = 0; (i < atoms->nr); i++)
{
do_atom(fio, &atoms->atom[i], egcNR, bRead, file_version, groups, i);
}
do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
- if (bRead && (file_version <= 20))
- {
- for (i = 0; i < atoms->nr; i++)
- {
- atoms->atomtype[i] = put_symtab(symtab, "?");
- atoms->atomtypeB[i] = put_symtab(symtab, "?");
- }
- }
- else
- {
- do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
- do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
- }
+ do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
+ do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
+
do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
if (file_version < 57)
{
if (bRead)
{
- groups->grpnr[g] = NULL;
+ groups->grpnr[g] = nullptr;
}
}
else
{
int j;
- if (file_version > 25)
+ gmx_fio_do_int(fio, atomtypes->nr);
+ j = atomtypes->nr;
+ if (bRead)
{
- gmx_fio_do_int(fio, atomtypes->nr);
- j = atomtypes->nr;
- if (bRead)
- {
- snew(atomtypes->radius, j);
- snew(atomtypes->vol, j);
- snew(atomtypes->surftens, j);
- snew(atomtypes->atomnumber, j);
- snew(atomtypes->gb_radius, j);
- snew(atomtypes->S_hct, j);
- }
- gmx_fio_ndo_real(fio, atomtypes->radius, j);
- gmx_fio_ndo_real(fio, atomtypes->vol, j);
- gmx_fio_ndo_real(fio, atomtypes->surftens, j);
- if (file_version >= 40)
- {
- gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
- }
- if (file_version >= 60)
- {
- gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
- gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
- }
+ snew(atomtypes->radius, j);
+ snew(atomtypes->vol, j);
+ snew(atomtypes->surftens, j);
+ snew(atomtypes->atomnumber, j);
+ snew(atomtypes->gb_radius, j);
+ snew(atomtypes->S_hct, j);
}
- else
+ gmx_fio_ndo_real(fio, atomtypes->radius, j);
+ gmx_fio_ndo_real(fio, atomtypes->vol, j);
+ gmx_fio_ndo_real(fio, atomtypes->surftens, j);
+ if (file_version >= 40)
{
- /* File versions prior to 26 cannot do GBSA,
- * so they dont use this structure
- */
- atomtypes->nr = 0;
- atomtypes->radius = NULL;
- atomtypes->vol = NULL;
- atomtypes->surftens = NULL;
- atomtypes->atomnumber = NULL;
- atomtypes->gb_radius = NULL;
- atomtypes->S_hct = NULL;
+ gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
+ }
+ if (file_version >= 60)
+ {
+ gmx_fio_ndo_real(fio, atomtypes->gb_radius, j);
+ gmx_fio_ndo_real(fio, atomtypes->S_hct, j);
}
}
else
{
symbuf = symtab->symbuf;
- while (symbuf != NULL)
+ while (symbuf != nullptr)
{
for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
{
{
mtop->ffparams.cmap_grid.ngrid = 0;
mtop->ffparams.cmap_grid.grid_spacing = 0;
- mtop->ffparams.cmap_grid.cmapdata = NULL;
+ mtop->ffparams.cmap_grid.cmapdata = nullptr;
}
if (file_version >= 57)
gmx_fio_do_string(fio, file_tag);
}
- if (fileVersion >= 26)
- {
- gmx_fio_do_int(fio, fileGeneration);
- }
- else
- {
- fileGeneration = 0;
- }
+ gmx_fio_do_int(fio, fileGeneration);
if (fileVersion >= 81)
{
}
gmx_fio_do_int(fio, tpx->natoms);
- if (fileVersion >= 28)
- {
- gmx_fio_do_int(fio, tpx->ngtc);
- }
- else
- {
- tpx->ngtc = 0;
- }
+ gmx_fio_do_int(fio, tpx->ngtc);
+
if (fileVersion < 62)
{
gmx_fio_do_int(fio, idum);
}
static int do_tpx(t_fileio *fio, gmx_bool bRead,
- t_inputrec *ir, t_state *state, gmx_mtop_t *mtop,
- gmx_bool bXVallocated)
+ t_inputrec *ir, t_state *state, rvec *x, rvec *v,
+ gmx_mtop_t *mtop)
{
t_tpxheader tpx;
- t_inputrec dum_ir;
gmx_mtop_t dum_top;
gmx_bool TopOnlyOK;
- rvec *xptr, *vptr;
int ePBC;
gmx_bool bPeriodicMols;
if (!bRead)
{
+ GMX_RELEASE_ASSERT(state != nullptr, "Cannot write a null state");
+ GMX_RELEASE_ASSERT(x == nullptr && v == nullptr, "Passing separate x and v pointers to do_tpx() is not supported when writing");
+
tpx.natoms = state->natoms;
tpx.ngtc = state->ngtc;
tpx.fep_state = state->fep_state;
tpx.lambda = state->lambda[efptFEP];
- tpx.bIr = (ir != NULL);
- tpx.bTop = (mtop != NULL);
- tpx.bX = (state->x != NULL);
- tpx.bV = (state->v != NULL);
+ tpx.bIr = (ir != nullptr);
+ tpx.bTop = (mtop != nullptr);
+ tpx.bX = (state->flags & (1 << estX));
+ tpx.bV = (state->flags & (1 << estV));
tpx.bF = FALSE;
tpx.bBox = TRUE;
}
+ else
+ {
+ GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr), "Passing x==NULL and v!=NULL is not supported");
+ }
- TopOnlyOK = (ir == NULL);
+ TopOnlyOK = (ir == nullptr);
int fileVersion; /* Version number of the code that wrote the file */
int fileGeneration; /* Generation version number of the code that wrote the file */
if (bRead)
{
- state->flags = 0;
- if (bXVallocated)
+ state->flags = 0;
+ init_gtc_state(state, tpx.ngtc, 0, 0);
+ if (x == nullptr)
{
- xptr = state->x;
- vptr = state->v;
- init_state(state, 0, tpx.ngtc, 0, 0, 0);
- state->natoms = tpx.natoms;
- state->nalloc = tpx.natoms;
- state->x = xptr;
- state->v = vptr;
- }
- else
- {
- init_state(state, tpx.natoms, tpx.ngtc, 0, 0, 0);
+ // v is also nullptr by the above assertion, so we may
+ // need to make memory in state for storing the contents
+ // of the tpx file.
+ if (tpx.bX)
+ {
+ state->flags |= (1 << estX);
+ }
+ if (tpx.bV)
+ {
+ state->flags |= (1 << estV);
+ }
+ state_change_natoms(state, tpx.natoms);
}
}
+ if (x == nullptr)
+ {
+ x = as_rvec_array(state->x.data());
+ v = as_rvec_array(state->v.data());
+ }
+
#define do_test(fio, b, p) if (bRead && (p != NULL) && !b) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
do_test(fio, tpx.bBox, state->box);
/* We initialize box_rel after reading the inputrec */
clear_mat(state->box_rel);
}
- if (fileVersion >= 28)
+ gmx_fio_ndo_rvec(fio, state->boxv, DIM);
+ if (fileVersion < 56)
{
- gmx_fio_ndo_rvec(fio, state->boxv, DIM);
- if (fileVersion < 56)
- {
- matrix mdum;
- gmx_fio_ndo_rvec(fio, mdum, DIM);
- }
+ matrix mdum;
+ gmx_fio_ndo_rvec(fio, mdum, DIM);
}
}
- if (state->ngtc > 0 && fileVersion >= 28)
+ if (state->ngtc > 0)
{
real *dumv;
snew(dumv, state->ngtc);
sfree(dumv);
}
- /* Prior to tpx version 26, the inputrec was here.
- * I moved it to enable partial forward-compatibility
- * for analysis/viewer programs.
- */
- if (fileVersion < 26)
- {
- do_test(fio, tpx.bIr, ir);
- if (tpx.bIr)
- {
- if (ir)
- {
- do_inputrec(fio, ir, bRead, fileVersion,
- mtop ? &mtop->ffparams.fudgeQQ : NULL);
- }
- else
- {
- do_inputrec(fio, &dum_ir, bRead, fileVersion,
- mtop ? &mtop->ffparams.fudgeQQ : NULL);
- done_inputrec(&dum_ir);
- }
-
- }
- }
-
do_test(fio, tpx.bTop, mtop);
if (tpx.bTop)
{
else
{
do_mtop(fio, &dum_top, bRead, fileVersion);
- done_mtop(&dum_top, TRUE);
+ done_mtop(&dum_top);
}
}
- do_test(fio, tpx.bX, state->x);
+ do_test(fio, tpx.bX, x);
if (tpx.bX)
{
if (bRead)
{
state->flags |= (1<<estX);
}
- gmx_fio_ndo_rvec(fio, state->x, state->natoms);
+ gmx_fio_ndo_rvec(fio, x, tpx.natoms);
}
- do_test(fio, tpx.bV, state->v);
+ do_test(fio, tpx.bV, v);
if (tpx.bV)
{
if (bRead)
{
state->flags |= (1<<estV);
}
- gmx_fio_ndo_rvec(fio, state->v, state->natoms);
+ gmx_fio_ndo_rvec(fio, v, tpx.natoms);
}
// No need to run do_test when the last argument is NULL
{
rvec *dummyForces;
snew(dummyForces, state->natoms);
- gmx_fio_ndo_rvec(fio, dummyForces, state->natoms);
+ gmx_fio_ndo_rvec(fio, dummyForces, tpx.natoms);
sfree(dummyForces);
}
*/
ePBC = -1;
bPeriodicMols = FALSE;
- if (fileVersion >= 26)
+
+ do_test(fio, tpx.bIr, ir);
+ if (tpx.bIr)
{
- do_test(fio, tpx.bIr, ir);
- if (tpx.bIr)
+ if (fileVersion >= 53)
{
- if (fileVersion >= 53)
+ /* Removed the pbc info from do_inputrec, since we always want it */
+ if (!bRead)
{
- /* Removed the pbc info from do_inputrec, since we always want it */
- if (!bRead)
- {
- ePBC = ir->ePBC;
- bPeriodicMols = ir->bPeriodicMols;
- }
- gmx_fio_do_int(fio, ePBC);
- gmx_fio_do_gmx_bool(fio, bPeriodicMols);
+ ePBC = ir->ePBC;
+ bPeriodicMols = ir->bPeriodicMols;
}
- if (fileGeneration <= tpx_generation && ir)
+ gmx_fio_do_int(fio, ePBC);
+ gmx_fio_do_gmx_bool(fio, bPeriodicMols);
+ }
+ if (fileGeneration <= tpx_generation && ir)
+ {
+ do_inputrec(fio, ir, bRead, fileVersion, mtop ? &mtop->ffparams.fudgeQQ : nullptr);
+ if (fileVersion < 51)
{
- do_inputrec(fio, ir, bRead, fileVersion, mtop ? &mtop->ffparams.fudgeQQ : NULL);
- if (fileVersion < 51)
- {
- set_box_rel(ir, state);
- }
- if (fileVersion < 53)
- {
- ePBC = ir->ePBC;
- bPeriodicMols = ir->bPeriodicMols;
- }
+ set_box_rel(ir, state);
}
- if (bRead && ir && fileVersion >= 53)
+ if (fileVersion < 53)
{
- /* We need to do this after do_inputrec, since that initializes ir */
- ir->ePBC = ePBC;
- ir->bPeriodicMols = bPeriodicMols;
+ ePBC = ir->ePBC;
+ bPeriodicMols = ir->bPeriodicMols;
}
}
+ if (bRead && ir && fileVersion >= 53)
+ {
+ /* We need to do this after do_inputrec, since that initializes ir */
+ ir->ePBC = ePBC;
+ ir->bPeriodicMols = bPeriodicMols;
+ }
}
if (bRead)
t_fileio *fio;
fio = open_tpx(fn, "r");
- do_tpxheader(fio, TRUE, tpx, TopOnlyOK, NULL, NULL);
+ do_tpxheader(fio, TRUE, tpx, TopOnlyOK, nullptr, nullptr);
close_tpx(fio);
}
fio = open_tpx(fn, "w");
do_tpx(fio, FALSE,
const_cast<t_inputrec *>(ir),
- const_cast<t_state *>(state),
- const_cast<gmx_mtop_t *>(mtop), FALSE);
+ const_cast<t_state *>(state), nullptr, nullptr,
+ const_cast<gmx_mtop_t *>(mtop));
close_tpx(fio);
}
t_fileio *fio;
fio = open_tpx(fn, "r");
- do_tpx(fio, TRUE, ir, state, mtop, FALSE);
+ do_tpx(fio, TRUE, ir, state, nullptr, nullptr, mtop);
close_tpx(fio);
}
t_state state;
int ePBC;
- state.x = x;
- state.v = v;
fio = open_tpx(fn, "r");
- ePBC = do_tpx(fio, TRUE, ir, &state, mtop, TRUE);
+ ePBC = do_tpx(fio, TRUE, ir, &state, x, v, mtop);
close_tpx(fio);
- *natoms = state.natoms;
+ *natoms = mtop->natoms;
if (box)
{
copy_mat(state.box, box);
}
- state.x = NULL;
- state.v = NULL;
- done_state(&state);
return ePBC;
}
ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
- *top = gmx_mtop_t_to_t_topology(&mtop);
+ *top = gmx_mtop_t_to_t_topology(&mtop, true);
return ePBC;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
-#include "gromacs/mdtypes/state.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
struct gmx_mtop_t;
struct t_atoms;
struct t_block;
struct t_inputrec;
+class t_state;
struct t_topology;
struct t_tpxheader
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/timecontrol.h"
#include "gromacs/fileio/tngio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xdrf.h"
* for skipping frames with -dt */
real tf; /* internal frame time */
t_trxframe *xframe;
- int nxframe;
t_fileio *fio;
tng_trajectory_t tng;
int natoms;
static void status_init(t_trxstatus *status)
{
status->flags = 0;
- status->nxframe = 0;
- status->xframe = NULL;
- status->fio = NULL;
+ status->xframe = nullptr;
+ status->fio = nullptr;
status->__frame = -1;
status->t0 = 0;
status->tf = 0;
- status->persistent_line = NULL;
- status->tng = NULL;
+ status->persistent_line = nullptr;
+ status->tng = nullptr;
}
void clear_trxframe(t_trxframe *fr, gmx_bool bFirst)
{
fr->not_ok = 0;
- fr->bTitle = FALSE;
fr->bStep = FALSE;
fr->bTime = FALSE;
fr->bLambda = FALSE;
{
fr->bDouble = FALSE;
fr->natoms = -1;
- fr->title = NULL;
fr->step = 0;
fr->time = 0;
fr->lambda = 0;
fr->fep_state = 0;
- fr->atoms = NULL;
+ fr->atoms = nullptr;
fr->prec = 0;
- fr->x = NULL;
- fr->v = NULL;
- fr->f = NULL;
+ fr->x = nullptr;
+ fr->v = nullptr;
+ fr->f = nullptr;
clear_mat(fr->box);
fr->bPBC = FALSE;
fr->ePBC = -1;
const int *ind, gmx_conect gc)
{
char title[STRLEN];
- rvec *xout = NULL, *vout = NULL, *fout = NULL;
+ rvec *xout = nullptr, *vout = nullptr, *fout = nullptr;
int i, ftp = -1;
real prec;
copy_rvec(fr->f[ind[i]], fout[i]);
}
}
- /* no break */
+ // fallthrough
case efXTC:
if (fr->bX)
{
if (ftp == efGRO)
{
write_hconf_indexed_p(gmx_fio_getfp(status->fio), title, fr->atoms, nind, ind,
- fr->x, fr->bV ? fr->v : NULL, fr->box);
+ fr->x, fr->bV ? fr->v : nullptr, fr->box);
}
else
{
}
break;
case efG96:
- write_g96_conf(gmx_fio_getfp(status->fio), fr, nind, ind);
+ sprintf(title, "frame t= %.3f", fr->time);
+ write_g96_conf(gmx_fio_getfp(status->fio), title, fr, nind, ind);
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe_indexed can not write %s",
{
sfree(fout);
}
- /* no break */
+ // fallthrough
case efXTC:
sfree(xout);
break;
gmx_incons("Sorry, can only prepare for TNG output.");
}
- if (*out == NULL)
+ if (*out == nullptr)
{
snew((*out), 1);
}
status_init(*out);
- if (in != NULL)
+ if (in != nullptr)
{
gmx_prepare_tng_writing(filename,
filemode,
break;
case efTRR:
gmx_trr_write_frame(status->fio, fr->step, fr->time, fr->lambda, fr->box, fr->natoms,
- fr->bX ? fr->x : NULL, fr->bV ? fr->v : NULL, fr->bF ? fr->f : NULL);
+ fr->bX ? fr->x : nullptr, fr->bV ? fr->v : nullptr, fr->bF ? fr->f : nullptr);
break;
case efGRO:
case efPDB:
if (gmx_fio_getftp(status->fio) == efGRO)
{
write_hconf_p(gmx_fio_getfp(status->fio), title, fr->atoms,
- fr->x, fr->bV ? fr->v : NULL, fr->box);
+ fr->x, fr->bV ? fr->v : nullptr, fr->box);
}
else
{
}
break;
case efG96:
- write_g96_conf(gmx_fio_getfp(status->fio), fr, -1, NULL);
+ write_g96_conf(gmx_fio_getfp(status->fio), title, fr, -1, nullptr);
break;
default:
gmx_fatal(FARGS, "Sorry, write_trxframe can not write %s",
fr.step = step;
fr.bTime = TRUE;
fr.time = time;
- fr.bAtoms = atoms != NULL;
+ fr.bAtoms = atoms != nullptr;
fr.atoms = const_cast<t_atoms *>(atoms);
fr.bX = TRUE;
fr.x = x;
- fr.bV = v != NULL;
+ fr.bV = v != nullptr;
fr.v = v;
fr.bBox = TRUE;
copy_mat(box, fr.box);
{
gmx_fio_close(status->fio);
}
+ sfree(status->persistent_line);
+#if GMX_USE_PLUGINS
+ sfree(status->vmdplugin);
+#endif
+ /* The memory in status->xframe is lost here,
+ * but the read_first_x/read_next_x functions are deprecated anyhow.
+ * read_first_frame/read_next_frame and close_trx should be used.
+ */
sfree(status);
}
fr->bBox = sh.box_size > 0;
if (status->flags & (TRX_READ_X | TRX_NEED_X))
{
- if (fr->x == NULL)
+ if (fr->x == nullptr)
{
snew(fr->x, sh.natoms);
}
}
if (status->flags & (TRX_READ_V | TRX_NEED_V))
{
- if (fr->v == NULL)
+ if (fr->v == nullptr)
{
snew(fr->v, sh.natoms);
}
}
if (status->flags & (TRX_READ_F | TRX_NEED_F))
{
- if (fr->f == NULL)
+ if (fr->f == nullptr)
{
snew(fr->f, sh.natoms);
}
double dbl;
atoms.nr = fr->natoms;
- atoms.atom = NULL;
- atoms.pdbinfo = NULL;
+ atoms.atom = nullptr;
+ atoms.pdbinfo = nullptr;
/* the other pointers in atoms should not be accessed if these are NULL */
snew(symtab, 1);
open_symtab(symtab);
- na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, NULL);
+ na = read_pdbfile(fp, title, &model_nr, &atoms, symtab, fr->x, &ePBC, boxpdb, TRUE, nullptr);
free_symtab(symtab);
sfree(symtab);
set_trxframe_ePBC(fr, ePBC);
break;
case efG96:
{
- t_symtab *symtab;
- snew(symtab, 1);
- open_symtab(symtab);
- read_g96_conf(gmx_fio_getfp(status->fio), NULL, fr,
+ t_symtab *symtab = nullptr;
+ read_g96_conf(gmx_fio_getfp(status->fio), nullptr, nullptr, fr,
symtab, status->persistent_line);
- free_symtab(symtab);
bRet = (fr->natoms > 0);
break;
}
}
break;
case efTNG:
- bRet = gmx_read_next_tng_frame(status->tng, fr, NULL, 0);
+ bRet = gmx_read_next_tng_frame(status->tng, fr, nullptr, 0);
break;
case efPDB:
bRet = pdb_next_x(status, gmx_fio_getfp(status->fio), fr);
int read_first_frame(const gmx_output_env_t *oenv, t_trxstatus **status,
const char *fn, t_trxframe *fr, int flags)
{
- t_fileio *fio;
+ t_fileio *fio = nullptr;
gmx_bool bFirst, bOK;
int ftp = fn2ftp(fn);
snew((*status), 1);
status_init( *status );
- (*status)->nxframe = 1;
initcount(*status);
(*status)->flags = flags;
/* allocate the persistent line */
snew((*status)->persistent_line, STRLEN+1);
}
- t_symtab *symtab;
- snew(symtab, 1);
- open_symtab(symtab);
- read_g96_conf(gmx_fio_getfp(fio), fn, fr, symtab, (*status)->persistent_line);
- free_symtab(symtab);
+ t_symtab *symtab = nullptr;
+ read_g96_conf(gmx_fio_getfp(fio), fn, nullptr, fr, symtab, (*status)->persistent_line);
gmx_fio_close(fio);
clear_trxframe(fr, FALSE);
if (flags & (TRX_READ_X | TRX_NEED_X))
break;
case efTNG:
fr->step = -1;
- if (!gmx_read_next_tng_frame((*status)->tng, fr, NULL, 0))
+ if (!gmx_read_next_tng_frame((*status)->tng, fr, nullptr, 0))
{
fr->not_ok = DATA_NOT_OK;
fr->natoms = 0;
read_first_frame(oenv, status, fn, &fr, TRX_NEED_X);
snew((*status)->xframe, 1);
- (*status)->nxframe = 1;
(*(*status)->xframe) = fr;
*t = (*status)->xframe->time;
*x = (*status)->xframe->x;
return bRet;
}
-void close_trj(t_trxstatus *status)
-{
- if (status == nullptr)
- {
- return;
- }
- gmx_tng_close(&status->tng);
- if (status->fio)
- {
- gmx_fio_close(status->fio);
- }
-
- /* The memory in status->xframe is lost here,
- * but the read_first_x/read_next_x functions are deprecated anyhow.
- * read_first_frame/read_next_frame and close_trx should be used.
- */
- sfree(status);
-}
-
void rewind_trj(t_trxstatus *status)
{
initcount(status);
t_topology *top;
snew(top, 1);
- epbc = read_tpx_top(fn, NULL, NULL, &natoms, NULL, NULL, top);
+ epbc = read_tpx_top(fn, nullptr, nullptr, &natoms, nullptr, nullptr, top);
if (ePBC)
{
*ePBC = epbc;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_trxframe *fr);
void close_trx(t_trxstatus *status);
-/* Close trajectory file as opened with read_first_x, read_frist_frame
- * or open_trx. Identical to close_trj.
+/* Close trajectory file as opened with read_first_x, read_first_frame
+ * or open_trx.
+ * Also frees memory in the structure.
*/
t_trxstatus *open_trx(const char *outfile, const char *filemode);
* status is the integer set in read_first_x.
*/
-void close_trj(t_trxstatus *status);
-/* Close trajectory file as opened with read_first_x, read_first_frame
- * or open_trx. Identical to close_trx.
- */
-
void rewind_trj(t_trxstatus *status);
/* Rewind trajectory file as opened with read_first_x */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
/* in case this library does not support the filetype, close it */
- if (vmdplugin->api == NULL)
+ if (vmdplugin->api == nullptr)
{
vmddlclose(handle);
}
sprintf(defpathenv, "%s\\University of Illinois\\VMD\\plugins\\WIN32\\molfile", progfolder);
#endif
- vmdplugin->api = NULL;
+ vmdplugin->api = nullptr;
vmdplugin->filetype = strrchr(fn, '.');
if (!vmdplugin->filetype)
{
* given at configure time. This last might be hard-coded to the
* default for VMD installs. */
pathenv = getenv("VMD_PLUGIN_PATH");
- if (pathenv == NULL)
+ if (pathenv == nullptr)
{
pathenv = getenv("VMDDIR");
- if (NULL == pathenv)
+ if (nullptr == pathenv)
{
printf("\nNeither VMD_PLUGIN_PATH or VMDDIR set. ");
printf("Using default location:\n%s\n", defpathenv);
strncpy(pathname, pathenv, sizeof(pathname));
#if !GMX_NATIVE_WINDOWS
strcat(pathname, "/*.so");
- glob(pathname, 0, NULL, &globbuf);
+ glob(pathname, 0, nullptr, &globbuf);
if (globbuf.gl_pathc == 0)
{
printf("\nNo VMD Plugins found\n"
"The architecture (e.g. 32bit versus 64bit) of GROMACS and VMD has to match.\n");
return 0;
}
- for (size_t i = 0; i < globbuf.gl_pathc && vmdplugin->api == NULL; i++)
+ for (size_t i = 0; i < globbuf.gl_pathc && vmdplugin->api == nullptr; i++)
{
/* FIXME: Undefined which plugin is chosen if more than one plugin
can read a certain file ending. Requires some additional command
return 0;
}
- if (vmdplugin->api == NULL)
+ if (vmdplugin->api == nullptr)
{
printf("\nNo plugin for %s found\n", vmdplugin->filetype);
return 0;
int read_first_vmd_frame(const char *fn, gmx_vmdplugin_t **vmdpluginp, t_trxframe *fr)
{
- molfile_timestep_metadata_t *metadata = NULL;
+ molfile_timestep_metadata_t *metadata = nullptr;
gmx_vmdplugin_t *vmdplugin;
snew(vmdplugin, 1);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
+#include <string>
+
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
wi->bAllowWarnings = bAllowWarnings;
wi->maxwarn = maxwarning;
- wi->nwarn_note = 0;
- wi->nwarn_warn = 0;
- wi->nwarn_error = 0;
+ warning_reset(wi);
strcpy(wi->filenm, "unknown");
wi->lineno = 0;
return wi;
}
+void warning_reset(warninp_t wi)
+{
+ wi->nwarn_note = 0;
+ wi->nwarn_warn = 0;
+ wi->nwarn_error = 0;
+}
+
void set_warning_line(warninp_t wi, const char *s, int line)
{
- if (s != NULL)
+ if (s != nullptr)
{
std::strcpy(wi->filenm, s);
}
char *temp, *temp2;
int i;
- if (s == NULL)
+ if (s == nullptr)
{
s = "Empty error message.";
}
}
}
+void warning(warninp_t wi, const std::string &s)
+{
+ warning(wi, s.c_str());
+}
+
void warning_note(warninp_t wi, const char *s)
{
wi->nwarn_note++;
low_warning(wi, "NOTE", wi->nwarn_note, s);
}
+void warning_note(warninp_t wi, const std::string &s)
+{
+ warning_note(wi, s.c_str());
+}
+
void warning_error(warninp_t wi, const char *s)
{
wi->nwarn_error++;
low_warning(wi, "ERROR", wi->nwarn_error, s);
}
+void warning_error(warninp_t wi, const std::string &s)
+{
+ warning_error(wi, s.c_str());
+}
+
static void print_warn_count(const char *type, int n)
{
if (n > 0)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_FILEIO_WARNINP_H
#define GMX_FILEIO_WARNINP_H
+#include <string>
+
#include "gromacs/utility/basedefinitions.h"
/* Abstract type for warning bookkeeping */
* So warning should only be called for issues that should be resolved,
* otherwise warning_note should be called.
*/
+//! Convenience wrapper.
+void
+warning(warninp_t wi, const std::string &s);
void
warning_note(warninp_t wi, const char *s);
* but 100% ok for other systems.
*/
+//! Convenience wrapper.
+void
+warning_note(warninp_t wi, const std::string &s);
+
void
warning_error(warninp_t wi, const char *s);
/* Issue an error, with the string s. If s == NULL, then warn_buf
* are printed, nwarn_error (local) is incremented.
*/
+//! Convenience wrapper.
+void
+warning_error(warninp_t wi, const std::string &s);
+
/*! \brief Issue an error with warning_error() and prevent further
* processing by calling check_warning_error().
*
gmx_bool warning_errors_exist(warninp_t wi);
/* Return whether any error-level warnings were issued to wi. */
+//! Resets the count for all kinds of warnings to zero.
+void warning_reset(warninp_t wi);
+
void
check_warning_error(warninp_t wi, int f_errno, const char *file, int line);
/* When warning_error has been called at least once gmx_fatal is called,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ps->nrgb = 0;
ps->maxrgb = 0;
- ps->rgb = NULL;
+ ps->rgb = nullptr;
ps->gen_ybox = 0;
ps->ostack = 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "xvgr.h"
+#include <cassert>
#include <cctype>
#include <cstring>
return (xvg_format == exvgXMGRACE || xvg_format == exvgXMGR);
}
-static char *xvgrstr(const char *gmx, const gmx_output_env_t *oenv,
+static char *xvgrstr(const std::string &gmx, const gmx_output_env_t *oenv,
char *buf, int buflen)
{
/* Supported greek letter names and corresponding xmgrace/xmgr symbols */
- const char *sym[] = { "beta", "chi", "delta", "eta", "lambda", "mu", "omega", "phi", "psi", "rho", "theta", NULL };
+ const char *sym[] = { "beta", "chi", "delta", "eta", "lambda", "mu", "omega", "phi", "psi", "rho", "theta", nullptr };
const char symc[] = { 'b', 'c', 'd', 'h', 'l', 'm', 'w', 'f', 'y', 'r', 'q', '\0' };
int xvgf;
gmx_bool bXVGR;
/* Check with the largest string we have ("lambda"), add one for \0 */
if (b + 6 + 1 >= buflen)
{
- gmx_fatal(FARGS, "Output buffer length in xvgstr (%d) too small to process xvg input string '%s'", buflen, gmx);
+ gmx_fatal(FARGS, "Output buffer length in xvgstr (%d) too small to process xvg input string '%s'", buflen, gmx.c_str());
}
if (gmx[g] == '\\')
{
{
/* Check for special symbol */
i = 0;
- while (sym[i] != NULL &&
- gmx_strncasecmp(sym[i], gmx+g, std::strlen(sym[i])) != 0)
+ while (sym[i] != nullptr &&
+ gmx_strncasecmp(sym[i], &gmx[g], std::strlen(sym[i])) != 0)
{
i++;
}
- if (sym[i] != NULL)
+ if (sym[i] != nullptr)
{
c = symc[i];
if (std::isupper(gmx[g]))
sprintf(buf+b, "%s%c%s", "\\8", c, "\\4");
break;
default:
- std::strncat(buf+b, gmx+g, std::strlen(sym[i]));
+ std::strncat(buf+b, &gmx[g], std::strlen(sym[i]));
b += std::strlen(sym[i]);
if (gmx[g+std::strlen(sym[i])] != ' ')
{
return buf;
}
-void xvgr_header(FILE *fp, const char *title, const char *xaxis,
- const char *yaxis, int exvg_graph_type,
+void xvgr_header(FILE *fp, const char *title, const std::string &xaxis,
+ const std::string &yaxis, int exvg_graph_type,
const gmx_output_env_t *oenv)
{
char buf[STRLEN];
}
}
-FILE *xvgropen_type(const char *fn, const char *title, const char *xaxis,
- const char *yaxis, int exvg_graph_type,
+FILE *xvgropen_type(const char *fn, const char *title, const std::string &xaxis,
+ const std::string &yaxis, int exvg_graph_type,
const gmx_output_env_t *oenv)
{
FILE *fp;
return fp;
}
-FILE *xvgropen(const char *fn, const char *title, const char *xaxis,
- const char *yaxis, const gmx_output_env_t *oenv)
+FILE *xvgropen(const char *fn, const char *title, const std::string &xaxis,
+ const std::string &yaxis, const gmx_output_env_t *oenv)
{
return xvgropen_type(fn, title, xaxis, yaxis, exvggtXNY, oenv);
}
curp = 0;
}
}
- if (fgets(*ptr + curp, len_remaining, fp) == NULL)
+ if (fgets(*ptr + curp, len_remaining, fp) == nullptr)
{
/* if last line, skip */
- return NULL;
+ return nullptr;
}
curp += len_remaining-1; /* overwrite the nul char in next iteration */
len_remaining = 1;
}
- while ((std::strchr(*ptr, '\n') == NULL) && (!feof(fp)));
+ while ((std::strchr(*ptr, '\n') == nullptr) && (!feof(fp)));
if (*len + STRLEN >= maxlen)
{
- return NULL; /* this line was too long */
+ return nullptr; /* this line was too long */
}
if (feof(fp))
{
/* We reached EOF before '\n', skip this last line. */
- return NULL;
+ return nullptr;
}
{
/* now remove newline */
int cur = 0;
#define prev (1-cur)
- if (NULL != ptr)
+ if (nullptr != ptr)
{
for (i = 0; (ptr[i] != '\0'); i++)
{
char *str;
ptr0 = std::strchr(line, '"');
- if (ptr0 != NULL)
+ if (ptr0 != nullptr)
{
ptr0++;
ptr1 = std::strchr(ptr0, '"');
- if (ptr1 != NULL)
+ if (ptr1 != nullptr)
{
str = gmx_strdup(ptr0);
str[ptr1-ptr0] = '\0';
{
FILE *fp;
char *ptr;
- char *base = NULL;
- char *fmt = NULL;
+ char *base = nullptr;
+ char *fmt = nullptr;
int k, line = 0, nny, nx, maxx, rval, legend_nalloc, set, nchar;
double lf;
- double **yy = NULL;
+ double **yy = nullptr;
char *tmpbuf;
int len = STRLEN;
*ny = 0;
fp = gmx_fio_fopen(fn, "r");
snew(tmpbuf, len);
- if (subtitle != NULL)
+ if (subtitle != nullptr)
{
- *subtitle = NULL;
+ *subtitle = nullptr;
}
legend_nalloc = 0;
- if (legend != NULL)
+ if (legend != nullptr)
{
- *legend = NULL;
+ *legend = nullptr;
}
- while ((ptr = fgets3(fp, &tmpbuf, &len, 10*STRLEN)) != NULL && ptr[0] != '&')
+ while ((ptr = fgets3(fp, &tmpbuf, &len, 10*STRLEN)) != nullptr && ptr[0] != '&')
{
line++;
trim(ptr);
if (ptr[0] == '@')
{
- if (legend != NULL)
+ if (legend != nullptr)
{
ptr++;
trim(ptr);
if (std::strncmp(ptr, "subtitle", 8) == 0)
{
ptr += 8;
- if (subtitle != NULL)
+ if (subtitle != nullptr)
{
*subtitle = read_xvgr_string(ptr);
}
{
if (*ny - 1 > legend_nalloc)
{
+ assert(legend);
srenew(*legend, *ny-1);
for (set = legend_nalloc; set < *ny-1; set++)
{
- (*legend)[set] = NULL;
+ (*legend)[set] = nullptr;
}
}
}
int read_xvg(const char *fn, double ***y, int *ny)
{
- return read_xvg_legend(fn, y, ny, NULL, NULL);
+ return read_xvg_legend(fn, y, ny, nullptr, nullptr);
}
void write_xvg(const char *fn, const char *title, int nx, int ny, real **y,
real **val;
t_nalloc = 0;
- *t = NULL;
- val = NULL;
- val_nalloc = NULL;
+ *t = nullptr;
+ val = nullptr;
+ val_nalloc = nullptr;
*nset = 0;
*dt = 0;
fp = gmx_fio_fopen(fn, "r");
srenew(val, *nset);
srenew(val_nalloc, *nset);
val_nalloc[set] = 0;
- val[set] = NULL;
+ val[set] = nullptr;
}
}
if (set == -1)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
+#include <string>
+
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
struct gmx_output_env_t;
/***************************************************
exvggtNONE, exvggtXNY, exvggtXYDY, exvggtXYDYDY, exvggtNR
};
-void xvgr_header(FILE *fp, const char *title, const char *xaxis,
- const char *yaxis, int exvg_graph_type,
+void xvgr_header(FILE *fp, const char *title, const std::string &xaxis,
+ const std::string &yaxis, int exvg_graph_type,
const struct gmx_output_env_t *oenv);
/* In most cases you want to use xvgropen_type, which does the same thing
* but takes a filename and opens it.
*/
-FILE *xvgropen_type(const char *fn, const char *title, const char *xaxis,
- const char *yaxis, int exvg_graph_type,
+FILE *xvgropen_type(const char *fn, const char *title, const std::string &xaxis,
+ const std::string &yaxis, int exvg_graph_type,
const struct gmx_output_env_t *oenv);
/* Open a file, and write a title, and axis-labels in Xvgr format
* or write nothing when oenv specifies so.
* The xvgr graph type enum is defined above.
*/
-FILE *xvgropen(const char *fn, const char *title, const char *xaxis,
- const char *yaxis, const struct gmx_output_env_t *oenv);
+FILE *xvgropen(const char *fn, const char *title, const std::string &xaxis,
+ const std::string &yaxis, const struct gmx_output_env_t *oenv);
/* Calls xvgropen_type with graph type xvggtXNY. */
/* Close xvgr file, and clean up internal file buffers correctly */
gmx_bool bTE, real te,
int nsets_in, int *nset, int *nval,
real *dt, real **t);
-#ifdef __cplusplus
-}
-#endif
-
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${GMXANA_SOURCES} PARENT_SCOPE)
if(BUILD_TESTING)
- add_subdirectory(legacytests)
+ add_subdirectory(tests)
endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* dihedrals to aromatic rings, COO, CONH2 or guanidinium are 2fold*/
if (Dih > edOmega && (dlist[i].atm.Cn[Dih-NONCHI+3] != -1))
{
- if ( ((std::strstr(name, "PHE") != NULL) && (Dih == edChi2)) ||
- ((std::strstr(name, "TYR") != NULL) && (Dih == edChi2)) ||
- ((std::strstr(name, "PTR") != NULL) && (Dih == edChi2)) ||
- ((std::strstr(name, "TRP") != NULL) && (Dih == edChi2)) ||
- ((std::strstr(name, "HIS") != NULL) && (Dih == edChi2)) ||
- ((std::strstr(name, "GLU") != NULL) && (Dih == edChi3)) ||
- ((std::strstr(name, "ASP") != NULL) && (Dih == edChi2)) ||
- ((std::strstr(name, "GLN") != NULL) && (Dih == edChi3)) ||
- ((std::strstr(name, "ASN") != NULL) && (Dih == edChi2)) ||
- ((std::strstr(name, "ARG") != NULL) && (Dih == edChi4)) )
+ if ( ((std::strstr(name, "PHE") != nullptr) && (Dih == edChi2)) ||
+ ((std::strstr(name, "TYR") != nullptr) && (Dih == edChi2)) ||
+ ((std::strstr(name, "PTR") != nullptr) && (Dih == edChi2)) ||
+ ((std::strstr(name, "TRP") != nullptr) && (Dih == edChi2)) ||
+ ((std::strstr(name, "HIS") != nullptr) && (Dih == edChi2)) ||
+ ((std::strstr(name, "GLU") != nullptr) && (Dih == edChi3)) ||
+ ((std::strstr(name, "ASP") != nullptr) && (Dih == edChi2)) ||
+ ((std::strstr(name, "GLN") != nullptr) && (Dih == edChi3)) ||
+ ((std::strstr(name, "ASN") != nullptr) && (Dih == edChi2)) ||
+ ((std::strstr(name, "ARG") != nullptr) && (Dih == edChi4)) )
{
multiplicity[j] = 2;
}
/* make a histogram pf culm. rotamer occupancy too */
snew(chi_prhist, nbin);
- make_histo(NULL, nframes, chi_prtrj, nbin, chi_prhist, 0, nbin);
+ make_histo(nullptr, nframes, chi_prtrj, nbin, chi_prhist, 0, nbin);
if (bAll)
{
sprintf(hisfile, "histo-chiprod%s.xvg", dlist[i].name);
total = 0;
teller = 0;
n_alloc = 0;
- *time = NULL;
- *trans_frac = NULL;
- *aver_angle = NULL;
+ *time = nullptr;
+ *trans_frac = nullptr;
+ *aver_angle = nullptr;
do
{
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
sfree(x);
sfree(angles[cur]);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
-void pswap(int *v1, int *v2)
+static void pswap(int *v1, int *v2)
{
int temp;
temp = *v1;
}
-void Swap (real *v1, real *v2)
+static void Swap (real *v1, real *v2)
{
real temp;
temp = *v1;
}
return iMin;
}
-
- else if (direction < 0)
+ else
{
while (iMax-iMin > 1)
{
}
}
return iMin-1;
-
- } /*end -ifelse direction*/
- return -1;
+ }
}
}
}
}
- else if (direction < 0)
+ else
{
for (i = stopindx; i >= startindx; i--)
{
}
}
- else
- {
- gmx_fatal(FARGS, "Startindex=stopindex=%d\n", startindx);
- }
-
return -1;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
sfree((*m)->m_ind);
sfree((*m)->erow);
sfree(*m);
- *m = NULL;
+ *m = nullptr;
}
real mat_energy(t_mat *m)
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "gromacs/topology/ifunc.h"
-#include "gromacs/topology/symtab.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-void replace_atom(t_topology *top, int inr, char *anm, char *resnm,
- real q, real m, int type)
-{
- t_atoms *atoms;
-
- atoms = &(top->atoms);
-
- /* Replace important properties of an atom by other properties */
- if ((inr < 0) || (inr > atoms->nr))
- {
- gmx_fatal(FARGS, "Replace_atom: inr (%d) not in %d .. %d", inr, 0, atoms->nr);
- }
- if (debug)
- {
- fprintf(debug, "Replacing atom %d ... ", inr);
- }
- /* Charge, mass and type */
- atoms->atom[inr].q = atoms->atom[inr].qB = q;
- atoms->atom[inr].m = atoms->atom[inr].mB = m;
- atoms->atom[inr].type = atoms->atom[inr].typeB = type;
-
- /* Residue name */
- atoms->resinfo[atoms->atom[inr].resind].name = put_symtab(&top->symtab, resnm);
- /* Atom name */
- atoms->atomname[inr] = put_symtab(&top->symtab, anm);
- if (debug)
- {
- fprintf(debug, " done\n");
- }
-}
-
-static void delete_from_interactions(t_idef *idef, int inr)
-{
- int i, j, k, nra, nnr;
- t_iatom *niatoms;
- gmx_bool bDel;
-
- /* Delete interactions including atom inr from lists */
- for (i = 0; (i < F_NRE); i++)
- {
- nra = interaction_function[i].nratoms;
- nnr = 0;
- snew(niatoms, idef->il[i].nr);
- for (j = 0; (j < idef->il[i].nr); j += nra+1)
- {
- bDel = FALSE;
- for (k = 0; (k < nra); k++)
- {
- if (idef->il[i].iatoms[j+k+1] == inr)
- {
- bDel = TRUE;
- }
- }
- if (!bDel)
- {
- /* If this does not need to be deleted, then copy it to temp array */
- for (k = 0; (k < nra+1); k++)
- {
- niatoms[nnr+k] = idef->il[i].iatoms[j+k];
- }
- nnr += nra+1;
- }
- }
- /* Copy temp array back */
- for (j = 0; (j < nnr); j++)
- {
- idef->il[i].iatoms[j] = niatoms[j];
- }
- idef->il[i].nr = nnr;
- sfree(niatoms);
- }
-}
-
-static void delete_from_block(t_block *block, int inr)
-{
- /* Update block data structure */
- int i, i1, j;
-
- for (i = 0; (i < block->nr); i++)
- {
- for (j = block->index[i]; (j < block->index[i+1]); j++)
- {
- if (j == inr)
- {
- /* This atom has to go */
- /* Change indices too */
- for (i1 = i+1; (i1 <= block->nr); i1++)
- {
- block->index[i1]--;
- }
- }
- }
- }
-}
-
-static void delete_from_blocka(t_blocka *block, int inr)
-{
- /* Update block data structure */
- int i, i1, j1, j, k;
-
- for (i = 0; (i < block->nr); i++)
- {
- for (j = block->index[i]; (j < block->index[i+1]); j++)
- {
- k = block->a[j];
- if (k == inr)
- {
- /* This atom has to go */
- for (j1 = j; (j1 < block->nra-1); j1++)
- {
- block->a[j1] = block->a[j1+1];
- }
- block->nra--;
- /* Change indices too */
- for (i1 = i+1; (i1 <= block->nr); i1++)
- {
- block->index[i1]--;
- }
- }
- }
- }
-}
-
-static void delete_from_atoms(t_atoms *atoms, int inr)
-{
- int i;
-
- /* Shift the atomnames down */
- for (i = inr; (i < atoms->nr-1); i++)
- {
- atoms->atomname[i] = atoms->atomname[i+1];
- }
-
- /* Shift the atom struct down */
- for (i = inr; (i < atoms->nr-1); i++)
- {
- atoms->atom[i] = atoms->atom[i+1];
- }
-
- if (atoms->pdbinfo)
- {
- /* Shift the pdbatom struct down */
- for (i = inr; (i < atoms->nr-1); i++)
- {
- atoms->pdbinfo[i] = atoms->pdbinfo[i+1];
- }
- }
- atoms->nr--;
-}
-
-void delete_atom(t_topology *top, int inr)
-{
- if ((inr < 0) || (inr >= top->atoms.nr))
- {
- gmx_fatal(FARGS, "Delete_atom: inr (%d) not in %d .. %d", inr, 0,
- top->atoms.nr);
- }
- if (debug)
- {
- fprintf(debug, "Deleting atom %d ...", inr);
- }
-
- /* First remove bonds etc. */
- delete_from_interactions(&top->idef, inr);
- /* Now charge groups etc. */
- delete_from_block(&(top->cgs), inr);
- delete_from_block(&(top->mols), inr);
- delete_from_blocka(&(top->excls), inr);
- /* Now from the atoms struct */
- delete_from_atoms(&top->atoms, inr);
- if (debug)
- {
- fprintf(debug, " done\n");
- }
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_trr_read_frame_header(status, &head, &bOK);
*natoms = head.natoms;
snew(*xav, *natoms);
- gmx_trr_read_frame_data(status, &head, box, *xav, NULL, NULL);
+ gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
if ((head.t >= -1.1) && (head.t <= -0.9))
{
{
fprintf(stderr, "Eigenvectors in %s were determined without fitting\n", file);
sfree(*xref);
- *xref = NULL;
+ *xref = nullptr;
}
gmx_trr_read_frame_header(status, &head, &bOK);
- gmx_trr_read_frame_data(status, &head, box, *xav, NULL, NULL);
+ gmx_trr_read_frame_data(status, &head, box, *xav, nullptr, nullptr);
}
else
{
*bFit = TRUE;
- *xref = NULL;
+ *xref = nullptr;
}
*bDMA = (head.lambda > 0.5);
if ((head.t <= -0.01) || (head.t >= 0.01))
*nvec = 0;
while (gmx_trr_read_frame_header(status, &head, &bOK))
{
- gmx_trr_read_frame_data(status, &head, box, x, NULL, NULL);
+ gmx_trr_read_frame_data(status, &head, box, x, nullptr, nullptr);
if (*nvec >= snew_size)
{
snew_size += 10;
if (WriteXref == eWXR_YES)
{
/* misuse lambda: 0/1 mass weighted fit no/yes */
- gmx_trr_write_frame(trrout, -1, -1, bDMR ? 1.0 : 0.0, zerobox, natoms, xref, NULL, NULL);
+ gmx_trr_write_frame(trrout, -1, -1, bDMR ? 1.0 : 0.0, zerobox, natoms, xref, nullptr, nullptr);
}
else if (WriteXref == eWXR_NOFIT)
{
/* misuse lambda: -1 no fit */
- gmx_trr_write_frame(trrout, -1, -1, -1.0, zerobox, natoms, x, NULL, NULL);
+ gmx_trr_write_frame(trrout, -1, -1, -1.0, zerobox, natoms, x, nullptr, nullptr);
}
/* misuse lambda: 0/1 mass weighted analysis no/yes */
- gmx_trr_write_frame(trrout, 0, 0, bDMA ? 1.0 : 0.0, zerobox, natoms, xav, NULL, NULL);
+ gmx_trr_write_frame(trrout, 0, 0, bDMA ? 1.0 : 0.0, zerobox, natoms, xav, nullptr, nullptr);
for (i = 0; i <= (end-begin); i++)
{
}
/* Store the eigenvalue in the time field */
- gmx_trr_write_frame(trrout, begin+i, eigval[vec], 0, zerobox, natoms, x, NULL, NULL);
+ gmx_trr_write_frame(trrout, begin+i, eigval[vec], 0, zerobox, natoms, x, nullptr, nullptr);
}
gmx_trr_close(trrout);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
rvec x[], int nca,
int caindex[], gmx_bool bFit)
{
- static rvec *xref = NULL;
- static real *mass = NULL;
+ static rvec *xref = nullptr;
+ static real *mass = nullptr;
const real d = 0.15; /* Rise per residue (nm) */
const real tw = 1.745; /* Twist per residue (rad) */
const real rad = 0.23; /* Radius of the helix (nm) */
gmx_fatal(FARGS, "Need at least 3 Calphas to fit to, (now %d)...\n", nca);
}
- if (xref == NULL)
+ if (xref == nullptr)
{
snew(xref, natoms);
snew(mass, natoms);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(pdbf, 1);
t_topology top;
- read_tps_conf(fn, &top, &pdbf->ePBC, &pdbf->x, NULL, pdbf->box, FALSE);
+ read_tps_conf(fn, &top, &pdbf->ePBC, &pdbf->x, nullptr, pdbf->box, FALSE);
pdbf->atoms = top.atoms;
fp = gmx_ffopen(fn, "r");
char buf[256], *ptr;
- while ((ptr = fgets2(buf, 255, fp)) != NULL)
+ while ((ptr = fgets2(buf, 255, fp)) != nullptr)
{
- if (std::strstr(buf, "Intermolecular") != NULL)
+ if (std::strstr(buf, "Intermolecular") != nullptr)
{
ptr = std::strchr(buf, '=');
sscanf(ptr+1, "%lf", &e);
pdbf->edocked = e;
}
- else if (std::strstr(buf, "Estimated Free") != NULL)
+ else if (std::strstr(buf, "Estimated Free") != nullptr)
{
ptr = std::strchr(buf, '=');
sscanf(ptr+1, "%lf", &e);
static t_pdbfile **read_em_all(const char *fn, int *npdbf)
{
- t_pdbfile **pdbf = 0;
+ t_pdbfile **pdbf = nullptr;
int i, maxpdbf;
char buf[256], name[256];
gmx_bool bExist;
gmx_stats_add_point(ed, i-start, pdbf[i]->edocked, 0, 0);
gmx_stats_add_point(ef, i-start, pdbf[i]->efree, 0, 0);
}
- gmx_stats_get_ase(ed, &aver, &sigma, NULL);
+ gmx_stats_get_ase(ed, &aver, &sigma, nullptr);
fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[FALSE], aver, sigma);
- gmx_stats_get_ase(ef, &aver, &sigma, NULL);
+ gmx_stats_get_ase(ef, &aver, &sigma, nullptr);
fprintf(fp, " <%12s> = %8.3f (+/- %6.3f)\n", etitles[TRUE], aver, sigma);
gmx_stats_free(ed);
gmx_stats_free(ef);
"energy or average energy."
};
t_filenm fnm[] = {
- { efPDB, "-f", NULL, ffREAD },
+ { efPDB, "-f", nullptr, ffREAD },
{ efXVG, "-od", "edocked", ffWRITE },
{ efXVG, "-of", "efree", ffWRITE },
{ efLOG, "-g", "anadock", ffWRITE }
#define NPA asize(pa)
FILE *fp;
- t_pdbfile **pdbf = NULL;
+ t_pdbfile **pdbf = nullptr;
int npdbf;
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc, 0,
- NULL, &oenv))
+ nullptr, &oenv))
{
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include <cassert>
#include <cmath>
#include <cstdlib>
#include <cstring>
#include <algorithm>
+#include <string>
#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
static void write_xvgr_graphs(const char *file, int ngraphs, int nsetspergraph,
const char *title, const char *subtitle,
- const char *xlabel, const char **ylabel,
+ const std::string &xlabel, const char **ylabel,
int n, real *x, real **y, real ***sy,
real scale_x, gmx_bool bZero, gmx_bool bSplit,
const gmx_output_env_t *oenv)
}
else
{
+ assert(sy);
ymin = sy[g][0][0];
ymax = sy[g][0][0];
for (s = 0; s < nsetspergraph; s++)
}
if (g == ngraphs-1)
{
- fprintf(out, "@ xaxis label \"%s\"\n", xlabel);
+ fprintf(out, "@ xaxis label \"%s\"\n", xlabel.c_str());
}
else
{
// better to be safe than sorry, so we check it with an assert.
// If we are in this comparison routine in the first place, neig2 should not be 0,
// so eigval2 should always be a valid pointer.
- GMX_RELEASE_ASSERT(eigval2 != NULL, "NULL pointer provided for eigval2");
+ GMX_RELEASE_ASSERT(eigval2 != nullptr, "NULL pointer provided for eigval2");
for (i = n; i < neig2; i++)
{
int noutvec, int *outvec, gmx_bool bSplit,
const gmx_output_env_t *oenv)
{
- FILE *xvgrout = NULL;
+ FILE *xvgrout = nullptr;
int nat, i, j, d, v, vec, nfr, nframes = 0, snew_size, frame;
- t_trxstatus *out = NULL;
+ t_trxstatus *out = nullptr;
t_trxstatus *status;
int noutvec_extr, imin, imax;
real *pmin, *pmax;
int *all_at;
matrix box;
rvec *xread, *x;
- real t, inp, **inprod = NULL;
+ real t, inp, **inprod = nullptr;
char str[STRLEN], str2[STRLEN], **ylabel, *c;
real fact;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
snew(x, natoms);
/* calculate x: a fitted struture of the selected atoms */
if (bFit)
{
- reset_x(nfit, ifit, nat, NULL, xread, w_rls);
+ reset_x(nfit, ifit, nat, nullptr, xread, w_rls);
do_fit(nat, w_rls, xref, xread);
}
for (i = 0; i < natoms; i++)
}
}
}
- write_trx(out, natoms, index, atoms, 0, t, box, xread, NULL, NULL);
+ write_trx(out, natoms, index, atoms, 0, t, box, xread, nullptr, nullptr);
}
nframes++;
}
if (projfile)
{
- GMX_RELEASE_ASSERT(inprod != NULL, "inprod must be non-NULL if projfile is non-NULL");
+ GMX_RELEASE_ASSERT(inprod != nullptr, "inprod must be non-NULL if projfile is non-NULL");
snew(ylabel, noutvec);
for (v = 0; v < noutvec; v++)
{
ylabel[v] = gmx_strdup(str);
}
sprintf(str, "projection on eigenvectors (%s)", proj_unit);
- write_xvgr_graphs(projfile, noutvec, 1, str, NULL, output_env_get_xvgr_tlabel(oenv),
+ write_xvgr_graphs(projfile, noutvec, 1, str, nullptr, output_env_get_xvgr_tlabel(oenv),
(const char **)ylabel,
- nframes, inprod[noutvec], inprod, NULL,
+ nframes, inprod[noutvec], inprod, nullptr,
output_env_get_time_factor(oenv), FALSE, bSplit, oenv);
}
{
t_atoms atoms;
rvec *x;
- real *b = NULL;
+ real *b = nullptr;
matrix box;
char *resnm, *atnm;
gmx_bool bPDB, b4D;
}
if ( ( b4D || bSplit ) && bPDB)
{
- GMX_RELEASE_ASSERT(inprod != NULL, "inprod must be non-NULL with 4D or split PDB output options");
+ GMX_RELEASE_ASSERT(inprod != nullptr, "inprod must be non-NULL with 4D or split PDB output options");
out = gmx_ffopen(threedplotfile, "w");
fprintf(out, "HEADER %s\n", str);
}
else
{
- write_sto_conf(threedplotfile, str, &atoms, x, NULL, ePBC, box);
+ write_sto_conf(threedplotfile, str, &atoms, x, nullptr, ePBC, box);
}
done_atom(&atoms);
}
snew(pmax, noutvec_extr);
if (extreme == 0)
{
- GMX_RELEASE_ASSERT(inprod != NULL, "inprod must be non-NULL");
+ GMX_RELEASE_ASSERT(inprod != nullptr, "inprod must be non-NULL");
fprintf(stderr, "%11s %17s %17s\n", "eigenvector", "Minimum", "Maximum");
fprintf(stderr,
"%11s %10s %10s %10s %10s\n", "", "value", "frame", "value", "frame");
*eigvec[outvec[v]][i][d]/sqrtm[i]);
}
}
- write_trx(out, natoms, index, atoms, 0, frame, topbox, xread, NULL, NULL);
+ write_trx(out, natoms, index, atoms, 0, frame, topbox, xread, nullptr, nullptr);
}
close_trx(out);
}
write_xvgr_graphs(outfile, noutvec, 4, "Eigenvector components",
"black: total, red: x, green: y, blue: z",
"Atom number", (const char **)ylabel,
- natoms, x, NULL, y, 1, FALSE, FALSE, oenv);
+ natoms, x, nullptr, y, 1, FALSE, FALSE, oenv);
fprintf(stderr, "\n");
}
y[g][i] = std::sqrt(eigval[eignr[v]]*norm2(eigvec[v][i]))/sqrtm[i];
}
}
- write_xvgr_graphs(outfile, noutvec, 1, "RMS fluctuation (nm) ", NULL,
+ write_xvgr_graphs(outfile, noutvec, 1, "RMS fluctuation (nm) ", nullptr,
"Atom number", (const char **)ylabel,
- natoms, x, y, NULL, 1, TRUE, FALSE, oenv);
+ natoms, x, y, nullptr, 1, TRUE, FALSE, oenv);
fprintf(stderr, "\n");
}
t_topology top;
int ePBC = -1;
- const t_atoms *atoms = NULL;
- rvec *xtop, *xref1, *xref2, *xrefp = NULL;
+ const t_atoms *atoms = nullptr;
+ rvec *xtop, *xref1, *xref2, *xrefp = nullptr;
gmx_bool bDMR1, bDMA1, bDMR2, bDMA2;
- int nvec1, nvec2, *eignr1 = NULL, *eignr2 = NULL;
- rvec *xav1, *xav2, **eigvec1 = NULL, **eigvec2 = NULL;
+ int nvec1, nvec2, *eignr1 = nullptr, *eignr2 = nullptr;
+ rvec *xav1, *xav2, **eigvec1 = nullptr, **eigvec2 = nullptr;
matrix topbox;
real totmass, *sqrtm, *w_rls, t;
int natoms;
const char *indexfile;
int i, j, d;
int nout, *iout, noutvec, *outvec, nfit;
- int *index = NULL, *ifit = NULL;
+ int *index = nullptr, *ifit = nullptr;
const char *VecFile, *Vec2File, *topfile;
const char *EigFile, *Eig2File;
const char *CompFile, *RmsfFile, *ProjOnVecFile;
const char *OverlapFile, *InpMatFile;
gmx_bool bFit1, bFit2, bM, bIndex, bTPS, bTop, bVec2, bProj;
gmx_bool bFirstToLast, bFirstLastSet, bTraj, bCompare, bPDB3D;
- real *eigval1 = NULL, *eigval2 = NULL;
+ real *eigval1 = nullptr, *eigval2 = nullptr;
int neig1, neig2;
double **xvgdata;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
{ efTRN, "-v", "eigenvec", ffREAD },
{ efTRN, "-v2", "eigenvec2", ffOPTRD },
- { efTRX, "-f", NULL, ffOPTRD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffOPTRD },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-eig", "eigenval", ffOPTRD },
{ efXVG, "-eig2", "eigenval2", ffOPTRD },
{ efXVG, "-comp", "eigcomp", ffOPTWR },
if (!parse_common_args(&argc, argv,
PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
neig1 = DIM*natoms;
/* Overwrite eigenvalues from separate files if the user provides them */
- if (EigFile != NULL)
+ if (EigFile != nullptr)
{
int neig_tmp = read_xvg(EigFile, &xvgdata, &i);
if (neig_tmp != neig1)
neig2 = 0;
}
- if (Eig2File != NULL)
+ if (Eig2File != nullptr)
{
neig2 = read_xvg(Eig2File, &xvgdata, &i);
srenew(eigval2, neig2);
{
bM = FALSE;
}
- if ((xref1 == NULL) && (bM || bTraj))
+ if ((xref1 == nullptr) && (bM || bTraj))
{
bTPS = TRUE;
}
- xtop = NULL;
+ xtop = nullptr;
nfit = 0;
- ifit = NULL;
- w_rls = NULL;
+ ifit = nullptr;
+ w_rls = nullptr;
if (!bTPS)
{
else
{
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
- &top, &ePBC, &xtop, NULL, topbox, bM);
+ &top, &ePBC, &xtop, nullptr, topbox, bM);
atoms = &top.atoms;
gpbc = gmx_rmpbc_init(&top.idef, ePBC, atoms->nr);
gmx_rmpbc(gpbc, atoms->nr, topbox, xtop);
/* Fitting is only required for the projection */
if (bProj && bFit1)
{
- if (xref1 == NULL)
+ if (xref1 == nullptr)
{
printf("\nNote: the structure in %s should be the same\n"
" as the one used for the fit in g_covar\n", topfile);
}
snew(xrefp, atoms->nr);
- if (xref1 != NULL)
+ if (xref1 != nullptr)
{
/* Safety check between selected fit-group and reference structure read from the eigenvector file */
if (natoms != nfit)
{
copy_rvec(xtop[ifit[i]], xrefp[ifit[i]]);
}
- reset_x(nfit, ifit, atoms->nr, NULL, xrefp, w_rls);
+ reset_x(nfit, ifit, atoms->nr, nullptr, xrefp, w_rls);
}
}
gmx_rmpbc_done(gpbc);
{
printf("Select eigenvectors for output, end your selection with 0\n");
nout = -1;
- iout = NULL;
+ iout = nullptr;
do
{
if (bProj)
{
- project(bTraj ? opt2fn("-f", NFILE, fnm) : NULL,
- bTop ? &top : NULL, ePBC, topbox,
+ project(bTraj ? opt2fn("-f", NFILE, fnm) : nullptr,
+ bTop ? &top : nullptr, ePBC, topbox,
ProjOnVecFile, TwoDPlotFile, ThreeDPlotFile, FilterFile, skip,
ExtremeFile, bFirstLastSet, max, nextr, atoms, natoms, index,
bFit1, xrefp, nfit, ifit, w_rls,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/correlationfunctions/autocorr.h"
#include "gromacs/correlationfunctions/expfit.h"
#include "gromacs/correlationfunctions/integrate.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
}
}
snew(a, nset-1);
- chi2 = multi_regression(NULL, n, y, nset-1, xx, a);
+ chi2 = multi_regression(nullptr, n, y, nset-1, xx, a);
printf("Fitting %d data points in %d sets\n", n, nset-1);
printf("chi2 = %g\n", chi2);
printf("A =");
}
}
-void histogram(const char *distfile, real binwidth, int n, int nset, real **val,
- const gmx_output_env_t *oenv)
+static void histogram(const char *distfile, real binwidth, int n, int nset, real **val,
+ const gmx_output_env_t *oenv)
{
FILE *fp;
int i, s;
FILE *fp;
int i, s, edge = 0;
double av, var, err;
- real *tmp = NULL;
+ real *tmp = nullptr;
fp = gmx_ffopen(avfile, "w");
if ((avbar_opt == avbarERROR) && (nset == 1))
fitparm[2] = std::sqrt(tau1_est*(n-1)*dt);
do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt*n, oenv,
bDebugMode(), effnERREST, fitparm, 0,
- NULL);
+ nullptr);
}
if (bSingleExpFit || fitparm[0] < 0 || fitparm[2] < 0 || fitparm[1] < 0
|| (fitparm[1] > 1 && !bAllowNegLTCorr) || fitparm[2] > (n-1)*dt)
fitparm[2] = (n-1)*dt;
fprintf(stdout, "Will fix tau2 at the total time: %g\n", fitparm[2]);
do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt*n, oenv, bDebugMode(),
- effnERREST, fitparm, 4, NULL);
+ effnERREST, fitparm, 4, nullptr);
}
if (bSingleExpFit || fitparm[0] < 0 || fitparm[1] < 0
|| (fitparm[1] > 1 && !bAllowNegLTCorr))
fitparm[1] = 1.0;
fitparm[2] = 0.0;
do_lmfit(nbs, ybs, fitsig, 0, tbs, 0, dt*n, oenv, bDebugMode(),
- effnERREST, fitparm, 6, NULL);
+ effnERREST, fitparm, 6, nullptr);
}
}
ee = optimal_error_estimate(sig[s], fitparm, n*dt);
fitsig[i] = 1;
}
}
- low_do_autocorr(NULL, oenv, NULL, n, 1, -1, &ac,
+ low_do_autocorr(nullptr, oenv, nullptr, n, 1, -1, &ac,
dt, eacNormal, 1, FALSE, TRUE,
FALSE, 0, 0, effnNONE);
ac_fit[0] = 0.5*acint;
ac_fit[1] = 0.95;
ac_fit[2] = 10*acint;
- do_lmfit(n/nb_min, ac, fitsig, dt, 0, 0, fitlen*dt, oenv,
- bDebugMode(), effnEXPEXP, ac_fit, 0, NULL);
+ do_lmfit(n/nb_min, ac, fitsig, dt, nullptr, 0, fitlen*dt, oenv,
+ bDebugMode(), effnEXPEXP, ac_fit, 0, nullptr);
ac_fit[3] = 1 - ac_fit[1];
fprintf(stdout, "Set %3d: ac erest %g a %g tau1 %g tau2 %g\n",
}
fprintf(debug, "RMS difference in derivatives is %g\n", std::sqrt(d2/nn));
}
- analyse_corr(nn, time, val[0], val[2], kt, NULL, NULL, NULL, fit_start,
+ analyse_corr(nn, time, val[0], val[2], kt, nullptr, nullptr, nullptr, fit_start,
temp);
sfree(kt);
}
int npargs, t_pargs *ppa, const gmx_output_env_t *oenv,
const char *fn_fitted)
{
- real *c1 = NULL, *sig = NULL;
+ real *c1 = nullptr, *sig = nullptr;
double *fitparm;
real tendfit, tbeginfit;
int i, efitfn, nparm;
}
else
{
- char *buf2 = NULL;
+ char *buf2 = nullptr;
int s, buflen = 0;
- if (NULL != fn_fitted)
+ if (nullptr != fn_fitted)
{
buflen = std::strlen(fn_fitted)+32;
snew(buf2, buflen);
}
for (s = 0; s < nset; s++)
{
- char *buf = NULL;
- if (NULL != fn_fitted)
+ char *buf = nullptr;
+ if (nullptr != fn_fitted)
{
snew(buf, buflen);
snprintf(buf, n, "%s_%d.xvg", buf2, s);
/* must correspond to enum avbar* declared at beginning of file */
static const char *avbar_opt[avbarNR+1] = {
- NULL, "none", "stddev", "error", "90", NULL
+ nullptr, "none", "stddev", "error", "90", nullptr
};
t_pargs pa[] = {
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(ppa);
return 0;
}
distfile = opt2fn_null("-dist", NFILE, fnm);
avfile = opt2fn_null("-av", NFILE, fnm);
eefile = opt2fn_null("-ee", NFILE, fnm);
- if (opt2parg_bSet("-fitfn", npargs, ppa) && acfile == NULL)
+ if (opt2parg_bSet("-fitfn", npargs, ppa) && acfile == nullptr)
{
fitfile = opt2fn("-g", NFILE, fnm);
}
{
for (s = 0; s < nset; s++)
{
- sum = evaluate_integral(n, t, val[s], NULL, aver_start, &stddev);
+ sum = evaluate_integral(n, t, val[s], nullptr, aver_start, &stddev);
printf("Integral %d %10.5f +/- %10.5f\n", s+1, sum, stddev);
}
}
}
- if (fitfile != NULL)
+ if (fitfile != nullptr)
{
print_fitted_function(fitfile,
opt2fn_null("-fitted", NFILE, fnm),
power_fit(n, nset, val, t);
}
- if (acfile != NULL)
+ if (acfile != nullptr)
{
if (bSubAv)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
}
- gmx_trr_write_frame(fio, i, time[i], 0, box, na, x, NULL, NULL);
+ gmx_trr_write_frame(fio, i, time[i], 0, box, na, x, nullptr, nullptr);
}
gmx_trr_close(fio);
sfree(x);
"records a histogram of the times between such transitions,",
"assuming the input trajectory frames are equally spaced in time."
};
- static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
+ static const char *opt[] = { nullptr, "angle", "dihedral", "improper", "ryckaert-bellemans", nullptr };
static gmx_bool bALL = FALSE, bChandler = FALSE, bAverCorr = FALSE, bPBC = TRUE;
static real binwidth = 1;
t_pargs pa[] = {
real aver, aver2, aversig; /* fraction trans dihedrals */
double tfrac = 0;
char title[256];
- real **dih = NULL; /* mega array with all dih. angles at all times*/
+ real **dih = nullptr; /* mega array with all dih. angles at all times*/
real *time, *trans_frac, *aver_angle;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efNDX, NULL, "angle", ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efNDX, nullptr, "angle", ffREAD },
{ efXVG, "-od", "angdist", ffWRITE },
{ efXVG, "-ov", "angaver", ffOPTWR },
{ efXVG, "-of", "dihfrac", ffOPTWR },
{ efXVG, "-ot", "dihtrans", ffOPTWR },
{ efXVG, "-oh", "trhisto", ffOPTWR },
{ efXVG, "-oc", "dihcorr", ffOPTWR },
- { efTRR, "-or", NULL, ffOPTWR }
+ { efTRR, "-or", nullptr, ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
+ sfree(ppa);
return 0;
}
maxang = 360.0;
bRb = FALSE;
- GMX_RELEASE_ASSERT(opt[0] != NULL, "Internal option inconsistency; opt[0]==NULL after processing");
+ GMX_RELEASE_ASSERT(opt[0] != nullptr, "Internal option inconsistency; opt[0]==NULL after processing");
switch (opt[0][0])
{
{
sprintf(title, "Dihedral Distribution: %s", grpname);
- calc_distribution_props(maxangstat, angstat, -180.0, 0, NULL, &S2);
+ calc_distribution_props(maxangstat, angstat, -180.0, 0, nullptr, &S2);
fprintf(stderr, "Order parameter S^2 = %g\n", S2);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
return FALSE;
}
- if (name == NULL && lc->names[index] == NULL)
+ if (name == nullptr && lc->names[index] == nullptr)
{
return TRUE;
}
- if ((name == NULL) != (lc->names[index] == NULL))
+ if ((name == nullptr) != (lc->names[index] == nullptr))
{
return FALSE;
}
static void xvg_init(xvg_t *ba)
{
- ba->filename = NULL;
+ ba->filename = nullptr;
ba->nset = 0;
ba->np_alloc = 0;
- ba->np = NULL;
- ba->y = NULL;
+ ba->np = nullptr;
+ ba->y = nullptr;
}
static void samples_init(samples_t *s, lambda_vec_t *native_lambda,
s->derivative = derivative;
s->ndu = 0;
- s->du = NULL;
- s->t = NULL;
+ s->du = nullptr;
+ s->t = nullptr;
s->start_time = s->delta_time = 0;
- s->hist = NULL;
- s->du_alloc = NULL;
- s->t_alloc = NULL;
- s->hist_alloc = NULL;
+ s->hist = nullptr;
+ s->du_alloc = nullptr;
+ s->t_alloc = nullptr;
+ s->hist_alloc = nullptr;
s->ndu_alloc = 0;
s->nt_alloc = 0;
r->start = 0;
r->end = s->ndu;
r->use = TRUE;
- r->s = NULL;
+ r->s = nullptr;
}
static void sample_coll_init(sample_coll_t *sc, lambda_vec_t *native_lambda,
sc->temp = temp;
sc->nsamples = 0;
- sc->s = NULL;
- sc->r = NULL;
+ sc->s = nullptr;
+ sc->r = nullptr;
sc->nsamples_alloc = 0;
sc->ntot = 0;
- sc->next = sc->prev = NULL;
+ sc->next = sc->prev = nullptr;
}
static void sample_coll_destroy(sample_coll_t *sc)
l->lambda = native_lambda;
l->temp = temp;
- l->next = NULL;
- l->prev = NULL;
+ l->next = nullptr;
+ l->prev = nullptr;
l->sc = &(l->sc_head);
- sample_coll_init(l->sc, native_lambda, NULL, 0.);
+ sample_coll_init(l->sc, native_lambda, nullptr, 0.);
l->sc->next = l->sc;
l->sc->prev = l->sc;
}
br->dg_stddev = 0;
br->dg_stddev_err = 0;
- br->a = NULL;
- br->b = NULL;
+ br->a = nullptr;
+ br->b = nullptr;
}
sc = sc->next;
}
- return NULL;
+ return nullptr;
}
/* insert li into an ordered list of lambda_colls */
}
/* write a collection of histograms to a file */
-void sim_data_histogram(sim_data_t *sd, const char *filename,
- int nbin_default, const gmx_output_env_t *oenv)
+static void sim_data_histogram(sim_data_t *sd, const char *filename,
+ int nbin_default, const gmx_output_env_t *oenv)
{
char label_x[STRLEN];
const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda";
FILE *fp;
lambda_data_t *bl;
int nsets = 0;
- char **setnames = NULL;
+ char **setnames = nullptr;
gmx_bool first_set = FALSE;
/* histogram data: */
- int *hist = NULL;
+ int *hist = nullptr;
int nbin = 0;
int nbin_alloc = 0;
double dx = 0;
{
if (!first_set)
{
- xvgr_new_dataset(fp, 0, 0, NULL, oenv);
+ xvgr_new_dataset(fp, 0, 0, nullptr, oenv);
}
sample_coll_make_hist(sc, &hist, &nbin_alloc, &nbin, &dx, &minval,
gmx_bool name_end_found = FALSE;
/* if the string is a NULL pointer, return a NULL pointer. */
- if (str == NULL)
+ if (str == nullptr)
{
- return NULL;
+ return nullptr;
}
while (*str != '\0')
{
}
str++;
}
- return NULL;
+ return nullptr;
}
const char **end,
const char *fn)
{
- gmx_bool initialize_lc = FALSE; /* whether to initialize the lambda
- components, or to check them */
- gmx_bool start_reached = FALSE; /* whether the start of component names
- has been reached */
- gmx_bool vector = FALSE; /* whether there are multiple components */
- int n = 0; /* current component number */
- const char *val_start = NULL; /* start of the component name, or NULL
- if not in a value */
+ gmx_bool initialize_lc = FALSE; /* whether to initialize the lambda
+ components, or to check them */
+ gmx_bool start_reached = FALSE; /* whether the start of component names
+ has been reached */
+ gmx_bool vector = FALSE; /* whether there are multiple components */
+ int n = 0; /* current component number */
+ const char *val_start = nullptr; /* start of the component name, or NULL
+ if not in a value */
char *strtod_end;
gmx_bool OK = TRUE;
initialize_lc = TRUE;
}
- if (lc_in == NULL)
+ if (lc_in == nullptr)
{
lc_in = lc_out;
}
if (std::isspace(*str) || *str == ')' || *str == ',' || *str == '\0')
{
/* end of value */
- if (lv == NULL)
+ if (lv == nullptr)
{
if (initialize_lc)
{
}
}
/* reset for the next identifier */
- val_start = NULL;
+ val_start = nullptr;
n++;
if (!vector)
{
}
else
{
- GMX_RELEASE_ASSERT(lc_in != NULL, "Internal inconsistency? lc_in==NULL");
+ GMX_RELEASE_ASSERT(lc_in != nullptr, "Internal inconsistency? lc_in==NULL");
if (n == lc_in->N)
{
return OK;
}
- else if (lv == NULL)
+ else if (lv == nullptr)
{
return FALSE;
}
const char **end,
const char *fn)
{
- return read_lambda_compvec(str, NULL, NULL, lc, end, fn);
+ return read_lambda_compvec(str, nullptr, nullptr, lc, end, fn);
}
/* read an initialized lambda vector from a string */
const char **end,
const char *fn)
{
- return read_lambda_compvec(str, lv, lv->lc, NULL, end, fn);
+ return read_lambda_compvec(str, lv, lv->lc, nullptr, end, fn);
}
const char *legend,
lambda_vec_t *lam)
{
- const char *ptr = NULL, *ptr2 = NULL;
+ const char *ptr = nullptr, *ptr2 = nullptr;
gmx_bool ok = FALSE;
gmx_bool bdhdl = FALSE;
const char *tostr = " to ";
- if (legend == NULL)
+ if (legend == nullptr)
{
gmx_fatal(FARGS, "There is no legend in file '%s', can not deduce lambda", fn);
}
do
{
ptr2 = std::strstr(ptr2, tostr);
- if (ptr2 != NULL)
+ if (ptr2 != nullptr)
{
ptr = ptr2;
ptr2++;
}
}
- while (ptr2 != NULL && *ptr2 != '\0');
+ while (ptr2 != nullptr && *ptr2 != '\0');
if (ptr)
{
ok = TRUE;
bdhdl = TRUE;
}
- else if (std::strchr(legend, 'D') != NULL && std::strchr(legend, 'H') != NULL)
+ else if (std::strchr(legend, 'D') != nullptr && std::strchr(legend, 'H') != nullptr)
{
ok = TRUE;
bdhdl = FALSE;
if (!bdhdl)
{
ptr = find_value(ptr);
- if (!ptr || !read_lambda_vector(ptr, lam, NULL, fn))
+ if (!ptr || !read_lambda_vector(ptr, lam, nullptr, fn))
{
gmx_fatal(FARGS, "lambda vector '%s' %s faulty", legend, fn);
}
return FALSE;
}
lambda_vec_init(&(ba->native_lambda), lc);
- if (!read_lambda_vector(ptr, &(ba->native_lambda), NULL, fn))
+ if (!read_lambda_vector(ptr, &(ba->native_lambda), nullptr, fn))
{
gmx_fatal(FARGS, "lambda vector in %s faulty", fn);
}
/* compatibility mode: check for lambda in other ways. */
/* plain text lambda string */
ptr = std::strstr(subtitle, "lambda");
- if (ptr == NULL)
+ if (ptr == nullptr)
{
/* xmgrace formatted lambda string */
ptr = std::strstr(subtitle, "\\xl\\f{}");
}
- if (ptr == NULL)
+ if (ptr == nullptr)
{
/* xmgr formatted lambda string */
ptr = std::strstr(subtitle, "\\8l\\4");
}
- if (ptr != NULL)
+ if (ptr != nullptr)
{
ptr = std::strstr(ptr, "=");
}
- if (ptr != NULL)
+ if (ptr != nullptr)
{
bFound = (sscanf(ptr+1, "%lf", &(native_lambda)) == 1);
/* add the lambda component name as an empty string */
}
/* searching backward to find the second directory separator */
dirsep = 0;
- digitptr = NULL;
+ digitptr = nullptr;
while (ptr >= fn)
{
if (ptr[0] != DIR_SEPARATOR && ptr[1] == DIR_SEPARATOR)
}
ba->temp = -1;
- if (subtitle != NULL)
+ if (subtitle != nullptr)
{
/* try to extract temperature */
ptr = std::strstr(subtitle, "T =");
- if (ptr != NULL)
+ if (ptr != nullptr)
{
ptr += 3;
if (sscanf(ptr, "%lf", &ba->temp) == 1)
}
}
snew(ba->lambda, ba->nset);
- if (legend == NULL)
+ if (legend == nullptr)
{
/* Check if we have a single set, no legend, nset=1 means t and dH/dl */
if (ba->nset == 1)
gmx_fatal(FARGS, "File %s contains multiple sets but no indication of the native lambda", fn);
}
- if (legend != NULL)
+ if (legend != nullptr)
{
for (i = 0; i < ba->nset-1; i++)
{
nhist = blk->nsub-2;
if (nhist == 0)
{
- return NULL;
+ return nullptr;
}
if (nhist > 2)
{
ener_file_t fp;
t_enxframe *fr;
int nre;
- gmx_enxnm_t *enm = NULL;
+ gmx_enxnm_t *enm = nullptr;
double first_t = -1;
double last_t = -1;
- samples_t **samples_rawdh = NULL; /* contains samples for raw delta_h */
- int *nhists = NULL; /* array to keep count & print at end */
- int *npts = NULL; /* array to keep count & print at end */
- lambda_vec_t **lambdas = NULL; /* array to keep count & print at end */
+ samples_t **samples_rawdh = nullptr; /* contains samples for raw delta_h */
+ int *nhists = nullptr; /* array to keep count & print at end */
+ int *npts = nullptr; /* array to keep count & print at end */
+ lambda_vec_t **lambdas = nullptr; /* array to keep count & print at end */
lambda_vec_t *native_lambda;
int nsamples = 0;
lambda_vec_t start_lambda;
snew(fr, 1);
snew(native_lambda, 1);
- start_lambda.lc = NULL;
+ start_lambda.lc = nullptr;
while (do_enx(fp, fr))
{
{
nhists[i] = 0;
npts[i] = 0;
- lambdas[i] = NULL;
- samples_rawdh[i] = NULL; /* init to NULL so we know which
- ones contain values */
+ lambdas[i] = nullptr;
+ samples_rawdh[i] = nullptr; /* init to NULL so we know which
+ ones contain values */
}
}
else
// nsamples is always >0 here, so samples_rawdh must be a valid pointer. Unfortunately
// cppcheck does not understand the logic unless the assert is inside the loop, but
// this is not performance-sensitive code.
- GMX_RELEASE_ASSERT(samples_rawdh != NULL, "samples_rawdh==NULL with nsamples>0");
+ GMX_RELEASE_ASSERT(samples_rawdh != nullptr, "samples_rawdh==NULL with nsamples>0");
if (samples_rawdh[i])
{
/* insert it into the existing list */
samples_rawdh[i]);
/* and make sure we'll allocate a new one this time
around */
- samples_rawdh[i] = NULL;
+ samples_rawdh[i] = nullptr;
}
}
}
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- fpb = NULL;
+ fpb = nullptr;
if (opt2bSet("-o", NFILE, fnm))
{
sprintf(buf, "%s (%s)", "\\DeltaG", "kT");
"\\lambda", buf, exvggtXYDY, oenv);
}
- fpi = NULL;
+ fpi = nullptr;
if (opt2bSet("-oi", NFILE, fnm))
{
sprintf(buf, "%s (%s)", "\\DeltaG", "kT");
for (f = 0; f < nresults; f++)
{
- if (fpi != NULL)
+ if (fpi != nullptr)
{
lambda_vec_print_short(results[f].a->native_lambda, buf);
fprintf(fpi, xvg2format, buf, dg_tot);
}
- if (fpb != NULL)
+ if (fpb != nullptr)
{
lambda_vec_print_intermediate(results[f].a->native_lambda,
results[f].b->native_lambda,
printf("\n");
- if (fpi != NULL)
+ if (fpi != nullptr)
{
lambda_vec_print_short(results[nresults-1].b->native_lambda, buf);
fprintf(fpi, xvg2format, buf, dg_tot);
xvgrclose(fpi);
}
- if (fpb != NULL)
+ if (fpb != nullptr)
{
xvgrclose(fpb);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_bundle *bun)
{
t_trxframe frout;
- static rvec *xout = NULL;
+ static rvec *xout = nullptr;
int i;
- if (xout == NULL)
+ if (xout == nullptr)
{
snew(xout, outat->nr);
}
frout.natoms = outat->nr;
frout.atoms = outat;
frout.x = xout;
- write_trxframe(status, &frout, NULL);
+ write_trxframe(status, &frout, nullptr);
}
int gmx_bundle(int argc, char *argv[])
"Use the [IT]z[it]-axis as reference instead of the average axis" }
};
FILE *flen, *fdist, *fz, *ftilt, *ftiltr, *ftiltl;
- FILE *fkink = NULL, *fkinkr = NULL, *fkinkl = NULL;
+ FILE *fkink = nullptr, *fkinkr = nullptr, *fkinkl = nullptr;
t_trxstatus *status;
t_trxstatus *fpdb;
t_topology top;
gmx_bool bKink;
rvec va, vb, vc, vr, vl;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
#define NLEG asize(leg)
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-ol", "bun_len", ffWRITE },
{ efXVG, "-od", "bun_dist", ffWRITE },
{ efXVG, "-oz", "bun_z", ffWRITE },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box, TRUE);
bKink = opt2bSet("-ok", NFILE, fnm) || opt2bSet("-okr", NFILE, fnm)
|| opt2bSet("-okl", NFILE, fnm);
}
else
{
- fpdb = NULL;
+ fpdb = nullptr;
}
read_first_frame(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &fr, TRX_NEED_X);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return (map[x][y] == '1') ? TRUE : FALSE;
}
-int *make_chi_ind(int nl, t_dlist dl[], int *ndih)
+static int *make_chi_ind(int nl, t_dlist dl[], int *ndih)
{
int *id;
int i, Xi, n;
return id;
}
-int bin(real chi, int mult)
-{
- mult = 3;
-
- return static_cast<int>(chi*mult/360.0);
-}
-
-
static void do_dihcorr(const char *fn, int nf, int ndih, real **dih, real dt,
int nlist, t_dlist dlist[], real time[], int maxchi,
gmx_bool bPhi, gmx_bool bPsi, gmx_bool bChi, gmx_bool bOmega,
#define NKKKCHI asize(kkkchi1)
#define NJC (NKKKPHI+NKKKPSI+NKKKCHI)
- FILE *fp, *ssfp[3] = {NULL, NULL, NULL};
+ FILE *fp, *ssfp[3] = {nullptr, nullptr, nullptr};
const char *sss[3] = { "sheet", "helix", "coil" };
real S2;
real *normhisto;
real **Jc, **Jcsig;
- int ****his_aa_ss = NULL;
+ int ****his_aa_ss = nullptr;
int ***his_aa, *histmp;
int i, j, k, m, n, nn, Dih, nres, hindex, angle;
gmx_bool bBfac, bOccup;
- char hisfile[256], hhisfile[256], sshisfile[256], title[256], *ss_str = NULL;
+ char hisfile[256], hhisfile[256], sshisfile[256], title[256], *ss_str = nullptr;
char **leg;
const char *residue_name;
int rt_size;
}
break;
default: /* covers edOmega and higher Chis than Chi1 */
- calc_distribution_props(nbin, histmp, -M_PI, 0, NULL, &S2);
+ calc_distribution_props(nbin, histmp, -M_PI, 0, nullptr, &S2);
break;
}
dlist[i].S2[Dih] = S2;
static void do_rama(int nf, int nlist, t_dlist dlist[], real **dih,
gmx_bool bViol, gmx_bool bRamOmega, const gmx_output_env_t *oenv)
{
- FILE *fp, *gp = NULL;
+ FILE *fp, *gp = nullptr;
gmx_bool bOm;
char fn[256];
int i, j, k, Xi1, Xi2, Phi, Psi, Om = 0, nlevels;
#define NMAT 120
- real **mat = NULL, phi, psi, omega, axis[NMAT], lo, hi;
+ real **mat = nullptr, phi, psi, omega, axis[NMAT], lo, hi;
t_rgb rlo = { 1.0, 0.0, 0.0 };
t_rgb rmid = { 1.0, 1.0, 1.0 };
t_rgb rhi = { 0.0, 0.0, 1.0 };
}
xvgrclose(fp);
- if (NULL != pdbfn)
+ if (nullptr != pdbfn)
{
real x0, y0, z0;
- if (NULL == atoms->pdbinfo)
+ atoms->havePdbInfo = TRUE;
+
+ if (nullptr == atoms->pdbinfo)
{
snew(atoms->pdbinfo, atoms->nr);
}
fprintf(fp, "REMARK generated by g_chi\n");
fprintf(fp, "REMARK "
"B-factor field contains negative of dihedral order parameters\n");
- write_pdbfile(fp, NULL, atoms, x, ePBC, box, ' ', 0, NULL, TRUE);
+ write_pdbfile(fp, nullptr, atoms, x, ePBC, box, ' ', 0, nullptr, TRUE);
x0 = y0 = z0 = 1000.0;
for (i = 0; (i < atoms->nr); i++)
{
static gmx_bool bAll = FALSE;
static gmx_bool bPhi = FALSE, bPsi = FALSE, bOmega = FALSE;
static real bfac_init = -1.0, bfac_max = 0;
- static const char *maxchistr[] = { NULL, "0", "1", "2", "3", "4", "5", "6", NULL };
+ static const char *maxchistr[] = { nullptr, "0", "1", "2", "3", "4", "5", "6", nullptr };
static gmx_bool bRama = FALSE, bShift = FALSE, bViol = FALSE, bRamOmega = FALSE;
static gmx_bool bNormHisto = TRUE, bChiProduct = FALSE, bHChi = FALSE, bRAD = FALSE, bPBC = TRUE;
static real core_frac = 0.5;
int i, **chi_lookup, *multiplicity;
t_filenm fnm[] = {
- { efSTX, "-s", NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
+ { efSTX, "-s", nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
{ efXVG, "-o", "order", ffWRITE },
{ efPDB, "-p", "order", ffOPTWR },
{ efDAT, "-ss", "ssdump", ffOPTRD },
NFILE, fnm, npargs, ppa, asize(desc), desc, asize(bugs), bugs,
&oenv))
{
+ sfree(ppa);
return 0;
}
/* Find the chi angles using atoms struct and a list of amino acids */
t_topology *top;
snew(top, 1);
- read_tps_conf(ftp2fn(efSTX, NFILE, fnm), top, &ePBC, &x, NULL, box, FALSE);
+ read_tps_conf(ftp2fn(efSTX, NFILE, fnm), top, &ePBC, &x, nullptr, box, FALSE);
t_atoms &atoms = top->atoms;
- if (atoms.pdbinfo == NULL)
+ if (atoms.pdbinfo == nullptr)
{
snew(atoms.pdbinfo, atoms.nr);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
/* print to two file pointers at once (i.e. stderr and log) */
static gmx_inline
int *nb;
} t_nnb;
-void cp_index(int nn, int from[], int to[])
+static void mc_optimize(FILE *log, t_mat *m, real *time,
+ int maxiter, int nrandom,
+ int seed, real kT,
+ const char *conv, gmx_output_env_t *oenv)
{
- int i;
-
- for (i = 0; (i < nn); i++)
- {
- to[i] = from[i];
- }
-}
-
-void mc_optimize(FILE *log, t_mat *m, real *time,
- int maxiter, int nrandom,
- int seed, real kT,
- const char *conv, gmx_output_env_t *oenv)
-{
- FILE *fp = NULL;
+ FILE *fp = nullptr;
real ecur, enext, emin, prob, enorm;
int i, j, iswap, jswap, nn, nuphill = 0;
t_mat *minimum;
minimum->nn = nn;
copy_t_mat(minimum, m);
- if (NULL != conv)
+ if (nullptr != conv)
{
fp = xvgropen(conv, "Convergence of the MC optimization",
"Energy", "Step", oenv);
fprintf(log, "Iter: %d Swapped %4d and %4d (energy: %g prob: %g)\n",
i, iswap, jswap, enext, prob);
- if (NULL != fp)
+ if (nullptr != fp)
{
fprintf(fp, "%6d %10g\n", i, enext);
}
(i < m->nn-1) ? m->mat[m->m_ind[i]][m->m_ind[i+1]] : 0);
}
- if (NULL != fp)
+ if (nullptr != fp)
{
xvgrclose(fp);
}
return std::sqrt(r2);
}
-static int rms_dist_comp(const void *a, const void *b)
+static bool rms_dist_comp(const t_dist &a, const t_dist &b)
{
- t_dist *da, *db;
-
- da = (t_dist *)a;
- db = (t_dist *)b;
-
- if (da->dist - db->dist < 0)
- {
- return -1;
- }
- else if (da->dist - db->dist > 0)
- {
- return 1;
- }
- return 0;
+ return a.dist < b.dist;
}
-static int clust_id_comp(const void *a, const void *b)
+static bool clust_id_comp(const t_clustid &a, const t_clustid &b)
{
- t_clustid *da, *db;
-
- da = (t_clustid *)a;
- db = (t_clustid *)b;
-
- return da->clust - db->clust;
+ return a.clust < b.clust;
}
-static int nrnb_comp(const void *a, const void *b)
+static bool nrnb_comp(const t_nnb &a, const t_nnb &b)
{
- t_nnb *da, *db;
-
- da = (t_nnb *)a;
- db = (t_nnb *)b;
-
- /* return the b-a, we want highest first */
- return db->nr - da->nr;
+ /* return b<a, we want highest first */
+ return b.nr < a.nr;
}
-void gather(t_mat *m, real cutoff, t_clusters *clust)
+static void gather(t_mat *m, real cutoff, t_clusters *clust)
{
t_clustid *c;
t_dist *d;
{
gmx_incons("gather algortihm");
}
- qsort(d, nn, sizeof(d[0]), rms_dist_comp);
+ std::sort(d, d+nn, rms_dist_comp);
/* Now we make a cluster index for all of the conformations */
c = new_clustid(n1);
while (bChange);
fprintf(stderr, "\nSorting and renumbering clusters\n");
/* Sort on cluster number */
- qsort(c, n1, sizeof(c[0]), clust_id_comp);
+ std::sort(c, c+n1, clust_id_comp);
/* Renumber clusters */
cid = 1;
sfree(d);
}
-gmx_bool jp_same(int **nnb, int i, int j, int P)
+static gmx_bool jp_same(int **nnb, int i, int j, int P)
{
gmx_bool bIn;
int k, ii, jj, pp;
int **nnb;
int i, j, k, cid, diff, maxval;
gmx_bool bChange;
- real **mcpy = NULL;
+ real **mcpy = nullptr;
if (rmsdcut < 0)
{
row[j].j = j;
row[j].dist = mat[i][j];
}
- qsort(row, n1, sizeof(row[0]), rms_dist_comp);
+ std::sort(row, row+n1, rms_dist_comp);
if (M > 0)
{
/* Put the M nearest neighbors in the list */
fprintf(stderr, "\nSorting and renumbering clusters\n");
/* Sort on cluster number */
- qsort(c, n1, sizeof(c[0]), clust_id_comp);
+ std::sort(c, c+n1, clust_id_comp);
/* Renumber clusters */
cid = 1;
sfree(row);
/* sort neighbor list on number of neighbors, largest first */
- qsort(nnb, n1, sizeof(nnb[0]), nrnb_comp);
+ std::sort(nnb, nnb+n1, nrnb_comp);
if (debug)
{
}
/* sort again on nnb[].nr, because we have new # neighbors: */
/* but we only need to sort upto i, i.e. when nnb[].nr>0 */
- qsort(nnb, i, sizeof(nnb[0]), nrnb_comp);
+ std::sort(nnb, nnb+i, nrnb_comp);
fprintf(stderr, "\b\b\b\b%4d", k);
/* new cluster id */
clust->ncl = k-1;
}
-rvec **read_whole_trj(const char *fn, int isize, int index[], int skip,
- int *nframe, real **time, const gmx_output_env_t *oenv, gmx_bool bPBC, gmx_rmpbc_t gpbc)
+static rvec **read_whole_trj(const char *fn, int isize, int index[], int skip,
+ int *nframe, real **time, const gmx_output_env_t *oenv, gmx_bool bPBC, gmx_rmpbc_t gpbc)
{
rvec **xx, *x;
matrix box;
max_nf = 0;
- xx = NULL;
- *time = NULL;
+ xx = nullptr;
+ *time = nullptr;
natom = read_first_x(oenv, &status, fn, &t, &x, box);
i = 0;
i0 = 0;
gmx_bool bFit, FILE *log, t_rgb rlo, t_rgb rhi,
const gmx_output_env_t *oenv)
{
- FILE *size_fp = NULL;
+ FILE *size_fp = nullptr;
char buf[STRLEN], buf1[40], buf2[40], buf3[40], *trxsfn;
- t_trxstatus *trxout = NULL;
- t_trxstatus *trxsout = NULL;
+ t_trxstatus *trxout = nullptr;
+ t_trxstatus *trxsout = nullptr;
int i, i1, cl, nstr, *structure, first = 0, midstr;
- gmx_bool *bWrite = NULL;
+ gmx_bool *bWrite = nullptr;
real r, clrmsd, midrmsd;
- rvec *xav = NULL;
+ rvec *xav = nullptr;
matrix zerobox;
clear_mat(zerobox);
ffprintf_d(stderr, log, buf, "\nFound %d clusters\n\n", clust->ncl);
- trxsfn = NULL;
+ trxsfn = nullptr;
if (trxfn)
{
/* do we write all structures? */
/* Prepare a reference structure for the orientation of the clusters */
if (bFit)
{
- reset_x(ifsize, fitidx, natom, NULL, xtps, mass);
+ reset_x(ifsize, fitidx, natom, nullptr, xtps, mass);
}
trxout = open_trx(trxfn, "w");
/* Calculate the average structure in each cluster, *
{
if (bFit)
{
- reset_x(ifsize, fitidx, natom, NULL, xx[i1], mass);
+ reset_x(ifsize, fitidx, natom, nullptr, xx[i1], mass);
}
if (nstr == 1)
{
if (bWrite[i])
{
write_trx(trxsout, iosize, outidx, atoms, i, time[structure[i]], zerobox,
- xx[structure[i]], NULL, NULL);
+ xx[structure[i]], nullptr, nullptr);
}
}
close_trx(trxsout);
}
if (bFit)
{
- reset_x(ifsize, fitidx, natom, NULL, xav, mass);
+ reset_x(ifsize, fitidx, natom, nullptr, xav, mass);
}
}
if (bFit)
{
do_fit(natom, mass, xtps, xav);
}
- write_trx(trxout, iosize, outidx, atoms, cl, time[midstr], zerobox, xav, NULL, NULL);
+ write_trx(trxout, iosize, outidx, atoms, cl, time[midstr], zerobox, xav, nullptr, nullptr);
}
}
/* clean up */
};
FILE *fp, *log;
- int nf, i, i1, i2, j;
+ int nf = 0, i, i1, i2, j;
gmx_int64_t nrms = 0;
matrix box;
- rvec *xtps, *usextps, *x1, **xx = NULL;
+ rvec *xtps, *usextps, *x1, **xx = nullptr;
const char *fn, *trx_out_fn;
t_clusters clust;
- t_mat *rms, *orig = NULL;
+ t_mat *rms, *orig = nullptr;
real *eigenvalues;
t_topology top;
int ePBC;
t_atoms useatoms;
- t_matrix *readmat = NULL;
+ t_matrix *readmat = nullptr;
real *eigenvectors;
int isize = 0, ifsize = 0, iosize = 0;
- int *index = NULL, *fitidx = NULL, *outidx = NULL;
+ int *index = nullptr, *fitidx = nullptr, *outidx = nullptr;
char *grpname;
- real rmsd, **d1, **d2, *time = NULL, time_invfac, *mass = NULL;
- char buf[STRLEN], buf1[80], title[STRLEN];
+ real rmsd, **d1, **d2, *time = nullptr, time_invfac, *mass = nullptr;
+ char buf[STRLEN], buf1[80];
gmx_bool bAnalyze, bUseRmsdCut, bJP_RMSD = FALSE, bReadMat, bReadTraj, bPBC = TRUE;
int method, ncluster = 0;
static const char *methodname[] = {
- NULL, "linkage", "jarvis-patrick", "monte-carlo",
- "diagonalization", "gromos", NULL
+ nullptr, "linkage", "jarvis-patrick", "monte-carlo",
+ "diagonalization", "gromos", nullptr
};
enum {
m_null, m_linkage, m_jarvis_patrick,
static real kT = 1e-3;
static int M = 10, P = 3;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_pargs pa[] = {
{ "-dista", FALSE, etBOOL, {&bRMSdist},
{ "-skip", FALSE, etINT, {&skip},
"Only analyze every nr-th frame" },
{ "-av", FALSE, etBOOL, {&bAverage},
- "Write average iso middle structure for each cluster" },
+ "Write average instead of middle structure for each cluster" },
{ "-wcl", FALSE, etINT, {&write_ncl},
"Write the structures for this number of clusters to numbered files" },
{ "-nst", FALSE, etINT, {&write_nst},
{ &bPBC }, "PBC check" }
};
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffOPTRD },
- { efTPS, "-s", NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffOPTRD },
+ { efTPS, "-s", nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXPM, "-dm", "rmsd", ffOPTRD },
{ efXPM, "-om", "rmsd-raw", ffWRITE },
{ efXPM, "-o", "rmsd-clust", ffWRITE },
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr,
&oenv))
{
return 0;
}
else
{
- trx_out_fn = NULL;
+ trx_out_fn = nullptr;
}
if (bReadMat && output_env_get_time_factor(oenv) != 1)
{
fprintf(stderr,
"\nWarning: assuming the time unit in %s is %s\n",
- opt2fn("-dm", NFILE, fnm), output_env_get_time_unit(oenv));
+ opt2fn("-dm", NFILE, fnm), output_env_get_time_unit(oenv).c_str());
}
if (trx_out_fn && !bReadTraj)
{
if (bReadTraj)
{
/* don't read mass-database as masses (and top) are not used */
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtps, NULL, box,
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtps, nullptr, box,
TRUE);
if (bPBC)
{
{
for (i = 0; i < nf; i++)
{
- reset_x(ifsize, fitidx, isize, NULL, xx[i], mass);
+ reset_x(ifsize, fitidx, isize, nullptr, xx[i], mass);
}
}
}
useatoms.nr = isize;
analyze_clusters(nf, &clust, rms->mat, isize, &useatoms, usextps, mass, xx, time,
ifsize, fitidx, iosize, outidx,
- bReadTraj ? trx_out_fn : NULL,
+ bReadTraj ? trx_out_fn : nullptr,
opt2fn_null("-sz", NFILE, fnm),
opt2fn_null("-tr", NFILE, fnm),
opt2fn_null("-ntr", NFILE, fnm),
}
else
{
- sprintf(buf, "Time (%s)", output_env_get_time_unit(oenv));
- sprintf(title, "RMS%sDeviation / Cluster Index",
- bRMSdist ? " Distance " : " ");
+ auto timeLabel = output_env_get_time_label(oenv);
+ auto title = gmx::formatString("RMS%sDeviation / Cluster Index",
+ bRMSdist ? " Distance " : " ");
if (minstruct > 1)
{
- write_xpm_split(fp, 0, title, "RMSD (nm)", buf, buf,
+ write_xpm_split(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel,
nf, nf, time, time, rms->mat, 0.0, rms->maxrms, &nlevels,
rlo_top, rhi_top, 0.0, ncluster,
&ncluster, TRUE, rlo_bot, rhi_bot);
}
else
{
- write_xpm(fp, 0, title, "RMSD (nm)", buf, buf,
+ write_xpm(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel,
nf, nf, time, time, rms->mat, 0.0, rms->maxrms,
rlo_top, rhi_top, &nlevels);
}
}
fprintf(stderr, "\n");
gmx_ffclose(fp);
- if (NULL != orig)
+ if (nullptr != orig)
{
fp = opt2FILE("-om", NFILE, fnm, "w");
- sprintf(buf, "Time (%s)", output_env_get_time_unit(oenv));
- sprintf(title, "RMS%sDeviation", bRMSdist ? " Distance " : " ");
- write_xpm(fp, 0, title, "RMSD (nm)", buf, buf,
+ auto timeLabel = output_env_get_time_label(oenv);
+ auto title = gmx::formatString("RMS%sDeviation", bRMSdist ? " Distance " : " ");
+ write_xpm(fp, 0, title, "RMSD (nm)", timeLabel, timeLabel,
nf, nf, time, time, orig->mat, 0.0, orig->maxrms,
rlo_top, rhi_top, &nlevels);
gmx_ffclose(fp);
do_view(oenv, opt2fn_null("-ntr", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn_null("-clid", NFILE, fnm), "-nxy");
}
- do_view(oenv, opt2fn_null("-conv", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn_null("-conv", NFILE, fnm), nullptr);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2007, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
+#include "gromacs/commandline/filenm.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/index.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/arraysize.h"
const gmx_output_env_t *oenv)
{
FILE *fp, *gp, *hp, *tp;
- int *index = NULL;
+ int *index = nullptr;
int nindex, natoms;
t_trxstatus *status;
- rvec *x = NULL, *v = NULL, dx;
+ rvec *x = nullptr, *v = nullptr, dx;
t_pbc pbc;
- char *gname;
- char timebuf[32];
gmx_bool bSame, bTPRwarn = TRUE;
/* Topology stuff */
t_trxframe fr;
t_tpxheader tpxh;
- gmx_mtop_t *mtop = NULL;
+ gmx_mtop_t *mtop = nullptr;
int ePBC = -1;
- t_block *mols = NULL;
- gmx_mtop_atomlookup_t alook;
- t_atom *atom;
+ t_block *mols = nullptr;
int ii, jj;
real temp, tfac;
/* Cluster size distribution (matrix) */
- real **cs_dist = NULL;
- real tf, dx2, cut2, *t_x = NULL, *t_y, cmid, cmax, cav, ekin;
+ real **cs_dist = nullptr;
+ real tf, dx2, cut2, *t_x = nullptr, *t_y, cmid, cmax, cav, ekin;
int i, j, k, ai, aj, ci, cj, nframe, nclust, n_x, max_size = 0;
int *clust_index, *clust_size, max_clust_size, max_clust_ind, nav, nhisto;
t_rgb rlo = { 1.0, 1.0, 1.0 };
clear_trxframe(&fr, TRUE);
- sprintf(timebuf, "Time (%s)", output_env_get_time_unit(oenv));
+ auto timeLabel = output_env_get_time_label(oenv);
tf = output_env_get_time_factor(oenv);
- fp = xvgropen(ncl, "Number of clusters", timebuf, "N", oenv);
- gp = xvgropen(acl, "Average cluster size", timebuf, "#molecules", oenv);
- hp = xvgropen(mcl, "Max cluster size", timebuf, "#molecules", oenv);
- tp = xvgropen(tempf, "Temperature of largest cluster", timebuf, "T (K)",
+ fp = xvgropen(ncl, "Number of clusters", timeLabel, "N", oenv);
+ gp = xvgropen(acl, "Average cluster size", timeLabel, "#molecules", oenv);
+ hp = xvgropen(mcl, "Max cluster size", timeLabel, "#molecules", oenv);
+ tp = xvgropen(tempf, "Temperature of largest cluster", timeLabel, "T (K)",
oenv);
if (!read_first_frame(oenv, &status, trx, &fr, TRX_NEED_X | TRX_READ_V))
gmx_fatal(FARGS, "tpr (%d atoms) and trajectory (%d atoms) do not match!",
tpxh.natoms, natoms);
}
- ePBC = read_tpx(tpr, NULL, NULL, &natoms, NULL, NULL, mtop);
+ ePBC = read_tpx(tpr, nullptr, nullptr, &natoms, nullptr, nullptr, mtop);
}
if (ndf <= -1)
{
printf("Using molecules rather than atoms. Not reading index file %s\n",
ndx);
}
- GMX_RELEASE_ASSERT(mtop != NULL, "Trying to access mtop->mols from NULL mtop pointer");
+ GMX_RELEASE_ASSERT(mtop != nullptr, "Trying to access mtop->mols from NULL mtop pointer");
mols = &(mtop->mols);
/* Make dummy index */
{
index[i] = i;
}
- gname = gmx_strdup("mols");
}
else
{
+ char *gname;
rd_index(ndx, 1, &nindex, &index, &gname);
+ sfree(gname);
}
- alook = gmx_mtop_atomlookup_init(mtop);
-
snew(clust_index, nindex);
snew(clust_size, nindex);
cut2 = cut*cut;
}
max_clust_size = 1;
max_clust_ind = -1;
+ int molb = 0;
do
{
if ((nskip == 0) || ((nskip > 0) && ((nframe % nskip) == 0)))
/* Compute distance */
if (bMol)
{
- GMX_RELEASE_ASSERT(mols != NULL, "Cannot access index[] from NULL mols pointer");
+ GMX_RELEASE_ASSERT(mols != nullptr, "Cannot access index[] from NULL mols pointer");
bSame = FALSE;
for (ii = mols->index[ai]; !bSame && (ii < mols->index[ai+1]); ii++)
{
{
if (clust_index[i] == max_clust_ind)
{
- ai = index[i];
- gmx_mtop_atomnr_to_atom(alook, ai, &atom);
- ekin += 0.5*atom->m*iprod(v[ai], v[ai]);
+ ai = index[i];
+ real m = mtopGetAtomMass(mtop, ai, &molb);
+ ekin += 0.5*m*iprod(v[ai], v[ai]);
}
}
temp = (ekin*2.0)/(3.0*tfac*max_clust_size*BOLTZ);
}
while (read_next_frame(oenv, status, &fr));
close_trx(status);
+ done_frame(&fr);
xvgrclose(fp);
xvgrclose(gp);
xvgrclose(hp);
xvgrclose(tp);
- gmx_mtop_atomlookup_destroy(alook);
-
if (max_clust_ind >= 0)
{
fp = gmx_ffopen(mcn, "w");
{
if (bMol)
{
- GMX_RELEASE_ASSERT(mols != NULL, "Cannot access index[] from NULL mols pointer");
+ GMX_RELEASE_ASSERT(mols != nullptr, "Cannot access index[] from NULL mols pointer");
for (j = mols->index[i]; (j < mols->index[i+1]); j++)
{
fprintf(fp, "%d\n", j+1);
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
cmid = 1;
fp = gmx_ffopen(xpm, "w");
- write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timebuf, "Size",
+ write_xpm3(fp, 0, "Cluster size distribution", "# clusters", timeLabel, "Size",
n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
rlo, rmid, rhi, &nlevels);
gmx_ffclose(fp);
}
fprintf(stderr, "cmid: %g, cmax: %g, max_size: %d\n", cmid, cmax, max_size);
fp = gmx_ffopen(xpmw, "w");
- write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timebuf,
+ write_xpm3(fp, 0, "Weighted cluster size distribution", "Fraction", timeLabel,
"Size", n_x, max_size, t_x, t_y, cs_dist, 0, cmid, cmax,
rlo, rmid, rhi, &nlevels);
gmx_ffclose(fp);
-
+ if (mtop)
+ {
+ done_mtop(mtop);
+ sfree(mtop);
+ }
+ sfree(t_x);
+ sfree(t_y);
+ for (i = 0; (i < n_x); i++)
+ {
+ sfree(cs_dist[i]);
+ }
+ sfree(cs_dist);
sfree(clust_index);
sfree(clust_size);
sfree(index);
"atom numbers of the largest cluster."
};
- static real cutoff = 0.35;
- static int nskip = 0;
- static int nlevels = 20;
- static int ndf = -1;
- static gmx_bool bMol = FALSE;
- static gmx_bool bPBC = TRUE;
- static rvec rlo = { 1.0, 1.0, 0.0 };
- static rvec rhi = { 0.0, 0.0, 1.0 };
+ real cutoff = 0.35;
+ int nskip = 0;
+ int nlevels = 20;
+ int ndf = -1;
+ gmx_bool bMol = FALSE;
+ gmx_bool bPBC = TRUE;
+ rvec rlo = { 1.0, 1.0, 0.0 };
+ rvec rhi = { 0.0, 0.0, 1.0 };
gmx_output_env_t *oenv;
t_rgb rgblo, rgbhi;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPR, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXPM, "-o", "csize", ffWRITE },
{ efXPM, "-ow", "csizew", ffWRITE },
{ efXVG, "-nc", "nclust", ffWRITE },
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
bMol, bPBC, fnTPR,
cutoff, nskip, nlevels, rgblo, rgbhi, ndf, oenv);
+ done_filenms(NFILE, fnm);
+ output_env_done(oenv);
+
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static const int NOTSET = -9368163;
-void calc_rm_cm(int isize, int index[], const t_atoms *atoms, rvec x[], rvec xcm)
+static void calc_rm_cm(int isize, int index[], const t_atoms *atoms, rvec x[], rvec xcm)
{
int i, d;
real tm, m;
}
}
-int build_res_index(int isize, int index[], t_atom atom[], int rindex[])
+static int build_res_index(int isize, int index[], t_atom atom[], int rindex[])
{
int i, r;
return r;
}
-int find_res_end(int i, int isize, int index[], const t_atoms *atoms)
+static int find_res_end(int i, int isize, int index[], const t_atoms *atoms)
{
int rnr;
return i;
}
-int debug_strcmp(char s1[], char s2[])
+static int debug_strcmp(char s1[], char s2[])
{
if (debug)
{
return std::strcmp(s1, s2);
}
-int find_next_match_atoms_in_res(int *i1, int index1[],
- int m1, char **atnms1[],
- int *i2, int index2[],
- int m2, char **atnms2[])
+static int find_next_match_atoms_in_res(int *i1, int index1[],
+ int m1, char **atnms1[],
+ int *i2, int index2[],
+ int m2, char **atnms2[])
{
int dx, dy, dmax, cmp;
gmx_bool bFW = FALSE;
return cmp;
}
-int find_first_atom_in_res(int rnr, int isize, int index[], t_atom atom[])
+static int find_first_atom_in_res(int rnr, int isize, int index[], t_atom atom[])
{
int i;
}
}
-void find_matching_names(int *isize1, int index1[], const t_atoms *atoms1,
- int *isize2, int index2[], const t_atoms *atoms2)
+static void find_matching_names(int *isize1, int index1[], const t_atoms *atoms1,
+ int *isize2, int index2[], const t_atoms *atoms2)
{
int i1, i2, ii1, ii2, m1, m2;
int atcmp, rescmp;
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
sfree(fit_x);
sfree(w_rls);
- w_rls = NULL;
+ w_rls = nullptr;
}
else
{
clear_rvec(xcm1);
clear_rvec(xcm2);
- w_rls = NULL;
+ w_rls = nullptr;
}
/* calculate the rms deviation */
srenew(atoms1->pdbinfo, atoms1->nr);
srenew(atoms1->atom, atoms1->nr); /* Why renew atom? */
+ atoms1->havePdbInfo = TRUE;
+
/* Avoid segfaults when writing the pdb-file */
for (i = 0; i < atoms1->nr; i++)
{
fp = gmx_ffopen(outfile, "w");
if (!bOne)
{
- write_pdbfile(fp, *top1->name, atoms1, x1, ePBC1, box1, ' ', 1, NULL, TRUE);
+ write_pdbfile(fp, *top1->name, atoms1, x1, ePBC1, box1, ' ', 1, nullptr, TRUE);
}
- write_pdbfile(fp, *top2->name, atoms2, x2, ePBC2, box2, ' ', bOne ? -1 : 2, NULL, TRUE);
+ write_pdbfile(fp, *top2->name, atoms2, x2, ePBC2, box2, ' ', bOne ? -1 : 2, nullptr, TRUE);
gmx_ffclose(fp);
break;
case efGRO:
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Apply corrections for periodic boundary conditions" }
};
- FILE *out = NULL; /* initialization makes all compilers happy */
+ FILE *out = nullptr; /* initialization makes all compilers happy */
t_trxstatus *status;
t_topology top;
int ePBC;
matrix box, zerobox;
real *sqrtm, *mat, *eigenvalues, sum, trace, inv_nframes;
real t, tstart, tend, **mat2;
- real xj, *w_rls = NULL;
+ real xj, *w_rls = nullptr;
real min, max, *axis;
int natoms, nat, nframes0, nframes, nlevels;
gmx_int64_t ndim, i, j, k, l;
t_rgb rlo, rmi, rhi;
real *eigenvectors;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "eigenval", ffWRITE },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "eigenval", ffWRITE },
{ efTRN, "-v", "eigenvec", ffWRITE },
{ efSTO, "-av", "average.pdb", ffWRITE },
- { efLOG, NULL, "covar", ffWRITE },
+ { efLOG, nullptr, "covar", ffWRITE },
{ efDAT, "-ascii", "covar", ffOPTWR },
{ efXPM, "-xpm", "covar", ffOPTWR },
{ efXPM, "-xpma", "covara", ffOPTWR }
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
xpmfile = opt2fn_null("-xpm", NFILE, fnm);
xpmafile = opt2fn_null("-xpma", NFILE, fnm);
- read_tps_conf(fitfile, &top, &ePBC, &xref, NULL, box, TRUE);
+ read_tps_conf(fitfile, &top, &ePBC, &xref, nullptr, box, TRUE);
atoms = &top.atoms;
if (bFit)
}
if (bFit)
{
- reset_x(nfit, ifit, atoms->nr, NULL, xref, w_rls);
+ reset_x(nfit, ifit, atoms->nr, nullptr, xref, w_rls);
}
snew(x, natoms);
}
if (bFit)
{
- reset_x(nfit, ifit, nat, NULL, xread, w_rls);
+ reset_x(nfit, ifit, nat, nullptr, xread, w_rls);
do_fit(nat, w_rls, xref, xread);
}
for (i = 0; i < natoms; i++)
}
}
while (read_next_x(oenv, status, &t, xread, box));
- close_trj(status);
+ close_trx(status);
inv_nframes = 1.0/nframes0;
for (i = 0; i < natoms; i++)
}
}
write_sto_conf_indexed(opt2fn("-av", NFILE, fnm), "Average structure",
- atoms, xread, NULL, epbcNONE, zerobox, natoms, index);
+ atoms, xread, nullptr, epbcNONE, zerobox, natoms, index);
sfree(xread);
fprintf(stderr, "Constructing covariance matrix (%dx%d) ...\n", static_cast<int>(ndim), static_cast<int>(ndim));
}
if (bFit)
{
- reset_x(nfit, ifit, nat, NULL, xread, w_rls);
+ reset_x(nfit, ifit, nat, nullptr, xread, w_rls);
do_fit(nat, w_rls, xref, xread);
}
if (bRef)
}
while (read_next_x(oenv, status, &t, xread, box) &&
(bRef || nframes < nframes0));
- close_trj(status);
+ close_trx(status);
gmx_rmpbc_done(gpbc);
fprintf(stderr, "Read %d frames\n", nframes);
fprintf(out, "Working directory: %s\n\n", str);
fprintf(out, "Read %d frames from %s (time %g to %g %s)\n", nframes, trxfile,
- output_env_conv_time(oenv, tstart), output_env_conv_time(oenv, tend), output_env_get_time_unit(oenv));
+ output_env_conv_time(oenv, tstart), output_env_conv_time(oenv, tend), output_env_get_time_unit(oenv).c_str());
if (bFit)
{
fprintf(out, "Read reference structure for fit from %s\n", fitfile);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int i, j;
int valloc, nalloc, nfr, nvfr;
int vshfr;
- real *xshfr = NULL;
- int *vfr = NULL;
+ real *xshfr = nullptr;
+ int *vfr = nullptr;
real refr = 0.0;
- real *cacf = NULL;
- real *time = NULL;
- real *djc = NULL;
+ real *cacf = nullptr;
+ real *time = nullptr;
+ real *djc = nullptr;
real corint = 0.0;
real prefactorav = 0.0;
real prefactor = 0.0;
rvec mja_tmp;
rvec mjd_tmp;
rvec mdvec;
- rvec *mu = NULL;
- rvec *xp = NULL;
- rvec *v0 = NULL;
- rvec *mjdsp = NULL;
- real *dsp2 = NULL;
+ rvec *mu = nullptr;
+ rvec *xp = nullptr;
+ rvec *v0 = nullptr;
+ rvec *mjdsp = nullptr;
+ real *dsp2 = nullptr;
real t0;
real rtmp;
rvec tmp;
- rvec *mtrans = NULL;
+ rvec *mtrans = nullptr;
/*
* Variables for the least-squares fit for Einstein-Helfand and Green-Kubo
real err = 0.0;
real *xfit;
real *yfit;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
/*
* indices for EH
xshfr[i] = 0.0;
}
}
- GMX_RELEASE_ASSERT(time != NULL, "Memory not allocated correctly - time array is NULL");
+ GMX_RELEASE_ASSERT(time != nullptr, "Memory not allocated correctly - time array is NULL");
if (nfr == 0)
{
printf("\n\nAverage translational dipole moment M_J [enm] after %d frames (|M|^2): %f %f %f (%f)\n", nfr, mja_tmp[XX], mja_tmp[YY], mja_tmp[ZZ], mj2);
printf("\n\nAverage molecular dipole moment M_D [enm] after %d frames (|M|^2): %f %f %f (%f)\n", nfr, mdvec[XX], mdvec[YY], mdvec[ZZ], md2);
- if (v0 != NULL)
+ if (v0 != nullptr)
{
if (bINT)
{
}
- if (v0 != NULL)
+ if (v0 != nullptr)
{
sfree(v0);
}
gmx_output_env_t *oenv;
t_topology top;
- char **grpname = NULL;
+ char **grpname = nullptr;
const char *indexfn;
t_trxframe fr;
- real *mass2 = NULL;
+ real *mass2 = nullptr;
matrix box;
int *index0;
- int *indexm = NULL;
+ int *indexm = nullptr;
int isize;
t_trxstatus *status;
int flags = 0;
int nmols;
int i;
real *qmol;
- FILE *outf = NULL;
- FILE *mcor = NULL;
- FILE *fmj = NULL;
- FILE *fmd = NULL;
- FILE *fmjdsp = NULL;
- FILE *fcur = NULL;
+ FILE *outf = nullptr;
+ FILE *mcor = nullptr;
+ FILE *fmj = nullptr;
+ FILE *fmd = nullptr;
+ FILE *fmjdsp = nullptr;
+ FILE *fcur = nullptr;
t_filenm fnm[] = {
- { efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
- { efNDX, NULL, NULL, ffOPTRD },
- { efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
+ { efTPS, nullptr, nullptr, ffREAD }, /* this is for the topology */
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD }, /* and this for the trajectory */
{ efXVG, "-o", "current", ffWRITE },
{ efXVG, "-caf", "caf", ffOPTWR },
{ efXVG, "-dsp", "dsp", ffWRITE },
/* At first the arguments will be parsed and the system information processed */
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
bACF = opt2bSet("-caf", NFILE, fnm);
bINT = opt2bSet("-mc", NFILE, fnm);
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, NULL, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box, TRUE);
indexfn = ftp2fn_null(efNDX, NFILE, fnm);
snew(grpname, 1);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/****************************************************************************/
/* used for sorting the list */
-int compare(void *a, void *b)
+static int compare(void *a, void *b)
{
t_electron *tmp1, *tmp2;
tmp1 = (t_electron *)a; tmp2 = (t_electron *)b;
return std::strcmp(tmp1->atomname, tmp2->atomname);
}
-int get_electrons(t_electron **eltab, const char *fn)
+static int get_electrons(t_electron **eltab, const char *fn)
{
char buffer[256]; /* to read in a line */
char tempname[80]; /* buffer to hold name */
gmx_fatal(FARGS, "Couldn't open %s. Exiting.\n", fn);
}
- if (NULL == fgets(buffer, 255, in))
+ if (nullptr == fgets(buffer, 255, in))
{
gmx_fatal(FARGS, "Error reading from file %s", fn);
}
for (i = 0; i < nr; i++)
{
- if (fgets(buffer, 255, in) == NULL)
+ if (fgets(buffer, 255, in) == nullptr)
{
gmx_fatal(FARGS, "reading datafile. Check your datafile.\n");
}
return nr;
}
-void center_coords(t_atoms *atoms, int *index_center, int ncenter,
- matrix box, rvec x0[])
+static void center_coords(t_atoms *atoms, int *index_center, int ncenter,
+ matrix box, rvec x0[])
{
int i, k, m;
real tmass, mm;
}
}
-void calc_electron_density(const char *fn, int **index, int gnx[],
- double ***slDensity, int *nslices, t_topology *top,
- int ePBC,
- int axis, int nr_grps, real *slWidth,
- t_electron eltab[], int nr, gmx_bool bCenter,
- int *index_center, int ncenter,
- gmx_bool bRelative, const gmx_output_env_t *oenv)
+static void calc_electron_density(const char *fn, int **index, int gnx[],
+ double ***slDensity, int *nslices, t_topology *top,
+ int ePBC,
+ int axis, int nr_grps, real *slWidth,
+ t_electron eltab[], int nr, gmx_bool bCenter,
+ int *index_center, int ncenter,
+ gmx_bool bRelative, const gmx_output_env_t *oenv)
{
rvec *x0; /* coordinates without pbc */
matrix box; /* box (3x3) */
t_electron *found; /* found by bsearch */
t_electron sought; /* thingie thought by bsearch */
real boxSz, aveBox;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
real t,
z;
(const void *)eltab, nr, sizeof(t_electron),
(int(*)(const void*, const void*))compare);
- if (found == NULL)
+ if (found == nullptr)
{
fprintf(stderr, "Couldn't find %s. Add it to the .dat file\n",
*(top->atoms.atomname[index[n][i]]));
gmx_rmpbc_done(gpbc);
/*********** done with status file **********/
- close_trj(status);
+ close_trx(status);
/* slDensity now contains the total number of electrons per slice, summed
over all frames. Now divide by nr_frames and volume of slice
sfree(x0); /* free memory used by coordinate array */
}
-void calc_density(const char *fn, int **index, int gnx[],
- double ***slDensity, int *nslices, t_topology *top, int ePBC,
- int axis, int nr_grps, real *slWidth, gmx_bool bCenter,
- int *index_center, int ncenter,
- gmx_bool bRelative, const gmx_output_env_t *oenv)
+static void calc_density(const char *fn, int **index, int gnx[],
+ double ***slDensity, int *nslices, t_topology *top, int ePBC,
+ int axis, int nr_grps, real *slWidth, gmx_bool bCenter,
+ int *index_center, int ncenter,
+ gmx_bool bRelative, const gmx_output_env_t *oenv)
{
rvec *x0; /* coordinates without pbc */
matrix box; /* box (3x3) */
real t,
z;
real boxSz, aveBox;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
if (axis < 0 || axis >= DIM)
{
gmx_rmpbc_done(gpbc);
/*********** done with status file **********/
- close_trj(status);
+ close_trx(status);
/* slDensity now contains the total mass per slice, summed over all
frames. Now divide by nr_frames and volume of slice
sfree(x0); /* free memory used by coordinate array */
}
-void plot_density(double *slDensity[], const char *afile, int nslices,
- int nr_grps, char *grpname[], real slWidth,
- const char **dens_opt,
- gmx_bool bCenter, gmx_bool bRelative, gmx_bool bSymmetrize,
- const gmx_output_env_t *oenv)
+static void plot_density(double *slDensity[], const char *afile, int nslices,
+ int nr_grps, char *grpname[], real slWidth,
+ const char **dens_opt,
+ gmx_bool bCenter, gmx_bool bRelative, gmx_bool bSymmetrize,
+ const gmx_output_env_t *oenv)
{
FILE *den;
- const char *title = NULL;
- const char *xlabel = NULL;
- const char *ylabel = NULL;
+ const char *title = nullptr;
+ const char *xlabel = nullptr;
+ const char *ylabel = nullptr;
int slice, n;
real ddd;
real axispos;
gmx_output_env_t *oenv;
static const char *dens_opt[] =
- { NULL, "mass", "number", "charge", "electron", NULL };
+ { nullptr, "mass", "number", "charge", "electron", nullptr };
static int axis = 2; /* normal to memb. default z */
static const char *axtitle = "Z";
static int nslices = 50; /* nr of slices defined */
int i;
t_filenm fnm[] = { /* files for g_density */
- { efTRX, "-f", NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efTPR, NULL, NULL, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efTPR, nullptr, nullptr, ffREAD },
{ efDAT, "-ei", "electrons", ffOPTRD }, /* file with nr. of electrons */
{ efXVG, "-o", "density", ffWRITE },
};
return 0;
}
- GMX_RELEASE_ASSERT(dens_opt[0] != NULL, "Option setting inconsistency; dens_opt[0] is NULL");
+ GMX_RELEASE_ASSERT(dens_opt[0] != nullptr, "Option setting inconsistency; dens_opt[0] is NULL");
if (bSymmetrize && !bCenter)
{
else
{
ncenter = 0;
- index_center = NULL;
+ index_center = nullptr;
}
fprintf(stderr, "\nSelect %d group%s to calculate density for:\n", ngrps, (ngrps > 1) ? "s" : "");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static int n1 = 0, n2 = 0;
static real xmin = -1, xmax = -1, bin = 0.02, dmin = 0, dmax = 0, amax = 0, rmax = 0;
static gmx_bool bMirror = FALSE, bSums = FALSE;
- static const char *eaver[] = { NULL, "z", "y", "x", NULL };
- static const char *eunit[] = { NULL, "nm-3", "nm-2", "count", NULL };
+ static const char *eaver[] = { nullptr, "z", "y", "x", nullptr };
+ static const char *eunit[] = { nullptr, "nm-3", "nm-2", "count", nullptr };
t_pargs pa[] = {
{ "-bin", FALSE, etREAL, {&bin},
int cav = 0, c1 = 0, c2 = 0;
char **grpname, buf[STRLEN];
const char *unit;
- int i, j, k, l, ngrps, anagrp, *gnx = NULL, nindex, nradial = 0, nfr, nmpower;
- int **ind = NULL, *index;
+ int i, j, k, l, ngrps, anagrp, *gnx = nullptr, nindex, nradial = 0, nfr, nmpower;
+ int **ind = nullptr, *index;
real **grid, maxgrid, m1, m2, box1, box2, *tickx, *tickz, invcellvol;
real invspa = 0, invspz = 0, axial, r, vol_old, vol, rowsum;
int nlev = 51;
gmx_output_env_t *oenv;
const char *label[] = { "x (nm)", "y (nm)", "z (nm)" };
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efDAT, "-od", "densmap", ffOPTWR },
{ efXPM, "-o", "densmap", ffWRITE }
};
npargs = asize(pa);
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
}
- GMX_RELEASE_ASSERT(eunit[0] != NULL, "Option setting inconsistency; eunit[0] is NULL");
+ GMX_RELEASE_ASSERT(eunit[0] != nullptr, "Option setting inconsistency; eunit[0] is NULL");
if (std::strcmp(eunit[0], "nm-3") == 0)
{
if (ftp2bSet(efTPS, NFILE, fnm) || !ftp2bSet(efNDX, NFILE, fnm))
{
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box,
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, nullptr, box,
bRadial);
}
if (!bRadial)
}
}
- GMX_RELEASE_ASSERT(eaver[0] != NULL, "Option setting inconsistency; eaver[0] is NULL");
+ GMX_RELEASE_ASSERT(eaver[0] != nullptr, "Option setting inconsistency; eaver[0] is NULL");
switch (eaver[0][0])
{
nfr++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
/* normalize gridpoints */
maxgrid = 0;
gmx_ffclose(fp);
}
- do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr);
return 0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* grpn - group number in index
*/
t_trxstatus *status;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
matrix box; /* Box - 3x3 -each step*/
rvec *x0; /* List of Coord without PBC*/
int i, j, /* loop indices, checks etc*/
ax1 = 0, ax2 = 0, /* tangent directions */
framenr = 0, /* frame number in trajectory*/
slicex, slicey, slicez; /*slice # of x y z position */
- real ***Densslice = NULL; /* Density-slice in one frame*/
+ real ***Densslice = nullptr; /* Density-slice in one frame*/
real dscale; /*physical scaling factor*/
real t, x, y, z; /* time and coordinates*/
rvec bbww;
/*Initialize Densdevel and PBC-remove*/
gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
- *Densdevel = NULL;
+ *Densdevel = nullptr;
do
{
/*Reset Densslice every nsttblock steps*/
/* The first conditional is for clang to understand that this branch is
* always taken the first time. */
- if (Densslice == NULL || framenr % nsttblock == 0)
+ if (Densslice == nullptr || framenr % nsttblock == 0)
{
snew(Densslice, *xslices);
for (i = 0; i < *xslices; i++)
/*Free memory we no longer need and exit.*/
gmx_rmpbc_done(gpbc);
- close_trj(status);
+ close_trx(status);
if (0)
{
real *sigma1, *sigma2;
double beginfit1[4];
double beginfit2[4];
- double *fit1 = NULL, *fit2 = NULL;
+ double *fit1 = nullptr, *fit2 = nullptr;
const double *avgfit1;
const double *avgfit2;
const real onehalf = 1.00/2.00;
- t_interf ***int1 = NULL, ***int2 = NULL; /*Interface matrices [t][x,y] - last index in row-major order*/
+ t_interf ***int1 = nullptr, ***int2 = nullptr; /*Interface matrices [t][x,y] - last index in row-major order*/
/*Create int1(t,xy) and int2(t,xy) arrays with correct number of interf_t elements*/
xysize = xslices*yslices;
snew(int1, tblocks);
/*Fit average density in z over whole trajectory to obtain tentative fit-parameters in fit1 and fit2*/
/*Fit 1st half of box*/
- do_lmfit(zslices, zDensavg, sigma1, binwidth, NULL, startpoint, splitpoint, oenv, FALSE, effnERF, beginfit1, 8, NULL);
+ do_lmfit(zslices, zDensavg, sigma1, binwidth, nullptr, startpoint, splitpoint, oenv, FALSE, effnERF, beginfit1, 8, nullptr);
/*Fit 2nd half of box*/
- do_lmfit(zslices, zDensavg, sigma2, binwidth, NULL, splitpoint, endpoint, oenv, FALSE, effnERF, beginfit2, 8, NULL);
+ do_lmfit(zslices, zDensavg, sigma2, binwidth, nullptr, splitpoint, endpoint, oenv, FALSE, effnERF, beginfit2, 8, nullptr);
/*Initialise the const arrays for storing the average fit parameters*/
avgfit1 = beginfit1;
fit2[k] = avgfit2[k];
}
/*Now fit and store in structures in row-major order int[n][i][j]*/
- do_lmfit(zslices, Densmap[n][i][j], sigma1, binwidth, NULL, startpoint, splitpoint, oenv, FALSE, effnERF, fit1, 0, NULL);
+ do_lmfit(zslices, Densmap[n][i][j], sigma1, binwidth, nullptr, startpoint, splitpoint, oenv, FALSE, effnERF, fit1, 0, nullptr);
int1[n][j+(yslices*i)]->Z = fit1[2];
int1[n][j+(yslices*i)]->t = fit1[3];
- do_lmfit(zslices, Densmap[n][i][j], sigma2, binwidth, NULL, splitpoint, endpoint, oenv, FALSE, effnERF, fit2, 0, NULL);
+ do_lmfit(zslices, Densmap[n][i][j], sigma2, binwidth, nullptr, splitpoint, endpoint, oenv, FALSE, effnERF, fit2, 0, nullptr);
int2[n][j+(yslices*i)]->Z = fit2[2];
int2[n][j+(yslices*i)]->t = fit2[3];
}
static void writesurftoxpms(t_interf ***surf1, t_interf ***surf2, int tblocks, int xbins, int ybins, int zbins, real bw, real bwz, char **outfiles, int maplevels )
{
- char numbuf[13];
+ char numbuf[STRLEN];
int n, i, j;
real **profile1, **profile2;
real max1, max2, min1, min2, *xticks, *yticks;
static gmx_bool b1d = FALSE;
static int nlevels = 100;
/*Densitymap - Densmap[t][x][y][z]*/
- real ****Densmap = NULL;
+ real ****Densmap = nullptr;
/* Surfaces surf[t][surf_x,surf_y]*/
t_interf ***surf1, ***surf2;
- static const char *meth[] = {NULL, "bisect", "functional", NULL};
+ static const char *meth[] = {nullptr, "bisect", "functional", nullptr};
int eMeth;
char **graphfiles, **rawfiles, **spectra; /* Filenames for xpm-surface maps, rawdata and powerspectra */
t_filenm fnm[] = {
- { efTPR, "-s", NULL, ffREAD }, /* this is for the topology */
- { efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
- { efNDX, "-n", NULL, ffREAD}, /* this is to select groups */
+ { efTPR, "-s", nullptr, ffREAD }, /* this is for the topology */
+ { efTRX, "-f", nullptr, ffREAD }, /* and this for the trajectory */
+ { efNDX, "-n", nullptr, ffREAD}, /* this is to select groups */
{ efDAT, "-o", "Density4D", ffOPTWR}, /* This is for outputting the entire 4D densityfield in binary format */
- { efOUT, "-or", NULL, ffOPTWRMULT}, /* This is for writing out the entire information in the t_interf arrays */
+ { efOUT, "-or", nullptr, ffOPTWRMULT}, /* This is for writing out the entire information in the t_interf arrays */
{ efXPM, "-og", "interface", ffOPTWRMULT}, /* This is for writing out the interface meshes - one xpm-file per tblock*/
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* This is for the trajectory averaged Fourier-spectra*/
};
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/smalloc.h"
/* Determines at which point in the array the fit should start */
-int calc_nbegin(int nx, real x[], real tbegin)
+static int calc_nbegin(int nx, real x[], real tbegin)
{
int nbegin;
return nbegin;
}
-real numerical_deriv(int nx, real x[], real y[], real fity[], real combined[], real dy[],
- real tendInt, int nsmooth)
+static real numerical_deriv(int nx, real x[], real y[], real fity[], real combined[], real dy[],
+ real tendInt, int nsmooth)
{
FILE *tmpfp;
int i, nbegin, i0, i1;
}
tmpfp = gmx_ffopen("integral_smth.xvg", "w");
- integralSmth = print_and_integrate(tmpfp, nx, x[1]-x[0], combined, NULL, 1);
+ integralSmth = print_and_integrate(tmpfp, nx, x[1]-x[0], combined, nullptr, 1);
printf("SMOOTH integral = %10.5e\n", integralSmth);
dy[0] = (combined[1]-combined[0])/(x[1]-x[0]);
return integralSmth;
}
-void do_four(const char *fn, const char *cn, int nx, real x[], real dy[],
- real eps0, real epsRF, const gmx_output_env_t *oenv)
+static void do_four(const char *fn, const char *cn, int nx, real x[], real dy[],
+ real eps0, real epsRF, const gmx_output_env_t *oenv)
{
FILE *fp, *cp;
t_complex *tmp, gw, hw, kw;
};
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
snew(y[4], nx);
snew(y[5], nx);
- integral = print_and_integrate(NULL, calc_nbegin(nx, y[0], tbegin),
- dt, y[1], NULL, 1);
+ integral = print_and_integrate(nullptr, calc_nbegin(nx, y[0], tbegin),
+ dt, y[1], nullptr, 1);
integral += do_lmfit(nx, y[1], y[2], dt, y[0], tbegin, tend,
- oenv, TRUE, eFitFn, fitparms, fix, NULL);
+ oenv, TRUE, eFitFn, fitparms, fix, nullptr);
for (i = 0; i < nx; i++)
{
y[3][i] = fit_function(eFitFn, fitparms, y[0][i]);
nx-1, y[0], y[5], eps0, epsRF, oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
- do_view(oenv, opt2fn("-c", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn("-c", NFILE, fnm), nullptr);
do_view(oenv, opt2fn("-d", NFILE, fnm), "-nxy");
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(gb, 1);
- if ((ptr = getenv("GMX_DIPOLE_SPACING")) != NULL)
+ if ((ptr = getenv("GMX_DIPOLE_SPACING")) != nullptr)
{
- double bw = strtod(ptr, NULL);
+ double bw = strtod(ptr, nullptr);
gb->spacing = bw;
}
else
sfree((*gb)->elem);
sfree((*gb)->count);
sfree((*gb));
- *gb = NULL;
+ *gb = nullptr;
}
static void add2gkr(t_gkrbin *gb, real r, real cosa, real phi)
int mindex[], rvec x[], rvec mu[],
int ePBC, const matrix box, const t_atom *atom, const int *nAtom)
{
- static rvec *xcm[2] = { NULL, NULL};
+ static rvec *xcm[2] = { nullptr, nullptr};
int gi, gj, j0, j1, i, j, k, n, grp0, grp1;
real qtot, q, cosa, rr, phi;
rvec dx;
xvgrclose(fp);
}
-gmx_bool read_mu_from_enx(ener_file_t fmu, int Vol, ivec iMu, rvec mu, real *vol,
- real *t, int nre, t_enxframe *fr)
+static gmx_bool read_mu_from_enx(ener_file_t fmu, int Vol, ivec iMu, rvec mu, real *vol,
+ real *t, int nre, t_enxframe *fr)
{
int i;
gmx_bool bCont;
/*
* Calculates epsilon according to M. Neumann, Mol. Phys. 50, 841 (1983)
*/
-real calc_eps(double M_diff, double volume, double epsRF, double temp)
+static real calc_eps(double M_diff, double volume, double epsRF, double temp)
{
double eps, A, teller, noemer;
double eps_0 = 8.854187817e-12; /* epsilon_0 in C^2 J^-1 m^-1 */
};
#define NLEGADIP asize(leg_adip)
- FILE *outdd, *outmtot, *outaver, *outeps, *caver = NULL;
- FILE *dip3d = NULL, *adip = NULL;
- rvec *x, *dipole = NULL, mu_t, quad, *dipsp = NULL;
- t_gkrbin *gkrbin = NULL;
- gmx_enxnm_t *enm = NULL;
+ FILE *outdd, *outmtot, *outaver, *outeps, *caver = nullptr;
+ FILE *dip3d = nullptr, *adip = nullptr;
+ rvec *x, *dipole = nullptr, mu_t, quad, *dipsp = nullptr;
+ t_gkrbin *gkrbin = nullptr;
+ gmx_enxnm_t *enm = nullptr;
t_enxframe *fr;
int nframes = 1000, nre, timecheck = 0, ncolour = 0;
- ener_file_t fmu = NULL;
+ ener_file_t fmu = nullptr;
int i, n, m, natom = 0, gnx_tot, teller, tel3;
t_trxstatus *status;
int *dipole_bin, ndipbin, ibin, iVol, idim = -1;
double M_diff = 0, epsilon, invtel, vol_aver;
double mu_ave, mu_mol, M2_ave = 0, M_ave2 = 0, M_av[DIM], M_av2[DIM];
double M[3], M2[3], M4[3], Gk = 0, g_k = 0;
- gmx_stats_t *Qlsq, mulsq, muframelsq = NULL;
+ gmx_stats_t *Qlsq, mulsq, muframelsq = nullptr;
ivec iMu;
- real **muall = NULL;
- rvec *slab_dipoles = NULL;
- const t_atom *atom = NULL;
- const t_block *mols = NULL;
- gmx_rmpbc_t gpbc = NULL;
+ real **muall = nullptr;
+ rvec *slab_dipoles = nullptr;
+ const t_atom *atom = nullptr;
+ const t_block *mols = nullptr;
+ gmx_rmpbc_t gpbc = nullptr;
gnx_tot = gnx[0];
if (ncos > 1)
if (!bMU)
{
- close_trj(status);
+ close_trx(status);
}
xvgrclose(outmtot);
}
}
-void dipole_atom2molindex(int *n, int *index, const t_block *mols)
+static void dipole_atom2molindex(int *n, int *index, const t_block *mols)
{
int nmol, i, j, m;
real mu_max = 5, mu_aver = -1, rcmax = 0;
real epsilonRF = 0.0, temp = 300;
gmx_bool bPairs = TRUE, bPhi = FALSE, bQuad = FALSE;
- const char *corrtype[] = {NULL, "none", "mol", "molsep", "total", NULL};
+ const char *corrtype[] = {nullptr, "none", "mol", "molsep", "total", nullptr};
const char *axtitle = "Z";
int nslices = 10; /* nr of slices defined */
int skip = 0, nFA = 0, nFB = 0, ncos = 1;
int *gnx;
int nFF[2];
int **grpindex;
- char **grpname = NULL;
+ char **grpname = nullptr;
gmx_bool bGkr, bMU, bSlab;
t_filenm fnm[] = {
- { efEDR, "-en", NULL, ffOPTRD },
- { efTRX, "-f", NULL, ffREAD },
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efEDR, "-en", nullptr, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-o", "Mtot", ffWRITE },
{ efXVG, "-eps", "epsilon", ffWRITE },
{ efXVG, "-a", "aver", ffWRITE },
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(ppa);
return 0;
}
}
snew(top, 1);
- ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm), NULL, box,
- &natoms, NULL, NULL, top);
+ ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm), nullptr, box,
+ &natoms, nullptr, nullptr, top);
snew(gnx, ncos);
snew(grpname, ncos);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real v;
} t_toppop;
-t_toppop *top = NULL;
+t_toppop *top = nullptr;
int ntop = 0;
typedef struct {
}
}
-int tpcomp(const void *a, const void *b)
+static int tpcomp(const void *a, const void *b)
{
t_toppop *tpa;
t_toppop *tpb;
while (((i+n) < disres->nr) &&
(forceparams[forceatoms[i+n]].disres.label == label));
- calc_disres_R_6(NULL, n, &forceatoms[i],
- (const rvec*)x, pbc, fcd, NULL);
+ calc_disres_R_6(nullptr, n, &forceatoms[i],
+ (const rvec*)x, pbc, fcd, nullptr);
- if (fcd->disres.Rt_6[0] <= 0)
+ if (fcd->disres.Rt_6[label] <= 0)
{
- gmx_fatal(FARGS, "ndr = %d, rt_6 = %f", ndr, fcd->disres.Rt_6[0]);
+ gmx_fatal(FARGS, "ndr = %d, rt_6 = %f", ndr, fcd->disres.Rt_6[label]);
}
- rt = gmx::invsixthroot(fcd->disres.Rt_6[0]);
+ rt = gmx::invsixthroot(fcd->disres.Rt_6[label]);
dr[clust_id].aver1[ndr] += rt;
dr[clust_id].aver2[ndr] += gmx::square(rt);
drt = 1.0/gmx::power3(rt);
dr[clust_id].aver_3[ndr] += drt;
- dr[clust_id].aver_6[ndr] += fcd->disres.Rt_6[0];
+ dr[clust_id].aver_6[ndr] += fcd->disres.Rt_6[label];
snew(fshift, SHIFTS);
interaction_function[F_DISRES].ifunc(n, &forceatoms[i], forceparams,
(const rvec*)x, f, fshift,
- pbc, g, lam, &dvdl, NULL, fcd, NULL);
+ pbc, g, lam, &dvdl, nullptr, fcd, nullptr);
sfree(fshift);
viol = fcd->disres.sumviol;
{
if (index[j] == forceparams[type].disres.label)
{
- vvindex[j] = gmx::invsixthroot(fcd->disres.Rt_6[0]);
+ vvindex[j] = gmx::invsixthroot(fcd->disres.Rt_6[label]);
}
}
}
real **matrix, *t_res, hi, *w_dr, rav, rviol;
t_rgb rlo = { 1, 1, 1 };
t_rgb rhi = { 0, 0, 0 };
- if (fn == NULL)
+ if (fn == nullptr)
{
return;
}
"Use inverse third power averaging or linear for matrix output" }
};
- FILE *out = NULL, *aver = NULL, *numv = NULL, *maxxv = NULL, *xvg = NULL;
+ FILE *out = nullptr, *aver = nullptr, *numv = nullptr, *maxxv = nullptr, *xvg = nullptr;
t_tpxheader header;
- t_inputrec ir;
gmx_mtop_t mtop;
rvec *xtop;
gmx_localtop_t *top;
- t_atoms *atoms = NULL;
+ t_atoms *atoms = nullptr;
t_fcdata fcd;
t_nrnb nrnb;
t_graph *g;
int ntopatoms, natoms, i, j, kkk;
t_trxstatus *status;
real t;
- rvec *x, *xav = NULL;
+ rvec *x, *xav = nullptr;
rvec4 *f;
matrix box;
gmx_bool bPDB;
int isize;
- int *index = NULL, *ind_fit = NULL;
+ int *index = nullptr, *ind_fit = nullptr;
char *grpname;
- t_cluster_ndx *clust = NULL;
- t_dr_result dr, *dr_clust = NULL;
+ t_cluster_ndx *clust = nullptr;
+ t_dr_result dr, *dr_clust = nullptr;
char **leg;
- real *vvindex = NULL, *w_rls = NULL;
+ real *vvindex = nullptr, *w_rls = nullptr;
t_mdatoms *mdatoms;
t_pbc pbc, *pbc_null;
int my_clust;
FILE *fplog;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
{ efXVG, "-ds", "drsum", ffWRITE },
{ efXVG, "-da", "draver", ffWRITE },
{ efXVG, "-dn", "drnum", ffWRITE },
{ efXVG, "-dm", "drmax", ffWRITE },
{ efXVG, "-dr", "restr", ffWRITE },
{ efLOG, "-l", "disres", ffWRITE },
- { efNDX, NULL, "viol", ffOPTRD },
+ { efNDX, nullptr, "viol", ffOPTRD },
{ efPDB, "-q", "viol", ffOPTWR },
{ efNDX, "-c", "clust", ffOPTRD },
{ efXPM, "-x", "matrix", ffOPTWR }
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
init5(ntop);
}
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
+
read_tpxheader(ftp2fn(efTPR, NFILE, fnm), &header, FALSE);
snew(xtop, header.natoms);
- read_tpx(ftp2fn(efTPR, NFILE, fnm), &ir, box, &ntopatoms, xtop, NULL, &mtop);
+ read_tpx(ftp2fn(efTPR, NFILE, fnm), ir, box, &ntopatoms, xtop, nullptr, &mtop);
bPDB = opt2bSet("-q", NFILE, fnm);
if (bPDB)
{
snew(atoms, 1);
*atoms = gmx_mtop_global_atoms(&mtop);
- if (atoms->pdbinfo == NULL)
+ if (atoms->pdbinfo == nullptr)
{
snew(atoms->pdbinfo, atoms->nr);
}
+ atoms->havePdbInfo = TRUE;
}
- top = gmx_mtop_generate_local_top(&mtop, ir.efep != efepNO);
+ top = gmx_mtop_generate_local_top(&mtop, ir->efep != efepNO);
- g = NULL;
- pbc_null = NULL;
- if (ir.ePBC != epbcNONE)
+ g = nullptr;
+ pbc_null = nullptr;
+ if (ir->ePBC != epbcNONE)
{
- if (ir.bPeriodicMols)
+ if (ir->bPeriodicMols)
{
pbc_null = &pbc;
}
isize = 0;
}
- ir.dr_tau = 0.0;
- init_disres(fplog, &mtop, &ir, NULL, &fcd, NULL, FALSE);
+ ir->dr_tau = 0.0;
+ init_disres(fplog, &mtop, ir, nullptr, &fcd, nullptr, FALSE);
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(f, 5*natoms);
"Largest Violation", "Time (ps)", "nm", oenv);
}
- mdatoms = init_mdatoms(fplog, &mtop, ir.efep != efepNO);
- atoms2md(&mtop, &ir, 0, NULL, mtop.natoms, mdatoms);
- update_mdatoms(mdatoms, ir.fepvals->init_lambda);
+ mdatoms = init_mdatoms(fplog, &mtop, ir->efep != efepNO);
+ atoms2md(&mtop, ir, -1, nullptr, mtop.natoms, mdatoms);
+ update_mdatoms(mdatoms, ir->fepvals->init_lambda);
init_nrnb(&nrnb);
- if (ir.ePBC != epbcNONE)
+ if (ir->ePBC != epbcNONE)
{
- gpbc = gmx_rmpbc_init(&top->idef, ir.ePBC, natoms);
+ gpbc = gmx_rmpbc_init(&top->idef, ir->ePBC, natoms);
}
j = 0;
do
{
- if (ir.ePBC != epbcNONE)
+ if (ir->ePBC != epbcNONE)
{
- if (ir.bPeriodicMols)
+ if (ir->bPeriodicMols)
{
- set_pbc(&pbc, ir.ePBC, box);
+ set_pbc(&pbc, ir->ePBC, box);
}
else
{
}
if (bPDB)
{
- reset_x(atoms->nr, ind_fit, atoms->nr, NULL, x, w_rls);
+ reset_x(atoms->nr, ind_fit, atoms->nr, nullptr, x, w_rls);
do_fit(atoms->nr, w_rls, x, x);
if (j == 0)
{
j++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
- if (ir.ePBC != epbcNONE)
+ close_trx(status);
+ if (ir->ePBC != epbcNONE)
{
gmx_rmpbc_done(gpbc);
}
{
dump_stats(fplog, j, fcd.disres.nres, &(top->idef.il[F_DISRES]),
top->idef.iparams, &dr, isize, index,
- bPDB ? atoms : NULL);
+ bPDB ? atoms : nullptr);
if (bPDB)
{
write_sto_conf(opt2fn("-q", NFILE, fnm),
"Coloured by average violation in Angstrom",
- atoms, xav, NULL, ir.ePBC, box);
+ atoms, xav, nullptr, ir->ePBC, box);
}
dump_disre_matrix(opt2fn_null("-x", NFILE, fnm), &dr, fcd.disres.nres,
j, &top->idef, &mtop, max_dr, nlevels, bThird);
{
fgets2(buf, STRLEN, tapeout);
}
- while (std::strstr(buf, "KAPPA") == NULL);
+ while (std::strstr(buf, "KAPPA") == nullptr);
if (bFirst)
{
/* Since we also have empty lines in the dssp output (temp) file,
nresidues = 0;
naccf = 0;
naccb = 0;
- for (nr = 0; (fgets2(buf, STRLEN, tapeout) != NULL); nr++)
+ for (nr = 0; (fgets2(buf, STRLEN, tapeout) != nullptr); nr++)
{
if (buf[13] == '!') /* Chain separator line has '!' at pos. 13 */
{
buf[39] = '\0';
/* Only calculate solvent accessible area if needed */
- if ((NULL != acc) && (buf[13] != '!'))
+ if ((nullptr != acc) && (buf[13] != '!'))
{
sscanf(&(buf[34]), "%d", &iacc);
acc[nr] = iacc;
if (bFirst)
{
- if (0 != acc)
+ if (nullptr != acc)
{
fprintf(stderr, "%d residues were classified as hydrophobic and %d as hydrophilic.\n", naccb, naccf);
}
sprintf(mat->title, "Secondary structure");
mat->legend[0] = 0;
- sprintf(mat->label_x, "%s", output_env_get_time_label(oenv));
+ sprintf(mat->label_x, "%s", output_env_get_time_label(oenv).c_str());
sprintf(mat->label_y, "Residue");
mat->bDiscrete = TRUE;
mat->ny = nr;
{
mat->axis_y[i] = i+1;
}
- mat->axis_x = NULL;
- mat->matrix = NULL;
+ mat->axis_x = nullptr;
+ mat->matrix = nullptr;
xsize = 0;
frame = 0;
bFirst = FALSE;
}
}
-void prune_ss_legend(t_matrix *mat)
+static void prune_ss_legend(t_matrix *mat)
{
gmx_bool *present;
int *newnum;
}
newnmap = 0;
- newmap = NULL;
+ newmap = nullptr;
for (i = 0; i < mat->nmap; i++)
{
newnum[i] = -1;
}
}
-void write_sas_mat(const char *fn, real **accr, int nframe, int nres, t_matrix *mat)
+static void write_sas_mat(const char *fn, real **accr, int nframe, int nres, t_matrix *mat)
{
real lo, hi;
int i, j, nlev;
}
}
-void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
- const gmx_output_env_t *oenv)
+static void analyse_ss(const char *outfile, t_matrix *mat, const char *ss_string,
+ const gmx_output_env_t *oenv)
{
FILE *fp;
t_mapping *map;
int *index;
rvec *xp, *x;
int *average_area;
- real **accr, *accr_ptr = NULL, *av_area, *norm_av_area;
+ real **accr, *accr_ptr = nullptr, *av_area, *norm_av_area;
char pdbfile[32], tmpfile[32];
char dssp[256];
const char *dptr;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efDAT, "-ssdump", "ssdump", ffOPTWR },
{ efMAP, "-map", "ss", ffLIBRD },
{ efXPM, "-o", "ss", ffWRITE },
if (!parse_common_args(&argc, argv,
PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fnAArea = opt2fn_null("-aa", NFILE, fnm);
bDoAccSurf = (fnArea || fnTArea || fnAArea);
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xp, NULL, box, FALSE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xp, nullptr, box, FALSE);
atoms = &(top.atoms);
check_oo(atoms);
bPhbres = bPhobics(atoms);
std::strcpy(pdbfile, "ddXXXXXX");
gmx_tmpnam(pdbfile);
- if ((tmpf = fopen(pdbfile, "w")) == NULL)
+ if ((tmpf = fopen(pdbfile, "w")) == nullptr)
{
sprintf(pdbfile, "%ctmp%cfilterXXXXXX", DIR_SEPARATOR, DIR_SEPARATOR);
gmx_tmpnam(pdbfile);
- if ((tmpf = fopen(pdbfile, "w")) == NULL)
+ if ((tmpf = fopen(pdbfile, "w")) == nullptr)
{
gmx_fatal(FARGS, "Can not open tmp file %s", pdbfile);
}
std::strcpy(tmpfile, "ddXXXXXX");
gmx_tmpnam(tmpfile);
- if ((tmpf = fopen(tmpfile, "w")) == NULL)
+ if ((tmpf = fopen(tmpfile, "w")) == nullptr)
{
sprintf(tmpfile, "%ctmp%cfilterXXXXXX", DIR_SEPARATOR, DIR_SEPARATOR);
gmx_tmpnam(tmpfile);
- if ((tmpf = fopen(tmpfile, "w")) == NULL)
+ if ((tmpf = fopen(tmpfile, "w")) == nullptr)
{
gmx_fatal(FARGS, "Can not open tmp file %s", tmpfile);
}
fclose(tmpf);
}
- if ((dptr = getenv("DSSP")) == NULL)
+ if ((dptr = getenv("DSSP")) == nullptr)
{
dptr = "/usr/local/bin/dssp";
}
}
else
{
- fTArea = NULL;
+ fTArea = nullptr;
}
- mat.map = NULL;
+ mat.map = nullptr;
mat.nmap = readcmap(opt2fn("-map", NFILE, fnm), &(mat.map));
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(average_area, atoms->nres);
snew(av_area, atoms->nres);
snew(norm_av_area, atoms->nres);
- accr = NULL;
+ accr = nullptr;
naccr = 0;
gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
}
gmx_rmpbc(gpbc, natoms, box, x);
tapein = gmx_ffopen(pdbfile, "w");
- write_pdbfile_indexed(tapein, NULL, atoms, x, ePBC, box, ' ', -1, gnx, index, NULL, TRUE);
+ write_pdbfile_indexed(tapein, nullptr, atoms, x, ePBC, box, ' ', -1, gnx, index, nullptr, TRUE);
gmx_ffclose(tapein);
if (0 != system(dssp))
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
- close_trj(status);
+ close_trx(status);
if (fTArea)
{
xvgrclose(fTArea);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
t_filenm fnm[] = {
- { efTRN, "-f", NULL, ffREAD },
- { efTPR, "-s", NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRN, "-f", nullptr, ffREAD },
+ { efTPR, "-s", nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
{ efXVG, "-dos", "dos", ffWRITE },
NFILE, fnm, npargs, ppa, asize(desc), desc,
asize(bugs), bugs, &oenv))
{
+ sfree(ppa);
return 0;
}
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
- read_tps_conf(ftp2fn(efTPR, NFILE, fnm), &top, &ePBC, NULL, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPR, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box, TRUE);
/* Handle index groups */
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &grpNatoms, &index, &grpname);
snew(c1, gnx);
for (i = 0; (i < gnx); i++)
{
- c1[i] = NULL;
+ c1[i] = nullptr;
}
read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_V);
}
while (read_next_frame(oenv, status, &fr));
- close_trj(status);
+ close_trx(status);
if (nframes < min_frames)
{
normalizeAutocorrelation = opt2parg_bool("-normalize", npargs, ppa);
/* Note that we always disable normalization here, regardless of user settings */
- low_do_autocorr(NULL, oenv, NULL, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE,
+ low_do_autocorr(nullptr, oenv, nullptr, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE,
FALSE, FALSE, -1, -1, 0);
snew(dos, DOS_NR);
for (j = 0; (j < DOS_NR); j++)
}
}
/* Normalize it */
- dostot = evaluate_integral(nframes/4, nu, dos[DOS], NULL, nframes/4, &stddev);
+ dostot = evaluate_integral(nframes/4, nu, dos[DOS], nullptr, nframes/4, &stddev);
if (bNormalizeDos)
{
for (j = 0; (j < nframes/4); j++)
dos[DOS_E][j] = (dos[DOS_DIFF][j]*wEdiff +
dos[DOS_SOLID][j]*wEsolid(nu[j], beta));
}
- DiffCoeff = evaluate_integral(nframes/2, tt, dos[VACF], NULL, nframes/2, &stddev);
+ DiffCoeff = evaluate_integral(nframes/2, tt, dos[VACF], nullptr, nframes/2, &stddev);
DiffCoeff = 1000*DiffCoeff/3.0;
fprintf(fplog, "Diffusion coefficient from VACF %g 10^-5 cm^2/s\n",
DiffCoeff);
fprintf(fplog, "Diffusion coefficient from DoS %g 10^-5 cm^2/s\n",
1000*DoS0/(12*tmass*beta));
- cP = BOLTZ * evaluate_integral(nframes/4, nu, dos[DOS_CP], NULL,
+ cP = BOLTZ * evaluate_integral(nframes/4, nu, dos[DOS_CP], nullptr,
nframes/4, &stddev);
fprintf(fplog, "Heat capacity %g J/mol K\n", 1000*cP/Nmol);
fprintf(fplog, "\nArrivederci!\n");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_filenm fnm[] =
{
- { efTRX, "-f", NULL, ffREAD },
- { efNDX, NULL, NULL, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffREAD },
{ efXVG, "-ot", "rkappa", ffOPTWR },
{ efXVG, "-oe", "insteff", ffOPTWR },
{ efDAT, "-o", "rkappa", ffOPTWR },
#define NFILE asize(fnm)
- const char *in_trajfile, *out_xvgrkfile = NULL, *out_xvginstefffile = NULL, *out_xvgrhistfile = NULL, *out_xvgkhistfile = NULL, *out_datfile = NULL;
+ const char *in_trajfile, *out_xvgrkfile = nullptr, *out_xvginstefffile = nullptr, *out_xvgrhistfile = nullptr, *out_xvgkhistfile = nullptr, *out_datfile = nullptr;
gmx_bool bHaveFirstFrame, bHaveNextFrame, indexOK = TRUE;
int ndon, nacc;
int *donindex, *accindex;
/*we rely on PBC autodetection (...currently)*/
int ePBC = -1;
- real *rvalues = NULL, *kappa2values = NULL, *rhist = NULL, *khist = NULL;
- t_pbc *pbc = NULL;
+ real *rvalues = nullptr, *kappa2values = nullptr, *rhist = nullptr, *khist = nullptr;
+ t_pbc *pbc = nullptr;
int i, bin;
- FILE *rkfp = NULL, *rhfp = NULL, *khfp = NULL, *datfp = NULL, *iefp = NULL;
+ FILE *rkfp = nullptr, *rhfp = nullptr, *khfp = nullptr, *datfp = nullptr, *iefp = nullptr;
gmx_bool bRKout, bRhistout, bKhistout, bDatout, bInstEffout, grident;
const char *rkleg[2] = { "R", "\\f{Symbol}k\\f{}\\S2\\N" };
int rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
printf("Select group with donor atom pairs defining the transition moment\n");
- get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
+ get_index(nullptr, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
printf("Select group with acceptor atom pairs defining the transition moment\n");
- get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
+ get_index(nullptr, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
/*check if groups are identical*/
grident = TRUE;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
int i, j, natoms, isize;
t_trxstatus *status;
- int *index = NULL, *index_all;
+ int *index = nullptr, *index_all;
char *grpname;
real angle, trans;
rvec *x, *v, *xout, *vout;
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
t_topology *top;
snew(top, 1);
- read_tps_conf(opt2fn("-f", NFILE, fnm), top, NULL, &x, &v, box, FALSE);
+ read_tps_conf(opt2fn("-f", NFILE, fnm), top, nullptr, &x, &v, box, FALSE);
t_atoms &atoms = top->atoms;
- if (atoms.pdbinfo == NULL)
+ if (atoms.pdbinfo == nullptr)
{
snew(atoms.pdbinfo, atoms.nr);
}
- natoms = atoms.nr;
+ atoms.havePdbInfo = TRUE;
+ natoms = atoms.nr;
snew(xout, natoms);
snew(vout, natoms);
atoms.resinfo[atoms.atom[j].resind].chainid = label;
}
- write_trx(status, atoms.nr, index_all, &atoms, i, angle, box, xout, vout, NULL);
+ write_trx(status, atoms.nr, index_all, &atoms, i, angle, box, xout, vout, nullptr);
}
close_trx(status);
#include "gromacs/utility/strdb.h"
-real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
+static real calc_mass(t_atoms *atoms, gmx_bool bGetMass, gmx_atomprop_t aps)
{
real tmass;
int i;
return tmass;
}
-real calc_geom(int isize, int *index, rvec *x, rvec geom_center, rvec minval,
- rvec maxval, gmx_bool bDiam)
+static real calc_geom(int isize, int *index, rvec *x, rvec geom_center, rvec minval,
+ rvec maxval, gmx_bool bDiam)
{
real diam2, d;
int ii, i, j;
return std::sqrt(diam2);
}
-void center_conf(int natom, rvec *x, rvec center, rvec geom_cent)
+static void center_conf(int natom, rvec *x, rvec center, rvec geom_cent)
{
int i;
rvec shift;
}
}
-void scale_conf(int natom, rvec x[], matrix box, rvec scale)
+static void scale_conf(int natom, rvec x[], matrix box, rvec scale)
{
int i, j;
}
}
-void read_bfac(const char *fn, int *n_bfac, double **bfac_val, int **bfac_nr)
+static void read_bfac(const char *fn, int *n_bfac, double **bfac_val, int **bfac_nr)
{
int i;
char **bfac_lines;
}
-void set_pdb_conf_bfac(int natoms, int nres, t_atoms *atoms, int n_bfac,
- double *bfac, int *bfac_nr, gmx_bool peratom)
+static void set_pdb_conf_bfac(int natoms, int nres, t_atoms *atoms, int n_bfac,
+ double *bfac, int *bfac_nr, gmx_bool peratom)
{
real bfac_min, bfac_max;
int i, n;
}
}
-void pdb_legend(FILE *out, int natoms, int nres, t_atoms *atoms, rvec x[])
+static void pdb_legend(FILE *out, int natoms, int nres, t_atoms *atoms, rvec x[])
{
real bfac_min, bfac_max, xmin, ymin, zmin;
int i;
}
}
-void visualize_images(const char *fn, int ePBC, matrix box)
+static void visualize_images(const char *fn, int ePBC, matrix box)
{
t_atoms atoms;
rvec *img;
}
calc_triclinic_images(box, img + 1);
- write_sto_conf(fn, "Images", &atoms, img, NULL, ePBC, box);
+ write_sto_conf(fn, "Images", &atoms, img, nullptr, ePBC, box);
done_atom(&atoms);
sfree(img);
}
-void visualize_box(FILE *out, int a0, int r0, matrix box, rvec gridsize)
+static void visualize_box(FILE *out, int a0, int r0, matrix box, rvec gridsize)
{
int *edge;
rvec *vert, shift;
}
}
-void calc_rotmatrix(rvec principal_axis, rvec targetvec, matrix rotmatrix)
+static void calc_rotmatrix(rvec principal_axis, rvec targetvec, matrix rotmatrix)
{
rvec rotvec;
real ux, uy, uz, costheta, sintheta;
resind_prev = -1;
for (i = 0; i < isize; i++)
{
- resind = atoms->atom[index == NULL ? i : index[i]].resind;
+ resind = atoms->atom[index == nullptr ? i : index[i]].resind;
if (resind != resind_prev)
{
atoms->resinfo[resind].nr = resnr_start;
{ 0, 0, 0 }, targetvec =
{ 0, 0, 0 };
static const char *btype[] =
- { NULL, "triclinic", "cubic", "dodecahedron", "octahedron", NULL },
+ { nullptr, "triclinic", "cubic", "dodecahedron", "octahedron", nullptr },
*label = "A";
static rvec visbox =
{ 0, 0, 0 };
FILE *out;
const char *infile, *outfile;
int outftp, inftp, natom, i, j, n_bfac, itype, ntype;
- double *bfac = NULL, c6, c12;
- int *bfac_nr = NULL;
- t_topology *top = NULL;
+ double *bfac = nullptr, c6, c12;
+ int *bfac_nr = nullptr;
+ t_topology *top = nullptr;
char *grpname, *sgrpname, *agrpname;
int isize, ssize, asize;
int *index, *sindex, *aindex;
gmx_output_env_t *oenv;
t_filenm fnm[] =
{
- { efSTX, "-f", NULL, ffREAD },
- { efNDX, "-n", NULL, ffOPTRD },
- { efSTO, NULL, NULL, ffOPTWR },
+ { efSTX, "-f", nullptr, ffREAD },
+ { efNDX, "-n", nullptr, ffOPTRD },
+ { efSTO, nullptr, nullptr, ffOPTWR },
{ efPQR, "-mead", "mead", ffOPTWR },
{ efDAT, "-bf", "bfact", ffOPTRD }
};
bScale = bScale || bRho;
bCalcGeom = bCenter || bRotate || bOrient || bScale;
- GMX_RELEASE_ASSERT(btype[0] != NULL, "Option setting inconsistency; btype[0] is NULL");
+ GMX_RELEASE_ASSERT(btype[0] != nullptr, "Option setting inconsistency; btype[0] is NULL");
bCalcDiam = (btype[0][0] == 'c' || btype[0][0] == 'd' || btype[0][0] == 'o');
read_tps_conf(infile, top_tmp, &ePBC, &x, &v, box, FALSE);
t_atoms &atoms = top_tmp->atoms;
natom = atoms.nr;
- if (atoms.pdbinfo == NULL)
+ if (atoms.pdbinfo == nullptr)
{
snew(atoms.pdbinfo, atoms.nr);
}
+ atoms.havePdbInfo = TRUE;
+
if (fn2ftp(infile) == efPDB)
{
get_pdb_atomnumber(&atoms, aps);
if (bMead || bGrasp || bCONECT)
{
- top = read_top(infile, NULL);
+ top = read_top(infile, nullptr);
}
if (bMead || bGrasp)
else
{
ssize = atoms.nr;
- sindex = NULL;
+ sindex = nullptr;
}
diam = calc_geom(ssize, sindex, x, gc, rmin, rmax, bCalcDiam);
rvec_sub(rmax, rmin, size);
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpnames);
/* Orient the principal axes along the coordinate axes */
- orient_princ(&atoms, isize, index, natom, x, bHaveV ? v : NULL, NULL);
+ orient_princ(&atoms, isize, index, natom, x, bHaveV ? v : nullptr, nullptr);
sfree(index);
sfree(grpnames);
}
else
{
ssize = atoms.nr;
- sindex = NULL;
+ sindex = nullptr;
}
printf("Translating %d atoms (out of %d) by %g %g %g nm\n", ssize, natom,
translation[XX], translation[YY], translation[ZZ]);
}
}
- if ((btype[0] != NULL) && (bSetSize || bDist || (btype[0][0] == 't' && bSetAng)))
+ if ((btype[0] != nullptr) && (bSetSize || bDist || (btype[0][0] == 't' && bSetAng)))
{
ePBC = epbcXYZ;
if (!(bSetSize || bDist))
}
else
{
- conect = NULL;
+ conect = nullptr;
}
if (bIndex)
}
else
{
- write_sto_conf_indexed(outfile, *top_tmp->name, &atoms, x, bHaveV ? v : NULL, ePBC, box, isize, index);
+ write_sto_conf_indexed(outfile, *top_tmp->name, &atoms, x, bHaveV ? v : nullptr, ePBC, box, isize, index);
}
}
else
{
if (resnr_start >= 0)
{
- renum_resnr(&atoms, atoms.nr, NULL, resnr_start);
+ renum_resnr(&atoms, atoms.nr, nullptr, resnr_start);
}
if ((outftp == efPDB) || (outftp == efPQR))
}
else
{
- write_sto_conf(outfile, *top_tmp->name, &atoms, x, bHaveV ? v : NULL, ePBC, box);
+ write_sto_conf(outfile, *top_tmp->name, &atoms, x, bHaveV ? v : nullptr, ePBC, box);
}
}
gmx_atomprop_destroy(aps);
- do_view(oenv, outfile, NULL);
+ do_view(oenv, outfile, nullptr);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int *set;
gmx_bool bVerbose = TRUE;
- if ((getenv("GMX_ENER_VERBOSE")) != NULL)
+ if ((getenv("GMX_ENER_VERBOSE")) != nullptr)
{
bVerbose = FALSE;
}
for (f = 0; f < nfiles; f++)
{
in = open_enx(fnms[f], "r");
- enm = NULL;
+ enm = nullptr;
do_enxnms(in, &nre, &enm);
if (f == 0)
fprintf(stderr,
"\nContinue conversion using only the first %d terms (n/y)?\n"
"(you should be sure that the energy terms match)\n", nremin);
- if (NULL == fgets(inputstring, STRLEN-1, stdin))
+ if (nullptr == fgets(inputstring, STRLEN-1, stdin))
{
gmx_fatal(FARGS, "Error reading user input");
}
ok = FALSE;
do
{
- if (NULL == fgets(inputstring, STRLEN-1, stdin))
+ if (nullptr == fgets(inputstring, STRLEN-1, stdin))
{
gmx_fatal(FARGS, "Error reading user input");
}
const char *bugs[] = {
"When combining trajectories the sigma and E^2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way."
};
- ener_file_t in = NULL, out = NULL;
- gmx_enxnm_t *enm = NULL;
+ ener_file_t in = nullptr, out = nullptr;
+ gmx_enxnm_t *enm = nullptr;
#if 0
ener_file_t in, out = NULL;
gmx_enxnm_t *enm = NULL;
t_energy *ee_sum;
gmx_int64_t lastfilestep, laststep, startstep_file = 0;
int noutfr;
- int nre, nremax, this_nre, nfile, f, i, kkk, nset, *set = NULL;
+ int nre, nremax, this_nre, nfile, f, i, kkk, nset, *set = nullptr;
double last_t;
char **fnms;
real *readtime, *settime, timestep, tadjust;
gmx_bool bNewFile, bFirst, bNewOutput;
gmx_output_env_t *oenv;
gmx_bool warned_about_dh = FALSE;
- t_enxblock *blocks = NULL;
+ t_enxblock *blocks = nullptr;
int nblocks = 0;
int nblocks_alloc = 0;
t_filenm fnm[] = {
- { efEDR, "-f", NULL, ffRDMULT },
+ { efEDR, "-f", nullptr, ffRDMULT },
{ efEDR, "-o", "fixed", ffWRITE },
};
bNewFile = TRUE;
bNewOutput = TRUE;
in = open_enx(fnms[f], "r");
- enm = NULL;
+ enm = nullptr;
do_enxnms(in, &this_nre, &enm);
if (f == 0)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ener_file_t in;
FILE *out;
int timecheck = 0;
- gmx_enxnm_t *enm = NULL;
+ gmx_enxnm_t *enm = nullptr;
t_enxframe *fr;
int teller = 0;
real sum;
gmx_bool bCont, bRef;
gmx_bool bCutmax, bCutmin;
- real **eneset, *time = NULL;
+ real **eneset, *time = nullptr;
int *set, i, j, k, prevk, m = 0, n, nre, nset, nenergy;
- char **groups = NULL;
+ char **groups = nullptr;
char groupname[255], fn[255];
int ngroups;
t_rgb rlo, rhi, rmid;
real emax, emid, emin;
real ***emat, **etot, *groupnr;
- double beta, expE, **e, *eaver, *efree = NULL, edum;
+ double beta, expE, **e, *eaver, *efree = nullptr, edum;
char label[234];
- char **ereflines, **erefres = NULL;
- real *eref = NULL, *edif = NULL;
+ char **ereflines, **erefres = nullptr;
+ real *eref = nullptr, *edif = nullptr;
int neref = 0;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efEDR, "-f", NULL, ffOPTRD },
+ { efEDR, "-f", nullptr, ffOPTRD },
{ efDAT, "-groups", "groups", ffREAD },
{ efDAT, "-eref", "eref", ffOPTRD },
{ efXPM, "-emat", "emat", ffWRITE },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
out = xvgropen(ftp2fn(efXVG, NFILE, fnm), "Mean Energy", "Residue", "kJ/mol",
oenv);
- xvgr_legend(out, 0, NULL, oenv);
+ xvgr_legend(out, 0, nullptr, oenv);
j = 0;
if (output_env_get_print_xvgr_codes(oenv))
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/ifunc.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/strconvert.h"
static real minthird = -1.0/3.0, minsixth = -1.0/6.0;
static const int NOTSET = -23451;
gmx_bool bHaveSums;
} enerdata_t;
+static void done_enerdata_t(int nset, enerdata_t *edat)
+{
+ sfree(edat->step);
+ sfree(edat->steps);
+ sfree(edat->points);
+ for (int i = 0; i < nset; i++)
+ {
+ sfree(edat->s[i].ener);
+ sfree(edat->s[i].es);
+ }
+ sfree(edat->s);
+}
+
static double mypow(double x, double y)
{
if (x > 0)
}
}
+static real blk_value(t_enxblock *blk, int sub, int index)
+{
+ range_check(index, 0, blk->sub[sub].nr);
+ if (blk->sub[sub].type == xdr_datatype_float)
+ {
+ return blk->sub[sub].fval[index];
+ }
+ else if (blk->sub[sub].type == xdr_datatype_double)
+ {
+ return blk->sub[sub].dval[index];
+ }
+ else
+ {
+ gmx_incons("Unknown datatype in t_enxblock");
+ }
+ return 0.0;
+}
+
static int *select_it(int nre, char *nm[], int *nset)
{
gmx_bool *bE;
int *set;
gmx_bool bVerbose = TRUE;
- if ((getenv("GMX_ENER_VERBOSE")) != NULL)
+ if ((getenv("GMX_ENER_VERBOSE")) != nullptr)
{
bVerbose = FALSE;
}
char *ptr, buf[STRLEN];
const char *fm4 = "%3d %-14s";
const char *fm2 = "%3d %-34s";
- char **newnm = NULL;
+ char **newnm = nullptr;
- if ((getenv("GMX_ENER_VERBOSE")) != NULL)
+ if ((getenv("GMX_ENER_VERBOSE")) != nullptr)
{
bVerbose = FALSE;
}
{
newnm[k] = gmx_strdup(nm[k].name);
/* Insert dashes in all the names */
- while ((ptr = std::strchr(newnm[k], ' ')) != NULL)
+ while ((ptr = std::strchr(newnm[k], ' ')) != nullptr)
{
*ptr = '-';
}
}
}
/* Look for the first space, and remove spaces from there */
- if ((ptr = std::strchr(ptr, ' ')) != NULL)
+ if ((ptr = std::strchr(ptr, ' ')) != nullptr)
{
trim(ptr);
}
matrix box;
/* all we need is the ir to be able to write the label */
- read_tpx(topnm, ir, box, &natoms, NULL, NULL, &mtop);
+ read_tpx(topnm, ir, box, &natoms, nullptr, nullptr, &mtop);
+ done_mtop(&mtop);
}
-static void get_orires_parms(const char *topnm,
+static void get_orires_parms(const char *topnm, t_inputrec *ir,
int *nor, int *nex, int **label, real **obs)
{
gmx_mtop_t mtop;
- gmx_localtop_t *top;
- t_inputrec ir;
+ t_topology top;
t_iparams *ip;
int natoms, i;
t_iatom *iatom;
int nb;
matrix box;
- read_tpx(topnm, &ir, box, &natoms, NULL, NULL, &mtop);
- top = gmx_mtop_generate_local_top(&mtop, ir.efep != efepNO);
+ read_tpx(topnm, ir, box, &natoms, nullptr, nullptr, &mtop);
+ top = gmx_mtop_t_to_t_topology(&mtop, FALSE);
- ip = top->idef.iparams;
- iatom = top->idef.il[F_ORIRES].iatoms;
+ ip = top.idef.iparams;
+ iatom = top.idef.il[F_ORIRES].iatoms;
/* Count how many distance restraint there are... */
- nb = top->idef.il[F_ORIRES].nr;
+ nb = top.idef.il[F_ORIRES].nr;
if (nb == 0)
{
gmx_fatal(FARGS, "No orientation restraints in topology!\n");
}
fprintf(stderr, "Found %d orientation restraints with %d experiments",
*nor, *nex);
+ done_top_mtop(&top, &mtop);
}
static int get_bounds(const char *topnm,
int nb, label1;
matrix box;
- read_tpx(topnm, ir, box, &natoms, NULL, NULL, mtop);
+ read_tpx(topnm, ir, box, &natoms, nullptr, nullptr, mtop);
snew(*ltop, 1);
top = gmx_mtop_generate_local_top(mtop, ir->efep != efepNO);
*ltop = top;
/* Subtract bounds from distances, to calculate violations */
calc_violations(violaver, violaver,
- nbounds, pair, bounds, NULL, &sumt, &sumaver);
+ nbounds, pair, bounds, nullptr, &sumt, &sumaver);
#ifdef DEBUG
fprintf(stdout, "\nSum of violations averaged over simulation: %g nm\n",
return esum;
}
-static char *ee_pr(double ee, char *buf)
+static void ee_pr(double ee, int buflen, char *buf)
{
- char tmp[100];
- double rnd;
-
- if (ee < 0)
- {
- sprintf(buf, "%s", "--");
- }
- else
+ snprintf(buf, buflen, "%s", "--");
+ if (ee >= 0)
{
/* Round to two decimals by printing. */
- sprintf(tmp, "%.1e", ee);
- sscanf(tmp, "%lf", &rnd);
- sprintf(buf, "%g", rnd);
+ char tmp[100];
+ snprintf(tmp, sizeof(tmp), "%.1e", ee);
+ double rnd = gmx::doubleFromString(tmp);
+ snprintf(buf, buflen, "%g", rnd);
}
-
- return buf;
}
static void remove_drift(int nset, int nbmin, int nbmax, real dt, enerdata_t *edat)
{
delta = edat->s[i].slope*dt;
- if (NULL != debug)
+ if (nullptr != debug)
{
fprintf(debug, "slope for set %d is %g\n", i, edat->s[i].slope);
}
fprintf(fp, "WARNING: Please verify that your simulations are converged and perform\n"
"a block-averaging error analysis (not implemented in g_energy yet)\n");
- if (debug != NULL)
+ if (debug != nullptr)
{
if (varv != NOTSET)
{
}
static void analyse_ener(gmx_bool bCorr, const char *corrfn,
+ const char *eviscofn, const char *eviscoifn,
gmx_bool bFee, gmx_bool bSum, gmx_bool bFluct,
gmx_bool bVisco, const char *visfn, int nmol,
gmx_int64_t start_step, double start_t,
FILE *fp;
/* Check out the printed manual for equations! */
double Dt, aver, stddev, errest, delta_t, totaldrift;
- enerdata_t *esum = NULL;
+ enerdata_t *esum = nullptr;
real integral, intBulk, Temp = 0, Pres = 0;
real pr_aver, pr_stddev, pr_errest;
- double beta = 0, expE, expEtot, *fee = NULL;
+ double beta = 0, expE, expEtot, *fee = nullptr;
gmx_int64_t nsteps;
int nexact, nnotexact;
int i, j, nout;
fee[i] = std::log(expE/edat->nframes)/beta + aver/nmol;
}
- if (std::strstr(leg[i], "empera") != NULL)
+ if (std::strstr(leg[i], "empera") != nullptr)
{
Temp = aver;
}
- else if (std::strstr(leg[i], "olum") != NULL)
+ else if (std::strstr(leg[i], "olum") != nullptr)
{
Vaver = aver;
}
- else if (std::strstr(leg[i], "essure") != NULL)
+ else if (std::strstr(leg[i], "essure") != nullptr)
{
Pres = aver;
}
totaldrift /= nmol;
}
+ ee_pr(pr_errest, sizeof(eebuf), eebuf);
fprintf(stdout, "%-24s %10g %10s %10g %10g",
- leg[i], pr_aver, ee_pr(pr_errest, eebuf), pr_stddev, totaldrift);
+ leg[i], pr_aver, eebuf, pr_stddev, totaldrift);
if (bFee)
{
fprintf(stdout, " %10g", fee[i]);
if (bSum)
{
totaldrift = (edat->nsteps - 1)*esum->s[0].slope;
+ ee_pr(esum->s[0].ee/nmol, sizeof(eebuf), eebuf);
fprintf(stdout, "%-24s %10g %10s %10s %10g (%s)",
- "Total", esum->s[0].av/nmol, ee_pr(esum->s[0].ee/nmol, eebuf),
+ "Total", esum->s[0].av/nmol, eebuf,
"--", totaldrift/nmol, enm[set[0]].unit);
/* pr_aver,pr_stddev,a,totaldrift */
if (bFee)
eneint[2][i+1] = eneint[2][i] + 0.5*(edat->s[5].es[i].sum + edat->s[7].es[i].sum)*Dt/edat->points[i];
}
- einstein_visco("evisco.xvg", "eviscoi.xvg",
+ einstein_visco(eviscofn, eviscoifn,
3, edat->nframes+1, eneint, Vaver, Temp, Dt, oenv);
for (i = 0; i < 3; i++)
real aver, beta;
real **eneset2;
double dE, sum;
- gmx_enxnm_t *enm = NULL;
+ gmx_enxnm_t *enm = nullptr;
t_enxframe *fr;
char buf[22];
/* read second energy file */
snew(fr, 1);
- enm = NULL;
+ enm = nullptr;
enx = open_enx(ene2fn, "r");
do_enxnms(enx, &(fr->nre), &enm);
srenew(eneset2[i], maxenergy);
}
}
- GMX_RELEASE_ASSERT(time != NULL, "trying to dereference NULL time pointer");
+ GMX_RELEASE_ASSERT(time != nullptr, "trying to dereference NULL time pointer");
if (fr->t != time[nenergy2])
{
nenergy = std::min(edat->nframes, nenergy2);
/* calculate fe difference dF = -kT ln < exp(-(E_B-E_A)/kT) >_A */
- fp = NULL;
+ fp = nullptr;
if (runavgfn)
{
fp = xvgropen(runavgfn, "Running average free energy difference",
/* coll data */
double temp = 0, start_time = 0, delta_time = 0, start_lambda = 0;
static int setnr = 0;
- double *native_lambda_vec = NULL;
- const char **lambda_components = NULL;
+ double *native_lambda_vec = nullptr;
+ const char **lambda_components = nullptr;
int n_lambda_vec = 0;
bool firstPass = true;
}
}
}
-
+ // Clean up!
+ sfree(native_lambda_vec);
+ sfree(lambda_components);
if (nblock_hist == 0 && nblock_dh == 0)
{
/* don't do anything */
"Volume", "Pressure"
};
- FILE *out = NULL, *fp_pairs = NULL, *fort = NULL, *fodt = NULL, *foten = NULL;
- FILE *fp_dhdl = NULL;
+ FILE *out = nullptr, *fp_pairs = nullptr, *fort = nullptr, *fodt = nullptr, *foten = nullptr;
+ FILE *fp_dhdl = nullptr;
ener_file_t fp;
int timecheck = 0;
gmx_mtop_t mtop;
- gmx_localtop_t *top = NULL;
- t_inputrec ir;
+ gmx_localtop_t *top = nullptr;
enerdata_t edat;
- gmx_enxnm_t *enm = NULL;
- t_enxframe *frame, *fr = NULL;
+ gmx_enxnm_t *enm = nullptr;
+ t_enxframe *frame, *fr = nullptr;
int cur = 0;
#define NEXT (1-cur)
int nre, teller, teller_disre, nfr;
gmx_int64_t start_step;
int nor = 0, nex = 0, norfr = 0, enx_i = 0;
real start_t;
- real *bounds = NULL, *violaver = NULL, *oobs = NULL, *orient = NULL, *odrms = NULL;
- int *index = NULL, *pair = NULL, norsel = 0, *orsel = NULL, *or_label = NULL;
+ real *bounds = nullptr, *violaver = nullptr, *oobs = nullptr, *orient = nullptr, *odrms = nullptr;
+ int *index = nullptr, *pair = nullptr, norsel = 0, *orsel = nullptr, *or_label = nullptr;
int nbounds = 0, npairs;
gmx_bool bDisRe, bDRAll, bORA, bORT, bODA, bODR, bODT, bORIRE, bOTEN, bDHDL;
gmx_bool bFoundStart, bCont, bVisco;
double sum, sumaver, sumt, dbl;
- double *time = NULL;
+ double *time = nullptr;
real Vaver;
- int *set = NULL, i, j, k, nset, sss;
- gmx_bool *bIsEner = NULL;
+ int *set = nullptr, i, j, k, nset, sss;
+ gmx_bool *bIsEner = nullptr;
char **pairleg, **odtleg, **otenleg;
- char **leg = NULL;
- char *anm_j, *anm_k, *resnm_j, *resnm_k;
+ char **leg = nullptr;
+ const char *anm_j, *anm_k, *resnm_j, *resnm_k;
int resnr_j, resnr_k;
const char *orinst_sub = "@ subtitle \"instantaneous\"\n";
char buf[256];
gmx_output_env_t *oenv;
- t_enxblock *blk = NULL;
- t_enxblock *blk_disre = NULL;
+ t_enxblock *blk_disre = nullptr;
int ndisre = 0;
int dh_blocks = 0, dh_hists = 0, dh_samples = 0, dh_lambdas = 0;
t_filenm fnm[] = {
- { efEDR, "-f", NULL, ffREAD },
- { efEDR, "-f2", NULL, ffOPTRD },
- { efTPR, "-s", NULL, ffOPTRD },
+ { efEDR, "-f", nullptr, ffREAD },
+ { efEDR, "-f2", nullptr, ffOPTRD },
+ { efTPR, "-s", nullptr, ffOPTRD },
{ efXVG, "-o", "energy", ffWRITE },
{ efXVG, "-viol", "violaver", ffOPTWR },
{ efXVG, "-pairs", "pairs", ffOPTWR },
{ efXVG, "-oten", "oriten", ffOPTWR },
{ efXVG, "-corr", "enecorr", ffOPTWR },
{ efXVG, "-vis", "visco", ffOPTWR },
+ { efXVG, "-evisco", "evisco", ffOPTWR },
+ { efXVG, "-eviscoi", "eviscoi", ffOPTWR },
{ efXVG, "-ravg", "runavgdf", ffOPTWR },
{ efXVG, "-odh", "dhdl", ffOPTWR }
};
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(ppa);
return 0;
}
bVisco = opt2bSet("-vis", NFILE, fnm);
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
+
if ((!bDisRe) && (!bDHDL))
{
if (bVisco)
(gmx_strcasecmp(interaction_function[j].longname, leg[i]) == 0);
}
}
-
if (bPrAll && nset > 1)
{
gmx_fatal(FARGS, "Printing averages can only be done when a single set is selected");
}
- time = NULL;
+ time = nullptr;
if (bORIRE || bOTEN)
{
- get_orires_parms(ftp2fn(efTPR, NFILE, fnm), &nor, &nex, &or_label, &oobs);
+ get_orires_parms(ftp2fn(efTPR, NFILE, fnm), ir,
+ &nor, &nex, &or_label, &oobs);
}
if (bORIRE)
fprintf(stderr, "Select the orientation restraint labels you want (-1 is all)\n");
fprintf(stderr, "End your selection with 0\n");
j = -1;
- orsel = NULL;
+ orsel = nullptr;
do
{
j++;
}
xvgr_legend(fodt, norsel, (const char**)odtleg, oenv);
}
+ for (i = 0; i < norsel; i++)
+ {
+ sfree(odtleg[i]);
+ }
+ sfree(odtleg);
}
}
if (bOTEN)
}
}
xvgr_legend(foten, bOvec ? nex*12 : nex*3, (const char**)otenleg, oenv);
+ for (j = 0; j < 3; j++)
+ {
+ sfree(otenleg[j]);
+ }
+ sfree(otenleg);
}
}
else if (bDisRe)
{
nbounds = get_bounds(ftp2fn(efTPR, NFILE, fnm), &bounds, &index, &pair, &npairs,
- &mtop, &top, &ir);
+ &mtop, &top, ir);
snew(violaver, npairs);
out = xvgropen(opt2fn("-o", NFILE, fnm), "Sum of Violations",
"Time (ps)", "nm", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp_pairs, "@ subtitle \"averaged (tau=%g) and instantaneous\"\n",
- ir.dr_tau);
+ ir->dr_tau);
}
}
}
else if (bDHDL)
{
- get_dhdl_parms(ftp2fn(efTPR, NFILE, fnm), &ir);
+ get_dhdl_parms(ftp2fn(efTPR, NFILE, fnm), ir);
}
/* Initiate energies and set them to zero */
edat.nsteps = 0;
edat.npoints = 0;
edat.nframes = 0;
- edat.step = NULL;
- edat.steps = NULL;
- edat.points = NULL;
+ edat.step = nullptr;
+ edat.steps = nullptr;
+ edat.points = nullptr;
edat.bHaveSums = TRUE;
snew(edat.s, nset);
* Define distance restraint legends. Can only be done after
* the first frame has been read... (Then we know how many there are)
*/
- blk_disre = find_block_id_enxframe(fr, enxDISRE, NULL);
+ blk_disre = find_block_id_enxframe(fr, enxDISRE, nullptr);
if (bDisRe && bDRAll && !leg && blk_disre)
{
t_iatom *fa;
ndisre, top->idef.il[F_DISRES].nr/3);
}
snew(pairleg, ndisre);
+ int molb = 0;
for (i = 0; i < ndisre; i++)
{
snew(pairleg[i], 30);
j = fa[3*i+1];
k = fa[3*i+2];
- gmx_mtop_atominfo_global(&mtop, j, &anm_j, &resnr_j, &resnm_j);
- gmx_mtop_atominfo_global(&mtop, k, &anm_k, &resnr_k, &resnm_k);
+ mtopGetAtomAndResidueName(&mtop, j, &molb, &anm_j, &resnr_j, &resnm_j, nullptr);
+ mtopGetAtomAndResidueName(&mtop, k, &molb, &anm_k, &resnr_k, &resnm_k, nullptr);
sprintf(pairleg[i], "%d %s %d %s (%d)",
resnr_j, anm_j, resnr_k, anm_k,
ip[fa[3*i]].disres.label);
*******************************************/
if (ndisre > 0)
{
- GMX_RELEASE_ASSERT(blk_disre != NULL, "Trying to dereference NULL blk_disre pointer");
+ GMX_RELEASE_ASSERT(blk_disre != nullptr, "Trying to dereference NULL blk_disre pointer");
#if !GMX_DOUBLE
float *disre_rt = blk_disre->sub[0].fval;
float *disre_rm3tav = blk_disre->sub[1].fval;
#endif
print_time(out, fr->t);
- if (violaver == NULL)
+ if (violaver == nullptr)
{
snew(violaver, ndisre);
}
}
else if (bDHDL)
{
- do_dhdl(fr, &ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists, &dh_samples, &dh_lambdas, oenv);
+ do_dhdl(fr, ir, &fp_dhdl, opt2fn("-odh", NFILE, fnm), bDp, &dh_blocks, &dh_hists, &dh_samples, &dh_lambdas, oenv);
}
/*******************************************
fprintf(out, "\n");
}
}
- blk = find_block_id_enxframe(fr, enx_i, NULL);
+ t_enxblock *blk = find_block_id_enxframe(fr, enx_i, nullptr);
if (bORIRE && blk)
{
-#if !GMX_DOUBLE
- xdr_datatype dt = xdr_datatype_float;
-#else
- xdr_datatype dt = xdr_datatype_double;
-#endif
- real *vals;
-
- if ( (blk->nsub != 1) || (blk->sub[0].type != dt) )
+ if (blk->nsub != 1)
{
- gmx_fatal(FARGS, "Orientational restraints read in incorrectly");
+ gmx_fatal(FARGS, "Orientational restraints read in incorrectly.");
}
-#if !GMX_DOUBLE
- vals = blk->sub[0].fval;
-#else
- vals = blk->sub[0].dval;
-#endif
if (blk->sub[0].nr != nor)
{
{
for (i = 0; i < nor; i++)
{
- orient[i] += vals[i];
+ orient[i] += blk_value(blk, 0, i);
}
}
if (bODR)
{
for (i = 0; i < nor; i++)
{
- odrms[i] += gmx::square(vals[i]-oobs[i]);
+ real v = blk_value(blk, 0, i);
+ odrms[i] += gmx::square(v - oobs[i]);
}
}
if (bORT)
fprintf(fort, " %10f", fr->t);
for (i = 0; i < norsel; i++)
{
- fprintf(fort, " %g", vals[orsel[i]]);
+ fprintf(fort, " %g", blk_value(blk, 0, orsel[i]));
}
fprintf(fort, "\n");
}
fprintf(fodt, " %10f", fr->t);
for (i = 0; i < norsel; i++)
{
- fprintf(fodt, " %g", vals[orsel[i]]-oobs[orsel[i]]);
+ fprintf(fodt, " %g", blk_value(blk, 0, orsel[i])-oobs[orsel[i]]);
}
fprintf(fodt, "\n");
}
norfr++;
}
- blk = find_block_id_enxframe(fr, enxORT, NULL);
+ blk = find_block_id_enxframe(fr, enxORT, nullptr);
if (bOTEN && blk)
{
-#if !GMX_DOUBLE
- xdr_datatype dt = xdr_datatype_float;
-#else
- xdr_datatype dt = xdr_datatype_double;
-#endif
- real *vals;
-
- if ( (blk->nsub != 1) || (blk->sub[0].type != dt) )
+ if (blk->nsub != 1)
{
gmx_fatal(FARGS, "Orientational restraints read in incorrectly");
}
-#if !GMX_DOUBLE
- vals = blk->sub[0].fval;
-#else
- vals = blk->sub[0].dval;
-#endif
if (blk->sub[0].nr != nex*12)
{
{
for (j = 0; j < (bOvec ? 12 : 3); j++)
{
- fprintf(foten, " %g", vals[i*12+j]);
+ fprintf(foten, " %g", blk_value(blk, 0, i*12+j));
}
}
fprintf(foten, "\n");
while (bCont && (timecheck == 0));
fprintf(stderr, "\n");
- close_enx(fp);
+ done_ener_file(fp);
if (out)
{
xvgrclose(out);
}
xvgrclose(out);
}
+ // Clean up orires variables.
+ sfree(or_label);
+ sfree(oobs);
+ sfree(orient);
+ sfree(odrms);
+ sfree(orsel);
if (bOTEN)
{
xvgrclose(foten);
{
double dt = (frame[cur].t-start_t)/(edat.nframes-1);
analyse_ener(opt2bSet("-corr", NFILE, fnm), opt2fn("-corr", NFILE, fnm),
+ opt2fn("-evisco", NFILE, fnm), opt2fn("-eviscoi", NFILE, fnm),
bFee, bSum, bFluct,
bVisco, opt2fn("-vis", NFILE, fnm),
nmol,
fec(opt2fn("-f2", NFILE, fnm), opt2fn("-ravg", NFILE, fnm),
reftemp, nset, set, leg, &edat, time, oenv);
}
-
+ // Clean up!
+ done_enerdata_t(nset, &edat);
+ sfree(time);
+ free_enxframe(&frame[0]);
+ free_enxframe(&frame[1]);
+ sfree(frame);
+ free_enxnms(nre, enm);
+ sfree(ppa);
+ sfree(set);
+ sfree(leg);
+ sfree(bIsEner);
{
const char *nxy = "-nxy";
do_view(oenv, opt2fn_null("-oten", NFILE, fnm), nxy);
do_view(oenv, opt2fn_null("-odh", NFILE, fnm), nxy);
}
+ output_env_done(oenv);
+ done_filenms(NFILE, fnm);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char *grpname;
int isize;
int *index;
- real *w_rls = NULL;
+ real *w_rls = nullptr;
t_trxstatus *in;
t_trxstatus *outl, *outh;
int nffr, i, fr, nat, j, d, m;
real flen, *filt, sum, *t;
rvec xcmtop, xcm, **x, *ptr, *xf, *xn, *xp, hbox;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
#define NLEG asize(leg)
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efTRO, "-ol", "lowpass", ffOPTWR },
{ efTRO, "-oh", "highpass", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
if (topfile)
{
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC,
- &xtop, NULL, topbox, TRUE);
+ &xtop, nullptr, topbox, TRUE);
if (bTop)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
}
else
{
- outl = 0;
+ outl = nullptr;
}
if (highfile)
{
}
else
{
- outh = 0;
+ outh = nullptr;
}
fr = 0;
}
if (outl && (bLowAll || fr % nf == nf - 1))
{
- write_trx(outl, nat, ind, topfile ? &(top.atoms) : NULL,
- 0, t[nf - 1], bFit ? topbox : boxf, xf, NULL, NULL);
+ write_trx(outl, nat, ind, topfile ? &(top.atoms) : nullptr,
+ 0, t[nf - 1], bFit ? topbox : boxf, xf, nullptr, nullptr);
}
if (outh)
{
boxf[j][d] = topbox[j][d] + box[nf - 1][j][d] - boxf[j][d];
}
}
- write_trx(outh, nat, ind, topfile ? &(top.atoms) : NULL,
- 0, t[nf - 1], bFit ? topbox : boxf, xf, NULL, NULL);
+ write_trx(outh, nat, ind, topfile ? &(top.atoms) : nullptr,
+ 0, t[nf - 1], bFit ? topbox : boxf, xf, nullptr, nullptr);
}
}
/* Cycle all the pointer and the box by one */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return str;
}
-void sort_ions(int nsa, int nw, int repl[], int index[],
- t_atoms *atoms, rvec x[],
- const char *p_name, const char *n_name)
+static void sort_ions(int nsa, int nw, int repl[], int index[],
+ t_atoms *atoms, rvec x[],
+ const char *p_name, const char *n_name)
{
int i, j, k, r, np, nn, starta, startr, npi, nni;
rvec *xt;
- char **pptr = NULL, **nptr = NULL, **paptr = NULL, **naptr = NULL;
+ char **pptr = nullptr, **nptr = nullptr, **paptr = nullptr, **naptr = nullptr;
snew(xt, atoms->nr);
const char *p_name, const char *n_name, char *grpname)
{
FILE *fpin, *fpout;
- char buf[STRLEN], buf2[STRLEN], *temp, **mol_line = NULL;
+ char buf[STRLEN], buf2[STRLEN], *temp, **mol_line = nullptr;
int line, i, nmol_line, sol_line, nsol_last;
gmx_bool bMolecules;
char temporary_filename[STRLEN];
{
line++;
std::strcpy(buf2, buf);
- if ((temp = std::strchr(buf2, '\n')) != NULL)
+ if ((temp = std::strchr(buf2, '\n')) != nullptr)
{
temp[0] = '\0';
}
if (buf2[0] == '[')
{
buf2[0] = ' ';
- if ((temp = std::strchr(buf2, '\n')) != NULL)
+ if ((temp = std::strchr(buf2, '\n')) != nullptr)
{
temp[0] = '\0';
}
int i, nw, nwa, nsa, nsalt, iqtot;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efSTO, "-o", NULL, ffWRITE },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efSTO, "-o", nullptr, ffWRITE },
{ efTOP, "-p", "topol", ffOPTRW }
};
#define NFILE asize(fnm)
}
sfree(atoms.pdbinfo);
- atoms.pdbinfo = NULL;
+ atoms.pdbinfo = nullptr;
}
- write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, NULL, ePBC, box);
+ write_sto_conf(ftp2fn(efSTO, NFILE, fnm), *top.name, &atoms, x, nullptr, ePBC, box);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define npargs asize(pa)
gmx_output_env_t *oenv;
- t_atoms *atoms = NULL;
+ t_atoms *atoms = nullptr;
int i, j, k;
FILE *out;
int igrp;
char *gn_grp;
matrix box;
gmx_bool bFreeze;
- rvec dx, *x = NULL, *v = NULL;
+ rvec dx, *x = nullptr, *v = nullptr;
t_filenm fnm[] = {
- { efSTX, "-f", NULL, ffREAD },
- { efNDX, "-n", NULL, ffOPTRD },
+ { efSTX, "-f", nullptr, ffREAD },
+ { efNDX, "-n", nullptr, ffOPTRD },
{ efITP, "-o", "posre", ffWRITE },
{ efNDX, "-of", "freeze", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, npargs, pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
xfn = opt2fn_null("-f", NFILE, fnm);
nfn = opt2fn_null("-n", NFILE, fnm);
- if (( nfn == NULL ) && ( xfn == NULL))
+ if (( nfn == nullptr ) && ( xfn == nullptr))
{
gmx_fatal(FARGS, "no index file and no structure file supplied");
}
}
const char *title = "";
- if (xfn != NULL)
+ if (xfn != nullptr)
{
fprintf(stderr, "\nReading structure file\n");
- t_topology *top = NULL;
+ t_topology *top = nullptr;
snew(top, 1);
- read_tps_conf(xfn, top, NULL, &x, &v, box, FALSE);
+ read_tps_conf(xfn, top, nullptr, &x, &v, box, FALSE);
title = *top->name;
atoms = &top->atoms;
- if (atoms->pdbinfo == NULL)
+ if (atoms->pdbinfo == nullptr)
{
snew(atoms->pdbinfo, atoms->nr);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-real calc_gyro(rvec x[], int gnx, int index[], t_atom atom[], real tm,
- rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
+static real calc_gyro(rvec x[], int gnx, int index[], t_atom atom[], real tm,
+ rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)
{
int i, ii, m;
real gyro, dx2, m0, Itot;
return std::sqrt(gyro/tm);
}
-void calc_gyro_z(rvec x[], matrix box,
- int gnx, int index[], t_atom atom[],
- int nz, real time, FILE *out)
+static void calc_gyro_z(rvec x[], matrix box,
+ int gnx, int index[], t_atom atom[],
+ int nz, real time, FILE *out)
{
- static dvec *inertia = NULL;
- static double *tm = NULL;
+ static dvec *inertia = nullptr;
+ static double *tm = nullptr;
int i, ii, j, zi;
real zf, w, sdet, e1, e2;
- if (inertia == NULL)
+ if (inertia == nullptr)
{
snew(inertia, nz);
snew(tm, nz);
rvec xcm, gvec, gvec1;
matrix box, trans;
gmx_bool bACF;
- real **moi_trans = NULL;
+ real **moi_trans = nullptr;
int max_moi = 0, delta_moi = 100;
rvec d, d1; /* eigenvalues of inertia tensor */
real t, t0, tm, gyro;
int j, m, gnx, nam, mol;
int *index;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
const char *leg[] = { "Rg", "Rg\\sX\\N", "Rg\\sY\\N", "Rg\\sZ\\N" };
const char *legI[] = { "Itot", "I1", "I2", "I3" };
#define NLEG asize(leg)
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "gyrate", ffWRITE },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "gyrate", ffWRITE },
{ efXVG, "-acf", "moi-acf", ffOPTWR },
};
#define NFILE asize(fnm)
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(ppa);
return 0;
}
bACF = opt2bSet("-acf", NFILE, fnm);
printf("Will print radius normalised by charge\n");
}
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, nullptr, box, TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
if (nmol > gnx || gnx % nmol != 0)
j++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
if (nz == 0)
{
gmx_rmpbc_done(gpbc);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* directions. */
/****************************************************************************/
-void calc_h2order(const char *fn, int index[], int ngx, rvec **slDipole,
- real **slOrder, real *slWidth, int *nslices,
- const t_topology *top, int ePBC,
- int axis, gmx_bool bMicel, int micel[], int nmic,
- const gmx_output_env_t *oenv)
+static void calc_h2order(const char *fn, int index[], int ngx, rvec **slDipole,
+ real **slOrder, real *slWidth, int *nslices,
+ const t_topology *top, int ePBC,
+ int axis, gmx_bool bMicel, int micel[], int nmic,
+ const gmx_output_env_t *oenv)
{
rvec *x0, /* coordinates with pbc */
dipole, /* dipole moment due to one molecules */
i, j, teller = 0,
slice = 0, /* current slice number */
*count; /* nr. of atoms in one slice */
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
if ((natoms = read_first_x(oenv, &status, fn, &t, &x0, box)) == 0)
{
sfree(x0); /* free memory used by coordinate arrays */
}
-void h2order_plot(rvec dipole[], real order[], const char *afile,
- int nslices, real slWidth, const gmx_output_env_t *oenv)
+static void h2order_plot(rvec dipole[], real order[], const char *afile,
+ int nslices, real slWidth, const gmx_output_env_t *oenv)
{
FILE *ord; /* xvgr files with order parameters */
int slice; /* loop index */
};
gmx_output_env_t *oenv;
- real *slOrder, /* av. cosine, per slice */
- slWidth = 0.0; /* width of a slice */
+ real *slOrder, /* av. cosine, per slice */
+ slWidth = 0.0; /* width of a slice */
rvec *slDipole;
- char *grpname, /* groupnames */
+ char *grpname, /* groupnames */
*micname;
- int ngx, /* nr. of atomsin sol group */
- nmic = 0; /* nr. of atoms in micelle */
- t_topology *top; /* topology */
+ int ngx, /* nr. of atomsin sol group */
+ nmic = 0; /* nr. of atoms in micelle */
+ t_topology *top; /* topology */
int ePBC;
- int *index, /* indices for solvent group */
- *micelle = NULL;
- gmx_bool bMicel = FALSE; /* think we're a micel */
- t_filenm fnm[] = { /* files for g_order */
- { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
- { efNDX, NULL, NULL, ffREAD }, /* index file */
- { efNDX, "-nm", NULL, ffOPTRD }, /* index with micelle atoms */
- { efTPR, NULL, NULL, ffREAD }, /* topology file */
- { efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
+ int *index, /* indices for solvent group */
+ *micelle = nullptr;
+ gmx_bool bMicel = FALSE; /* think we're a micel */
+ t_filenm fnm[] = { /* files for g_order */
+ { efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
+ { efNDX, nullptr, nullptr, ffREAD }, /* index file */
+ { efNDX, "-nm", nullptr, ffOPTRD }, /* index with micelle atoms */
+ { efTPR, nullptr, nullptr, ffREAD }, /* topology file */
+ { efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
};
#define NFILE asize(fnm)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (i = 0; (i < hb->d.nrd); i++)
{
snew(hb->hbmap[i], hb->a.nra);
- if (hb->hbmap[i] == NULL)
+ if (hb->hbmap[i] == nullptr)
{
gmx_fatal(FARGS, "Could not allocate enough memory for hbmap");
}
for (j = 0; (j > hb->a.nra); j++)
{
- hb->hbmap[i][j] = NULL;
+ hb->hbmap[i][j] = nullptr;
}
}
}
static void set_hb(t_hbdata *hb, int id, int ih, int ia, int frame, int ihb)
{
- unsigned int *ghptr = NULL;
+ unsigned int *ghptr = nullptr;
if (ihb == hbHB)
{
}
else if (grpd != hb->d.grp[id])
{
- gmx_fatal(FARGS, "Inconsistent donor groups, %d iso %d, atom %d",
+ gmx_fatal(FARGS, "Inconsistent donor groups, %d instead of %d, atom %d",
grpd, hb->d.grp[id], d+1);
}
if ((ia = hb->a.aptr[a]) == NOTSET)
}
else if (grpa != hb->a.grp[ia])
{
- gmx_fatal(FARGS, "Inconsistent acceptor groups, %d iso %d, atom %d",
+ gmx_fatal(FARGS, "Inconsistent acceptor groups, %d instead of %d, atom %d",
grpa, hb->a.grp[ia], a+1);
}
}
else if (grpd != hb->d.grp[id])
{
- gmx_fatal(FARGS, "Inconsistent donor groups, %d iso %d, atom %d",
+ gmx_fatal(FARGS, "Inconsistent donor groups, %d instead of %d, atom %d",
grpd, hb->d.grp[id], d+1);
}
if ((ia = hb->a.aptr[a]) == NOTSET)
}
else if (grpa != hb->a.grp[ia])
{
- gmx_fatal(FARGS, "Inconsistent acceptor groups, %d iso %d, atom %d",
+ gmx_fatal(FARGS, "Inconsistent acceptor groups, %d instead of %d, atom %d",
grpa, hb->a.grp[ia], a+1);
}
}
{
try
{
- if (hb->hbmap[id][ia] == NULL)
+ if (hb->hbmap[id][ia] == nullptr)
{
snew(hb->hbmap[id][ia], 1);
snew(hb->hbmap[id][ia]->h, hb->maxhydro);
}
}
-void pbc_correct_gem(rvec dx, matrix box, rvec hbox);
-void pbc_in_gridbox(rvec dx, matrix box);
+static void pbc_correct_gem(rvec dx, matrix box, rvec hbox);
+static void pbc_in_gridbox(rvec dx, matrix box);
static void build_grid(t_hbdata *hb, rvec x[], rvec xshell,
gmx_bool bBox, matrix box, rvec hbox,
sfree(g[z]);
}
sfree(g);
- g = NULL;
+ g = nullptr;
}
-void pbc_correct_gem(rvec dx, matrix box, rvec hbox)
+static void pbc_correct_gem(rvec dx, matrix box, rvec hbox)
{
int m;
gmx_bool bDone = FALSE;
}
}
-void pbc_in_gridbox(rvec dx, matrix box)
+static void pbc_in_gridbox(rvec dx, matrix box)
{
int m;
gmx_bool bDone = FALSE;
}
sfree(hb1->h[0]);
sfree(hb1->g[0]);
- hb1->h[0] = NULL;
- hb1->g[0] = NULL;
+ hb1->h[0] = nullptr;
+ hb1->g[0] = nullptr;
hb1->history[0] = hbNo;
}
}
real k = 1, kp = 1, kow = 1;
real Q = 0, chi2, tau_hb, dtau, tau_rlx, e_1, sigma_k, sigma_kp, ddg;
double tmp, sn2 = 0, sc2 = 0, sk2 = 0, scn = 0, sck = 0, snk = 0;
- gmx_bool bError = (sigma_ct != NULL) && (sigma_nt != NULL) && (sigma_kt != NULL);
+ gmx_bool bError = (sigma_ct != nullptr) && (sigma_nt != nullptr) && (sigma_kt != nullptr);
for (i0 = 0; (i0 < n-2) && ((t[i0]-t[0]) < fit_start); i0++)
{
sc2, sn2, sk2, sck, snk, scn);
}
/* Determine integral of the correlation function */
- tau_hb = evaluate_integral(n, t, ct, NULL, (t[n-1]-t[0])/2, &dtau);
+ tau_hb = evaluate_integral(n, t, ct, nullptr, (t[n-1]-t[0])/2, &dtau);
printf("Integral %10.3f %s%8.3f %10.3f\n", 1/tau_hb,
bError ? " " : "", tau_hb, calc_dg(tau_hb, temp));
e_1 = std::exp(-1.0);
for (i = 0; i < len; i++)
{
ct[i] *= ct_fac;
- if (gt != NULL)
+ if (gt != nullptr)
{
gt[i] *= gt_fac;
}
};
gmx_bool bNorm = FALSE;
double nhb = 0;
- real *rhbex = NULL, *ht, *gt, *ght, *dght, *kt;
+ real *rhbex = nullptr, *ht, *gt, *ght, *dght, *kt;
real *ct, tail, tail2, dtail, *cct;
const real tol = 1e-3;
int nframes = hb->nframes;
- unsigned int **h = NULL, **g = NULL;
+ unsigned int **h = nullptr, **g = nullptr;
int nh, nhbonds, nhydro;
t_hbond *hbh;
int acType;
- int *dondata = NULL;
+ int *dondata = nullptr;
enum {
AC_NONE, AC_NN, AC_GEM, AC_LUZAR
}
/* The autocorrelation function is normalized after summation only */
- low_do_autocorr(NULL, oenv, NULL, nframes, 1, -1, &rhbex, hb->time[1]-hb->time[0],
+ low_do_autocorr(nullptr, oenv, nullptr, nframes, 1, -1, &rhbex, hb->time[1]-hb->time[0],
eacNormal, 1, FALSE, bNorm, FALSE, 0, -1, 0);
/* Cross correlation analysis for thermodynamics */
}
xvgrclose(fp);
- analyse_corr(nn, hb->time, ct, ght, kt, NULL, NULL, NULL,
+ analyse_corr(nn, hb->time, ct, ght, kt, nullptr, nullptr, nullptr,
fit_start, temp);
- do_view(oenv, fn, NULL);
+ do_view(oenv, fn, nullptr);
sfree(rhbex);
sfree(ct);
sfree(gt);
t_hbdata *hb,
const gmx_output_env_t *oenv)
{
- FILE *fp = NULL;
+ FILE *fp = nullptr;
const char *leg[] = { "Nbound", "Nfree" };
if (!fn || !hb)
{
- return NULL;
+ return nullptr;
}
fp = xvgropen(fn, "Donor properties", output_env_get_xvgr_tlabel(oenv), "Number", oenv);
}
else
{
- fplog = NULL;
+ fplog = nullptr;
}
for (grp = gr0; grp <= (bTwo ? gr1 : gr0); grp++)
{
"The option [TT]-sel[tt] that used to work on selected hbonds is out of order, and therefore not available for the time being."
};
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
/* { efNDX, "-sel", "select", ffOPTRD },*/
{ efXVG, "-num", "hbnum", ffWRITE },
{ efLOG, "-g", "hbond", ffOPTWR },
t_trxstatus *status;
int trrStatus = 1;
t_topology top;
- t_inputrec ir;
t_pargs *ppa;
int npargs, natoms, nframes = 0, shatom;
int *isize;
int grp, nabin, nrbin, resdist, ihb;
char **leg;
t_hbdata *hb;
- FILE *fp, *fpnhb = NULL, *donor_properties = NULL;
+ FILE *fp, *fpnhb = nullptr, *donor_properties = nullptr;
t_gridcell ***grid;
t_ncell *icell, *jcell;
ivec ngrid;
gmx_bool bParallel;
gmx_bool bEdge_yjj, bEdge_xjj;
- t_hbdata **p_hb = NULL; /* one per thread, then merge after the frame loop */
- int **p_adist = NULL, **p_rdist = NULL; /* a histogram for each thread. */
+ t_hbdata **p_hb = nullptr; /* one per thread, then merge after the frame loop */
+ int **p_adist = nullptr, **p_rdist = nullptr; /* a histogram for each thread. */
const bool bOMP = GMX_OPENMP;
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, npargs,
ppa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
+ sfree(ppa);
return 0;
}
hb = mk_hbdata(bHBmap, opt2bSet("-dan", NFILE, fnm), bMerge || bContact);
/* get topology */
- read_tpx_top(ftp2fn(efTPR, NFILE, fnm), &ir, box, &natoms, NULL, NULL, &top);
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
+ read_tpx_top(ftp2fn(efTPR, NFILE, fnm), ir, box, &natoms, nullptr, nullptr, &top);
snew(grpnames, grNR);
snew(index, grNR);
top.atoms.nr, natoms);
}
- bBox = ir.ePBC != epbcNONE;
+ bBox = (ir->ePBC != epbcNONE);
grid = init_grid(bBox, box, (rcut > r2cut) ? rcut : r2cut, ngrid);
nabin = static_cast<int>(acut/abin);
nrbin = static_cast<int>(rcut/rbin);
snew(p_rdist[i], nrbin+1);
p_hb[i]->max_frames = 0;
- p_hb[i]->nhb = NULL;
- p_hb[i]->ndist = NULL;
- p_hb[i]->n_bound = NULL;
- p_hb[i]->time = NULL;
- p_hb[i]->nhx = NULL;
+ p_hb[i]->nhb = nullptr;
+ p_hb[i]->ndist = nullptr;
+ p_hb[i]->n_bound = nullptr;
+ p_hb[i]->time = nullptr;
+ p_hb[i]->nhx = nullptr;
p_hb[i]->bHBmap = hb->bHBmap;
p_hb[i]->bDAnr = hb->bDAnr;
free_grid(ngrid, &grid);
- close_trj(status);
+ close_trx(status);
if (donor_properties)
{
sprintf(mat.title, bContact ? "Contact Existence Map" :
"Hydrogen Bond Existence Map");
sprintf(mat.legend, bContact ? "Contacts" : "Hydrogen Bonds");
- sprintf(mat.label_x, "%s", output_env_get_xvgr_tlabel(oenv));
+ sprintf(mat.label_x, "%s", output_env_get_xvgr_tlabel(oenv).c_str());
sprintf(mat.label_y, bContact ? "Contact Index" : "Hydrogen Bond Index");
mat.bDiscrete = TRUE;
mat.nmap = 2;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
} t_xvgrfile;
t_xvgrfile xf[efhNR] = {
- { NULL, NULL, TRUE, "radius", "Helix radius", NULL, "r (nm)", 0.0 },
- { NULL, NULL, TRUE, "twist", "Twist per residue", NULL, "Angle (deg)", 0.0 },
- { NULL, NULL, TRUE, "rise", "Rise per residue", NULL, "Rise (nm)", 0.0 },
- { NULL, NULL, FALSE, "len-ahx", "Length of the Helix", NULL, "Length (nm)", 0.0 },
- { NULL, NULL, FALSE, "dip-ahx", "Helix Backbone Dipole", NULL, "rq (nm e)", 0.0 },
- { NULL, NULL, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", NULL, "RMS (nm)", 0.0 },
- { NULL, NULL, FALSE, "rmsa-ahx", "Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
- { NULL, NULL, FALSE, "cd222", "Ellipticity at 222 nm", NULL, "nm", 0.0 },
- { NULL, NULL, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", NULL, "deg", 0.0 },
- { NULL, NULL, TRUE, "caphi", "Average Ca-Ca Dihedral", NULL, "\\8F\\4(deg)", 0.0 },
- { NULL, NULL, TRUE, "phi", "Average \\8F\\4 angles", NULL, "deg", 0.0 },
- { NULL, NULL, TRUE, "psi", "Average \\8Y\\4 angles", NULL, "deg", 0.0 },
- { NULL, NULL, TRUE, "hb3", "Average n-n+3 hbond length", NULL, "nm", 0.0 },
- { NULL, NULL, TRUE, "hb4", "Average n-n+4 hbond length", NULL, "nm", 0.0 },
- { NULL, NULL, TRUE, "hb5", "Average n-n+5 hbond length", NULL, "nm", 0.0 },
- { NULL, NULL, FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz", 0.0 },
- { NULL, NULL, FALSE, "helicity", "Helicity per Residue", "Residue", "% of time", 0.0 }
+ { nullptr, nullptr, TRUE, "radius", "Helix radius", nullptr, "r (nm)", 0.0 },
+ { nullptr, nullptr, TRUE, "twist", "Twist per residue", nullptr, "Angle (deg)", 0.0 },
+ { nullptr, nullptr, TRUE, "rise", "Rise per residue", nullptr, "Rise (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "len-ahx", "Length of the Helix", nullptr, "Length (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "dip-ahx", "Helix Backbone Dipole", nullptr, "rq (nm e)", 0.0 },
+ { nullptr, nullptr, TRUE, "rms-ahx", "RMS Deviation from Ideal Helix", nullptr, "RMS (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "rmsa-ahx", "Average RMSD per Residue", "Residue", "RMS (nm)", 0.0 },
+ { nullptr, nullptr, FALSE, "cd222", "Ellipticity at 222 nm", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, TRUE, "pprms", "RMS Distance from \\8a\\4-helix", nullptr, "deg", 0.0 },
+ { nullptr, nullptr, TRUE, "caphi", "Average Ca-Ca Dihedral", nullptr, "\\8F\\4(deg)", 0.0 },
+ { nullptr, nullptr, TRUE, "phi", "Average \\8F\\4 angles", nullptr, "deg", 0.0 },
+ { nullptr, nullptr, TRUE, "psi", "Average \\8Y\\4 angles", nullptr, "deg", 0.0 },
+ { nullptr, nullptr, TRUE, "hb3", "Average n-n+3 hbond length", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, TRUE, "hb4", "Average n-n+4 hbond length", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, TRUE, "hb5", "Average n-n+5 hbond length", nullptr, "nm", 0.0 },
+ { nullptr, nullptr, FALSE, "JCaHa", "J-Coupling Values", "Residue", "Hz", 0.0 },
+ { nullptr, nullptr, FALSE, "helicity", "Helicity per Residue", "Residue", "% of time", 0.0 }
};
gmx_output_env_t *oenv;
real t;
real rms;
matrix box;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
gmx_bool bRange;
t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
{ efSTO, "-cz", "zconf", ffWRITE },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
/* Read reference frame from tpx file to compute helix length */
snew(xref, top->atoms.nr);
read_tpx(ftp2fn(efTPR, NFILE, fnm),
- NULL, NULL, &natoms, xref, NULL, NULL);
+ nullptr, nullptr, &natoms, xref, nullptr, nullptr);
calc_hxprops(nres, bb, xref);
do_start_end(nres, bb, &nbb, bbindex, &nca, caindex, bRange, rStart, rEnd);
sfree(xref);
if (teller == 1)
{
write_sto_conf(opt2fn("-cz", NFILE, fnm), "Helix fitted to Z-Axis",
- &(top->atoms), x, NULL, ePBC, box);
+ &(top->atoms), x, nullptr, ePBC, box);
}
xf[efhRAD].val = radius(xf[efhRAD].fp2, nca, caindex, x);
gmx_rmpbc_done(gpbc);
- close_trj(status);
+ close_trx(status);
for (i = 0; (i < nres); i++)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"purposes, we also write out the actual Euler rotation angles as [TT]theta[1-3].xvg[tt]"
};
- t_topology *top = NULL;
+ t_topology *top = nullptr;
real t;
- rvec *x = NULL;
+ rvec *x = nullptr;
matrix box;
t_trxstatus *status;
int natoms;
int ePBC;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
static gmx_bool bSC = FALSE;
static gmx_bool bIncremental = FALSE;
#define NPA asize(pa)
t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efDAT, "-oaxis", "helixaxis", ffWRITE },
{ efDAT, "-ocenter", "center", ffWRITE },
{ efXVG, "-orise", "rise", ffWRITE },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
gmx_ffclose(fptheta2);
gmx_ffclose(fptheta3);
- close_trj(status);
+ close_trx(status);
return 0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real sgang1, real sgang2, real ****intfpos,
gmx_output_env_t *oenv)
{
- FILE *fpsg = NULL, *fpsk = NULL;
+ FILE *fpsg = nullptr, *fpsk = nullptr;
t_topology top;
int ePBC;
t_trxstatus *status;
rvec *xtop, *x;
matrix box;
real sg, sk, sgintf;
- int **index = NULL;
- char **grpname = NULL;
+ int **index = nullptr;
+ char **grpname = nullptr;
int i, j, k, n, *isize, ng, nslicez, framenr;
- real ***sg_grid = NULL, ***sk_grid = NULL, ***sg_fravg = NULL, ***sk_fravg = NULL, ****sk_4d = NULL, ****sg_4d = NULL;
+ real ***sg_grid = nullptr, ***sk_grid = nullptr, ***sg_fravg = nullptr, ***sk_fravg = nullptr, ****sk_4d = nullptr, ****sg_4d = nullptr;
int *perm;
int ndx1, ndx2;
int bins;
* i.e 1D Row-major order in (t,x,y) */
- read_tps_conf(fnTPS, &top, &ePBC, &xtop, NULL, box, FALSE);
+ read_tps_conf(fnTPS, &top, &ePBC, &xtop, nullptr, box, FALSE);
*nslicex = static_cast<int>(box[XX][XX]/binw + onehalf); /*Calculate slicenr from binwidth*/
*nslicey = static_cast<int>(box[YY][YY]/binw + onehalf);
gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
top.atoms.nr, natoms);
}
- check_index(NULL, ng, index[0], NULL, natoms);
+ check_index(nullptr, ng, index[0], nullptr, natoms);
/*Prepare structures for temporary storage of frame info*/
}
}
- sg_4d = NULL;
- sk_4d = NULL;
+ sg_4d = nullptr;
+ sk_4d = nullptr;
*nframes = 0;
framenr = 0;
find_tetra_order_grid(top, ePBC, natoms, box, x, isize[0], index[0],
&sg, &sk, *nslicex, *nslicey, nslicez, sg_grid, sk_grid);
- GMX_RELEASE_ASSERT(sk_fravg != NULL, "Trying to dereference NULL sk_fravg pointer");
+ GMX_RELEASE_ASSERT(sk_fravg != nullptr, "Trying to dereference NULL sk_fravg pointer");
for (i = 0; i < *nslicex; i++)
{
for (j = 0; j < *nslicey; j++)
if (framenr%tblock == 0)
{
- GMX_RELEASE_ASSERT(sk_4d != NULL, "Trying to dereference NULL sk_4d pointer");
+ GMX_RELEASE_ASSERT(sk_4d != nullptr, "Trying to dereference NULL sk_4d pointer");
sk_4d[*nframes] = sk_fravg;
sg_4d[*nframes] = sg_fravg;
(*nframes)++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
sfree(grpname);
sfree(index);
static void writesurftoxpms(real ***surf, int tblocks, int xbins, int ybins, real bw, char **outfiles, int maplevels )
{
- char numbuf[8];
+ char numbuf[STRLEN];
int n, i, j;
real **profile1, **profile2;
real max1, max2, min1, min2, *xticks, *yticks;
static gmx_bool bRawOut = FALSE;
int frames, xslices, yslices; /* Dimensions of interface arrays*/
real ***intfpos; /* Interface arrays (intfnr,t,xy) -potentially large */
- static const char *normal_axis[] = { NULL, "z", "x", "y", NULL };
+ static const char *normal_axis[] = { nullptr, "z", "x", "y", nullptr };
t_pargs pa[] = {
{ "-d", FALSE, etENUM, {normal_axis},
};
t_filenm fnm[] = { /* files for g_order */
- { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
- { efNDX, "-n", NULL, ffREAD }, /* index file */
- { efTPR, "-s", NULL, ffREAD }, /* topology file */
+ { efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
+ { efNDX, "-n", nullptr, ffREAD }, /* index file */
+ { efTPR, "-s", nullptr, ffREAD }, /* topology file */
{ efXPM, "-o", "intf", ffWRMULT}, /* XPM- surface maps */
{ efOUT, "-or", "raw", ffOPTWRMULT }, /* xvgr output file */
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
gmx_output_env_t *oenv;
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
- GMX_RELEASE_ASSERT(normal_axis[0] != NULL, "Option setting inconsistency; normal_axis[0] is NULL");
+ GMX_RELEASE_ASSERT(normal_axis[0] != nullptr, "Option setting inconsistency; normal_axis[0] is NULL");
if (std::strcmp(normal_axis[0], "x") == 0)
{
axis = XX;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(ld, 1);
for (; (i < nre); i++)
{
- if ((std::strstr(names[i].name, ligand) != NULL) &&
- (std::strstr(names[i].name, self) == NULL))
+ if ((std::strstr(names[i].name, ligand) != nullptr) &&
+ (std::strstr(names[i].name, self) == nullptr))
{
- if (std::strstr(names[i].name, "LJ") != NULL)
+ if (std::strstr(names[i].name, "LJ") != nullptr)
{
ld->nlj++;
srenew(ld->lj, ld->nlj);
ld->lj[ld->nlj-1] = i;
}
- else if (std::strstr(names[i].name, "Coul") != NULL)
+ else if (std::strstr(names[i].name, "Coul") != nullptr)
{
ld->nqq++;
srenew(ld->qq, ld->nqq);
return ld;
}
-real calc_lie(t_liedata *ld, t_energy ee[], real lie_lj, real lie_qq,
- real fac_lj, real fac_qq)
+static real calc_lie(t_liedata *ld, t_energy ee[], real lie_lj, real lie_qq,
+ real fac_lj, real fac_qq)
{
int i;
real lj_tot, qq_tot;
int nre, nframes = 0, ct = 0;
ener_file_t fp;
t_liedata *ld;
- gmx_enxnm_t *enm = NULL;
+ gmx_enxnm_t *enm = nullptr;
t_enxframe *fr;
real lie;
double lieaver = 0, lieav2 = 0;
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/eigio.h"
#include "gromacs/gmxana/gmx_ana.h"
-void make_t_edx(struct edix *edx, int natoms, rvec *pos, int index[])
+static void make_t_edx(struct edix *edx, int natoms, rvec *pos, int index[])
{
edx->nr = natoms;
edx->anrs = index;
edx->x = pos;
}
-void write_t_edx(FILE *fp, struct edix edx, const char *comment)
+static void write_t_edx(FILE *fp, struct edix edx, const char *comment)
{
/*here we copy only the pointers into the t_edx struct
no data is copied and edx.box is ignored */
}
}
-int sscan_list(int *list[], const char *str, const char *listname)
+static int sscan_list(int *list[], const char *str, const char *listname)
{
/*this routine scans a string of the form 1,3-6,9 and returns the
selected numbers (in this case 1 3 4 5 6 9) in NULL-terminated array of integers.
int number = 0;
int end_number = 0;
- char *start = NULL; /*holds the string of the number behind a ','*/
- char *end = NULL; /*holds the string of the number behind a '-' */
+ char *start = nullptr; /*holds the string of the number behind a ','*/
+ char *end = nullptr; /*holds the string of the number behind a '-' */
- int nvecs = 0; /* counts the number of vectors in the list*/
+ int nvecs = 0; /* counts the number of vectors in the list*/
- step = NULL;
+ step = nullptr;
snew(pos, n+4);
startpos = pos;
std::strcpy(pos, str);
pos[n+1] = '1';
pos[n+2] = '\0';
- *list = NULL;
+ *list = nullptr;
while ((c = *pos) != 0)
{
{
/*store number*/
srenew(*list, nvecs+1);
- (*list)[nvecs++] = number = std::strtol(start, NULL, 10);
+ (*list)[nvecs++] = number = std::strtol(start, nullptr, 10);
status = sBefore;
if (number == 0)
{
if (c == ',')
{
/*store numbers*/
- end_number = std::strtol(end, NULL, 10);
- number = std::strtol(start, NULL, 10);
+ end_number = std::strtol(end, nullptr, 10);
+ number = std::strtol(start, nullptr, 10);
status = sBefore;
if (number == 0)
{
srenew(*list, nvecs+end_number-number+1);
if (step)
{
- istep = strtol(step, NULL, 10);
- step = NULL;
+ istep = strtol(step, nullptr, 10);
+ step = nullptr;
}
else
{
return nvecs;
} /*sscan_list*/
-void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
+static void write_eigvec(FILE* fp, int natoms, int eig_list[], rvec** eigvecs, int nvec, const char *grouptitle, real steps[])
{
/* eig_list is a zero-terminated list of indices into the eigvecs array.
eigvecs are coordinates of eigenvectors
#define MAGIC 670
-void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
- int nvec, int *eig_listen[], real* evStepList[])
+static void write_the_whole_thing(FILE* fp, t_edipar *edpars, rvec** eigvecs,
+ int nvec, int *eig_listen[], real* evStepList[])
{
/* write edi-file */
/*Eigenvectors */
- write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", NULL);
+ write_eigvec(fp, edpars->ned, eig_listen[evMON], eigvecs, nvec, "COMPONENTS GROUP 1", nullptr);
write_eigvec(fp, edpars->ned, eig_listen[evLINFIX], eigvecs, nvec, "COMPONENTS GROUP 2", evStepList[evLINFIX]);
write_eigvec(fp, edpars->ned, eig_listen[evLINACC], eigvecs, nvec, "COMPONENTS GROUP 3", evStepList[evLINACC]);
write_eigvec(fp, edpars->ned, eig_listen[evRADFIX], eigvecs, nvec, "COMPONENTS GROUP 4", evStepList[evRADFIX]);
- write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", NULL);
- write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", NULL);
+ write_eigvec(fp, edpars->ned, eig_listen[evRADACC], eigvecs, nvec, "COMPONENTS GROUP 5", nullptr);
+ write_eigvec(fp, edpars->ned, eig_listen[evRADCON], eigvecs, nvec, "COMPONENTS GROUP 6", nullptr);
write_eigvec(fp, edpars->ned, eig_listen[evFLOOD], eigvecs, nvec, "COMPONENTS GROUP 7", evStepList[evFLOOD]);
write_t_edx(fp, edpars->sori, "NORIGIN, XORIGIN");
}
-int read_conffile(const char *confin, rvec **x)
+static int read_conffile(const char *confin, rvec **x)
{
t_topology top;
matrix box;
printf("read coordnumber from file %s\n", confin);
- read_tps_conf(confin, &top, NULL, x, NULL, box, FALSE);
+ read_tps_conf(confin, &top, nullptr, x, nullptr, box, FALSE);
printf("number of coordinates in file %d\n", top.atoms.nr);
return top.atoms.nr;
}
-void read_eigenvalues(int vecs[], const char *eigfile, real values[],
- gmx_bool bHesse, real kT, int natoms_average_struct)
+static void read_eigenvalues(int vecs[], const char *eigfile, real values[],
+ gmx_bool bHesse, real kT, int natoms_average_struct)
{
int neig, nrow, i;
double **eigval;
}
-void init_edx(struct edix *edx)
+static void init_edx(struct edix *edx)
{
edx->nr = 0;
snew(edx->x, 1);
snew(edx->anrs, 1);
}
-void filter2edx(struct edix *edx, int nindex, int index[], int ngro,
- int igro[], const rvec *x, const char* structure)
+static void filter2edx(struct edix *edx, int nindex, int index[], int ngro,
+ int igro[], const rvec *x, const char* structure)
{
/* filter2edx copies coordinates from x to edx which are given in index
*/
}
}
-void get_structure(const t_atoms *atoms, const char *IndexFile,
- const char *StructureFile, struct edix *edx, int nfit,
- int ifit[], int nav, int index[])
+static void get_structure(const t_atoms *atoms, const char *IndexFile,
+ const char *StructureFile, struct edix *edx, int nfit,
+ int ifit[], int nav, int index[])
{
int *igro; /*index corresponding to target or origin structure*/
int ngro;
enum {
evStepNr = evRADFIX + 1
};
- static const char* evSelections[evNr] = {NULL, NULL, NULL, NULL, NULL, NULL};
+ static const char* evSelections[evNr] = {nullptr, nullptr, nullptr, nullptr, nullptr, nullptr};
static const char* evOptions[evNr] = {"-linfix", "-linacc", "-flood", "-radfix", "-radacc", "-radcon", "-mon"};
- static const char* evParams[evStepNr] = {NULL, NULL};
+ static const char* evParams[evStepNr] = {nullptr, nullptr};
static const char* evStepOptions[evStepNr] = {"-linstep", "-accdir", "-not_used", "-radstep"};
static const char* ConstForceStr;
static real * evStepList[evStepNr];
#define NPA asize(pa)
rvec *xref1;
- int nvec1, *eignr1 = NULL;
- rvec *xav1, **eigvec1 = NULL;
- t_atoms *atoms = NULL;
+ int nvec1, *eignr1 = nullptr;
+ rvec *xav1, **eigvec1 = nullptr;
+ t_atoms *atoms = nullptr;
int nav; /* Number of atoms in the average structure */
char *grpname;
const char *indexfile;
int i;
int *index, *ifit;
- int nfit; /* Number of atoms in the reference/fit structure */
- int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
+ int nfit; /* Number of atoms in the reference/fit structure */
+ int ev_class; /* parameter _class i.e. evMON, evRADFIX etc. */
int nvecs;
- real *eigval1 = NULL; /* in V3.3 this is parameter of read_eigenvectors */
+ real *eigval1 = nullptr; /* in V3.3 this is parameter of read_eigenvectors */
const char *EdiFile;
const char *TargetFile;
t_filenm fnm[] = {
{ efTRN, "-f", "eigenvec", ffREAD },
{ efXVG, "-eig", "eigenval", ffOPTRD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efSTX, "-tar", "target", ffOPTRD},
{ efSTX, "-ori", "origin", ffOPTRD},
{ efEDI, "-o", "sam", ffWRITE }
#define NFILE asize(fnm)
edi_params.outfrq = 100; edi_params.slope = 0.0; edi_params.maxedsteps = 0;
if (!parse_common_args(&argc, argv, 0,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
else /* if there are no eigenvectors for this option set list to zero */
{
- listen[ev_class] = NULL;
+ listen[ev_class] = nullptr;
snew(listen[ev_class], 1);
listen[ev_class][0] = 0;
}
&xref1, &edi_params.fitmas, &xav1, &edi_params.pcamas, &nvec1, &eignr1, &eigvec1, &eigval1);
read_tps_conf(ftp2fn(efTPS, NFILE, fnm),
- &top, &ePBC, &xtop, NULL, topbox, 0);
+ &top, &ePBC, &xtop, nullptr, topbox, 0);
atoms = &top.atoms;
printf("\n");
- if (xref1 == NULL)
+ if (xref1 == nullptr)
{
if (bFit1)
{
}
else
{
- make_t_edx(&edi_params.star, 0, NULL, index);
+ make_t_edx(&edi_params.star, 0, nullptr, index);
}
/* Store origin positions */
}
else
{
- make_t_edx(&edi_params.sori, 0, NULL, index);
+ make_t_edx(&edi_params.sori, 0, nullptr, index);
}
/* Write edi-file */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
const char *spec = " !&|";
- return (c != '\0' && std::strchr(spec, c) == NULL);
+ return (c != '\0' && std::strchr(spec, c) == nullptr);
}
static int parse_names(char **string, int *n_names, char **names)
(*string)++;
s = gmx_strdup((*string));
sp = std::strchr(s, c);
- if (sp != NULL)
+ if (sp != nullptr)
{
(*string) += sp-s + 1;
sp[0] = '\0';
{
char buf[STRLEN];
int j, nchain;
- int i, a, natoms, *start = NULL, *end = NULL, ca_start, ca_end;
+ int i, a, natoms, *start = nullptr, *end = nullptr, ca_start, ca_end;
rvec vec;
natoms = atoms->nr;
static gmx_bool check_have_atoms(const t_atoms *atoms, char *string)
{
- if (atoms == NULL)
+ if (atoms == nullptr)
{
printf("Can not process '%s' without atom info, use option -f\n", string);
return FALSE;
if (check_have_atoms(atoms, ostring) &&
parse_names(string, &n_names, names))
{
- if (atoms->atomtype == NULL)
+ if (!(atoms->haveType))
{
printf("Need a run input file to select atom types\n");
}
}
}
- string = NULL;
+ string = nullptr;
snew(index, natoms);
snew(index1, natoms);
}
printf("\n");
printf("> ");
- if (NULL == fgets(inp_string, STRLEN, stdin))
+ if (nullptr == fgets(inp_string, STRLEN, stdin))
{
gmx_fatal(FARGS, "Error reading user input");
}
return natoms;
}
-void merge_blocks(t_blocka *dest, t_blocka *source)
+static void merge_blocks(t_blocka *dest, t_blocka *source)
{
int i, nra0, i0;
t_blocka *block, *block2;
char **gnames, **gnames2;
t_filenm fnm[] = {
- { efSTX, "-f", NULL, ffOPTRD },
- { efNDX, "-n", NULL, ffOPTRDMULT },
- { efNDX, "-o", NULL, ffWRITE }
+ { efSTX, "-f", nullptr, ffOPTRD },
+ { efNDX, "-n", nullptr, ffOPTRDMULT },
+ { efNDX, "-o", nullptr, ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, NPA, pa, asize(desc), desc,
- 0, NULL, &oenv))
+ 0, nullptr, &oenv))
{
return 0;
}
fprintf(stderr, "\nReading structure file\n");
read_tps_conf(stxfile, top, &ePBC, &x, &v, box, FALSE);
atoms = &top->atoms;
- if (atoms->pdbinfo == NULL)
+ if (atoms->pdbinfo == nullptr)
{
snew(atoms->pdbinfo, atoms->nr);
}
}
else
{
- atoms = NULL;
- x = NULL;
+ atoms = nullptr;
+ x = nullptr;
}
/* read input file(s) */
block = new_blocka();
- gnames = NULL;
+ gnames = nullptr;
printf("Going to read %d old index file(s)\n", nndxin);
if (nndxin)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define FARAWAY 10000
-int *res_ndx(t_atoms *atoms)
+static int *res_ndx(t_atoms *atoms)
{
int *rndx;
int i, r0;
if (atoms->nr <= 0)
{
- return NULL;
+ return nullptr;
}
snew(rndx, atoms->nr);
r0 = atoms->atom[0].resind;
return rndx;
}
-int *res_natm(t_atoms *atoms)
+static int *res_natm(t_atoms *atoms)
{
int *natm;
int i, j, r0;
if (atoms->nr <= 0)
{
- return NULL;
+ return nullptr;
}
snew(natm, atoms->nres);
r0 = atoms->atom[0].resind;
"Discretize distance in this number of levels" }
};
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXPM, "-mean", "dm", ffWRITE },
{ efXPM, "-frames", "dmf", ffOPTWR },
{ efXVG, "-no", "num", ffOPTWR },
};
#define NFILE asize(fnm)
- FILE *out = NULL, *fp;
+ FILE *out = nullptr, *fp;
t_topology top;
int ePBC;
t_atoms useatoms;
int *tot_n;
matrix box = {{0}};
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
if (!parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fprintf(stderr, "Will calculate number of different contacts\n");
}
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, FALSE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, nullptr, box, FALSE);
fprintf(stderr, "Select group for analysis\n");
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
- close_trj(status);
+ close_trx(status);
gmx_rmpbc_done(gpbc);
if (bFrames)
{
int natoms, ind_min[2] = {0, 0}, ind_mini = 0, ind_minj = 0;
real rmin, rmax, rmint, tmint;
gmx_bool bFirst;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
natoms = read_first_x(oenv, &status, trxfn, &t, &x, box);
- check_index(NULL, n, index, NULL, natoms);
+ check_index(nullptr, n, index, nullptr, natoms);
out = xvgropen(outfn, "Minimum distance to periodic image",
output_env_get_time_label(oenv), "Distance (nm)", oenv);
rmint = box[XX][XX];
tmint = 0;
- if (NULL != top)
+ if (nullptr != top)
{
gpbc = gmx_rmpbc_init(&top->idef, ePBC, natoms);
}
bFirst = TRUE;
do
{
- if (NULL != top)
+ if (nullptr != top)
{
gmx_rmpbc(gpbc, natoms, box, x);
}
}
while (read_next_x(oenv, status, &t, x, box));
- if (NULL != top)
+ if (nullptr != top)
{
gmx_rmpbc_done(gpbc);
}
fprintf(stdout,
"\nThe shortest periodic distance is %g (nm) at time %g (%s),\n"
"between atoms %d and %d\n",
- rmint, output_env_conv_time(oenv, tmint), output_env_get_time_unit(oenv),
+ rmint, output_env_conv_time(oenv, tmint), output_env_get_time_unit(oenv).c_str(),
index[ind_mini]+1, index[ind_minj]+1);
}
for (j = 0; (j < j1); j++)
{
jx = index3[j];
- if (index2 == NULL)
+ if (index2 == nullptr)
{
i0 = j + 1;
}
{
nmin_j++;
}
- else if (r2 > rcut2)
+ else
{
nmax_j++;
}
*rmax = std::sqrt(rmax2);
}
-void dist_plot(const char *fn, const char *afile, const char *dfile,
- const char *nfile, const char *rfile, const char *xfile,
- real rcut, gmx_bool bMat, const t_atoms *atoms,
- int ng, int *index[], int gnx[], char *grpn[], gmx_bool bSplit,
- gmx_bool bMin, int nres, int *residue, gmx_bool bPBC, int ePBC,
- gmx_bool bGroup, gmx_bool bEachResEachTime, gmx_bool bPrintResName,
- const gmx_output_env_t *oenv)
+static void dist_plot(const char *fn, const char *afile, const char *dfile,
+ const char *nfile, const char *rfile, const char *xfile,
+ real rcut, gmx_bool bMat, const t_atoms *atoms,
+ int ng, int *index[], int gnx[], char *grpn[], gmx_bool bSplit,
+ gmx_bool bMin, int nres, int *residue, gmx_bool bPBC, int ePBC,
+ gmx_bool bGroup, gmx_bool bEachResEachTime, gmx_bool bPrintResName,
+ const gmx_output_env_t *oenv)
{
FILE *atm, *dist, *num;
t_trxstatus *trxout;
char buf[256];
char **leg;
- real t, dmin, dmax, **mindres = NULL, **maxdres = NULL;
+ real t, dmin, dmax, **mindres = nullptr, **maxdres = nullptr;
int nmin, nmax;
t_trxstatus *status;
int i = -1, j, k;
rvec *x0;
matrix box;
gmx_bool bFirst;
- FILE *respertime = NULL;
+ FILE *respertime = nullptr;
if (read_first_x(oenv, &status, fn, &t, &x0, box) == 0)
{
sprintf(buf, "%simum Distance", bMin ? "Min" : "Max");
dist = xvgropen(dfile, buf, output_env_get_time_label(oenv), "Distance (nm)", oenv);
sprintf(buf, "Number of Contacts %s %g nm", bMin ? "<" : ">", rcut);
- num = nfile ? xvgropen(nfile, buf, output_env_get_time_label(oenv), "Number", oenv) : NULL;
- atm = afile ? gmx_ffopen(afile, "w") : NULL;
- trxout = xfile ? open_trx(xfile, "w") : NULL;
+ num = nfile ? xvgropen(nfile, buf, output_env_get_time_label(oenv), "Number", oenv) : nullptr;
+ atm = afile ? gmx_ffopen(afile, "w") : nullptr;
+ trxout = xfile ? open_trx(xfile, "w") : nullptr;
if (bMat)
{
{
oindex[0] = bMin ? min1 : max1;
oindex[1] = bMin ? min2 : max2;
- write_trx(trxout, 2, oindex, atoms, i, t, box, x0, NULL, NULL);
+ write_trx(trxout, 2, oindex, atoms, i, t, box, x0, nullptr, nullptr);
}
bFirst = FALSE;
/*dmin should be minimum distance for residue and group*/
}
while (read_next_x(oenv, status, &t, x0, box));
- close_trj(status);
+ close_trx(status);
xvgrclose(dist);
if (num)
{
sfree(x0);
}
-int find_residues(const t_atoms *atoms, int n, int index[], int **resindex)
+static int find_residues(const t_atoms *atoms, int n, int index[], int **resindex)
{
int i;
int nres = 0, resnr, presnr = 0;
return nres;
}
-void dump_res(FILE *out, int nres, int *resindex, int index[])
+static void dump_res(FILE *out, int nres, int *resindex, int index[])
{
int i, j;
"Write residue names" }
};
gmx_output_env_t *oenv;
- t_topology *top = NULL;
+ t_topology *top = nullptr;
int ePBC = -1;
rvec *x;
matrix box;
const char *trxfnm, *tpsfnm, *ndxfnm, *distfnm, *numfnm, *atmfnm, *oxfnm, *resfnm;
char **grpname;
int *gnx;
- int **index, *residues = NULL;
+ int **index, *residues = nullptr;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-od", "mindist", ffWRITE },
{ efXVG, "-on", "numcont", ffOPTWR },
{ efOUT, "-o", "atm-pair", ffOPTWR },
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
atmfnm = ftp2fn_null(efOUT, NFILE, fnm);
oxfnm = opt2fn_null("-ox", NFILE, fnm);
resfnm = opt2fn_null("-or", NFILE, fnm);
- if (bPI || resfnm != NULL)
+ if (bPI || resfnm != nullptr)
{
/* We need a tps file */
tpsfnm = ftp2fn(efTPS, NFILE, fnm);
if (tpsfnm || resfnm || !ndxfnm)
{
snew(top, 1);
- bTop = read_tps_conf(tpsfnm, top, &ePBC, &x, NULL, box, FALSE);
+ bTop = read_tps_conf(tpsfnm, top, &ePBC, &x, nullptr, box, FALSE);
if (bPI && !bTop)
{
printf("\nWARNING: Without a run input file a trajectory with broken molecules will not give the correct periodic image distance\n\n");
}
}
- get_index(top ? &(top->atoms) : NULL, ndxfnm, ng, gnx, index, grpname);
+ get_index(top ? &(top->atoms) : nullptr, ndxfnm, ng, gnx, index, grpname);
if (bMat && (ng == 1))
{
if (resfnm)
{
- GMX_RELEASE_ASSERT(top != NULL, "top pointer cannot be NULL when finding residues");
+ GMX_RELEASE_ASSERT(top != nullptr, "top pointer cannot be NULL when finding residues");
nres = find_residues(&(top->atoms), gnx[0], index[0], &residues);
if (debug)
else
{
dist_plot(trxfnm, atmfnm, distfnm, numfnm, resfnm, oxfnm,
- rcutoff, bMat, top ? &(top->atoms) : NULL,
+ rcutoff, bMat, top ? &(top->atoms) : nullptr,
ng, index, gnx, grpname, bSplit, !bMax, nres, residues, bPBC, ePBC,
bGroup, bEachResEachTime, bPrintResName, oenv);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static int *select_ftype(const char *opt, int *nft, int *mult)
{
- int *ft = NULL, ftype;
+ int *ft = nullptr, ftype;
if (opt[0] == 'a')
{
"angle distributions etc. It uses a run input file ([REF].tpx[ref]) for the",
"definitions of the angles, dihedrals etc."
};
- static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
+ static const char *opt[] = { nullptr, "angle", "dihedral", "improper", "ryckaert-bellemans", nullptr };
static gmx_bool bH = TRUE;
static real hq = -1;
t_pargs pa[] = {
int *nr;
char **grpnames;
t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, "angle", ffWRITE }
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, "angle", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- GMX_RELEASE_ASSERT(opt[0] != 0, "Options inconsistency; opt[0] is NULL");
+ GMX_RELEASE_ASSERT(opt[0] != nullptr, "Options inconsistency; opt[0] is NULL");
ft = select_ftype(opt[0], &nft, &mult);
- top = read_top(ftp2fn(efTPR, NFILE, fnm), NULL);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), nullptr);
ntype = calc_ntype(nft, ft, &(top->idef));
snew(grpnames, ntype);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"Do a least squares fit of the second to the first structure before interpolating" }
};
const char *leg[] = { "Ref = 1\\Sst\\N conf", "Ref = 2\\Snd\\N conf" };
- FILE *fp = NULL;
+ FILE *fp = nullptr;
int i, isize, is_lsq, nat1, nat2;
t_trxstatus *status;
int *index, *index_lsq, *index_all, *dummy;
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv))
+ 0, nullptr, &oenv))
{
return 0;
}
t_topology *top;
snew(top, 1);
- read_tps_conf(opt2fn("-f1", NFILE, fnm), top, NULL, &x1, NULL, box, FALSE);
+ read_tps_conf(opt2fn("-f1", NFILE, fnm), top, nullptr, &x1, nullptr, box, FALSE);
nat1 = top->atoms.nr;
- read_tps_conf(opt2fn("-f2", NFILE, fnm), top, NULL, &x2, NULL, box, FALSE);
+ read_tps_conf(opt2fn("-f2", NFILE, fnm), top, nullptr, &x2, nullptr, box, FALSE);
nat2 = top->atoms.nr;
if (nat1 != nat2)
{
for (i = 0; (i < ninterm); i++)
{
fac = dointerp(nat1, x1, x2, xx, i, ninterm, first, last);
- write_trx(status, nat1, dummy, &atoms, i, fac, box, xx, NULL, NULL);
+ write_trx(status, nat1, dummy, &atoms, i, fac, box, xx, nullptr, nullptr);
if (bRMS)
{
rms1 = rmsdev_ind(isize, index, mass, x1, xx);
return curr->nframes-curr->n_offs[nx00];
}
-t_corr *init_corr(int nrgrp, int type, int axis, real dim_factor,
- int nmol, gmx_bool bTen, gmx_bool bMass, real dt, const t_topology *top,
- real beginfit, real endfit)
+static t_corr *init_corr(int nrgrp, int type, int axis, real dim_factor,
+ int nmol, gmx_bool bTen, gmx_bool bMass, real dt, const t_topology *top,
+ real beginfit, real endfit)
{
t_corr *curr;
int i;
curr->delta_t = dt;
curr->beginfit = (1 - 2*GMX_REAL_EPS)*beginfit;
curr->endfit = (1 + 2*GMX_REAL_EPS)*endfit;
- curr->x0 = NULL;
- curr->n_offs = NULL;
+ curr->x0 = nullptr;
+ curr->n_offs = nullptr;
curr->nframes = 0;
curr->nlast = 0;
curr->dim_factor = dim_factor;
}
for (i = 0; (i < nrgrp); i++)
{
- curr->ndata[i] = NULL;
- curr->data[i] = NULL;
+ curr->ndata[i] = nullptr;
+ curr->data[i] = nullptr;
if (bTen)
{
- curr->datam[i] = NULL;
+ curr->datam[i] = nullptr;
}
}
- curr->time = NULL;
- curr->lsq = NULL;
+ curr->time = nullptr;
+ curr->lsq = nullptr;
curr->nmol = nmol;
if (curr->nmol > 0)
{
if (DD)
{
fprintf(out, "# MSD gathered over %g %s with %d restarts\n",
- msdtime, output_env_get_time_unit(oenv), curr->nrestart);
+ msdtime, output_env_get_time_unit(oenv).c_str(), curr->nrestart);
fprintf(out, "# Diffusion constants fitted from time %g to %g %s\n",
- beginfit, endfit, output_env_get_time_unit(oenv));
+ beginfit, endfit, output_env_get_time_unit(oenv).c_str());
for (i = 0; i < curr->ngrp; i++)
{
fprintf(out, "# D[%10s] = %.4f (+/- %.4f) (1e-5 cm^2/s)\n",
gmx_stats_t lsq1;
int i, j;
real a, b, D, Dav, D2av, VarD, sqrtD, sqrtD_max, scale;
- t_pdbinfo *pdbinfo = NULL;
- const int *mol2a = NULL;
+ t_pdbinfo *pdbinfo = nullptr;
+ const int *mol2a = nullptr;
out = xvgropen(fn, "Diffusion Coefficients / Molecule", "Molecule", "D", oenv);
gmx_stats_add_point(lsq1, xx, yy, dx, dy);
}
}
- gmx_stats_get_ab(lsq1, elsqWEIGHT_NONE, &a, &b, NULL, NULL, NULL, NULL);
+ gmx_stats_get_ab(lsq1, elsqWEIGHT_NONE, &a, &b, nullptr, nullptr, nullptr, nullptr);
gmx_stats_free(lsq1);
D = a*FACTOR/curr->dim_factor;
if (D < 0)
{
scale *= 10;
}
- GMX_RELEASE_ASSERT(pdbinfo != NULL, "Internal error - pdbinfo not set for PDB input");
+ GMX_RELEASE_ASSERT(pdbinfo != nullptr, "Internal error - pdbinfo not set for PDB input");
for (i = 0; i < top->atoms.nr; i++)
{
pdbinfo[i].bfac *= scale;
}
- write_sto_conf(fn_pdb, "molecular MSD", &top->atoms, x, NULL, ePBC, box);
+ write_sto_conf(fn_pdb, "molecular MSD", &top->atoms, x, nullptr, ePBC, box);
}
}
* fx and nx are file pointers to things like read_first_x and
* read_next_x
*/
-int corr_loop(t_corr *curr, const char *fn, const t_topology *top, int ePBC,
- gmx_bool bMol, int gnx[], int *index[],
- t_calc_func *calc1, gmx_bool bTen, int *gnx_com, int *index_com[],
- real dt, real t_pdb, rvec **x_pdb, matrix box_pdb,
- const gmx_output_env_t *oenv)
+static int corr_loop(t_corr *curr, const char *fn, const t_topology *top, int ePBC,
+ gmx_bool bMol, int gnx[], int *index[],
+ t_calc_func *calc1, gmx_bool bTen, int *gnx_com, int *index_com[],
+ real dt, real t_pdb, rvec **x_pdb, matrix box_pdb,
+ const gmx_output_env_t *oenv)
{
rvec *x[2]; /* the coordinates to read */
rvec *xa[2]; /* the coordinates to calculate displacements for */
#define prev (1-cur)
matrix box;
gmx_bool bFirst;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
natoms = read_first_x(oenv, &status, fn, &curr->t0, &(x[cur]), box);
#ifdef DEBUG
fprintf(stderr, "Read %d atoms for first frame\n", natoms);
#endif
- if ((gnx_com != NULL) && natoms < top->atoms.nr)
+ if ((gnx_com != nullptr) && natoms < top->atoms.nr)
{
fprintf(stderr, "WARNING: The trajectory only contains part of the system (%d of %d atoms) and therefore the COM motion of only this part of the system will be removed\n", natoms, top->atoms.nr);
}
t = curr->t0;
if (x_pdb)
{
- *x_pdb = NULL;
+ *x_pdb = nullptr;
}
if (bMol)
t_pdb > t - 0.5*(t - t_prev) &&
t_pdb < t + 0.5*(t - t_prev))))
{
- if (*x_pdb == NULL)
+ if (*x_pdb == nullptr)
{
snew(*x_pdb, natoms);
}
{
for (i = 0; (i < curr->ngrp); i++)
{
- curr->ndata[i] = NULL;
- curr->data[i] = NULL;
+ curr->ndata[i] = nullptr;
+ curr->data[i] = nullptr;
if (bTen)
{
- curr->datam[i] = NULL;
+ curr->datam[i] = nullptr;
}
}
- curr->time = NULL;
+ curr->time = nullptr;
}
maxframes += 10;
for (i = 0; (i < curr->ngrp); i++)
for (i = 0; (i < curr->ngrp); i++)
{
/* calculate something useful, like mean square displacements */
- calc_corr(curr, i, gnx[i], index[i], xa[cur], (gnx_com != NULL), com,
+ calc_corr(curr, i, gnx[i], index[i], xa[cur], (gnx_com != nullptr), com,
calc1, bTen);
}
cur = prev;
while (read_next_x(oenv, status, &t, x[cur], box));
fprintf(stderr, "\nUsed %d restart points spaced %g %s over %g %s\n\n",
curr->nrestart,
- output_env_conv_time(oenv, dt), output_env_get_time_unit(oenv),
+ output_env_conv_time(oenv, dt), output_env_get_time_unit(oenv).c_str(),
output_env_conv_time(oenv, curr->time[curr->nframes-1]),
- output_env_get_time_unit(oenv) );
+ output_env_get_time_unit(oenv).c_str() );
if (bMol)
{
gmx_rmpbc_done(gpbc);
}
- close_trj(status);
+ close_trx(status);
return natoms;
}
*n = nmol;
}
-void do_corr(const char *trx_file, const char *ndx_file, const char *msd_file,
- const char *mol_file, const char *pdb_file, real t_pdb,
- int nrgrp, t_topology *top, int ePBC,
- gmx_bool bTen, gmx_bool bMW, gmx_bool bRmCOMM,
- int type, real dim_factor, int axis,
- real dt, real beginfit, real endfit, const gmx_output_env_t *oenv)
+static void do_corr(const char *trx_file, const char *ndx_file, const char *msd_file,
+ const char *mol_file, const char *pdb_file, real t_pdb,
+ int nrgrp, t_topology *top, int ePBC,
+ gmx_bool bTen, gmx_bool bMW, gmx_bool bRmCOMM,
+ int type, real dim_factor, int axis,
+ real dt, real beginfit, real endfit, const gmx_output_env_t *oenv)
{
t_corr *msd;
int *gnx; /* the selected groups' sizes */
real *DD, *SigmaD, a, a2, b, r, chi2;
rvec *x;
matrix box;
- int *gnx_com = NULL; /* the COM removal group size */
- int **index_com = NULL; /* the COM removal group atom indices */
- char **grpname_com = NULL; /* the COM removal group name */
+ int *gnx_com = nullptr; /* the COM removal group size */
+ int **index_com = nullptr; /* the COM removal group atom indices */
+ char **grpname_com = nullptr; /* the COM removal group name */
snew(gnx, nrgrp);
snew(index, nrgrp);
}
msd = init_corr(nrgrp, type, axis, dim_factor,
- mol_file == NULL ? 0 : gnx[0], bTen, bMW, dt, top,
+ mol_file == nullptr ? 0 : gnx[0], bTen, bMW, dt, top,
beginfit, endfit);
nat_trx =
corr_loop(msd, trx_file, top, ePBC, mol_file ? gnx[0] : 0, gnx, index,
- (mol_file != NULL) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
+ (mol_file != nullptr) ? calc1_mol : (bMW ? calc1_mw : calc1_norm),
bTen, gnx_com, index_com, dt, t_pdb,
- pdb_file ? &x : NULL, box, oenv);
+ pdb_file ? &x : nullptr, box, oenv);
/* Correct for the number of points */
for (j = 0; (j < msd->ngrp); j++)
if (mol_file)
{
- if (pdb_file && x == NULL)
+ if (pdb_file && x == nullptr)
{
fprintf(stderr, "\nNo frame found need time tpdb = %g ps\n"
"Can not write %s\n\n", t_pdb, pdb_file);
}
i = top->atoms.nr;
top->atoms.nr = nat_trx;
- if (pdb_file && top->atoms.pdbinfo == NULL)
+ if (pdb_file && top->atoms.pdbinfo == nullptr)
{
snew(top->atoms.pdbinfo, top->atoms.nr);
}
top->atoms.nr = i;
}
- DD = NULL;
- SigmaD = NULL;
+ DD = nullptr;
+ SigmaD = nullptr;
if (beginfit == -1)
{
}
}
fprintf(stdout, "Fitting from %g to %g %s\n\n", beginfit, endfit,
- output_env_get_time_unit(oenv));
+ output_env_get_time_unit(oenv).c_str());
N = i1-i0;
if (N <= 2)
"the diffusion coefficient of the molecule.",
"This option implies option [TT]-mol[tt]."
};
- static const char *normtype[] = { NULL, "no", "x", "y", "z", NULL };
- static const char *axtitle[] = { NULL, "no", "x", "y", "z", NULL };
+ static const char *normtype[] = { nullptr, "no", "x", "y", "z", nullptr };
+ static const char *axtitle[] = { nullptr, "no", "x", "y", "z", nullptr };
static int ngroup = 1;
static real dt = 10;
static real t_pdb = 0;
};
t_filenm fnm[] = {
- { efTRX, NULL, NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "msd", ffWRITE },
+ { efTRX, nullptr, nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "msd", ffWRITE },
{ efXVG, "-mol", "diff_mol", ffOPTWR },
{ efPDB, "-pdb", "diff_mol", ffOPTWR }
};
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fprintf(stderr, "Calculating diffusion coefficients for molecules.\n");
}
- GMX_RELEASE_ASSERT(normtype[0] != 0, "Options inconsistency; normtype[0] is NULL");
- GMX_RELEASE_ASSERT(axtitle[0] != 0, "Options inconsistency; axtitle[0] is NULL");
+ GMX_RELEASE_ASSERT(normtype[0] != nullptr, "Options inconsistency; normtype[0] is NULL");
+ GMX_RELEASE_ASSERT(axtitle[0] != nullptr, "Options inconsistency; axtitle[0] is NULL");
if (normtype[0][0] != 'n')
{
gmx_fatal(FARGS, "Can only calculate the full tensor for 3D msd");
}
- bTop = read_tps_conf(tps_file, &top, &ePBC, &xdum, NULL, box, bMW || bRmCOMM);
+ bTop = read_tps_conf(tps_file, &top, &ePBC, &xdum, nullptr, box, bMW || bRmCOMM);
if (mol_file && !bTop)
{
gmx_fatal(FARGS,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return nh;
}
-static size_t get_nvsite_mt(gmx_moltype_t *mt)
-{
- static int vs_func[] = {
- F_VSITE2, F_VSITE3, F_VSITE3FD, F_VSITE3FAD,
- F_VSITE3OUT, F_VSITE4FD, F_VSITE4FDN, F_VSITEN
- };
- int i, ft;
- size_t nh = 0;
- for (i = 0; (i < asize(vs_func)); i++)
- {
- ft = vs_func[i];
- nh += mt->ilist[ft].nr/(interaction_function[ft].nratoms+1);
- }
- return nh;
-}
-
static int get_nharm(const gmx_mtop_t *mtop)
{
int nh = 0;
eigensolver(hess, ndim, begin-1, end-1, eigenvalues, eigenvectors);
/* And scale the output eigenvectors */
- if (bM && eigenvectors != NULL)
+ if (bM && eigenvectors != nullptr)
{
for (int i = 0; i < (end-begin+1); i++)
{
/* Cannot check symmetry since we only store half matrix */
/* divide elements hess[i][j] by sqrt(mas[i])*sqrt(mas[j]) when required */
- GMX_RELEASE_ASSERT(sparse_hessian != NULL, "NULL matrix pointer provided to nma_sparse_hessian");
+ GMX_RELEASE_ASSERT(sparse_hessian != nullptr, "NULL matrix pointer provided to nma_sparse_hessian");
if (bM)
{
sparse_eigensolver(sparse_hessian, neig, eigenvalues, eigenvectors, 10000000);
/* Scale output eigenvectors */
- if (bM && eigenvectors != NULL)
+ if (bM && eigenvectors != nullptr)
{
for (i = 0; i < neig; i++)
{
real value, omega, nu;
real factor_gmx_to_omega2;
real factor_omega_to_wavenumber;
- real *spectrum = NULL;
+ real *spectrum = nullptr;
real wfac;
gmx_output_env_t *oenv;
const char *qcleg[] = {
"Heat Capacity cV (J/mol K)",
"Enthalpy H (kJ/mol)"
};
- real * full_hessian = NULL;
- gmx_sparsematrix_t * sparse_hessian = NULL;
+ real * full_hessian = nullptr;
+ gmx_sparsematrix_t * sparse_hessian = nullptr;
t_filenm fnm[] = {
{ efMTX, "-f", "hessian", ffREAD },
- { efTPR, NULL, NULL, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
{ efXVG, "-of", "eigenfreq", ffWRITE },
{ efXVG, "-ol", "eigenval", ffWRITE },
{ efXVG, "-os", "spectrum", ffOPTWR },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
snew(top_x, tpx.natoms);
int natoms_tpx;
- read_tpx(ftp2fn(efTPR, NFILE, fnm), NULL, box, &natoms_tpx,
- top_x, NULL, &mtop);
+ read_tpx(ftp2fn(efTPR, NFILE, fnm), nullptr, box, &natoms_tpx,
+ top_x, nullptr, &mtop);
int nharm = 0;
if (bCons)
{
}
std::vector<size_t> atom_index = get_atom_index(&mtop);
- top = gmx_mtop_t_to_t_topology(&mtop);
+ top = gmx_mtop_t_to_t_topology(&mtop, true);
bM = TRUE;
int ndim = DIM*atom_index.size();
* If this is not valid we convert to full matrix storage,
* but warn the user that we might run out of memory...
*/
- if ((sparse_hessian != NULL) && (end == ndim))
+ if ((sparse_hessian != nullptr) && (end == ndim))
{
fprintf(stderr, "Cannot use sparse Hessian to calculate all eigenvectors.\n");
}
}
gmx_sparsematrix_destroy(sparse_hessian);
- sparse_hessian = NULL;
+ sparse_hessian = nullptr;
fprintf(stderr, "Converted sparse to full matrix storage.\n");
}
snew(eigenvalues, nrow);
- if (full_hessian != NULL)
+ if (full_hessian != nullptr)
{
/* Using full matrix storage */
eigenvectors = allocateEigenvectors(nrow, begin, end, false);
}
else
{
- qc = NULL;
+ qc = nullptr;
}
printf("Writing eigenfrequencies - negative eigenvalues will be set to zero.\n");
}
}
/* Spectrum ? */
- spec = NULL;
+ spec = nullptr;
if (opt2bSet("-os", NFILE, fnm) && (maxspec > 0))
{
snew(spectrum, maxspec);
nu = 1e-12*omega/(2*M_PI);
value = omega*factor_omega_to_wavenumber;
fprintf (out, "%6d %15g\n", i, value);
- if (NULL != spec)
+ if (nullptr != spec)
{
wfac = eigenvalues[i-begin]/(width*std::sqrt(2*M_PI));
for (j = 0; (j < maxspec); j++)
spectrum[j] += wfac*std::exp(-gmx::square(j-value)/(2*gmx::square(width)));
}
}
- if (NULL != qc)
+ if (nullptr != qc)
{
qcv = cv_corr(nu, T);
qu = u_corr(nu, T);
}
}
xvgrclose(out);
- if (NULL != spec)
+ if (nullptr != spec)
{
for (j = 0; (j < maxspec); j++)
{
}
xvgrclose(spec);
}
- if (NULL != qc)
+ if (nullptr != qc)
{
printf("Quantum corrections for harmonic degrees of freedom\n");
printf("Use appropriate -first and -last options to get reliable results.\n");
* will not be strictly orthogonal in plain cartesian scalar products.
*/
const real *eigenvectorPtr;
- if (full_hessian != NULL)
+ if (full_hessian != nullptr)
{
eigenvectorPtr = eigenvectors;
}
eigenvectorPtr = eigenvectors + (begin - 1)*atom_index.size();
}
write_eigenvectors(opt2fn("-v", NFILE, fnm), atom_index.size(), eigenvectorPtr, FALSE, begin, end,
- eWXR_NO, NULL, FALSE, top_x, bM, eigenvalues);
+ eWXR_NO, nullptr, FALSE, top_x, bM, eigenvalues);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_atoms *atoms;
rvec *xtop, *xref, *xav, *xout1, *xout2;
gmx_bool bDMR, bDMA, bFit;
- int nvec, *eignr = NULL;
- rvec **eigvec = NULL;
+ int nvec, *eignr = nullptr;
+ rvec **eigvec = nullptr;
matrix box;
real *eigval, *invsqrtm, t, disp;
int natoms;
t_filenm fnm[] = {
{ efTRN, "-v", "eigenvec", ffREAD },
{ efXVG, "-e", "eigenval", ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efTRO, "-o", "ensemble", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit,
&xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, box, bDMA);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box, bDMA);
atoms = &top.atoms;
printf("\nSelect an index group of %d elements that corresponds to the eigenvectors\n", natoms);
{
printf("Select eigenvectors for output, end your selection with 0\n");
nout = -1;
- iout = NULL;
+ iout = nullptr;
do
{
nout++;
copy_rvec(xout1[i], xout2[index[i]]);
}
t = s+1;
- write_trx(out, natoms, index, atoms, 0, t, box, xout2, NULL, NULL);
+ write_trx(out, natoms, index, atoms, 0, t, box, xout2, nullptr, nullptr);
fprintf(stderr, "\rGenerated %d structures", s+1);
fflush(stderr);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int ePBC;
t_atoms *atoms;
rvec *xtop, *xref, *xav, *xout;
- int nvec, *eignr = NULL;
- rvec **eigvec = NULL;
+ int nvec, *eignr = nullptr;
+ rvec **eigvec = nullptr;
matrix box;
int natoms;
int i, j, k, kmode, d;
t_filenm fnm[] =
{
- { efTPS, NULL, NULL, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
{ efTRN, "-v", "eigenvec", ffREAD },
{ efTRO, "-o", "nmtraj", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, 0,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
read_eigenvectors(opt2fn("-v", NFILE, fnm), &natoms, &bFit,
&xref, &bDMR, &xav, &bDMA, &nvec, &eignr, &eigvec, &eigval);
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, box, bDMA);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box, bDMA);
/* Find vectors and phases */
}
}
}
- write_trx(out, natoms, dummy, atoms, i, static_cast<real>(i)/nframes, box, xout, NULL, NULL);
+ write_trx(out, natoms, dummy, atoms, i, static_cast<real>(i)/nframes, box, xout, nullptr, nullptr);
}
fprintf(stderr, "\n");
const char *sgslfn, const char *skslfn,
const gmx_output_env_t *oenv)
{
- FILE *fpsg = NULL, *fpsk = NULL;
+ FILE *fpsg = nullptr, *fpsk = nullptr;
t_topology top;
int ePBC;
t_trxstatus *status;
char **grpname;
int i, *isize, ng, nframes;
real *sg_slice, *sg_slice_tot, *sk_slice, *sk_slice_tot;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
- read_tps_conf(fnTPS, &top, &ePBC, &xtop, NULL, box, FALSE);
+ read_tps_conf(fnTPS, &top, &ePBC, &xtop, nullptr, box, FALSE);
snew(sg_slice, nslice);
snew(sk_slice, nslice);
gmx_fatal(FARGS, "Topology (%d atoms) does not match trajectory (%d atoms)",
top.atoms.nr, natoms);
}
- check_index(NULL, ng, index[0], NULL, natoms);
+ check_index(nullptr, ng, index[0], nullptr, natoms);
fpsg = xvgropen(sgfn, "S\\sg\\N Angle Order Parameter", "Time (ps)", "S\\sg\\N",
oenv);
nframes++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
gmx_rmpbc_done(gpbc);
sfree(grpname);
}
}
-void calc_order(const char *fn, int *index, int *a, rvec **order,
- real ***slOrder, real *slWidth, int nslices, gmx_bool bSliced,
- gmx_bool bUnsat, const t_topology *top, int ePBC, int ngrps, int axis,
- gmx_bool permolecule, gmx_bool radial, gmx_bool distcalc, const char *radfn,
- real ***distvals,
- const gmx_output_env_t *oenv)
+static void calc_order(const char *fn, int *index, int *a, rvec **order,
+ real ***slOrder, real *slWidth, int nslices, gmx_bool bSliced,
+ gmx_bool bUnsat, const t_topology *top, int ePBC, int ngrps, int axis,
+ gmx_bool permolecule, gmx_bool radial, gmx_bool distcalc, const char *radfn,
+ real ***distvals,
+ const gmx_output_env_t *oenv)
{
/* if permolecule = TRUE, order parameters will be calculed per molecule
* and stored in slOrder with #slices = # molecules */
gmx_bool use_unitvector = FALSE; /* use a specified unit vector instead of axis to specify unit normal*/
rvec direction, com, dref, dvec;
int comsize, distsize;
- int *comidx = NULL, *distidx = NULL;
- char *grpname = NULL;
+ int *comidx = nullptr, *distidx = nullptr;
+ char *grpname = nullptr;
t_pbc pbc;
real arcdist, tmpdist;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
/* PBC added for center-of-mass vector*/
/* Initiate the pbc structure */
}
if (distcalc)
{
- if (grpname != NULL)
+ if (grpname != nullptr)
{
sfree(grpname);
}
sfree(x0); /* free memory used by coordinate arrays */
sfree(x1);
- if (comidx != NULL)
+ if (comidx != nullptr)
{
sfree(comidx);
}
- if (distidx != NULL)
+ if (distidx != nullptr)
{
sfree(distidx);
}
- if (grpname != NULL)
+ if (grpname != nullptr)
{
sfree(grpname);
}
}
-void order_plot(rvec order[], real *slOrder[], const char *afile, const char *bfile,
- const char *cfile, int ngrps, int nslices, real slWidth, gmx_bool bSzonly,
- gmx_bool permolecule, real **distvals, const gmx_output_env_t *oenv)
+static void order_plot(rvec order[], real *slOrder[], const char *afile, const char *bfile,
+ const char *cfile, int ngrps, int nslices, real slWidth, gmx_bool bSzonly,
+ gmx_bool permolecule, real **distvals, const gmx_output_env_t *oenv)
{
FILE *ord, *slOrd; /* xvgr files with order parameters */
int atom, slice; /* atom corresponding to order para.*/
xvgrclose(slOrd);
}
-void write_bfactors(t_filenm *fnm, int nfile, int *index, int *a, int nslices, int ngrps, real **order, const t_topology *top, real **distvals, gmx_output_env_t *oenv)
+static void write_bfactors(t_filenm *fnm, int nfile, int *index, int *a, int nslices, int ngrps, real **order, const t_topology *top, real **distvals, gmx_output_env_t *oenv)
{
/*function to write order parameters as B factors in PDB file using
first frame of trajectory*/
nout = nslices*ngrps;
read_first_frame(oenv, &status, ftp2fn(efTRX, nfile, fnm), &fr, TRX_NEED_X);
- close_trj(status);
+ close_trx(status);
frout = fr;
frout.natoms = nout;
frout.bF = FALSE;
frout.bV = FALSE;
- frout.x = 0;
+ frout.x = nullptr;
snew(frout.x, nout);
init_t_atoms(&useatoms, nout, TRUE);
}
}
- write_sto_conf(opt2fn("-ob", nfile, fnm), "Order parameters", &useatoms, frout.x, NULL, frout.ePBC, frout.box);
+ write_sto_conf(opt2fn("-ob", nfile, fnm), "Order parameters", &useatoms, frout.x, nullptr, frout.ePBC, frout.box);
sfree(frout.x);
done_atom(&useatoms);
static int nslices = 1; /* nr of slices defined */
static gmx_bool bSzonly = FALSE; /* True if only Sz is wanted */
static gmx_bool bUnsat = FALSE; /* True if carbons are unsat. */
- static const char *normal_axis[] = { NULL, "z", "x", "y", NULL };
+ static const char *normal_axis[] = { nullptr, "z", "x", "y", nullptr };
static gmx_bool permolecule = FALSE; /*compute on a per-molecule basis */
static gmx_bool radial = FALSE; /*compute a radial membrane normal */
static gmx_bool distcalc = FALSE; /*calculate distance from a reference group */
*a; /* atom numbers in each group */
t_blocka *block; /* data from index file */
t_filenm fnm[] = { /* files for g_order */
- { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
- { efNDX, "-n", NULL, ffREAD }, /* index file */
- { efNDX, "-nr", NULL, ffOPTRD }, /* index for radial axis calculation */
- { efTPR, NULL, NULL, ffREAD }, /* topology file */
+ { efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
+ { efNDX, "-n", nullptr, ffREAD }, /* index file */
+ { efNDX, "-nr", nullptr, ffOPTRD }, /* index for radial axis calculation */
+ { efTPR, nullptr, nullptr, ffREAD }, /* topology file */
{ efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
{ efXVG, "-od", "deuter", ffWRITE }, /* xvgr output file */
- { efPDB, "-ob", NULL, ffOPTWR }, /* write Scd as B factors to PDB if permolecule */
+ { efPDB, "-ob", nullptr, ffOPTWR }, /* write Scd as B factors to PDB if permolecule */
{ efXVG, "-os", "sliced", ffWRITE }, /* xvgr output file */
{ efXVG, "-Sg", "sg-ang", ffOPTWR }, /* xvgr output file */
{ efXVG, "-Sk", "sk-dist", ffOPTWR }, /* xvgr output file */
};
gmx_bool bSliced = FALSE; /* True if box is sliced */
#define NFILE asize(fnm)
- real **distvals = NULL;
+ real **distvals = nullptr;
const char *sgfnm, *skfnm, *ndxfnm, *tpsfnm, *trxfnm;
gmx_output_env_t *oenv;
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
- GMX_RELEASE_ASSERT(normal_axis[0] != NULL, "Options inconsistency; normal_axis[0] is NULL");
+ GMX_RELEASE_ASSERT(normal_axis[0] != nullptr, "Options inconsistency; normal_axis[0] is NULL");
if (std::strcmp(normal_axis[0], "x") == 0)
{
axis = XX;
opt2fn("-Sgsl", NFILE, fnm), opt2fn("-Sksl", NFILE, fnm),
oenv);
/* view xvgr files */
- do_view(oenv, opt2fn("-Sg", NFILE, fnm), NULL);
- do_view(oenv, opt2fn("-Sk", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn("-Sg", NFILE, fnm), nullptr);
+ do_view(oenv, opt2fn("-Sk", NFILE, fnm), nullptr);
if (nslices > 1)
{
- do_view(oenv, opt2fn("-Sgsl", NFILE, fnm), NULL);
- do_view(oenv, opt2fn("-Sksl", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn("-Sgsl", NFILE, fnm), nullptr);
+ do_view(oenv, opt2fn("-Sksl", NFILE, fnm), nullptr);
}
}
else
}
- do_view(oenv, opt2fn("-o", NFILE, fnm), NULL); /* view xvgr file */
- do_view(oenv, opt2fn("-os", NFILE, fnm), NULL); /* view xvgr file */
- do_view(oenv, opt2fn("-od", NFILE, fnm), NULL); /* view xvgr file */
+ do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr); /* view xvgr file */
+ do_view(oenv, opt2fn("-os", NFILE, fnm), nullptr); /* view xvgr file */
+ do_view(oenv, opt2fn("-od", NFILE, fnm), nullptr); /* view xvgr file */
}
- if (distvals != NULL)
+ if (distvals != nullptr)
{
for (i = 0; i < nslices; ++i)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include "gromacs/commandline/pargs.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fft/calcgrid.h"
#include "gromacs/fileio/checkpoint.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/broadcaststructs.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformintdistribution.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
-/* We use the same defines as in broadcaststructs.cpp here */
-#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
-#define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
-#define snew_bc(cr, d, nr) { if (!MASTER(cr)) {snew((d), (nr)); }}
/* #define TAKETIME */
/* #define DEBUG */
real tmp2 = 0;
gmx_bool bFraction;
- int *numbers = NULL;
+ int *numbers = nullptr;
/* Index variables for parallel work distribution */
int startglobal, stopglobal;
int i;
int nq; /* number of charged particles */
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
if (MASTER(cr))
nq = 0;
aloop = gmx_mtop_atomloop_all_init(mtop);
-
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
if (is_charge(atom->q))
const gmx_mtop_t *mtop, FILE *fp_out, gmx_bool bVerbose, unsigned int seed,
t_commrec *cr)
{
- rvec *x = NULL; /* The coordinates */
- real *q = NULL; /* The charges */
- real edir = 0.0; /* real space error */
- real erec = 0.0; /* reciprocal space error */
- real derr = 0.0; /* difference of real and reciprocal space error */
- real derr0 = 0.0; /* difference of real and reciprocal space error */
- real beta = 0.0; /* splitting parameter beta */
- real beta0 = 0.0; /* splitting parameter beta */
- int ncharges; /* The number of atoms with charges */
- int nsamples; /* The number of samples used for the calculation of the
- * self-energy error term */
+ rvec *x = nullptr; /* The coordinates */
+ real *q = nullptr; /* The charges */
+ real edir = 0.0; /* real space error */
+ real erec = 0.0; /* reciprocal space error */
+ real derr = 0.0; /* difference of real and reciprocal space error */
+ real derr0 = 0.0; /* difference of real and reciprocal space error */
+ real beta = 0.0; /* splitting parameter beta */
+ real beta0 = 0.0; /* splitting parameter beta */
+ int ncharges; /* The number of atoms with charges */
+ int nsamples; /* The number of samples used for the calculation of the
+ * self-energy error term */
int i = 0;
if (MASTER(cr))
}
/* Prepare an x and q array with only the charged atoms */
- ncharges = prepare_x_q(&q, &x, mtop, state->x, cr);
+ ncharges = prepare_x_q(&q, &x, mtop, as_rvec_array(state->x.data()), cr);
if (MASTER(cr))
{
calc_q2all(mtop, &(info->q2all), &(info->q2allnr));
real user_beta = -1.0;
real fracself = 1.0;
t_inputinfo info;
- t_state state; /* The state from the tpr input file */
- gmx_mtop_t mtop; /* The topology from the tpr input file */
- t_inputrec *ir = NULL; /* The inputrec from the tpr file */
- FILE *fp = NULL;
+ t_state state; /* The state from the tpr input file */
+ gmx_mtop_t mtop; /* The topology from the tpr input file */
+ t_inputrec *ir = nullptr; /* The inputrec from the tpr file */
+ FILE *fp = nullptr;
t_commrec *cr;
unsigned long PCA_Flags;
gmx_bool bTUNE = FALSE;
static t_filenm fnm[] = {
- { efTPR, "-s", NULL, ffREAD },
+ { efTPR, "-s", nullptr, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
{ efTPR, "-so", "tuned", ffOPTWR }
};
- gmx_output_env_t *oenv = NULL;
+ gmx_output_env_t *oenv = nullptr;
t_pargs pa[] = {
{ "-beta", FALSE, etREAL, {&user_beta},
if (!parse_common_args(&argc, argv, PCA_Flags,
NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv))
+ 0, nullptr, &oenv))
{
+ sfree(cr);
return 0;
}
if (MASTER(cr))
{
- /* Read in the tpr file */
- snew(ir, 1);
+ ir = new t_inputrec();
read_tpr_file(opt2fn("-s", NFILE, fnm), &info, &state, &mtop, ir, user_beta, fracself);
/* Open logfile for reading */
fp = fopen(opt2fn("-o", NFILE, fnm), "w");
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
- calc_grid(stdout, state.box, info.fourier_sp[0], &(info.nkx[0]), &(info.nky[0]), &(info.nkz[0]));
+ calcFftGrid(stdout, state.box, info.fourier_sp[0], minimalPmeGridSize(info.pme_order[0]),
+ &(info.nkx[0]), &(info.nky[0]), &(info.nkz[0]));
if ( (ir->nkx != info.nkx[0]) || (ir->nky != info.nky[0]) || (ir->nkz != info.nkz[0]) )
{
gmx_fatal(FARGS, "Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = %d x %d x %d",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-o", "polystat", ffWRITE },
{ efXVG, "-v", "polyvec", ffOPTWR },
{ efXVG, "-p", "persist", ffOPTWR },
char *grpname;
t_trxstatus *status;
real t;
- rvec *x, *bond = NULL;
+ rvec *x, *bond = nullptr;
matrix box;
int natoms, i, j, frame, ind0, ind1, a, d, d2, ord[DIM] = {0};
dvec cm, sum_eig = {0, 0, 0};
double **gyr, **gyr_all, eig[DIM], **eigv;
double sum_eed2, sum_eed2_tot, sum_gyro, sum_gyro_tot, sum_pers_tot;
- int *ninp = NULL;
- double *sum_inp = NULL, pers;
+ int *ninp = nullptr;
+ double *sum_inp = nullptr, pers;
double *intd, ymax, ymin;
double mmol, m;
char title[STRLEN];
"<R\\sg\\N eig1>", "<R\\sg\\N eig2>", "<R\\sg\\N eig3>"
};
char **legp, buf[STRLEN];
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
if (!parse_common_args(&argc, argv,
PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
snew(top, 1);
ePBC = read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
- NULL, box, &natoms, NULL, NULL, top);
+ nullptr, box, &natoms, nullptr, nullptr, top);
fprintf(stderr, "Select a group of polymer mainchain atoms:\n");
get_index(&top->atoms, ftp2fn_null(efNDX, NFILE, fnm),
}
else
{
- outv = NULL;
+ outv = nullptr;
}
if (opt2bSet("-p", NFILE, fnm))
}
else
{
- outp = NULL;
+ outp = nullptr;
}
if (opt2bSet("-i", NFILE, fnm))
}
else
{
- intd = NULL;
- outi = NULL;
+ intd = nullptr;
+ outi = nullptr;
}
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* this routine integrates the array data and returns the resulting array */
/* routine uses simple trapezoid rule */
-void p_integrate(double *result, double data[], int ndata, double slWidth)
+static void p_integrate(double *result, double data[], int ndata, double slWidth)
{
int i, slice;
double sum;
return;
}
-void calc_potential(const char *fn, int **index, int gnx[],
- double ***slPotential, double ***slCharge,
- double ***slField, int *nslices,
- const t_topology *top, int ePBC,
- int axis, int nr_grps, double *slWidth,
- double fudge_z, gmx_bool bSpherical, gmx_bool bCorrect,
- const gmx_output_env_t *oenv)
+static void calc_potential(const char *fn, int **index, int gnx[],
+ double ***slPotential, double ***slCharge,
+ double ***slField, int *nslices,
+ const t_topology *top, int ePBC,
+ int axis, int nr_grps, double *slWidth,
+ double fudge_z, gmx_bool bSpherical, gmx_bool bCorrect,
+ const gmx_output_env_t *oenv)
{
rvec *x0; /* coordinates without pbc */
matrix box; /* box (3x3) */
real t;
double z;
rvec xcm;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
switch (axis)
{
gmx_rmpbc_done(gpbc);
/*********** done with status file **********/
- close_trj(status);
+ close_trx(status);
/* slCharge now contains the total charge per slice, summed over all
frames. Now divide by nr_frames and integrate twice
sfree(x0); /* free memory used by coordinate array */
}
-void plot_potential(double *potential[], double *charge[], double *field[],
- const char *afile, const char *bfile, const char *cfile,
- int nslices, int nr_grps, const char *grpname[], double slWidth,
- const gmx_output_env_t *oenv)
+static void plot_potential(double *potential[], double *charge[], double *field[],
+ const char *afile, const char *bfile, const char *cfile,
+ int nslices, int nr_grps, const char *grpname[], double slWidth,
+ const gmx_output_env_t *oenv)
{
FILE *pot, /* xvgr file with potential */
*cha, /* xvgr file with charges */
int ePBC;
int **index; /* indices for all groups */
t_filenm fnm[] = { /* files for g_order */
- { efTRX, "-f", NULL, ffREAD }, /* trajectory file */
- { efNDX, NULL, NULL, ffREAD }, /* index file */
- { efTPR, NULL, NULL, ffREAD }, /* topology file */
+ { efTRX, "-f", nullptr, ffREAD }, /* trajectory file */
+ { efNDX, nullptr, nullptr, ffREAD }, /* index file */
+ { efTPR, nullptr, nullptr, ffREAD }, /* topology file */
{ efXVG, "-o", "potential", ffWRITE }, /* xvgr output file */
{ efXVG, "-oc", "charge", ffWRITE }, /* xvgr output file */
{ efXVG, "-of", "field", ffWRITE }, /* xvgr output file */
opt2fn("-oc", NFILE, fnm), opt2fn("-of", NFILE, fnm),
nslices, ngrps, (const char**)grpname, slWidth, oenv);
- do_view(oenv, opt2fn("-o", NFILE, fnm), NULL); /* view xvgr file */
- do_view(oenv, opt2fn("-oc", NFILE, fnm), NULL); /* view xvgr file */
- do_view(oenv, opt2fn("-of", NFILE, fnm), NULL); /* view xvgr file */
+ do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr); /* view xvgr file */
+ do_view(oenv, opt2fn("-oc", NFILE, fnm), nullptr); /* view xvgr file */
+ do_view(oenv, opt2fn("-of", NFILE, fnm), nullptr); /* view xvgr file */
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/smalloc.h"
-void
+static void
calc_principal_axes(const t_topology *top,
rvec *x,
int *index,
FILE * fmoi;
matrix axes, box;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
char ** legend;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-a1", "paxis1", ffWRITE },
{ efXVG, "-a2", "paxis2", ffWRITE },
{ efXVG, "-a3", "paxis3", ffWRITE },
if (!parse_common_args(&argc, argv,
PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
sfree(legend);
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, NULL, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box, TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
gmx_rmpbc_done(gpbc);
- close_trj(status);
+ close_trx(status);
xvgrclose(axis1);
xvgrclose(axis2);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int j;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPR, NULL, NULL, ffREAD },
- { efXVG, NULL, "rama", ffWRITE }
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efXVG, nullptr, "rama", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, 0, NULL, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, 0, nullptr, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
fprintf(stderr, "\n");
xvgrclose(out);
- do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
+ do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* equalize principal components: */
/* orient principal axes, get principal components */
- orient_princ(atoms, isize, index, natoms, x, NULL, princ);
+ orient_princ(atoms, isize, index, natoms, x, nullptr, princ);
/* calc our own principal components */
clear_rvec(vec);
};
int ewhat;
const char *what[ewNR + 1] =
- { NULL, "rmsd", "rho", "rhosc", NULL };
+ { nullptr, "rmsd", "rho", "rhosc", nullptr };
const char *whatname[ewNR] =
- { NULL, "RMSD", "Rho", "Rho sc" };
+ { nullptr, "RMSD", "Rho", "Rho sc" };
const char *whatlabel[ewNR] =
- { NULL, "RMSD (nm)", "Rho", "Rho sc" };
+ { nullptr, "RMSD (nm)", "Rho", "Rho sc" };
const char *whatxvgname[ewNR] =
- { NULL, "RMSD", "\\8r\\4", "\\8r\\4\\ssc\\N" };
+ { nullptr, "RMSD", "\\8r\\4", "\\8r\\4\\ssc\\N" };
const char *whatxvglabel[ewNR] =
- { NULL, "RMSD (nm)", "\\8r\\4", "\\8r\\4\\ssc\\N" };
+ { nullptr, "RMSD (nm)", "\\8r\\4", "\\8r\\4\\ssc\\N" };
/* strings and things for fitting methods */
enum
{
};
int efit;
const char *fit[efNR + 1] =
- { NULL, "rot+trans", "translation", "none", NULL };
+ { nullptr, "rot+trans", "translation", "none", nullptr };
const char *fitgraphlabel[efNR + 1] =
- { NULL, "lsq fit", "translational fit", "no fit" };
+ { nullptr, "lsq fit", "translational fit", "no fit" };
static int nrms = 1;
static gmx_bool bMassWeighted = TRUE;
t_pargs pa[] =
int i, j, k, m, teller, teller2, tel_mat, tel_mat2;
#define NFRAME 5000
int maxframe = NFRAME, maxframe2 = NFRAME;
- real t, *w_rls, *w_rms, *w_rls_m = NULL, *w_rms_m = NULL;
+ real t, *w_rls, *w_rms, *w_rls_m = nullptr, *w_rms_m = nullptr;
gmx_bool bNorm, bAv, bFreq2, bFile2, bMat, bBond, bDelta, bMirror, bMass;
gmx_bool bFit, bReset;
t_topology top;
int ePBC;
- t_iatom *iatom = NULL;
+ t_iatom *iatom = nullptr;
matrix box = {{0}};
- rvec *x, *xp, *xm = NULL, **mat_x = NULL, **mat_x2, *mat_x2_j = NULL, vec1,
+ rvec *x, *xp, *xm = nullptr, **mat_x = nullptr, **mat_x2, *mat_x2_j = nullptr, vec1,
vec2;
t_trxstatus *status;
char buf[256], buf2[256];
int ncons = 0;
FILE *fp;
- real rlstot = 0, **rls, **rlsm = NULL, *time, *time2, *rlsnorm = NULL,
- **rmsd_mat = NULL, **bond_mat = NULL, *axis, *axis2, *del_xaxis,
+ real rlstot = 0, **rls, **rlsm = nullptr, *time, *time2, *rlsnorm = nullptr,
+ **rmsd_mat = nullptr, **bond_mat = nullptr, *axis, *axis2, *del_xaxis,
*del_yaxis, rmsd_max, rmsd_min, rmsd_avg, bond_max, bond_min, ang;
- real **rmsdav_mat = NULL, av_tot, weight, weight_tot;
- real **delta = NULL, delta_max, delta_scalex = 0, delta_scaley = 0,
+ real **rmsdav_mat = nullptr, av_tot, weight, weight_tot;
+ real **delta = nullptr, delta_max, delta_scalex = 0, delta_scaley = 0,
*delta_tot;
int delta_xsize = 0, del_lev = 100, mx, my, abs_my;
- gmx_bool bA1, bA2, bPrev, bTop, *bInMat = NULL;
- int ifit, *irms, ibond = 0, *ind_bond1 = NULL, *ind_bond2 = NULL, n_ind_m =
+ gmx_bool bA1, bA2, bPrev, bTop, *bInMat = nullptr;
+ int ifit, *irms, ibond = 0, *ind_bond1 = nullptr, *ind_bond2 = nullptr, n_ind_m =
0;
- int *ind_fit, **ind_rms, *ind_m = NULL, *rev_ind_m = NULL, *ind_rms_m =
- NULL;
+ int *ind_fit, **ind_rms, *ind_m = nullptr, *rev_ind_m = nullptr, *ind_rms_m =
+ nullptr;
char *gn_fit, **gn_rms;
t_rgb rlo, rhi;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_filenm fnm[] =
{
- { efTPS, NULL, NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
- { efTRX, "-f2", NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "rmsd", ffWRITE },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTRX, "-f2", nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "rmsd", ffWRITE },
{ efXVG, "-mir", "rmsdmir", ffOPTWR },
{ efXVG, "-a", "avgrp", ffOPTWR },
{ efXVG, "-dist", "rmsd-dist", ffOPTWR },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr,
&oenv))
{
return 0;
}
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xp,
- NULL, box, TRUE);
+ nullptr, box, TRUE);
snew(w_rls, top.atoms.nr);
snew(w_rms, top.atoms.nr);
}
if (bReset)
{
- reset_x(ifit, ind_fit, top.atoms.nr, NULL, xp, w_rls);
+ reset_x(ifit, ind_fit, top.atoms.nr, nullptr, xp, w_rls);
}
if (bMirror)
{
if (bReset)
{
- reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
+ reset_x(ifit, ind_fit, natoms, nullptr, x, w_rls);
}
if (ewhat == ewRhoSc)
{
}
if (bReset)
{
- reset_x(ifit, ind_fit, natoms, NULL, xp, w_rls);
+ reset_x(ifit, ind_fit, natoms, nullptr, xp, w_rls);
}
if (bFit)
{
}
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
if (bFile2)
{
if (bReset)
{
- reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
+ reset_x(ifit, ind_fit, natoms, nullptr, x, w_rls);
}
if (ewhat == ewRhoSc)
{
}
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
}
else
{
else
{
sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat],
- time[prev*freq]-time[0], output_env_get_time_label(oenv));
+ time[prev*freq]-time[0], output_env_get_time_label(oenv).c_str());
}
fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
whatxvglabel[ewhat], oenv);
xvgrclose(fp);
}
do_view(oenv, opt2fn_null("-a", NFILE, fnm), "-graphtype bar");
- do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
- do_view(oenv, opt2fn_null("-mir", NFILE, fnm), NULL);
- do_view(oenv, opt2fn_null("-m", NFILE, fnm), NULL);
- do_view(oenv, opt2fn_null("-bm", NFILE, fnm), NULL);
- do_view(oenv, opt2fn_null("-dist", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr);
+ do_view(oenv, opt2fn_null("-mir", NFILE, fnm), nullptr);
+ do_view(oenv, opt2fn_null("-m", NFILE, fnm), nullptr);
+ do_view(oenv, opt2fn_null("-bm", NFILE, fnm), nullptr);
+ do_view(oenv, opt2fn_null("-dist", NFILE, fnm), nullptr);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fp = gmx_ffopen(eq_fn, "r");
neq = 0;
- equiv = NULL;
+ equiv = nullptr;
while (get_a_line(fp, line, STRLEN))
{
lp = line;
/* this is not efficient, but I'm lazy */
srenew(equiv, neq+1);
- equiv[neq] = NULL;
+ equiv[neq] = nullptr;
na = 0;
if (sscanf(lp, "%s %n", atomname, &n) == 1)
{
equiv[neq][na].aname = gmx_strdup(atomname);
if (na > 0)
{
- equiv[neq][na].nname = NULL;
+ equiv[neq][na].nname = nullptr;
}
na++;
lp += n;
srenew(equiv[neq], na+1);
equiv[neq][na].set = false;
equiv[neq][na].rnr = 0;
- equiv[neq][na].rname = NULL;
- equiv[neq][na].aname = NULL;
+ equiv[neq][na].rname = nullptr;
+ equiv[neq][na].aname = nullptr;
/* next */
neq++;
else
{
neq = 0;
- equiv = NULL;
+ equiv = nullptr;
}
groupnr = 0;
}
}
-real rms_diff(int natom, real **d, real **d_r)
+static real rms_diff(int natom, real **d, real **d_r)
{
int i, j;
real r, r2;
int *index, *noe_index;
char *grpname;
real **d_r, **d, **dtot, **dtot2, **mean, **rms, **rmsc, *resnr;
- real **dtot1_3 = NULL, **dtot1_6 = NULL;
+ real **dtot1_3 = nullptr, **dtot1_6 = nullptr;
real rmsnow, meanmax, rmsmax, rmscmax;
real max1_3, max1_6;
- t_noe_gr *noe_gr = NULL;
- t_noe **noe = NULL;
+ t_noe_gr *noe_gr = nullptr;
+ t_noe **noe = nullptr;
t_rgb rlo, rhi;
gmx_bool bRMS, bScale, bMean, bNOE, bNMR3, bNMR6, bNMR;
"Use periodic boundary conditions when computing distances" }
};
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efDAT, "-equiv", "equiv", ffOPTRD },
- { efXVG, NULL, "distrmsd", ffWRITE },
+ { efXVG, nullptr, "distrmsd", ffWRITE },
{ efXPM, "-rms", "rmsdist", ffOPTWR },
{ efXPM, "-scl", "rmsscale", ffOPTWR },
{ efXPM, "-mean", "rmsmean", ffOPTWR },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
/* get topology and index */
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, FALSE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, nullptr, box, FALSE);
if (!bPBC)
{
xvgrclose(fp);
- close_trj(status);
+ close_trx(status);
calc_rms(isize, teller, dtot, dtot2, rms, &rmsmax, rmsc, &rmscmax, mean, &meanmax);
fprintf(stderr, "rmsmax = %g, rmscmax = %g\n", rmsmax, rmscmax);
write_noe(opt2FILE("-noe", NFILE, fnm, "w"), gnr, noe, noe_gr, scalemax);
}
- do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
+ do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
return 0;
}
*/
#include "gmxpre.h"
+#include <cassert>
#include <cmath>
#include <cstring>
if ((ri->nr == atoms->resinfo[atoms->atom[i].resind].nr) &&
(ri->ic == atoms->resinfo[atoms->atom[i].resind].ic) &&
(std::strcmp(*atoms->resinfo[atoms->atom[i].resind].name, rresnm) == 0) &&
- (std::strstr(*atoms->atomname[i], atomnm) != NULL))
+ (std::strstr(*atoms->atomname[i], atomnm) != nullptr))
{
break;
}
return atoms->pdbinfo[i].bfac;
}
-void correlate_aniso(const char *fn, t_atoms *ref, t_atoms *calc,
- const gmx_output_env_t *oenv)
+static void correlate_aniso(const char *fn, t_atoms *ref, t_atoms *calc,
+ const gmx_output_env_t *oenv)
{
FILE *fp;
int i, j;
start = 0;
av = 0;
m = 0;
+ if (!f)
+ {
+ assert(U);
+ }
for (i = 0; i < isize; i++)
{
- av += w_rls[index[i]]*(f != NULL ? f[i] : U[i][uind]);
+ av += w_rls[index[i]]*(f != nullptr ? f[i] : U[i][uind]);
m += w_rls[index[i]];
if (i+1 == isize ||
atoms->atom[index[i]].resind != atoms->atom[index[i+1]].resind)
{
av /= m;
- if (f != NULL)
+ if (f != nullptr)
{
for (j = start; j <= i; j++)
{
}
}
-void print_dir(FILE *fp, real *Uaver)
+static void print_dir(FILE *fp, real *Uaver)
{
real eigvec[DIM*DIM];
real tmp[DIM*DIM];
real bfac, pdb_bfac, *Uaver;
double **U, *xav;
int aid;
- rvec *rmsd_x = NULL;
+ rvec *rmsd_x = nullptr;
double *rmsf, invcount, totmass;
int d;
real count = 0;
rvec xcm;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
gmx_output_env_t *oenv;
const char *leg[2] = { "MD", "X-Ray" };
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efPDB, "-q", NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efPDB, "-q", nullptr, ffOPTRD },
{ efPDB, "-oq", "bfac", ffOPTWR },
{ efPDB, "-ox", "xaver", ffOPTWR },
{ efXVG, "-o", "rmsf", ffWRITE },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, NULL,
+ NFILE, fnm, asize(pargs), pargs, asize(desc), desc, 0, nullptr,
&oenv))
{
return 0;
devfn = opt2fn_null("-od", NFILE, fnm);
dirfn = opt2fn_null("-dir", NFILE, fnm);
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xref, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xref, nullptr, box, TRUE);
const char *title = *top.name;
snew(w_rls, top.atoms.nr);
t_topology *top_pdb;
snew(top_pdb, 1);
/* Read coordinates twice */
- read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, NULL, NULL, NULL, pdbbox, FALSE);
+ read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, nullptr, nullptr, nullptr, pdbbox, FALSE);
snew(pdbatoms, 1);
*pdbatoms = top_pdb->atoms;
- read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, NULL, &pdbx, NULL, pdbbox, FALSE);
+ read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, nullptr, &pdbx, nullptr, pdbbox, FALSE);
/* TODO Should this assert that top_pdb->atoms.nr == top.atoms.nr?
* See discussion at https://gerrit.gromacs.org/#/c/6430/1 */
title = *top_pdb->name;
refatoms = &top.atoms;
pdbx = xref;
snew(pdbatoms->pdbinfo, pdbatoms->nr);
+ pdbatoms->havePdbInfo = TRUE;
copy_mat(box, pdbbox);
}
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
if (bFit)
{
{
for (d = 0; d < DIM*DIM; d++)
{
- average_residues(NULL, U, d, isize, index, w_rls, &top.atoms);
+ average_residues(nullptr, U, d, isize, index, w_rls, &top.atoms);
}
}
}
if (bRes)
{
- average_residues(rmsf, NULL, 0, isize, index, w_rls, &top.atoms);
+ average_residues(rmsf, nullptr, 0, isize, index, w_rls, &top.atoms);
}
/* Write RMSD output */
fp = xvgropen(devfn, "RMS Deviation", label, "(nm)", oenv);
rvec_inc(pdbx[index[i]], xcm);
}
write_sto_conf_indexed(opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx,
- NULL, ePBC, pdbbox, isize, index);
+ nullptr, ePBC, pdbbox, isize, index);
}
if (opt2bSet("-ox", NFILE, fnm))
{
}
}
/* Write a .pdb file with B-factors and optionally anisou records */
- write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, NULL,
+ write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, nullptr,
ePBC, pdbbox, isize, index);
sfree(bFactorX);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int i, m, teller, n_alloc, natoms, nvec, ai, aj, ak;
unsigned long mode;
real t, t0, t1, dt;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_topology *top;
int ePBC;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffREAD },
{ efXVG, "-o", "rotacf", ffWRITE }
};
#define NFILE asize(fnm)
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(ppa);
return 0;
}
snew(c1, nvec);
for (i = 0; (i < nvec); i++)
{
- c1[i] = NULL;
+ c1[i] = nullptr;
}
n_alloc = 0;
teller++;
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
fprintf(stderr, "\nDone with trajectory\n");
gmx_rmpbc_done(gpbc);
teller, nvec, c1, dt, mode, bAver);
}
- do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
+ do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
return 0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real xf;
matrix box, R;
real *w_rls;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
nfr_all = 0;
{
copy_rvec(x[index[i]], xi[nfr][i]);
}
- reset_x(gnx, NULL, gnx, NULL, xi[nfr], w_rls);
+ reset_x(gnx, nullptr, gnx, nullptr, xi[nfr], w_rls);
nfr++;
if (nfr % 100 == 0)
{
nfr_all++;
}
while (read_next_x(oenv, status, &ti[nfr], x, box));
- close_trj(status);
+ close_trx(status);
sfree(x);
gmx_rmpbc_done(gpbc);
"the rotation matrix."
};
const char *reffit[] =
- { NULL, "none", "xyz", "xy", NULL };
+ { nullptr, "none", "xyz", "xy", nullptr };
static int skip = 1;
static gmx_bool bFitXY = FALSE, bMW = TRUE;
t_pargs pa[] = {
int natoms, i;
char *grpname;
int gnx;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
int *index;
gmx_output_env_t *oenv;
real *w_rls;
const char *leg[] = { "xx", "xy", "xz", "yx", "yy", "yz", "zx", "zy", "zz" };
#define NLEG asize(leg)
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "rotmat", ffWRITE }
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "rotmat", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x_ref, NULL, box, bMW);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x_ref, nullptr, box, bMW);
gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
- GMX_RELEASE_ASSERT(reffit[0] != NULL, "Options inconsistency; reffit[0] is NULL");
+ GMX_RELEASE_ASSERT(reffit[0] != nullptr, "Options inconsistency; reffit[0] is NULL");
if (reffit[0][0] != 'n')
{
get_refx(oenv, ftp2fn(efTRX, NFILE, fnm), reffit[0][2] == 'z' ? 3 : 2, skip,
if (reffit[0][0] == 'n')
{
- reset_x(gnx, index, natoms, NULL, x_ref, w_rls);
+ reset_x(gnx, index, natoms, nullptr, x_ref, w_rls);
}
out = xvgropen(ftp2fn(efXVG, NFILE, fnm),
{
gmx_rmpbc(gpbc, natoms, box, x);
- reset_x(gnx, index, natoms, NULL, x, w_rls);
+ reset_x(gnx, index, natoms, nullptr, x, w_rls);
if (bFitXY)
{
gmx_rmpbc_done(gpbc);
- close_trj(status);
+ close_trx(status);
xvgrclose(out);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static t_charge *mk_charge(const t_atoms *atoms, const t_block *cgs, int *nncg)
{
- t_charge *cg = NULL;
+ t_charge *cg = nullptr;
char buf[32];
int i, j, ncg, resnr, anr;
real qq;
"Use separate files for each interaction (may be MANY)" }
};
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPR, NULL, NULL, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
};
#define NFILE asize(fnm)
gmx_output_env_t *oenv;
if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
teller = 0;
- time = NULL;
+ time = nullptr;
do
{
srenew(time, teller+1);
}
while (read_next_x(oenv, status, &t, x, box));
fprintf(stderr, "\n");
- close_trj(status);
+ close_trx(status);
if (bSep)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static unsigned int seed = 0;
static int nthreads = -1;
- static const char *emode[] = { NULL, "direct", "mc", NULL };
- static const char *emethod[] = { NULL, "debye", "fft", NULL };
+ static const char *emode[] = { nullptr, "direct", "mc", nullptr };
+ static const char *emethod[] = { nullptr, "debye", "fft", nullptr };
gmx_neutron_atomic_structurefactors_t *gnsf;
gmx_sans_t *gsans;
#endif
};
FILE *fp;
- const char *fnTPX, *fnTRX, *fnDAT = NULL;
+ const char *fnTPX, *fnTRX, *fnDAT = nullptr;
t_trxstatus *status;
- t_topology *top = NULL;
- gmx_rmpbc_t gpbc = NULL;
+ t_topology *top = nullptr;
+ gmx_rmpbc_t gpbc = nullptr;
gmx_bool bFFT = FALSE, bDEBYE = FALSE;
gmx_bool bMC = FALSE;
int ePBC = -1;
rvec *x;
int natoms;
real t;
- char **grpname = NULL;
- int *index = NULL;
+ char **grpname = nullptr;
+ int *index = nullptr;
int isize;
int i;
- char *hdr = NULL;
- char *suffix = NULL;
- t_filenm *fnmdup = NULL;
- gmx_radial_distribution_histogram_t *prframecurrent = NULL, *pr = NULL;
- gmx_static_structurefactor_t *sqframecurrent = NULL, *sq = NULL;
+ char *hdr = nullptr;
+ char *suffix = nullptr;
+ t_filenm *fnmdup = nullptr;
+ gmx_radial_distribution_histogram_t *prframecurrent = nullptr, *pr = nullptr;
+ gmx_static_structurefactor_t *sqframecurrent = nullptr, *sq = nullptr;
gmx_output_env_t *oenv;
#define NFILE asize(fnm)
t_filenm fnm[] = {
- { efTPR, "-s", NULL, ffREAD },
- { efTRX, "-f", NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTPR, "-s", nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efDAT, "-d", "nsfactor", ffOPTRD },
{ efXVG, "-pr", "pr", ffWRITE },
{ efXVG, "-sq", "sq", ffWRITE },
nthreads = gmx_omp_get_max_threads();
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
gmx_omp_set_num_threads(nthreads);
/* Now try to parse opts for modes */
- GMX_RELEASE_ASSERT(emethod[0] != NULL, "Options inconsistency; emethod[0] is NULL");
+ GMX_RELEASE_ASSERT(emethod[0] != nullptr, "Options inconsistency; emethod[0] is NULL");
switch (emethod[0][0])
{
case 'd':
snew(grpname, 1);
snew(index, 1);
- read_tps_conf(fnTPX, top, &ePBC, &x, NULL, box, TRUE);
+ read_tps_conf(fnTPX, top, &ePBC, &x, nullptr, box, TRUE);
printf("\nPlease select group for SANS spectra calculation:\n");
get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, grpname);
gmx_rmpbc(gpbc, top->atoms.nr, box, x);
}
/* allocate memory for pr */
- if (pr == NULL)
+ if (pr == nullptr)
{
/* in case its first frame to read */
snew(pr, 1);
prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
/* copy prframecurrent -> pr and summ up pr->gr[i] */
/* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
- if (pr->gr == NULL)
+ if (pr->gr == nullptr)
{
/* check if we use pr->gr first time */
snew(pr->gr, prframecurrent->grn);
sfree(sqframecurrent);
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
/* normalize histo */
normalize_probability(pr->grn, pr->gr);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"Energy of the incoming X-ray (keV) "}
};
#define NPA asize(pa)
- const char *fnTPS, *fnTRX, *fnNDX, *fnDAT = NULL;
+ const char *fnTPS, *fnTRX, *fnNDX, *fnDAT = nullptr;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efDAT, "-d", "sfactor", ffOPTRD },
{ efXVG, "-sq", "sq", ffWRITE },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
- NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, NPA, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/matio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/xvgr.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/gmxana/gstat.h"
{
FILE *fp;
real *min_eig, *max_eig;
- real *axis_x, *axis_y, *axis_z, *axis = NULL;
+ real *axis_x, *axis_y, *axis_z, *axis = nullptr;
double *P;
real **PP, *W, *E, **WW, **EE, *S, **SS, *M, *bE;
rvec xxx;
npargs = asize(pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
- NFILE, fnm, npargs, pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
}
else
{
- et_val = NULL;
+ et_val = nullptr;
}
if (fn_ene && et_val)
opt2fn("-ls", NFILE, fnm), opt2fn("-lsh", NFILE, fnm),
opt2fn("-lss", NFILE, fnm),
opt2fn("-ls3", NFILE, fnm), opt2fn("-g", NFILE, fnm),
- n, nset, val, fn_ge != NULL, e_nset, et_val, Tref,
+ n, nset, val, fn_ge != nullptr, e_nset, et_val, Tref,
pmax, gmax,
- opt2parg_bSet("-emin", NPA, pa) ? &emin : NULL,
- opt2parg_bSet("-emax", NPA, pa) ? &emax : NULL,
+ opt2parg_bSet("-emin", NPA, pa) ? &emin : nullptr,
+ opt2parg_bSet("-emax", NPA, pa) ? &emax : nullptr,
nlevels, pmin,
idim, ibox,
opt2parg_bSet("-xmin", NPA, pa), rmin,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/smalloc.h"
-real pot(real x, real qq, real c6, real cn, int npow)
+static real pot(real x, real qq, real c6, real cn, int npow)
{
return cn*pow(x, -npow)-c6/gmx::power6(x)+qq*ONE_4PI_EPS0/x;
}
-real bhpot(real x, real A, real B, real C)
+static real bhpot(real x, real A, real B, real C)
{
return A*std::exp(-B*x) - C/gmx::power6(x);
}
-real dpot(real x, real qq, real c6, real cn, int npow)
+static real dpot(real x, real qq, real c6, real cn, int npow)
{
return -(npow*cn*std::pow(x, -npow-1)-6*c6/(x*gmx::power6(x))+qq*ONE_4PI_EPS0/gmx::square(x));
}
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc),
- desc, 0, NULL, &oenv))
+ desc, 0, nullptr, &oenv))
{
return 0;
}
}
xvgrclose(fp);
- do_view(oenv, ftp2fn(efXVG, NFILE, fnm), NULL);
+ do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char str[STRLEN];
gmx_bool bTPS;
rvec xref, dx, dxh1, dxh2, outer;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_pbc pbc;
const char *legr[] = {
"<cos(\\8q\\4\\s1\\N)>",
};
t_filenm fnm[] = {
- { efTRX, NULL, NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "sori", ffWRITE },
+ { efTRX, nullptr, nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "sori", ffWRITE },
{ efXVG, "-no", "snor", ffWRITE },
{ efXVG, "-ro", "sord", ffWRITE },
{ efXVG, "-co", "scum", ffWRITE },
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
bTPS = (opt2bSet("-s", NFILE, fnm) || !opt2bSet("-n", NFILE, fnm) || bCom);
if (bTPS)
{
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, box,
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box,
bCom);
}
}
else
{
- get_index(NULL, ftp2fn(efNDX, NFILE, fnm), 2, isize, index, grpname);
+ get_index(nullptr, ftp2fn(efNDX, NFILE, fnm), 2, isize, index, grpname);
}
if (bCom)
/* clean up */
sfree(x);
- close_trj(status);
+ close_trx(status);
gmx_rmpbc_done(gpbc);
/* Add the bin for the exact maximum to the previous bin */
}
xvgrclose(fp);
- do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
- do_view(oenv, opt2fn("-no", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr);
+ do_view(oenv, opt2fn("-no", NFILE, fnm), nullptr);
do_view(oenv, opt2fn("-ro", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-co", NFILE, fnm), "-nxy");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int i, nidx, nidxp;
int v;
int j, k;
- int ***bin = NULL;
+ int ***bin = nullptr;
int nbin[3];
FILE *flp;
int x, y, z, minx, miny, minz, maxx, maxy, maxz;
int tot, maxval, minval;
double norm;
gmx_output_env_t *oenv;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
t_filenm fnm[] = {
- { efTPS, NULL, NULL, ffREAD }, /* this is for the topology */
- { efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
- { efNDX, NULL, NULL, ffOPTRD }
+ { efTPS, nullptr, nullptr, ffREAD }, /* this is for the topology */
+ { efTRX, "-f", nullptr, ffREAD }, /* and this for the trajectory */
+ { efNDX, nullptr, nullptr, ffOPTRD }
};
#define NFILE asize(fnm)
return 0;
}
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, box, TRUE);
sfree(xtop);
atoms = &(top.atoms);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
-void spol_atom2molindex(int *n, int *index, const t_block *mols)
+static void spol_atom2molindex(int *n, int *index, const t_block *mols)
{
int nmol, i, j, m;
int gmx_spol(int argc, char *argv[])
{
t_topology *top;
- t_inputrec *ir;
t_atom *atom;
t_trxstatus *status;
int nrefat, natoms, nf, ntot;
double sdip, sdip2, sinp, sdinp, nmol;
int *hist;
t_pbc pbc;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
const char *desc[] = {
};
t_filenm fnm[] = {
- { efTRX, NULL, NULL, ffREAD },
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efXVG, NULL, "scdist", ffWRITE }
+ { efTRX, nullptr, nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efXVG, nullptr, "scdist", ffWRITE }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
snew(top, 1);
- snew(ir, 1);
+ // TODO: Only ePBC is used, not the full inputrec.
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
read_tpx_top(ftp2fn(efTPR, NFILE, fnm),
- ir, box, &natoms, NULL, NULL, top);
+ ir, box, &natoms, nullptr, nullptr, top);
/* get index groups */
printf("Select a group of reference particles and a solvent group:\n");
/* clean up */
sfree(x);
- close_trj(status);
+ close_trx(status);
fprintf(stderr, "Average number of molecules within %g nm is %.1f\n",
rmax, static_cast<real>(ntot)/nf);
}
xvgrclose(fp);
- do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
+ do_view(oenv, opt2fn("-o", NFILE, fnm), nullptr);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char *fn_tcf, const char *fn_cub,
const char *fn_vk, const gmx_output_env_t *oenv)
{
- FILE *fp, *fp_vk, *fp_cub = NULL;
+ FILE *fp, *fp_vk, *fp_cub = nullptr;
int nk, ntc;
- real **tcaf, **tcafc = NULL, eta, *sig;
+ real **tcaf, **tcafc = nullptr, eta, *sig;
int i, j, k, kc;
int ncorr;
double fitparms[3];
tcaf[k][0] = 1.0;
fitparms[0] = 1;
fitparms[1] = 1;
- do_lmfit(ncorr, tcaf[k], sig, dt, 0, 0, ncorr*dt,
- oenv, bDebugMode(), effnVAC, fitparms, 0, NULL);
+ do_lmfit(ncorr, tcaf[k], sig, dt, nullptr, 0, ncorr*dt,
+ oenv, bDebugMode(), effnVAC, fitparms, 0, nullptr);
eta = 1000*fitparms[1]*rho/
(4*fitparms[0]*PICO*norm2(kfac[k])/(NANO*NANO));
fprintf(stdout, "k %6.3f tau %6.3f eta %8.5f 10^-3 kg/(m s)\n",
tcafc[k][0] = 1.0;
fitparms[0] = 1;
fitparms[1] = 1;
- do_lmfit(ncorr, tcafc[k], sig, dt, 0, 0, ncorr*dt,
- oenv, bDebugMode(), effnVAC, fitparms, 0, NULL);
+ do_lmfit(ncorr, tcafc[k], sig, dt, nullptr, 0, ncorr*dt,
+ oenv, bDebugMode(), effnVAC, fitparms, 0, nullptr);
eta = 1000*fitparms[1]*rho/
(4*fitparms[0]*PICO*norm2(kfac[kset_c[k]])/(NANO*NANO));
fprintf(stdout,
matrix box;
gmx_bool bTop;
int gnx;
- int *index, *atndx = NULL, at;
+ int *index, *atndx = nullptr, at;
char *grpname;
char title[256];
real t0, t1, dt, m, mtot, sysmass, rho, sx, cx;
#define NHISTO 360
t_filenm fnm[] = {
- { efTRN, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRN, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-ot", "transcur", ffOPTWR },
{ efXVG, "-oa", "tcaf_all", ffWRITE },
{ efXVG, "-o", "tcaf", ffWRITE },
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(ppa);
return 0;
}
- bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, NULL, NULL, box,
+ bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box,
TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
nframes++;
}
while (read_next_frame(oenv, status, &fr));
- close_trj(status);
+ close_trx(status);
dt = (t1-t0)/(nframes-1);
#include <cstring>
#include <algorithm>
+#include <string>
#include "gromacs/commandline/pargs.h"
#include "gromacs/commandline/viewit.h"
fprintf(fp, " %g", time);
for (i = 0; i < n; i++)
{
- if (index != NULL)
+ if (index != nullptr)
{
ii = index[i];
}
for (i = 0; i < isize[g]; i++)
{
ind = index[g][i];
- if (mass != NULL)
+ if (mass != nullptr)
{
m = mass[ind];
svmul(m, x[ind], tmp);
}
}
}
- if (mass != NULL)
+ if (mass != nullptr)
{
for (d = 0; d < DIM; d++)
{
int ngrps, int isize[], int **index, gmx_bool bDim[],
const char *sffmt)
{
- static rvec *xav = NULL;
+ static rvec *xav = nullptr;
if (bCom)
{
- if (xav == NULL)
+ if (xav == nullptr)
{
snew(xav, ngrps);
}
average_data(x, xav, mass, ngrps, isize, index);
- low_print_data(fp, time, xav, ngrps, NULL, bDim, sffmt);
+ low_print_data(fp, time, xav, ngrps, nullptr, bDim, sffmt);
}
else
{
static void write_trx_x(t_trxstatus *status, const t_trxframe *fr, real *mass, gmx_bool bCom,
int ngrps, int isize[], int **index)
{
- static rvec *xav = NULL;
- static t_atoms *atoms = NULL;
+ static rvec *xav = nullptr;
+ static t_atoms *atoms = nullptr;
t_trxframe fr_av;
int i;
if (bCom)
{
- if (xav == NULL)
+ if (xav == nullptr)
{
snew(xav, ngrps);
snew(atoms, 1);
fr_av.natoms = ngrps;
fr_av.atoms = atoms;
fr_av.x = xav;
- write_trxframe(status, &fr_av, NULL);
+ write_trxframe(status, &fr_av, nullptr);
}
else
{
- write_trxframe_indexed(status, fr, isize[0], index[0], NULL);
+ write_trxframe_indexed(status, fr, isize[0], index[0], nullptr);
}
}
static real ekrot(rvec x[], rvec v[], real mass[], int isize, int index[])
{
- static real **TCM = NULL, **L;
+ real TCM[5][5], L[5][5];
double tm, m0, lxx, lxy, lxz, lyy, lyz, lzz, ekrot;
rvec a0, ocm;
dvec dx, b0;
dvec xcm, vcm, acm;
int i, j, m, n;
- if (TCM == NULL)
- {
- snew(TCM, DIM);
- for (i = 0; i < DIM; i++)
- {
- snew(TCM[i], DIM);
- }
- snew(L, DIM);
- for (i = 0; i < DIM; i++)
- {
- snew(L[i], DIM);
- }
- }
-
clear_dvec(xcm);
clear_dvec(vcm);
clear_dvec(acm);
L[YY][ZZ] = -lyz;
L[ZZ][ZZ] = lxx + lyy;
- m_inv_gen(L, DIM, TCM);
+ m_inv_gen(&L[0][0], DIM, &TCM[0][0]);
/* Compute omega (hoeksnelheid) */
clear_rvec(ocm);
*(atoms->resinfo[atoms->atom[maxi].resind].name),
atoms->resinfo[atoms->atom[maxi].resind].nr);
- if (atoms->pdbinfo == NULL)
+ if (atoms->pdbinfo == nullptr)
{
snew(atoms->pdbinfo, atoms->nr);
}
+ atoms->havePdbInfo = TRUE;
+
if (onedim == -1)
{
for (i = 0; i < isize; i++)
atoms->pdbinfo[index[i]].bfac = sum[index[i]][onedim]*scale;
}
}
- write_sto_conf_indexed(fname, title, atoms, x, NULL, ePBC, box, isize, index);
+ write_sto_conf_indexed(fname, title, atoms, x, nullptr, ePBC, box, isize, index);
}
}
int i, m, in, nnn;
real vn, vnmax;
- if (*histo == NULL)
+ if (*histo == nullptr)
{
vnmax = 0;
for (i = 0; (i < gnx); i++)
"(specified with [TT]-av[tt] or [TT]-af[tt]).[PAR]",
"Option [TT]-vd[tt] computes a velocity distribution, i.e. the",
"norm of the vector is plotted. In addition in the same graph",
- "the kinetic energy distribution is given."
+ "the kinetic energy distribution is given.",
+ "",
+ "See [gmx-trajectory] for plotting similar data for selections."
};
static gmx_bool bMol = FALSE, bCom = FALSE, bPBC = TRUE, bNoJump = FALSE;
static gmx_bool bX = TRUE, bY = TRUE, bZ = TRUE, bNorm = FALSE, bFP = FALSE;
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Make molecules whole for COM" },
{ "-mol", FALSE, etBOOL, {&bMol},
- "Index contains molecule numbers iso atom numbers" },
+ "Index contains molecule numbers instead of atom numbers" },
{ "-nojump", FALSE, etBOOL, {&bNoJump},
"Remove jumps of atoms across the box" },
{ "-x", FALSE, etBOOL, {&bX},
{ "-scale", FALSE, etREAL, {&scale},
"Scale factor for [REF].pdb[ref] output, 0 is autoscale" }
};
- FILE *outx = NULL, *outv = NULL, *outf = NULL, *outb = NULL, *outt = NULL;
- FILE *outekt = NULL, *outekr = NULL;
+ FILE *outx = nullptr, *outv = nullptr, *outf = nullptr, *outb = nullptr, *outt = nullptr;
+ FILE *outekt = nullptr, *outekr = nullptr;
t_topology top;
int ePBC;
real *mass, time;
const char *indexfn;
t_trxframe fr;
- int flags, nvhisto = 0, *vhisto = NULL;
- rvec *xtop, *xp = NULL;
- rvec *sumx = NULL, *sumv = NULL, *sumf = NULL;
+ int flags, nvhisto = 0, *vhisto = nullptr;
+ rvec *xtop, *xp = nullptr;
+ rvec *sumx = nullptr, *sumv = nullptr, *sumf = nullptr;
matrix topbox;
t_trxstatus *status;
- t_trxstatus *status_out = NULL;
- gmx_rmpbc_t gpbc = NULL;
+ t_trxstatus *status_out = nullptr;
+ gmx_rmpbc_t gpbc = nullptr;
int i, j;
int nr_xfr, nr_vfr, nr_ffr;
char **grpname;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-ox", "coord", ffOPTWR },
{ efTRX, "-oxt", "coord", ffOPTWR },
{ efXVG, "-ov", "veloc", ffOPTWR },
if (!parse_common_args(&argc, argv,
PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
sprintf(sffmt6, "%s%s%s%s%s%s", sffmt, sffmt, sffmt, sffmt, sffmt, sffmt);
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC,
- &xtop, NULL, topbox,
+ &xtop, nullptr, topbox,
bCom && (bOX || bOXT || bOV || bOT || bEKT || bEKR));
sfree(xtop);
if ((bMol || bCV || bCF) && !bTop)
}
else
{
- mass = NULL;
+ mass = nullptr;
}
flags = 0;
+ std::string label(output_env_get_xvgr_tlabel(oenv));
if (bOX)
{
flags = flags | TRX_READ_X;
outx = xvgropen(opt2fn("-ox", NFILE, fnm),
bCom ? "Center of mass" : "Coordinate",
- output_env_get_xvgr_tlabel(oenv), "Coordinate (nm)", oenv);
+ label, "Coordinate (nm)", oenv);
make_legend(outx, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOXT)
flags = flags | TRX_READ_V;
outv = xvgropen(opt2fn("-ov", NFILE, fnm),
bCom ? "Center of mass velocity" : "Velocity",
- output_env_get_xvgr_tlabel(oenv), "Velocity (nm/ps)", oenv);
+ label, "Velocity (nm/ps)", oenv);
make_legend(outv, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOF)
{
flags = flags | TRX_READ_F;
outf = xvgropen(opt2fn("-of", NFILE, fnm), "Force",
- output_env_get_xvgr_tlabel(oenv), "Force (kJ mol\\S-1\\N nm\\S-1\\N)",
+ label, "Force (kJ mol\\S-1\\N nm\\S-1\\N)",
oenv);
make_legend(outf, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOB)
{
outb = xvgropen(opt2fn("-ob", NFILE, fnm), "Box vector elements",
- output_env_get_xvgr_tlabel(oenv), "(nm)", oenv);
+ label, "(nm)", oenv);
xvgr_legend(outb, 6, box_leg, oenv);
}
bDum[DIM] = TRUE;
flags = flags | TRX_READ_V;
outt = xvgropen(opt2fn("-ot", NFILE, fnm), "Temperature",
- output_env_get_xvgr_tlabel(oenv), "(K)", oenv);
+ label, "(K)", oenv);
make_legend(outt, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bEKT)
bDum[DIM] = TRUE;
flags = flags | TRX_READ_V;
outekt = xvgropen(opt2fn("-ekt", NFILE, fnm), "Center of mass translation",
- output_env_get_xvgr_tlabel(oenv), "Energy (kJ mol\\S-1\\N)", oenv);
+ label, "Energy (kJ mol\\S-1\\N)", oenv);
make_legend(outekt, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bEKR)
bDum[DIM] = TRUE;
flags = flags | TRX_READ_X | TRX_READ_V;
outekr = xvgropen(opt2fn("-ekr", NFILE, fnm), "Center of mass rotation",
- output_env_get_xvgr_tlabel(oenv), "Energy (kJ mol\\S-1\\N)", oenv);
+ label, "Energy (kJ mol\\S-1\\N)", oenv);
make_legend(outekr, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bVD)
}
if (bOF && fr.bF)
{
- print_data(outf, time, fr.f, NULL, bCom, ngroups, isize, index, bDim, sffmt);
+ print_data(outf, time, fr.f, nullptr, bCom, ngroups, isize, index, bDim, sffmt);
}
if (bOB && fr.bBox)
{
}
while (read_next_frame(oenv, status, &fr));
- if (gpbc != NULL)
+ if (gpbc != nullptr)
{
gmx_rmpbc_done(gpbc);
}
/* clean up a bit */
- close_trj(status);
+ close_trx(status);
if (bOX)
{
/* view it */
view_all(oenv, NFILE, fnm);
+ done_top(&top);
+ // Free index and isize only if they are distinct from index0 and isize0
+ if (bMol)
+ {
+ for (int i = 0; i < ngroups; i++)
+ {
+ sfree(index[i]);
+ }
+ sfree(index);
+ sfree(isize);
+ }
+ for (int i = 0; i < ngroups; i++)
+ {
+ sfree(index0[i]);
+ sfree(grpname[i]);
+ }
+ sfree(index0);
+ sfree(isize0);
+ sfree(grpname);
+ done_filenms(NFILE, fnm);
+ done_frame(&fr);
+ output_env_done(oenv);
+
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <string>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tngio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/fileio/xvgr.h"
timestep[i] = 0;
}
- close_trj(status);
+ close_trx(status);
if (fr.bX)
{
sfree(fr.x);
gmx_bool ok;
char inputstring[STRLEN], *chptr;
+ auto timeUnit = output_env_get_time_unit(oenv);
if (bSetTime)
{
fprintf(stderr, "\n\nEnter the new start time (%s) for each file.\n"
"same amount as in the previous. Use it when the time in the\n"
"new run continues from the end of the previous one,\n"
"since this takes possible overlap into account.\n\n",
- output_env_get_time_unit(oenv));
+ timeUnit.c_str());
fprintf(
stderr,
" File Current start (%s) New start (%s)\n"
"---------------------------------------------------------\n",
- output_env_get_time_unit(oenv), output_env_get_time_unit(oenv));
+ timeUnit.c_str(), timeUnit.c_str());
for (i = 0; i < nfiles; i++)
{
fprintf(stderr, "%25s %10.3f %s ", fnms[i],
- output_env_conv_time(oenv, readtime[i]), output_env_get_time_unit(oenv));
+ output_env_conv_time(oenv, readtime[i]), timeUnit.c_str());
ok = FALSE;
do
{
- if (NULL == fgets(inputstring, STRLEN - 1, stdin))
+ if (nullptr == fgets(inputstring, STRLEN - 1, stdin))
{
gmx_fatal(FARGS, "Error reading user input" );
}
case TIME_EXPLICIT:
fprintf(stderr, "%25s %10.3f %s %10.3f %s",
fnms[i],
- output_env_conv_time(oenv, settime[i]), output_env_get_time_unit(oenv),
- output_env_conv_time(oenv, timestep[i]), output_env_get_time_unit(oenv));
+ output_env_conv_time(oenv, settime[i]), timeUnit.c_str(),
+ output_env_conv_time(oenv, timestep[i]), timeUnit.c_str());
if (i > 0 &&
cont_type[i-1] == TIME_EXPLICIT && settime[i] == settime[i-1])
{
{
if (index)
{
- write_trxframe_indexed(fp_out[j], &trx[i], isize, index, NULL);
+ write_trxframe_indexed(fp_out[j], &trx[i], isize, index, nullptr);
}
else
{
- write_trxframe(fp_out[j], &trx[i], NULL);
+ write_trxframe(fp_out[j], &trx[i], nullptr);
}
}
}
"the trajectory does not match that in the [REF].xvg[ref] file then the program",
"tries to be smart. Beware."
};
- static gmx_bool bVels = TRUE;
static gmx_bool bCat = FALSE;
static gmx_bool bSort = TRUE;
static gmx_bool bKeepLast = FALSE;
{ &end }, "Last time to use (%t)" },
{ "-dt", FALSE, etTIME,
{ &dt }, "Only write frame when t MOD dt = first time (%t)" },
- { "-vel", FALSE, etBOOL,
- { &bVels }, "Read and write velocities if possible" },
{ "-settime", FALSE, etBOOL,
{ &bSetTime }, "Change starting time interactively" },
{ "-sort", FALSE, etBOOL,
};
#define npargs asize(pa)
int ftpin, i, frame, frame_out;
- t_trxstatus *status, *trxout = NULL;
+ t_trxstatus *status, *trxout = nullptr;
real t_corr;
t_trxframe fr, frout;
char **fnms, **fnms_out, *out_file;
gmx_bool lastTimeSet = FALSE;
real last_frame_time, searchtime;
int isize = 0, j;
- int *index = NULL, imax;
+ int *index = nullptr, imax;
char *grpname;
- real **val = NULL, *t = NULL, dt_remd;
+ real **val = nullptr, *t = nullptr, dt_remd;
int n, nset, ftpout = -1, prevEndStep = 0, filetype;
gmx_off_t fpos;
gmx_output_env_t *oenv;
t_filenm fnm[] =
{
- { efTRX, "-f", NULL, ffRDMULT },
- { efTRO, "-o", NULL, ffWRMULT },
+ { efTRX, "-f", nullptr, ffRDMULT },
+ { efTRO, "-o", nullptr, ffWRMULT },
{ efNDX, "-n", "index", ffOPTRD },
{ efXVG, "-demux", "remd", ffOPTRD }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
- asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
+ auto timeUnit = output_env_get_time_unit(oenv);
bIndex = ftp2bSet(efNDX, NFILE, fnm);
bDeMux = ftp2bSet(efXVG, NFILE, fnm);
}
if (bIndex)
{
- trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
- fnms[0], isize, NULL, index, grpname);
+ trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr, &trxout,
+ fnms[0], isize, nullptr, index, grpname);
}
else
{
- trjtools_gmx_prepare_tng_writing(out_file, 'w', NULL, &trxout,
- fnms[0], -1, NULL, NULL, NULL);
+ trjtools_gmx_prepare_tng_writing(out_file, 'w', nullptr, &trxout,
+ fnms[0], -1, nullptr, nullptr, nullptr);
}
}
else
}
lastTimeSet = TRUE;
bKeepLastAppend = TRUE;
- close_trj(status);
+ close_trx(status);
trxout = open_trx(out_file, "a");
}
else if (bOverwrite)
lasttime = fr.time;
lastTimeSet = TRUE;
fpos = gmx_fio_ftell(stfio);
- close_trj(status);
+ close_trx(status);
trxout = open_trx(out_file, "r+");
if (gmx_fio_seek(trx_get_fileio(trxout), fpos))
{
"spacing than the rest,\n"
"might be a gap or overlap that couldn't be corrected "
"automatically.\n", output_env_conv_time(oenv, frout.time),
- output_env_get_time_unit(oenv));
+ timeUnit.c_str());
}
}
}
{
fprintf(stderr, "\nContinue writing frames from %s t=%g %s, "
"frame=%d \n",
- fnms[i], output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv),
+ fnms[i], output_env_conv_time(oenv, frout.time), timeUnit.c_str(),
frame);
bNewFile = FALSE;
}
if (bIndex)
{
write_trxframe_indexed(trxout, &frout, isize, index,
- NULL);
+ nullptr);
}
else
{
- write_trxframe(trxout, &frout, NULL);
+ write_trxframe(trxout, &frout, nullptr);
}
if ( ((frame % 10) == 0) || (frame < 10) )
{
fprintf(stderr, " -> frame %6d time %8.3f %s \r",
- frame_out, output_env_conv_time(oenv, frout.time), output_env_get_time_unit(oenv));
+ frame_out, output_env_conv_time(oenv, frout.time), timeUnit.c_str());
fflush(stderr);
}
}
}
while (read_next_frame(oenv, status, &fr));
- close_trj(status);
+ close_trx(status);
}
if (trxout)
{
close_trx(trxout);
}
fprintf(stderr, "\nLast frame written was %d, time %f %s\n",
- frame, output_env_conv_time(oenv, last_ok_t), output_env_get_time_unit(oenv));
+ frame, output_env_conv_time(oenv, last_ok_t), timeUnit.c_str());
}
return 0;
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/groio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/trxio.h"
std::strcat(out_file, ext);
}
-void check_trr(const char *fn)
+static void check_trr(const char *fn)
{
if (fn2ftp(fn) != efTRR)
{
}
}
-void do_trunc(const char *fn, real t0)
+static void do_trunc(const char *fn, real t0)
{
t_fileio *in;
FILE *fp;
in = gmx_trr_open(fn, "r");
fp = gmx_fio_getfp(in);
- if (fp == NULL)
+ if (fp == nullptr)
{
fprintf(stderr, "Sorry, can not trunc %s, truncation of this filetype is not supported\n", fn);
gmx_trr_close(in);
bStop = FALSE;
while (!bStop && gmx_trr_read_frame_header(in, &sh, &bOK))
{
- gmx_trr_read_frame_data(in, &sh, NULL, NULL, NULL, NULL);
+ gmx_trr_read_frame_data(in, &sh, nullptr, nullptr, nullptr, nullptr);
fpos = gmx_ftell(fp);
t = sh.t;
if (t >= t0)
const char *input_file,
const char *output_file)
{
- gmx_mtop_t *mtop = NULL;
+ gmx_mtop_t *mtop = nullptr;
if (fn2bTPX(tps_file) &&
efTNG != fn2ftp(input_file) &&
{
int temp_natoms = -1;
snew(mtop, 1);
- read_tpx(tps_file, NULL, NULL, &temp_natoms,
- NULL, NULL, mtop);
+ read_tpx(tps_file, nullptr, nullptr, &temp_natoms,
+ nullptr, nullptr, mtop);
}
return mtop;
};
const char *pbc_opt[epNR + 1] =
{
- NULL, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
- NULL
+ nullptr, "none", "mol", "res", "atom", "nojump", "cluster", "whole",
+ nullptr
};
int unitcell_enum;
const char *unitcell_opt[euNR+1] =
- { NULL, "rect", "tric", "compact", NULL };
+ { nullptr, "rect", "tric", "compact", nullptr };
enum
{
ecSel, ecTric, ecRect, ecZero, ecNR
};
const char *center_opt[ecNR+1] =
- { NULL, "tric", "rect", "zero", NULL };
+ { nullptr, "tric", "rect", "zero", nullptr };
int ecenter;
int fit_enum;
};
const char *fit[efNR + 1] =
{
- NULL, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
- "progressive", NULL
+ nullptr, "none", "rot+trans", "rotxy+transxy", "translation", "transxy",
+ "progressive", nullptr
};
static gmx_bool bSeparate = FALSE, bVels = TRUE, bForce = FALSE, bCONECT = FALSE;
static int skip_nr = 1, ndec = 3, nzero = 0;
static real tzero = 0, delta_t = 0, timestep = 0, ttrunc = -1, tdump = -1, split_t = 0;
static rvec newbox = {0, 0, 0}, shift = {0, 0, 0}, trans = {0, 0, 0};
- static char *exec_command = NULL;
+ static char *exec_command = nullptr;
static real dropunder = 0, dropover = 0;
static gmx_bool bRound = FALSE;
};
#define NPA asize(pa)
- FILE *out = NULL;
- t_trxstatus *trxout = NULL;
+ FILE *out = nullptr;
+ t_trxstatus *trxout = nullptr;
t_trxstatus *trxin;
int file_nr;
t_trxframe fr, frout;
int flags;
- rvec *xmem = NULL, *vmem = NULL, *fmem = NULL;
- rvec *xp = NULL, x_shift, hbox;
- real *w_rls = NULL;
+ rvec *xmem = nullptr, *vmem = nullptr, *fmem = nullptr;
+ rvec *xp = nullptr, x_shift, hbox;
+ real *w_rls = nullptr;
int m, i, d, frame, outframe, natoms, nout, ncent, newstep = 0, model_nr;
#define SKIP 10
t_topology top;
- gmx_mtop_t *mtop = NULL;
- gmx_conect gc = NULL;
+ gmx_mtop_t *mtop = nullptr;
+ gmx_conect gc = nullptr;
int ePBC = -1;
- t_atoms *atoms = NULL, useatoms;
+ t_atoms *atoms = nullptr, useatoms;
matrix top_box;
- int *index, *cindex;
- char *grpnm;
+ int *index = nullptr, *cindex = nullptr;
+ char *grpnm = nullptr;
int *frindex, nrfri;
char *frname;
int ifit, my_clust = -1;
int *ind_fit;
char *gn_fit;
- t_cluster_ndx *clust = NULL;
- t_trxstatus **clust_status = NULL;
- int *clust_status_id = NULL;
+ t_cluster_ndx *clust = nullptr;
+ t_trxstatus **clust_status = nullptr;
+ int *clust_status_id = nullptr;
int ntrxopen = 0;
- int *nfwritten = NULL;
+ int *nfwritten = nullptr;
int ndrop = 0, ncol, drop0 = 0, drop1 = 0, dropuse = 0;
double **dropval;
real tshift = 0, t0 = -1, dt = 0.001, prec;
gmx_bool bFit, bPFit, bReset;
int nfitdim;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
gmx_bool bRmPBC, bPBCWhole, bPBCcomRes, bPBCcomMol, bPBCcomAtom, bPBC, bNoJump, bCluster;
gmx_bool bCopy, bDoIt, bIndex, bTDump, bSetTime, bTPS = FALSE, bDTset = FALSE;
gmx_bool bExec, bTimeStep = FALSE, bDumpFrame = FALSE, bSetPrec, bNeedPrec;
gmx_bool bHaveFirstFrame, bHaveNextFrame, bSetBox, bSetUR, bSplit = FALSE;
gmx_bool bSubTraj = FALSE, bDropUnder = FALSE, bDropOver = FALSE, bTrans = FALSE;
gmx_bool bWriteFrame, bSplitHere;
- const char *top_file, *in_file, *out_file = NULL;
+ const char *top_file, *in_file, *out_file = nullptr;
char out_file2[256], *charpt;
- char *outf_base = NULL;
- const char *outf_ext = NULL;
+ char *outf_base = nullptr;
+ const char *outf_ext = nullptr;
char top_title[256], title[256], filemode[5];
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTRO, "-o", NULL, ffWRITE },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTRO, "-o", nullptr, ffWRITE },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efNDX, "-fr", "frames", ffOPTRD },
{ efNDX, "-sub", "cluster", ffOPTRD },
{ efXVG, "-drop", "drop", ffOPTRD }
PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW |
PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc,
- 0, NULL, &oenv))
+ 0, nullptr, &oenv))
{
return 0;
}
top_file = ftp2fn(efTPS, NFILE, fnm);
- init_top(&top);
/* Check command line */
in_file = opt2fn("-f", NFILE, fnm);
if (bSeparate || bSplit)
{
outf_ext = std::strrchr(out_file, '.');
- if (outf_ext == NULL)
+ if (outf_ext == nullptr)
{
gmx_fatal(FARGS, "Output file name '%s' does not contain a '.'", out_file);
}
gmx_fatal(FARGS, "Can only use the sub option with output file types "
"xtc and trr");
}
- clust = cluster_index(NULL, opt2fn("-sub", NFILE, fnm));
+ clust = cluster_index(nullptr, opt2fn("-sub", NFILE, fnm));
/* Check for number of files disabled, as FOPEN_MAX is not the correct
* number to check for. In my linux box it is only 16.
snew(nfwritten, clust->clust->nr);
for (i = 0; (i < clust->clust->nr); i++)
{
- clust_status[i] = NULL;
+ clust_status[i] = nullptr;
clust_status_id[i] = -1;
}
bSeparate = bSplit = FALSE;
if (bTPS)
{
- read_tps_conf(top_file, &top, &ePBC, &xp, NULL, top_box,
+ read_tps_conf(top_file, &top, &ePBC, &xp, nullptr, top_box,
bReset || bPBCcomRes);
std::strncpy(top_title, *top.name, 255);
top_title[255] = '\0';
}
/* get frame number index */
- frindex = NULL;
+ frindex = nullptr;
if (opt2bSet("-fr", NFILE, fnm))
{
printf("Select groups of frame number indices:\n");
gmx_fatal(FARGS, "Could not read a frame from %s", in_file);
}
natoms = fr.natoms;
- close_trj(trxin);
+ close_trx(trxin);
sfree(fr.x);
snew(index, natoms);
for (i = 0; i < natoms; i++)
gmx_rmpbc(gpbc, top.atoms.nr, top_box, xp);
}
copy_rvec(xp[index[0]], x_shift);
- reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, NULL, xp, w_rls);
+ reset_x_ndim(nfitdim, ifit, ind_fit, atoms->nr, nullptr, xp, w_rls);
rvec_dec(x_shift, xp[index[0]]);
}
else
/* get memory for stuff to go in .pdb file, and initialize
* the pdbinfo structure part if the input has it.
*/
- init_t_atoms(&useatoms, atoms->nr, (atoms->pdbinfo != NULL));
+ init_t_atoms(&useatoms, atoms->nr, atoms->havePdbInfo);
sfree(useatoms.resinfo);
useatoms.resinfo = atoms->resinfo;
for (i = 0; (i < nout); i++)
{
useatoms.atomname[i] = atoms->atomname[index[i]];
useatoms.atom[i] = atoms->atom[index[i]];
- if (atoms->pdbinfo != NULL)
+ if (atoms->havePdbInfo)
{
useatoms.pdbinfo[i] = atoms->pdbinfo[index[i]];
}
filemode[0],
trxin,
&trxout,
- NULL,
+ nullptr,
nout,
mtop,
index,
break;
case efXTC:
case efTRR:
- out = NULL;
+ out = nullptr;
if (!bSplit && !bSubTraj)
{
trxout = open_trx(out_file, filemode);
gmx_rmpbc_trxfr(gpbc, &fr);
}
- reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
+ reset_x_ndim(nfitdim, ifit, ind_fit, natoms, nullptr, fr.x, w_rls);
do_fit(natoms, w_rls, xp, fr.x);
}
/* store this set of coordinates for future use */
if (bPFit || bNoJump)
{
- if (xp == NULL)
+ if (xp == nullptr)
{
snew(xp, natoms);
}
if (bTDump)
{
fprintf(stderr, "\nDumping frame at t= %g %s\n",
- output_env_conv_time(oenv, frout_time), output_env_get_time_unit(oenv));
+ output_env_conv_time(oenv, frout_time), output_env_get_time_unit(oenv).c_str());
}
/* check for writing at each delta_t */
if (bReset)
{
- reset_x_ndim(nfitdim, ifit, ind_fit, natoms, NULL, fr.x, w_rls);
+ reset_x_ndim(nfitdim, ifit, ind_fit, natoms, nullptr, fr.x, w_rls);
if (bFit)
{
do_fit_ndim(nfitdim, natoms, w_rls, xp, fr.x);
clust->clust->index[my_clust]))
{
close_trx(clust_status[my_clust]);
- clust_status[my_clust] = NULL;
+ clust_status[my_clust] = nullptr;
clust_status_id[my_clust] = -2;
ntrxopen--;
if (ntrxopen < 0)
{
case efGRO:
write_hconf_p(out, title, &useatoms,
- frout.x, frout.bV ? frout.v : NULL, frout.box);
+ frout.x, frout.bV ? frout.v : nullptr, frout.box);
break;
case efPDB:
fprintf(out, "REMARK GENERATED BY TRJCONV\n");
frout.ePBC, frout.box, ' ', model_nr, gc, TRUE);
break;
case efG96:
- frout.title = title;
+ const char *outputTitle = "";
if (bSeparate || bTDump)
{
- frout.bTitle = TRUE;
+ outputTitle = title;
if (bTPS)
{
frout.bAtoms = TRUE;
}
else
{
- frout.bTitle = (outframe == 0);
+ if (outframe == 0)
+ {
+ outputTitle = title;
+ }
frout.bAtoms = FALSE;
frout.bStep = TRUE;
frout.bTime = TRUE;
}
- write_g96_conf(out, &frout, -1, NULL);
+ write_g96_conf(out, outputTitle, &frout, -1, nullptr);
}
if (bSeparate || bSplitHere)
{
gmx_ffclose(out);
- out = NULL;
+ out = nullptr;
}
break;
default:
}
fprintf(stderr, "\n");
- close_trj(trxin);
+ close_trx(trxin);
sfree(outf_base);
if (bRmPBC)
{
close_trx(trxout);
}
- else if (out != NULL)
+ else if (out != nullptr)
{
gmx_ffclose(out);
}
}
sfree(mtop);
-
- do_view(oenv, out_file, NULL);
-
+ done_top(&top);
+ sfree(xp);
+ sfree(xmem);
+ sfree(vmem);
+ sfree(fmem);
+ sfree(grpnm);
+ sfree(index);
+ sfree(cindex);
+ done_filenms(NFILE, fnm);
+ done_frame(&fr);
+
+ do_view(oenv, out_file, nullptr);
+
+ output_env_done(oenv);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int natoms, nwat, ncut;
char **grpname;
int i, j, d, *isize, isize_ref = 0, isize_sol;
- int sa, sr, *swi, **index, *ind_ref = NULL, *ind_sol;
+ int sa, sr, *swi, **index, *ind_ref = nullptr, *ind_sol;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efTRO, "-o", "ordered", ffOPTWR },
{ efXVG, "-nshell", "nshell", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, NULL, box, TRUE);
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &x, nullptr, box, TRUE);
sfree(x);
/* get index groups */
swi[i] = i;
}
- out = NULL;
- fp = NULL;
+ out = nullptr;
+ fp = nullptr;
bNShell = ((opt2bSet("-nshell", NFILE, fnm)) ||
(opt2parg_bSet("-r", asize(pa), pa)));
bPDBout = FALSE;
}
}
}
- write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, NULL, NULL);
+ write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, nullptr, nullptr);
}
}
while (read_next_x(oenv, status, &t, x, box));
- close_trj(status);
+ close_trx(status);
if (out)
{
close_trx(out);
#endif
#include "gromacs/commandline/pargs.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fft/calcgrid.h"
#include "gromacs/fileio/checkpoint.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/math/utilities.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
/* Enum for situations that can occur during log file parsing, the
* corresponding string entries can be found in do_the_tests() in
fp = fopen(fn_out, "r");
fprintf(stdout, "\n\n");
- while (fgets(buf, STRLEN-1, fp) != NULL)
+ while (fgets(buf, STRLEN-1, fp) != nullptr)
{
fprintf(stdout, "%s", buf);
}
iFound = eFoundDDStr; /* Skip some case statements */
}
- while (fgets(line, STRLEN, fp) != NULL)
+ while (fgets(line, STRLEN, fp) != nullptr)
{
/* Remove leading spaces */
ltrim(line);
/* Check for TERM and INT signals from user: */
- if (std::strstr(line, errSIG) != NULL)
+ if (std::strstr(line, errSIG) != nullptr)
{
fclose(fp);
cleandata(perfdata, test_nr);
/* Check whether cycle resetting worked */
if (presteps > 0 && !bFoundResetStr)
{
- if (std::strstr(line, matchstrcr) != NULL)
+ if (std::strstr(line, matchstrcr) != nullptr)
{
sprintf(dumstring, "step %s", "%" GMX_SCNd64);
sscanf(line, dumstring, &resetsteps);
if (gmx_fexist(errfile))
{
fp = fopen(errfile, "r");
- while (fgets(line, STRLEN, fp) != NULL)
+ while (fgets(line, STRLEN, fp) != nullptr)
{
if (str_starts(line, "Fatal error:") )
{
- if (fgets(line, STRLEN, fp) != NULL)
+ if (fgets(line, STRLEN, fp) != nullptr)
{
fprintf(stderr, "\nWARNING: An error occurred during this benchmark:\n"
"%s\n", line);
/* Get the commands we need to set up the runs from environment variables */
if (!bThreads)
{
- if ( (cp = getenv("MPIRUN")) != NULL)
+ if ( (cp = getenv("MPIRUN")) != nullptr)
{
*cmd_mpirun = gmx_strdup(cp);
}
*cmd_mpirun = gmx_strdup(empty_mpirun);
}
- if (*cmd_mdrun == NULL)
+ if (*cmd_mdrun == nullptr)
{
/* The use of MDRUN is deprecated, but made available in 5.1
for backward compatibility. It may be removed in a future
version. */
- if ( (cp = getenv("MDRUN" )) != NULL)
+ if ( (cp = getenv("MDRUN" )) != nullptr)
{
*cmd_mdrun = gmx_strdup(cp);
}
const char *cmd_mdrun,
gmx_bool bNeedGpuSupport)
{
- char *command = NULL;
+ char *command = nullptr;
char *cp;
char line[STRLEN];
FILE *fp;
while (!feof(fp) )
{
cp = fgets(line, STRLEN, fp);
- if (cp != NULL)
+ if (cp != nullptr)
{
if (str_starts(line, match_mdrun) )
{
sfree(command);
}
-/*! \brief Helper struct so we can parse the string with eligible GPU
- IDs outside do_the_tests. */
-typedef struct eligible_gpu_ids
-{
- int n; /**< Length of ids */
- int *ids; /**< Array of length n. NULL if no GPUs in use */
-} t_eligible_gpu_ids;
-
/* Handles the no-GPU case by emitting an empty string. */
-static char *make_gpu_id_command_line(int numRanks, int numPmeRanks, const t_eligible_gpu_ids *gpu_ids)
+static char *make_gpu_id_command_line(int numRanks, int numPmeRanks, const std::vector<int> &gpu_ids)
{
char *command_line, *ptr;
const char *flag = "-gpu_id ";
/* If the user has given no eligible GPU IDs, or we're trying the
* default behaviour, then there is nothing for g_tune_pme to give
* to mdrun -gpu_id */
- if (gpu_ids->n > 0 && numPmeRanks > -1)
+ if (!gpu_ids.empty() && numPmeRanks > -1)
{
- int numPpRanks, max_num_ranks_for_each_GPU;
- int gpu_id, rank;
+ size_t numPpRanks, max_num_ranks_for_each_GPU;
/* Write the option flag */
std::strcpy(ptr, flag);
ptr += flag_length;
numPpRanks = numRanks - numPmeRanks;
- max_num_ranks_for_each_GPU = numPpRanks / gpu_ids->n;
- if (max_num_ranks_for_each_GPU * gpu_ids->n != numPpRanks)
+ max_num_ranks_for_each_GPU = numPpRanks / gpu_ids.size();
+ if (max_num_ranks_for_each_GPU * gpu_ids.size() != numPpRanks)
{
/* Some GPUs will receive more work than others, which
* we choose to be those with the lowest indices */
}
/* Loop over all eligible GPU ids */
- for (gpu_id = 0, rank = 0; gpu_id < gpu_ids->n; gpu_id++)
+ for (size_t gpu_id = 0, rank = 0; gpu_id < gpu_ids.size(); gpu_id++)
{
- int rank_for_this_GPU;
+ size_t rank_for_this_GPU;
/* Loop over all PP ranks for GPU with ID gpu_id, building the
assignment string. */
for (rank_for_this_GPU = 0;
rank_for_this_GPU < max_num_ranks_for_each_GPU && rank < numPpRanks;
rank++, rank_for_this_GPU++)
{
- *ptr = '0' + gpu_ids->ids[gpu_id];
+ *ptr = '0' + gpu_ids[gpu_id];
ptr++;
}
}
const char *simulation_tpr, /* This tpr will be simulated */
int nnodes, /* Number of ranks to use */
int nPMEnodes, /* Number of PME ranks to use */
- const t_eligible_gpu_ids *gpu_ids) /* Struct containing GPU IDs for
+ const std::vector<int> &gpu_ids) /* Vector of GPU IDs for
* constructing mdrun command lines */
{
char *command, *cmd_gpu_ids;
const char *fn_best_tpr, /* tpr file with the best performance */
const char *fn_sim_tpr) /* name of tpr file to be launched */
{
- t_inputrec *ir;
- t_state state;
- gmx_mtop_t mtop;
- char buf[200];
+ t_state state;
+ gmx_mtop_t mtop;
+ char buf[200];
- snew(ir, 1);
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
read_tpx_state(fn_best_tpr, ir, &state, &mtop);
/* Reset nsteps and init_step to the value of the input .tpr file */
fprintf(stdout, buf, ir->nsteps);
fflush(stdout);
write_tpx_state(fn_sim_tpr, ir, &state, &mtop);
-
- sfree(ir);
}
static gmx_bool can_scale_rvdw(int vdwtype)
FILE *fp) /* Write the output here */
{
int i, j, d;
- t_inputrec *ir;
t_state state;
gmx_mtop_t mtop;
real nlist_buffer; /* Thickness of the buffer regions for PME-switch potentials */
}
fprintf(stdout, ".\n");
-
- snew(ir, 1);
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
read_tpx_state(fn_sim_tpr, ir, &state, &mtop);
/* Check if some kind of PME was chosen */
/* Scale the Fourier grid spacing */
ir->nkx = ir->nky = ir->nkz = 0;
- calc_grid(NULL, state.box, fourierspacing*fac, &ir->nkx, &ir->nky, &ir->nkz);
+ calcFftGrid(nullptr, state.box, fourierspacing*fac, minimalPmeGridSize(ir->pme_order),
+ &ir->nkx, &ir->nky, &ir->nkz);
/* Adjust other radii since various conditions need to be fulfilled */
if (eelPME == ir->coulombtype)
}
fflush(stdout);
fflush(fp);
- sfree(ir);
}
{
char numstring[STRLEN];
char newfilename[STRLEN];
- const char *fn = NULL;
+ const char *fn = nullptr;
int i;
const char *opt;
int presteps, /* DLB equilibration steps, is checked */
gmx_int64_t cpt_steps, /* Time step counter in the checkpoint */
gmx_bool bCheck, /* Check whether benchmark mdrun works */
- const t_eligible_gpu_ids *gpu_ids) /* Struct containing GPU IDs for
+ const std::vector<int> &gpu_ids) /* Vector of GPU IDs for
* constructing mdrun command lines */
{
int i, nr, k, ret, count = 0, totaltests;
- int *nPMEnodes = NULL;
- t_perf *pd = NULL;
+ int *nPMEnodes = nullptr;
+ t_perf *pd = nullptr;
int cmdline_length;
char *command, *cmd_stub;
char buf[STRLEN];
/* Loop over various numbers of PME nodes: */
for (i = 0; i < *pmeentries; i++)
{
- char *cmd_gpu_ids = NULL;
+ char *cmd_gpu_ids = nullptr;
pd = &perfdata[k][i];
gmx_bool bFree; /* Is a free energy simulation requested? */
gmx_bool bNM; /* Is a normal mode analysis requested? */
gmx_bool bSwap; /* Is water/ion position swapping requested? */
- t_inputrec ir;
t_state state;
gmx_mtop_t mtop;
/* Check tpr file for options that trigger extra output files */
- read_tpx_state(opt2fn("-s", nfile, fnm), &ir, &state, &mtop);
- bFree = (efepNO != ir.efep );
- bNM = (eiNM == ir.eI );
- bSwap = (eswapNO != ir.eSwapCoords);
- bTpi = EI_TPI(ir.eI);
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
+ read_tpx_state(opt2fn("-s", nfile, fnm), ir, &state, &mtop);
+ bFree = (efepNO != ir->efep );
+ bNM = (eiNM == ir->eI );
+ bSwap = (eswapNO != ir->eSwapCoords);
+ bTpi = EI_TPI(ir->eI);
/* Set these output files on the tuning command-line */
- if (ir.bPull)
+ if (ir->bPull)
{
setopt("-pf", nfile, fnm);
setopt("-px", nfile, fnm);
setopt("-swap", nfile, fnm);
}
- *rcoulomb = ir.rcoulomb;
+ *rcoulomb = ir->rcoulomb;
/* Return the estimate for the number of PME nodes */
- return pme_load_estimate(&mtop, &ir, state.box);
+ float npme = pme_load_estimate(&mtop, ir, state.box);
+ return npme;
}
int presteps = 1500; /* Do a full cycle reset after presteps steps */
gmx_bool bOverwrite = FALSE, bKeepTPR;
gmx_bool bLaunch = FALSE;
- char *ExtraArgs = NULL;
- char **tpr_names = NULL;
- const char *simulation_tpr = NULL;
- char *deffnm = NULL;
+ char *ExtraArgs = nullptr;
+ char **tpr_names = nullptr;
+ const char *simulation_tpr = nullptr;
+ char *deffnm = nullptr;
int best_npme, best_tpr;
int sim_part = 1; /* For benchmarks with checkpoint files */
char bbuf[STRLEN];
/* Default program names if nothing else is found */
- char *cmd_mpirun = NULL, *cmd_mdrun = NULL;
+ char *cmd_mpirun = nullptr, *cmd_mdrun = nullptr;
char *cmd_args_bench, *cmd_args_launch;
- char *cmd_np = NULL;
+ char *cmd_np = nullptr;
/* IDs of GPUs that are eligible for computation */
- char *eligible_gpu_ids = NULL;
- t_eligible_gpu_ids *gpu_ids = NULL;
+ char *eligible_gpu_ids = nullptr;
- t_perf **perfdata = NULL;
+ t_perf **perfdata = nullptr;
t_inputinfo *info;
int i;
FILE *fp;
{ efLOG, "-err", "bencherr", ffWRITE },
{ efTPR, "-so", "tuned", ffWRITE },
/* mdrun: */
- { efTPR, NULL, NULL, ffREAD },
- { efTRN, "-o", NULL, ffWRITE },
- { efCOMPRESSED, "-x", NULL, ffOPTWR },
- { efCPT, "-cpi", NULL, ffOPTRD },
- { efCPT, "-cpo", NULL, ffOPTWR },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efTRN, "-o", nullptr, ffWRITE },
+ { efCOMPRESSED, "-x", nullptr, ffOPTWR },
+ { efCPT, "-cpi", nullptr, ffOPTRD },
+ { efCPT, "-cpo", nullptr, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
int nthreads = 1;
const char *procstring[] =
- { NULL, "np", "n", "none", NULL };
+ { nullptr, "np", "n", "none", nullptr };
const char *npmevalues_opt[] =
- { NULL, "auto", "all", "subset", NULL };
+ { nullptr, "auto", "all", "subset", nullptr };
gmx_bool bAppendFiles = TRUE;
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bBenchmark = TRUE;
gmx_bool bCheck = TRUE;
- gmx_output_env_t *oenv = NULL;
+ gmx_output_env_t *oenv = nullptr;
t_pargs pa[] = {
/***********************/
if (!parse_common_args(&argc, argv, PCA_NOEXIT_ON_ARGS,
NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv))
+ 0, nullptr, &oenv))
{
return 0;
}
// procstring[0] is used inside two different conditionals further down
- GMX_RELEASE_ASSERT(procstring[0] != NULL, "Options inconsistency; procstring[0] is NULL");
+ GMX_RELEASE_ASSERT(procstring[0] != nullptr, "Options inconsistency; procstring[0] is NULL");
/* Store the remaining unparsed command line entries in a string which
* is then attached to the mdrun command line */
bench_nsteps, fnm, NFILE, sim_part, presteps,
asize(pa), pa);
/* Check any GPU IDs passed make sense, and fill the data structure for them */
- snew(gpu_ids, 1);
- parse_digits_from_string(eligible_gpu_ids, &gpu_ids->n, &gpu_ids->ids);
+ auto gpu_ids = gmx::parseDigitsFromString(eligible_gpu_ids);
/* Determine the maximum and minimum number of PME nodes to test,
* the actual list of settings is build in do_the_tests(). */
get_program_paths(bThreads, &cmd_mpirun, &cmd_mdrun);
if (bBenchmark && repeats > 0)
{
- check_mdrun_works(bThreads, cmd_mpirun, cmd_np, cmd_mdrun, NULL != eligible_gpu_ids);
+ check_mdrun_works(bThreads, cmd_mpirun, cmd_np, cmd_mdrun, nullptr != eligible_gpu_ids);
}
/* Print some header info to file */
snew(perfdata, ntprs);
if (bBenchmark)
{
- GMX_RELEASE_ASSERT(npmevalues_opt[0] != NULL, "Options inconsistency; npmevalues_opt[0] is NULL");
+ GMX_RELEASE_ASSERT(npmevalues_opt[0] != nullptr, "Options inconsistency; npmevalues_opt[0] is NULL");
do_the_tests(fp, tpr_names, maxPMEnodes, minPMEnodes, npme_fixed, npmevalues_opt[0], perfdata, &pmeentries,
repeats, nnodes, ntprs, bThreads, cmd_mpirun, cmd_np, cmd_mdrun,
cmd_args_bench, fnm, NFILE, presteps, cpt_steps, bCheck, gpu_ids);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define NPA asize(pa)
t_filenm fnm[] = {
- { efTRX, NULL, NULL, ffREAD },
- { efTPS, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRX, nullptr, nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXPM, "-om", "vanhove", ffOPTWR },
{ efXVG, "-or", "vanhove_r", ffOPTWR },
{ efXVG, "-ot", "vanhove_t", ffOPTWR }
real *time, t, invbin = 0, rmax2 = 0, rint2 = 0, d2;
real invsbin = 0, matmax, normfac, dt, *tickx, *ticky;
char buf[STRLEN], **legend;
- real **mat = NULL;
- int *pt = NULL, **pr = NULL, *mcount = NULL, *tcount = NULL, *rcount = NULL;
+ real **mat = nullptr;
+ int *pt = nullptr, **pr = nullptr, *mcount = nullptr, *tcount = nullptr, *rcount = nullptr;
FILE *fp;
t_rgb rlo = {1, 1, 1}, rhi = {0, 0, 0};
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
exit(0);
}
- read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, NULL, boxtop,
+ read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, boxtop,
FALSE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
nalloc = 0;
- time = NULL;
- sbox = NULL;
- sx = NULL;
+ time = nullptr;
+ sbox = nullptr;
+ sx = nullptr;
clear_mat(avbox);
read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
srenew(sbox, nalloc);
srenew(sx, nalloc);
}
- GMX_RELEASE_ASSERT(time != NULL, "Memory allocation failure; time array is NULL");
- GMX_RELEASE_ASSERT(sbox != NULL, "Memory allocation failure; sbox array is NULL");
+ GMX_RELEASE_ASSERT(time != nullptr, "Memory allocation failure; time array is NULL");
+ GMX_RELEASE_ASSERT(sbox != nullptr, "Memory allocation failure; sbox array is NULL");
time[nfr] = t;
copy_mat(box, sbox[nfr]);
/* clean up */
sfree(x);
- close_trj(status);
+ close_trx(status);
fprintf(stderr, "Read %d frames\n", nfr);
xvgrclose(fp);
}
- do_view(oenv, matfile, NULL);
- do_view(oenv, orfile, NULL);
- do_view(oenv, otfile, NULL);
+ do_view(oenv, matfile, nullptr);
+ do_view(oenv, orfile, nullptr);
+ do_view(oenv, otfile, nullptr);
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
rvec mv_mol;
/* Array for the correlation function */
real **c1;
- real *normm = NULL;
+ real *normm = nullptr;
gmx_output_env_t *oenv;
#define NHISTO 360
t_filenm fnm[] = {
- { efTRN, "-f", NULL, ffREAD },
- { efTPS, NULL, NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTRN, "-f", nullptr, ffREAD },
+ { efTPS, nullptr, nullptr, ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efXVG, "-o", "vac", ffWRITE },
{ efXVG, "-os", "spectrum", ffOPTWR }
};
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(ppa);
return 0;
}
if (bTPS)
{
- bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, NULL, NULL, box,
+ bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, nullptr, nullptr, box,
TRUE);
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
}
snew(c1, gnx);
for (i = 0; (i < gnx); i++)
{
- c1[i] = NULL;
+ c1[i] = nullptr;
}
read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_V);
}
while (read_next_frame(oenv, status, &fr));
- close_trj(status);
+ close_trx(status);
if (counter >= 4)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <cassert>
#include <cctype>
#include <cmath>
#include <cstdio>
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/random/tabulatednormaldistribution.h"
#include "gromacs/random/threefry.h"
} t_UmbrellaOptions;
//! Make an umbrella window (may contain several histograms)
-t_UmbrellaWindow * initUmbrellaWindows(int nwin)
+static t_UmbrellaWindow * initUmbrellaWindows(int nwin)
{
t_UmbrellaWindow *win;
int i;
snew(win, nwin);
for (i = 0; i < nwin; i++)
{
- win[i].Histo = win[i].cum = 0;
- win[i].k = win[i].pos = win[i].z = 0;
- win[i].N = win[i].Ntot = 0;
- win[i].g = win[i].tau = win[i].tausmooth = 0;
- win[i].bContrib = 0;
- win[i].ztime = 0;
- win[i].forceAv = 0;
- win[i].aver = win[i].sigma = 0;
- win[i].bsWeight = 0;
+ win[i].Histo = win[i].cum = nullptr;
+ win[i].k = win[i].pos = win[i].z = nullptr;
+ win[i].N = win[i].Ntot = nullptr;
+ win[i].g = win[i].tau = win[i].tausmooth = nullptr;
+ win[i].bContrib = nullptr;
+ win[i].ztime = nullptr;
+ win[i].forceAv = nullptr;
+ win[i].aver = win[i].sigma = nullptr;
+ win[i].bsWeight = nullptr;
}
return win;
}
//! Delete an umbrella window (may contain several histograms)
-void freeUmbrellaWindows(t_UmbrellaWindow *win, int nwin)
+static void freeUmbrellaWindows(t_UmbrellaWindow *win, int nwin)
{
int i, j;
for (i = 0; i < nwin; i++)
/*! \brief
* Read and setup tabulated umbrella potential
*/
-void setup_tab(const char *fn, t_UmbrellaOptions *opt)
+static void setup_tab(const char *fn, t_UmbrellaOptions *opt)
{
int i, ny, nl;
double **y;
}
//! Read the header of an PDO file (position, force const, nr of groups)
-void read_pdo_header(FILE * file, t_UmbrellaHeader * header, t_UmbrellaOptions *opt)
+static void read_pdo_header(FILE * file, t_UmbrellaHeader * header, t_UmbrellaOptions *opt)
{
char line[2048];
char Buffer0[256], Buffer1[256], Buffer2[256], Buffer3[256], Buffer4[256];
std::istringstream ist;
/* line 1 */
- if (fgets(line, 2048, file) == NULL)
+ if (fgets(line, 2048, file) == nullptr)
{
gmx_fatal(FARGS, "Error reading header from pdo file\n");
}
}
/* line 2 */
- if (fgets(line, 2048, file) == NULL)
+ if (fgets(line, 2048, file) == nullptr)
{
gmx_fatal(FARGS, "Error reading header from pdo file\n");
}
}
/* line3 */
- if (fgets(line, 2048, file) == NULL)
+ if (fgets(line, 2048, file) == nullptr)
{
gmx_fatal(FARGS, "Error reading header from pdo file\n");
}
ist >> Buffer0 >> Buffer1 >> header->nSkip;
/* line 4 */
- if (fgets(line, 2048, file) == NULL)
+ if (fgets(line, 2048, file) == nullptr)
{
gmx_fatal(FARGS, "Error reading header from pdo file\n");
}
ist >> Buffer0 >> Buffer1 >> Buffer2 >> header->Reference;
/* line 5 */
- if (fgets(line, 2048, file) == NULL)
+ if (fgets(line, 2048, file) == nullptr)
{
gmx_fatal(FARGS, "Error reading header from pdo file\n");
}
for (i = 0; i < header->nPull; ++i)
{
- if (fgets(line, 2048, file) == NULL)
+ if (fgets(line, 2048, file) == nullptr)
{
gmx_fatal(FARGS, "Error reading header from pdo file\n");
}
}
}
- if (fgets(line, 2048, file) == NULL)
+ if (fgets(line, 2048, file) == nullptr)
{
gmx_fatal(FARGS, "Cannot read from file\n");
}
char *p;
int slen;
- if (fgets(ptr, *len-1, fp) == NULL)
+ if (fgets(ptr, *len-1, fp) == nullptr)
{
- return NULL;
+ return nullptr;
}
p = ptr;
- while ((std::strchr(ptr, '\n') == NULL) && (!feof(fp)))
+ while ((std::strchr(ptr, '\n') == nullptr) && (!feof(fp)))
{
/* This line is longer than len characters, let's increase len! */
*len += STRLEN;
p += STRLEN;
srenew(ptr, *len);
- if (fgets(p-1, STRLEN, fp) == NULL)
+ if (fgets(p-1, STRLEN, fp) == nullptr)
{
break;
}
* At the moment, this warning is avoided by hiding the format string
* the variable fmtlf.
*/
-void read_pdo_data(FILE * file, t_UmbrellaHeader * header,
- int fileno, t_UmbrellaWindow * win,
- t_UmbrellaOptions *opt,
- gmx_bool bGetMinMax, real *mintmp, real *maxtmp)
+static void read_pdo_data(FILE * file, t_UmbrellaHeader * header,
+ int fileno, t_UmbrellaWindow * win,
+ t_UmbrellaOptions *opt,
+ gmx_bool bGetMinMax, real *mintmp, real *maxtmp)
{
int i, inttemp, bins, count, ntot;
real minval, maxval, minfound = 1e20, maxfound = -1e20;
double temp, time, time0 = 0, dt;
- char *ptr = 0;
- t_UmbrellaWindow * window = 0;
+ char *ptr = nullptr;
+ t_UmbrellaWindow * window = nullptr;
gmx_bool timeok, dt_ok = 1;
- char *tmpbuf = 0, fmt[256], fmtign[256], fmtlf[5] = "%lf";
+ char *tmpbuf = nullptr, fmt[256], fmtign[256], fmtlf[5] = "%lf";
int len = STRLEN, dstep = 1;
const int blocklen = 4096;
- int *lennow = 0;
+ int *lennow = nullptr;
if (!bGetMinMax)
{
snew(window->g, window->nPull);
snew(window->bsWeight, window->nPull);
- window->bContrib = 0;
+ window->bContrib = nullptr;
if (opt->bCalcTauInt)
{
}
else
{
- window->ztime = 0;
+ window->ztime = nullptr;
}
snew(lennow, window->nPull);
window->g[i] = 1.;
if (opt->bCalcTauInt)
{
- window->ztime[i] = 0;
+ window->ztime[i] = nullptr;
}
}
count = 0;
snew(tmpbuf, len);
- while ( (ptr = fgets3(file, tmpbuf, &len)) != NULL)
+ while ( (ptr = fgets3(file, tmpbuf, &len)) != nullptr)
{
trim(ptr);
* by this routine (not recommended). Since we now support autocorrelations, it is better to set
* an appropriate autocorrelation times instead of using this function.
*/
-void enforceEqualWeights(t_UmbrellaWindow * window, int nWindows)
+static void enforceEqualWeights(t_UmbrellaWindow * window, int nWindows)
{
int i, k, j, NEnforced;
double ratio;
/*! \brief Simple linear interpolation between two given tabulated points
*/
-double tabulated_pot(double dist, t_UmbrellaOptions *opt)
+static double tabulated_pot(double dist, t_UmbrellaOptions *opt)
{
int jl, ju;
double pl, pu, dz, dp;
* After rapid convergence (using only substiantal contributions), we always switch to
* full precision.
*/
-void setup_acc_wham(double *profile, t_UmbrellaWindow * window, int nWindows,
- t_UmbrellaOptions *opt)
+static void setup_acc_wham(double *profile, t_UmbrellaWindow * window, int nWindows,
+ t_UmbrellaOptions *opt)
{
int i, j, k, nGrptot = 0, nContrib = 0, nTot = 0;
double U, min = opt->min, dz = opt->dz, temp, ztot_half, distance, ztot, contrib1, contrib2;
}
//! Compute the PMF (one of the two main WHAM routines)
-void calc_profile(double *profile, t_UmbrellaWindow * window, int nWindows,
- t_UmbrellaOptions *opt, gmx_bool bExact)
+static void calc_profile(double *profile, t_UmbrellaWindow * window, int nWindows,
+ t_UmbrellaOptions *opt, gmx_bool bExact)
{
double ztot_half, ztot, min = opt->min, dz = opt->dz;
}
//! Compute the free energy offsets z (one of the two main WHAM routines)
-double calc_z(double * profile, t_UmbrellaWindow * window, int nWindows,
- t_UmbrellaOptions *opt, gmx_bool bExact)
+static double calc_z(double * profile, t_UmbrellaWindow * window, int nWindows,
+ t_UmbrellaOptions *opt, gmx_bool bExact)
{
double min = opt->min, dz = opt->dz, ztot_half, ztot;
double maxglob = -1e20;
}
//! Make PMF symmetric around 0 (useful e.g. for membranes)
-void symmetrizeProfile(double* profile, t_UmbrellaOptions *opt)
+static void symmetrizeProfile(double* profile, t_UmbrellaOptions *opt)
{
int i, j, bins = opt->bins;
double *prof2, min = opt->min, max = opt->max, dz = opt->dz, zsym, deltaz, profsym;
}
//! Set energy unit (kJ/mol,kT,kCal/mol) and set it to zero at opt->zProf0
-void prof_normalization_and_unit(double * profile, t_UmbrellaOptions *opt)
+static void prof_normalization_and_unit(double * profile, t_UmbrellaOptions *opt)
{
int i, bins, imin;
double unit_factor = 1., diff;
}
//! Make an array of random integers (used for bootstrapping)
-void getRandomIntArray(int nPull, int blockLength, int* randomArray, gmx::DefaultRandomEngine * rng)
+static void getRandomIntArray(int nPull, int blockLength, int* randomArray, gmx::DefaultRandomEngine * rng)
{
gmx::UniformIntDistribution<int> dist(0, blockLength-1);
* This is used when bootstapping new trajectories and thereby create new histogtrams,
* but it is not required if we bootstrap complete histograms.
*/
-void copy_pullgrp_to_synthwindow(t_UmbrellaWindow *synthWindow,
- t_UmbrellaWindow *thisWindow, int pullid)
+static void copy_pullgrp_to_synthwindow(t_UmbrellaWindow *synthWindow,
+ t_UmbrellaWindow *thisWindow, int pullid)
{
synthWindow->N [0] = thisWindow->N [pullid];
synthWindow->Histo [0] = thisWindow->Histo [pullid];
* which are distributed according to the histograms. Required to generate
* the "synthetic" histograms for the Bootstrap method
*/
-void calc_cumulatives(t_UmbrellaWindow *window, int nWindows,
- t_UmbrellaOptions *opt, const char *fnhist, const char *xlabel)
+static void calc_cumulatives(t_UmbrellaWindow *window, int nWindows,
+ t_UmbrellaOptions *opt, const char *fnhist, const char *xlabel)
{
int i, j, k, nbin;
double last;
- char *fn = 0, *buf = 0;
- FILE *fp = 0;
+ char *fn = nullptr, *buf = nullptr;
+ FILE *fp = nullptr;
if (opt->bs_verbose)
{
*
* This is used to generate a random sequence distributed according to a histogram
*/
-void searchCumulative(double xx[], int n, double x, int *j)
+static void searchCumulative(double xx[], int n, double x, int *j)
{
int ju, jm, jl;
}
//! Bootstrap new trajectories and thereby generate new (bootstrapped) histograms
-void create_synthetic_histo(t_UmbrellaWindow *synthWindow, t_UmbrellaWindow *thisWindow,
- int pullid, t_UmbrellaOptions *opt)
+static void create_synthetic_histo(t_UmbrellaWindow *synthWindow, t_UmbrellaWindow *thisWindow,
+ int pullid, t_UmbrellaOptions *opt)
{
int N, i, nbins, r_index, ibin;
double r, tausteps = 0.0, a, ap, dt, x, invsqrt2, g, y, sig = 0., z, mu = 0.;
* If bs_index>=0, a number is added to the output file name to allow the ouput of all
* sets of bootstrapped histograms.
*/
-void print_histograms(const char *fnhist, t_UmbrellaWindow * window, int nWindows,
- int bs_index, t_UmbrellaOptions *opt, const char *xlabel)
+static void print_histograms(const char *fnhist, t_UmbrellaWindow * window, int nWindows,
+ int bs_index, t_UmbrellaOptions *opt, const char *xlabel)
{
- char *fn = 0, *buf = 0, title[256];
+ char *fn = nullptr, *buf = nullptr, title[256];
FILE *fp;
int bins, l, i, j;
}
//! Used for qsort to sort random numbers
-int func_wham_is_larger(const void *a, const void *b)
+static int func_wham_is_larger(const void *a, const void *b)
{
double *aa, *bb;
aa = (double*)a;
}
//! Make random weights for histograms for the Bayesian bootstrap of complete histograms)
-void setRandomBsWeights(t_UmbrellaWindow *synthwin, int nAllPull, t_UmbrellaOptions *opt)
+static void setRandomBsWeights(t_UmbrellaWindow *synthwin, int nAllPull, t_UmbrellaOptions *opt)
{
int i;
double *r;
}
//! The main bootstrapping routine
-void do_bootstrapping(const char *fnres, const char* fnprof, const char *fnhist,
- const char *xlabel, char* ylabel, double *profile,
- t_UmbrellaWindow * window, int nWindows, t_UmbrellaOptions *opt)
+static void do_bootstrapping(const char *fnres, const char* fnprof, const char *fnhist,
+ const char *xlabel, char* ylabel, double *profile,
+ t_UmbrellaWindow * window, int nWindows, t_UmbrellaOptions *opt)
{
t_UmbrellaWindow * synthWindow;
double *bsProfile, *bsProfiles_av, *bsProfiles_av2, maxchange = 1e20, tmp, stddev;
- int i, j, *randomArray = 0, winid, pullid, ib;
+ int i, j, *randomArray = nullptr, winid, pullid, ib;
int iAllPull, nAllPull, *allPull_winId, *allPull_pullId;
FILE *fp;
gmx_bool bExact = FALSE;
}
//! Return type of input file based on file extension (xvg, pdo, or tpr)
-int whaminFileType(char *fn)
+static int whaminFileType(char *fn)
{
int len;
len = std::strlen(fn);
}
//! Read the files names in pdo-files.dat, pullf/x-files.dat, tpr-files.dat
-void read_wham_in(const char *fn, char ***filenamesRet, int *nfilesRet,
- t_UmbrellaOptions *opt)
+static void read_wham_in(const char *fn, char ***filenamesRet, int *nfilesRet,
+ t_UmbrellaOptions *opt)
{
- char **filename = 0, tmp[WHAM_MAXFILELEN+2];
+ char **filename = nullptr, tmp[WHAM_MAXFILELEN+2];
int nread, sizenow, i, block = 1;
FILE *fp;
fp = gmx_ffopen(fn, "r");
nread = 0;
sizenow = 0;
- while (fgets(tmp, sizeof(tmp), fp) != NULL)
+ while (fgets(tmp, sizeof(tmp), fp) != nullptr)
{
if (std::strlen(tmp) >= WHAM_MAXFILELEN)
{
}
//! Open a file or a pipe to a gzipped file
-FILE *open_pdo_pipe(const char *fn, t_UmbrellaOptions *opt, gmx_bool *bPipeOpen)
+static FILE *open_pdo_pipe(const char *fn, t_UmbrellaOptions *opt, gmx_bool *bPipeOpen)
{
- char Buffer[1024], gunzip[1024], *Path = 0;
- FILE *pipe = 0;
+ char Buffer[1024], gunzip[1024], *Path = nullptr;
+ FILE *pipe = nullptr;
static gmx_bool bFirst = 1;
/* gzipped pdo file? */
printf("Executing command '%s'\n", Buffer);
}
#if HAVE_PIPES
- if ((pipe = popen(Buffer, "r")) == NULL)
+ if ((pipe = popen(Buffer, "r")) == nullptr)
{
gmx_fatal(FARGS, "Unable to open pipe to `%s'\n", Buffer);
}
}
//! Close file or pipe
-void pdo_close_file(FILE *fp)
+static void pdo_close_file(FILE *fp)
{
#if HAVE_PIPES
pclose(fp);
}
//! Reading all pdo files
-void read_pdo_files(char **fn, int nfiles, t_UmbrellaHeader* header,
- t_UmbrellaWindow *window, t_UmbrellaOptions *opt)
+static void read_pdo_files(char **fn, int nfiles, t_UmbrellaHeader* header,
+ t_UmbrellaWindow *window, t_UmbrellaOptions *opt)
{
FILE *file;
real mintmp, maxtmp, done = 0.;
}
read_pdo_header(file, header, opt);
/* here only determine min and max of this window */
- read_pdo_data(file, header, i, NULL, opt, TRUE, &mintmp, &maxtmp);
+ read_pdo_data(file, header, i, nullptr, opt, TRUE, &mintmp, &maxtmp);
if (maxtmp > opt->max)
{
opt->max = maxtmp;
file = open_pdo_pipe(fn[i], opt, &bPipeOpen);
read_pdo_header(file, header, opt);
/* load data into window */
- read_pdo_data(file, header, i, window, opt, FALSE, NULL, NULL);
+ read_pdo_data(file, header, i, window, opt, FALSE, nullptr, nullptr);
if ((window+i)->Ntot[0] == 0)
{
fprintf(stderr, "\nWARNING, no data points read from file %s (check -b option)\n", fn[i]);
#define int2YN(a) (((a) == 0) ? ("N") : ("Y"))
//! Read pull groups from a tpr file (including position, force const, geometry, number of groups)
-void read_tpr_header(const char *fn, t_UmbrellaHeader* header, t_UmbrellaOptions *opt, t_coordselection *coordsel)
+static void read_tpr_header(const char *fn, t_UmbrellaHeader* header, t_UmbrellaOptions *opt, t_coordselection *coordsel)
{
- t_inputrec ir;
- int i;
- t_state state;
- static int first = 1;
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
+ t_state state;
+ static int first = 1;
/* printf("Reading %s \n",fn); */
- read_tpx_state(fn, &ir, &state, NULL);
+ read_tpx_state(fn, ir, &state, nullptr);
- if (!ir.bPull)
+ if (!ir->bPull)
{
gmx_fatal(FARGS, "This is not a tpr with COM pulling");
}
- if (ir.pull->ncoord == 0)
+ if (ir->pull->ncoord == 0)
{
gmx_fatal(FARGS, "No pull coordinates found in %s", fn);
}
/* Read overall pull info */
- header->npullcrds = ir.pull->ncoord;
- header->bPrintCOM = ir.pull->bPrintCOM;
- header->bPrintRefValue = ir.pull->bPrintRefValue;
- header->bPrintComp = ir.pull->bPrintComp;
+ header->npullcrds = ir->pull->ncoord;
+ header->bPrintCOM = ir->pull->bPrintCOM;
+ header->bPrintRefValue = ir->pull->bPrintRefValue;
+ header->bPrintComp = ir->pull->bPrintComp;
/* Read pull coordinates */
snew(header->pcrd, header->npullcrds);
- for (i = 0; i < ir.pull->ncoord; i++)
+ for (int i = 0; i < ir->pull->ncoord; i++)
{
- header->pcrd[i].pull_type = ir.pull->coord[i].eType;
- header->pcrd[i].geometry = ir.pull->coord[i].eGeom;
- header->pcrd[i].ngroup = ir.pull->coord[i].ngroup;
- header->pcrd[i].k = ir.pull->coord[i].k;
- header->pcrd[i].init_dist = ir.pull->coord[i].init;
+ header->pcrd[i].pull_type = ir->pull->coord[i].eType;
+ header->pcrd[i].geometry = ir->pull->coord[i].eGeom;
+ header->pcrd[i].ngroup = ir->pull->coord[i].ngroup;
+ header->pcrd[i].k = ir->pull->coord[i].k;
+ header->pcrd[i].init_dist = ir->pull->coord[i].init;
- copy_ivec(ir.pull->coord[i].dim, header->pcrd[i].dim);
+ copy_ivec(ir->pull->coord[i].dim, header->pcrd[i].dim);
header->pcrd[i].ndim = header->pcrd[i].dim[XX] + header->pcrd[i].dim[YY] + header->pcrd[i].dim[ZZ];
std::strcpy(header->pcrd[i].coord_unit,
- pull_coordinate_units(&ir.pull->coord[i]));
+ pull_coordinate_units(&ir->pull->coord[i]));
- if (ir.efep != efepNO && ir.pull->coord[i].k != ir.pull->coord[i].kB)
+ if (ir->efep != efepNO && ir->pull->coord[i].k != ir->pull->coord[i].kB)
{
gmx_fatal(FARGS, "Seems like you did free-energy perturbation, and you perturbed the force constant."
" This is not supported.\n");
}
- if (coordsel && (coordsel->n != ir.pull->ncoord))
+ if (coordsel && (coordsel->n != ir->pull->ncoord))
{
gmx_fatal(FARGS, "Found %d pull coordinates in %s, but %d columns in the respective line\n"
- "coordinate selection file (option -is)\n", ir.pull->ncoord, fn, coordsel->n);
+ "coordinate selection file (option -is)\n", ir->pull->ncoord, fn, coordsel->n);
}
}
int geom = -1;
ivec thedim = { 0, 0, 0 };
bool geometryIsSet = false;
- for (i = 0; i < ir.pull->ncoord; i++)
+ for (int i = 0; i < ir->pull->ncoord; i++)
{
- if (coordsel == NULL || coordsel->bUse[i])
+ if (coordsel == nullptr || coordsel->bUse[i])
{
if (header->pcrd[i].pull_type != epullUMBRELLA)
{
{
printf("\nFile %s, %d coordinates, with these options:\n", fn, header->npullcrds);
int maxlen = 0;
- for (i = 0; i < ir.pull->ncoord; i++)
+ for (int i = 0; i < ir->pull->ncoord; i++)
{
int lentmp = strlen(epullg_names[header->pcrd[i].geometry]);
maxlen = (lentmp > maxlen) ? lentmp : maxlen;
char fmt[STRLEN];
sprintf(fmt, "\tGeometry %%-%ds k = %%-8g position = %%-8g dimensions [%%s %%s %%s] (%%d dimensions). Used: %%s\n",
maxlen+1);
- for (i = 0; i < ir.pull->ncoord; i++)
+ for (int i = 0; i < ir->pull->ncoord; i++)
{
- bool use = (coordsel == NULL || coordsel->bUse[i]);
+ bool use = (coordsel == nullptr || coordsel->bUse[i]);
printf(fmt,
epullg_names[header->pcrd[i].geometry], header->pcrd[i].k, header->pcrd[i].init_dist,
int2YN(header->pcrd[i].dim[XX]), int2YN(header->pcrd[i].dim[YY]), int2YN(header->pcrd[i].dim[ZZ]),
header->pcrd[i].ndim, use ? "Yes" : "No");
- printf("\tPull group coordinates of %d groups expected in pullx files.\n", ir.pull->bPrintCOM ? header->pcrd[i].ngroup : 0);
+ printf("\tPull group coordinates of %d groups expected in pullx files.\n", ir->pull->bPrintCOM ? header->pcrd[i].ngroup : 0);
}
printf("\tReference value of the coordinate%s expected in pullx files.\n",
header->bPrintRefValue ? "" : " not");
first = 0;
}
-//! 2-norm in a ndim-dimensional space
-double dist_ndim(double **dx, int ndim, int line)
-{
- int i;
- double r2 = 0.;
- for (i = 0; i < ndim; i++)
- {
- r2 += gmx::square(dx[i][line]);
- }
- return std::sqrt(r2);
-}
-
//! Read pullx.xvg or pullf.xvg
-void read_pull_xf(const char *fn, t_UmbrellaHeader * header,
- t_UmbrellaWindow * window,
- t_UmbrellaOptions *opt,
- gmx_bool bGetMinMax, real *mintmp, real *maxtmp,
- t_coordselection *coordsel)
+static void read_pull_xf(const char *fn, t_UmbrellaHeader * header,
+ t_UmbrellaWindow * window,
+ t_UmbrellaOptions *opt,
+ gmx_bool bGetMinMax, real *mintmp, real *maxtmp,
+ t_coordselection *coordsel)
{
- double **y = 0, pos = 0., t, force, time0 = 0., dt;
+ double **y = nullptr, pos = 0., t, force, time0 = 0., dt;
int ny, nt, bins, ibin, i, g, gUsed, dstep = 1;
int nColExpect, ntot, column;
real min, max, minfound = 1e20, maxfound = -1e20;
gmx_bool dt_ok, timeok;
const char *quantity;
const int blocklen = 4096;
- int *lennow = 0;
+ int *lennow = nullptr;
static gmx_bool bFirst = TRUE;
/*
if (!bGetMinMax)
{
+ assert(window);
bins = opt->bins;
min = opt->min;
max = opt->max;
snew(window->Ntot, window->nPull);
snew(window->g, window->nPull);
snew(window->bsWeight, window->nPull);
- window->bContrib = 0;
+ window->bContrib = nullptr;
if (opt->bCalcTauInt)
{
}
else
{
- window->ztime = NULL;
+ window->ztime = nullptr;
}
snew(lennow, window->nPull);
if (opt->bCalcTauInt)
{
- window->ztime[g] = NULL;
+ window->ztime[g] = nullptr;
}
}
}
//! read pullf-files.dat or pullx-files.dat and tpr-files.dat
-void read_tpr_pullxf_files(char **fnTprs, char **fnPull, int nfiles,
- t_UmbrellaHeader* header,
- t_UmbrellaWindow *window, t_UmbrellaOptions *opt)
+static void read_tpr_pullxf_files(char **fnTprs, char **fnPull, int nfiles,
+ t_UmbrellaHeader* header,
+ t_UmbrellaWindow *window, t_UmbrellaOptions *opt)
{
int i;
real mintmp, maxtmp;
{
gmx_fatal(FARGS, "Expected the %d'th file in input file to be a tpr file\n", i);
}
- read_tpr_header(fnTprs[i], header, opt, (opt->nCoordsel > 0) ? &opt->coordsel[i] : NULL);
+ read_tpr_header(fnTprs[i], header, opt, (opt->nCoordsel > 0) ? &opt->coordsel[i] : nullptr);
if (whaminFileType(fnPull[i]) != whamin_pullxf)
{
gmx_fatal(FARGS, "Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n", i);
}
- read_pull_xf(fnPull[i], header, NULL, opt, TRUE, &mintmp, &maxtmp,
- (opt->nCoordsel > 0) ? &opt->coordsel[i] : NULL);
+ read_pull_xf(fnPull[i], header, nullptr, opt, TRUE, &mintmp, &maxtmp,
+ (opt->nCoordsel > 0) ? &opt->coordsel[i] : nullptr);
if (maxtmp > opt->max)
{
opt->max = maxtmp;
{
gmx_fatal(FARGS, "Expected the %d'th file in input file to be a tpr file\n", i);
}
- read_tpr_header(fnTprs[i], header, opt, (opt->nCoordsel > 0) ? &opt->coordsel[i] : NULL);
+ read_tpr_header(fnTprs[i], header, opt, (opt->nCoordsel > 0) ? &opt->coordsel[i] : nullptr);
if (whaminFileType(fnPull[i]) != whamin_pullxf)
{
gmx_fatal(FARGS, "Expected the %d'th file in input file to be a xvg (pullx/pullf) file\n", i);
}
- read_pull_xf(fnPull[i], header, window+i, opt, FALSE, NULL, NULL,
- (opt->nCoordsel > 0) ? &opt->coordsel[i] : NULL);
+ read_pull_xf(fnPull[i], header, window+i, opt, FALSE, nullptr, nullptr,
+ (opt->nCoordsel > 0) ? &opt->coordsel[i] : nullptr);
if (window[i].Ntot[0] == 0)
{
fprintf(stderr, "\nWARNING, no data points read from file %s (check -b option)\n", fnPull[i]);
* Note: Here we consider tau[int] := int_0^inf ACF(t) as the integrated autocorrelation times.
* The factor `g := 1 + 2*tau[int]` subsequently enters the uncertainty.
*/
-void readIntegratedAutocorrelationTimes(t_UmbrellaWindow *window, int nwins, const char* fn)
+static void readIntegratedAutocorrelationTimes(t_UmbrellaWindow *window, int nwins, const char* fn)
{
int nlines, ny, i, ig;
double **iact;
* If opt->bAllowReduceIact==FALSE, the ACTs are never reduced, only increased
* by the smoothing
*/
-void smoothIact(t_UmbrellaWindow *window, int nwins, t_UmbrellaOptions *opt)
+static void smoothIact(t_UmbrellaWindow *window, int nwins, t_UmbrellaOptions *opt)
{
int i, ig, j, jg;
double pos, dpos2, siglim, siglim2, gaufact, invtwosig2, w, weight, tausm;
/*! \brief Try to compute the autocorrelation time for each umbrealla window
*/
-void calcIntegratedAutocorrelationTimes(t_UmbrellaWindow *window, int nwins,
- t_UmbrellaOptions *opt, const char *fn, const char *xlabel)
+static void calcIntegratedAutocorrelationTimes(t_UmbrellaWindow *window, int nwins,
+ t_UmbrellaOptions *opt, const char *fn, const char *xlabel)
{
int i, ig, ncorr, ntot, j, k, *count, restart;
real *corr, c0, dt, tmp;
real *ztime, av, tausteps;
- FILE *fp, *fpcorr = 0;
+ FILE *fp, *fpcorr = nullptr;
if (opt->verbose)
{
/*! \brief
* compute average and sigma of each umbrella histogram
*/
-void averageSigma(t_UmbrellaWindow *window, int nwins)
+static void averageSigma(t_UmbrellaWindow *window, int nwins)
{
int i, ig, ntot, k;
real av, sum2, sig, diff, *ztime, nSamplesIndep;
/*! \brief
* Use histograms to compute average force on pull group.
*/
-void computeAverageForce(t_UmbrellaWindow *window, int nWindows, t_UmbrellaOptions *opt)
+static void computeAverageForce(t_UmbrellaWindow *window, int nWindows, t_UmbrellaOptions *opt)
{
int i, j, bins = opt->bins, k;
double dz, min = opt->min, max = opt->max, displAv, temp, distance, ztot, ztot_half, w, weight;
/*! \brief
* Check if the complete reaction coordinate is covered by the histograms
*/
-void checkReactionCoordinateCovered(t_UmbrellaWindow *window, int nwins,
- t_UmbrellaOptions *opt)
+static void checkReactionCoordinateCovered(t_UmbrellaWindow *window, int nwins,
+ t_UmbrellaOptions *opt)
{
int i, ig, j, bins = opt->bins, bBoundary;
real avcount = 0, z, relcount, *count;
*
* This speeds up the convergence by roughly a factor of 2
*/
-void guessPotByIntegration(t_UmbrellaWindow *window, int nWindows, t_UmbrellaOptions *opt, const char *xlabel)
+static void guessPotByIntegration(t_UmbrellaWindow *window, int nWindows, t_UmbrellaOptions *opt, const char *xlabel)
{
int i, j, ig, bins = opt->bins, nHist, winmin, groupmin;
double dz, min = opt->min, *pot, pos, hispos, dist, diff, fAv, distmin, *f;
*
* TO DO: ptr=fgets(...) is never freed (small memory leak)
*/
-void readPullCoordSelection(t_UmbrellaOptions *opt, char **fnTpr, int nTpr)
+static void readPullCoordSelection(t_UmbrellaOptions *opt, char **fnTpr, int nTpr)
{
FILE *fp;
int i, iline, n, len = STRLEN, temp;
- char *ptr = 0, *tmpbuf = 0;
+ char *ptr = nullptr, *tmpbuf = nullptr;
char fmt[1024], fmtign[1024];
int block = 1, sizenow;
fp = gmx_ffopen(opt->fnCoordSel, "r");
- opt->coordsel = NULL;
+ opt->coordsel = nullptr;
snew(tmpbuf, len);
sizenow = 0;
iline = 0;
- while ( (ptr = fgets3(fp, tmpbuf, &len)) != NULL)
+ while ( (ptr = fgets3(fp, tmpbuf, &len)) != nullptr)
{
trim(ptr);
n = wordcount(ptr);
"the histograms."
};
- const char *en_unit[] = {NULL, "kJ", "kCal", "kT", NULL};
- const char *en_unit_label[] = {"", "E (kJ mol\\S-1\\N)", "E (kcal mol\\S-1\\N)", "E (kT)", NULL};
- const char *en_bsMethod[] = { NULL, "b-hist", "hist", "traj", "traj-gauss", NULL };
+ const char *en_unit[] = {nullptr, "kJ", "kCal", "kT", nullptr};
+ const char *en_unit_label[] = {"", "E (kJ mol\\S-1\\N)", "E (kcal mol\\S-1\\N)", "E (kT)", nullptr};
+ const char *en_bsMethod[] = { nullptr, "b-hist", "hist", "traj", "traj-gauss", nullptr };
static t_UmbrellaOptions opt;
t_pargs pa[] = {
int i, j, l, nfiles, nwins, nfiles2;
t_UmbrellaHeader header;
- t_UmbrellaWindow * window = NULL;
+ t_UmbrellaWindow * window = nullptr;
double *profile, maxchange = 1e20;
gmx_bool bMinSet, bMaxSet, bAutoSet, bExact = FALSE;
char **fninTpr, **fninPull, **fninPdo;
opt.max = 0;
opt.bAuto = TRUE;
opt.nCoordsel = 0;
- opt.coordsel = NULL;
+ opt.coordsel = nullptr;
/* bootstrapping stuff */
opt.nBootStrap = 0;
opt.stepUpdateContrib = 100;
if (!parse_common_args(&argc, argv, 0,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &opt.oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &opt.oenv))
{
return 0;
}
}
/* Read file that selects the pull group to be used */
- if (opt.fnCoordSel != NULL)
+ if (opt.fnCoordSel != nullptr)
{
readPullCoordSelection(&opt, fninTpr, nfiles);
}
}
else
{ /* reading pdo files */
- if (opt.fnCoordSel != NULL)
+ if (opt.fnCoordSel != nullptr)
{
gmx_fatal(FARGS, "Reading a -is file is not supported with PDO input files.\n"
"Use awk or a similar tool to pick the required pull groups from your PDO files\n");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return bb;
}
-void wheel(const char *fn, int nres, char *resnm[], int r0, real rot0, char *title)
+static void wheel(const char *fn, int nres, char *resnm[], int r0, real rot0, char *title)
{
const real fontsize = 16;
const real gray = 0.9;
ps_close(out);
}
-void wheel2(const char *fn, int nres, char *resnm[], real rot0, char *title)
+static void wheel2(const char *fn, int nres, char *resnm[], real rot0, char *title)
{
const real fontsize = 14;
const real gray = 0.9;
gmx_output_env_t *oenv;
static real rot0 = 0;
static gmx_bool bNum = TRUE;
- static char *title = NULL;
+ static char *title = nullptr;
static int r0 = 1;
t_pargs pa [] = {
{ "-r0", FALSE, etINT, {&r0},
"Toggle numbers" }
};
t_filenm fnm[] = {
- { efDAT, "-f", NULL, ffREAD },
- { efEPS, "-o", NULL, ffWRITE }
+ { efDAT, "-f", nullptr, ffREAD },
+ { efEPS, "-o", nullptr, ffWRITE }
};
#define NFILE asize(fnm)
char **resnm;
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
{
if (std::strcmp(argv[i], "-r0") == 0)
{
- r0 = std::strtol(argv[++i], NULL, 10);
+ r0 = std::strtol(argv[++i], nullptr, 10);
fprintf(stderr, "First residue is %d\n", r0);
}
else if (std::strcmp(argv[i], "-rot0") == 0)
{
- rot0 = strtod(argv[++i], NULL);
+ rot0 = strtod(argv[++i], nullptr);
fprintf(stderr, "Initial rotation is %g\n", rot0);
}
else if (std::strcmp(argv[i], "-T") == 0)
#include "gromacs/gmxana/gmx_ana.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/filestream.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
ecSel, ecHalves, ecAdd, ecSub, ecMult, ecDiv, ecNR
};
-void get_params(const char *mpin, const char *mpout, t_psrec *psr)
+static void get_params(const char *mpin, const char *mpout, t_psrec *psr)
{
- static const char *gmx_bools[BOOL_NR+1] = { "no", "yes", NULL };
+ static const char *gmx_bools[BOOL_NR+1] = { "no", "yes", nullptr };
/* this must correspond to t_rgb *linecolors[] below */
- static const char *colors[] = { "none", "black", "white", NULL };
+ static const char *colors[] = { "none", "black", "white", nullptr };
warninp_t wi;
t_inpfile *inp;
const char *tmp;
wi = init_warning(FALSE, 0);
- if (mpin != NULL)
+ if (mpin != nullptr)
{
- inp = read_inpfile(mpin, &ninp, wi);
+ gmx::TextInputFile stream(mpin);
+ inp = read_inpfile(&stream, mpin, &ninp, wi);
}
else
{
- inp = NULL;
+ inp = nullptr;
}
ETYPE("black&white", psr->bw, gmx_bools);
RTYPE("linewidth", psr->linewidth, 1.0);
check_warning_error(wi, FARGS);
- if (mpout != NULL)
+ if (mpout != nullptr)
{
- write_inpfile(mpout, ninp, inp, TRUE, wi);
+ gmx::TextOutputFile stream(mpout);
+ write_inpfile(&stream, mpout, ninp, inp, TRUE, WriteMdpHeader::yes, wi);
+ stream.close();
}
done_warning(wi, FARGS);
t_rgb blue = { 0, 0, 1 };
#define BLACK (&black)
/* this must correspond to *colors[] in get_params */
-t_rgb *linecolors[] = { NULL, &black, &white, NULL };
+t_rgb *linecolors[] = { nullptr, &black, &white, nullptr };
-gmx_bool diff_maps(int nmap1, t_mapping *map1, int nmap2, t_mapping *map2)
+static gmx_bool diff_maps(int nmap1, t_mapping *map1, int nmap2, t_mapping *map2)
{
int i;
gmx_bool bDiff, bColDiff = FALSE;
return bDiff;
}
-void leg_discrete(t_psdata ps, real x0, real y0, char *label,
- real fontsize, char *font, int nmap, t_mapping map[])
+static void leg_discrete(t_psdata ps, real x0, real y0, char *label,
+ real fontsize, char *font, int nmap, t_mapping map[])
{
int i;
real yhh;
}
}
-void leg_continuous(t_psdata ps, real x0, real x, real y0, char *label,
- real fontsize, char *font,
- int nmap, t_mapping map[],
- int mapoffset)
+static void leg_continuous(t_psdata ps, real x0, real x, real y0, char *label,
+ real fontsize, char *font,
+ int nmap, t_mapping map[],
+ int mapoffset)
{
int i;
real xx0;
boxxh = fontsize;
}
- GMX_RELEASE_ASSERT(map != NULL, "NULL map array provided to leg_continuous()");
+ GMX_RELEASE_ASSERT(map != nullptr, "NULL map array provided to leg_continuous()");
/* LANDSCAPE */
xx0 = x0-((nmap-mapoffset)*boxxh)/2.0;
- boxxh/2, yhh, map[nmap-1].desc, eXCenter);
}
-void leg_bicontinuous(t_psdata ps, real x0, real x, real y0, char *label1,
- char *label2, real fontsize, char *font,
- int nmap1, t_mapping map1[], int nmap2, t_mapping map2[])
+static void leg_bicontinuous(t_psdata ps, real x0, real x, real y0, char *label1,
+ char *label2, real fontsize, char *font,
+ int nmap1, t_mapping map1[], int nmap2, t_mapping map2[])
{
real xx1, xx2, x1, x2;
*dh = dhh;
}
-int add_maps(t_mapping **newmap,
- int nmap1, t_mapping map1[], int nmap2, t_mapping map2[])
+static int add_maps(t_mapping **newmap,
+ int nmap1, t_mapping map1[], int nmap2, t_mapping map2[])
{
static char mapper[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789!@#$%^&*()-_=+{}|;:',<.>/?";
int nsymbols;
return nmap;
}
-void xpm_mat(const char *outf, int nmat, t_matrix *mat, t_matrix *mat2,
- gmx_bool bDiag, gmx_bool bFirstDiag)
+static void xpm_mat(const char *outf, int nmat, t_matrix *mat, t_matrix *mat2,
+ gmx_bool bDiag, gmx_bool bFirstDiag)
{
FILE *out;
int i, x, y, col;
int nmap;
- t_mapping *map = NULL;
+ t_mapping *map = nullptr;
out = gmx_ffopen(outf, "w");
axisnm, *major, *minor);
}
-void ps_mat(const char *outf, int nmat, t_matrix mat[], t_matrix mat2[],
- gmx_bool bFrame, gmx_bool bDiag, gmx_bool bFirstDiag,
- gmx_bool bTitle, gmx_bool bTitleOnce, gmx_bool bYonce, int elegend,
- real size, real boxx, real boxy, const char *m2p, const char *m2pout,
- int mapoffset)
+static void ps_mat(const char *outf, int nmat, t_matrix mat[], t_matrix mat2[],
+ gmx_bool bFrame, gmx_bool bDiag, gmx_bool bFirstDiag,
+ gmx_bool bTitle, gmx_bool bTitleOnce, gmx_bool bYonce, int elegend,
+ real size, real boxx, real boxy, const char *m2p, const char *m2pout,
+ int mapoffset)
{
const char *libm2p;
char *legend;
real x0, y0, xx;
real w, h, dw, dh;
int nmap1 = 0, nmap2 = 0, leg_nmap;
- t_mapping *map1 = NULL, *map2 = NULL, *leg_map;
+ t_mapping *map1 = nullptr, *map2 = nullptr, *leg_map;
gmx_bool bMap1, bNextMap1, bDiscrete;
/* memory leak: */
libm2p = m2p ? gmxlibfn(m2p) : m2p;
- get_params(libm2p, m2pout, &psrec);
+ try
+ {
+ get_params(libm2p, m2pout, &psrec);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
psr = &psrec;
{
ps_comment(out, "Now it's legend time!");
ps_linewidth(out, static_cast<int>(psr->linewidth));
- if (mat2 == NULL || elegend != elSecond)
+ if (mat2 == nullptr || elegend != elSecond)
{
bDiscrete = mat[0].bDiscrete;
legend = mat[0].legend;
ps_close(out);
}
-void make_axis_labels(int nmat, t_matrix *mat)
+static void make_axis_labels(int nmat, t_matrix *mat)
{
int i, j;
for (i = 0; (i < nmat); i++)
{
/* Make labels for x axis */
- if (mat[i].axis_x == NULL)
+ if (mat[i].axis_x == nullptr)
{
snew(mat[i].axis_x, mat[i].nx);
for (j = 0; (j < mat[i].nx); j++)
}
}
/* Make labels for y axis */
- if (mat[i].axis_y == NULL)
+ if (mat[i].axis_y == nullptr)
{
snew(mat[i].axis_y, mat[i].ny);
for (j = 0; (j < mat[i].ny); j++)
}
}
-void prune_mat(int nmat, t_matrix *mat, t_matrix *mat2, int skip)
+static void prune_mat(int nmat, t_matrix *mat, t_matrix *mat2, int skip)
{
int i, x, y, xs, ys;
}
}
-void zero_lines(int nmat, t_matrix *mat, t_matrix *mat2)
+static void zero_lines(int nmat, t_matrix *mat, t_matrix *mat2)
{
int i, x, y, m;
t_matrix *mats;
}
}
-void write_combined_matrix(int ecombine, const char *fn,
- int nmat, t_matrix *mat1, t_matrix *mat2,
- real *cmin, real *cmax)
+static void write_combined_matrix(int ecombine, const char *fn,
+ int nmat, t_matrix *mat1, t_matrix *mat2,
+ real *cmin, real *cmax)
{
int i, j, k, nlevels;
FILE *out;
" not match.\n", k, mat1[k].nx, mat1[k].ny, mat2[k].nx, mat2[k].ny);
}
printf("Combining two %dx%d matrices\n", mat1[k].nx, mat1[k].ny);
- rmat1 = matrix2real(&mat1[k], NULL);
- rmat2 = matrix2real(&mat2[k], NULL);
- if (NULL == rmat1 || NULL == rmat2)
+ rmat1 = matrix2real(&mat1[k], nullptr);
+ rmat2 = matrix2real(&mat2[k], nullptr);
+ if (nullptr == rmat1 || nullptr == rmat2)
{
gmx_fatal(FARGS, "Could not extract real data from %s xpm matrices. Note that, e.g.,\n"
"g_rms and g_mdmat provide such data, but not do_dssp.\n",
- (NULL == rmat1 && NULL == rmat2) ? "both" : "one of the" );
+ (nullptr == rmat1 && nullptr == rmat2) ? "both" : "one of the" );
}
rlo = 1e38;
rhi = -1e38;
gmx_ffclose(out);
}
-void do_mat(int nmat, t_matrix *mat, t_matrix *mat2,
- gmx_bool bFrame, gmx_bool bZeroLine, gmx_bool bDiag, gmx_bool bFirstDiag, gmx_bool bTitle,
- gmx_bool bTitleOnce, gmx_bool bYonce, int elegend,
- real size, real boxx, real boxy,
- const char *epsfile, const char *xpmfile, const char *m2p,
- const char *m2pout, int skip, int mapoffset)
+static void do_mat(int nmat, t_matrix *mat, t_matrix *mat2,
+ gmx_bool bFrame, gmx_bool bZeroLine, gmx_bool bDiag, gmx_bool bFirstDiag, gmx_bool bTitle,
+ gmx_bool bTitleOnce, gmx_bool bYonce, int elegend,
+ real size, real boxx, real boxy,
+ const char *epsfile, const char *xpmfile, const char *m2p,
+ const char *m2pout, int skip, int mapoffset)
{
int i, j, k;
zero_lines(nmat, mat, mat);
}
- if (epsfile != NULL)
+ if (epsfile != nullptr)
{
ps_mat(epsfile, nmat, mat, mat2, bFrame, bDiag, bFirstDiag,
bTitle, bTitleOnce, bYonce, elegend,
size, boxx, boxy, m2p, m2pout, mapoffset);
}
- if (xpmfile != NULL)
+ if (xpmfile != nullptr)
{
xpm_mat(xpmfile, nmat, mat, mat2, bDiag, bFirstDiag);
}
}
-void gradient_map(rvec grad, int nmap, t_mapping map[])
+static void gradient_map(rvec grad, int nmap, t_mapping map[])
{
int i;
real c;
}
}
-void gradient_mat(rvec grad, int nmat, t_matrix mat[])
+static void gradient_mat(rvec grad, int nmat, t_matrix mat[])
{
int m;
}
}
-void rainbow_map(gmx_bool bBlue, int nmap, t_mapping map[])
+static void rainbow_map(gmx_bool bBlue, int nmap, t_mapping map[])
{
int i;
real c, r, g, b;
}
}
-void rainbow_mat(gmx_bool bBlue, int nmat, t_matrix mat[])
+static void rainbow_mat(gmx_bool bBlue, int nmat, t_matrix mat[])
{
int m;
};
gmx_output_env_t *oenv;
- const char *fn, *epsfile = NULL, *xpmfile = NULL;
+ const char *fn, *epsfile = nullptr, *xpmfile = nullptr;
int i, nmat, nmat2, etitle, elegend, ediag, erainbow, ecombine;
- t_matrix *mat = NULL, *mat2 = NULL;
+ t_matrix *mat = nullptr, *mat2 = nullptr;
gmx_bool bTitle, bTitleOnce, bDiag, bFirstDiag, bGrad;
static gmx_bool bFrame = TRUE, bZeroLine = FALSE, bYonce = FALSE;
static real size = 400, boxx = 0, boxy = 0, cmin = 0, cmax = 0;
enum {
etSel, etTop, etOnce, etYlabel, etNone, etNR
};
- const char *title[] = { NULL, "top", "once", "ylabel", "none", NULL };
+ const char *title[] = { nullptr, "top", "once", "ylabel", "none", nullptr };
/* MUST correspond to enum elXxx as defined at top of file */
- const char *legend[] = { NULL, "both", "first", "second", "none", NULL };
+ const char *legend[] = { nullptr, "both", "first", "second", "none", nullptr };
enum {
edSel, edFirst, edSecond, edNone, edNR
};
- const char *diag[] = { NULL, "first", "second", "none", NULL };
+ const char *diag[] = { nullptr, "first", "second", "none", nullptr };
enum {
erSel, erNo, erBlue, erRed, erNR
};
- const char *rainbow[] = { NULL, "no", "blue", "red", NULL };
+ const char *rainbow[] = { nullptr, "no", "blue", "red", nullptr };
/* MUST correspond to enum ecXxx as defined at top of file */
const char *combine[] = {
- NULL, "halves", "add", "sub", "mult", "div", NULL
+ nullptr, "halves", "add", "sub", "mult", "div", nullptr
};
static int skip = 1, mapoffset = 0;
t_pargs pa[] = {
};
#define NPA asize(pa)
t_filenm fnm[] = {
- { efXPM, "-f", NULL, ffREAD },
+ { efXPM, "-f", nullptr, ffREAD },
{ efXPM, "-f2", "root2", ffOPTRD },
- { efM2P, "-di", NULL, ffLIBOPTRD },
+ { efM2P, "-di", nullptr, ffLIBOPTRD },
{ efM2P, "-do", "out", ffOPTWR },
- { efEPS, "-o", NULL, ffOPTWR },
- { efXPM, "-xpm", NULL, ffOPTWR }
+ { efEPS, "-o", nullptr, ffOPTWR },
+ { efXPM, "-xpm", nullptr, ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, NPA, pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
epsfile = ftp2fn_null(efEPS, NFILE, fnm);
xpmfile = opt2fn_null("-xpm", NFILE, fnm);
- if (epsfile == NULL && xpmfile == NULL)
+ if (epsfile == nullptr && xpmfile == nullptr)
{
if (ecombine != ecHalves)
{
"WARNING: can only write result of arithmetic combination "
"of two matrices to .xpm file\n"
" file %s will not be written\n", epsfile);
- epsfile = NULL;
+ epsfile = nullptr;
}
bDiag = ediag != edNone;
}
}
- if ((mat2 == NULL) && (elegend != elNone))
+ if ((mat2 == nullptr) && (elegend != elNone))
{
elegend = elFirst;
}
if (ecombine && ecombine != ecHalves)
{
write_combined_matrix(ecombine, xpmfile, nmat, mat, mat2,
- opt2parg_bSet("-cmin", NPA, pa) ? &cmin : NULL,
- opt2parg_bSet("-cmax", NPA, pa) ? &cmax : NULL);
+ opt2parg_bSet("-cmin", NPA, pa) ? &cmin : nullptr,
+ opt2parg_bSet("-cmax", NPA, pa) ? &cmax : nullptr);
}
else
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ak = index[i+2];
al = index[i+3];
phi = RAD2DEG*
- dih_angle(x[ai], x[aj], x[ak], x[al], NULL,
+ dih_angle(x[ai], x[aj], x[ak], x[al], nullptr,
r_ij, r_kj, r_kl, m, n,
&sign, &t1, &t2, &t3);
phitot += phi;
}
bb[i].phi = RAD2DEG*
- dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], NULL,
+ dih_angle(x[bb[i].Cprev], x[bb[i].N], x[bb[i].CA], x[bb[i].C], nullptr,
r_ij, r_kj, r_kl, m, n,
&sign, &t1, &t2, &t3);
bb[i].psi = RAD2DEG*
- dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], NULL,
+ dih_angle(x[bb[i].N], x[bb[i].CA], x[bb[i].C], x[bb[i].Nnext], nullptr,
r_ij, r_kj, r_kl, m, n,
&sign, &t1, &t2, &t3);
bb[i].pprms2 = gmx::square(bb[i].phi-PHI_AHX)+gmx::square(bb[i].psi-PSI_AHX);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real t; /* Interface thickness */
} t_interf;
-static void init_interf(t_interf *surf)
+static inline void init_interf(t_interf *surf)
{
surf->Z = 0;
surf->t = 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include <cstring>
+#include <algorithm>
+
#include "gromacs/listed-forces/bonded.h"
#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/utility/cstringutil.h"
static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };
#define NPP (sizeof(pp_pat)/sizeof(pp_pat[0]))
-static int d_comp(const void *a, const void *b)
+static bool d_comp(const t_dih &a, const t_dih &b)
{
- t_dih *da, *db;
-
- da = (t_dih *)a;
- db = (t_dih *)b;
-
- if (da->ai[1] < db->ai[1])
+ if (a.ai[1] < b.ai[1])
{
- return -1;
+ return true;
}
- else if (da->ai[1] == db->ai[1])
+ else if (a.ai[1] == b.ai[1])
{
- return (da->ai[2] - db->ai[2]);
+ return a.ai[2] < b.ai[2];
}
else
{
- return 1;
+ return false;
}
}
rvec r_ij, r_kj, r_kl, m, n;
real sign;
t_dih *dd;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
gpbc = gmx_rmpbc_init(xr->idef, xr->ePBC, xr->natoms);
gmx_rmpbc(gpbc, xr->natoms, xr->box, xr->x);
dd = &(xr->dih[i]);
dd->ang = dih_angle(xr->x[dd->ai[0]], xr->x[dd->ai[1]],
xr->x[dd->ai[2]], xr->x[dd->ai[3]],
- NULL,
+ nullptr,
r_ij, r_kj, r_kl, m, n, &sign, &t1, &t2, &t3);
}
}
key.ai[1] = ia[2];
key.ai[2] = ia[3];
- if ((dd = (t_dih *)bsearch(&key, xr->dih, xr->ndih, (size_t)sizeof(key), d_comp))
- != NULL)
+ dd = std::lower_bound(xr->dih, xr->dih+xr->ndih, key, d_comp);
+ if (dd < xr->dih+xr->ndih && !d_comp(key, *dd))
{
dd->mult = idef->iparams[ft].pdihs.mult;
dd->phi0 = idef->iparams[ft].pdihs.phiA;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fclose(fp);
- return (gmx_neutron_atomic_structurefactors_t *) gnsf;
+ return gnsf;
}
gmx_sans_t *gmx_sans_init (const t_topology *top, gmx_neutron_atomic_structurefactors_t *gnsf)
{
- gmx_sans_t *gsans = NULL;
+ gmx_sans_t *gsans = nullptr;
int i, j;
/* Try to assing scattering length from nsfactor.dat */
snew(gsans, 1);
}
}
- return (gmx_sans_t *) gsans;
+ return gsans;
}
gmx_radial_distribution_histogram_t *calc_radial_distribution_histogram (
real mcover,
unsigned int seed)
{
- gmx_radial_distribution_histogram_t *pr = NULL;
+ gmx_radial_distribution_histogram_t *pr = nullptr;
rvec dist;
double rmax;
int i, j;
double **tgr;
int tid;
int nthreads;
- gmx::DefaultRandomEngine *trng = NULL;
+ gmx::DefaultRandomEngine *trng = nullptr;
#endif
gmx_int64_t mc = 0, mc_max;
gmx::DefaultRandomEngine rng(seed);
pr->r[i] = (pr->binwidth*i+pr->binwidth*0.5);
}
- return (gmx_radial_distribution_histogram_t *) pr;
+ return pr;
}
gmx_static_structurefactor_t *convert_histogram_to_intensity_curve (gmx_radial_distribution_histogram_t *pr, double start_q, double end_q, double q_step)
{
- gmx_static_structurefactor_t *sq = NULL;
+ gmx_static_structurefactor_t *sq = nullptr;
int i, j;
/* init data */
snew(sq, 1);
}
}
- return (gmx_static_structurefactor_t *) sq;
+ return sq;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
-void addtoavgenergy(t_complex *list, real *result, int size, int tsteps)
+static void addtoavgenergy(t_complex *list, real *result, int size, int tsteps)
{
int i;
for (i = 0; i < size; i++)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
trans[ZZ][m] = -trans[ZZ][m];
}
}
- rotate_atoms(natoms, NULL, x, trans);
+ rotate_atoms(natoms, nullptr, x, trans);
if (v)
{
- rotate_atoms(natoms, NULL, v, trans);
+ rotate_atoms(natoms, nullptr, v, trans);
}
for (i = 0; i < natoms; i++)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(gsf->b, nralloc);
snew(gsf->c, nralloc);
snew(gsf->p, nralloc);
- gsf->n = NULL;
+ gsf->n = nullptr;
gsf->nratoms = line_no;
while (get_a_line(fp, line, STRLEN))
{
sf->energy = energy;
/* Read the topology informations */
- read_tps_conf (fnTPS, &top, &ePBC, &xtop, NULL, box, TRUE);
+ read_tps_conf (fnTPS, &top, &ePBC, &xtop, nullptr, box, TRUE);
sfree (xtop);
/* groups stuff... */
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-set(testname "LegacyToolsTests")
-set(exename "legacy-tools-test")
+set(exename gmxana-test)
gmx_add_gtest_executable(
${exename}
- # files with code for test fixtures
- gmx_traj_tests.cpp
- )
-gmx_register_integration_test(
- ${testname}
- ${exename}
+ gmx_traj.cpp
+ gmx_trjconv.cpp
)
+gmx_register_gtest_test(GmxAnaTest ${exename} INTEGRATION_TEST)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2013,2014,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx traj.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ */
+#include "gmxpre.h"
+
+#include "config.h"
+
+#include "gromacs/gmxana/gmx_ana.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/stdiohelper.h"
+#include "testutils/textblockmatchers.h"
+
+namespace
+{
+
+class GmxTraj : public gmx::test::CommandLineTestBase,
+ public ::testing::WithParamInterface<const char *>
+{
+ public:
+ void runTest(const char *fileName)
+ {
+ auto &cmdline = commandLine();
+ cmdline.append("traj");
+ setInputFile("-s", "spc2.gro");
+ setInputFile("-f", fileName);
+ setOutputFile("-ox", "spc2.xvg", gmx::test::NoTextMatch());
+
+ gmx::test::StdioTestHelper stdioHelper(&fileManager());
+ stdioHelper.redirectStringToStdin("0\n");
+
+ ASSERT_EQ(0, gmx_traj(cmdline.argc(), cmdline.argv()));
+ }
+};
+
+/* TODO These tests are actually not very effective, because gmx-traj
+ * can only return 0 or exit via gmx_fatal() (which currently also
+ * exits the test binary). So, "no XDR/TNG support in the binary"
+ * leads to the reading test appearing to pass. Still, no fatal error
+ * and no segfault is useful information while modifying such code. */
+
+TEST_P(GmxTraj, WithDifferentInputFormats)
+{
+ runTest(GetParam());
+}
+
+/*! \brief Helper array of input files present in the source repo
+ * database. These all have two identical frames of two SPC water
+ * molecules, which were generated via trjconv from the .gro
+ * version. */
+const char *const trajectoryFileNames[] = {
+ "spc2-traj.trr",
+#if GMX_USE_TNG
+ "spc2-traj.tng",
+#endif
+ "spc2-traj.xtc",
+ "spc2-traj.gro",
+ "spc2-traj.pdb",
+ "spc2-traj.g96"
+};
+
+INSTANTIATE_TEST_CASE_P(NoFatalErrorWhenWritingFrom,
+ GmxTraj, ::testing::ValuesIn(trajectoryFileNames));
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \internal \file
* \brief
- * Tests for gmx traj
+ * Tests for gmx trjconv.
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
*/
-
#include "gmxpre.h"
#include "config.h"
#include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/utility/arrayref.h"
#include "testutils/cmdlinetest.h"
-#include "testutils/integrationtests.h"
+#include "testutils/stdiohelper.h"
+#include "testutils/textblockmatchers.h"
namespace
{
-class GmxTraj : public gmx::test::IntegrationTestFixture,
- public ::testing::WithParamInterface<const char *>
-{
- public:
- GmxTraj() : groFileName(fileManager_.getInputFilePath("spc2.gro")),
- xvgFileName(fileManager_.getTemporaryFilePath("spc2.xvg"))
- {
- }
-
- int runTest(const char *fileName)
- {
- gmx::test::CommandLine caller;
- caller.append("traj");
-
- caller.addOption("-s", groFileName);
- caller.addOption("-ox", xvgFileName);
-
- std::string inputTrajectoryFileName = fileManager_.getInputFilePath(fileName);
- caller.addOption("-f", inputTrajectoryFileName);
-
- redirectStringToStdin("0\n");
-
- return gmx_traj(caller.argc(), caller.argv());
- }
-
- std::string groFileName;
- std::string xvgFileName;
-};
-
-/* TODO These tests are actually not very effective, because gmx-traj
- * can only return 0 or exit via gmx_fatal() (which currently also
- * exits the test binary). So, "no XDR/TNG support in the binary"
- * leads to the reading test appearing to pass. Still, no fatal error
- * and no segfault is useful information while modifying such code. */
-
-TEST_P(GmxTraj, WithDifferentInputFormats)
-{
- runTest(GetParam());
-}
-
-// ==
-
-class TrjconvWithIndexGroupSubset : public gmx::test::IntegrationTestFixture,
+class TrjconvWithIndexGroupSubset : public gmx::test::CommandLineTestBase,
public ::testing::WithParamInterface<const char *>
{
public:
- int runTest(const char *fileName)
+ void runTest(const char *fileName)
{
- gmx::test::CommandLine caller;
- caller.append("trjconv");
+ auto &cmdline = commandLine();
+ cmdline.append("trjconv");
- caller.addOption("-s", fileManager_.getInputFilePath("spc2.gro"));
+ setInputFile("-s", "spc2.gro");
+ setInputFile("-f", fileName);
+ setInputFile("-n", "spc2.ndx");
+ setOutputFile("-o", "spc-traj.tng", gmx::test::NoTextMatch());
- std::string inputTrajectoryFileName = fileManager_.getInputFilePath(fileName);
- caller.addOption("-f", inputTrajectoryFileName);
-
- std::string ndxFileName = fileManager_.getInputFilePath("spc2.ndx");
- caller.addOption("-n", ndxFileName);
-
- caller.addOption("-o", fileManager_.getTemporaryFilePath("spc-traj.tng"));
-
- redirectStringToStdin("SecondWaterMolecule\n");
+ gmx::test::StdioTestHelper stdioHelper(&fileManager());
+ stdioHelper.redirectStringToStdin("SecondWaterMolecule\n");
/* TODO Ideally, we would then check that the output file
has only 3 of the 6 atoms (which it does), but the
infrastructure for doing that automatically is still
being built. This would also fix the TODO below. */
- return gmx_trjconv(caller.argc(), caller.argv());
+ ASSERT_EQ(0, gmx_trjconv(cmdline.argc(), cmdline.argv()));
}
};
/* TODO These tests are actually not very effective, because trjconv
runTest(GetParam());
}
-// ==
-
/*! \brief Helper array of input files present in the source repo
* database. These all have two identical frames of two SPC water
* molecules, which were generated via trjconv from the .gro
* version. */
-const char *trajectoryFileNames[] = {
+const char *const trajectoryFileNames[] = {
"spc2-traj.trr",
#if GMX_USE_TNG
"spc2-traj.tng",
"spc2-traj.g96"
};
-#ifdef __INTEL_COMPILER
-#pragma warning( disable : 177 )
-#endif
-
-INSTANTIATE_TEST_CASE_P(NoFatalErrorWhenWritingFrom,
- GmxTraj,
- ::testing::ValuesIn(gmx::ArrayRef<const char*>(trajectoryFileNames)));
-
INSTANTIATE_TEST_CASE_P(NoFatalErrorWhenWritingFrom,
TrjconvWithIndexGroupSubset,
- ::testing::ValuesIn(gmx::ArrayRef<const char*>(trajectoryFileNames)));
+ ::testing::ValuesIn(trajectoryFileNames));
} // namespace
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
cr->nnodes = gmx_node_num();
cr->nodeid = gmx_node_rank();
+ if (PAR(cr) || MULTISIM(cr))
+ {
+ MPI_Comm_split(MPI_COMM_WORLD, gmx_physicalnode_id_hash(), cr->nodeid, &cr->mpi_comm_physicalnode);
+ }
cr->sim_nodeid = cr->nodeid;
cr->mpi_comm_mysim = MPI_COMM_WORLD;
cr->mpi_comm_mygroup = MPI_COMM_WORLD;
#if GMX_LIB_MPI
gmx_fill_commrec_from_mpi(cr);
#else
- cr->mpi_comm_mysim = NULL;
- cr->mpi_comm_mygroup = NULL;
+ cr->mpi_comm_mysim = nullptr;
+ cr->mpi_comm_mygroup = nullptr;
cr->nnodes = 1;
cr->sim_nodeid = 0;
cr->nodeid = cr->sim_nodeid;
return cr;
}
+static void done_mpi_in_place_buf(mpi_in_place_buf_t *buf)
+{
+ if (nullptr != buf)
+ {
+ sfree(buf->ibuf);
+ sfree(buf->libuf);
+ sfree(buf->fbuf);
+ sfree(buf->dbuf);
+ sfree(buf);
+ }
+}
+
+void done_commrec(t_commrec *cr)
+{
+#if GMX_MPI
+ if (PAR(cr) || MULTISIM(cr))
+ {
+ MPI_Comm_free(&cr->mpi_comm_physicalnode);
+ }
+#endif
+ if (nullptr != cr->dd)
+ {
+ // TODO: implement
+ // done_domdec(cr->dd);
+ }
+ if (nullptr != cr->ms)
+ {
+ done_mpi_in_place_buf(cr->ms->mpb);
+ sfree(cr->ms);
+ }
+ done_mpi_in_place_buf(cr->mpb);
+ sfree(cr);
+}
+
t_commrec *reinitialize_commrec_for_this_thread(const t_commrec gmx_unused *cro)
{
#if GMX_THREAD_MPI
return cr;
#else
- return NULL;
+ return nullptr;
#endif
}
ng, ni);
}
- if (getenv("GMX_NO_NODECOMM") == NULL &&
+ if (getenv("GMX_NO_NODECOMM") == nullptr &&
((ng > 1 && ng < n) || (ni > 1 && ni < n)))
{
nc->bUse = TRUE;
#endif
}
+void gmx_barrier_physical_node(const t_commrec gmx_unused *cr)
+{
+#if !GMX_MPI
+ gmx_call("gmx_barrier_physical_node");
+#else
+ MPI_Barrier(cr->mpi_comm_physicalnode);
+#endif
+}
+
void gmx_bcast(int gmx_unused nbytes, void gmx_unused *b, const t_commrec gmx_unused *cr)
{
#if !GMX_MPI
{
/* This is here because of the silly MPI specification
that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
- MPI_Reduce(r, NULL, nr, MPI_DOUBLE, MPI_SUM, 0, cr->nc.comm_intra);
+ MPI_Reduce(r, nullptr, nr, MPI_DOUBLE, MPI_SUM, 0, cr->nc.comm_intra);
}
MPI_Bcast(r, nr, MPI_DOUBLE, 0, cr->nc.comm_intra);
}
{
/* This is here because of the silly MPI specification
that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
- MPI_Reduce(r, NULL, nr, MPI_FLOAT, MPI_SUM, 0, cr->nc.comm_intra);
+ MPI_Reduce(r, nullptr, nr, MPI_FLOAT, MPI_SUM, 0, cr->nc.comm_intra);
}
MPI_Bcast(r, nr, MPI_FLOAT, 0, cr->nc.comm_intra);
}
{
/* This is here because of the silly MPI specification
that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
- MPI_Reduce(r, NULL, nr, MPI_INT, MPI_SUM, 0, cr->nc.comm_intra);
+ MPI_Reduce(r, nullptr, nr, MPI_INT, MPI_SUM, 0, cr->nc.comm_intra);
}
MPI_Bcast(r, nr, MPI_INT, 0, cr->nc.comm_intra);
}
{
/* This is here because of the silly MPI specification
that MPI_IN_PLACE should be put in sendbuf instead of recvbuf */
- MPI_Reduce(r, NULL, nr, MPI_INT64_T, MPI_SUM, 0, cr->nc.comm_intra);
+ MPI_Reduce(r, nullptr, nr, MPI_INT64_T, MPI_SUM, 0, cr->nc.comm_intra);
}
MPI_Bcast(r, nr, MPI_INT64_T, 0, cr->nc.comm_intra);
}
const char *opt2fn_master(const char *opt, int nfile, const t_filenm fnm[],
t_commrec *cr)
{
- return SIMMASTER(cr) ? opt2fn(opt, nfile, fnm) : NULL;
+ return SIMMASTER(cr) ? opt2fn(opt, nfile, fnm) : nullptr;
}
void gmx_fatal_collective(int f_errno, const char *file, int line,
/* Any result except MPI_UNEQUAL allows us to call MPI_Finalize */
bFinalize = (result != MPI_UNEQUAL);
#else
+ GMX_UNUSED_VALUE(comm);
bFinalize = TRUE;
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_commrec *init_commrec(void);
/* Allocate, initialize and return the commrec. */
+void done_commrec(struct t_commrec *cr);
+/* Free memory associated with the commrec. */
+
struct t_commrec *reinitialize_commrec_for_this_thread(const struct t_commrec *cro);
/* Initialize communication records for thread-parallel simulations.
Must be called on all threads before any communication takes place by
void gmx_barrier(const struct t_commrec *cr);
/* Wait till all processes in cr->mpi_comm_mygroup have reached the barrier */
+void gmx_barrier_physical_node(const struct t_commrec *cr);
+/* Wait till all processes in cr->mpi_comm_physical_node have reached the barrier */
+
void gmx_bcast(int nbytes, void *b, const struct t_commrec *cr);
/* Broadcast nbytes bytes from the master to cr->mpi_comm_mygroup */
# Sources that should always be built
file(GLOB NONBONDED_SOURCES *.cpp nb_kernel_c/*.c)
-if("${GMX_SIMD}" STREQUAL "SSE2" AND NOT GMX_DOUBLE)
+if("${GMX_SIMD_ACTIVE}" STREQUAL "SSE2" AND NOT GMX_DOUBLE)
file(GLOB NONBONDED_SSE2_SINGLE_SOURCES nb_kernel_sse2_single/*.c)
endif()
-if("${GMX_SIMD}" STREQUAL "SSE4.1" AND NOT GMX_DOUBLE)
+if("${GMX_SIMD_ACTIVE}" STREQUAL "SSE4.1" AND NOT GMX_DOUBLE)
file(GLOB NONBONDED_SSE4_1_SINGLE_SOURCES nb_kernel_sse4_1_single/*.c)
endif()
-if("${GMX_SIMD}" STREQUAL "AVX_128_FMA" AND NOT GMX_DOUBLE)
+if("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_128_FMA" AND NOT GMX_DOUBLE)
file(GLOB NONBONDED_AVX_128_FMA_SINGLE_SOURCES nb_kernel_avx_128_fma_single/*.c)
endif()
-if((("${GMX_SIMD}" STREQUAL "AVX_256")
- OR ("${GMX_SIMD}" STREQUAL "AVX2_256")
- OR ("${GMX_SIMD}" STREQUAL "AVX_512")
- OR ("${GMX_SIMD}" STREQUAL "AVX_512_KNL"))
+if((("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_256")
+ OR ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX2_256")
+ OR ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512")
+ OR ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
AND NOT GMX_DOUBLE)
file(GLOB NONBONDED_AVX_256_SINGLE_SOURCES nb_kernel_avx_256_single/*.c)
endif()
-if("${GMX_SIMD}" STREQUAL "SSE2" AND GMX_DOUBLE)
+if("${GMX_SIMD_ACTIVE}" STREQUAL "SSE2" AND GMX_DOUBLE)
file(GLOB NONBONDED_SSE2_DOUBLE_SOURCES nb_kernel_sse2_double/*.c)
endif()
-if("${GMX_SIMD}" STREQUAL "SSE4.1" AND GMX_DOUBLE)
+if("${GMX_SIMD_ACTIVE}" STREQUAL "SSE4.1" AND GMX_DOUBLE)
file(GLOB NONBONDED_SSE4_1_DOUBLE_SOURCES nb_kernel_sse4_1_double/*.c)
endif()
-if("${GMX_SIMD}" STREQUAL "AVX_128_FMA" AND GMX_DOUBLE)
+if("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_128_FMA" AND GMX_DOUBLE)
file(GLOB NONBONDED_AVX_128_FMA_DOUBLE_SOURCES nb_kernel_avx_128_fma_double/*.c)
endif()
-if((("${GMX_SIMD}" STREQUAL "AVX_256")
- OR ("${GMX_SIMD}" STREQUAL "AVX2_256")
- OR ("${GMX_SIMD}" STREQUAL "AVX_512")
- OR ("${GMX_SIMD}" STREQUAL "AVX_512_KNL"))
+if((("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_256")
+ OR ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX2_256")
+ OR ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512")
+ OR ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
AND GMX_DOUBLE)
file(GLOB NONBONDED_AVX_256_DOUBLE_SOURCES nb_kernel_avx_256_double/*.c)
endif()
-if("${GMX_SIMD}" STREQUAL "SPARC64_HPC_ACE" AND GMX_DOUBLE)
+if("${GMX_SIMD_ACTIVE}" STREQUAL "SPARC64_HPC_ACE" AND GMX_DOUBLE)
file(GLOB NONBONDED_SPARC64_HPC_ACE_DOUBLE_SOURCES nb_kernel_sparc64_hpc_ace_double/*.c)
endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const real * shiftvec;
real * fshift;
real tabscale = 0;
- const real * VFtab = NULL;
+ const real * VFtab = nullptr;
const real * x;
real * f;
real facel, krf, crf;
tj[STATE_A] = ntiA+2*typeA[jnr];
tj[STATE_B] = ntiB+2*typeB[jnr];
- if (nlist->excl_fep == NULL || nlist->excl_fep[k])
+ if (nlist->excl_fep == nullptr || nlist->excl_fep[k])
{
c6[STATE_A] = nbfp[tj[STATE_A]];
c6[STATE_B] = nbfp[tj[STATE_B]];
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
else
{
tabscale = 0;
- VFtab = NULL;
+ VFtab = nullptr;
}
ewtab = fr->ic->tabq_coul_FDV0;
ewtabscale = fr->ic->tabq_scale;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
else
{
tabscale = 0;
- VFtab = NULL;
+ VFtab = nullptr;
}
/* avoid compiler warnings for cases that cannot happen */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Static data structures to find kernels */
-static nb_kernel_info_t * kernel_list = NULL;
+static nb_kernel_info_t * kernel_list = nullptr;
static unsigned int kernel_list_size = 0;
-static int * kernel_list_hash = NULL;
+static int * kernel_list_hash = nullptr;
static unsigned int kernel_list_hash_size = 0;
static unsigned int
return 0;
}
-void
-nb_kernel_list_hash_destroy()
-{
- sfree(kernel_list_hash);
- kernel_list_hash = NULL;
- kernel_list_hash_size = 0;
-}
-
-
nb_kernel_t *
nb_kernel_list_findkernel(FILE gmx_unused * log,
const char * arch,
if (kernel_list_hash_size == 0)
{
- return NULL;
+ return nullptr;
}
index = nb_kernel_hash_func(arch,
other,
vf) % kernel_list_hash_size;
- kernelinfo_ptr = NULL;
+ kernelinfo_ptr = nullptr;
while ( (i = kernel_list_hash[index]) != -1)
{
if (!gmx_strcasecmp_min(kernel_list[i].architecture, arch) &&
index = (index+1) % kernel_list_hash_size;
}
- if (debug && kernelinfo_ptr != NULL)
+ if (debug && kernelinfo_ptr != nullptr)
{
fprintf(debug,
"NB kernel %s() with architecture '%s' used for neighborlist with\n"
}
/* If we did not find any kernel the pointer will still be NULL */
- return (kernelinfo_ptr != NULL) ? kernelinfo_ptr->kernelptr : NULL;
+ return (kernelinfo_ptr != nullptr) ? kernelinfo_ptr->kernelptr : nullptr;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_t (t_nblist * nlist,
rvec * x,
rvec * f,
- t_forcerec * fr,
+ struct t_forcerec * fr,
t_mdatoms * mdatoms,
nb_kernel_data_t * kernel_data,
t_nrnb * nrnb);
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define gmx_mm_castsi128_ps _mm_castsi128_ps
#define gmx_mm_extract_epi32 _mm_extract_epi32
-/* Work around gcc bug with wrong type for mask formal parameter to maskload/maskstore */
-#if GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
-# define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), _mm_castsi128_ps(mask))
-# define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), _mm_castsi128_ps(mask), (x))
-# define gmx_mm256_maskload_ps(mem, mask) _mm256_maskload_ps((mem), _mm256_castsi256_ps(mask))
-# define gmx_mm256_maskstore_ps(mem, mask, x) _mm256_maskstore_ps((mem), _mm256_castsi256_ps(mask), (x))
-#else
-# define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), (mask))
-# define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), (mask), (x))
-# define gmx_mm256_maskload_ps(mem, mask) _mm256_maskload_ps((mem), (mask))
-# define gmx_mm256_maskstore_ps(mem, mask, x) _mm256_maskstore_ps((mem), (mask), (x))
-#endif
+#define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), (mask))
+#define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), (mask), (x))
+#define gmx_mm256_maskload_ps(mem, mask) _mm256_maskload_ps((mem), (mask))
+#define gmx_mm256_maskstore_ps(mem, mask, x) _mm256_maskstore_ps((mem), (mask), (x))
/* Normal sum of four xmm registers */
#define gmx_mm_sum4_ps(t0, t1, t2, t3) _mm_add_ps(_mm_add_ps(t0, t1), _mm_add_ps(t2, t3))
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return _mm256_insertf128_ps(_mm256_castps128_ps256(lo), hi, 0x1);
}
-/* Work around gcc bug with wrong type for mask formal parameter to maskload/maskstore */
-#if GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
-# define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), _mm_castsi128_ps(mask))
-# define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), _mm_castsi128_ps(mask), (x))
-# define gmx_mm256_maskload_ps(mem, mask) _mm256_maskload_ps((mem), _mm256_castsi256_ps(mask))
-# define gmx_mm256_maskstore_ps(mem, mask, x) _mm256_maskstore_ps((mem), _mm256_castsi256_ps(mask), (x))
-#else
-# define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), (mask))
-# define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), (mask), (x))
-# define gmx_mm256_maskload_ps(mem, mask) _mm256_maskload_ps((mem), (mask))
-# define gmx_mm256_maskstore_ps(mem, mask, x) _mm256_maskstore_ps((mem), (mask), (x))
-#endif
+#define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), (mask))
+#define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), (mask), (x))
+#define gmx_mm256_maskload_ps(mem, mask) _mm256_maskload_ps((mem), (mask))
+#define gmx_mm256_maskstore_ps(mem, mask, x) _mm256_maskstore_ps((mem), (mask), (x))
/* Transpose lower/upper half of 256-bit registers separately */
#define GMX_MM256_HALFTRANSPOSE4_PS(ymm0, ymm1, ymm2, ymm3) { \
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014.2015')
+FileHeader = create_copyright_header('2012,2013,2014.2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014.2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014.2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_allvsall(t_nblist gmx_unused * nlist,
rvec * xx,
rvec * ff,
- t_forcerec * fr,
+ struct t_forcerec * fr,
t_mdatoms * mdatoms,
nb_kernel_data_t * kernel_data,
t_nrnb * nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_allvsall(t_nblist * nlist,
rvec * x,
rvec * f,
- t_forcerec * fr,
+ struct t_forcerec * fr,
t_mdatoms * mdatoms,
nb_kernel_data_t * kernel_data,
t_nrnb * nrnb);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_allvsallgb(t_nblist gmx_unused * nlist,
rvec * xx,
rvec * ff,
- t_forcerec * fr,
+ struct t_forcerec * fr,
t_mdatoms * mdatoms,
nb_kernel_data_t * kernel_data,
t_nrnb * nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nb_kernel_allvsallgb(t_nblist * nlist,
rvec * x,
rvec * f,
- t_forcerec * fr,
+ struct t_forcerec * fr,
t_mdatoms * mdatoms,
nb_kernel_data_t * kernel_data,
t_nrnb * nrnb);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# 'cutoff' means the interaction is set to 0.0 outside the cutoff
#
-FileHeader = create_copyright_header('2012,2013,2014,2015')
+FileHeader = create_copyright_header('2012,2013,2014,2015,2017')
FileHeader += """/*
* Note: this file was generated by the GROMACS """+Arch+""" kernel generator.
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
(t_nblist * gmx_restrict nlist,
rvec * gmx_restrict xx,
rvec * gmx_restrict ff,
- t_forcerec * gmx_restrict fr,
+ struct t_forcerec * gmx_restrict fr,
t_mdatoms * gmx_restrict mdatoms,
nb_kernel_data_t gmx_unused * gmx_restrict kernel_data,
t_nrnb * gmx_restrict nrnb)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Add the generic kernels to the structure stored statically in nb_kernel.c */
nb_kernel_list_add_kernels(kernellist_c, kernellist_c_size);
- if (!(fr != NULL && fr->use_simd_kernels == FALSE))
+ if (!(fr != nullptr && fr->use_simd_kernels == FALSE))
{
/* Add interaction-specific kernels for different architectures */
/* Single precision */
/* We typically call this setup routine before starting timers,
* but if that has not been done for whatever reason we do it now.
*/
- gmx_nonbonded_setup(NULL, FALSE);
+ gmx_nonbonded_setup(nullptr, FALSE);
}
/* Not used yet */
other = "";
- nl->kernelptr_vf = NULL;
- nl->kernelptr_v = NULL;
- nl->kernelptr_f = NULL;
+ nl->kernelptr_vf = nullptr;
+ nl->kernelptr_v = nullptr;
+ nl->kernelptr_f = nullptr;
elec = gmx_nbkernel_elec_names[nl->ielec];
elec_mod = eintmod_names[nl->ielecmod];
{
/* Try to find a specific kernel first */
- for (i = 0; i < narch && nl->kernelptr_vf == NULL; i++)
+ for (i = 0; i < narch && nl->kernelptr_vf == nullptr; i++)
{
nl->kernelptr_vf = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
}
- for (i = 0; i < narch && nl->kernelptr_f == NULL; i++)
+ for (i = 0; i < narch && nl->kernelptr_f == nullptr; i++)
{
nl->kernelptr_f = (void *) nb_kernel_list_findkernel(log, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "Force");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
/* If there is not force-only optimized kernel, is there a potential & force one? */
- if (nl->kernelptr_f == NULL)
+ if (nl->kernelptr_f == nullptr)
{
- nl->kernelptr_f = (void *) nb_kernel_list_findkernel(NULL, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
+ nl->kernelptr_f = (void *) nb_kernel_list_findkernel(nullptr, arch_and_padding[i].arch, elec, elec_mod, vdw, vdw_mod, geom, other, "PotentialAndForce");
nl->simd_padding_width = arch_and_padding[i].simd_padding_width;
}
}
(nl->ivdw != GMX_NBKERNEL_VDW_NONE) && (nl->ivdwmod == eintmodPOTSWITCH) &&
bElecAndVdwSwitchDiffers)
{
- nl->kernelptr_vf = NULL;
- nl->kernelptr_f = NULL;
+ nl->kernelptr_vf = nullptr;
+ nl->kernelptr_f = nullptr;
}
/* Give up, pick a generic one instead.
* We only do this for particle-particle kernels; by leaving the water-optimized kernel
* pointers to NULL, the water optimization will automatically be disabled for this interaction.
*/
- if (nl->kernelptr_vf == NULL && !gmx_strcasecmp_min(geom, "Particle-Particle"))
+ if (nl->kernelptr_vf == nullptr && !gmx_strcasecmp_min(geom, "Particle-Particle"))
{
nl->kernelptr_vf = (void *) gmx_nb_generic_kernel;
nl->kernelptr_f = (void *) gmx_nb_generic_kernel;
int n, n0, n1, i, i0, i1;
t_nblists * nblists;
nb_kernel_data_t kernel_data;
- nb_kernel_t * kernelptr = NULL;
+ nb_kernel_t * kernelptr = nullptr;
rvec * f;
kernel_data.flags = flags;
continue;
}
/* Neighborlists whose kernelptr==NULL will always be empty */
- if (kernelptr != NULL)
+ if (kernelptr != nullptr)
{
(*kernelptr)(&(nlist[i]), x, f, fr, mdatoms, &kernel_data, nrnb);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*nbfs = 0.0;
for (i = 0; (i < eNR_NBKERNEL_ALLVSALLGB); i++)
{
- if (std::strstr(nbdata[i].name, "W3-W3") != NULL)
+ if (std::strstr(nbdata[i].name, "W3-W3") != nullptr)
{
*nbfs += 9e-6*nrnb->n[i];
}
- else if (std::strstr(nbdata[i].name, "W3") != NULL)
+ else if (std::strstr(nbdata[i].name, "W3") != nullptr)
{
*nbfs += 3e-6*nrnb->n[i];
}
- else if (std::strstr(nbdata[i].name, "W4-W4") != NULL)
+ else if (std::strstr(nbdata[i].name, "W4-W4") != nullptr)
{
*nbfs += 10e-6*nrnb->n[i];
}
- else if (std::strstr(nbdata[i].name, "W4") != NULL)
+ else if (std::strstr(nbdata[i].name, "W4") != nullptr)
{
*nbfs += 4e-6*nrnb->n[i];
}
*mflop += mni*flop;
frac = 100.0*mni*flop/tflop;
tfrac += frac;
- if (out != NULL)
+ if (out != nullptr)
{
fprintf(out, " %-32s %16.6f %15.3f %6.1f\n",
nbdata[i].name, mni, mni*flop, frac);
mflop = mflop/time_per_node;
wallclocktime = nsteps*delta_t;
- if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
+ if (getenv("GMX_DETAILED_PERF_STATS") == nullptr)
{
fprintf(out, "%12s %12s %12s\n",
"", "(ns/day)", "(hour/ns)");
}
else
{
- if (getenv("GMX_DETAILED_PERF_STATS") == NULL)
+ if (getenv("GMX_DETAILED_PERF_STATS") == nullptr)
{
fprintf(out, "%12s %14s\n",
"", "(steps/hour)");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* This file is completely threadsafe - keep it that way! */
#include "gmxpre.h"
+#include "add_par.h"
+
#include <string.h>
#include <algorithm>
ps->param[ps->nr].ai() = ai;
ps->param[ps->nr].aj() = aj;
clear_atom_list(2, ps->param[ps->nr].a);
- if (c == NULL)
+ if (c == nullptr)
{
clear_force_param(0, ps->param[ps->nr].c);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string.h>
+#include <cassert>
#include <cmath>
#include "gromacs/gmxpreprocess/gpp_atomtype.h"
/* Type==-1 is used as a signal that this interaction is all-zero and should not be added. */
if (!bNB && type >= 0)
{
+ assert(il);
nral = NRAL(ftype);
delta = nr*(nral+1);
srenew(il->iatoms, il->nr+delta);
ffp = &mtop->ffparams;
ffp->ntypes = 0;
ffp->atnr = atnr;
- ffp->functype = NULL;
- ffp->iparams = NULL;
+ ffp->functype = nullptr;
+ ffp->iparams = nullptr;
ffp->reppow = reppow;
- enter_function(&(nbtypes[F_LJ]), (t_functype)F_LJ, comb, reppow, ffp, NULL,
+ enter_function(&(nbtypes[F_LJ]), (t_functype)F_LJ, comb, reppow, ffp, nullptr,
&maxtypes, TRUE, TRUE);
- enter_function(&(nbtypes[F_BHAM]), (t_functype)F_BHAM, comb, reppow, ffp, NULL,
+ enter_function(&(nbtypes[F_BHAM]), (t_functype)F_BHAM, comb, reppow, ffp, nullptr,
&maxtypes, TRUE, TRUE);
for (mt = 0; mt < mtop->nmoltype; mt++)
for (i = 0; (i < F_NRE); i++)
{
molt->ilist[i].nr = 0;
- molt->ilist[i].iatoms = NULL;
+ molt->ilist[i].iatoms = nullptr;
plist = mi[mt].plist;
}
mtop->bIntermolecularInteractions = FALSE;
- if (intermolecular_interactions != NULL)
+ if (intermolecular_interactions != nullptr)
{
/* Process the intermolecular interaction list */
snew(mtop->intermolecular_ilist, F_NRE);
for (i = 0; (i < F_NRE); i++)
{
mtop->intermolecular_ilist[i].nr = 0;
- mtop->intermolecular_ilist[i].iatoms = NULL;
+ mtop->intermolecular_ilist[i].iatoms = nullptr;
plist = intermolecular_interactions->plist;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char *ptr;
cptr = strrchr(filename, DIR_SEPARATOR);
- if (cptr != NULL)
+ if (cptr != nullptr)
{
/* Skip the separator */
cptr += 1;
strcpy(filebase, cptr);
/* Remove the extension */
ptr = strrchr(filebase, '.');
- if (ptr != NULL)
+ if (ptr != nullptr)
{
ptr[0] = '\0';
}
file_fullpath = low_gmxlibfn(file, TRUE, FALSE);
- if (file_fullpath == NULL)
+ if (file_fullpath == nullptr)
{
return FALSE;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/smalloc.h"
#define DIHEDRAL_WAS_SET_IN_RTP 0
-static gmx_bool was_dihedral_set_in_rtp(t_param *dih)
+static gmx_bool was_dihedral_set_in_rtp(const t_param *dih)
{
return dih->c[MAXFORCEPARAM-1] == DIHEDRAL_WAS_SET_IN_RTP;
}
static int acomp(const void *a1, const void *a2)
{
- t_param *p1, *p2;
- int ac;
+ const t_param *p1, *p2;
+ int ac;
- p1 = (t_param *)a1;
- p2 = (t_param *)a2;
+ p1 = static_cast<const t_param *>(a1);
+ p2 = static_cast<const t_param *>(a2);
if ((ac = (p1->aj()-p2->aj())) != 0)
{
return ac;
static int pcomp(const void *a1, const void *a2)
{
- t_param *p1, *p2;
- int pc;
+ const t_param *p1, *p2;
+ int pc;
- p1 = (t_param *)a1;
- p2 = (t_param *)a2;
+ p1 = static_cast<const t_param *>(a1);
+ p2 = static_cast<const t_param *>(a2);
if ((pc = (p1->ai()-p2->ai())) != 0)
{
return pc;
static int dcomp(const void *d1, const void *d2)
{
- t_param *p1, *p2;
- int dc;
+ const t_param *p1, *p2;
+ int dc;
- p1 = (t_param *)d1;
- p2 = (t_param *)d2;
+ p1 = static_cast<const t_param *>(d1);
+ p2 = static_cast<const t_param *>(d2);
/* First sort by J & K (the two central) atoms */
if ((dc = (p1->aj()-p2->aj())) != 0)
{
static int idcomp(const void *a, const void *b)
{
- t_param *pa, *pb;
- int d;
+ const t_param *pa, *pb;
+ int d;
- pa = (t_param *)a;
- pb = (t_param *)b;
+ pa = static_cast<const t_param *>(a);
+ pb = static_cast<const t_param *>(b);
if ((d = (pa->a[0]-pb->a[0])) != 0)
{
return d;
/* Add all the impropers from the residue database to the list. */
nimproper = 0;
start = 0;
- if (hb != NULL)
+ if (hb != nullptr)
{
for (i = 0; (i < atoms->nres); i++)
{
srenew(*improper, nalloc);
}
/* Not broken out */
- set_p(&((*improper)[nimproper]), ai, NULL, impropers->b[j].s);
+ set_p(&((*improper)[nimproper]), ai, nullptr, impropers->b[j].s);
nimproper++;
}
}
return NRE;
}
-gmx_bool is_hydro(t_atoms *atoms, int ai)
+static gmx_bool is_hydro(t_atoms *atoms, int ai)
{
return ((*(atoms->atomname[ai]))[0] == 'H');
}
real boltz, sd;
real ekin, temp, mass, scal;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
+ const t_atom *atom;
gmx::TabulatedNormalDistribution<real> normalDist;
boltz = BOLTZ*tempi;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(vsiteconflist, 1);
snew(vsitetoplist, 1);
- while (fgets2(pline, STRLEN-2, ddb) != NULL)
+ while (fgets2(pline, STRLEN-2, ddb) != nullptr)
{
strip_comment(pline);
trim(pline);
if (pline[0] == OPENDIR)
{
strncpy(dirstr, pline+1, STRLEN-2);
- if ((ch = strchr (dirstr, CLOSEDIR)) != NULL)
+ if ((ch = strchr (dirstr, CLOSEDIR)) != nullptr)
{
(*ch) = 0;
}
srenew(vsitetoplist[i].bond, k+1);
strncpy(vsitetoplist[i].bond[k].atom1, s1, MAXNAME-1);
strncpy(vsitetoplist[i].bond[k].atom2, s2, MAXNAME-1);
- vsitetoplist[i].bond[k].value = strtod(s3, NULL);
+ vsitetoplist[i].bond[k].value = strtod(s3, nullptr);
}
else if (n == 4)
{
strncpy(vsitetoplist[i].angle[k].atom1, s1, MAXNAME-1);
strncpy(vsitetoplist[i].angle[k].atom2, s2, MAXNAME-1);
strncpy(vsitetoplist[i].angle[k].atom3, s3, MAXNAME-1);
- vsitetoplist[i].angle[k].value = strtod(s4, NULL);
+ vsitetoplist[i].angle[k].value = strtod(s4, nullptr);
}
else
{
}
else
{
- return NULL;
+ return nullptr;
}
}
{ NOTSET, NOTSET, NOTSET, NOTSET, NOTSET, NOTSET };
c[0] = b;
- add_param(plist, ai, aj, c, NULL);
+ add_param(plist, ai, aj, c, nullptr);
}
static void add_vsites(t_params plist[], int vsite_type[],
srenew(*newcgnr, at->nr+*nadd);
for (j = 0; j < NMASS; j++)
{
- (*newatomname)[at->nr+*nadd-1-j] = NULL;
+ (*newatomname)[at->nr+*nadd-1-j] = nullptr;
}
/* Dummy masses will be placed at the center-of-mass in each ring. */
srenew(*newatomname, at->nr+*nadd);
srenew(*newvsite_type, at->nr+*nadd);
srenew(*newcgnr, at->nr+*nadd);
- (*newatomname)[at->nr+*nadd-1] = NULL;
+ (*newatomname)[at->nr+*nadd-1] = nullptr;
/* Calc the dummy mass initial position */
rvec_sub(x[ats[atHH]], x[ats[atOH]], r1);
t_atom *newatom;
t_params *params;
char ***newatomname;
- char *resnm = NULL;
+ char *resnm = nullptr;
int ndb, f;
char **db;
int nvsiteconf, nvsitetop, cmplength;
{ "CG", /* PHE */
"CD1", "HD1", "CD2", "HD2",
"CE1", "HE1", "CE2", "HE2",
- "CZ", "HZ", NULL },
+ "CZ", "HZ", nullptr },
{ "CB", /* TRP */
"CG",
"CD1", "HD1", "CD2",
"NE1", "HE1", "CE2", "CE3", "HE3",
"CZ2", "HZ2", "CZ3", "HZ3",
- "CH2", "HH2", NULL },
+ "CH2", "HH2", nullptr },
{ "CG", /* TYR */
"CD1", "HD1", "CD2", "HD2",
"CE1", "HE1", "CE2", "HE2",
- "CZ", "OH", "HH", NULL },
+ "CZ", "OH", "HH", nullptr },
{ "CG", /* HIS */
"ND1", "HD1", "CD2", "HD2",
- "CE1", "HE1", "NE2", "HE2", NULL }
+ "CE1", "HE1", "NE2", "HE2", nullptr }
};
if (debug)
ndb = fflib_search_file_end(ffdir, ".vsd", FALSE, &db);
nvsiteconf = 0;
- vsiteconflist = NULL;
+ vsiteconflist = nullptr;
nvsitetop = 0;
- vsitetop = NULL;
+ vsitetop = nullptr;
for (f = 0; f < ndb; f++)
{
read_vsite_database(db[f], &vsiteconflist, &nvsiteconf, &vsitetop, &nvsitetop);
strcpy(nexttpname, get_atomtype_name(get_atype(heavies[0], at, nrtp, rtp, rt), atype));
ch = get_dummymass_name(vsiteconflist, nvsiteconf, tpname, nexttpname);
- if (ch == NULL)
+ if (ch == nullptr)
{
if (ndb > 0)
{
for (j = 0; j < NMASS; j++)
{
- newatomname[at->nr+nadd-1-j] = NULL;
+ newatomname[at->nr+nadd-1-j] = nullptr;
}
/* calculate starting position for the masses */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/3dtransforms.h"
#include "gromacs/math/utilities.h"
t_filenm fnm[] = {
{ efSTX, "-f", "conf", ffREAD },
{ efSTO, "-o", "out", ffWRITE },
- { efTRX, "-trj", NULL, ffOPTRD }
+ { efTRX, "-trj", nullptr, ffOPTRD }
};
#define NFILE asize(fnm)
- static rvec nrbox = {1, 1, 1};
- static int seed = 0; /* seed for random number generator */
- static gmx_bool bRandom = FALSE; /* False: no random rotations */
- static gmx_bool bRenum = TRUE; /* renumber residues */
- static rvec dist = {0, 0, 0}; /* space added between molecules ? */
- static rvec max_rot = {180, 180, 180}; /* maximum rotation */
+ rvec nrbox = {1, 1, 1};
+ int seed = 0; /* seed for random number generator */
+ gmx_bool bRandom = FALSE; /* False: no random rotations */
+ gmx_bool bRenum = TRUE; /* renumber residues */
+ rvec dist = {0, 0, 0}; /* space added between molecules ? */
+ rvec max_rot = {180, 180, 180}; /* maximum rotation */
t_pargs pa[] = {
{ "-nbox", FALSE, etRVEC, {nrbox}, "Number of boxes" },
{ "-dist", FALSE, etRVEC, {dist}, "Distance between boxes" },
}
if (bTRX)
{
- close_trj(status);
+ close_trx(status);
}
/* make box bigger */
write_sto_conf(opt2fn("-o", NFILE, fnm), *top->name, atoms, x, v, ePBC, box);
+ sfree(x);
+ sfree(v);
+ sfree(xrot);
+ sfree(vrot);
+ sfree(xx);
+ done_top(top);
+ sfree(top);
+ done_filenms(NFILE, fnm);
+ output_env_done(oenv);
+
return 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return;
}
-void dump_ab(FILE *out, int natom, int nab[], t_hack *ab[], gmx_bool bHeader)
+static void dump_ab(FILE *out, int natom, int nab[], t_hack *ab[], gmx_bool bHeader)
{
int i, j;
/* first the termini */
for (i = 0; i < nterpairs; i++)
{
- if (ntdb[i] != NULL)
+ if (ntdb[i] != nullptr)
{
copy_t_hackblock(ntdb[i], &hb[rN[i]]);
}
- if (ctdb[i] != NULL)
+ if (ctdb[i] != nullptr)
{
merge_t_hackblock(ctdb[i], &hb[rC[i]]);
}
ahptr = search_h_db(nah, ah, *pdba->resinfo[rnr].rtp);
if (ahptr)
{
- if (hb[rnr].name == NULL)
+ if (hb[rnr].name == nullptr)
{
hb[rnr].name = gmx_strdup(ahptr->name);
}
}
if (!bIgnore &&
- ( ( ( hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL ) &&
+ ( ( ( hbr->hack[j].tp > 0 || hbr->hack[j].oname == nullptr ) &&
strcmp(atomname, hbr->hack[j].ai()) == 0 ) ||
- ( hbr->hack[j].oname != NULL &&
+ ( hbr->hack[j].oname != nullptr &&
strcmp(atomname, hbr->hack[j].oname) == 0) ) )
{
/* now expand all hacks for this atom */
(*abi)[*nabi + k].bXSet = FALSE;
/* if we're adding (oname==NULL) and don't have a new name (nname)
yet, build it from atomname */
- if ( (*abi)[*nabi + k].nname == NULL)
+ if ( (*abi)[*nabi + k].nname == nullptr)
{
- if ( (*abi)[*nabi + k].oname == NULL)
+ if ( (*abi)[*nabi + k].oname == nullptr)
{
(*abi)[*nabi + k].nname = gmx_strdup(atomname);
(*abi)[*nabi + k].nname[0] = 'H';
(*nabi) += hbr->hack[j].nr;
/* add hacks to atoms we've just added */
- if (hbr->hack[j].tp > 0 || hbr->hack[j].oname == NULL)
+ if (hbr->hack[j].tp > 0 || hbr->hack[j].oname == nullptr)
{
for (k = 0; k < hbr->hack[j].nr; k++)
{
rnr = pdba->atom[i].resind;
for (j = 0; j < nab[i]; j++)
{
- if (ab[i][j].oname == NULL)
+ if (ab[i][j].oname == nullptr)
{
/* we're adding */
- if (ab[i][j].nname == NULL)
+ if (ab[i][j].nname == nullptr)
{
gmx_incons("ab[i][j].nname not allocated");
}
nadd++;
}
}
- else if (ab[i][j].nname == NULL)
+ else if (ab[i][j].nname == nullptr)
{
/* we're deleting */
nadd--;
for (j = 0; j < nab[i]; j += ab[i][j].nr)
{
/* check if we're adding: */
- if (ab[i][j].oname == NULL && ab[i][j].tp > 0)
+ if (ab[i][j].oname == nullptr && ab[i][j].tp > 0)
{
bFoundAll = TRUE;
for (m = 0; (m < ab[i][j].nctl && bFoundAll); m++)
int **nabptr, t_hack ***abptr,
gmx_bool bUpdate_pdba, gmx_bool bKeep_old_pdba)
{
- t_atoms *newpdba = NULL, *pdba = NULL;
+ t_atoms *newpdba = nullptr, *pdba = nullptr;
int nadd;
int i, newi, j, natoms, nalreadypresent;
- int *nab = NULL;
- t_hack **ab = NULL;
+ int *nab = nullptr;
+ t_hack **ab = nullptr;
t_hackblock *hb;
rvec *xn;
gmx_bool bKeep_ab;
for (i = 0; (i < natoms); i++)
{
/* check if this atom wasn't scheduled for deletion */
- if (nab[i] == 0 || (ab[i][0].nname != NULL) )
+ if (nab[i] == 0 || (ab[i][0].nname != nullptr) )
{
if (newi >= natoms+nadd)
{
nalreadypresent = 0;
for (j = 0; j < nab[i]; j++)
{
- if (ab[i][j].oname == NULL) /* add */
+ if (ab[i][j].oname == nullptr) /* add */
{
newi++;
if (newi >= natoms+nadd)
fprintf(debug, " + %d", newi+1);
}
}
- if (ab[i][j].nname != NULL &&
- (ab[i][j].oname == NULL ||
+ if (ab[i][j].nname != nullptr &&
+ (ab[i][j].oname == nullptr ||
strcmp(ab[i][j].oname, *newpdba->atomname[newi]) == 0))
{
/* add or replace */
- if (ab[i][j].oname == NULL && ab[i][j].bAlreadyPresent)
+ if (ab[i][j].oname == nullptr && ab[i][j].bAlreadyPresent)
{
/* This atom is already present, copy it from the input. */
nalreadypresent++;
}
snew(newpdba->atomname[newi], 1);
*newpdba->atomname[newi] = gmx_strdup(ab[i][j].nname);
- if (ab[i][j].oname != NULL && ab[i][j].atom) /* replace */
- { /* newpdba->atom[newi].m = ab[i][j].atom->m; */
+ if (ab[i][j].oname != nullptr && ab[i][j].atom) /* replace */
+ { /* newpdba->atom[newi].m = ab[i][j].atom->m; */
/* newpdba->atom[newi].q = ab[i][j].atom->q; */
/* newpdba->atom[newi].type = ab[i][j].atom->type; */
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
} t_define;
static int ndef = 0;
-static t_define *defs = NULL;
+static t_define *defs = nullptr;
static int nincl = 0;
-static char **incl = 0;
+static char **incl = nullptr;
/* enum used for handling ifdefs */
enum {
{
const char *ptr;
- while ((ptr = strstr(buf, word)) != NULL)
+ while ((ptr = strstr(buf, word)) != nullptr)
{
/* Check if we did not find part of a longer word */
if (ptr &&
buf = ptr + strlen(word);
}
- return NULL;
+ return nullptr;
}
static gmx_bool find_directive(char *buf, char **name, char **val)
}
}
/* Check if anything is remaining */
- *val = (*buf != 0) ? buf : NULL;
+ *val = (*buf != 0) ? buf : nullptr;
return TRUE;
}
{
int i;
- if (include == NULL)
+ if (include == nullptr)
{
return;
}
sfree(incl[i]);
}
sfree(incl);
- incl = NULL;
+ incl = nullptr;
nincl = 0;
}
}
else
{
- defs[i].def = NULL;
+ defs[i].def = nullptr;
}
}
sfree(defs[i].def);
}
sfree(defs);
- defs = NULL;
+ defs = nullptr;
ndef = 0;
}
}
else
{
- add_define(cppopts[i] + 2, NULL);
+ add_define(cppopts[i] + 2, nullptr);
}
}
i++;
snew(cpp, 1);
*handle = cpp;
- cpp->fn = NULL;
+ cpp->fn = nullptr;
/* Find the file. First check whether it is in the current directory. */
if (gmx_fexist(filenm))
{
{
gmx_fatal(FARGS, "Topology include file \"%s\" not found", filenm);
}
- if (NULL != debug)
+ if (nullptr != debug)
{
fprintf(debug, "GMXCPP: cpp file open %s\n", cpp->fn);
}
ptr = strrchr(cpp->fn, '/');
ptr2 = strrchr(cpp->fn, DIR_SEPARATOR);
- if (ptr == NULL || (ptr2 != NULL && ptr2 > ptr))
+ if (ptr == nullptr || (ptr2 != nullptr && ptr2 > ptr))
{
ptr = ptr2;
}
- if (ptr == NULL)
+ if (ptr == nullptr)
{
- cpp->path = NULL;
- cpp->cwd = NULL;
+ cpp->path = nullptr;
+ cpp->cwd = nullptr;
}
else
{
snew(cpp->cwd, STRLEN);
gmx_getcwd(cpp->cwd, STRLEN);
- if (NULL != debug)
+ if (nullptr != debug)
{
fprintf(debug, "GMXCPP: cwd %s\n", cpp->cwd);
}
gmx_chdir(cpp->path);
- if (NULL != debug)
+ if (nullptr != debug)
{
fprintf(debug, "GMXCPP: chdir to %s\n", cpp->path);
}
}
cpp->line_len = 0;
- cpp->line = NULL;
+ cpp->line = nullptr;
cpp->line_nr = 0;
cpp->nifdef = 0;
- cpp->ifdefs = NULL;
- cpp->child = NULL;
- cpp->parent = NULL;
- if (cpp->fp == NULL)
+ cpp->ifdefs = nullptr;
+ cpp->child = nullptr;
+ cpp->parent = nullptr;
+ if (cpp->fp == nullptr)
{
- if (NULL != debug)
+ if (nullptr != debug)
{
fprintf(debug, "GMXCPP: opening file %s\n", cpp->fn);
}
cpp->fp = fopen(cpp->fn, "r");
}
- if (cpp->fp == NULL)
+ if (cpp->fp == nullptr)
{
switch (errno)
{
inc_fn, i0, len);
}
/* Open include file and store it as a child in the handle structure */
- status = cpp_open_file(inc_fn, &(handle->child), NULL);
+ status = cpp_open_file(inc_fn, &(handle->child), nullptr);
sfree(inc_fn);
if (status != eCPP_OK)
{
- handle->child = NULL;
+ handle->child = nullptr;
return status;
}
/* Make a linked list of open files and move on to the include file */
if (!bEOF)
{
/* Read the actual line now. */
- if (fgets2(buf, n-1, handle->fp) == NULL)
+ if (fgets2(buf, n-1, handle->fp) == nullptr)
{
/* Recheck EOF, since we could have been at the end before
* the fgets2 call, but we need to read past the end to know.
if (bEOF)
{
- if (handle->parent == NULL)
+ if (handle->parent == nullptr)
{
return eCPP_EOF;
}
cpp_close_file(handlep);
*handlep = handle->parent;
- handle->child = NULL;
+ handle->child = nullptr;
return cpp_read_line(handlep, n, buf);
}
else
{
nn = 0;
ptr = buf;
- while ((ptr = strstrw(ptr, defs[i].name)) != NULL)
+ while ((ptr = strstrw(ptr, defs[i].name)) != nullptr)
{
nn++;
ptr += strlen(defs[i].name);
len = strlen(buf) + nn*std::max(four, four+strlen(defs[i].def)-strlen(defs[i].name));
snew(name, len);
ptr = buf;
- while ((ptr2 = strstrw(ptr, defs[i].name)) != NULL)
+ while ((ptr2 = strstrw(ptr, defs[i].name)) != nullptr)
{
strncat(name, ptr, (int)(ptr2-ptr));
strcat(name, defs[i].def);
fprintf(debug, "GMXCPP: closing file %s\n", handle->fn);
}
fclose(handle->fp);
- if (NULL != handle->cwd)
+ if (nullptr != handle->cwd)
{
- if (NULL != debug)
+ if (nullptr != debug)
{
fprintf(debug, "GMXCPP: chdir to %s\n", handle->cwd);
}
return eCPP_UNKNOWN;
}
}
- handle->fp = NULL;
+ handle->fp = nullptr;
handle->line_nr = 0;
- if (NULL != handle->fn)
+ if (nullptr != handle->fn)
{
sfree(handle->fn);
- handle->fn = NULL;
+ handle->fn = nullptr;
}
- if (NULL != handle->line)
+ if (nullptr != handle->line)
{
sfree(handle->line);
- handle->line = NULL;
+ handle->line = nullptr;
}
- if (NULL != handle->ifdefs)
+ if (nullptr != handle->ifdefs)
{
sfree(handle->ifdefs);
}
handle->nifdef = 0;
- if (NULL != handle->path)
+ if (nullptr != handle->path)
{
sfree(handle->path);
}
- if (NULL != handle->cwd)
+ if (nullptr != handle->cwd)
{
sfree(handle->cwd);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if ((nt < 0) || (nt >= ga->nr))
{
- return NULL;
+ return nullptr;
}
return *(ga->atomname[nt]);
snew(ga, 1);
ga->nr = 0;
- ga->atom = NULL;
- ga->atomname = NULL;
- ga->nb = NULL;
- ga->bondatomtype = NULL;
- ga->radius = NULL;
- ga->vol = NULL;
- ga->surftens = NULL;
- ga->atomnumber = NULL;
- ga->gb_radius = NULL;
- ga->S_hct = NULL;
+ ga->atom = nullptr;
+ ga->atomname = nullptr;
+ ga->nb = nullptr;
+ ga->bondatomtype = nullptr;
+ ga->radius = nullptr;
+ ga->vol = nullptr;
+ ga->surftens = nullptr;
+ ga->atomnumber = nullptr;
+ ga->gb_radius = nullptr;
+ ga->S_hct = nullptr;
return ga;
}
{
if (strcmp(*ga->atomname[i], name) == 0)
{
- if (NULL != debug)
+ if (nullptr != debug)
{
fprintf(debug, "Trying to add atomtype %s again. Skipping it.\n", name);
}
}
/* Renumber nlist */
- nbsnew = NULL;
+ nbsnew = nullptr;
snew(nbsnew, plist[ftype].nr);
nrfp = NRFP(ftype);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if ((nt < 0) || (nt >= ga->nr))
{
- return NULL;
+ return nullptr;
}
return *(ga->atomname[nt]);
ga->nr = 0;
sfree(ga);
- *at = NULL;
+ *at = nullptr;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real c[MAXFORCEPARAM]; /* Force parameters (eg. b0 = c[0]) */
char s[MAXSLEN]; /* A string (instead of parameters), *
* read from the .rtp file in pdb2gmx */
+ const int &ai() const { return a[0]; }
int &ai() { return a[0]; }
+ const int &aj() const { return a[1]; }
int &aj() { return a[1]; }
+ const int &ak() const { return a[2]; }
int &ak() { return a[2]; }
+ const int &al() const { return a[3]; }
int &al() { return a[3]; }
+ const int &am() const { return a[4]; }
int &am() { return a[4]; }
real &c0() { return c[0]; }
#include <sys/types.h>
#include "gromacs/commandline/pargs.h"
+#include "gromacs/ewald/pme.h"
#include "gromacs/fft/calcgrid.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdlib/perf_est.h"
+#include "gromacs/mdrunutility/mdmodules.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
w_a1 = w_a2 = -1;
w_period2 = -1.0;
- w_moltype = NULL;
+ w_moltype = nullptr;
for (molt = 0; molt < mtop->nmoltype; molt++)
{
moltype = &mtop->moltype[molt];
}
}
if (!bFound &&
- (w_moltype == NULL || period2 < w_period2))
+ (w_moltype == nullptr || period2 < w_period2))
{
w_moltype = moltype;
w_a1 = a1;
}
}
- if (w_moltype != NULL)
+ if (w_moltype != nullptr)
{
bWarn = (w_period2 < gmx::square(min_steps_warn*dt));
/* A check that would recognize most water models */
static void check_vel(gmx_mtop_t *mtop, rvec v[])
{
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
+ const t_atom *atom;
int a;
aloop = gmx_mtop_atomloop_all_init(mtop);
warninp_t wi)
{
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
+ const t_atom *atom;
int a, nshells = 0;
char warn_buf[STRLEN];
gmx_bool bMorse,
warninp_t wi)
{
- t_molinfo *molinfo = NULL;
+ t_molinfo *molinfo = nullptr;
int nmolblock;
gmx_molblock_t *molblock, *molbs;
int mb, i, nrmols, nmismatch;
}
t_topology *conftop;
+ rvec *x = nullptr;
+ rvec *v = nullptr;
snew(conftop, 1);
- init_state(state, 0, 0, 0, 0, 0);
- read_tps_conf(confin, conftop, NULL, &state->x, &state->v, state->box, FALSE);
- state->natoms = state->nalloc = conftop->atoms.nr;
+ read_tps_conf(confin, conftop, nullptr, &x, &v, state->box, FALSE);
+ state->natoms = conftop->atoms.nr;
if (state->natoms != sys->natoms)
{
gmx_fatal(FARGS, "number of coordinates in coordinate file (%s, %d)\n"
" does not match topology (%s, %d)",
confin, state->natoms, topfile, sys->natoms);
}
+ /* It would be nice to get rid of the copies below, but we don't know
+ * a priori if the number of atoms in confin matches what we expect.
+ */
+ state->flags |= (1 << estX);
+ if (v != NULL)
+ {
+ state->flags |= (1 << estV);
+ }
+ state_change_natoms(state, state->natoms);
+ for (int i = 0; i < state->natoms; i++)
+ {
+ copy_rvec(x[i], state->x[i]);
+ }
+ sfree(x);
+ if (v != nullptr)
+ {
+ for (int i = 0; i < state->natoms; i++)
+ {
+ copy_rvec(v[i], state->v[i]);
+ }
+ sfree(v);
+ }
/* This call fixes the box shape for runs with pressure scaling */
set_box_rel(ir, state);
{
real *mass;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
+ const t_atom *atom;
snew(mass, state->natoms);
aloop = gmx_mtop_atomloop_all_init(sys);
opts->seed = static_cast<int>(gmx::makeRandomSeed());
fprintf(stderr, "Setting gen_seed to %d\n", opts->seed);
}
- maxwell_speed(opts->tempi, opts->seed, sys, state->v);
+ state->flags |= (1 << estV);
+ maxwell_speed(opts->tempi, opts->seed, sys, as_rvec_array(state->v.data()));
- stop_cm(stdout, state->natoms, mass, state->x, state->v);
+ stop_cm(stdout, state->natoms, mass, as_rvec_array(state->x.data()), as_rvec_array(state->v.data()));
sfree(mass);
}
{
clear_rvec(state->v[i]);
}
- close_trj(fp);
+ close_trx(fp);
/* Search for a frame without velocities */
bReadVel = FALSE;
read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X);
copy_state(slog, &fr, bReadVel, state, &use_time);
}
- close_trj(fp);
+ close_trx(fp);
/* Set the relative box lengths for preserving the box shape.
* Note that this call can lead to differences in the last bit
}
static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
- char *fn,
+ const char *fn,
int rc_scaling, int ePBC,
rvec com,
warninp_t wi)
t_atom *atom;
snew(top, 1);
- read_tps_conf(fn, top, NULL, &x, &v, box, FALSE);
+ read_tps_conf(fn, top, nullptr, &x, &v, box, FALSE);
natoms = top->atoms.nr;
done_top(top);
sfree(top);
}
static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
- char *fnA, char *fnB,
+ const char *fnA, const char *fnB,
int rc_scaling, int ePBC,
rvec com, rvec comB,
warninp_t wi)
return nrdf;
}
-void
+static void
spline1d( double dx,
double * y,
int n,
}
-void
+static void
interpolate1d( double xmin,
double dx,
double * ya,
}
-void
+static void
setup_cmap (int grid_spacing,
int nc,
real * grid,
}
}
-void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
+static void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
{
int i, nelem;
rvec *v)
{
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
+ const t_atom *atom;
int a;
double sum_mv2 = 0;
* Prints a note for each unbound atoms and a warning if any is present.
*/
static void checkForUnboundAtoms(const gmx_moltype_t *molt,
+ gmx_bool bVerbose,
warninp_t wi)
{
const t_atoms *atoms = &molt->atoms;
if (atoms->atom[a].ptype != eptVSite &&
count[a] == 0)
{
- fprintf(stderr, "\nAtom %d '%s' in moleculetype '%s' is not bound by a potential or constraint to any other atom in the same moleculetype.\n",
- a + 1, *atoms->atomname[a], *molt->name);
-
+ if (bVerbose)
+ {
+ fprintf(stderr, "\nAtom %d '%s' in moleculetype '%s' is not bound by a potential or constraint to any other atom in the same moleculetype.\n",
+ a + 1, *atoms->atomname[a], *molt->name);
+ }
numDanglingAtoms++;
}
}
if (numDanglingAtoms > 0)
{
char buf[STRLEN];
- sprintf(buf, "In moleculetype '%s' %d atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake.",
+ sprintf(buf, "In moleculetype '%s' %d atoms are not bound by a potential or constraint to any other atom in the same moleculetype. Although technically this might not cause issues in a simulation, this often means that the user forgot to add a bond/potential/constraint or put multiple molecules in the same moleculetype definition by mistake. Run with -v to get information for each atom.",
*molt->name, numDanglingAtoms);
warning_note(wi, buf);
}
/* Checks all moleculetypes for unbound atoms */
static void checkForUnboundAtoms(const gmx_mtop_t *mtop,
+ gmx_bool bVerbose,
warninp_t wi)
{
for (int mt = 0; mt < mtop->nmoltype; mt++)
{
- checkForUnboundAtoms(&mtop->moltype[mt], wi);
+ checkForUnboundAtoms(&mtop->moltype[mt], bVerbose, wi);
}
}
/* Calculate the buffer size for simple atom vs atoms list */
ls.cluster_size_i = 1;
ls.cluster_size_j = 1;
- calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
- &ls, &n_nonlin_vsite, &rlist_1x1);
+ calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
+ buffer_temp, &ls, &n_nonlin_vsite, &rlist_1x1);
/* Set the pair-list buffer size in ir */
verletbuf_get_list_setup(FALSE, FALSE, &ls);
- calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
- &ls, &n_nonlin_vsite, &ir->rlist);
+ calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
+ buffer_temp, &ls, &n_nonlin_vsite, &ir->rlist);
if (n_nonlin_vsite > 0)
{
int gmx_grompp(int argc, char *argv[])
{
- static const char *desc[] = {
+ const char *desc[] = {
"[THISMODULE] (the gromacs preprocessor)",
"reads a molecular topology file, checks the validity of the",
"file, expands the topology from a molecular description to an atomic",
"Specifying the [TT]-pp[tt] flag will get the pre-processed",
"topology file written out so that you can verify its contents.[PAR]",
- "When using position restraints a file with restraint coordinates",
- "can be supplied with [TT]-r[tt], otherwise restraining will be done",
- "with respect to the conformation from the [TT]-c[tt] option.",
- "For free energy calculation the the coordinates for the B topology",
- "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
- "those of the A topology.[PAR]",
+ "When using position restraints, a file with restraint coordinates",
+ "must be supplied with [TT]-r[tt] (can be the same file as supplied",
+ "for [TT]-c[tt]). For free energy calculations, separate reference",
+ "coordinates for the B topology can be supplied with [TT]-rb[tt],",
+ "otherwise they will be equal to those of the A topology.[PAR]",
"Starting coordinates can be read from trajectory with [TT]-t[tt].",
"The last frame with coordinates and velocities will be read,",
int nmi;
t_molinfo *mi, *intermolecular_interactions;
gpp_atomtype_t atype;
- t_inputrec *ir;
int nvsite, comb, mt;
t_params *plist;
- t_state *state;
matrix box;
real fudgeQQ;
double reppow;
- char fn[STRLEN], fnB[STRLEN];
const char *mdparin;
int ntype;
gmx_bool bNeedVel, bGenVel;
char warn_buf[STRLEN];
t_filenm fnm[] = {
- { efMDP, NULL, NULL, ffREAD },
+ { efMDP, nullptr, nullptr, ffREAD },
{ efMDP, "-po", "mdout", ffWRITE },
- { efSTX, "-c", NULL, ffREAD },
- { efSTX, "-r", NULL, ffOPTRD },
- { efSTX, "-rb", NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
- { efTOP, NULL, NULL, ffREAD },
+ { efSTX, "-c", nullptr, ffREAD },
+ { efSTX, "-r", "restraint", ffOPTRD },
+ { efSTX, "-rb", "restraint", ffOPTRD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efTOP, nullptr, nullptr, ffREAD },
{ efTOP, "-pp", "processed", ffOPTWR },
- { efTPR, "-o", NULL, ffWRITE },
- { efTRN, "-t", NULL, ffOPTRD },
- { efEDR, "-e", NULL, ffOPTRD },
+ { efTPR, "-o", nullptr, ffWRITE },
+ { efTRN, "-t", nullptr, ffOPTRD },
+ { efEDR, "-e", nullptr, ffOPTRD },
/* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
{ efGRO, "-imd", "imdgroup", ffOPTWR },
{ efTRN, "-ref", "rotref", ffOPTRW }
#define NFILE asize(fnm)
/* Command line options */
- static gmx_bool bRenum = TRUE;
- static gmx_bool bRmVSBds = TRUE, bZero = FALSE;
- static int i, maxwarn = 0;
- static real fr_time = -1;
+ gmx_bool bRenum = TRUE;
+ gmx_bool bRmVSBds = TRUE, bZero = FALSE;
+ int i, maxwarn = 0;
+ real fr_time = -1;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" },
"Renumber atomtypes and minimize number of atomtypes" }
};
- /* Initiate some variables */
- snew(ir, 1);
- snew(opts, 1);
- init_ir(ir, opts);
-
/* Parse the command line */
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
+ /* Initiate some variables */
+ gmx::MDModules mdModules;
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
+ snew(opts, 1);
+ snew(opts->include, STRLEN);
+ snew(opts->define, STRLEN);
+
wi = init_warning(TRUE, maxwarn);
/* PARAMETER file processing */
mdparin = opt2fn("-f", NFILE, fnm);
set_warning_line(wi, mdparin, -1);
- get_ir(mdparin, opt2fn("-po", NFILE, fnm), ir, opts, wi);
+ try
+ {
+ get_ir(mdparin, opt2fn("-po", NFILE, fnm), &mdModules, ir, opts, WriteMdpHeader::yes, wi);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
if (bVerbose)
{
pr_symtab(debug, 0, "Just opened", &sys->symtab);
}
- strcpy(fn, ftp2fn(efTOP, NFILE, fnm));
+ const char *fn = ftp2fn(efTOP, NFILE, fnm);
if (!gmx_fexist(fn))
{
gmx_fatal(FARGS, "%s does not exist", fn);
}
- snew(state, 1);
+
+ t_state state;
new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm),
- opts, ir, bZero, bGenVel, bVerbose, state,
+ opts, ir, bZero, bGenVel, bVerbose, &state,
atype, sys, &nmi, &mi, &intermolecular_interactions,
plist, &comb, &reppow, &fudgeQQ,
opts->bMorse,
*/
check_warning_error(wi, FARGS);
- if (opt2bSet("-r", NFILE, fnm))
- {
- sprintf(fn, "%s", opt2fn("-r", NFILE, fnm));
- }
- else
- {
- sprintf(fn, "%s", opt2fn("-c", NFILE, fnm));
- }
- if (opt2bSet("-rb", NFILE, fnm))
- {
- sprintf(fnB, "%s", opt2fn("-rb", NFILE, fnm));
- }
- else
+ if (nint_ftype(sys, mi, F_POSRES) > 0 ||
+ nint_ftype(sys, mi, F_FBPOSRES) > 0)
{
- strcpy(fnB, fn);
- }
+ const char *fn = opt2fn("-r", NFILE, fnm);
+ const char *fnB;
+
+ if (opt2bSet("-rb", NFILE, fnm))
+ {
+ fnB = opt2fn("-rb", NFILE, fnm);
+ }
+ else
+ {
+ fnB = fn;
+ }
- if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
- {
if (bVerbose)
{
fprintf(stderr, "Reading position restraint coords from %s", fn);
/* Check velocity for virtual sites and shells */
if (bGenVel)
{
- check_vel(sys, state->v);
+ check_vel(sys, as_rvec_array(state.v.data()));
}
/* check for shells and inpurecs */
/* check masses */
check_mol(sys, wi);
- checkForUnboundAtoms(sys, wi);
+ checkForUnboundAtoms(sys, bVerbose, wi);
for (i = 0; i < sys->nmoltype; i++)
{
}
else
{
- buffer_temp = calc_temp(sys, ir, state->v);
+ buffer_temp = calc_temp(sys, ir, as_rvec_array(state.v.data()));
}
if (buffer_temp > 0)
{
}
}
- set_verlet_buffer(sys, ir, buffer_temp, state->box, wi);
+ set_verlet_buffer(sys, ir, buffer_temp, state.box, wi);
}
}
}
/* Init the temperature coupling state */
- init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
+ init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
if (bVerbose)
{
fprintf(stderr, "getting data from old trajectory ...\n");
}
cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm),
- bNeedVel, bGenVel, fr_time, ir, state, sys, oenv);
+ bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
}
if (ir->ePBC == epbcXY && ir->nwall != 2)
{
- clear_rvec(state->box[ZZ]);
+ clear_rvec(state.box[ZZ]);
}
if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
{
set_warning_line(wi, mdparin, -1);
- check_chargegroup_radii(sys, ir, state->x, wi);
+ check_chargegroup_radii(sys, ir, as_rvec_array(state.x.data()), wi);
}
if (EEL_FULL(ir->coulombtype) || EVDW_PME(ir->vdwtype))
{
/* Calculate the optimal grid dimensions */
- copy_mat(state->box, box);
+ copy_mat(state.box, box);
if (ir->ePBC == epbcXY && ir->nwall == 2)
{
svmul(ir->wall_ewald_zfac, box[ZZ], box[ZZ]);
set_warning_line(wi, mdparin, -1);
warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
}
- calc_grid(stdout, box, ir->fourier_spacing,
- &(ir->nkx), &(ir->nky), &(ir->nkz));
+ const int minGridSize = minimalPmeGridSize(ir->pme_order);
+ calcFftGrid(stdout, box, ir->fourier_spacing, minGridSize,
+ &(ir->nkx), &(ir->nky), &(ir->nkz));
+ if (ir->nkx < minGridSize ||
+ ir->nky < minGridSize ||
+ ir->nkz < minGridSize)
+ {
+ warning_error(wi, "The PME grid size should be >= 2*(pme-order - 1); either manually increase the grid size or decrease pme-order");
+ }
}
/* MRS: eventually figure out better logic for initializing the fep
potentially conflict if not handled correctly. */
if (ir->efep != efepNO)
{
- state->fep_state = ir->fepvals->init_fep_state;
+ state.fep_state = ir->fepvals->init_fep_state;
for (i = 0; i < efptNR; i++)
{
/* init_lambda trumps state definitions*/
if (ir->fepvals->init_lambda >= 0)
{
- state->lambda[i] = ir->fepvals->init_lambda;
+ state.lambda[i] = ir->fepvals->init_lambda;
}
else
{
- if (ir->fepvals->all_lambda[i] == NULL)
+ if (ir->fepvals->all_lambda[i] == nullptr)
{
gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
}
else
{
- state->lambda[i] = ir->fepvals->all_lambda[i][state->fep_state];
+ state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
}
}
}
}
- struct pull_t *pull = NULL;
+ struct pull_t *pull = nullptr;
if (ir->bPull)
{
- pull = set_pull_init(ir, sys, state->x, state->box, state->lambda[efptMASS], oenv);
+ pull = set_pull_init(ir, sys, as_rvec_array(state.x.data()), state.box, state.lambda[efptMASS], oenv);
}
/* Modules that supply external potential for pull coordinates
if (ir->bRot)
{
- set_reference_positions(ir->rot, state->x, state->box,
+ set_reference_positions(ir->rot, as_rvec_array(state.x.data()), state.box,
opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm),
wi);
}
if (EEL_PME(ir->coulombtype))
{
- float ratio = pme_load_estimate(sys, ir, state->box);
+ float ratio = pme_load_estimate(sys, ir, state.box);
fprintf(stderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
/* With free energy we might need to do PME both for the A and B state
* charges. This will double the cost, but the optimal performance will
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, state, sys);
+ write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
/* Output IMD group, if bIMD is TRUE */
- write_IMDgroup_to_file(ir->bIMD, ir, state, sys, NFILE, fnm);
+ write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
- done_state(state);
- sfree(state);
done_atomtype(atype);
- done_mtop(sys, TRUE);
+ done_mtop(sys);
done_inputrec_strings();
return 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int compaddh(const void *a, const void *b)
{
- t_hackblock *ah, *bh;
+ const t_hackblock *ah, *bh;
- ah = (t_hackblock *)a;
- bh = (t_hackblock *)b;
+ ah = static_cast<const t_hackblock *>(a);
+ bh = static_cast<const t_hackblock *>(b);
return gmx_strcasecmp(ah->name, bh->name);
}
hack->nctl = ns - 3;
if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
{
- gmx_fatal(FARGS, "Error in hdb file %s:\nWrong number of control atoms (%d iso %d) on line:\n%s\n", fn, hack->nctl, ncontrol[hack->tp], line);
+ gmx_fatal(FARGS, "Error in hdb file %s:\nWrong number of control atoms (%d instead of %d) on line:\n%s\n", fn, hack->nctl, ncontrol[hack->tp], line);
}
for (i = 0; (i < hack->nctl); i++)
{
}
for (; i < 4; i++)
{
- hack->a[i] = NULL;
+ hack->a[i] = nullptr;
}
- hack->oname = NULL;
+ hack->oname = nullptr;
hack->nname = gmx_strdup(hn);
- hack->atom = NULL;
+ hack->atom = nullptr;
hack->cgnr = NOTSET;
hack->bXSet = FALSE;
for (i = 0; i < DIM; i++)
"while reading Hydrogen Database %s residue %s",
nab, i-1, aah[nah].name, hfn);
}
- if (NULL == fgets(buf, STRLEN, in))
+ if (nullptr == fgets(buf, STRLEN, in))
{
gmx_fatal(FARGS, "Error reading from file %s", hfn);
}
*/
nhdbf = fflib_search_file_end(ffdir, ".hdb", FALSE, &hdbf);
nah = 0;
- *ah = NULL;
+ *ah = nullptr;
for (f = 0; f < nhdbf; f++)
{
read_h_db_file(hdbf[f], &nah, ah);
if (nh <= 0)
{
- return NULL;
+ return nullptr;
}
ahkey.name = key;
- result = (t_hackblock *)bsearch(&ahkey, ah, nh, (size_t)sizeof(ah[0]), compaddh);
+ result = static_cast<t_hackblock *>(bsearch(&ahkey, ah, nh, (size_t)sizeof(ah[0]), compaddh));
return result;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
free_t_bonded(&rbs->b[i]);
}
sfree(rbs->b);
- rbs->b = NULL;
+ rbs->b = nullptr;
rbs->nb = 0;
}
}
}
sfree(*h);
- *h = NULL;
+ *h = nullptr;
}
void free_t_hackblock(int nhb, t_hackblock **hb)
{
int i;
- hb->name = NULL;
+ hb->name = nullptr;
hb->nhack = 0;
hb->maxhack = 0;
- hb->hack = NULL;
+ hb->hack = nullptr;
for (i = 0; i < ebtsNR; i++)
{
hb->rb[i].nb = 0;
- hb->rb[i].b = NULL;
+ hb->rb[i].b = nullptr;
}
}
int i;
hack->nr = 0;
- hack->oname = NULL;
- hack->nname = NULL;
- hack->atom = NULL;
+ hack->oname = nullptr;
+ hack->nname = nullptr;
+ hack->atom = nullptr;
hack->cgnr = NOTSET;
hack->tp = 0;
hack->nctl = 0;
for (i = 0; i < 4; i++)
{
- hack->a[i] = NULL;
+ hack->a[i] = nullptr;
}
for (i = 0; i < DIM; i++)
{
return bRet;
}
-int
+static int
rbonded_find_atoms_in_list(t_rbonded *b, t_rbonded blist[], int nlist, int natoms)
{
int i, k;
{
d->rb[i].type = s->rb[i].type;
d->rb[i].nb = 0;
- d->rb[i].b = NULL;
+ d->rb[i].b = nullptr;
}
merge_t_bondeds(s->rb, d->rb, FALSE, FALSE);
}
}
else
{
- d->atom = NULL;
+ d->atom = nullptr;
}
for (i = 0; i < 4; i++)
{
*d = *s;
d->name = safe_strdup(s->name);
d->nhack = 0;
- d->hack = NULL;
+ d->hack = nullptr;
for (i = 0; i < ebtsNR; i++)
{
d->rb[i].nb = 0;
- d->rb[i].b = NULL;
+ d->rb[i].b = nullptr;
}
merge_t_hackblock(s, d);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* This file is completely threadsafe - keep it that way! */
#include "gmxpre.h"
+#include "hizzie.h"
+
#include <stdio.h>
#include <string.h>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_GMXPREPROCESS_HIZZIE_H
#define GMX_GMXPREPROCESS_HIZZIE_H
+#include "gromacs/math/vectypes.h"
+#include "gromacs/topology/atoms.h"
+
void set_histp(t_atoms *pdba, rvec *x, real angle, real distance);
/* calculate HIStidine protonation state */
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/atoms.h"
#include "gromacs/topology/atomsbuilder.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/cstringutil.h"
}
if (enum_rot == en_rotXYZ || enum_rot == en_rotZ)
{
- rotate_conf(xout->size(), as_rvec_array(xout->data()), NULL, alfa, beta, gamma);
+ rotate_conf(xout->size(), as_rvec_array(xout->data()), nullptr, alfa, beta, gamma);
}
for (size_t i = 0; i < xout->size(); ++i)
{
static void insert_mols(int nmol_insrt, int ntry, int seed,
real defaultDistance, real scaleFactor,
- t_topology *top, std::vector<RVec> *x,
+ t_atoms *atoms, t_symtab *symtab, std::vector<RVec> *x,
const std::set<int> &removableAtoms,
const t_atoms &atoms_insrt, const std::vector<RVec> &x_insrt,
int ePBC, matrix box,
fprintf(stderr, "Initialising inter-atomic distances...\n");
gmx_atomprop_t aps = gmx_atomprop_init();
std::vector<real> exclusionDistances(
- makeExclusionDistances(&top->atoms, aps, defaultDistance, scaleFactor));
+ makeExclusionDistances(atoms, aps, defaultDistance, scaleFactor));
const std::vector<real> exclusionDistances_insrt(
makeExclusionDistances(&atoms_insrt, aps, defaultDistance, scaleFactor));
gmx_atomprop_destroy(aps);
set_pbc(&pbc, ePBC, box);
/* With -ip, take nmol_insrt from file posfn */
- double **rpos = NULL;
+ double **rpos = nullptr;
const bool insertAtPositions = !posfn.empty();
if (insertAtPositions)
{
nmol_insrt, posfn.c_str());
}
- gmx::AtomsBuilder builder(&top->atoms, &top->symtab);
- gmx::AtomsRemover remover(top->atoms);
+ gmx::AtomsBuilder builder(atoms, symtab);
+ gmx::AtomsRemover remover(*atoms);
{
- const int finalAtomCount = top->atoms.nr + nmol_insrt * atoms_insrt.nr;
- const int finalResidueCount = top->atoms.nres + nmol_insrt * atoms_insrt.nres;
+ const int finalAtomCount = atoms->nr + nmol_insrt * atoms_insrt.nr;
+ const int finalResidueCount = atoms->nres + nmol_insrt * atoms_insrt.nres;
builder.reserve(finalAtomCount, finalResidueCount);
x->reserve(finalAtomCount);
exclusionDistances.reserve(finalAtomCount);
gmx::AnalysisNeighborhoodPositions pos(*x);
gmx::AnalysisNeighborhoodSearch search = nb.initSearch(&pbc, pos);
if (isInsertionAllowed(&search, exclusionDistances, x_n, exclusionDistances_insrt,
- top->atoms, removableAtoms, &remover))
+ *atoms, removableAtoms, &remover))
{
x->insert(x->end(), x_n.begin(), x_n.end());
exclusionDistances.insert(exclusionDistances.end(),
fprintf(stderr, "Added %d molecules (out of %d requested)\n",
mol - failed, nmol_insrt);
- const int originalAtomCount = top->atoms.nr;
- const int originalResidueCount = top->atoms.nres;
- remover.refreshAtomCount(top->atoms);
+ const int originalAtomCount = atoms->nr;
+ const int originalResidueCount = atoms->nres;
+ remover.refreshAtomCount(*atoms);
remover.removeMarkedElements(x);
- remover.removeMarkedAtoms(&top->atoms);
- if (top->atoms.nr < originalAtomCount)
+ remover.removeMarkedAtoms(atoms);
+ if (atoms->nr < originalAtomCount)
{
fprintf(stderr, "Replaced %d residues (%d atoms)\n",
- originalResidueCount - top->atoms.nres,
- originalAtomCount - top->atoms.nr);
+ originalResidueCount - atoms->nres,
+ originalAtomCount - atoms->nr);
}
- if (rpos != NULL)
+ if (rpos != nullptr)
{
for (int i = 0; i < DIM; ++i)
{
InsertMolecules()
: bBox_(false), nmolIns_(0), nmolTry_(10), seed_(0),
defaultDistance_(0.105), scaleFactor_(0.57), enumRot_(en_rotXYZ),
- top_(NULL), ePBC_(-1)
+ top_(nullptr), ePBC_(-1)
{
clear_rvec(newBox_);
clear_rvec(deltaR_);
}
virtual ~InsertMolecules()
{
- if (top_ != NULL)
+ if (top_ != nullptr)
{
- done_top(top_);
+ done_mtop(top_);
sfree(top_);
}
}
// From ITopologyProvider
- virtual t_topology *getTopology(bool /*required*/) { return top_; }
+ virtual gmx_mtop_t *getTopology(bool /*required*/) { return top_; }
virtual int getAtomCount() { return 0; }
// From ICommandLineOptionsModule
RotationType enumRot_;
Selection replaceSel_;
- t_topology *top_;
+ gmx_mtop_t *top_;
std::vector<RVec> x_;
matrix box_;
int ePBC_;
snew(top_, 1);
if (!inputConfFile_.empty())
{
- readConformation(inputConfFile_.c_str(), top_, &x_, NULL,
+ readConformation(inputConfFile_.c_str(), top_, &x_, nullptr,
&ePBC_, box_, "solute");
- if (top_->atoms.nr == 0)
+ if (top_->natoms == 0)
{
fprintf(stderr, "Note: no atoms in %s\n", inputConfFile_.c_str());
}
int ePBC_dummy;
matrix box_dummy;
readConformation(insertConfFile_.c_str(), top_insrt, &x_insrt,
- NULL, &ePBC_dummy, box_dummy, "molecule");
+ nullptr, &ePBC_dummy, box_dummy, "molecule");
if (top_insrt->atoms.nr == 0)
{
gmx_fatal(FARGS, "No molecule in %s, please check your input",
insertConfFile_.c_str());
}
- if (top_->name == NULL)
+ if (top_->name == nullptr)
{
top_->name = top_insrt->name;
}
}
}
+ // TODO: Adapt to use mtop throughout.
+ t_atoms atoms = gmx_mtop_global_atoms(top_);
+
/* add nmol_ins molecules of atoms_ins
in random orientation at random place */
insert_mols(nmolIns_, nmolTry_, seed_, defaultDistance_, scaleFactor_,
- top_, &x_, removableAtoms, top_insrt->atoms, x_insrt,
+ &atoms, &top_->symtab, &x_, removableAtoms, top_insrt->atoms, x_insrt,
ePBC_, box_, positionFile_, deltaR_, enumRot_);
/* write new configuration to file confout */
fprintf(stderr, "Writing generated configuration to %s\n",
outputConfFile_.c_str());
- write_sto_conf(outputConfFile_.c_str(), *top_->name, &top_->atoms,
- as_rvec_array(x_.data()), NULL, ePBC_, box_);
+ write_sto_conf(outputConfFile_.c_str(), *top_->name, &atoms,
+ as_rvec_array(x_.data()), nullptr, ePBC_, box_);
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
- top_->atoms.nr, top_->atoms.nres);
+ atoms.nr, atoms.nres);
+ done_atom(&atoms);
done_top(top_insrt);
sfree(top_insrt);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Defines a function to write a flat key-value tree to look like
+ * old-style mdp output.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_gmxpreprocess
+ */
+#include "gmxpre.h"
+
+#include "keyvaluetreemdpwriter.h"
+
+#include <string>
+
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
+
+namespace gmx
+{
+
+void writeKeyValueTreeAsMdp(TextWriter *writer,
+ const KeyValueTreeObject &tree)
+{
+ for (const auto &prop : tree.properties())
+ {
+ const auto &value = prop.value();
+ GMX_RELEASE_ASSERT(!value.isObject(), "Only flat key-value trees can be written as mdp");
+
+ // Recognize a special key prefix that identifies comment
+ // lines. This mechanism is not pretty, but our plan is to
+ // write key-value trees, rather than old-style mdp, and
+ // comments will need different handling then.
+ if (prop.key().compare(0, 7, "comment") == 0)
+ {
+ GMX_RELEASE_ASSERT(prop.value().isType<std::string>(), "Comments must have string-typed values");
+ auto comment = prop.value().cast<std::string>();
+ // TODO Consider implementing an MdpTextWriter that can
+ // format an array of strings suitably, e.g. by prefixing
+ // each line like "; %s". We'd need to implement arrays of
+ // objects, such a comment key to be able to refer to an
+ // array of strings. Also, we'd want to have a plan to
+ // write such comments in whatever replaces the mdp
+ // format.
+ writer->writeLine(comment);
+ }
+ else
+ {
+ writer->writeString(formatString("%-24s = ", prop.key().c_str()));
+ if (value.isArray())
+ {
+ bool first = true;
+ for (const auto &elem : value.asArray().values())
+ {
+ GMX_RELEASE_ASSERT(!elem.isObject() && !elem.isArray(),
+ "Arrays of objects not currently implemented");
+ if (!first)
+ {
+ writer->writeString(" ");
+ }
+ writer->writeString(simpleValueToString(elem));
+ first = false;
+ }
+ }
+ else
+ {
+ writer->writeString(simpleValueToString(value));
+ }
+ writer->writeLine();
+ }
+ }
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares a function to write a flat key-value tree to look like
+ * old-style mdp output.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_gmxpreprocess
+ */
+#ifndef GMX_GMXPREPROCESS_KEYVALUETREEMDPWRITER_H
+#define GMX_GMXPREPROCESS_KEYVALUETREEMDPWRITER_H
+
+namespace gmx
+{
+
+class KeyValueTreeObject;
+class TextWriter;
+
+/*! \brief Write a flat key-value \c tree to \c writer in mdp style.
+ *
+ * Sub-objects will output nothing, so they can be used to
+ * contain a special key-value pair to create a comment, as
+ * well as the normal key and value. The comment pair will
+ * have a key of "comment", and the value will be used as a
+ * comment (if non-empty). */
+void writeKeyValueTreeAsMdp(TextWriter *writer,
+ const KeyValueTreeObject &tree);
+
+} // namespace gmx
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/gmxpreprocess/fflibutil.h"
#include "gromacs/gmxpreprocess/gpp_atomtype.h"
#include "gromacs/gmxpreprocess/gpp_nextnb.h"
char buf[1024], elem[16], type[16], nbbuf[16], **newbuf;
int i, nb, nnnm, line = 1;
double qq, mm;
- t_nm2type *nm2t = NULL;
+ t_nm2type *nm2t = nullptr;
fp = fflib_open(fn);
- if (NULL == fp)
+ if (nullptr == fp)
{
gmx_fatal(FARGS, "Can not find %s in library directory", fn);
}
do
{
/* Read a line from the file */
- bCont = (fgets2(buf, 1023, fp) != NULL);
+ bCont = (fgets2(buf, 1023, fp) != nullptr);
if (bCont)
{
}
else
{
- newbuf = NULL;
+ newbuf = nullptr;
}
nm2t[nnnm].elem = gmx_strdup(elem);
nm2t[nnnm].type = gmx_strdup(type);
nff = fflib_search_file_end(ffdir, ".n2t", FALSE, &ff);
*nnm = 0;
- nm = NULL;
+ nm = nullptr;
for (f = 0; f < nff; f++)
{
rd_nm2type_file(ff[f], nnm, &nm);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/gmxlib/conformation-utilities.h"
#include "gromacs/gmxpreprocess/fflibutil.h"
#include "gromacs/gmxpreprocess/genhydro.h"
char *nn;
int i;
- nn = NULL;
+ nn = nullptr;
i = 0;
while (i < nrr && ((!bCompareFFRTPname && strcmp(name, rr[i].gmx) != 0) ||
char *nn;
gmx_bool bFFRTPTERRNM;
- bFFRTPTERRNM = (getenv("GMX_NO_FFRTP_TER_RENAME") == NULL);
+ bFFRTPTERRNM = (getenv("GMX_NO_FFRTP_TER_RENAME") == nullptr);
for (r = 0; r < pdba->nres; r++)
{
nn = search_resrename(nrr, rr, *pdba->resinfo[r].rtp, bStart, bEnd, FALSE);
- if (bFFRTPTERRNM && nn == NULL && (bStart || bEnd))
+ if (bFFRTPTERRNM && nn == nullptr && (bStart || bEnd))
{
/* This is a terminal residue, but the residue name,
* currently stored in .rtp, is not a standard residue name,
*pdba->resinfo[r].rtp, bStart, bEnd, TRUE);
}
- if (nn != NULL && strcmp(*pdba->resinfo[r].rtp, nn) != 0)
+ if (nn != nullptr && strcmp(*pdba->resinfo[r].rtp, nn) != 0)
{
if (bVerbose)
{
for (i = 0; (i < pdba->nres); i++)
{
- if (pdba->resinfo[i].rtp == NULL)
+ if (pdba->resinfo[i].rtp == nullptr)
{
pdba->resinfo[i].rtp = pdba->resinfo[i].name;
}
{
resnm = *pdba->resinfo[i].name;
if ((bFullCompare && (gmx_strcasecmp(resnm, oldnm) == 0)) ||
- (!bFullCompare && strstr(resnm, oldnm) != NULL))
+ (!bFullCompare && strstr(resnm, oldnm) != nullptr))
{
/* Rename the residue name (not the rtp name) */
pdba->resinfo[i].name = put_symtab(symtab, newnm);
/* We have not set the rtp name yes, use the residue name */
bbnm = *pdba->resinfo[i].name;
if ((bFullCompare && (gmx_strcasecmp(bbnm, oldnm) == 0)) ||
- (!bFullCompare && strstr(bbnm, oldnm) != NULL))
+ (!bFullCompare && strstr(bbnm, oldnm) != nullptr))
{
/* Change the rtp builing block name */
pdba->resinfo[i].rtp = put_symtab(symtab, newnm);
/* We have not set the rtp name yes, use the residue name */
bbnm = *pdba->resinfo[i].name;
if ((bFullCompare && (strcmp(bbnm, oldnm) == 0)) ||
- (!bFullCompare && strstr(bbnm, oldnm) != NULL))
+ (!bFullCompare && strstr(bbnm, oldnm) != nullptr))
{
ptr = gettp(i, nrr, rr);
pdba->resinfo[i].rtp = put_symtab(symtab, ptr);
}
}
-void write_posres(char *fn, t_atoms *pdba, real fc)
+static void write_posres(char *fn, t_atoms *pdba, real fc)
{
FILE *fp;
int i;
printf("Reading %s...\n", inf);
t_topology *top;
snew(top, 1);
- read_tps_conf(inf, top, ePBC, x, NULL, box, FALSE);
+ read_tps_conf(inf, top, ePBC, x, nullptr, box, FALSE);
strncpy(title, *top->name, STRLEN);
title[STRLEN-1] = '\0';
*atoms = top->atoms;
sfree(top);
natom = atoms->nr;
- if (atoms->pdbinfo == NULL)
+ if (atoms->pdbinfo == nullptr)
{
snew(atoms->pdbinfo, atoms->nr);
}
rename_pdbres(atoms, "SOL", watres, FALSE, symtab);
rename_pdbres(atoms, "WAT", watres, FALSE, symtab);
- rename_atoms("xlateat.dat", NULL,
- atoms, symtab, NULL, TRUE, rt, TRUE, bVerbose);
+ rename_atoms("xlateat.dat", nullptr,
+ atoms, symtab, nullptr, TRUE, rt, TRUE, bVerbose);
if (natom == 0)
{
if (outf)
{
- write_sto_conf(outf, title, atoms, *x, NULL, *ePBC, box);
+ write_sto_conf(outf, title, atoms, *x, nullptr, *ePBC, box);
}
return natom;
}
-void process_chain(t_atoms *pdba, rvec *x,
- gmx_bool bTrpU, gmx_bool bPheU, gmx_bool bTyrU,
- gmx_bool bLysMan, gmx_bool bAspMan, gmx_bool bGluMan,
- gmx_bool bHisMan, gmx_bool bArgMan, gmx_bool bGlnMan,
- real angle, real distance, t_symtab *symtab,
- int nrr, const rtprename_t *rr)
+static void process_chain(t_atoms *pdba, rvec *x,
+ gmx_bool bTrpU, gmx_bool bPheU, gmx_bool bTyrU,
+ gmx_bool bLysMan, gmx_bool bAspMan, gmx_bool bGluMan,
+ gmx_bool bHisMan, gmx_bool bArgMan, gmx_bool bGlnMan,
+ real angle, real distance, t_symtab *symtab,
+ int nrr, const rtprename_t *rr)
{
/* Rename aromatics, lys, asp and histidine */
if (bTyrU)
char altloc; /* alternate location indicator */
} t_pdbindex;
-int pdbicomp(const void *a, const void *b)
+static int pdbicomp(const void *a, const void *b)
{
t_pdbindex *pa, *pb;
int d;
pdba = *pdbaptr;
natoms = pdba->nr;
- pdbnew = NULL;
+ pdbnew = nullptr;
snew(xnew, 1);
snew(pdbi, natoms);
return pdba->nr;
}
-void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end,
- gmx_residuetype_t *rt)
+static void find_nc_ter(t_atoms *pdba, int r0, int r1, int *r_start, int *r_end,
+ gmx_residuetype_t *rt)
{
int i;
const char *p_startrestype;
old_prev_chainnum = -1;
new_chainnum = -1;
- this_atomname = NULL;
+ this_atomname = nullptr;
this_atomnum = -1;
- this_resname = NULL;
+ this_resname = nullptr;
this_resnum = -1;
this_chainid = '?';
prev_chainid = this_chainid;
this_atomname = *(pdba->atomname[i]);
- this_atomnum = (pdba->pdbinfo != NULL) ? pdba->pdbinfo[i].atomnr : i+1;
+ this_atomnum = (pdba->pdbinfo != nullptr) ? pdba->pdbinfo[i].atomnr : i+1;
this_resname = *ri->name;
this_resnum = ri->nr;
this_chainid = ri->chainid;
prev_resname, prev_resnum, prev_chainid, prev_atomnum, prev_atomname,
this_resname, this_resnum, this_chainid, this_atomnum, this_atomname);
- if (NULL == fgets(select, STRLEN-1, stdin))
+ if (nullptr == fgets(select, STRLEN-1, stdin))
{
gmx_fatal(FARGS, "Error reading from stdin");
}
};
- FILE *fp, *top_file, *top_file2, *itp_file = NULL;
+ FILE *fp, *top_file, *top_file2, *itp_file = nullptr;
int natom, nres;
t_atoms pdba_all, *pdba;
t_atoms *atoms;
int nrrn;
char **rrn;
int nrtprename;
- rtprename_t *rtprename = NULL;
+ rtprename_t *rtprename = nullptr;
int nah, nNtdb, nCtdb, ntdblist;
t_hackblock *ntdb, *ctdb, **tdblist;
int nssbonds;
t_filenm fnm[] = {
{ efSTX, "-f", "eiwit.pdb", ffREAD },
{ efSTO, "-o", "conf", ffWRITE },
- { efTOP, NULL, NULL, ffWRITE },
+ { efTOP, nullptr, nullptr, ffWRITE },
{ efITP, "-i", "posre", ffWRITE },
{ efNDX, "-n", "clean", ffOPTWR },
{ efSTO, "-q", "clean.pdb", ffOPTWR }
};
#define NFILE asize(fnm)
-
- /* Command line arguments must be static */
- static gmx_bool bNewRTP = FALSE;
- static gmx_bool bInter = FALSE, bCysMan = FALSE;
- static gmx_bool bLysMan = FALSE, bAspMan = FALSE, bGluMan = FALSE, bHisMan = FALSE;
- static gmx_bool bGlnMan = FALSE, bArgMan = FALSE;
- static gmx_bool bTerMan = FALSE, bUnA = FALSE, bHeavyH;
- static gmx_bool bSort = TRUE, bAllowMissing = FALSE, bRemoveH = FALSE;
- static gmx_bool bDeuterate = FALSE, bVerbose = FALSE, bChargeGroups = TRUE, bCmap = TRUE;
- static gmx_bool bRenumRes = FALSE, bRTPresname = FALSE;
- static real angle = 135.0, distance = 0.3, posre_fc = 1000;
- static real long_bond_dist = 0.25, short_bond_dist = 0.05;
- static const char *vsitestr[] = { NULL, "none", "hydrogens", "aromatics", NULL };
- static const char *watstr[] = { NULL, "select", "none", "spc", "spce", "tip3p", "tip4p", "tip5p", NULL };
- static const char *chainsep[] = { NULL, "id_or_ter", "id_and_ter", "ter", "id", "interactive", NULL };
- static const char *merge[] = {NULL, "no", "all", "interactive", NULL };
- static const char *ff = "select";
+ gmx_bool bNewRTP = FALSE;
+ gmx_bool bInter = FALSE, bCysMan = FALSE;
+ gmx_bool bLysMan = FALSE, bAspMan = FALSE, bGluMan = FALSE, bHisMan = FALSE;
+ gmx_bool bGlnMan = FALSE, bArgMan = FALSE;
+ gmx_bool bTerMan = FALSE, bUnA = FALSE, bHeavyH = FALSE;
+ gmx_bool bSort = TRUE, bAllowMissing = FALSE, bRemoveH = FALSE;
+ gmx_bool bDeuterate = FALSE, bVerbose = FALSE, bChargeGroups = TRUE, bCmap = TRUE;
+ gmx_bool bRenumRes = FALSE, bRTPresname = FALSE;
+ real angle = 135.0, distance = 0.3, posre_fc = 1000;
+ real long_bond_dist = 0.25, short_bond_dist = 0.05;
+ const char *vsitestr[] = { nullptr, "none", "hydrogens", "aromatics", nullptr };
+ const char *watstr[] = { nullptr, "select", "none", "spc", "spce", "tip3p", "tip4p", "tip5p", nullptr };
+ const char *chainsep[] = { nullptr, "id_or_ter", "id_and_ter", "ter", "id", "interactive", nullptr };
+ const char *merge[] = {nullptr, "no", "all", "interactive", nullptr };
+ const char *ff = "select";
t_pargs pa[] = {
{ "-newrtp", FALSE, etBOOL, {&bNewRTP},
#define NPARGS asize(pa)
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa, asize(desc), desc,
- 0, NULL, &oenv))
+ 0, nullptr, &oenv))
{
return 0;
}
/* Force field selection, interactive or direct */
- choose_ff(strcmp(ff, "select") == 0 ? NULL : ff,
+ choose_ff(strcmp(ff, "select") == 0 ? nullptr : ff,
forcefield, sizeof(forcefield),
ffdir, sizeof(ffdir));
nrrn = fflib_search_file_end(ffdir, ".r2b", FALSE, &rrn);
nrtprename = 0;
- rtprename = NULL;
+ rtprename = nullptr;
for (i = 0; i < nrrn; i++)
{
fp = fflib_open(rrn[i]);
}
clear_mat(box);
- if (watermodel != NULL && (strstr(watermodel, "4p") ||
- strstr(watermodel, "4P")))
+ if (watermodel != nullptr && (strstr(watermodel, "4p") ||
+ strstr(watermodel, "4P")))
{
watres = "HO4";
}
- else if (watermodel != NULL && (strstr(watermodel, "5p") ||
- strstr(watermodel, "5P")))
+ else if (watermodel != nullptr && (strstr(watermodel, "5p") ||
+ strstr(watermodel, "5P")))
{
watres = "HO5";
}
nchainmerges = 0;
- this_atomname = NULL;
+ this_atomname = nullptr;
this_atomnum = -1;
- this_resname = NULL;
+ this_resname = nullptr;
this_resnum = -1;
this_chainid = '?';
this_chainnumber = -1;
}
this_atomname = *pdba_all.atomname[i];
- this_atomnum = (pdba_all.pdbinfo != NULL) ? pdba_all.pdbinfo[i].atomnr : i+1;
+ this_atomnum = (pdba_all.pdbinfo != nullptr) ? pdba_all.pdbinfo[i].atomnr : i+1;
this_resname = *ri->name;
this_resnum = ri->nr;
this_chainid = ri->chainid;
prev_resname, prev_resnum, prev_chainid, prev_atomnum, prev_atomname,
this_resname, this_resnum, this_chainid, this_atomnum, this_atomname);
- if (NULL == fgets(select, STRLEN-1, stdin))
+ if (nullptr == fgets(select, STRLEN-1, stdin))
{
gmx_fatal(FARGS, "Error reading from stdin");
}
printf("Reading residue database... (%s)\n", forcefield);
nrtpf = fflib_search_file_end(ffdir, ".rtp", TRUE, &rtpf);
nrtp = 0;
- restp = NULL;
+ restp = nullptr;
for (i = 0; i < nrtpf; i++)
{
read_resall(rtpf[i], &nrtp, &restp, atype, &symtab, FALSE);
nincl = 0;
nmol = 0;
- incls = NULL;
- mols = NULL;
+ incls = nullptr;
+ mols = nullptr;
for (chain = 0; (chain < nch); chain++)
{
cc = &(chains[chain]);
{
sprintf(fn, "chain_%c%d.pdb", cc->chainid, cc->chainnum);
}
- write_sto_conf(fn, title, pdba, x, NULL, ePBC, box);
+ write_sto_conf(fn, title, pdba, x, nullptr, ePBC, box);
}
{
printf("No suitable end (N or 5') terminus found in database - assuming this residue\n"
"is already in a terminus-specific form and skipping terminus selection.\n");
- cc->ntdb[i] = NULL;
+ cc->ntdb[i] = nullptr;
}
else
{
}
else
{
- cc->ntdb[i] = NULL;
+ cc->ntdb[i] = nullptr;
}
/* And the C terminus */
{
printf("No suitable end (C or 3') terminus found in database - assuming this residue\n"
"is already in a terminus-specific form and skipping terminus selection.\n");
- cc->ctdb[i] = NULL;
+ cc->ctdb[i] = nullptr;
}
else
{
}
else
{
- cc->ctdb[i] = NULL;
+ cc->ctdb[i] = nullptr;
}
}
/* lookup hackblocks and rtp for all residues */
requires some re-thinking of code in gen_vsite.c, which I won't
do now :( AF 26-7-99 */
- rename_atoms(NULL, ffdir,
+ rename_atoms(nullptr, ffdir,
pdba, &symtab, restp_chain, FALSE, rt, FALSE, bVerbose);
match_atomnames_with_rtp(restp_chain, hb_chain, pdba, x, bVerbose);
printf("Generating any missing hydrogen atoms and/or adding termini.\n");
natom = add_h(&pdba, &x, nah, ah,
cc->nterpairs, cc->ntdb, cc->ctdb, cc->r_start, cc->r_end, bAllowMissing,
- NULL, NULL, TRUE, FALSE);
+ nullptr, nullptr, TRUE, FALSE);
printf("Now there are %d residues with %d atoms\n",
pdba->nres, pdba->nr);
if (debug)
{
- write_pdbfile(debug, title, pdba, x, ePBC, box, ' ', 0, NULL, TRUE);
+ write_pdbfile(debug, title, pdba, x, ePBC, box, ' ', 0, nullptr, TRUE);
}
if (debug)
if (cc->bAllWat)
{
- top_file2 = NULL;
+ top_file2 = nullptr;
}
else
if (bITP)
{
sprintf(fn, "chain_%c.pdb", cc->chainid);
}
- write_sto_conf(fn, "", pdba, x, NULL, ePBC, box);
+ write_sto_conf(fn, "", pdba, x, nullptr, ePBC, box);
}
}
- if (watermodel == NULL)
+ if (watermodel == nullptr)
{
for (chain = 0; chain < nch; chain++)
{
{
make_new_box(atoms->nr, x, box, box_space, FALSE);
}
- write_sto_conf(ftp2fn(efSTO, NFILE, fnm), title, atoms, x, NULL, ePBC, box);
+ write_sto_conf(ftp2fn(efSTO, NFILE, fnm), title, atoms, x, nullptr, ePBC, box);
printf("\t\t--------- PLEASE NOTE ------------\n");
printf("You have successfully generated a topology from: %s.\n",
opt2fn("-f", NFILE, fnm));
- if (watermodel != NULL)
+ if (watermodel != nullptr)
{
printf("The %s force field and the %s water model are used.\n",
ffname, watermodel);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/niceheader.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strdb.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
/* this must correspond to enum in pdb2top.h */
const char *hh[ehisNR] = { "HISD", "HISE", "HISH", "HIS1" };
}
int sel;
- if (ffsel != NULL)
+ if (ffsel != nullptr)
{
sel = -1;
int cwdsel = -1;
FILE *fp = gmx_ffopen(docFileName.c_str(), "r");
get_a_line(fp, buf, STRLEN);
gmx_ffclose(fp);
- desc.push_back(buf);
+ desc.emplace_back(buf);
}
else
{
{
pret = fgets(buf, STRLEN, stdin);
- if (pret != NULL)
+ if (pret != nullptr)
{
- sel = strtol(buf, NULL, 10);
+ sel = strtol(buf, nullptr, 10);
sel--;
}
}
- while (pret == NULL || (sel < 0) || (sel >= nff));
+ while (pret == nullptr || (sel < 0) || (sel >= nff));
/* Check for a current limitation of the fflib code.
* It will always read from the first ff directory in the list.
if (strcmp(wmsel, "none") == 0)
{
- *watermodel = NULL;
+ *watermodel = nullptr;
return;
}
{
fprintf(stderr, "No file '%s' found, will not include a water model\n",
fn_watermodels);
- *watermodel = NULL;
+ *watermodel = nullptr;
return;
}
fp = fflib_open(fn_list);
printf("\nSelect the Water Model:\n");
nwm = 0;
- model = NULL;
+ model = nullptr;
while (get_a_line(fp, buf, STRLEN))
{
srenew(model, nwm+1);
{
pret = fgets(buf, STRLEN, stdin);
- if (pret != NULL)
+ if (pret != nullptr)
{
- sel = strtol(buf, NULL, 10);
+ sel = strtol(buf, nullptr, 10);
sel--;
}
}
- while (pret == NULL || sel < 0 || sel > nwm);
+ while (pret == nullptr || sel < 0 || sel > nwm);
if (sel == nwm)
{
- *watermodel = NULL;
+ *watermodel = nullptr;
}
else
{
char ffdir_parent[STRLEN];
char *p;
- nice_header(out, filename);
- fprintf(out, ";\tThis is a %s topology file\n;\n", bITP ? "include" : "standalone");
try
{
+ gmx::TextWriter writer(out);
+ gmx::niceHeader(&writer, filename, ';');
+ writer.writeLine(gmx::formatString(";\tThis is a %s topology file", bITP ? "include" : "standalone"));
+ writer.writeLine(";");
+
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix(";\t");
- gmx::printBinaryInformation(out, gmx::getProgramContext(), settings);
+ gmx::printBinaryInformation(&writer, gmx::getProgramContext(), settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- if (strchr(ffdir, '/') == NULL)
+ if (strchr(ffdir, '/') == nullptr)
{
fprintf(out, ";\tForce field was read from the standard GROMACS share directory.\n;\n\n");
}
fprintf(out, "; Include forcefield parameters\n");
p = strrchr(ffdir, '/');
- p = (ffdir[0] == '.' || p == NULL) ? ffdir : p+1;
+ p = (ffdir[0] == '.' || p == nullptr) ? ffdir : p+1;
fprintf(out, "#include \"%s/%s\"\n\n", p, fflib_forcefield_itp());
}
fprintf(out, "; Include water topology\n");
p = strrchr(ffdir, '/');
- p = (ffdir[0] == '.' || p == NULL) ? ffdir : p+1;
+ p = (ffdir[0] == '.' || p == nullptr) ? ffdir : p+1;
fprintf(out, "#include \"%s/%s.itp\"\n", p, water);
fprintf(out, "\n");
for (i = 0; (i < nincl); i++)
{
incl = strrchr(incls[i], DIR_SEPARATOR);
- if (incl == NULL)
+ if (incl == nullptr)
{
incl = incls[i];
}
gmx_fatal(FARGS, "Trying to make impossible special bond (%s-%s)!",
ssbonds[i].a1, ssbonds[i].a2);
}
- add_param(ps, ai, aj, NULL, NULL);
+ add_param(ps, ai, aj, nullptr, nullptr);
}
}
fprintf(stderr, "Warning: Short Bond (%d-%d = %g nm)\n",
ai+1, aj+1, std::sqrt(dist2));
}
- add_param(psb, ai, aj, NULL, hb[resind].rb[ebtsBONDS].b[j].s);
+ add_param(psb, ai, aj, nullptr, hb[resind].rb[ebtsBONDS].b[j].s);
}
}
/* add bonds from list of hacks (each added atom gets a bond) */
for (j = 0; j < hb[resind].nhack; j++)
{
if ( ( hb[resind].hack[j].tp > 0 ||
- hb[resind].hack[j].oname == NULL ) &&
+ hb[resind].hack[j].oname == nullptr ) &&
strcmp(hb[resind].hack[j].a[0], *(atoms->atomname[i])) == 0)
{
switch (hb[resind].hack[j].tp)
{
- case 9: /* COOH terminus */
- add_param(psb, i, i+1, NULL, NULL); /* C-O */
- add_param(psb, i, i+2, NULL, NULL); /* C-OA */
- add_param(psb, i+2, i+3, NULL, NULL); /* OA-H */
+ case 9: /* COOH terminus */
+ add_param(psb, i, i+1, nullptr, nullptr); /* C-O */
+ add_param(psb, i, i+2, nullptr, nullptr); /* C-OA */
+ add_param(psb, i+2, i+3, nullptr, nullptr); /* OA-H */
break;
default:
for (k = 0; (k < hb[resind].hack[j].nr); k++)
{
- add_param(psb, i, i+k+1, NULL, NULL);
+ add_param(psb, i, i+k+1, nullptr, nullptr);
}
}
}
static int pcompar(const void *a, const void *b)
{
- t_param *pa, *pb;
- int d;
- pa = (t_param *)a;
- pb = (t_param *)b;
+ const t_param *pa, *pb;
+ int d;
+ pa = static_cast<const t_param *>(a);
+ pb = static_cast<const t_param *>(b);
d = pa->a[0] - pb->a[0];
if (d == 0)
}
}
-void add_atom_to_restp(t_restp *restp, int at_start, const t_hack *hack)
+static void add_atom_to_restp(t_restp *restp, int at_start, const t_hack *hack)
{
char buf[STRLEN];
int k;
/* first the termini */
for (i = 0; i < nterpairs; i++)
{
- if (rn[i] >= 0 && ntdb[i] != NULL)
+ if (rn[i] >= 0 && ntdb[i] != nullptr)
{
copy_t_hackblock(ntdb[i], &(*hb)[rn[i]]);
}
- if (rc[i] >= 0 && ctdb[i] != NULL)
+ if (rc[i] >= 0 && ctdb[i] != nullptr)
{
merge_t_hackblock(ctdb[i], &(*hb)[rc[i]]);
}
}
bRM = merge_t_bondeds(res->rb, (*hb)[i].rb, tern >= 0, terc >= 0);
- if (bRM && ((tern >= 0 && ntdb[tern] == NULL) ||
- (terc >= 0 && ctdb[terc] == NULL)))
+ if (bRM && ((tern >= 0 && ntdb[tern] == nullptr) ||
+ (terc >= 0 && ctdb[terc] == nullptr)))
{
gmx_fatal(FARGS, "There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb).");
}
/* find atom in restp */
for (l = 0; l < (*restp)[i].natom; l++)
{
- if ( ( (*hb)[i].hack[j].oname == NULL &&
+ if ( ( (*hb)[i].hack[j].oname == nullptr &&
strcmp((*hb)[i].hack[j].a[0], *(*restp)[i].atomname[l]) == 0 ) ||
- ( (*hb)[i].hack[j].oname != NULL &&
+ ( (*hb)[i].hack[j].oname != nullptr &&
strcmp((*hb)[i].hack[j].oname, *(*restp)[i].atomname[l]) == 0 ) )
{
break;
/* Deleting can happen also only on the input atoms,
* not necessarily always on the rtp entry.
*/
- if (!((*hb)[i].hack[j].oname != NULL &&
- (*hb)[i].hack[j].nname != NULL) &&
- !((*hb)[i].hack[j].oname != NULL &&
- (*hb)[i].hack[j].nname == NULL))
+ if (!((*hb)[i].hack[j].oname != nullptr &&
+ (*hb)[i].hack[j].nname != nullptr) &&
+ !((*hb)[i].hack[j].oname != nullptr &&
+ (*hb)[i].hack[j].nname == nullptr))
{
gmx_fatal(FARGS,
"atom %s not found in buiding block %d%s "
"while combining tdb and rtp",
- (*hb)[i].hack[j].oname != NULL ?
+ (*hb)[i].hack[j].oname != nullptr ?
(*hb)[i].hack[j].oname : (*hb)[i].hack[j].a[0],
i+1, *resinfo[i].rtp);
}
}
else
{
- if ( (*hb)[i].hack[j].oname == NULL)
+ if ( (*hb)[i].hack[j].oname == nullptr)
{
/* we're adding: */
add_atom_to_restp(&(*restp)[i], l, &(*hb)[i].hack[j]);
else
{
/* oname != NULL */
- if ( (*hb)[i].hack[j].nname == NULL)
+ if ( (*hb)[i].hack[j].nname == nullptr)
{
/* we're deleting */
if (debug)
bDeleted = FALSE;
for (j = 0; j < hbr->nhack; j++)
{
- if (hbr->hack[j].oname != NULL && hbr->hack[j].nname != NULL &&
+ if (hbr->hack[j].oname != nullptr && hbr->hack[j].nname != nullptr &&
gmx_strcasecmp(oldnm, hbr->hack[j].oname) == 0)
{
/* This is a replace entry. */
for (k = 0; k < hbr->nhack; k++)
{
if (k != j &&
- hbr->hack[k].oname != NULL && hbr->hack[k].nname != NULL &&
+ hbr->hack[k].oname != nullptr && hbr->hack[k].nname != nullptr &&
gmx_strcasecmp(hbr->hack[k].nname, hbr->hack[j].oname) == 0)
{
/* The replace in hack[j] replaces an atom that
bFoundInAdd = FALSE;
for (k = 0; k < hbr->nhack; k++)
{
- if (hbr->hack[k].oname == NULL &&
- hbr->hack[k].nname != NULL &&
+ if (hbr->hack[k].oname == nullptr &&
+ hbr->hack[k].nname != nullptr &&
atomname_cmp_nr(newnm, &hbr->hack[k], &anmnr))
{
if (anmnr <= 1)
snew(pdba->atomname[atind], 1);
*pdba->atomname[atind] = gmx_strdup(newnm);
}
- else if (hbr->hack[j].oname != NULL && hbr->hack[j].nname == NULL &&
+ else if (hbr->hack[j].oname != nullptr && hbr->hack[j].nname == nullptr &&
gmx_strcasecmp(oldnm, hbr->hack[j].oname) == 0)
{
/* This is a delete entry, check if this atom is present
/* Skip this CMAP entry if it refers to residues before the
* first or after the last residue.
*/
- if (((strchr(pname, '-') != NULL) && (residx == 0)) ||
- ((strchr(pname, '+') != NULL) && (residx == nres-1)))
+ if (((strchr(pname, '-') != nullptr) && (residx == 0)) ||
+ ((strchr(pname, '+') != nullptr) && (residx == nres-1)))
{
bAddCMAP = FALSE;
break;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_atom *at = atoms->atom;
char ** const * anm = atoms->atomname;
- bPrevious = (strchr(type, '-') != NULL);
- bNext = (strchr(type, '+') != NULL);
+ bPrevious = (strchr(type, '-') != nullptr);
+ bNext = (strchr(type, '+') != nullptr);
if (!bPrevious)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/confio.h"
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/unique_cptr.h"
using gmx::RVec;
return exclusionDistances;
}
+void readConformation(const char *confin, gmx_mtop_t *top,
+ std::vector<RVec> *x, std::vector<RVec> *v,
+ int *ePBC, matrix box, const char *statusTitle)
+{
+ fprintf(stderr, "Reading %s configuration%s\n", statusTitle,
+ v ? " and velocities" : "");
+ rvec *x_tmp = nullptr, *v_tmp = nullptr;
+ bool dummy;
+ readConfAndTopology(confin, &dummy, top, ePBC, x ? &x_tmp : nullptr, v ? &v_tmp : nullptr, box);
+ const gmx::sfree_guard xguard(x_tmp);
+ const gmx::sfree_guard vguard(v_tmp);
+ if (x && x_tmp)
+ {
+ *x = std::vector<RVec>(x_tmp, x_tmp + top->natoms);
+ }
+ if (v && v_tmp)
+ {
+ *v = std::vector<RVec>(v_tmp, v_tmp + top->natoms);
+ }
+ fprintf(stderr, "%s\nContaining %d atoms in %d residues\n",
+ *top->name, top->natoms, gmx_mtop_nres(top));
+}
+
void readConformation(const char *confin, t_topology *top,
std::vector<RVec> *x, std::vector<RVec> *v,
int *ePBC, matrix box, const char *statusTitle)
{
fprintf(stderr, "Reading %s configuration%s\n", statusTitle,
v ? " and velocities" : "");
- rvec *x_tmp = NULL, *v_tmp = NULL;
- read_tps_conf(confin, top, ePBC, x ? &x_tmp : NULL, v ? &v_tmp : NULL, box, FALSE);
- gmx::scoped_guard_sfree xguard(x_tmp);
- gmx::scoped_guard_sfree vguard(v_tmp);
+ rvec *x_tmp = nullptr, *v_tmp = nullptr;
+ read_tps_conf(confin, top, ePBC, x ? &x_tmp : nullptr, v ? &v_tmp : nullptr, box, FALSE);
+ const gmx::sfree_guard xguard(x_tmp);
+ const gmx::sfree_guard vguard(v_tmp);
if (x && x_tmp)
{
*x = std::vector<RVec>(x_tmp, x_tmp + top->atoms.nr);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/real.h"
struct gmx_atomprop;
+struct gmx_mtop_t;
struct t_atoms;
struct t_topology;
makeExclusionDistances(const t_atoms *a, gmx_atomprop *aps,
real defaultDistance, real scaleFactor);
+void readConformation(const char *confin, gmx_mtop_t *top,
+ std::vector<gmx::RVec> *x, std::vector<gmx::RVec> *v,
+ int *ePBC, matrix box, const char *statusTitle);
/*! \brief Read a conformation from a file, allocate and fill data structures.
*
* Used by solvate and insert-molecules. The returned pointers *x and
#include "gromacs/fileio/warninp.h"
#include "gromacs/gmxlib/chargegroup.h"
#include "gromacs/gmxlib/network.h"
+#include "gromacs/gmxpreprocess/keyvaluetreemdpwriter.h"
#include "gromacs/gmxpreprocess/toputil.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/calc_verletbuf.h"
+#include "gromacs/mdrunutility/mdmodules.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/pull-params.h"
+#include "gromacs/options/options.h"
+#include "gromacs/options/treesupport.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/ikeyvaluetreeerror.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/keyvaluetreetransform.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringcompare.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
#define MAXPTR 254
#define NOGID 255
char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
- char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
- efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
} gmx_inputrec_strings;
-static gmx_inputrec_strings *is = NULL;
+static gmx_inputrec_strings *is = nullptr;
void init_inputrec_strings()
{
void done_inputrec_strings()
{
sfree(is);
- is = NULL;
+ is = nullptr;
}
};
static const char *constraints[eshNR+1] = {
- "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
+ "none", "h-bonds", "all-bonds", "h-angles", "all-angles", nullptr
};
static const char *couple_lam[ecouplamNR+1] = {
- "vdw-q", "vdw", "q", "none", NULL
+ "vdw-q", "vdw", "q", "none", nullptr
};
-void init_ir(t_inputrec *ir, t_gromppopts *opts)
-{
- snew(opts->include, STRLEN);
- snew(opts->define, STRLEN);
- snew(ir->fepvals, 1);
- snew(ir->expandedvals, 1);
- snew(ir->simtempvals, 1);
-}
-
static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
{
CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
}
- if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
+ if (getenv("GMX_DO_GALACTIC_DYNAMICS") == nullptr)
{
sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
CHECK(ir->epsilon_r < 0);
if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
{
- if (ir->pme_order < 3)
+ // TODO: Move these checks into the ewald module with the options class
+ int orderMin = 3;
+ int orderMax = (ir->coulombtype == eelP3M_AD ? 8 : 12);
+
+ if (ir->pme_order < orderMin || ir->pme_order > orderMax)
{
- warning_error(wi, "pme-order can not be smaller than 3");
+ sprintf(warn_buf, "With coulombtype = %s, you should have %d <= pme-order <= %d", eel_names[ir->coulombtype], orderMin, orderMax);
+ warning_error(wi, warn_buf);
}
}
}
ltrim(copy);
}
- if (ptr == NULL)
+ if (ptr == nullptr)
{
sfree(copy0);
}
char *names[MAXPTR];
double dbl;
- opts->wall_atomtype[0] = NULL;
- opts->wall_atomtype[1] = NULL;
+ opts->wall_atomtype[0] = nullptr;
+ opts->wall_atomtype[1] = nullptr;
ir->wall_atomtype[0] = -1;
ir->wall_atomtype[1] = -1;
}
}
-void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
- t_expanded *expand, warninp_t wi)
+static void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
+ t_expanded *expand, warninp_t wi)
{
int ninp;
t_inpfile *inp;
couple_lambda_value == ecouplamVDWQ);
}
+namespace
+{
+
+class MdpErrorHandler : public gmx::IKeyValueTreeErrorHandler
+{
+ public:
+ explicit MdpErrorHandler(warninp_t wi)
+ : wi_(wi), mapping_(nullptr)
+ {
+ }
+
+ void setBackMapping(const gmx::IKeyValueTreeBackMapping &mapping)
+ {
+ mapping_ = &mapping;
+ }
+
+ virtual bool onError(gmx::UserInputError *ex, const gmx::KeyValueTreePath &context)
+ {
+ ex->prependContext(gmx::formatString("Error in mdp option \"%s\":",
+ getOptionName(context).c_str()));
+ std::string message = gmx::formatExceptionMessageToString(*ex);
+ warning_error(wi_, message.c_str());
+ return true;
+ }
+
+ private:
+ std::string getOptionName(const gmx::KeyValueTreePath &context)
+ {
+ if (mapping_ != nullptr)
+ {
+ gmx::KeyValueTreePath path = mapping_->originalPath(context);
+ GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
+ return path[0];
+ }
+ GMX_ASSERT(context.size() == 1, "Inconsistent context for mdp option parsing");
+ return context[0];
+ }
+
+ warninp_t wi_;
+ const gmx::IKeyValueTreeBackMapping *mapping_;
+};
+
+} // namespace
+
void get_ir(const char *mdparin, const char *mdparout,
- t_inputrec *ir, t_gromppopts *opts,
- warninp_t wi)
+ gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
+ WriteMdpHeader writeMdpHeader, warninp_t wi)
{
char *dumstr[2];
double dumdub[2][6];
t_expanded *expand = ir->expandedvals;
init_inputrec_strings();
- inp = read_inpfile(mdparin, &ninp, wi);
+ gmx::TextInputFile stream(mdparin);
+ inp = read_inpfile(&stream, mdparin, &ninp, wi);
snew(dumstr[0], STRLEN);
snew(dumstr[1], STRLEN);
CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
CTYPE ("Preprocessor information: use cpp syntax.");
CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
- STYPE ("include", opts->include, NULL);
+ STYPE ("include", opts->include, nullptr);
CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
- STYPE ("define", opts->define, NULL);
+ STYPE ("define", opts->define, nullptr);
CCTYPE ("RUN CONTROL PARAMETERS");
EETYPE("integrator", ir->eI, ei_names);
CTYPE ("number of steps for center of mass motion removal");
ITYPE ("nstcomm", ir->nstcomm, 100);
CTYPE ("group(s) for center of mass motion removal");
- STYPE ("comm-grps", is->vcm, NULL);
+ STYPE ("comm-grps", is->vcm, nullptr);
CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
CTYPE ("Friction coefficient (amu/ps) and random seed");
CTYPE ("This selects the subset of atoms for the compressed");
CTYPE ("trajectory file. You can select multiple groups. By");
CTYPE ("default, all atoms will be written.");
- STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
+ STYPE ("compressed-x-grps", is->x_compressed_groups, nullptr);
CTYPE ("Selection of energy groups");
- STYPE ("energygrps", is->energy, NULL);
+ STYPE ("energygrps", is->energy, nullptr);
/* Neighbor searching */
CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
CTYPE ("Extension of the potential lookup tables beyond the cut-off");
RTYPE ("table-extension", ir->tabext, 1.0);
CTYPE ("Separate tables between energy group pairs");
- STYPE ("energygrp-table", is->egptable, NULL);
+ STYPE ("energygrp-table", is->egptable, nullptr);
CTYPE ("Spacing for the PME/PPPM FFT grid");
RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
CTYPE ("Groups to couple separately");
- STYPE ("tc-grps", is->tcgrps, NULL);
+ STYPE ("tc-grps", is->tcgrps, nullptr);
CTYPE ("Time constant (ps) and reference temperature (K)");
- STYPE ("tau-t", is->tau_t, NULL);
- STYPE ("ref-t", is->ref_t, NULL);
+ STYPE ("tau-t", is->tau_t, nullptr);
+ STYPE ("ref-t", is->ref_t, nullptr);
CTYPE ("pressure coupling");
EETYPE("pcoupl", ir->epc, epcoupl_names);
EETYPE("pcoupltype", ir->epct, epcoupltype_names);
ITYPE ("nstpcouple", ir->nstpcouple, -1);
CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
RTYPE ("tau-p", ir->tau_p, 1.0);
- STYPE ("compressibility", dumstr[0], NULL);
- STYPE ("ref-p", dumstr[1], NULL);
+ STYPE ("compressibility", dumstr[0], nullptr);
+ STYPE ("ref-p", dumstr[1], nullptr);
CTYPE ("Scaling of reference coordinates, No, All or COM");
EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
CCTYPE ("OPTIONS FOR QMMM calculations");
EETYPE("QMMM", ir->bQMMM, yesno_names);
CTYPE ("Groups treated Quantum Mechanically");
- STYPE ("QMMM-grps", is->QMMM, NULL);
+ STYPE ("QMMM-grps", is->QMMM, nullptr);
CTYPE ("QM method");
- STYPE("QMmethod", is->QMmethod, NULL);
+ STYPE("QMmethod", is->QMmethod, nullptr);
CTYPE ("QMMM scheme");
EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
CTYPE ("QM basisset");
- STYPE("QMbasis", is->QMbasis, NULL);
+ STYPE("QMbasis", is->QMbasis, nullptr);
CTYPE ("QM charge");
- STYPE ("QMcharge", is->QMcharge, NULL);
+ STYPE ("QMcharge", is->QMcharge, nullptr);
CTYPE ("QM multiplicity");
- STYPE ("QMmult", is->QMmult, NULL);
+ STYPE ("QMmult", is->QMmult, nullptr);
CTYPE ("Surface Hopping");
- STYPE ("SH", is->bSH, NULL);
+ STYPE ("SH", is->bSH, nullptr);
CTYPE ("CAS space options");
- STYPE ("CASorbitals", is->CASorbitals, NULL);
- STYPE ("CASelectrons", is->CASelectrons, NULL);
- STYPE ("SAon", is->SAon, NULL);
- STYPE ("SAoff", is->SAoff, NULL);
- STYPE ("SAsteps", is->SAsteps, NULL);
+ STYPE ("CASorbitals", is->CASorbitals, nullptr);
+ STYPE ("CASelectrons", is->CASelectrons, nullptr);
+ STYPE ("SAon", is->SAon, nullptr);
+ STYPE ("SAoff", is->SAoff, nullptr);
+ STYPE ("SAsteps", is->SAsteps, nullptr);
CTYPE ("Scale factor for MM charges");
RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
CTYPE ("Optimization of QM subsystem");
- STYPE ("bOPT", is->bOPT, NULL);
- STYPE ("bTS", is->bTS, NULL);
+ STYPE ("bOPT", is->bOPT, nullptr);
+ STYPE ("bTS", is->bTS, nullptr);
/* Simulated annealing */
CCTYPE("SIMULATED ANNEALING");
CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
- STYPE ("annealing", is->anneal, NULL);
+ STYPE ("annealing", is->anneal, nullptr);
CTYPE ("Number of time points to use for specifying annealing in each group");
- STYPE ("annealing-npoints", is->anneal_npoints, NULL);
+ STYPE ("annealing-npoints", is->anneal_npoints, nullptr);
CTYPE ("List of times at the annealing points for each group");
- STYPE ("annealing-time", is->anneal_time, NULL);
+ STYPE ("annealing-time", is->anneal_time, nullptr);
CTYPE ("Temp. at each annealing point, for each group.");
- STYPE ("annealing-temp", is->anneal_temp, NULL);
+ STYPE ("annealing-temp", is->anneal_temp, nullptr);
/* Startup run */
CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
/* Energy group exclusions */
CCTYPE ("ENERGY GROUP EXCLUSIONS");
CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
- STYPE ("energygrp-excl", is->egpexcl, NULL);
+ STYPE ("energygrp-excl", is->egpexcl, nullptr);
/* Walls */
CCTYPE ("WALLS");
ITYPE ("nwall", ir->nwall, 0);
EETYPE("wall-type", ir->wall_type, ewt_names);
RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
- STYPE ("wall-atomtype", is->wall_atomtype, NULL);
- STYPE ("wall-density", is->wall_density, NULL);
+ STYPE ("wall-atomtype", is->wall_atomtype, nullptr);
+ STYPE ("wall-density", is->wall_density, nullptr);
RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
/* COM pulling */
/* Interactive MD */
ir->bIMD = FALSE;
CCTYPE("Group to display and/or manipulate in interactive MD session");
- STYPE ("IMD-group", is->imd_grp, NULL);
+ STYPE ("IMD-group", is->imd_grp, nullptr);
if (is->imd_grp[0] != '\0')
{
snew(ir->imd, 1);
CTYPE ("Orientation restraints force constant and tau for time averaging");
RTYPE ("orire-fc", ir->orires_fc, 0.0);
RTYPE ("orire-tau", ir->orires_tau, 0.0);
- STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
+ STYPE ("orire-fitgrp", is->orirefitgrp, nullptr);
CTYPE ("Output frequency for trace(SD) and S to energy file");
ITYPE ("nstorireout", ir->nstorireout, 100);
/* free energy variables */
CCTYPE ("Free energy variables");
EETYPE("free-energy", ir->efep, efep_names);
- STYPE ("couple-moltype", is->couple_moltype, NULL);
+ STYPE ("couple-moltype", is->couple_moltype, nullptr);
EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
ITYPE ("init-lambda-state", fep->init_fep_state, -1);
RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
ITYPE ("nstdhdl", fep->nstdhdl, 50);
- STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
- STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
- STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
- STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
- STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
- STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
- STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
+ STYPE ("fep-lambdas", is->fep_lambda[efptFEP], nullptr);
+ STYPE ("mass-lambdas", is->fep_lambda[efptMASS], nullptr);
+ STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
+ STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
+ STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
+ STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
+ STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
- STYPE ("init-lambda-weights", is->lambda_weights, NULL);
+ STYPE ("init-lambda-weights", is->lambda_weights, nullptr);
EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
ITYPE ("sc-power", fep->sc_power, 1);
/* Non-equilibrium MD stuff */
CCTYPE("Non-equilibrium MD stuff");
- STYPE ("acc-grps", is->accgrps, NULL);
- STYPE ("accelerate", is->acc, NULL);
- STYPE ("freezegrps", is->freeze, NULL);
- STYPE ("freezedim", is->frdim, NULL);
+ STYPE ("acc-grps", is->accgrps, nullptr);
+ STYPE ("accelerate", is->acc, nullptr);
+ STYPE ("freezegrps", is->freeze, nullptr);
+ STYPE ("freezedim", is->frdim, nullptr);
RTYPE ("cos-acceleration", ir->cos_accel, 0);
- STYPE ("deform", is->deform, NULL);
+ STYPE ("deform", is->deform, nullptr);
/* simulated tempering variables */
CCTYPE("simulated tempering variables");
}
/* Electric fields */
- CCTYPE("Electric fields");
- CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
- CTYPE ("and a phase angle (real)");
- STYPE ("E-x", is->efield_x, NULL);
- CTYPE ("Time dependent (pulsed) electric field. Format is omega, time for pulse");
- CTYPE ("peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving");
- CTYPE ("the field to be a cosine function.");
- STYPE ("E-xt", is->efield_xt, NULL);
- STYPE ("E-y", is->efield_y, NULL);
- STYPE ("E-yt", is->efield_yt, NULL);
- STYPE ("E-z", is->efield_z, NULL);
- STYPE ("E-zt", is->efield_zt, NULL);
+ {
+ gmx::KeyValueTreeObject convertedValues = flatKeyValueTreeFromInpFile(ninp, inp);
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
+ mdModules->initMdpTransform(transform.rules());
+ for (const auto &path : transform.mappedPaths())
+ {
+ GMX_ASSERT(path.size() == 1, "Inconsistent mapping back to mdp options");
+ mark_einp_set(ninp, inp, path[0].c_str());
+ }
+ MdpErrorHandler errorHandler(wi);
+ auto result
+ = transform.transform(convertedValues, &errorHandler);
+ ir->params = new gmx::KeyValueTreeObject(result.object());
+ mdModules->adjustInputrecBasedOnModules(ir);
+ errorHandler.setBackMapping(result.backMapping());
+ mdModules->assignOptionsToModules(*ir->params, &errorHandler);
+ }
/* Ion/water position swapping ("computational electrophysiology") */
CCTYPE("Ion/water position swapping for computational electrophysiology setups");
snew(ir->swap->grp[i].molname, STRLEN);
}
CTYPE("Two index groups that contain the compartment-partitioning atoms");
- STYPE("split-group0", ir->swap->grp[eGrpSplit0].molname, NULL);
- STYPE("split-group1", ir->swap->grp[eGrpSplit1].molname, NULL);
+ STYPE("split-group0", ir->swap->grp[eGrpSplit0].molname, nullptr);
+ STYPE("split-group1", ir->swap->grp[eGrpSplit1].molname, nullptr);
CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
CTYPE("Name of solvent molecules");
- STYPE("solvent-group", ir->swap->grp[eGrpSolvent].molname, NULL);
+ STYPE("solvent-group", ir->swap->grp[eGrpSolvent].molname, nullptr);
CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
int ig = eSwapFixedGrpNR + i;
sprintf(buf, "iontype%d-name", i);
- STYPE(buf, ir->swap->grp[ig].molname, NULL);
+ STYPE(buf, ir->swap->grp[ig].molname, nullptr);
sprintf(buf, "iontype%d-in-A", i);
ITYPE(buf, ir->swap->grp[ig].nmolReq[0], -1);
sprintf(buf, "iontype%d-in-B", i);
/* User defined thingies */
CCTYPE ("User defined thingies");
- STYPE ("user1-grps", is->user1, NULL);
- STYPE ("user2-grps", is->user2, NULL);
+ STYPE ("user1-grps", is->user1, nullptr);
+ STYPE ("user2-grps", is->user2, nullptr);
ITYPE ("userint1", ir->userint1, 0);
ITYPE ("userint2", ir->userint2, 0);
ITYPE ("userint3", ir->userint3, 0);
RTYPE ("userreal4", ir->userreal4, 0);
#undef CTYPE
- write_inpfile(mdparout, ninp, inp, FALSE, wi);
+ {
+ gmx::TextOutputFile stream(mdparout);
+ write_inpfile(&stream, mdparout, ninp, inp, FALSE, writeMdpHeader, wi);
+
+ // Transform module data into a flat key-value tree for output.
+ gmx::KeyValueTreeBuilder builder;
+ gmx::KeyValueTreeObjectBuilder builderObject = builder.rootObject();
+ mdModules->buildMdpOutput(&builderObject);
+ {
+ gmx::TextWriter writer(&stream);
+ writeKeyValueTreeAsMdp(&writer, builder.build());
+ }
+ stream.close();
+ }
+
for (i = 0; (i < ninp); i++)
{
sfree(inp[i].name);
ir->nstcomm = 0;
}
- opts->couple_moltype = NULL;
+ opts->couple_moltype = nullptr;
if (strlen(is->couple_moltype) > 0)
{
if (ir->efep != efepNO)
/* ORIENTATION RESTRAINT PARAMETERS */
- if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
+ if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, nullptr) != 1)
{
warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
}
{
/* All atoms are part of one (or no) group, no index required */
groups->ngrpnr[gtype] = 0;
- groups->grpnr[gtype] = NULL;
+ groups->grpnr[gtype] = nullptr;
}
else
{
double *nrdf_tc, *nrdf_vcm, nrdf_uc, *nrdf_vcm_sub;
ivec *dof_vcm;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
int mb, mol, ftype, as;
gmx_molblock_t *molb;
gmx_moltype_t *molt;
snew(nrdf2, natoms);
aloop = gmx_mtop_atomloop_all_init(mtop);
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
nrdf2[i] = 0;
sfree(nrdf_vcm_sub);
}
-static void decode_cos(char *s, t_cosines *cosine)
-{
- char *t;
- char format[STRLEN], f1[STRLEN];
- double a, phi;
- int i;
-
- t = gmx_strdup(s);
- trim(t);
-
- cosine->n = 0;
- cosine->a = NULL;
- cosine->phi = NULL;
- if (strlen(t))
- {
- if (sscanf(t, "%d", &(cosine->n)) != 1)
- {
- gmx_fatal(FARGS, "Cannot parse cosine multiplicity from string '%s'", t);
- }
- if (cosine->n <= 0)
- {
- cosine->n = 0;
- }
- else
- {
- snew(cosine->a, cosine->n);
- snew(cosine->phi, cosine->n);
-
- sprintf(format, "%%*d");
- for (i = 0; (i < cosine->n); i++)
- {
- double gmx_unused canary;
-
- strcpy(f1, format);
- strcat(f1, "%lf%lf%lf");
- if (sscanf(t, f1, &a, &phi, &canary) != 2)
- {
- gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
- }
- cosine->a[i] = a;
- cosine->phi[i] = phi;
- strcat(format, "%*lf%*lf");
- }
- }
- }
- sfree(t);
-}
-
static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
const char *option, const char *val, int flag)
{
}
-void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
+static void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
{
int ig, i;
{
fprintf(stderr, "processing index file...\n");
}
- if (ndx == NULL)
+ if (ndx == nullptr)
{
snew(grps, 1);
snew(grps->index, 1);
{
ir->opts.annealing[i] = eannNO;
ir->opts.anneal_npoints[i] = 0;
- ir->opts.anneal_time[i] = NULL;
- ir->opts.anneal_temp[i] = NULL;
+ ir->opts.anneal_time[i] = nullptr;
+ ir->opts.anneal_temp[i] = nullptr;
}
if (nSA > 0)
{
gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
}
- decode_cos(is->efield_x, &(ir->ex[XX]));
- decode_cos(is->efield_xt, &(ir->et[XX]));
- decode_cos(is->efield_y, &(ir->ex[YY]));
- decode_cos(is->efield_yt, &(ir->et[YY]));
- decode_cos(is->efield_z, &(ir->ex[ZZ]));
- decode_cos(is->efield_zt, &(ir->et[ZZ]));
-
for (i = 0; (i < grps->nr); i++)
{
sfree(gnames[i]);
*/
tol = 1e-5;
ptr = getenv("GMX_LJCOMB_TOL");
- if (ptr != NULL)
+ if (ptr != nullptr)
{
double dbl;
double gmx_unused canary;
rvec acc;
gmx_mtop_atomloop_block_t aloopb;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
ivec AbsRef;
char warn_buf[STRLEN];
bCharge = FALSE;
aloopb = gmx_mtop_atomloop_block_init(sys);
+ const t_atom *atom;
while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
{
if (atom->q != 0 || atom->qB != 0)
clear_rvec(acc);
snew(mgrp, sys->groups.grps[egcACC].nr);
aloop = gmx_mtop_atomloop_all_init(sys);
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/readinp.h"
#include "gromacs/gmxpreprocess/grompp-impl.h"
+namespace gmx
+{
+class MDModules;
+}
+
struct gmx_groups_t;
struct gmx_mtop_t;
struct gmx_output_env_t;
struct pull_params_t;
struct pull_t;
struct t_grpopts;
+struct t_inpfile;
struct t_inputrec;
struct t_rot;
+struct warninp;
+typedef warninp *warninp_t;
enum {
eshNONE, eshHBONDS, eshALLBONDS, eshHANGLES, eshALLANGLES, eshNR
ecouplamVDWQ, ecouplamVDW, ecouplamQ, ecouplamNONE, ecouplamNR
};
-typedef struct {
+struct t_gromppopts
+{
int warnings;
int nshake;
char *include;
int couple_lam0;
int couple_lam1;
gmx_bool bCoupleIntra;
-} t_gromppopts;
+};
/*! \brief Initialise object to hold strings parsed from an .mdp file */
void init_inputrec_strings();
/*! \brief Clean up object that holds strings parsed from an .mdp file */
void done_inputrec_strings();
-void init_ir(t_inputrec *ir, t_gromppopts *opts);
-/* Initiate stuff */
-
void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
warninp_t wi);
/* Validate inputrec data.
/* Even more checks, charge group radii vs. cut-off's only. */
void get_ir(const char *mdparin, const char *mdparout,
- t_inputrec *ir, t_gromppopts *opts,
- warninp_t wi);
+ gmx::MDModules *mdModules, t_inputrec *ir, t_gromppopts *opts,
+ WriteMdpHeader writeMdpHeader, warninp_t wi);
/* Read the input file, and retrieve data for inputrec.
* More data are read, but the are only evaluated when the next
* function is called. Also prints the input file back to mdparout.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string.h>
#include "gromacs/fileio/readinp.h"
+#include "gromacs/fileio/warninp.h"
#include "gromacs/gmxpreprocess/readir.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/pull-params.h"
{
sprintf(wbuf, "%s should contain %d pull group indices with geometry %s",
buf, pcrd->ngroup, epullg_names[pcrd->eGeom]);
- set_warning_line(wi, NULL, -1);
+ set_warning_line(wi, nullptr, -1);
warning_error(wi, wbuf);
}
for (int g = 0; g < pcrd->ngroup; g++)
double t_start;
pull = ir->pull;
- pull_work = init_pull(NULL, pull, ir, 0, NULL, mtop, NULL, oenv, lambda, FALSE, 0);
- md = init_mdatoms(NULL, mtop, ir->efep);
- atoms2md(mtop, ir, 0, NULL, mtop->natoms, md);
+ pull_work = init_pull(nullptr, pull, ir, 0, nullptr, mtop, nullptr, oenv, lambda, FALSE, ContinuationOptions());
+ md = init_mdatoms(nullptr, mtop, ir->efep);
+ atoms2md(mtop, ir, -1, nullptr, mtop->natoms, md);
if (ir->efep)
{
update_mdatoms(md, lambda);
t_start = ir->init_t + ir->init_step*ir->delta_t;
- pull_calc_coms(NULL, pull_work, md, &pbc, t_start, x, NULL);
+ pull_calc_coms(nullptr, pull_work, md, &pbc, t_start, x, nullptr);
fprintf(stderr, "Pull group natoms pbc atom distance at start reference at t=0\n");
for (c = 0; c < pull->ncoord; c++)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/trrio.h"
+#include "gromacs/fileio/warninp.h"
#include "gromacs/gmxpreprocess/readir.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/block.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
gmx_fatal(FARGS, "Number of atoms in file %s (%d) does not match the number of atoms in rotation group (%d)!\n",
reffile, header.natoms, rotg->nat);
}
- gmx_trr_read_single_frame(reffile, &header.step, &header.t, &header.lambda, f_box, &header.natoms, rotg->x_ref, NULL, NULL);
+ gmx_trr_read_single_frame(reffile, &header.step, &header.t, &header.lambda, f_box, &header.natoms, rotg->x_ref, nullptr, nullptr);
/* Check whether the box is unchanged and output a warning if not: */
check_box_unchanged(f_box, box, reffile, wi);
ii = rotg->ind[i];
copy_rvec(x[ii], rotg->x_ref[i]);
}
- gmx_trr_write_single_frame(reffile, g, 0.0, 0.0, box, rotg->nat, rotg->x_ref, NULL, NULL);
+ gmx_trr_write_single_frame(reffile, g, 0.0, 0.0, box, rotg->nat, rotg->x_ref, nullptr, nullptr);
}
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Skip blank or comment-only lines */
do
{
- if (fgets2(buf, STRLEN, in) != NULL)
+ if (fgets2(buf, STRLEN, in) != nullptr)
{
strip_comment(buf);
trim(buf);
{
tp = rtp->atom[j].type;
tpnm = get_atomtype_name(tp, atype);
- if (tpnm == NULL)
+ if (tpnm == nullptr)
{
gmx_fatal(FARGS, "Incorrect atomtype (%d)", tp);
}
/* Read Atoms */
maxentries = 0;
- r0->atom = NULL;
- r0->atomname = NULL;
- r0->cgnr = NULL;
+ r0->atom = nullptr;
+ r0->atomname = nullptr;
+ r0->cgnr = nullptr;
i = 0;
- while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == NULL))
+ while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == nullptr))
{
if (sscanf(line, "%s%s%lf%d", buf, buf1, &q, &cg) != 4)
{
return TRUE;
}
-gmx_bool read_bondeds(int bt, FILE *in, char *line, t_restp *rtp)
+static gmx_bool read_bondeds(int bt, FILE *in, char *line, t_restp *rtp)
{
char str[STRLEN];
int j, n, ni, maxrb;
maxrb = rtp->rb[bt].nb;
- while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == NULL))
+ while (get_a_line(in, line, STRLEN) && (strchr(line, '[') == nullptr))
{
if (rtp->rb[bt].nb >= maxrb)
{
}
for (; j < MAXATOMLIST; j++)
{
- rtp->rb[bt].b[rtp->rb[bt].nb].a[j] = NULL;
+ rtp->rb[bt].b[rtp->rb[bt].nb].a[j] = nullptr;
}
while (isspace(line[n]))
{
}
}
-static int comprtp(const void *a, const void *b)
-{
- t_restp *ra, *rb;
-
- ra = (t_restp *)a;
- rb = (t_restp *)b;
-
- return gmx_strcasecmp(ra->resname, rb->resname);
-}
-
-int get_bt(char* header)
+static int get_bt(char* header)
{
int i;
return NOTSET;
}
-void clear_t_restp(t_restp *rrtp)
+static void clear_t_restp(t_restp *rrtp)
{
memset((void *)rrtp, 0, sizeof(t_restp));
}
/* print all the ebtsNR type numbers */
-void print_resall_header(FILE *out, t_restp rtp[])
+static void print_resall_header(FILE *out, t_restp rtp[])
{
fprintf(out, "[ bondedtypes ]\n");
fprintf(out, "; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih\n");
srenew(rrtp, nrtp);
fprintf(stderr, "\nSorting it all out...\n");
- qsort(rrtp, nrtp, (size_t)sizeof(rrtp[0]), comprtp);
+ std::sort(rrtp, rrtp+nrtp, [](const t_restp &a, const t_restp &b) {return gmx_strcasecmp(a.resname, b.resname) < 0; });
check_rtp(nrtp, rrtp, rrdb);
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/boxutilities.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/nbsearch.h"
#include "gromacs/topology/atomprop.h"
int res0;
} t_moltypes;
-static void sort_molecule(t_atoms *atoms, std::vector<RVec> *x,
+static void sort_molecule(t_atoms **atoms_solvt, std::vector<RVec> *x,
std::vector<RVec> *v)
{
int atnr, i, j, moltp = 0, nrmoltypes, resi_o, resi_n, resnr;
t_moltypes *moltypes;
+ t_atoms *atoms, *newatoms;
fprintf(stderr, "Sorting configuration\n");
- /* copy each residue from atoms to a molecule in *molecule */
- moltypes = NULL;
+ atoms = *atoms_solvt;
+
+ /* copy each residue from *atoms to a molecule in *molecule */
+ moltypes = nullptr;
nrmoltypes = 0;
for (i = 0; i < atoms->nr; i++)
{
}
/* now put them there: */
- t_atoms *newatoms;
snew(newatoms, 1);
init_t_atoms(newatoms, atoms->nr, FALSE);
newatoms->nres = atoms->nres;
- srenew(newatoms->resinfo, atoms->nres);
+ snew(newatoms->resinfo, atoms->nres);
std::vector<RVec> newx(x->size());
std::vector<RVec> newv(v->size());
sfree(atoms->atomname);
sfree(atoms->resinfo);
sfree(atoms->atom);
- *atoms = *newatoms;
- sfree(newatoms);
+ sfree(atoms);
+ *atoms_solvt = newatoms;
std::swap(*x, newx);
std::swap(*v, newv);
}
// but not in all).
t_atoms newAtoms;
init_t_atoms(&newAtoms, 0, FALSE);
- gmx::AtomsBuilder builder(&newAtoms, NULL);
+ gmx::AtomsBuilder builder(&newAtoms, nullptr);
builder.reserve(atoms->nr * nmol, atoms->nres * nmol);
std::vector<RVec> newX(atoms->nr * nmol);
std::vector<RVec> newV(!v->empty() ? atoms->nr * nmol : 0);
sfree(atoms->atom);
sfree(atoms->atomname);
sfree(atoms->resinfo);
- sfree(atoms->pdbinfo);
atoms->nr = newAtoms.nr;
atoms->nres = newAtoms.nres;
atoms->atom = newAtoms.atom;
atoms->atomname = newAtoms.atomname;
atoms->resinfo = newAtoms.resinfo;
- atoms->pdbinfo = newAtoms.pdbinfo;
newX.resize(atoms->nr);
std::swap(*x, newX);
char *filename = gmxlibfn(fn);
snew(top_solvt, 1);
- readConformation(filename, top_solvt, &x_solvt, !v->empty() ? &v_solvt : NULL,
+ readConformation(filename, top_solvt, &x_solvt, !v->empty() ? &v_solvt : nullptr,
&ePBC_solvt, box_solvt, "solvent");
t_atoms *atoms_solvt = &top_solvt->atoms;
if (0 == atoms_solvt->nr)
sfree(filename);
fprintf(stderr, "\n");
- /* apply pbc for solvent configuration for whole molecules */
- rm_res_pbc(atoms_solvt, &x_solvt, box_solvt);
-
/* initialise distance arrays for solvent configuration */
fprintf(stderr, "Initialising inter-atomic distances...\n");
const std::vector<real> exclusionDistances(
fprintf(stderr, "Generating solvent configuration\n");
t_pbc pbc;
set_pbc(&pbc, ePBC, box);
- replicateSolventBox(atoms_solvt, &x_solvt, &v_solvt, &exclusionDistances_solvt,
- box_solvt, box);
- if (ePBC != epbcNONE)
+ if (!gmx::boxesAreEqual(box_solvt, box))
{
- removeSolventBoxOverlap(atoms_solvt, &x_solvt, &v_solvt, &exclusionDistances_solvt, pbc);
+ if (TRICLINIC(box_solvt))
+ {
+ gmx_fatal(FARGS, "Generating from non-rectangular solvent boxes is currently not supported.\n"
+ "You can try to pass the same box for -cp and -cs.");
+ }
+ /* apply pbc for solvent configuration for whole molecules */
+ rm_res_pbc(atoms_solvt, &x_solvt, box_solvt);
+ replicateSolventBox(atoms_solvt, &x_solvt, &v_solvt, &exclusionDistances_solvt,
+ box_solvt, box);
+ if (ePBC != epbcNONE)
+ {
+ removeSolventBoxOverlap(atoms_solvt, &x_solvt, &v_solvt, &exclusionDistances_solvt, pbc);
+ }
}
if (top->atoms.nr > 0)
{
}
/* Sort the solvent mixture, not the protein... */
- sort_molecule(atoms_solvt, &x_solvt, &v_solvt);
+ sort_molecule(&atoms_solvt, &x_solvt, &v_solvt);
// Merge the two configurations.
x->insert(x->end(), x_solvt.begin(), x_solvt.end());
bSkip = FALSE;
line++;
strcpy(buf2, buf);
- if ((temp = strchr(buf2, '\n')) != NULL)
+ if ((temp = strchr(buf2, '\n')) != nullptr)
{
temp[0] = '\0';
}
if (buf2[0] == '[')
{
buf2[0] = ' ';
- if ((temp = strchr(buf2, '\n')) != NULL)
+ if ((temp = strchr(buf2, '\n')) != nullptr)
{
temp[0] = '\0';
}
}
if (bSkip)
{
- if ((temp = strchr(buf, '\n')) != NULL)
+ if ((temp = strchr(buf, '\n')) != nullptr)
{
temp[0] = '\0';
}
t_filenm fnm[] = {
{ efSTX, "-cp", "protein", ffOPTRD },
{ efSTX, "-cs", "spc216", ffLIBRD},
- { efSTO, NULL, NULL, ffWRITE},
- { efTOP, NULL, NULL, ffOPTRW},
+ { efSTO, nullptr, nullptr, ffWRITE},
+ { efTOP, nullptr, nullptr, ffOPTRW},
};
#define NFILE asize(fnm)
- static real defaultDistance = 0.105, r_shell = 0, scaleFactor = 0.57;
- static rvec new_box = {0.0, 0.0, 0.0};
- static gmx_bool bReadV = FALSE;
- static int max_sol = 0;
+ real defaultDistance = 0.105, r_shell = 0, scaleFactor = 0.57;
+ rvec new_box = {0.0, 0.0, 0.0};
+ gmx_bool bReadV = FALSE;
+ int max_sol = 0;
gmx_output_env_t *oenv;
t_pargs pa[] = {
{ "-box", FALSE, etRVEC, {new_box},
/* Generate a solute configuration */
conf_prot = opt2fn("-cp", NFILE, fnm);
readConformation(conf_prot, top, &x,
- bReadV ? &v : NULL, &ePBC, box, "solute");
+ bReadV ? &v : nullptr, &ePBC, box, "solute");
if (bReadV && v.empty())
{
fprintf(stderr, "Note: no velocities found\n");
fprintf(stderr, "Writing generated configuration to %s\n", confout);
const char *outputTitle = (bProt ? *top->name : "Generated by gmx solvate");
write_sto_conf(confout, outputTitle, &top->atoms, as_rvec_array(x.data()),
- !v.empty() ? as_rvec_array(v.data()) : NULL, ePBC, box);
+ !v.empty() ? as_rvec_array(v.data()) : nullptr, ePBC, box);
/* print size of generated configuration */
fprintf(stderr, "\nOutput configuration contains %d atoms in %d residues\n",
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
const char *sbfile = "specbond.dat";
- t_specbond *sb = NULL;
+ t_specbond *sb = nullptr;
char r1buf[32], r2buf[32], a1buf[32], a2buf[32], nr1buf[32], nr2buf[32];
double length;
int nb1, nb2;
int mk_specbonds(t_atoms *pdba, rvec x[], gmx_bool bInteractive,
t_ssbond **specbonds, gmx_bool bVerbose)
{
- t_specbond *sb = NULL;
- t_ssbond *bonds = NULL;
+ t_specbond *sb = nullptr;
+ t_ssbond *bonds = nullptr;
int nsb;
int nspec, nbonds;
int *specp, *sgp;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"replace", "add", "delete"
};
-int find_kw(char *keyw)
+static int find_kw(char *keyw)
{
int i;
}
else
{
- *nname = NULL;
+ *nname = nullptr;
}
}
a->type = get_atomtype_type(buf[i++], atype);
ndel = 0;
for (j = 0; j < tb[i].nhack; j++)
{
- if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
+ if (tb[i].hack[j].oname != nullptr && tb[i].hack[j].nname != nullptr)
{
nrepl++;
}
- else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
+ else if (tb[i].hack[j].oname == nullptr && tb[i].hack[j].nname != nullptr)
{
nadd++;
}
- else if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
+ else if (tb[i].hack[j].oname != nullptr && tb[i].hack[j].nname == nullptr)
{
ndel++;
}
- else if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname == NULL)
+ else if (tb[i].hack[j].oname == nullptr && tb[i].hack[j].nname == nullptr)
{
gmx_fatal(FARGS, "invalid hack (%s) in termini database", tb[i].name);
}
fprintf(out, "[ %s ]\n", kw_names[ekwRepl-ebtsNR-1]);
for (j = 0; j < tb[i].nhack; j++)
{
- if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname != NULL)
+ if (tb[i].hack[j].oname != nullptr && tb[i].hack[j].nname != nullptr)
{
fprintf(out, "%s\t", tb[i].hack[j].oname);
print_atom(out, tb[i].hack[j].atom, atype);
fprintf(out, "[ %s ]\n", kw_names[ekwAdd-ebtsNR-1]);
for (j = 0; j < tb[i].nhack; j++)
{
- if (tb[i].hack[j].oname == NULL && tb[i].hack[j].nname != NULL)
+ if (tb[i].hack[j].oname == nullptr && tb[i].hack[j].nname != nullptr)
{
print_ab(out, &(tb[i].hack[j]), tb[i].hack[j].nname);
print_atom(out, tb[i].hack[j].atom, atype);
fprintf(out, "[ %s ]\n", kw_names[ekwDel-ebtsNR-1]);
for (j = 0; j < tb[i].nhack; j++)
{
- if (tb[i].hack[j].oname != NULL && tb[i].hack[j].nname == NULL)
+ if (tb[i].hack[j].oname != nullptr && tb[i].hack[j].nname == nullptr)
{
fprintf(out, "%s\n", tb[i].hack[j].oname);
}
fflib_filename_base(fn, filebase, STRLEN);
/* Remove the C/N termini extension */
ptr = strrchr(filebase, '.');
- if (ptr != NULL)
+ if (ptr != nullptr)
{
ptr[0] = '\0';
}
clear_t_hack(&(tb[nb].hack[nh]));
for (i = 0; i < 4; i++)
{
- tb[nb].hack[nh].a[i] = NULL;
+ tb[nb].hack[nh].a[i] = nullptr;
}
tb[nb].nhack++;
read_atom(line+n, kwnr == ekwAdd,
&tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
&tb[nb].hack[nh].cgnr);
- if (tb[nb].hack[nh].nname == NULL)
+ if (tb[nb].hack[nh].nname == nullptr)
{
- if (tb[nb].hack[nh].oname != NULL)
+ if (tb[nb].hack[nh].oname != nullptr)
{
tb[nb].hack[nh].nname = gmx_strdup(tb[nb].hack[nh].oname);
}
}
for (; j < MAXATOMLIST; j++)
{
- tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
+ tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = nullptr;
}
strcpy(buf, "");
sscanf(line+n, "%s", buf);
*/
ntdbf = fflib_search_file_end(ffdir, ext, FALSE, &tdbf);
ntb = 0;
- *tbptr = NULL;
+ *tbptr = nullptr;
for (f = 0; f < ntdbf; f++)
{
read_ter_db_file(tdbf[f], &ntb, tbptr, atype);
restp = get_restp(rtpname_match, nrtp, rtp);
n = 0;
- list = NULL;
+ list = nullptr;
for (i = 0; i < nb; i++)
{
{
/* advance to next |-separated field */
s = strchr(s, '|');
- if (s != NULL)
+ if (s != nullptr)
{
s++;
}
}
}
- while (!found && s != NULL);
+ while (!found && s != nullptr);
}
/* All residue-specific termini have been added. We might have to fall
/* A conjunction hyphen normally indicates a residue-specific
terminus, which is named like "GLY-COOH". A generic terminus
won't have a hyphen. */
- bool bFoundAnyHyphen = (c != NULL);
+ bool bFoundAnyHyphen = (c != nullptr);
/* '-' as the last character indicates charge, so if that's
the only one found e.g. "COO-", then it was not a conjunction
hyphen, so this is a generic terminus */
/* Check that we haven't already added a residue-specific version
* of this terminus.
*/
- for (j = 0; j < n && strstr((*list[j]).name, s) == NULL; j++)
+ for (j = 0; j < n && strstr((*list[j]).name, s) == nullptr; j++)
{
;
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test(GmxPreprocessTests gmxpreprocess-test
genconf.cpp
insert-molecules.cpp
+ readir.cpp
solvate.cpp
)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Test routines that parse mdp fields from grompp input and writes
+ * mdp back out.
+ *
+ * In particular these will provide test coverage as we refactor to
+ * use a new Options-based key-value-style mdp implementation to
+ * support a more modular mdrun.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ */
+#include "gmxpre.h"
+
+#include "gromacs/gmxpreprocess/readir.h"
+
+#include <string>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/fileio/warninp.h"
+#include "gromacs/mdrunutility/mdmodules.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textreader.h"
+#include "gromacs/utility/textwriter.h"
+#include "gromacs/utility/unique_cptr.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testfilemanager.h"
+
+namespace gmx
+{
+namespace test
+{
+
+class GetIrTest : public ::testing::Test
+{
+ public:
+ GetIrTest() : fileManager_(), data_(), checker_(data_.rootChecker()),
+ ir_(), mdModules_(), opts_(),
+ wi_(init_warning(FALSE, 0)), wiGuard_(wi_)
+
+ {
+ snew(opts_.include, STRLEN);
+ snew(opts_.define, STRLEN);
+ }
+ ~GetIrTest()
+ {
+ done_inputrec_strings();
+ sfree(opts_.include);
+ sfree(opts_.define);
+ }
+ /*! \brief Test mdp reading and writing
+ *
+ * \todo Modernize read_inp and write_inp to use streams,
+ * which will make these tests run faster, because they don't
+ * use disk files. */
+ void runTest(const std::string &inputMdpFileContents)
+ {
+ auto inputMdpFilename = fileManager_.getTemporaryFilePath("input.mdp");
+ auto outputMdpFilename = fileManager_.getTemporaryFilePath("output.mdp");
+
+ TextWriter::writeFileFromString(inputMdpFilename, inputMdpFileContents);
+
+ get_ir(inputMdpFilename.c_str(), outputMdpFilename.c_str(),
+ &mdModules_, &ir_, &opts_, WriteMdpHeader::no, wi_);
+ bool failure = warning_errors_exist(wi_);
+ checker_.checkBoolean(failure, "Error parsing mdp file");
+ warning_reset(wi_);
+
+ auto outputMdpContents = TextReader::readFileToString(outputMdpFilename);
+ checker_.checkString(outputMdpContents, "OutputMdpFile");
+ }
+
+ TestFileManager fileManager_;
+ TestReferenceData data_;
+ TestReferenceChecker checker_;
+ t_inputrec ir_;
+ MDModules mdModules_;
+ t_gromppopts opts_;
+ warninp_t wi_;
+ unique_cptr<warninp, free_warning> wiGuard_;
+};
+
+TEST_F(GetIrTest, HandlesDifferentKindsOfMdpLines)
+{
+ const char *inputMdpFile[] = {
+ "; File to run my simulation",
+ "title = simulation",
+ ";",
+ "xtc_grps = System ; was Protein",
+ "include = -I/home/me/stuff",
+ "",
+ "tau-t = 0.1 0.3",
+ "tinit = 0.3",
+ "init_step = 0",
+ "nstcomm = 100",
+ "integrator = steep"
+ };
+ runTest(joinStrings(inputMdpFile, "\n"));
+}
+
+// This case is used often by SimulationRunner::useEmptyMdpFile (see
+// comments there for explanation). When we remove the group scheme,
+// that usage will have to disappear, and so can this test.
+TEST_F(GetIrTest, HandlesOnlyCutoffScheme)
+{
+ const char *inputMdpFile = "cutoff-scheme = Group\n";
+ runTest(inputMdpFile);
+}
+
+// TODO Stop accepting any of these
+TEST_F(GetIrTest, UserErrorsSilentlyTolerated)
+{
+ const char *inputMdpFile[] = {
+ "title simulation",
+ "xtc_grps = ",
+ "= -I/home/me/stuff",
+ "="
+ };
+ runTest(joinStrings(inputMdpFile, "\n"));
+}
+
+TEST_F(GetIrTest, EmptyInputWorks)
+{
+ const char *inputMdpFile = "";
+ runTest(inputMdpFile);
+}
+
+// This test observes how the electric-field keys behave, since they
+// are currently the only ones using the new Options-style handling.
+TEST_F(GetIrTest, ProducesOutputFromElectricField)
+{
+ const char *inputMdpFile = "E-x = 1 1.2 -1";
+ runTest(inputMdpFile);
+}
+
+} // namespace
+} // namespace
2SOL OW 4 1.555 1.511 0.703 0.8690 1.2450 1.6650
2SOL HW1 5 1.498 1.495 0.784 0.1690 0.2750 1.5650
2SOL HW2 6 1.496 1.521 0.623 0.2690 2.2750 1.4650
- 1MeOH Me1 7 1.970 1.460 4.319 -0.8587 -0.1344 -0.0643
- 1MeOH O2 8 1.978 1.415 4.192 0.0623 -0.1787 0.0036
- 1MeOH H3 9 1.905 1.460 4.140 -0.5020 -0.9564 0.0997
- 2SOL OW 10 1.555 1.511 3.813 0.8690 1.2450 1.6650
- 2SOL HW1 11 1.498 1.495 3.894 0.1690 0.2750 1.5650
- 2SOL HW2 12 1.496 1.521 3.733 0.2690 2.2750 1.4650
- 1MeOH Me1 13 1.970 1.460 7.429 -0.8587 -0.1344 -0.0643
- 1MeOH O2 14 1.978 1.415 7.302 0.0623 -0.1787 0.0036
- 1MeOH H3 15 1.905 1.460 7.250 -0.5020 -0.9564 0.0997
- 2SOL OW 16 1.555 1.511 6.923 0.8690 1.2450 1.6650
- 2SOL HW1 17 1.498 1.495 7.004 0.1690 0.2750 1.5650
- 2SOL HW2 18 1.496 1.521 6.843 0.2690 2.2750 1.4650
- 1MeOH Me1 19 1.970 4.570 1.209 -0.8587 -0.1344 -0.0643
- 1MeOH O2 20 1.978 4.525 1.082 0.0623 -0.1787 0.0036
- 1MeOH H3 21 1.905 4.570 1.030 -0.5020 -0.9564 0.0997
- 2SOL OW 22 1.555 4.621 0.703 0.8690 1.2450 1.6650
- 2SOL HW1 23 1.498 4.605 0.784 0.1690 0.2750 1.5650
- 2SOL HW2 24 1.496 4.631 0.623 0.2690 2.2750 1.4650
- 1MeOH Me1 25 1.970 4.570 4.319 -0.8587 -0.1344 -0.0643
- 1MeOH O2 26 1.978 4.525 4.192 0.0623 -0.1787 0.0036
- 1MeOH H3 27 1.905 4.570 4.140 -0.5020 -0.9564 0.0997
- 2SOL OW 28 1.555 4.621 3.813 0.8690 1.2450 1.6650
- 2SOL HW1 29 1.498 4.605 3.894 0.1690 0.2750 1.5650
- 2SOL HW2 30 1.496 4.631 3.733 0.2690 2.2750 1.4650
- 1MeOH Me1 31 1.970 4.570 7.429 -0.8587 -0.1344 -0.0643
- 1MeOH O2 32 1.978 4.525 7.302 0.0623 -0.1787 0.0036
- 1MeOH H3 33 1.905 4.570 7.250 -0.5020 -0.9564 0.0997
- 2SOL OW 34 1.555 4.621 6.923 0.8690 1.2450 1.6650
- 2SOL HW1 35 1.498 4.605 7.004 0.1690 0.2750 1.5650
- 2SOL HW2 36 1.496 4.631 6.843 0.2690 2.2750 1.4650
- 1MeOH Me1 37 5.080 1.460 1.209 -0.8587 -0.1344 -0.0643
- 1MeOH O2 38 5.088 1.415 1.082 0.0623 -0.1787 0.0036
- 1MeOH H3 39 5.015 1.460 1.030 -0.5020 -0.9564 0.0997
- 2SOL OW 40 4.665 1.511 0.703 0.8690 1.2450 1.6650
- 2SOL HW1 41 4.608 1.495 0.784 0.1690 0.2750 1.5650
- 2SOL HW2 42 4.606 1.521 0.623 0.2690 2.2750 1.4650
- 1MeOH Me1 43 5.080 1.460 4.319 -0.8587 -0.1344 -0.0643
- 1MeOH O2 44 5.088 1.415 4.192 0.0623 -0.1787 0.0036
- 1MeOH H3 45 5.015 1.460 4.140 -0.5020 -0.9564 0.0997
- 2SOL OW 46 4.665 1.511 3.813 0.8690 1.2450 1.6650
- 2SOL HW1 47 4.608 1.495 3.894 0.1690 0.2750 1.5650
- 2SOL HW2 48 4.606 1.521 3.733 0.2690 2.2750 1.4650
- 1MeOH Me1 49 5.080 1.460 7.429 -0.8587 -0.1344 -0.0643
- 1MeOH O2 50 5.088 1.415 7.302 0.0623 -0.1787 0.0036
- 1MeOH H3 51 5.015 1.460 7.250 -0.5020 -0.9564 0.0997
- 2SOL OW 52 4.665 1.511 6.923 0.8690 1.2450 1.6650
- 2SOL HW1 53 4.608 1.495 7.004 0.1690 0.2750 1.5650
- 2SOL HW2 54 4.606 1.521 6.843 0.2690 2.2750 1.4650
- 1MeOH Me1 55 5.080 4.570 1.209 -0.8587 -0.1344 -0.0643
- 1MeOH O2 56 5.088 4.525 1.082 0.0623 -0.1787 0.0036
- 1MeOH H3 57 5.015 4.570 1.030 -0.5020 -0.9564 0.0997
- 2SOL OW 58 4.665 4.621 0.703 0.8690 1.2450 1.6650
- 2SOL HW1 59 4.608 4.605 0.784 0.1690 0.2750 1.5650
- 2SOL HW2 60 4.606 4.631 0.623 0.2690 2.2750 1.4650
- 1MeOH Me1 61 5.080 4.570 4.319 -0.8587 -0.1344 -0.0643
- 1MeOH O2 62 5.088 4.525 4.192 0.0623 -0.1787 0.0036
- 1MeOH H3 63 5.015 4.570 4.140 -0.5020 -0.9564 0.0997
- 2SOL OW 64 4.665 4.621 3.813 0.8690 1.2450 1.6650
- 2SOL HW1 65 4.608 4.605 3.894 0.1690 0.2750 1.5650
- 2SOL HW2 66 4.606 4.631 3.733 0.2690 2.2750 1.4650
- 1MeOH Me1 67 5.080 4.570 7.429 -0.8587 -0.1344 -0.0643
- 1MeOH O2 68 5.088 4.525 7.302 0.0623 -0.1787 0.0036
- 1MeOH H3 69 5.015 4.570 7.250 -0.5020 -0.9564 0.0997
- 2SOL OW 70 4.665 4.621 6.923 0.8690 1.2450 1.6650
- 2SOL HW1 71 4.608 4.605 7.004 0.1690 0.2750 1.5650
- 2SOL HW2 72 4.606 4.631 6.843 0.2690 2.2750 1.4650
+ 3MeOH Me1 7 1.970 1.460 4.319 -0.8587 -0.1344 -0.0643
+ 3MeOH O2 8 1.978 1.415 4.192 0.0623 -0.1787 0.0036
+ 3MeOH H3 9 1.905 1.460 4.140 -0.5020 -0.9564 0.0997
+ 4SOL OW 10 1.555 1.511 3.813 0.8690 1.2450 1.6650
+ 4SOL HW1 11 1.498 1.495 3.894 0.1690 0.2750 1.5650
+ 4SOL HW2 12 1.496 1.521 3.733 0.2690 2.2750 1.4650
+ 5MeOH Me1 13 1.970 1.460 7.429 -0.8587 -0.1344 -0.0643
+ 5MeOH O2 14 1.978 1.415 7.302 0.0623 -0.1787 0.0036
+ 5MeOH H3 15 1.905 1.460 7.250 -0.5020 -0.9564 0.0997
+ 6SOL OW 16 1.555 1.511 6.923 0.8690 1.2450 1.6650
+ 6SOL HW1 17 1.498 1.495 7.004 0.1690 0.2750 1.5650
+ 6SOL HW2 18 1.496 1.521 6.843 0.2690 2.2750 1.4650
+ 7MeOH Me1 19 1.970 4.570 1.209 -0.8587 -0.1344 -0.0643
+ 7MeOH O2 20 1.978 4.525 1.082 0.0623 -0.1787 0.0036
+ 7MeOH H3 21 1.905 4.570 1.030 -0.5020 -0.9564 0.0997
+ 8SOL OW 22 1.555 4.621 0.703 0.8690 1.2450 1.6650
+ 8SOL HW1 23 1.498 4.605 0.784 0.1690 0.2750 1.5650
+ 8SOL HW2 24 1.496 4.631 0.623 0.2690 2.2750 1.4650
+ 9MeOH Me1 25 1.970 4.570 4.319 -0.8587 -0.1344 -0.0643
+ 9MeOH O2 26 1.978 4.525 4.192 0.0623 -0.1787 0.0036
+ 9MeOH H3 27 1.905 4.570 4.140 -0.5020 -0.9564 0.0997
+ 10SOL OW 28 1.555 4.621 3.813 0.8690 1.2450 1.6650
+ 10SOL HW1 29 1.498 4.605 3.894 0.1690 0.2750 1.5650
+ 10SOL HW2 30 1.496 4.631 3.733 0.2690 2.2750 1.4650
+ 11MeOH Me1 31 1.970 4.570 7.429 -0.8587 -0.1344 -0.0643
+ 11MeOH O2 32 1.978 4.525 7.302 0.0623 -0.1787 0.0036
+ 11MeOH H3 33 1.905 4.570 7.250 -0.5020 -0.9564 0.0997
+ 12SOL OW 34 1.555 4.621 6.923 0.8690 1.2450 1.6650
+ 12SOL HW1 35 1.498 4.605 7.004 0.1690 0.2750 1.5650
+ 12SOL HW2 36 1.496 4.631 6.843 0.2690 2.2750 1.4650
+ 13MeOH Me1 37 5.080 1.460 1.209 -0.8587 -0.1344 -0.0643
+ 13MeOH O2 38 5.088 1.415 1.082 0.0623 -0.1787 0.0036
+ 13MeOH H3 39 5.015 1.460 1.030 -0.5020 -0.9564 0.0997
+ 14SOL OW 40 4.665 1.511 0.703 0.8690 1.2450 1.6650
+ 14SOL HW1 41 4.608 1.495 0.784 0.1690 0.2750 1.5650
+ 14SOL HW2 42 4.606 1.521 0.623 0.2690 2.2750 1.4650
+ 15MeOH Me1 43 5.080 1.460 4.319 -0.8587 -0.1344 -0.0643
+ 15MeOH O2 44 5.088 1.415 4.192 0.0623 -0.1787 0.0036
+ 15MeOH H3 45 5.015 1.460 4.140 -0.5020 -0.9564 0.0997
+ 16SOL OW 46 4.665 1.511 3.813 0.8690 1.2450 1.6650
+ 16SOL HW1 47 4.608 1.495 3.894 0.1690 0.2750 1.5650
+ 16SOL HW2 48 4.606 1.521 3.733 0.2690 2.2750 1.4650
+ 17MeOH Me1 49 5.080 1.460 7.429 -0.8587 -0.1344 -0.0643
+ 17MeOH O2 50 5.088 1.415 7.302 0.0623 -0.1787 0.0036
+ 17MeOH H3 51 5.015 1.460 7.250 -0.5020 -0.9564 0.0997
+ 18SOL OW 52 4.665 1.511 6.923 0.8690 1.2450 1.6650
+ 18SOL HW1 53 4.608 1.495 7.004 0.1690 0.2750 1.5650
+ 18SOL HW2 54 4.606 1.521 6.843 0.2690 2.2750 1.4650
+ 19MeOH Me1 55 5.080 4.570 1.209 -0.8587 -0.1344 -0.0643
+ 19MeOH O2 56 5.088 4.525 1.082 0.0623 -0.1787 0.0036
+ 19MeOH H3 57 5.015 4.570 1.030 -0.5020 -0.9564 0.0997
+ 20SOL OW 58 4.665 4.621 0.703 0.8690 1.2450 1.6650
+ 20SOL HW1 59 4.608 4.605 0.784 0.1690 0.2750 1.5650
+ 20SOL HW2 60 4.606 4.631 0.623 0.2690 2.2750 1.4650
+ 21MeOH Me1 61 5.080 4.570 4.319 -0.8587 -0.1344 -0.0643
+ 21MeOH O2 62 5.088 4.525 4.192 0.0623 -0.1787 0.0036
+ 21MeOH H3 63 5.015 4.570 4.140 -0.5020 -0.9564 0.0997
+ 22SOL OW 64 4.665 4.621 3.813 0.8690 1.2450 1.6650
+ 22SOL HW1 65 4.608 4.605 3.894 0.1690 0.2750 1.5650
+ 22SOL HW2 66 4.606 4.631 3.733 0.2690 2.2750 1.4650
+ 23MeOH Me1 67 5.080 4.570 7.429 -0.8587 -0.1344 -0.0643
+ 23MeOH O2 68 5.088 4.525 7.302 0.0623 -0.1787 0.0036
+ 23MeOH H3 69 5.015 4.570 7.250 -0.5020 -0.9564 0.0997
+ 24SOL OW 70 4.665 4.621 6.923 0.8690 1.2450 1.6650
+ 24SOL HW1 71 4.608 4.605 7.004 0.1690 0.2750 1.5650
+ 24SOL HW2 72 4.606 4.631 6.843 0.2690 2.2750 1.4650
6.22000 6.22000 9.33000
]]></String>
</File>
2SOL OW 4 1.698 1.407 0.645 -1.2387 0.8962 1.6553
2SOL HW1 5 1.659 1.331 0.696 -0.6962 -0.1507 1.4304
2SOL HW2 6 1.692 1.387 0.547 -2.2872 1.0137 1.0656
- 1MeOH Me1 7 1.585 1.592 4.352 0.8537 -0.1691 -0.0463
- 1MeOH O2 8 1.685 1.637 4.273 -0.0004 0.1383 0.1293
- 1MeOH H3 9 1.676 1.592 4.184 0.7621 0.3943 0.6637
- 2SOL OW 10 1.814 1.383 3.773 -1.4910 -1.6216 0.4741
- 2SOL HW1 11 1.793 1.301 3.826 -0.5070 -1.1559 0.9799
- 2SOL HW2 12 1.848 1.357 3.683 -1.2346 -2.3848 -0.4273
- 1MeOH Me1 13 1.762 1.718 7.425 0.2370 -0.8319 0.1066
- 1MeOH O2 14 1.849 1.637 7.361 0.1204 0.0852 0.1186
- 1MeOH H3 15 1.807 1.609 7.275 0.6829 -0.3736 0.7554
- 2SOL OW 16 1.692 1.322 6.906 -2.1305 0.6607 0.3189
- 2SOL HW1 17 1.607 1.312 6.959 -1.2802 0.0971 0.9514
- 2SOL HW2 18 1.685 1.264 6.824 -2.6759 -0.0653 -0.4788
- 1MeOH Me1 19 1.778 4.890 1.139 -0.7633 -0.1096 -0.4061
- 1MeOH O2 20 1.689 4.789 1.133 -0.0583 0.0804 0.1611
- 1MeOH H3 21 1.726 4.720 1.071 -0.9541 0.4031 0.3223
- 2SOL OW 22 1.730 4.376 0.734 1.6869 1.1401 -0.9653
- 2SOL HW1 23 1.757 4.453 0.677 0.5389 1.3424 -0.6790
- 2SOL HW2 24 1.722 4.294 0.677 1.8069 0.4843 -1.9735
- 1MeOH Me1 25 1.915 4.493 3.688 -0.0613 0.8412 0.2196
- 1MeOH O2 26 1.950 4.564 3.798 0.1668 0.0002 -0.0894
- 1MeOH H3 27 1.882 4.545 3.868 0.6563 0.7941 -0.3396
- 2SOL OW 28 1.589 4.631 4.241 -1.6140 -1.0182 -1.1982
- 2SOL HW1 29 1.522 4.638 4.167 -0.9032 -0.0582 -1.3169
- 2SOL HW2 30 1.544 4.650 4.328 -2.5524 -0.8151 -0.4639
- 1MeOH Me1 31 1.890 4.570 6.773 -0.8166 0.2929 0.0827
- 1MeOH O2 32 1.833 4.669 6.846 0.0582 0.1025 -0.1481
- 1MeOH H3 33 1.826 4.636 6.940 -0.5178 0.6434 -0.7033
- 2SOL OW 34 1.638 4.576 7.380 0.4363 -2.1961 -0.2531
- 2SOL HW1 35 1.611 4.489 7.339 -0.2236 -1.3607 -0.8074
- 2SOL HW2 36 1.604 4.582 7.473 -0.0878 -2.6112 0.7539
- 1MeOH Me1 37 4.610 1.735 0.740 0.4965 0.2520 0.6705
- 1MeOH O2 38 4.743 1.732 0.764 -0.0063 0.1606 -0.1000
- 1MeOH H3 39 4.766 1.637 0.789 0.3066 1.0179 0.2155
- 2SOL OW 40 4.989 1.276 1.016 -2.0450 -0.8883 0.3261
- 2SOL HW1 41 4.904 1.277 1.069 -1.4679 0.1226 0.6194
- 2SOL HW2 42 5.050 1.206 1.053 -1.7367 -1.8215 1.0296
- 1MeOH Me1 43 5.153 1.247 4.010 0.1022 0.8451 -0.1869
- 1MeOH O2 44 5.123 1.361 4.075 0.1661 -0.0369 0.0830
- 1MeOH H3 45 5.024 1.376 4.065 0.9227 0.5631 0.0906
- 2SOL OW 46 4.611 1.617 4.010 -0.5106 -1.5002 -1.6019
- 2SOL HW1 47 4.624 1.587 3.915 0.3484 -0.6863 -1.4003
- 2SOL HW2 48 4.528 1.673 4.015 -1.5361 -1.0046 -2.0063
- 1MeOH Me1 49 4.557 1.735 7.114 0.3121 -0.2458 0.7757
- 1MeOH O2 50 4.681 1.735 7.169 -0.0478 0.1792 0.0377
- 1MeOH H3 51 4.731 1.657 7.129 -0.0685 0.5690 0.9210
- 2SOL OW 52 5.034 1.284 7.111 -1.6638 -1.1382 -1.0069
- 2SOL HW1 53 4.949 1.233 7.121 -1.4843 -0.5900 0.0458
- 2SOL HW2 54 5.111 1.219 7.108 -1.1439 -2.2280 -1.0590
- 1MeOH Me1 55 5.110 4.719 1.150 -0.7942 -0.1897 0.3047
- 1MeOH O2 56 5.033 4.609 1.147 0.1057 -0.0432 0.1510
- 1MeOH H3 57 4.994 4.602 1.055 -0.2441 -0.2414 1.0290
- 2SOL OW 58 4.668 4.510 0.713 0.4804 2.0402 -0.8273
- 2SOL HW1 59 4.655 4.609 0.720 0.0534 1.5847 0.1980
- 2SOL HW2 60 4.603 4.473 0.646 -0.3570 2.0943 -1.6972
- 1MeOH Me1 61 4.704 4.648 4.369 0.7064 -0.5020 -0.0927
- 1MeOH O2 62 4.825 4.667 4.312 0.0359 0.0786 0.1684
- 1MeOH H3 63 4.813 4.659 4.213 0.7429 -0.1979 0.7652
- 2SOL OW 64 4.916 4.545 3.756 -2.0765 -0.8670 -0.1174
- 2SOL HW1 65 4.855 4.468 3.778 -1.0802 -1.0537 0.5256
- 2SOL HW2 66 4.949 4.535 3.663 -2.0165 -1.3549 -1.2216
- 1MeOH Me1 67 5.133 4.487 6.891 -0.0721 -0.4007 0.7706
- 1MeOH O2 68 5.034 4.419 6.951 0.0725 -0.1401 -0.1046
- 1MeOH H3 69 4.967 4.486 6.985 0.4032 -0.9760 0.2481
- 2SOL OW 70 4.642 4.683 7.280 1.1586 1.9203 -0.2175
- 2SOL HW1 71 4.722 4.737 7.308 1.3671 0.8073 0.1808
- 2SOL HW2 72 4.564 4.710 7.336 0.5573 2.5967 0.5836
- 6.22000 6.22000 9.33000
+ 3MeOH Me1 7 1.585 1.592 4.252 0.8537 -0.1691 -0.0463
+ 3MeOH O2 8 1.685 1.637 4.173 -0.0004 0.1383 0.1293
+ 3MeOH H3 9 1.676 1.592 4.084 0.7621 0.3943 0.6637
+ 4SOL OW 10 1.814 1.383 3.673 -1.4910 -1.6216 0.4741
+ 4SOL HW1 11 1.793 1.301 3.726 -0.5070 -1.1559 0.9799
+ 4SOL HW2 12 1.848 1.357 3.583 -1.2346 -2.3848 -0.4273
+ 5MeOH Me1 13 1.762 1.718 7.225 0.2370 -0.8319 0.1066
+ 5MeOH O2 14 1.849 1.637 7.161 0.1204 0.0852 0.1186
+ 5MeOH H3 15 1.807 1.609 7.075 0.6829 -0.3736 0.7554
+ 6SOL OW 16 1.692 1.322 6.706 -2.1305 0.6607 0.3189
+ 6SOL HW1 17 1.607 1.312 6.759 -1.2802 0.0971 0.9514
+ 6SOL HW2 18 1.685 1.264 6.624 -2.6759 -0.0653 -0.4788
+ 7MeOH Me1 19 1.778 4.790 1.139 -0.7633 -0.1096 -0.4061
+ 7MeOH O2 20 1.689 4.689 1.133 -0.0583 0.0804 0.1611
+ 7MeOH H3 21 1.726 4.620 1.071 -0.9541 0.4031 0.3223
+ 8SOL OW 22 1.730 4.276 0.734 1.6869 1.1401 -0.9653
+ 8SOL HW1 23 1.757 4.353 0.677 0.5389 1.3424 -0.6790
+ 8SOL HW2 24 1.722 4.194 0.677 1.8069 0.4843 -1.9735
+ 9MeOH Me1 25 1.915 4.393 3.588 -0.0613 0.8412 0.2196
+ 9MeOH O2 26 1.950 4.464 3.698 0.1668 0.0002 -0.0894
+ 9MeOH H3 27 1.882 4.445 3.768 0.6563 0.7941 -0.3396
+ 10SOL OW 28 1.589 4.531 4.141 -1.6140 -1.0182 -1.1982
+ 10SOL HW1 29 1.522 4.538 4.067 -0.9032 -0.0582 -1.3169
+ 10SOL HW2 30 1.544 4.550 4.228 -2.5524 -0.8151 -0.4639
+ 11MeOH Me1 31 1.890 4.470 6.573 -0.8166 0.2929 0.0827
+ 11MeOH O2 32 1.833 4.569 6.646 0.0582 0.1025 -0.1481
+ 11MeOH H3 33 1.826 4.536 6.740 -0.5178 0.6434 -0.7033
+ 12SOL OW 34 1.638 4.476 7.180 0.4363 -2.1961 -0.2531
+ 12SOL HW1 35 1.611 4.389 7.139 -0.2236 -1.3607 -0.8074
+ 12SOL HW2 36 1.604 4.482 7.273 -0.0878 -2.6112 0.7539
+ 13MeOH Me1 37 4.510 1.735 0.740 0.4965 0.2520 0.6705
+ 13MeOH O2 38 4.643 1.732 0.764 -0.0063 0.1606 -0.1000
+ 13MeOH H3 39 4.666 1.637 0.789 0.3066 1.0179 0.2155
+ 14SOL OW 40 4.889 1.276 1.016 -2.0450 -0.8883 0.3261
+ 14SOL HW1 41 4.804 1.277 1.069 -1.4679 0.1226 0.6194
+ 14SOL HW2 42 4.950 1.206 1.053 -1.7367 -1.8215 1.0296
+ 15MeOH Me1 43 5.053 1.247 3.910 0.1022 0.8451 -0.1869
+ 15MeOH O2 44 5.023 1.361 3.975 0.1661 -0.0369 0.0830
+ 15MeOH H3 45 4.924 1.376 3.965 0.9227 0.5631 0.0906
+ 16SOL OW 46 4.511 1.617 3.910 -0.5106 -1.5002 -1.6019
+ 16SOL HW1 47 4.524 1.587 3.815 0.3484 -0.6863 -1.4003
+ 16SOL HW2 48 4.428 1.673 3.915 -1.5361 -1.0046 -2.0063
+ 17MeOH Me1 49 4.457 1.735 6.914 0.3121 -0.2458 0.7757
+ 17MeOH O2 50 4.581 1.735 6.969 -0.0478 0.1792 0.0377
+ 17MeOH H3 51 4.631 1.657 6.929 -0.0685 0.5690 0.9210
+ 18SOL OW 52 4.934 1.284 6.911 -1.6638 -1.1382 -1.0069
+ 18SOL HW1 53 4.849 1.233 6.921 -1.4843 -0.5900 0.0458
+ 18SOL HW2 54 5.011 1.219 6.908 -1.1439 -2.2280 -1.0590
+ 19MeOH Me1 55 5.010 4.619 1.150 -0.7942 -0.1897 0.3047
+ 19MeOH O2 56 4.933 4.509 1.147 0.1057 -0.0432 0.1510
+ 19MeOH H3 57 4.894 4.502 1.055 -0.2441 -0.2414 1.0290
+ 20SOL OW 58 4.568 4.410 0.713 0.4804 2.0402 -0.8273
+ 20SOL HW1 59 4.555 4.509 0.720 0.0534 1.5847 0.1980
+ 20SOL HW2 60 4.503 4.373 0.646 -0.3570 2.0943 -1.6972
+ 21MeOH Me1 61 4.604 4.548 4.269 0.7064 -0.5020 -0.0927
+ 21MeOH O2 62 4.725 4.567 4.212 0.0359 0.0786 0.1684
+ 21MeOH H3 63 4.713 4.559 4.113 0.7429 -0.1979 0.7652
+ 22SOL OW 64 4.816 4.445 3.656 -2.0765 -0.8670 -0.1174
+ 22SOL HW1 65 4.755 4.368 3.678 -1.0802 -1.0537 0.5256
+ 22SOL HW2 66 4.849 4.435 3.563 -2.0165 -1.3549 -1.2216
+ 23MeOH Me1 67 5.033 4.387 6.691 -0.0721 -0.4007 0.7706
+ 23MeOH O2 68 4.934 4.319 6.751 0.0725 -0.1401 -0.1046
+ 23MeOH H3 69 4.867 4.386 6.785 0.4032 -0.9760 0.2481
+ 24SOL OW 70 4.542 4.583 7.080 1.1586 1.9203 -0.2175
+ 24SOL HW1 71 4.622 4.637 7.108 1.3671 0.8073 0.1808
+ 24SOL HW2 72 4.464 4.610 7.136 0.5573 2.5967 0.5836
+ 6.02000 6.02000 9.03000
]]></String>
</File>
</OutputFiles>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include =
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define =
+
+; RUN CONTROL PARAMETERS
+integrator = md
+; Start time and timestep in ps
+tinit = 0
+dt = 0.001
+nsteps = 0
+; For exact run continuation or redoing part of a run
+init-step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm-mode = Linear
+; number of steps for center of mass motion removal
+nstcomm = 100
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 1000
+nstcalcenergy = 100
+nstenergy = 1000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 0
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps =
+; Selection of energy groups
+energygrps =
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = Verlet
+; nblist update frequency
+nstlist = 10
+; ns algorithm (simple or grid)
+ns-type = Grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 1
+; Separate tables between energy group pairs
+energygrp-table =
+; Spacing for the PME/PPPM FFT grid
+fourierspacing = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier-nx = 0
+fourier-ny = 0
+fourier-nz = 0
+; EWALD/PME/PPPM parameters
+pme-order = 4
+ewald-rtol = 1e-05
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+
+; IMPLICIT SOLVENT ALGORITHM
+implicit-solvent = No
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb-algorithm = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii = 1
+; Dielectric coefficient of the implicit solvent
+gb-epsilon-solvent = 80
+; Salt concentration in M for Generalized Born models
+gb-saltconc = 0
+; Scaling factors used in the OBC GB model. Default values are OBC(II)
+gb-obc-alpha = 1
+gb-obc-beta = 0.8
+gb-obc-gamma = 4.85
+gb-dielectric-offset = 0.009
+sa-algorithm = Ace-approximation
+; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
+; The value -1 will set default value for Still/HCT/OBC GB-models.
+sa-surface-tension = -1
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps =
+; Time constant (ps) and reference temperature (K)
+tau-t =
+ref-t =
+; pressure coupling
+pcoupl = No
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+; Optimization of QM subsystem
+bOPT =
+bTS =
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen-vel = no
+gen-temp = 300
+gen-seed = -1
+
+; OPTIONS FOR BONDS
+constraints = none
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle = 30
+; Convert harmonic bonds to morse potentials
+morse = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+pull = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed = no
+disre-fc = 1000
+disre-tau = 0
+; Output frequency for pair distances to energy file
+nstdisreout = 100
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
+; Electric fields
+; Format for E-x, etc. is: number of cosines (int; only 1 is supported),
+; amplitude (real; V/nm), and phase (real; value is meaningless
+; for a cosine of frequency 0.
+; Format for E-xt, etc. is: omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Sigma = 0 removes the pulse,
+; leaving the field to be a cosine function.
+E-x = 1 0 -1
+E-xt = 0 0 0
+E-y = 1 0 -1
+E-yt = 0 0 0
+E-z = 1 0 -1
+E-zt = 0 0 0
+</String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include = -I/home/me/stuff
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define =
+
+; RUN CONTROL PARAMETERS
+integrator = steep
+; Start time and timestep in ps
+tinit = 0.3
+dt = 0.001
+nsteps = 0
+; For exact run continuation or redoing part of a run
+init_step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm-mode = Linear
+; number of steps for center of mass motion removal
+nstcomm = 100
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 1000
+nstcalcenergy = 100
+nstenergy = 1000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 0
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps = System
+; Selection of energy groups
+energygrps =
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = Verlet
+; nblist update frequency
+nstlist = 10
+; ns algorithm (simple or grid)
+ns-type = Grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 1
+; Separate tables between energy group pairs
+energygrp-table =
+; Spacing for the PME/PPPM FFT grid
+fourierspacing = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier-nx = 0
+fourier-ny = 0
+fourier-nz = 0
+; EWALD/PME/PPPM parameters
+pme-order = 4
+ewald-rtol = 1e-05
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+
+; IMPLICIT SOLVENT ALGORITHM
+implicit-solvent = No
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb-algorithm = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii = 1
+; Dielectric coefficient of the implicit solvent
+gb-epsilon-solvent = 80
+; Salt concentration in M for Generalized Born models
+gb-saltconc = 0
+; Scaling factors used in the OBC GB model. Default values are OBC(II)
+gb-obc-alpha = 1
+gb-obc-beta = 0.8
+gb-obc-gamma = 4.85
+gb-dielectric-offset = 0.009
+sa-algorithm = Ace-approximation
+; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
+; The value -1 will set default value for Still/HCT/OBC GB-models.
+sa-surface-tension = -1
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps =
+; Time constant (ps) and reference temperature (K)
+tau-t = 0.1 0.3
+ref-t =
+; pressure coupling
+pcoupl = No
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+; Optimization of QM subsystem
+bOPT =
+bTS =
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen-vel = no
+gen-temp = 300
+gen-seed = -1
+
+; OPTIONS FOR BONDS
+constraints = none
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle = 30
+; Convert harmonic bonds to morse potentials
+morse = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+pull = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed = no
+disre-fc = 1000
+disre-tau = 0
+; Output frequency for pair distances to energy file
+nstdisreout = 100
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
+; Electric fields
+; Format for E-x, etc. is: number of cosines (int; only 1 is supported),
+; amplitude (real; V/nm), and phase (real; value is meaningless
+; for a cosine of frequency 0.
+; Format for E-xt, etc. is: omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Sigma = 0 removes the pulse,
+; leaving the field to be a cosine function.
+E-x = 1 0 -1
+E-xt = 0 0 0
+E-y = 1 0 -1
+E-yt = 0 0 0
+E-z = 1 0 -1
+E-zt = 0 0 0
+</String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include =
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define =
+
+; RUN CONTROL PARAMETERS
+integrator = md
+; Start time and timestep in ps
+tinit = 0
+dt = 0.001
+nsteps = 0
+; For exact run continuation or redoing part of a run
+init-step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm-mode = Linear
+; number of steps for center of mass motion removal
+nstcomm = 100
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 1000
+nstcalcenergy = 100
+nstenergy = 1000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 0
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps =
+; Selection of energy groups
+energygrps =
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = Group
+; nblist update frequency
+nstlist = 10
+; ns algorithm (simple or grid)
+ns-type = Grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 1
+; Separate tables between energy group pairs
+energygrp-table =
+; Spacing for the PME/PPPM FFT grid
+fourierspacing = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier-nx = 0
+fourier-ny = 0
+fourier-nz = 0
+; EWALD/PME/PPPM parameters
+pme-order = 4
+ewald-rtol = 1e-05
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+
+; IMPLICIT SOLVENT ALGORITHM
+implicit-solvent = No
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb-algorithm = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii = 1
+; Dielectric coefficient of the implicit solvent
+gb-epsilon-solvent = 80
+; Salt concentration in M for Generalized Born models
+gb-saltconc = 0
+; Scaling factors used in the OBC GB model. Default values are OBC(II)
+gb-obc-alpha = 1
+gb-obc-beta = 0.8
+gb-obc-gamma = 4.85
+gb-dielectric-offset = 0.009
+sa-algorithm = Ace-approximation
+; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
+; The value -1 will set default value for Still/HCT/OBC GB-models.
+sa-surface-tension = -1
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps =
+; Time constant (ps) and reference temperature (K)
+tau-t =
+ref-t =
+; pressure coupling
+pcoupl = No
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+; Optimization of QM subsystem
+bOPT =
+bTS =
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen-vel = no
+gen-temp = 300
+gen-seed = -1
+
+; OPTIONS FOR BONDS
+constraints = none
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle = 30
+; Convert harmonic bonds to morse potentials
+morse = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+pull = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed = no
+disre-fc = 1000
+disre-tau = 0
+; Output frequency for pair distances to energy file
+nstdisreout = 100
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
+; Electric fields
+; Format for E-x, etc. is: number of cosines (int; only 1 is supported),
+; amplitude (real; V/nm), and phase (real; value is meaningless
+; for a cosine of frequency 0.
+; Format for E-xt, etc. is: omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Sigma = 0 removes the pulse,
+; leaving the field to be a cosine function.
+E-x = 1 0 -1
+E-xt = 0 0 0
+E-y = 1 0 -1
+E-yt = 0 0 0
+E-z = 1 0 -1
+E-zt = 0 0 0
+</String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include =
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define =
+
+; RUN CONTROL PARAMETERS
+integrator = md
+; Start time and timestep in ps
+tinit = 0
+dt = 0.001
+nsteps = 0
+; For exact run continuation or redoing part of a run
+init-step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm-mode = Linear
+; number of steps for center of mass motion removal
+nstcomm = 100
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 1000
+nstcalcenergy = 100
+nstenergy = 1000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 0
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps =
+; Selection of energy groups
+energygrps =
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = Verlet
+; nblist update frequency
+nstlist = 10
+; ns algorithm (simple or grid)
+ns-type = Grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 1
+; Separate tables between energy group pairs
+energygrp-table =
+; Spacing for the PME/PPPM FFT grid
+fourierspacing = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier-nx = 0
+fourier-ny = 0
+fourier-nz = 0
+; EWALD/PME/PPPM parameters
+pme-order = 4
+ewald-rtol = 1e-05
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+
+; IMPLICIT SOLVENT ALGORITHM
+implicit-solvent = No
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb-algorithm = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii = 1
+; Dielectric coefficient of the implicit solvent
+gb-epsilon-solvent = 80
+; Salt concentration in M for Generalized Born models
+gb-saltconc = 0
+; Scaling factors used in the OBC GB model. Default values are OBC(II)
+gb-obc-alpha = 1
+gb-obc-beta = 0.8
+gb-obc-gamma = 4.85
+gb-dielectric-offset = 0.009
+sa-algorithm = Ace-approximation
+; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
+; The value -1 will set default value for Still/HCT/OBC GB-models.
+sa-surface-tension = -1
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps =
+; Time constant (ps) and reference temperature (K)
+tau-t =
+ref-t =
+; pressure coupling
+pcoupl = No
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+; Optimization of QM subsystem
+bOPT =
+bTS =
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen-vel = no
+gen-temp = 300
+gen-seed = -1
+
+; OPTIONS FOR BONDS
+constraints = none
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle = 30
+; Convert harmonic bonds to morse potentials
+morse = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+pull = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed = no
+disre-fc = 1000
+disre-tau = 0
+; Output frequency for pair distances to energy file
+nstdisreout = 100
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
+; Electric fields
+; Format for E-x, etc. is: number of cosines (int; only 1 is supported),
+; amplitude (real; V/nm), and phase (real; value is meaningless
+; for a cosine of frequency 0.
+; Format for E-xt, etc. is: omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Sigma = 0 removes the pulse,
+; leaving the field to be a cosine function.
+E-x = 1 1.2 -1
+E-xt = 0 0 0
+E-y = 1 0 -1
+E-yt = 0 0 0
+E-z = 1 0 -1
+E-zt = 0 0 0
+</String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Bool Name="Error parsing mdp file">false</Bool>
+ <String Name="OutputMdpFile">
+; VARIOUS PREPROCESSING OPTIONS
+; Preprocessor information: use cpp syntax.
+; e.g.: -I/home/joe/doe -I/home/mary/roe
+include =
+; e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)
+define =
+
+; RUN CONTROL PARAMETERS
+integrator = md
+; Start time and timestep in ps
+tinit = 0
+dt = 0.001
+nsteps = 0
+; For exact run continuation or redoing part of a run
+init-step = 0
+; Part index is updated automatically on checkpointing (keeps files separate)
+simulation-part = 1
+; mode for center of mass motion removal
+comm-mode = Linear
+; number of steps for center of mass motion removal
+nstcomm = 100
+; group(s) for center of mass motion removal
+comm-grps =
+
+; LANGEVIN DYNAMICS OPTIONS
+; Friction coefficient (amu/ps) and random seed
+bd-fric = 0
+ld-seed = -1
+
+; ENERGY MINIMIZATION OPTIONS
+; Force tolerance and initial step-size
+emtol = 10
+emstep = 0.01
+; Max number of iterations in relax-shells
+niter = 20
+; Step size (ps^2) for minimization of flexible constraints
+fcstep = 0
+; Frequency of steepest descents steps when doing CG
+nstcgsteep = 1000
+nbfgscorr = 10
+
+; TEST PARTICLE INSERTION OPTIONS
+rtpi = 0.05
+
+; OUTPUT CONTROL OPTIONS
+; Output frequency for coords (x), velocities (v) and forces (f)
+nstxout = 0
+nstvout = 0
+nstfout = 0
+; Output frequency for energies to log file and energy file
+nstlog = 1000
+nstcalcenergy = 100
+nstenergy = 1000
+; Output frequency and precision for .xtc file
+nstxout-compressed = 0
+compressed-x-precision = 1000
+; This selects the subset of atoms for the compressed
+; trajectory file. You can select multiple groups. By
+; default, all atoms will be written.
+compressed-x-grps =
+; Selection of energy groups
+energygrps =
+
+; NEIGHBORSEARCHING PARAMETERS
+; cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)
+cutoff-scheme = Verlet
+; nblist update frequency
+nstlist = 10
+; ns algorithm (simple or grid)
+ns-type = Grid
+; Periodic boundary conditions: xyz, no, xy
+pbc = xyz
+periodic-molecules = no
+; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
+; a value of -1 means: use rlist
+verlet-buffer-tolerance = 0.005
+; nblist cut-off
+rlist = 1
+; long-range cut-off for switched potentials
+
+; OPTIONS FOR ELECTROSTATICS AND VDW
+; Method for doing electrostatics
+coulombtype = Cut-off
+coulomb-modifier = Potential-shift-Verlet
+rcoulomb-switch = 0
+rcoulomb = 1
+; Relative dielectric constant for the medium and the reaction field
+epsilon-r = 1
+epsilon-rf = 0
+; Method for doing Van der Waals
+vdw-type = Cut-off
+vdw-modifier = Potential-shift-Verlet
+; cut-off lengths
+rvdw-switch = 0
+rvdw = 1
+; Apply long range dispersion corrections for Energy and Pressure
+DispCorr = No
+; Extension of the potential lookup tables beyond the cut-off
+table-extension = 1
+; Separate tables between energy group pairs
+energygrp-table =
+; Spacing for the PME/PPPM FFT grid
+fourierspacing = 0.12
+; FFT grid size, when a value is 0 fourierspacing will be used
+fourier-nx = 0
+fourier-ny = 0
+fourier-nz = 0
+; EWALD/PME/PPPM parameters
+pme-order = 4
+ewald-rtol = 1e-05
+ewald-rtol-lj = 0.001
+lj-pme-comb-rule = Geometric
+ewald-geometry = 3d
+epsilon-surface = 0
+
+; IMPLICIT SOLVENT ALGORITHM
+implicit-solvent = No
+
+; GENERALIZED BORN ELECTROSTATICS
+; Algorithm for calculating Born radii
+gb-algorithm = Still
+; Frequency of calculating the Born radii inside rlist
+nstgbradii = 1
+; Cutoff for Born radii calculation; the contribution from atoms
+; between rlist and rgbradii is updated every nstlist steps
+rgbradii = 1
+; Dielectric coefficient of the implicit solvent
+gb-epsilon-solvent = 80
+; Salt concentration in M for Generalized Born models
+gb-saltconc = 0
+; Scaling factors used in the OBC GB model. Default values are OBC(II)
+gb-obc-alpha = 1
+gb-obc-beta = 0.8
+gb-obc-gamma = 4.85
+gb-dielectric-offset = 0.009
+sa-algorithm = Ace-approximation
+; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA
+; The value -1 will set default value for Still/HCT/OBC GB-models.
+sa-surface-tension = -1
+
+; OPTIONS FOR WEAK COUPLING ALGORITHMS
+; Temperature coupling
+tcoupl = No
+nsttcouple = -1
+nh-chain-length = 10
+print-nose-hoover-chain-variables = no
+; Groups to couple separately
+tc-grps =
+; Time constant (ps) and reference temperature (K)
+tau-t =
+ref-t =
+; pressure coupling
+pcoupl = No
+pcoupltype = Isotropic
+nstpcouple = -1
+; Time constant (ps), compressibility (1/bar) and reference P (bar)
+tau-p = 1
+compressibility =
+ref-p =
+; Scaling of reference coordinates, No, All or COM
+refcoord-scaling = No
+
+; OPTIONS FOR QMMM calculations
+QMMM = no
+; Groups treated Quantum Mechanically
+QMMM-grps =
+; QM method
+QMmethod =
+; QMMM scheme
+QMMMscheme = normal
+; QM basisset
+QMbasis =
+; QM charge
+QMcharge =
+; QM multiplicity
+QMmult =
+; Surface Hopping
+SH =
+; CAS space options
+CASorbitals =
+CASelectrons =
+SAon =
+SAoff =
+SAsteps =
+; Scale factor for MM charges
+MMChargeScaleFactor = 1
+; Optimization of QM subsystem
+bOPT =
+bTS =
+
+; SIMULATED ANNEALING
+; Type of annealing for each temperature group (no/single/periodic)
+annealing =
+; Number of time points to use for specifying annealing in each group
+annealing-npoints =
+; List of times at the annealing points for each group
+annealing-time =
+; Temp. at each annealing point, for each group.
+annealing-temp =
+
+; GENERATE VELOCITIES FOR STARTUP RUN
+gen-vel = no
+gen-temp = 300
+gen-seed = -1
+
+; OPTIONS FOR BONDS
+constraints = none
+; Type of constraint algorithm
+constraint-algorithm = Lincs
+; Do not constrain the start configuration
+continuation = no
+; Use successive overrelaxation to reduce the number of shake iterations
+Shake-SOR = no
+; Relative tolerance of shake
+shake-tol = 0.0001
+; Highest order in the expansion of the constraint coupling matrix
+lincs-order = 4
+; Number of iterations in the final step of LINCS. 1 is fine for
+; normal simulations, but use 2 to conserve energy in NVE runs.
+; For energy minimization with constraints it should be 4 to 8.
+lincs-iter = 1
+; Lincs will write a warning to the stderr if in one step a bond
+; rotates over more degrees than
+lincs-warnangle = 30
+; Convert harmonic bonds to morse potentials
+morse = no
+
+; ENERGY GROUP EXCLUSIONS
+; Pairs of energy groups for which all non-bonded interactions are excluded
+energygrp-excl =
+
+; WALLS
+; Number of walls, type, atom types, densities and box-z scale factor for Ewald
+nwall = 0
+wall-type = 9-3
+wall-r-linpot = -1
+wall-atomtype =
+wall-density =
+wall-ewald-zfac = 3
+
+; COM PULLING
+pull = no
+
+; ENFORCED ROTATION
+; Enforced rotation: No or Yes
+rotation = no
+
+; Group to display and/or manipulate in interactive MD session
+IMD-group =
+
+; NMR refinement stuff
+; Distance restraints type: No, Simple or Ensemble
+disre = No
+; Force weighting of pairs in one distance restraint: Conservative or Equal
+disre-weighting = Conservative
+; Use sqrt of the time averaged times the instantaneous violation
+disre-mixed = no
+disre-fc = 1000
+disre-tau = 0
+; Output frequency for pair distances to energy file
+nstdisreout = 100
+; Orientation restraints: No or Yes
+orire = no
+; Orientation restraints force constant and tau for time averaging
+orire-fc = 0
+orire-tau = 0
+orire-fitgrp =
+; Output frequency for trace(SD) and S to energy file
+nstorireout = 100
+
+; Free energy variables
+free-energy = no
+couple-moltype =
+couple-lambda0 = vdw-q
+couple-lambda1 = vdw-q
+couple-intramol = no
+init-lambda = -1
+init-lambda-state = -1
+delta-lambda = 0
+nstdhdl = 50
+fep-lambdas =
+mass-lambdas =
+coul-lambdas =
+vdw-lambdas =
+bonded-lambdas =
+restraint-lambdas =
+temperature-lambdas =
+calc-lambda-neighbors = 1
+init-lambda-weights =
+dhdl-print-energy = no
+sc-alpha = 0
+sc-power = 1
+sc-r-power = 6
+sc-sigma = 0.3
+sc-coul = no
+separate-dhdl-file = yes
+dhdl-derivatives = yes
+dh_hist_size = 0
+dh_hist_spacing = 0.1
+
+; Non-equilibrium MD stuff
+acc-grps =
+accelerate =
+freezegrps =
+freezedim =
+cos-acceleration = 0
+deform =
+
+; simulated tempering variables
+simulated-tempering = no
+simulated-tempering-scaling = geometric
+sim-temp-low = 300
+sim-temp-high = 300
+
+; Ion/water position swapping for computational electrophysiology setups
+; Swap positions along direction: no, X, Y, Z
+swapcoords = no
+adress = no
+
+; User defined thingies
+user1-grps =
+user2-grps =
+userint1 = 0
+userint2 = 0
+userint3 = 0
+userint4 = 0
+userreal1 = 0
+userreal2 = 0
+userreal3 = 0
+userreal4 = 0
+; Electric fields
+; Format for E-x, etc. is: number of cosines (int; only 1 is supported),
+; amplitude (real; V/nm), and phase (real; value is meaningless
+; for a cosine of frequency 0.
+; Format for E-xt, etc. is: omega (1/ps), time for the pulse peak (ps),
+; and sigma (ps) width of the pulse. Sigma = 0 removes the pulse,
+; leaving the field to be a cosine function.
+E-x = 1 0 -1
+E-xt = 0 0 0
+E-y = 1 0 -1
+E-yt = 0 0 0
+E-z = 1 0 -1
+E-zt = 0 0 0
+</String>
+</ReferenceData>
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char ai[32], aj[32];
double e_diss;
const char *fn = "edissoc.dat";
- t_2morse *t2m = NULL;
+ t_2morse *t2m = nullptr;
int maxn2m = 0, n2m = 0;
int nread;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return d_invalid;
}
-static directive **necessary = NULL;
+static directive **necessary = nullptr;
static void set_nec(directive **n, ...)
/* Must always have at least one extra argument */
void DS_Init(DirStack **DS)
{
- if (necessary == NULL)
+ if (necessary == nullptr)
{
int i;
}
}
}
- *DS = NULL;
+ *DS = nullptr;
}
{
DirStack *D;
- while (*DS != NULL)
+ while (*DS != nullptr)
{
D = *DS;
*DS = (*DS)->prev;
DirStack *D;
D = DS;
- while ((D != NULL) && (D->d != d))
+ while ((D != nullptr) && (D->d != d))
{
D = D->prev;
}
- return (D != NULL);
+ return (D != nullptr);
}
int DS_Check_Order(DirStack *DS, directive d)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cassert>
#include <cmath>
+#include <algorithm>
+
#include <sys/types.h>
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
#include "gromacs/gmxpreprocess/gpp_nextnb.h"
#include "gromacs/gmxpreprocess/grompp-impl.h"
+#include "gromacs/gmxpreprocess/readir.h"
#include "gromacs/gmxpreprocess/topdirs.h"
#include "gromacs/gmxpreprocess/toppush.h"
#include "gromacs/gmxpreprocess/topshake.h"
#include "gromacs/mdlib/genborn.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
#define OPENDIR '[' /* starting sign for directive */
return q;
}
-static void sum_q(t_atoms *atoms, int n, double *qt, double *qBt)
+/*! \brief Returns the rounded charge of a molecule, when close to integer, otherwise returns the original charge.
+ *
+ * The results of this routine are only used for checking and for
+ * printing warning messages. Thus we can assume that charges of molecules
+ * should be integer. If the user wanted non-integer molecular charge,
+ * an undesired warning is printed and the user should use grompp -maxwarn 1.
+ *
+ * \param qMol The total, unrounded, charge of the molecule
+ * \param sumAbsQ The sum of absolute values of the charges, used for determining the tolerance for the rounding.
+ */
+static double roundedMoleculeCharge(double qMol, double sumAbsQ)
{
- double qmolA, qmolB;
- int i;
-
- /* sum charge */
- qmolA = 0;
- qmolB = 0;
- for (i = 0; i < atoms->nr; i++)
+ /* We use a tolerance of 1e-6 for inaccuracies beyond the 6th decimal
+ * of the charges for ascii float truncation in the topology files.
+ * Although the summation here uses double precision, the charges
+ * are read and stored in single precision when real=float. This can
+ * lead to rounding errors of half the least significant bit.
+ * Note that, unfortunately, we can not assume addition of random
+ * rounding errors. It is not entirely unlikely that many charges
+ * have a near half-bit rounding error with the same sign.
+ */
+ double tolAbs = 1e-6;
+ double tol = std::max(tolAbs, 0.5*GMX_REAL_EPS*sumAbsQ);
+ double qRound = std::round(qMol);
+ if (std::abs(qMol - qRound) <= tol)
{
- qmolA += atoms->atom[i].q;
- qmolB += atoms->atom[i].qB;
+ return qRound;
}
- /* Unfortunately an absolute comparison,
- * but this avoids unnecessary warnings and gmx-users mails.
- */
- if (fabs(qmolA) >= 1e-6 || fabs(qmolB) >= 1e-6)
+ else
{
- *qt += n*qmolA;
- *qBt += n*qmolB;
+ return qMol;
}
}
+static void sum_q(const t_atoms *atoms, int numMols,
+ double *qTotA, double *qTotB)
+{
+ /* sum charge */
+ double qmolA = 0;
+ double qmolB = 0;
+ double sumAbsQA = 0;
+ double sumAbsQB = 0;
+ for (int i = 0; i < atoms->nr; i++)
+ {
+ qmolA += atoms->atom[i].q;
+ qmolB += atoms->atom[i].qB;
+ sumAbsQA += std::abs(atoms->atom[i].q);
+ sumAbsQB += std::abs(atoms->atom[i].qB);
+ }
+
+ *qTotA += numMols*roundedMoleculeCharge(qmolA, sumAbsQA);
+ *qTotB += numMols*roundedMoleculeCharge(qmolB, sumAbsQB);
+}
+
static void get_nbparm(char *nb_str, char *comb_str, int *nb, int *comb,
warninp_t wi)
{
}
if (*nb == -1)
{
- *nb = strtol(nb_str, NULL, 10);
+ *nb = strtol(nb_str, nullptr, 10);
}
if ((*nb < 1) || (*nb >= eNBF_NR))
{
}
if (*comb == -1)
{
- *comb = strtol(comb_str, NULL, 10);
+ *comb = strtol(comb_str, nullptr, 10);
}
if ((*comb < 1) || (*comb >= eCOMB_NR))
{
int n, len;
int ncppopts = 0;
const char *cppadds[2];
- char **cppopts = NULL;
+ char **cppopts = nullptr;
const char *option[2] = { "-D", "-I" };
const char *nopt[2] = { "define", "include" };
const char *ptr;
}
}
srenew(cppopts, ++ncppopts);
- cppopts[ncppopts-1] = NULL;
+ cppopts[ncppopts-1] = nullptr;
return cppopts;
}
-int
+static int
find_gb_bondlength(t_params *plist, int ai, int aj, real *length)
{
int i, j, a1, a2;
}
-int
+static int
find_gb_anglelength(t_params *plist, int ai, int ak, real *length)
{
int i, j, a1, a2, a3;
return status;
}
-int
+static int
generate_gb_exclusion_interactions(t_molinfo *mi, gpp_atomtype_t atype, t_nextnb *nnb)
{
int j, n, ai, aj, ti, tj;
const t_atoms *mol_atoms;
atoms->nr = 0;
- atoms->atom = NULL;
+ atoms->atom = nullptr;
for (mb = 0; mb < nmolb; mb++)
{
gmx_bool bFEP,
gmx_bool bGenborn,
gmx_bool bZero,
- warninp_t wi)
+ gmx_bool usingFullRangeElectrostatics,
+ warninp_t wi)
{
FILE *out;
int i, sl, nb_funct;
- char *pline = NULL, **title = NULL;
+ char *pline = nullptr, **title = nullptr;
char line[STRLEN], errbuf[256], comb_str[256], nb_str[256];
char genpairs[32];
char *dirstr, *dummy2;
int nrcopies, nmol, nmolb = 0, nscan, ncombs, ncopy;
double fLJ, fQQ, fPOW;
- gmx_molblock_t *molb = NULL;
- t_molinfo *mi0 = NULL;
+ gmx_molblock_t *molb = nullptr;
+ t_molinfo *mi0 = nullptr;
DirStack *DS;
directive d, newd;
t_nbparam **nbparam, **pair;
/* File handling variables */
int status, done;
gmx_cpp_t handle;
- char *tmp_line = NULL;
+ char *tmp_line = nullptr;
char warn_buf[STRLEN];
const char *floating_point_arithmetic_tip =
"Total charge should normally be an integer. See\n"
}
else
{
- out = NULL;
+ out = nullptr;
}
/* open input file */
DS_Init(&DS); /* directive stack */
nmol = 0; /* no molecules yet... */
d = d_invalid; /* first thing should be a directive */
- nbparam = NULL; /* The temporary non-bonded matrix */
- pair = NULL; /* The temporary pair interaction matrix */
- block2 = NULL; /* the extra exclusions */
+ nbparam = nullptr; /* The temporary non-bonded matrix */
+ pair = nullptr; /* The temporary pair interaction matrix */
+ block2 = nullptr; /* the extra exclusions */
nb_funct = F_LJ;
*reppow = 12.0; /* Default value for repulsion power */
- *intermolecular_interactions = NULL;
+ *intermolecular_interactions = nullptr;
/* Init the number of CMAP torsion angles and grid spacing */
plist[F_CMAP].grid_spacing = 0;
* skip spaces and tabs on either side of directive
*/
dirstr = gmx_strdup((pline+1));
- if ((dummy2 = strchr (dirstr, CLOSEDIR)) != NULL)
+ if ((dummy2 = strchr (dirstr, CLOSEDIR)) != nullptr)
{
(*dummy2) = 0;
}
if (d == d_intermolecular_interactions)
{
- if (*intermolecular_interactions == NULL)
+ if (*intermolecular_interactions == nullptr)
{
/* We (mis)use the moleculetype processing
* to process the intermolecular interactions
break;
case d_atomtypes:
push_at(symtab, atype, batype, pline, nb_funct,
- &nbparam, bGenPairs ? &pair : NULL, wi);
+ &nbparam, bGenPairs ? &pair : nullptr, wi);
break;
case d_bondtypes:
- push_bt(d, plist, 2, NULL, batype, pline, wi);
+ push_bt(d, plist, 2, nullptr, batype, pline, wi);
break;
case d_constrainttypes:
- push_bt(d, plist, 2, NULL, batype, pline, wi);
+ push_bt(d, plist, 2, nullptr, batype, pline, wi);
break;
case d_pairtypes:
if (bGenPairs)
}
else
{
- push_bt(d, plist, 2, atype, NULL, pline, wi);
+ push_bt(d, plist, 2, atype, nullptr, pline, wi);
}
break;
case d_angletypes:
- push_bt(d, plist, 3, NULL, batype, pline, wi);
+ push_bt(d, plist, 3, nullptr, batype, pline, wi);
break;
case d_dihedraltypes:
/* Special routine that can read both 2 and 4 atom dihedral definitions. */
if (!bReadMolType)
{
int ntype;
- if (opts->couple_moltype != NULL &&
+ if (opts->couple_moltype != nullptr &&
(opts->couple_lam0 == ecouplamNONE ||
opts->couple_lam0 == ecouplamQ ||
opts->couple_lam1 == ecouplamNONE ||
opts->couple_lam1 == ecouplamQ))
{
dcatt = add_atomtype_decoupled(symtab, atype,
- &nbparam, bGenPairs ? &pair : NULL);
+ &nbparam, bGenPairs ? &pair : nullptr);
}
ntype = get_atomtype_ntypes(atype);
ncombs = (ntype*(ntype+1))/2;
push_molt(symtab, &nmol, molinfo, pline, wi);
srenew(block2, nmol);
- block2[nmol-1].nr = 0;
- mi0 = &((*molinfo)[nmol-1]);
+ block2[nmol-1].nr = 0;
+ mi0 = &((*molinfo)[nmol-1]);
+ mi0->atoms.haveMass = TRUE;
+ mi0->atoms.haveCharge = TRUE;
+ mi0->atoms.haveType = TRUE;
+ mi0->atoms.haveBState = TRUE;
+ mi0->atoms.havePdbInfo = FALSE;
break;
}
case d_atoms:
molb[nmolb].nmol = nrcopies;
nmolb++;
- bCouple = (opts->couple_moltype != NULL &&
+ bCouple = (opts->couple_moltype != nullptr &&
(gmx_strcasecmp("system", opts->couple_moltype) == 0 ||
strcmp(*(mi0->name), opts->couple_moltype) == 0));
if (bCouple)
}
}
sfree(pline);
- pline = NULL;
+ pline = nullptr;
}
}
while (!done);
{
title = put_symtab(symtab, "");
}
+
if (fabs(qt) > 1e-4)
{
sprintf(warn_buf, "System has non-zero total charge: %.6f\n%s\n", qt, floating_point_arithmetic_tip);
sprintf(warn_buf, "State B has non-zero total charge: %.6f\n%s\n", qBt, floating_point_arithmetic_tip);
warning_note(wi, warn_buf);
}
+ if (usingFullRangeElectrostatics && (fabs(qt) > 1e-4 || fabs(qBt) > 1e-4))
+ {
+ warning(wi, "You are using Ewald electrostatics in a system with net charge. This can lead to severe artifacts, such as ions moving into regions with low dielectric, due to the uniform background charge. We suggest to neutralize your system with counter ions, possibly in combination with a physiological salt concentration.");
+ please_cite(stdout, "Hub2014a");
+ }
+
DS_Done (&DS);
for (i = 0; i < nmol; i++)
{
done_bond_atomtype(&batype);
- if (*intermolecular_interactions != NULL)
+ if (*intermolecular_interactions != nullptr)
{
sfree(mi0->atoms.atom);
}
}
else
{
- tmpfile = NULL;
+ tmpfile = nullptr;
}
if (bVerbose)
nrmols, molinfo, intermolecular_interactions,
plist, combination_rule, repulsion_power,
opts, fudgeQQ, nmolblock, molblock,
- ir->efep != efepNO, bGenborn, bZero, wi);
+ ir->efep != efepNO, bGenborn, bZero,
+ EEL_FULL(ir->coulombtype), wi);
+
if ((*combination_rule != eCOMB_GEOMETRIC) &&
(ir->vdwtype == evdwUSER))
{
* not by the gromacs routines
*/
int qm_max = 0, qm_nr = 0, link_nr = 0, link_max = 0;
- int *qm_arr = NULL, *link_arr = NULL;
+ int *qm_arr = nullptr, *link_arr = nullptr;
gmx_bool *bQMMM, *blink;
/* First we search and select the QM atoms in an qm_arr array that
#include "gromacs/gmxpreprocess/gpp_atomtype.h"
#include "gromacs/gmxpreprocess/grompp-impl.h"
-#include "gromacs/gmxpreprocess/readir.h"
struct gmx_molblock_t;
+struct gmx_mtop_t;
+struct t_gromppopts;
+struct t_inputrec;
+struct warninp;
+typedef warninp *warninp_t;
double check_mol(gmx_mtop_t *mtop, warninp_t wi);
/* Check mass and charge */
#include <stdlib.h>
#include <cmath>
+#include <cstring>
#include <algorithm>
return;
}
- ft = strtol(alc[nral], NULL, 10);
+ ft = strtol(alc[nral], nullptr, 10);
ftype = ifunc_index(d, ft);
nrfp = NRFP(ftype);
nrfpA = interaction_function[ftype].nrfpA;
if (nn >= 3 && strlen(alc[2]) == 1 && isdigit(alc[2][0]))
{
nral = 2;
- ft = strtol(alc[nral], NULL, 10);
+ ft = strtol(alc[nral], nullptr, 10);
/* Move atom types around a bit and use 'X' for wildcard atoms
* to create a 4-atom dihedral definition with arbitrary atoms in
* position 1 and 4.
else if (nn == 5 && strlen(alc[4]) == 1 && isdigit(alc[4][0]))
{
nral = 4;
- ft = strtol(alc[nral], NULL, 10);
+ ft = strtol(alc[nral], nullptr, 10);
}
else
{
}
start += nchar_consumed;
- ft = strtol(alc[nral], NULL, 10);
- nxcmap = strtol(alc[nral+1], NULL, 10);
- nycmap = strtol(alc[nral+2], NULL, 10);
+ ft = strtol(alc[nral], nullptr, 10);
+ nxcmap = strtol(alc[nral+1], nullptr, 10);
+ nycmap = strtol(alc[nral+2], nullptr, 10);
/* Check for equal grid spacing in x and y dims */
if (nxcmap != nycmap)
ncmap = nxcmap*nycmap;
ftype = ifunc_index(d, ft);
- nrfpA = strtol(alc[6], NULL, 10)*strtol(alc[6], NULL, 10);
- nrfpB = strtol(alc[7], NULL, 10)*strtol(alc[7], NULL, 10);
+ nrfpA = strtol(alc[6], nullptr, 10)*strtol(alc[6], nullptr, 10);
+ nrfpB = strtol(alc[7], nullptr, 10)*strtol(alc[7], nullptr, 10);
nrfp = nrfpA+nrfpB;
/* Allocate memory for the CMAP grid */
}
nn = sscanf(line+start+sl, " %s ", s);
sl += strlen(s);
- bt[F_CMAP].cmap[i+(bt[F_CMAP].ncmap)-nrfp] = strtod(s, NULL);
+ bt[F_CMAP].cmap[i+(bt[F_CMAP].ncmap)-nrfp] = strtod(s, nullptr);
if (nn == 1)
{
warning_error_and_exit(wi, errbuf, FARGS);
}
}
- resnr = strtol(resnumberic, NULL, 10);
+ resnr = strtol(resnumberic, nullptr, 10);
if (nr > 0)
{
at->nr++;
}
-void push_cg(t_block *block, int *lastindex, int index, int a)
+static void push_cg(t_block *block, int *lastindex, int index, int a)
{
if (debug)
{
{
int i, j, ti, tj, ntype;
gmx_bool bFound;
- t_param *pi = NULL;
+ t_param *pi = nullptr;
int nr = bt[ftype].nr;
int nral = NRAL(ftype);
int nrfp = interaction_function[ftype].nrfpA;
{
int nparam_found;
gmx_bool bFound, bSame;
- t_param *pi = NULL;
- t_param *pj = NULL;
+ t_param *pi = nullptr;
+ t_param *pj = nullptr;
int nr = bt[ftype].nr;
int nral = NRAL(ftype);
int nrfpA = interaction_function[ftype].nrfpA;
}
for (j = i+1; (j < nral); j++)
{
+ GMX_ASSERT(j < MAXATOMLIST + 1, "Values from nral=NRAL() will satisfy this, we assert to keep gcc 4 happy");
if (aa[i] == aa[j])
{
sprintf(errbuf, "Duplicate atom index (%d) in %s", aa[i], dir2str(d));
- warning(wi, errbuf);
+ if (ftype == F_ANGRES)
+ {
+ /* Since the angle restraints uses 2 pairs of atoms to
+ * defines an angle between vectors, it can be useful
+ * to use one atom twice, so we only issue a note here.
+ */
+ warning_note(wi, errbuf);
+ }
+ else
+ {
+ warning_error(wi, errbuf);
+ }
}
}
}
if (aa[i] == aa[j])
{
sprintf(errbuf, "Duplicate atom index (%d) in %s", aa[i], dir2str(d));
- warning(wi, errbuf);
+ warning_error(wi, errbuf);
}
}
}
{
char *ptr;
int type, ftype, j, n, ret, nj, a;
- int *atc = NULL;
- double *weight = NULL, weight_tot;
+ int *atc = nullptr;
+ double *weight = nullptr, weight_tot;
t_param param;
char errbuf[STRLEN];
snew(b2->a, b2->nr);
for (i = 0; (i < b2->nr); i++)
{
- b2->a[i] = NULL;
+ b2->a[i] = nullptr;
}
}
/* Empty the LJ14 pairlist */
plist[F_LJ14].nr = 0;
- plist[F_LJ14].param = NULL;
+ plist[F_LJ14].param = nullptr;
}
static void generate_LJCpairsNB(t_molinfo *mol, int nb_funct, t_params *nbp, warninp_t wi)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
plist[i].nr = 0;
plist[i].maxnr = 0;
- plist[i].param = NULL;
+ plist[i].param = nullptr;
/* CMAP */
plist[i].ncmap = 0;
- plist[i].cmap = NULL;
+ plist[i].cmap = nullptr;
plist[i].grid_spacing = 0;
plist[i].nc = 0;
plist[i].nct = 0;
- plist[i].cmap_types = NULL;
+ plist[i].cmap_types = nullptr;
}
}
/* FREEING MEMORY */
-void done_bt (t_params *pl)
+static void done_bt (t_params *pl)
{
sfree(pl->param);
}
/* PRINTING STRUCTURES */
-void print_bt(FILE *out, directive d, gpp_atomtype_t at,
- int ftype, int fsubtype, t_params plist[],
- gmx_bool bFullDih)
+static void print_bt(FILE *out, directive d, gpp_atomtype_t at,
+ int ftype, int fsubtype, t_params plist[],
+ gmx_bool bFullDih)
{
/* This dihp is a DIRTY patch because the dih-types do not use
* all four atoms to determine the type.
{
ri = at->atom[i].resind;
if ((i == 0 || ri != at->atom[i-1].resind) &&
- at->resinfo[ri].rtp != NULL)
+ at->resinfo[ri].rtp != nullptr)
{
qres = get_residue_charge(at, i);
fprintf(out, "; residue %3d %-3s rtp %-4s q ",
fprintf(out, "\n");
}
tpA = at->atom[i].type;
- if ((tpnmA = get_atomtype_name(tpA, atype)) == NULL)
+ if ((tpnmA = get_atomtype_name(tpA, atype)) == nullptr)
{
gmx_fatal(FARGS, "tpA = %d, i= %d in print_atoms", tpA, i);
}
if (PERTURBED(at->atom[i]))
{
tpB = at->atom[i].typeB;
- if ((tpnmB = get_atomtype_name(tpB, atype)) == NULL)
+ if ((tpnmB = get_atomtype_name(tpB, atype)) == nullptr)
{
gmx_fatal(FARGS, "tpB = %d, i= %d in print_atoms", tpB, i);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/strconvert.h"
typedef struct {
t_iatom a[4];
}
nrbond = nrang = nridih = 0;
- bonds = NULL;
- angles = NULL;
- idihs = NULL;
+ bonds = nullptr;
+ angles = nullptr;
+ idihs = nullptr;
nrset++;
/* now set the vsite parameters: */
get_bondeds(NRAL(ftype), plist[ftype].param[i].a, at2vb,
for (i = 0; (i < ps->nr); i++) /* for all bonds in the plist */
{
int vsnral = 0;
- const int *first_atoms = NULL;
+ const int *first_atoms = nullptr;
bKeep = FALSE;
bRemove = FALSE;
for (i = 0; (i < ps->nr); i++) /* for all angles in the plist */
{
int vsnral = 0;
- const int *first_atoms = NULL;
+ const int *first_atoms = nullptr;
bKeep = FALSE;
bAll3FAD = TRUE;
{
int k, m, n, nvsite;
int vsnral = 0;
- const int *first_atoms = NULL;
+ const int *first_atoms = nullptr;
int atom;
gmx_bool bKeep, bUsed, bPresent;
t_pindex *pindex;
at2vsitecon_t *at2vc;
- pindex = 0; /* avoid warnings */
+ pindex = nullptr; /* avoid warnings */
/* make vsite_type array */
snew(vsite_type, natoms);
for (i = 0; i < natoms; i++)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "x2top.h"
#include <cmath>
+#include <cstring>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/readinp.h"
#include "gromacs/gmxpreprocess/gen_ad.h"
#include "gromacs/gmxpreprocess/gpp_nextnb.h"
#include "gromacs/gmxpreprocess/hackblock.h"
return FALSE;
}
-void mk_bonds(int nnm, t_nm2type nmt[],
- t_atoms *atoms, const rvec x[], t_params *bond, int nbond[],
- gmx_bool bPBC, matrix box)
+static void mk_bonds(int nnm, t_nm2type nmt[],
+ t_atoms *atoms, const rvec x[], t_params *bond, int nbond[],
+ gmx_bool bPBC, matrix box)
{
t_param b;
int i, j;
fflush(stderr);
}
-int *set_cgnr(t_atoms *atoms, gmx_bool bUsePDBcharge, real *qtot, real *mtot)
+static int *set_cgnr(t_atoms *atoms, gmx_bool bUsePDBcharge, real *qtot, real *mtot)
{
int i, n = 1;
int *cgnr;
return cgnr;
}
-gpp_atomtype_t set_atom_type(t_symtab *tab, t_atoms *atoms, t_params *bonds,
- int *nbonds, int nnm, t_nm2type nm2t[])
+static gpp_atomtype_t set_atom_type(t_symtab *tab, t_atoms *atoms, t_params *bonds,
+ int *nbonds, int nnm, t_nm2type nm2t[])
{
gpp_atomtype_t atype;
int nresolved;
return atype;
}
-void lo_set_force_const(t_params *plist, real c[], int nrfp, gmx_bool bRound,
- gmx_bool bDih, gmx_bool bParam)
+static void lo_set_force_const(t_params *plist, real c[], int nrfp, gmx_bool bRound,
+ gmx_bool bDih, gmx_bool bParam)
{
int i, j;
double cc;
}
}
-void set_force_const(t_params plist[], real kb, real kt, real kp, gmx_bool bRound,
- gmx_bool bParam)
+static void set_force_const(t_params plist[], real kb, real kt, real kp, gmx_bool bRound,
+ gmx_bool bParam)
{
real c[MAXFORCEPARAM];
lo_set_force_const(&plist[F_PDIHS], c, 3, bRound, TRUE, bParam);
}
-void calc_angles_dihs(t_params *ang, t_params *dih, const rvec x[], gmx_bool bPBC,
- matrix box)
+static void calc_angles_dihs(t_params *ang, t_params *dih, const rvec x[], gmx_bool bPBC,
+ matrix box)
{
int i, ai, aj, ak, al, t1, t2, t3;
rvec r_ij, r_kj, r_kl, m, n;
ai = ang->param[i].ai();
aj = ang->param[i].aj();
ak = ang->param[i].ak();
- th = RAD2DEG*bond_angle(x[ai], x[aj], x[ak], bPBC ? &pbc : NULL,
+ th = RAD2DEG*bond_angle(x[ai], x[aj], x[ak], bPBC ? &pbc : nullptr,
r_ij, r_kj, &costh, &t1, &t2);
if (debug)
{
aj = dih->param[i].aj();
ak = dih->param[i].ak();
al = dih->param[i].al();
- ph = RAD2DEG*dih_angle(x[ai], x[aj], x[ak], x[al], bPBC ? &pbc : NULL,
+ ph = RAD2DEG*dih_angle(x[ai], x[aj], x[ak], x[al], bPBC ? &pbc : nullptr,
r_ij, r_kj, r_kl, m, n, &sign, &t1, &t2, &t3);
if (debug)
{
for (i = 0; (i < atoms->nr); i++)
{
tp = atoms->atom[i].type;
- if ((tpnm = get_atomtype_name(tp, atype)) == NULL)
+ if ((tpnm = get_atomtype_name(tp, atype)) == nullptr)
{
gmx_fatal(FARGS, "tp = %d, i = %d in print_rtp", tp, i);
}
{ efRTP, "-r", "out", ffOPTWR }
};
#define NFILE asize(fnm)
- static real kb = 4e5, kt = 400, kp = 5;
- static t_restp rtp_header_settings;
- static gmx_bool bRemoveDihedralIfWithImproper = FALSE;
- static gmx_bool bGenerateHH14Interactions = TRUE;
- static gmx_bool bKeepAllGeneratedDihedrals = FALSE;
- static int nrexcl = 3;
- static gmx_bool bParam = TRUE, bRound = TRUE;
- static gmx_bool bPairs = TRUE, bPBC = TRUE;
- static gmx_bool bUsePDBcharge = FALSE, bVerbose = FALSE;
- static const char *molnm = "ICE";
- static const char *ff = "oplsaa";
+ real kb = 4e5, kt = 400, kp = 5;
+ t_restp rtp_header_settings = { 0 };
+ gmx_bool bRemoveDihedralIfWithImproper = FALSE;
+ gmx_bool bGenerateHH14Interactions = TRUE;
+ gmx_bool bKeepAllGeneratedDihedrals = FALSE;
+ int nrexcl = 3;
+ gmx_bool bParam = TRUE, bRound = TRUE;
+ gmx_bool bPairs = TRUE, bPBC = TRUE;
+ gmx_bool bUsePDBcharge = FALSE, bVerbose = FALSE;
+ const char *molnm = "ICE";
+ const char *ff = "oplsaa";
t_pargs pa[] = {
{ "-ff", FALSE, etSTR, {&ff},
"Force field for your simulation. Type \"select\" for interactive selection." },
}
/* Force field selection, interactive or direct */
- choose_ff(strcmp(ff, "select") == 0 ? NULL : ff,
+ choose_ff(strcmp(ff, "select") == 0 ? nullptr : ff,
forcefield, sizeof(forcefield),
ffdir, sizeof(ffdir));
/* Read coordinates */
t_topology *top;
snew(top, 1);
- read_tps_conf(opt2fn("-f", NFILE, fnm), top, &epbc, &x, NULL, box, FALSE);
+ read_tps_conf(opt2fn("-f", NFILE, fnm), top, &epbc, &x, nullptr, box, FALSE);
t_atoms *atoms = &top->atoms;
natoms = atoms->nr;
- if (atoms->pdbinfo == NULL)
+ if (atoms->pdbinfo == nullptr)
{
snew(atoms->pdbinfo, natoms);
}
init_nnb(&nnb, atoms->nr, 4);
gen_nnb(&nnb, plist);
print_nnb(&nnb, "NNB");
- gen_pad(&nnb, atoms, &rtp_header_settings, plist, excls, NULL, TRUE);
+ gen_pad(&nnb, atoms, &rtp_header_settings, plist, excls, nullptr, TRUE);
done_nnb(&nnb);
if (!bPairs)
fp = ftp2FILE(efTOP, NFILE, fnm, "w");
print_top_header(fp, ftp2fn(efTOP, NFILE, fnm), TRUE, ffdir, 1.0);
- write_top(fp, NULL, mymol.name, atoms, FALSE, bts, plist, excls, atype,
+ write_top(fp, nullptr, mymol.name, atoms, FALSE, bts, plist, excls, atype,
cgnr, rtp_header_settings.nrexcl);
- print_top_mols(fp, mymol.name, ffdir, NULL, 0, NULL, 1, &mymol);
+ print_top_mols(fp, mymol.name, ffdir, nullptr, 0, nullptr, 1, &mymol);
gmx_ffclose(fp);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
else
{
- xl[n].res = NULL;
+ xl[n].res = nullptr;
}
/* Replace underscores in the string by spaces */
- while ((_ptr = strchr(abuf, '_')) != 0)
+ while ((_ptr = strchr(abuf, '_')) != nullptr)
{
*_ptr = ' ';
}
for (i = 0; (i < nxlate); i++)
{
sfree(xlatom[i].filebase);
- if (xlatom[i].res != NULL)
+ if (xlatom[i].res != nullptr)
{
sfree(xlatom[i].res);
}
gmx_bool bStartTerm, bEndTerm;
nxlate = 0;
- xlatom = NULL;
- if (xlfile != NULL)
+ xlatom = nullptr;
+ if (xlfile != nullptr)
{
fp = libopen(xlfile);
get_xlatoms(xlfile, fp, &nxlate, &xlatom);
for (i = 0; (i < nxlate) && !bRenamed; i++)
{
/* Check if the base file name of the rtp and arn entry match */
- if (restp == NULL ||
+ if (restp == nullptr ||
gmx_strcasecmp(restp[resind].filebase, xlatom[i].filebase) == 0)
{
/* Match the residue name */
- bMatch = (xlatom[i].res == NULL ||
+ bMatch = (xlatom[i].res == nullptr ||
(gmx_strcasecmp("protein-nterm", xlatom[i].res) == 0 &&
gmx_residuetype_is_protein(rt, rnm) && bStartTerm) ||
(gmx_strcasecmp("protein-cterm", xlatom[i].res) == 0 &&
#include "config.h"
+#include "gromacs/utility/basedefinitions.h"
+
/*! \file
* \brief CUDA arch dependent definitions.
*
static __forceinline__ __device__
T gmx_shfl_up_sync(const unsigned int activeMask,
const T var,
- unsigned int offset)
+ unsigned int offset,
+ int width = warp_size)
{
#if GMX_CUDA_VERSION < 9000
GMX_UNUSED_VALUE(activeMask);
- return __shfl_up(var, offset);
+ return __shfl_up(var, offset, width);
#else
- return __shfl_up_sync(activeMask, var, offset);
+ return __shfl_up_sync(activeMask, var, offset, width);
#endif
}
static __forceinline__ __device__
T gmx_shfl_down_sync(const unsigned int activeMask,
const T var,
- unsigned int offset)
+ unsigned int offset,
+ int width = warp_size)
{
#if GMX_CUDA_VERSION < 9000
GMX_UNUSED_VALUE(activeMask);
- return __shfl_down(var, offset);
+ return __shfl_down(var, offset, width);
#else
- return __shfl_down_sync(activeMask, var, offset);
+ return __shfl_down_sync(activeMask, var, offset, width);
#endif
}
+/*! \brief Allow disabling CUDA textures using the GMX_DISABLE_CUDA_TEXTURES macro.
+ *
+ * This option will not influence functionality. All features using textures ought
+ * to have fallback for texture-less reads (direct/LDG loads), all new code needs
+ * to provide fallback code.
+ */
+#if defined GMX_DISABLE_CUDA_TEXTURES
+#define DISABLE_CUDA_TEXTURES 1
+#else
+#define DISABLE_CUDA_TEXTURES 0
+#endif
+
+/* CUDA architecture technical characteristics. Needs macros because it is used
+ * in the __launch_bounds__ function qualifiers and might need it in preprocessor
+ * conditionals.
+ *
+ */
+#if GMX_PTX_ARCH > 0
+ #if GMX_PTX_ARCH <= 210 // CC 2.x
+ #define GMX_CUDA_MAX_BLOCKS_PER_MP 8
+ #define GMX_CUDA_MAX_THREADS_PER_MP 1536
+ #elif GMX_PTX_ARCH <= 370 // CC 3.x
+ #define GMX_CUDA_MAX_BLOCKS_PER_MP 16
+ #define GMX_CUDA_MAX_THREADS_PER_MP 2048
+ #else // CC 5.x, 6.x
+ /* Note that this final branch covers all future architectures (current gen
+ * is 6.x as of writing), hence assuming that these *currently defined* upper
+ * limits will not be lowered.
+ */
+ #define GMX_CUDA_MAX_BLOCKS_PER_MP 32
+ #define GMX_CUDA_MAX_THREADS_PER_MP 2048
+ #endif
+#else
+ #define GMX_CUDA_MAX_BLOCKS_PER_MP 0
+ #define GMX_CUDA_MAX_THREADS_PER_MP 0
+#endif
+
#endif /* CUDA_ARCH_UTILS_CUH_ */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_GPU_UTILS_CUDA_KERNEL_UTILS_CUH
+#define GMX_GPU_UTILS_CUDA_KERNEL_UTILS_CUH
+
+/*! \file
+ * \brief CUDA device util functions (callable from GPU kernels).
+ *
+ * \author Szilard Pall <pall.szilard@gmail.com>
+ */
+
+#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
+
+/*! Load directly or using __ldg() when supported. */
+template<typename T>
+__device__ __forceinline__ T LDG(const T* ptr)
+{
+#if GMX_PTX_ARCH >= 350
+ /* CC >=3.5 supports constant loads through texture or L1 */
+ return __ldg(ptr);
+#else
+ /* Device does not have LDG support, fall back to direct load. */
+ return *ptr;
+#endif
+}
+
+
+#endif /* GMX_GPU_UTILS_CUDA_KERNEL_UTILS_CUH */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return cu_copy_H2D_generic(d_dest, h_src, bytes, true, s);
}
-int cu_copy_H2D_alloc(void ** d_dest, void * h_src, size_t bytes)
-{
- cudaError_t stat;
-
- if (d_dest == NULL || h_src == NULL || bytes == 0)
- {
- return -1;
- }
-
- stat = cudaMalloc(d_dest, bytes);
- CU_RET_ERR(stat, "cudaMalloc failed in cu_copy_H2D_alloc");
-
- return cu_copy_H2D(*d_dest, h_src, bytes);
-}
-
float cu_event_elapsed(cudaEvent_t start, cudaEvent_t end)
{
float t = 0.0;
* The CUDA device information is queried and set at detection and contains
* both information about the device/hardware returned by the runtime as well
* as additional data like support status.
+ *
+ * \todo extract an object to manage NVML details
*/
struct gmx_device_info_t
{
int id; /* id of the CUDA device */
cudaDeviceProp prop; /* CUDA device properties */
int stat; /* result of the device check */
- gmx_bool nvml_initialized; /* If NVML was initialized */
unsigned int nvml_orig_app_sm_clock; /* The original SM clock before we changed it */
unsigned int nvml_orig_app_mem_clock; /* The original memory clock before we changed it */
gmx_bool nvml_app_clocks_changed; /* If application clocks have been changed */
unsigned int nvml_set_app_mem_clock; /* The memory clock we set */
#if HAVE_NVML
nvmlDevice_t nvml_device_id; /* NVML device id */
+ // TODO This can become a bool with a more useful name
nvmlEnableState_t nvml_is_restricted; /* Status of application clocks permission */
#endif /* HAVE_NVML */
};
/*! Launches asynchronous host to device memory copy in stream s. */
int cu_copy_H2D_async(void * /*d_dest*/, void * /*h_src*/, size_t /*bytes*/, cudaStream_t /*s = 0*/);
-/*! Allocates device memory and launches synchronous host to device memory copy. */
-int cu_copy_H2D_alloc(void ** /*d_dest*/, void * /*h_src*/, size_t /*bytes*/);
-
/*! Frees device memory and resets the size and allocation size to -1. */
void cu_free_buffered(void *d_ptr, int *n = NULL, int *nalloc = NULL);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define REAL_FUNC_TERM ;
#define REAL_FUNC_TERM_WITH_RETURN(arg) ;
-#define NULL_FUNC_QUALIFIER static
+#define NULL_FUNC_QUALIFIER gmx_unused static
#define NULL_FUNC_ARGUMENT(arg) /*arg*/
#define NULL_FUNC_TERM {}
#define NULL_FUNC_TERM_WITH_RETURN(arg) { return (arg); }
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_host_alloc_t **nb_alloc,
gmx_host_free_t **nb_free)
{
- *nb_alloc = NULL;
- *nb_free = NULL;
+ *nb_alloc = nullptr;
+ *nb_free = nullptr;
}
#include "gromacs/hardware/gpu_hw_info.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/snprintf.h"
#if HAVE_NVML
#include <nvml.h>
return 0;
}
-#if HAVE_NVML
-/* TODO: We should actually be using md_print_warn in md_logging.c,
- * but we can't include mpi.h in CUDA code.
- */
-static void md_print_info(FILE *fplog,
- const char *fmt, ...)
-{
- va_list ap;
-
- if (fplog != NULL)
- {
- /* We should only print to stderr on the master node,
- * in most cases fplog is only set on the master node, so this works.
- */
- va_start(ap, fmt);
- vfprintf(stderr, fmt, ap);
- va_end(ap);
-
- va_start(ap, fmt);
- vfprintf(fplog, fmt, ap);
- va_end(ap);
- }
-}
-#endif /*HAVE_NVML*/
-
-/* TODO: We should actually be using md_print_warn in md_logging.c,
- * but we can't include mpi.h in CUDA code.
- * This is replicated from nbnxn_cuda_data_mgmt.cu.
- */
-static void md_print_warn(FILE *fplog,
- const char *fmt, ...)
-{
- va_list ap;
-
- if (fplog != NULL)
- {
- /* We should only print to stderr on the master node,
- * in most cases fplog is only set on the master node, so this works.
- */
- va_start(ap, fmt);
- fprintf(stderr, "\n");
- vfprintf(stderr, fmt, ap);
- fprintf(stderr, "\n");
- va_end(ap);
-
- va_start(ap, fmt);
- fprintf(fplog, "\n");
- vfprintf(fplog, fmt, ap);
- fprintf(fplog, "\n");
- va_end(ap);
- }
-}
-
#if HAVE_NVML_APPLICATION_CLOCKS
/*! \brief Determines and adds the NVML device ID to the passed \cuda_dev.
*
static bool addNVMLDeviceId(gmx_device_info_t* cuda_dev)
{
nvmlDevice_t nvml_device_id;
- unsigned int nvml_device_count = 0;
- nvmlReturn_t nvml_stat = nvmlDeviceGetCount ( &nvml_device_count );
- cuda_dev->nvml_initialized = false;
+ unsigned int nvml_device_count = 0;
+ nvmlReturn_t nvml_stat = nvmlDeviceGetCount ( &nvml_device_count );
+ bool nvmlWasInitialized = false;
HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetCount failed" );
for (unsigned int nvml_device_idx = 0; nvml_stat == NVML_SUCCESS && nvml_device_idx < nvml_device_count; ++nvml_device_idx)
{
static_cast<unsigned int>(cuda_dev->prop.pciDeviceID) == nvml_pci_info.device &&
static_cast<unsigned int>(cuda_dev->prop.pciDomainID) == nvml_pci_info.domain)
{
- cuda_dev->nvml_initialized = true;
+ nvmlWasInitialized = true;
cuda_dev->nvml_device_id = nvml_device_id;
break;
}
}
- return cuda_dev->nvml_initialized;
+ return nvmlWasInitialized;
}
/*! \brief Reads and returns the application clocks for device.
/*! \brief Tries to set application clocks for the GPU with the given index.
*
- * The variable \gpuid is the index of the GPU in the gpu_info.cuda_dev array
- * to handle the application clocks for. Application clocks are set to the
- * max supported value to increase performance if application clock permissions
- * allow this. For future GPU architectures a more sophisticated scheme might be
- * required.
+ * Application clocks are set to the max supported value to increase
+ * performance if application clock permissions allow this. For future
+ * GPU architectures a more sophisticated scheme might be required.
+ *
+ * \todo Refactor this into a detection phase and a work phase. Also
+ * refactor to remove compile-time dependence on logging header.
*
- * \param[out] fplog log file to write to
- * \param[in] gpuid index of the GPU to set application clocks for
- * \param[in] gpu_info GPU info of all detected devices in the system.
+ * \param mdlog log file to write to
+ * \param[in] cuda_dev GPU device info for the GPU in use
* \returns true if no error occurs during application clocks handling.
*/
-static gmx_bool init_gpu_application_clocks(FILE gmx_unused *fplog, int gmx_unused gpuid, const gmx_gpu_info_t gmx_unused *gpu_info)
+static gmx_bool init_gpu_application_clocks(
+ const gmx::MDLogger &mdlog,
+ gmx_device_info_t *cuda_dev)
{
- const cudaDeviceProp *prop = &gpu_info->gpu_dev[gpuid].prop;
- int cuda_version_number = prop->major * 10 + prop->minor;
+ const cudaDeviceProp *prop = &cuda_dev->prop;
+ int cuda_compute_capability = prop->major * 10 + prop->minor;
gmx_bool bGpuCanUseApplicationClocks =
- ((0 == gmx_wcmatch("*Tesla*", prop->name) && cuda_version_number >= 35 ) ||
- (0 == gmx_wcmatch("*Quadro*", prop->name) && cuda_version_number >= 52 ));
+ ((0 == gmx_wcmatch("*Tesla*", prop->name) && cuda_compute_capability >= 35 ) ||
+ (0 == gmx_wcmatch("*Quadro*", prop->name) && cuda_compute_capability >= 52 ));
if (!bGpuCanUseApplicationClocks)
{
return true;
}
#if !HAVE_NVML
- int cuda_driver = 0;
- int cuda_runtime = 0;
- cudaDriverGetVersion(&cuda_driver);
- cudaRuntimeGetVersion(&cuda_runtime);
- md_print_warn( fplog, "NOTE: GROMACS was configured without NVML support hence it can not exploit\n"
- " application clocks of the detected %s GPU to improve performance.\n"
- " Recompile with the NVML library (compatible with the driver used) or set application clocks manually.\n",
- prop->name);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: GROMACS was configured without NVML support hence it can not exploit\n"
+ " application clocks of the detected %s GPU to improve performance.\n"
+ " Recompile with the NVML library (compatible with the driver used) or set application clocks manually.",
+ prop->name);
return true;
#else
if (!bCompiledWithApplicationClockSupport)
{
- int cuda_driver = 0;
- int cuda_runtime = 0;
- cudaDriverGetVersion(&cuda_driver);
- cudaRuntimeGetVersion(&cuda_runtime);
- md_print_warn( fplog, "NOTE: GROMACS was compiled with an old NVML library which does not support\n"
- " managing application clocks of the detected %s GPU to improve performance.\n"
- " If your GPU supports application clocks, upgrade NVML (and driver) and recompile or set the clocks manually.\n",
- prop->name );
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: GROMACS was compiled with an old NVML library which does not support\n"
+ " managing application clocks of the detected %s GPU to improve performance.\n"
+ " If your GPU supports application clocks, upgrade NVML (and driver) and recompile or set the clocks manually.",
+ prop->name );
return true;
}
return false;
}
- gmx_device_info_t *cuda_dev = &(gpu_info->gpu_dev[gpuid]);
-
if (!addNVMLDeviceId(cuda_dev))
{
return false;
cuda_dev->nvml_is_restricted = NVML_FEATURE_ENABLED;
cuda_dev->nvml_app_clocks_changed = false;
- nvml_stat = nvmlDeviceGetAPIRestriction(cuda_dev->nvml_device_id, NVML_RESTRICTED_API_SET_APPLICATION_CLOCKS, &(cuda_dev->nvml_is_restricted));
- HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetAPIRestriction failed" );
-
- /* Note: Distinguishing between different types of GPUs here might be necessary in the future,
- e.g. if max application clocks should not be used for certain GPUs. */
- if (nvml_stat == NVML_SUCCESS && cuda_dev->nvml_orig_app_sm_clock < max_sm_clock && cuda_dev->nvml_is_restricted == NVML_FEATURE_DISABLED)
+ if (cuda_dev->nvml_orig_app_sm_clock >= max_sm_clock)
{
- md_print_info(fplog, "Changing GPU application clocks for %s to (%d,%d)\n", cuda_dev->prop.name, max_mem_clock, max_sm_clock);
- nvml_stat = nvmlDeviceSetApplicationsClocks(cuda_dev->nvml_device_id, max_mem_clock, max_sm_clock);
- HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceSetApplicationsClock failed" );
- cuda_dev->nvml_app_clocks_changed = true;
- cuda_dev->nvml_set_app_sm_clock = max_sm_clock;
- cuda_dev->nvml_set_app_mem_clock = max_mem_clock;
+ //TODO: This should probably be integrated into the GPU Properties table.
+ GMX_LOG(mdlog.info).appendTextFormatted(
+ "Application clocks (GPU clocks) for %s are (%d,%d)",
+ cuda_dev->prop.name, cuda_dev->nvml_orig_app_mem_clock, cuda_dev->nvml_orig_app_sm_clock);
+ return true;
}
- else if (nvml_stat == NVML_SUCCESS && cuda_dev->nvml_orig_app_sm_clock < max_sm_clock)
+
+ if (cuda_compute_capability >= 60)
{
- md_print_warn(fplog, "Can not change application clocks for %s to optimal values due to insufficient permissions. Current values are (%d,%d), max values are (%d,%d).\nUse sudo nvidia-smi -acp UNRESTRICTED or contact your admin to change application clocks.\n", cuda_dev->prop.name, cuda_dev->nvml_orig_app_mem_clock, cuda_dev->nvml_orig_app_sm_clock, max_mem_clock, max_sm_clock);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "Cannot change application clocks for %s to optimal values due to insufficient permissions. Current values are (%d,%d), max values are (%d,%d).\nPlease contact your admin to change application clocks.\n",
+ cuda_dev->prop.name, cuda_dev->nvml_orig_app_mem_clock, cuda_dev->nvml_orig_app_sm_clock, max_mem_clock, max_sm_clock);
+ return true;
}
- else if (nvml_stat == NVML_SUCCESS && cuda_dev->nvml_orig_app_sm_clock == max_sm_clock)
+
+ nvml_stat = nvmlDeviceGetAPIRestriction(cuda_dev->nvml_device_id, NVML_RESTRICTED_API_SET_APPLICATION_CLOCKS, &(cuda_dev->nvml_is_restricted));
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetAPIRestriction failed" );
+
+ if (nvml_stat != NVML_SUCCESS)
{
- md_print_info(fplog, "Application clocks (GPU clocks) for %s are (%d,%d)\n", cuda_dev->prop.name, cuda_dev->nvml_orig_app_mem_clock, cuda_dev->nvml_orig_app_sm_clock);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "Cannot change GPU application clocks to optimal values due to NVML error (%d): %s.",
+ nvml_stat, nvmlErrorString(nvml_stat));
+ return false;
}
- else
+
+ if (cuda_dev->nvml_is_restricted != NVML_FEATURE_DISABLED)
{
- md_print_warn( fplog, "Can not change GPU application clocks to optimal values due to NVML error (%d): %s.\n", nvml_stat, nvmlErrorString(nvml_stat));
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "Cannot change application clocks for %s to optimal values due to insufficient permissions. Current values are (%d,%d), max values are (%d,%d).\nUse sudo nvidia-smi -acp UNRESTRICTED or contact your admin to change application clocks.",
+ cuda_dev->prop.name, cuda_dev->nvml_orig_app_mem_clock, cuda_dev->nvml_orig_app_sm_clock, max_mem_clock, max_sm_clock);
+ return true;
}
- return (nvml_stat == NVML_SUCCESS);
+
+ /* Note: Distinguishing between different types of GPUs here might be necessary in the future,
+ e.g. if max application clocks should not be used for certain GPUs. */
+ GMX_LOG(mdlog.warning).appendTextFormatted(
+ "Changing GPU application clocks for %s to (%d,%d)",
+ cuda_dev->prop.name, max_mem_clock, max_sm_clock);
+ nvml_stat = nvmlDeviceSetApplicationsClocks(cuda_dev->nvml_device_id, max_mem_clock, max_sm_clock);
+ HANDLE_NVML_RET_ERR( nvml_stat, "nvmlDeviceGetApplicationsClock failed" );
+ cuda_dev->nvml_app_clocks_changed = true;
+ cuda_dev->nvml_set_app_sm_clock = max_sm_clock;
+ cuda_dev->nvml_set_app_mem_clock = max_mem_clock;
+
+ return true;
#endif /* HAVE_NVML */
}
#endif /* HAVE_NVML_APPLICATION_CLOCKS */
}
-gmx_bool init_gpu(FILE gmx_unused *fplog, int mygpu, char *result_str,
- const struct gmx_gpu_info_t *gpu_info,
- const struct gmx_gpu_opt_t *gpu_opt)
+void init_gpu(const gmx::MDLogger &mdlog, int rank,
+ gmx_device_info_t *deviceInfo)
{
cudaError_t stat;
char sbuf[STRLEN];
- int gpuid;
- assert(gpu_info);
- assert(result_str);
+ assert(deviceInfo);
- if (mygpu < 0 || mygpu >= gpu_opt->n_dev_use)
+ stat = cudaSetDevice(deviceInfo->id);
+ if (stat != cudaSuccess)
{
- sprintf(sbuf, "Trying to initialize an inexistent GPU: "
- "there are %d %s-selected GPU(s), but #%d was requested.",
- gpu_opt->n_dev_use, gpu_opt->bUserSet ? "user" : "auto", mygpu);
- gmx_incons(sbuf);
+ snprintf(sbuf, STRLEN, "On rank %d failed to initialize GPU #%d",
+ rank, deviceInfo->id);
+ CU_RET_ERR(stat, sbuf);
}
- gpuid = gpu_info->gpu_dev[gpu_opt->dev_use[mygpu]].id;
-
- stat = cudaSetDevice(gpuid);
- strncpy(result_str, cudaGetErrorString(stat), STRLEN);
-
if (debug)
{
- fprintf(stderr, "Initialized GPU ID #%d: %s\n", gpuid, gpu_info->gpu_dev[gpuid].prop.name);
+ fprintf(stderr, "Initialized GPU ID #%d: %s\n", deviceInfo->id, deviceInfo->prop.name);
}
//Ignoring return value as NVML errors should be treated not critical.
- if (stat == cudaSuccess)
- {
- init_gpu_application_clocks(fplog, gpuid, gpu_info);
- }
- return (stat == cudaSuccess);
+ init_gpu_application_clocks(mdlog, deviceInfo);
}
-gmx_bool free_cuda_gpu(
- int gmx_unused mygpu, char *result_str,
- const gmx_gpu_info_t gmx_unused *gpu_info,
- const gmx_gpu_opt_t gmx_unused *gpu_opt
- )
+gmx_bool free_cuda_gpu(const gmx_device_info_t *deviceInfo,
+ char *result_str)
{
cudaError_t stat;
gmx_bool reset_gpu_application_clocks_status = true;
- int gpuid;
assert(result_str);
fprintf(stderr, "Cleaning up context on GPU ID #%d\n", gpuid);
}
- gpuid = gpu_opt ? gpu_opt->dev_use[mygpu] : -1;
- if (gpuid != -1)
+ if (deviceInfo != nullptr)
{
- reset_gpu_application_clocks_status = reset_gpu_application_clocks( &(gpu_info->gpu_dev[gpuid]) );
+ reset_gpu_application_clocks_status = reset_gpu_application_clocks(deviceInfo);
}
stat = cudaDeviceReset();
return (stat == cudaSuccess) && reset_gpu_application_clocks_status;
}
+gmx_device_info_t *getDeviceInfo(const gmx_gpu_info_t &gpu_info,
+ int deviceId)
+{
+ if (deviceId < 0 || deviceId >= gpu_info.n_dev)
+ {
+ gmx_incons("Invalid GPU deviceId requested");
+ }
+ return &gpu_info.gpu_dev[deviceId];
+}
+
/*! \brief Returns true if the gpu characterized by the device properties is
* supported by the native gpu acceleration.
*
return (dev_prop->major >= 2);
}
-/*! \brief Helper function that checks whether a given GPU status indicates compatible GPU.
- *
- * \param[in] stat GPU status.
- * \returns true if the provided status is egpuCompatible, otherwise false.
- */
-static bool is_compatible_gpu(int stat)
-{
- return (stat == egpuCompatible);
-}
-
/*! \brief Checks if a GPU with a given ID is supported by the native GROMACS acceleration.
*
* Returns a status value which indicates compatibility or one of the following
return retval;
}
-void pick_compatible_gpus(const gmx_gpu_info_t *gpu_info,
- gmx_gpu_opt_t *gpu_opt)
+bool isGpuCompatible(const gmx_gpu_info_t &gpu_info,
+ int index)
{
- int i, ncompat;
- int *compat;
-
- assert(gpu_info);
- /* gpu_dev/n_dev have to be either NULL/0 or not (NULL/0) */
- assert((gpu_info->n_dev != 0 ? 0 : 1) ^ (gpu_info->gpu_dev == NULL ? 0 : 1));
-
- snew(compat, gpu_info->n_dev);
- ncompat = 0;
- for (i = 0; i < gpu_info->n_dev; i++)
- {
- if (is_compatible_gpu(gpu_info->gpu_dev[i].stat))
- {
- ncompat++;
- compat[ncompat - 1] = i;
- }
- }
+ assert(gpu_info.n_dev == 0 || gpu_info.gpu_dev);
- gpu_opt->n_dev_compatible = ncompat;
- snew(gpu_opt->dev_compatible, ncompat);
- memcpy(gpu_opt->dev_compatible, compat, ncompat*sizeof(*compat));
- sfree(compat);
+ return (index >= gpu_info.n_dev ?
+ false :
+ gpu_info.gpu_dev[index].stat == egpuCompatible);
}
-gmx_bool check_selected_gpus(int *checkres,
- const gmx_gpu_info_t *gpu_info,
- gmx_gpu_opt_t *gpu_opt)
+const char *getGpuCompatibilityDescription(const gmx_gpu_info_t &gpu_info,
+ int index)
{
- int i, id;
- bool bAllOk;
-
- assert(checkres);
- assert(gpu_info);
- assert(gpu_opt->n_dev_use >= 0);
-
- if (gpu_opt->n_dev_use == 0)
- {
- return TRUE;
- }
-
- assert(gpu_opt->dev_use);
-
- /* we will assume that all GPUs requested are valid IDs,
- otherwise we'll bail anyways */
-
- bAllOk = true;
- for (i = 0; i < gpu_opt->n_dev_use; i++)
- {
- id = gpu_opt->dev_use[i];
-
- /* devices are stored in increasing order of IDs in gpu_dev */
- gpu_opt->dev_use[i] = id;
-
- checkres[i] = (id >= gpu_info->n_dev) ?
- egpuNonexistent : gpu_info->gpu_dev[id].stat;
-
- bAllOk = bAllOk && is_compatible_gpu(checkres[i]);
- }
-
- return bAllOk;
+ return (index >= gpu_info.n_dev ?
+ gpu_detect_res_str[egpuNonexistent] :
+ gpu_detect_res_str[gpu_info.gpu_dev[index].stat]);
}
void free_gpu_info(const gmx_gpu_info_t *gpu_info)
sfree(gpu_info->gpu_dev);
}
-void get_gpu_device_info_string(char *s, const gmx_gpu_info_t *gpu_info, int index)
+void get_gpu_device_info_string(char *s, const gmx_gpu_info_t &gpu_info, int index)
{
assert(s);
- assert(gpu_info);
- if (index < 0 && index >= gpu_info->n_dev)
+ if (index < 0 && index >= gpu_info.n_dev)
{
return;
}
- gmx_device_info_t *dinfo = &gpu_info->gpu_dev[index];
+ gmx_device_info_t *dinfo = &gpu_info.gpu_dev[index];
bool bGpuExists =
dinfo->stat == egpuCompatible ||
}
}
-int get_gpu_device_id(const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt,
- int idx)
-{
- assert(gpu_info);
- assert(gpu_opt);
- assert(idx >= 0 && idx < gpu_opt->n_dev_use);
-
- return gpu_info->gpu_dev[gpu_opt->dev_use[idx]].id;
-}
-
int get_current_cuda_gpu_device_id(void)
{
int gpuid;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2010, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/gpu_macros.h"
#include "gromacs/utility/basedefinitions.h"
+struct gmx_device_info_t;
struct gmx_gpu_info_t;
-struct gmx_gpu_opt_t;
+
+namespace gmx
+{
+class MDLogger;
+}
/*! \brief Detect all GPUs in the system.
*
GPU_FUNC_QUALIFIER
int detect_gpus(struct gmx_gpu_info_t *GPU_FUNC_ARGUMENT(gpu_info), char *GPU_FUNC_ARGUMENT(err_str)) GPU_FUNC_TERM_WITH_RETURN(-1)
-/*! \brief Select the compatible GPUs
- *
- * This function selects the compatible gpus and initializes
- * gpu_info->dev_use and gpu_info->n_dev_use.
+/*! \brief Return whether the GPU with given \c index is compatible, ie suitable for use.
*
- * Given the list of GPUs available in the system check each device in
- * gpu_info->gpu_dev and place the indices of the compatible GPUs into
- * dev_use with this marking the respective GPUs as "available for use."
- * Note that \p detect_gpus must have been called before.
- *
- * \param[in] gpu_info pointer to structure holding GPU information
- * \param[in,out] gpu_opt pointer to structure holding GPU options
+ * \param[in] gpu_info Information about detected GPUs
+ * \param[in] index index of GPU to ask about
+ * \returns Whether the GPU is compatible.
*/
GPU_FUNC_QUALIFIER
-void pick_compatible_gpus(const struct gmx_gpu_info_t *GPU_FUNC_ARGUMENT(gpu_info),
- gmx_gpu_opt_t *GPU_FUNC_ARGUMENT(gpu_opt)) GPU_FUNC_TERM
+bool isGpuCompatible(const gmx_gpu_info_t &GPU_FUNC_ARGUMENT(gpu_info),
+ int GPU_FUNC_ARGUMENT(index)) GPU_FUNC_TERM_WITH_RETURN(false)
-/*! \brief Check the existence/compatibility of a set of GPUs specified by their device IDs.
- *
- * Given the a list of gpu_opt->n_dev_use GPU device IDs stored in
- * gpu_opt->dev_use check the existence and compatibility
- * of the respective GPUs. Also provide the caller with an array containing
- * the result of checks in \p checkres.
+/*! \brief Return a string describing how compatible the GPU with given \c index is.
*
- * \param[out] checkres check result for each ID passed in requested_devs
- * \param[in] gpu_info pointer to structure holding GPU information
- * \param[out] gpu_opt pointer to structure holding GPU options
- * \returns TRUE if every the requested GPUs are compatible
+ * \param[in] gpu_info Information about detected GPUs
+ * \param[in] index index of GPU to ask about
+ * \returns A null-terminated C string describing the compatibility status, useful for error messages.
*/
GPU_FUNC_QUALIFIER
-gmx_bool check_selected_gpus(int *GPU_FUNC_ARGUMENT(checkres),
- const struct gmx_gpu_info_t *GPU_FUNC_ARGUMENT(gpu_info),
- gmx_gpu_opt_t *GPU_FUNC_ARGUMENT(gpu_opt)) GPU_FUNC_TERM_WITH_RETURN(-1)
+const char *getGpuCompatibilityDescription(const gmx_gpu_info_t &GPU_FUNC_ARGUMENT(gpu_info),
+ int GPU_FUNC_ARGUMENT(index)) GPU_FUNC_TERM_WITH_RETURN("")
/*! \brief Frees the gpu_dev and dev_use array fields of \p gpu_info.
*
GPU_FUNC_QUALIFIER
void free_gpu_info(const struct gmx_gpu_info_t *GPU_FUNC_ARGUMENT(gpu_info)) GPU_FUNC_TERM
-/*! \brief Initializes the GPU with the given index.
+/*! \brief Initializes the GPU described by \c deviceInfo.
*
- * The varible \p mygpu is the index of the GPU to initialize in the
- * gpu_info.gpu_dev array.
+ * TODO Doxygen complains about these - probably a Doxygen bug, since
+ * the patterns here are the same as elsewhere in this header.
*
- * \param[out] fplog log file to write to
- * \param[in] mygpu index of the GPU to initialize
- * \param[out] result_str the message related to the error that occurred
- * during the initialization (if there was any).
- * \param[in] gpu_info GPU info of all detected devices in the system.
- * \param[in] gpu_opt options for using the GPUs in gpu_info
- * \returns true if no error occurs during initialization.
+ * param[in] mdlog log file to write to
+ * param[in] rank MPI rank of this process (for error output)
+ * \param[inout] deviceInfo device info of the GPU to initialize
+ *
+ * Issues a fatal error for any critical errors that occur during
+ * initialization.
*/
GPU_FUNC_QUALIFIER
-gmx_bool init_gpu(FILE *GPU_FUNC_ARGUMENT(fplog),
- int GPU_FUNC_ARGUMENT(mygpu),
- char *GPU_FUNC_ARGUMENT(result_str),
- const struct gmx_gpu_info_t *GPU_FUNC_ARGUMENT(gpu_info),
- const gmx_gpu_opt_t *GPU_FUNC_ARGUMENT(gpu_opt)) GPU_FUNC_TERM_WITH_RETURN(-1)
+void init_gpu(const gmx::MDLogger &GPU_FUNC_ARGUMENT(mdlog),
+ int GPU_FUNC_ARGUMENT(rank),
+ gmx_device_info_t *GPU_FUNC_ARGUMENT(deviceInfo)) GPU_FUNC_TERM
/*! \brief Frees up the CUDA GPU used by the active context at the time of calling.
*
* The context is explicitly destroyed and therefore all data uploaded to the GPU
* is lost. This should only be called when none of this data is required anymore.
*
- * \param[in] mygpu index of the GPU clean up for
+ * \param[in] deviceInfo device info of the GPU to clean up for
* \param[out] result_str the message related to the error that occurred
* during the initialization (if there was any).
- * \param[in] gpu_info GPU info of all detected devices in the system.
- * \param[in] gpu_opt options for using the GPUs in gpu_info
- * \returns true if no error occurs during the freeing.
- */
-CUDA_FUNC_QUALIFIER
-gmx_bool free_cuda_gpu(int CUDA_FUNC_ARGUMENT(mygpu),
- char *CUDA_FUNC_ARGUMENT(result_str),
- const gmx_gpu_info_t *CUDA_FUNC_ARGUMENT(gpu_info),
- const gmx_gpu_opt_t *CUDA_FUNC_ARGUMENT(gpu_opt)) CUDA_FUNC_TERM_WITH_RETURN(TRUE)
-
-/*! \brief Returns the device ID of the CUDA GPU currently in use.
- *
- * The GPU used is the one that is active at the time of the call in the active context.
*
- * \returns device ID of the GPU in use at the time of the call
+ * \returns true if no error occurs during the freeing.
*/
CUDA_FUNC_QUALIFIER
-int get_current_cuda_gpu_device_id(void) CUDA_FUNC_TERM_WITH_RETURN(-1)
+gmx_bool free_cuda_gpu(const gmx_device_info_t *CUDA_FUNC_ARGUMENT(deviceInfo),
+ char *CUDA_FUNC_ARGUMENT(result_str)) CUDA_FUNC_TERM_WITH_RETURN(TRUE)
-/*! \brief Returns an identifier for the GPU with a given index into the array of used GPUs.
+/*! \brief Return a pointer to the device info for \c deviceId
*
- * Getter function which, given an index into the array of GPUs in use
- * (dev_use) -- typically an MPI rank --, returns an identifier of the
- * respective GPU.
+ * \param[in] gpu_info GPU info of all detected devices in the system.
+ * \param[in] deviceId ID for the GPU device requested.
*
- * \param[in] gpu_info Pointer to structure holding GPU information
- * \param[in] gpu_opt Pointer to structure holding GPU options
- * \param[in] idx Index into the array of used GPUs
- * \returns device ID of the requested GPU
+ * \returns Pointer to the device info for \c deviceId.
*/
GPU_FUNC_QUALIFIER
-int get_gpu_device_id(const struct gmx_gpu_info_t *GPU_FUNC_ARGUMENT(gpu_info),
- const gmx_gpu_opt_t *GPU_FUNC_ARGUMENT(gpu_opt),
- int GPU_FUNC_ARGUMENT(idx)) GPU_FUNC_TERM_WITH_RETURN(-1)
+gmx_device_info_t *getDeviceInfo(const gmx_gpu_info_t &GPU_FUNC_ARGUMENT(gpu_info),
+ int GPU_FUNC_ARGUMENT(deviceId)) GPU_FUNC_TERM_WITH_RETURN(NULL)
-/*! \brief Returns the name for the OpenCL GPU with a given index into the array of used GPUs.
+/*! \brief Returns the device ID of the CUDA GPU currently in use.
*
- * Getter function which, given an index into the array of GPUs in use
- * (dev_use) -- typically a tMPI/MPI rank --, returns the device name for the
- * respective OpenCL GPU.
+ * The GPU used is the one that is active at the time of the call in the active context.
*
- * \param[in] gpu_info Pointer to structure holding GPU information
- * \param[in] gpu_opt Pointer to structure holding GPU options
- * \param[in] idx Index into the array of used GPUs
- * \returns A string with the name of the requested OpenCL GPU
+ * \returns device ID of the GPU in use at the time of the call
*/
-OPENCL_FUNC_QUALIFIER
-char* get_ocl_gpu_device_name(const struct gmx_gpu_info_t *OPENCL_FUNC_ARGUMENT(gpu_info),
- const gmx_gpu_opt_t *OPENCL_FUNC_ARGUMENT(gpu_opt),
- int OPENCL_FUNC_ARGUMENT(idx)) OPENCL_FUNC_TERM_WITH_RETURN(NULL)
+CUDA_FUNC_QUALIFIER
+int get_current_cuda_gpu_device_id(void) CUDA_FUNC_TERM_WITH_RETURN(-1)
/*! \brief Formats and returns a device information string for a given GPU.
*
* ID, name, compute capability, and detection status.
*
* \param[out] s pointer to output string (has to be allocated externally)
- * \param[in] gpu_info pointer to structure holding GPU information
+ * \param[in] gpu_info Information about detected GPUs
* \param[in] index an index *directly* into the array of available GPUs
*/
GPU_FUNC_QUALIFIER
void get_gpu_device_info_string(char *GPU_FUNC_ARGUMENT(s),
- const struct gmx_gpu_info_t *GPU_FUNC_ARGUMENT(gpu_info),
+ const struct gmx_gpu_info_t &GPU_FUNC_ARGUMENT(gpu_info),
int GPU_FUNC_ARGUMENT(index)) GPU_FUNC_TERM
/*! \brief Returns the size of the gpu_dev_info struct.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
-/*! \brief Helper function that checks whether a given GPU status indicates compatible GPU.
- *
- * \param[in] stat GPU status.
- * \returns true if the provided status is egpuCompatible, otherwise false.
- */
-static bool is_compatible_gpu(int stat)
-{
- return (stat == egpuCompatible);
-}
-
/*! \brief Return true if executing on compatible OS for AMD OpenCL.
*
* This is assumed to be true for OS X version of at least 10.10.4 and
*/
static int is_gmx_supported_gpu_id(struct gmx_device_info_t *ocl_gpu_device)
{
+ if ((getenv("GMX_OCL_DISABLE_COMPATIBILITY_CHECK")) != NULL)
+ {
+ return egpuCompatible;
+ }
+
/* Only AMD and NVIDIA GPUs are supported for now */
switch (ocl_gpu_device->vendor_e)
{
}
//! This function is documented in the header file
-void pick_compatible_gpus(const gmx_gpu_info_t *gpu_info,
- gmx_gpu_opt_t *gpu_opt)
+bool isGpuCompatible(const gmx_gpu_info_t &gpu_info,
+ int index)
{
- int i, ncompat;
- int *compat;
-
- assert(gpu_info);
- /* gpu_dev/n_dev have to be either NULL/0 or not (NULL/0) */
- assert((gpu_info->n_dev != 0 ? 0 : 1) ^ (gpu_info->gpu_dev == NULL ? 0 : 1));
-
- snew(compat, gpu_info->n_dev);
- ncompat = 0;
- for (i = 0; i < gpu_info->n_dev; i++)
- {
- if (is_compatible_gpu(gpu_info->gpu_dev[i].stat))
- {
- ncompat++;
- compat[ncompat - 1] = i;
- }
- }
-
- gpu_opt->n_dev_compatible = ncompat;
- snew(gpu_opt->dev_compatible, ncompat);
- memcpy(gpu_opt->dev_compatible, compat, ncompat*sizeof(*compat));
- sfree(compat);
+ return (index >= gpu_info.n_dev ?
+ false :
+ gpu_info.gpu_dev[index].stat == egpuCompatible);
}
//! This function is documented in the header file
-gmx_bool check_selected_gpus(int *checkres,
- const gmx_gpu_info_t *gpu_info,
- gmx_gpu_opt_t *gpu_opt)
+const char *getGpuCompatibilityDescription(const gmx_gpu_info_t &gpu_info,
+ int index)
{
- int i, id;
- bool bAllOk;
-
- assert(checkres);
- assert(gpu_info);
- assert(gpu_opt->n_dev_use >= 0);
-
- if (gpu_opt->n_dev_use == 0)
- {
- return TRUE;
- }
-
- assert(gpu_opt->dev_use);
-
- /* we will assume that all GPUs requested are valid IDs,
- otherwise we'll bail anyways */
-
- bAllOk = true;
- for (i = 0; i < gpu_opt->n_dev_use; i++)
- {
- id = gpu_opt->dev_use[i];
-
- /* devices are stored in increasing order of IDs in gpu_dev */
- gpu_opt->dev_use[i] = id;
-
- checkres[i] = (id >= gpu_info->n_dev) ?
- egpuNonexistent : gpu_info->gpu_dev[id].stat;
-
- bAllOk = bAllOk && is_compatible_gpu(checkres[i]);
- }
-
- return bAllOk;
+ return (index >= gpu_info.n_dev ?
+ gpu_detect_res_str[egpuNonexistent] :
+ gpu_detect_res_str[gpu_info.gpu_dev[index].stat]);
}
//! This function is documented in the header file
-void get_gpu_device_info_string(char gmx_unused *s, const gmx_gpu_info_t gmx_unused *gpu_info, int gmx_unused index)
+void get_gpu_device_info_string(char *s, const gmx_gpu_info_t &gpu_info, int index)
{
assert(s);
- assert(gpu_info);
- if (index < 0 && index >= gpu_info->n_dev)
+ if (index < 0 && index >= gpu_info.n_dev)
{
return;
}
- gmx_device_info_t *dinfo = &gpu_info->gpu_dev[index];
+ gmx_device_info_t *dinfo = &gpu_info.gpu_dev[index];
bool bGpuExists =
dinfo->stat == egpuCompatible ||
}
//! This function is documented in the header file
-gmx_bool init_gpu(FILE gmx_unused *fplog,
- int mygpu,
- char *result_str,
- const gmx_gpu_info_t gmx_unused *gpu_info,
- const gmx_gpu_opt_t *gpu_opt
- )
+void init_gpu(const gmx::MDLogger & /*mdlog*/,
+ int /* rank */,
+ gmx_device_info_t *deviceInfo)
{
- assert(result_str);
-
- result_str[0] = 0;
-
- if (mygpu < 0 || mygpu >= gpu_opt->n_dev_use)
- {
- char sbuf[STRLEN];
- sprintf(sbuf, "Trying to initialize an inexistent GPU: "
- "there are %d %s-selected GPU(s), but #%d was requested.",
- gpu_opt->n_dev_use, gpu_opt->bUserSet ? "user" : "auto", mygpu);
- gmx_incons(sbuf);
- }
+ assert(deviceInfo);
// If the device is NVIDIA, for safety reasons we disable the JIT
// caching as this is known to be broken at least until driver 364.19;
// the cache does not always get regenerated when the source code changes,
// e.g. if the path to the kernel sources remains the same
- if (gpu_info->gpu_dev[mygpu].vendor_e == OCL_VENDOR_NVIDIA)
+ if (deviceInfo->vendor_e == OCL_VENDOR_NVIDIA)
{
// Ignore return values, failing to set the variable does not mean
// that something will go wrong later.
setenv("CUDA_CACHE_DISABLE", "1", 0);
#endif
}
-
- return TRUE;
-}
-
-//! This function is documented in the header file
-int get_gpu_device_id(const gmx_gpu_info_t *,
- const gmx_gpu_opt_t *gpu_opt,
- int idx)
-{
- assert(gpu_opt);
- assert(idx >= 0 && idx < gpu_opt->n_dev_use);
-
- return gpu_opt->dev_use[idx];
}
//! This function is documented in the header file
-char* get_ocl_gpu_device_name(const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt,
- int idx)
+gmx_device_info_t *getDeviceInfo(const gmx_gpu_info_t &gpu_info,
+ int deviceId)
{
- assert(gpu_info);
- assert(gpu_opt);
- assert(idx >= 0 && idx < gpu_opt->n_dev_use);
-
- return gpu_info->gpu_dev[gpu_opt->dev_use[idx]].device_name;
+ if (deviceId < 0 || deviceId >= gpu_info.n_dev)
+ {
+ gmx_incons("Invalid GPU deviceId requested");
+ }
+ return &gpu_info.gpu_dev[deviceId];
}
//! This function is documented in the header file
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/programcontext.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
+#include "gromacs/utility/unique_cptr.h"
namespace gmx
{
namespace ocl
{
-/*! \brief RAII helper to use with scoped_cptr
- *
- * Can't use fclose because the template requires a function that
- * returns void.
- *
- * \todo Either generalise scoped_cptr somehow, or (better) make
- * general infrastructure for reading and writing binary lumps.
- * Neither of these is a priority while JIT caching is inactive.
- */
-static void fclose_wrapper(FILE *fp)
-{
- assert(fp != NULL);
- fclose(fp);
-}
-
std::string makeBinaryCacheFilename(const std::string &kernelFilename,
cl_device_id deviceId)
{
cl_device_id deviceId)
{
// TODO all this file reading stuff should become gmx::BinaryReader
- FILE *f = fopen(filename.c_str(), "rb");
- scoped_cptr<FILE, fclose_wrapper> fileGuard(f);
+ const auto f = create_unique_with_deleter(fopen(filename.c_str(), "rb"), fclose);
if (!f)
{
GMX_THROW(FileIOError("Failed to open binary cache file " + filename));
}
// TODO more stdio error handling
- fseek(f, 0, SEEK_END);
+ fseek(f.get(), 0, SEEK_END);
unsigned char *binary;
- scoped_cptr<unsigned char> binaryGuard;
- size_t fileSize = ftell(f);
+ unique_cptr<unsigned char> binaryGuard;
+ size_t fileSize = ftell(f.get());
snew(binary, fileSize);
binaryGuard.reset(binary);
- fseek(f, 0, SEEK_SET);
- size_t readCount = fread(binary, 1, fileSize, f);
+ fseek(f.get(), 0, SEEK_SET);
+ size_t readCount = fread(binary, 1, fileSize, f.get());
if (readCount != fileSize)
{
}
// TODO all this file writing stuff should become gmx::BinaryWriter
- unsigned char *binary;
+ unsigned char *binary;
snew(binary, fileSize);
- scoped_cptr<unsigned char> binaryGuard(binary);
+ const unique_cptr<unsigned char> binaryGuard(binary);
cl_error = clGetProgramInfo(program, CL_PROGRAM_BINARIES, sizeof(binary), &binary, NULL);
if (cl_error != CL_SUCCESS)
GMX_THROW(InternalError("Could not get OpenCL program binary, error was " + ocl_get_error_string(cl_error)));
}
- FILE *f = fopen(filename.c_str(), "wb");
- scoped_cptr<FILE, fclose_wrapper> fileGuard(f);
+ const auto f = create_unique_with_deleter(fopen(filename.c_str(), "wb"), fclose);
if (!f)
{
GMX_THROW(FileIOError("Failed to open binary cache file " + filename));
}
- fwrite(binary, 1, fileSize, f);
+ fwrite(binary, 1, fileSize, f.get());
}
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
+#include "gromacs/utility/unique_cptr.h"
#include "ocl_caching.h"
}
char *buildLog = nullptr;
- scoped_cptr<char> buildLogGuard;
+ unique_cptr<char> buildLogGuard;
if (buildLogSize != 0)
{
/* Allocate memory to fit the build log,
/*! \brief Builds a string with build options for the OpenCL kernels
*
* \throws std::bad_alloc if out of memory. */
-std::string
+static std::string
makePreprocessorOptions(const std::string &kernelRootPath,
size_t warpSize,
ocl_vendor_id_t deviceVendorId,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
#include "gromacs/gpu_utils/oclutils.h"
-#include "gromacs/hardware/gpu_hw_info.h"
namespace gmx
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* identifying this particular device to host operation. The event can further
* be used to queue a wait for this operation or to query profiling information.
*/
-int ocl_copy_D2H_generic(void * h_dest, cl_mem d_src,
- size_t offset, size_t bytes,
- bool bAsync,
- cl_command_queue command_queue,
- cl_event *copy_event)
+static int ocl_copy_D2H_generic(void * h_dest, cl_mem d_src,
+ size_t offset, size_t bytes,
+ bool bAsync,
+ cl_command_queue command_queue,
+ cl_event *copy_event)
{
cl_int gmx_unused cl_error;
case -1003: return "CL_INVALID_D3D10_RESOURCE_KHR";
case -1004: return "CL_D3D10_RESOURCE_ALREADY_ACQUIRED_KHR";
case -1005: return "CL_D3D10_RESOURCE_NOT_ACQUIRED_KHR";
- default: return "Unknown OpenCL error";
+ default: return "Unknown OpenCL error: " +
+ std::to_string(static_cast<int32_t>(error));
}
}
include(${_gmx_import_file})
unset(_gmx_import_file)
+get_target_property(_libs libgromacs INTERFACE_LINK_LIBRARIES)
+if (_libs MATCHES "tng_io::tng_io")
+ include(CMakeFindDependencyMacro)
+ find_dependency(TNG_IO)
+endif()
+unset(_libs)
+
set(GROMACS_INCLUDE_DIRS)
set(_include_dirs "@INSTALLED_HEADER_INCLUDE_DIRS@")
foreach (_dir ${_include_dirs})
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015, by the GROMACS development team, led by
+# Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_libgromacs_sources(
cpuinfo.cpp
detecthardware.cpp
+ hardwareassign.cpp
hardwaretopology.cpp
+ gpu_hw_info.cpp
+ printhardware.cpp
)
if (BUILD_TESTING)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares and defines architecture booleans to minimize preprocessed code
+ *
+ * \ingroup module_hardware
+ */
+#ifndef GMX_ARCHITECTURE_H
+#define GMX_ARCHITECTURE_H
+
+namespace gmx
+{
+
+//! Enum for GROMACS CPU hardware detection support
+enum class Architecture
+{
+ Unknown, //! Not one of the cases below
+ X86, //! X86
+ Arm, //! ARM
+ PowerPC //! IBM PowerPC
+};
+
+//! Constant that tells what the architecture is
+static constexpr Architecture c_architecture =
+#if defined __i386__ || defined __i386 || defined _X86_ || defined _M_IX86 || \
+ defined __x86_64__ || defined __amd64__ || defined _M_X64 || defined _M_AMD64
+ Architecture::X86;
+#elif defined __arm__ || defined __arm || defined _M_ARM || defined __aarch64_
+ Architecture::Arm;
+#elif defined __powerpc__ || defined __ppc__ || defined __PPC__
+ Architecture::PowerPC;
+#else
+ Architecture::Unknown;
+#endif
+
+} // namespace gmx
+
+#endif // GMX_ARCHITECTURE_H
# include "gromacs/utility/basedefinitions.h"
#endif
+#include "architecture.h"
+
namespace gmx
{
unsigned int * ecx,
unsigned int * edx)
{
-#if defined __i386__ || defined __i386 || defined _X86_ || defined _M_IX86 || \
- defined __x86_64__ || defined __amd64__ || defined _M_X64 || defined _M_AMD64
-
-# if defined __GNUC__ || GMX_X86_GCC_INLINE_ASM
-
- // any compiler that understands gcc inline assembly
- *eax = level;
- *ecx = ecxval;
- *ebx = 0;
- *edx = 0;
-
-# if (defined __i386__ || defined __i386 || defined _X86_ || defined _M_IX86) && defined(__PIC__)
- // Avoid clobbering the global offset table in 32-bit pic code (ebx register)
- __asm__ __volatile__ ("xchgl %%ebx, %1 \n\t"
- "cpuid \n\t"
- "xchgl %%ebx, %1 \n\t"
- : "+a" (*eax), "+r" (*ebx), "+c" (*ecx), "+d" (*edx));
-# else
- // i386 without PIC, or x86-64. Things are easy and we can clobber any reg we want
- __asm__ __volatile__ ("cpuid \n\t"
- : "+a" (*eax), "+b" (*ebx), "+c" (*ecx), "+d" (*edx));
-# endif
- return 0;
-
-# elif defined _MSC_VER
-
- // MSVC (and icc on windows) on ia32 or x86-64
- int cpuInfo[4];
- __cpuidex(cpuInfo, level, ecxval);
- *eax = static_cast<unsigned int>(cpuInfo[0]);
- *ebx = static_cast<unsigned int>(cpuInfo[1]);
- *ecx = static_cast<unsigned int>(cpuInfo[2]);
- *edx = static_cast<unsigned int>(cpuInfo[3]);
- return 0;
-
+ if (c_architecture == Architecture::X86)
+ {
+#if defined __GNUC__ || GMX_X86_GCC_INLINE_ASM
+
+ // any compiler that understands gcc inline assembly
+ *eax = level;
+ *ecx = ecxval;
+ *ebx = 0;
+ *edx = 0;
+
+# if (defined __i386__ || defined __i386 || defined _X86_ || defined _M_IX86) && defined(__PIC__)
+ // Avoid clobbering the global offset table in 32-bit pic code (ebx register)
+ __asm__ __volatile__ ("xchgl %%ebx, %1 \n\t"
+ "cpuid \n\t"
+ "xchgl %%ebx, %1 \n\t"
+ : "+a" (*eax), "+r" (*ebx), "+c" (*ecx), "+d" (*edx));
# else
+ // i386 without PIC, or x86-64. Things are easy and we can clobber any reg we want
+ __asm__ __volatile__ ("cpuid \n\t"
+ : "+a" (*eax), "+b" (*ebx), "+c" (*ecx), "+d" (*edx));
+# endif
+ return 0;
- // We are on x86, but without compiler support for cpuid if we get here
- *eax = 0;
- *ebx = 0;
- *ecx = 0;
- *edx = 0;
- return 1;
+#elif defined _MSC_VER
-# endif // check for inline asm on x86
+ // MSVC (and icc on windows) on ia32 or x86-64
+ int cpuInfo[4];
+ __cpuidex(cpuInfo, level, ecxval);
+ *eax = static_cast<unsigned int>(cpuInfo[0]);
+ *ebx = static_cast<unsigned int>(cpuInfo[1]);
+ *ecx = static_cast<unsigned int>(cpuInfo[2]);
+ *edx = static_cast<unsigned int>(cpuInfo[3]);
+ return 0;
#else
- // We are not on x86
- *eax = 0;
- *ebx = 0;
- *ecx = 0;
- *edx = 0;
- return 1;
+ // We are on x86, but without compiler support for cpuid if we get here
+ *eax = 0;
+ *ebx = 0;
+ *ecx = 0;
+ *edx = 0;
+ return 1;
-#endif // x86
+#endif // check for inline asm on x86
+ }
+ else
+ {
+ // We are not on x86
+ *eax = 0;
+ *ebx = 0;
+ *ecx = 0;
+ *edx = 0;
+ return 1;
+ }
}
}
if (cpuInfo.count("CPU architecture"))
{
- *family = std::strtol(cpuInfo.at("CPU architecture").c_str(), NULL, 10);
+ *family = std::strtol(cpuInfo.at("CPU architecture").c_str(), nullptr, 10);
// For some 64-bit CPUs it appears to say 'AArch64' instead
if (*family == 0 && cpuInfo.at("CPU architecture").find("AArch64") != std::string::npos)
{
}
if (cpuInfo.count("CPU variant"))
{
- *model = std::strtol(cpuInfo.at("CPU variant").c_str(), NULL, 16);
+ *model = std::strtol(cpuInfo.at("CPU variant").c_str(), nullptr, 16);
}
if (cpuInfo.count("CPU revision"))
{
- *stepping = std::strtol(cpuInfo.at("CPU revision").c_str(), NULL, 10);
+ *stepping = std::strtol(cpuInfo.at("CPU revision").c_str(), nullptr, 10);
}
if (cpuInfo.count("Features"))
{
CpuInfo result;
-#if defined __i386__ || defined __i386 || defined _X86_ || defined _M_IX86 || \
- defined __x86_64__ || defined __amd64__ || defined _M_X64 || defined _M_AMD64
-
- result.vendor_ = detectX86Vendor();
- detectX86Features(&result.brandString_, &result.family_, &result.model_,
- &result.stepping_, &result.features_);
- result.logicalProcessors_ = detectX86LogicalProcessors();
-#else // not x86
-
-# if defined __arm__ || defined __arm || defined _M_ARM || defined __aarch64__
- result.vendor_ = CpuInfo::Vendor::Arm;
-# elif defined __powerpc__ || defined __ppc__ || defined __PPC__
- result.vendor_ = CpuInfo::Vendor::Ibm;
-# endif
+ if (c_architecture == Architecture::X86)
+ {
+ result.vendor_ = detectX86Vendor();
-# if defined __aarch64__ || ( defined _M_ARM && _M_ARM >= 8 )
- result.features_.insert(Feature::Arm_Neon); // ARMv8 always has Neon
- result.features_.insert(Feature::Arm_NeonAsimd); // ARMv8 always has Neon-asimd
-# endif
+ if (result.vendor_ == CpuInfo::Vendor::Intel)
+ {
+ result.features_.insert(CpuInfo::Feature::X86_Intel);
+ }
+ else if (result.vendor_ == CpuInfo::Vendor::Amd)
+ {
+ result.features_.insert(CpuInfo::Feature::X86_Amd);
+ }
+ detectX86Features(&result.brandString_, &result.family_, &result.model_,
+ &result.stepping_, &result.features_);
+ result.logicalProcessors_ = detectX86LogicalProcessors();
+ }
+ else
+ {
+ // Not x86
+ if (c_architecture == Architecture::Arm)
+ {
+ result.vendor_ = CpuInfo::Vendor::Arm;
+ }
+ else if (c_architecture == Architecture::PowerPC)
+ {
+ result.vendor_ = CpuInfo::Vendor::Ibm;
+ }
-# if defined sun
- result.vendor_ = CpuInfo::Vendor::Oracle;
-# endif
+#if defined __aarch64__ || ( defined _M_ARM && _M_ARM >= 8 )
+ result.features_.insert(Feature::Arm_Neon); // ARMv8 always has Neon
+ result.features_.insert(Feature::Arm_NeonAsimd); // ARMv8 always has Neon-asimd
+#endif
- // On Linux we might be able to find information in /proc/cpuinfo. If vendor or brand
- // is set to a known value this routine will not overwrite it.
- detectProcCpuInfo(&result.vendor_, &result.brandString_, &result.family_,
- &result.model_, &result.stepping_, &result.features_);
+#if defined sun
+ result.vendor_ = CpuInfo::Vendor::Oracle;
+#endif
-#endif // x86 or not
+ // On Linux we might be able to find information in /proc/cpuinfo. If vendor or brand
+ // is set to a known value this routine will not overwrite it.
+ detectProcCpuInfo(&result.vendor_, &result.brandString_, &result.family_,
+ &result.model_, &result.stepping_, &result.features_);
+ }
if (!result.logicalProcessors_.empty())
{
CpuInfo::s_featureStrings_ =
{
{ CpuInfo::Feature::X86_Aes, "aes" },
+ { CpuInfo::Feature::X86_Amd, "amd" },
{ CpuInfo::Feature::X86_Apic, "apic" },
{ CpuInfo::Feature::X86_Avx, "avx" },
{ CpuInfo::Feature::X86_Avx2, "avx2" },
{ CpuInfo::Feature::X86_Fma4, "fma4" },
{ CpuInfo::Feature::X86_Hle, "hle" },
{ CpuInfo::Feature::X86_Htt, "htt" },
+ { CpuInfo::Feature::X86_Intel, "intel" },
{ CpuInfo::Feature::X86_Lahf, "lahf" },
{ CpuInfo::Feature::X86_MisalignSse, "misalignsse" },
{ CpuInfo::Feature::X86_Mmx, "mmx" },
}
else if (arg == "-features")
{
+ // Separate the feature strings with spaces. Note that in the
+ // GROMACS cmake code, surrounding whitespace is first
+ // stripped by the CPU detection routine, and then added back
+ // in the code for making the SIMD suggestion.
for (auto &f : cpuInfo.featureSet() )
{
- printf(" %s", cpuInfo.featureString(f).c_str());
+ printf("%s ", cpuInfo.featureString(f).c_str());
}
- printf(" \n"); // extra space so we can grep output for " <feature> " in CMake
+ printf("\n");
}
else if (arg == "-topology")
{
enum class Feature
{
X86_Aes, //!< x86 advanced encryption standard accel.
+ X86_Amd, //!< This is an AMD x86 processor
X86_Apic, //!< APIC support
X86_Avx, //!< Advanced vector extensions
X86_Avx2, //!< AVX2 including gather support (not used yet)
X86_Fma4, //!< 4-operand FMA, only on AMD for now
X86_Hle, //!< Hardware lock elision
X86_Htt, //!< Hyper-Threading supported (but maybe not enabled)
+ X86_Intel, //!< This is an Intel x86 processor
X86_Lahf, //!< LAHF/SAHF support in 64 bits
X86_MisalignSse, //!< Support for misaligned SSE data instructions
X86_Mmx, //!< MMX registers and instructions
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "thread_mpi/threads.h"
-#include "gromacs/gmxlib/md_logging.h"
-#include "gromacs/gmxlib/network.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/cpuinfo.h"
-#include "gromacs/hardware/gpu_hw_info.h"
#include "gromacs/hardware/hardwaretopology.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/simd/support.h"
-#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/sysinfo.h"
+#include "architecture.h"
+
#ifdef HAVE_UNISTD_H
# include <unistd.h> // sysconf()
#endif
+namespace gmx
+{
+
//! Convenience macro to help us avoid ifdefs each time we use sysconf
#if !defined(_SC_NPROCESSORS_ONLN) && defined(_SC_NPROC_ONLN)
# define _SC_NPROCESSORS_ONLN _SC_NPROC_ONLN
# define _SC_NPROCESSORS_CONF _SC_NPROC_CONF
#endif
-#if defined (__i386__) || defined (__x86_64__) || defined (_M_IX86) || defined (_M_X64)
-//! Constant used to help minimize preprocessed code
-static const bool isX86 = true;
-#else
-//! Constant used to help minimize preprocessed code
-static const bool isX86 = false;
-#endif
-
-#if defined __powerpc__ || defined __ppc__ || defined __PPC__
-static const bool isPowerPC = true;
-#else
-static const bool isPowerPC = false;
-#endif
-
//! Constant used to help minimize preprocessed code
static const bool bGPUBinary = GMX_GPU != GMX_GPU_NONE;
-/* Note that some of the following arrays must match the "GPU support
- * enumeration" in src/config.h.cmakein, so that GMX_GPU looks up an
- * array entry. */
-
-/* Both CUDA and OpenCL (on the supported/tested platforms) supports
- * GPU device sharing.
- */
-static const bool gpuSharingSupport[] = { false, true, true };
-static const bool bGpuSharingSupported = gpuSharingSupport[GMX_GPU];
-
-/* Both CUDA and OpenCL (on the tested/supported platforms) supports everything.
- */
-static const bool multiGpuSupport[] = {
- false, true, true
-};
-static const bool bMultiGpuPerNodeSupported = multiGpuSupport[GMX_GPU];
-
-/* Names of the GPU detection/check results (see e_gpu_detect_res_t in hw_info.h). */
-const char * const gpu_detect_res_str[egpuNR] =
-{
- "compatible", "inexistent", "incompatible", "insane"
-};
-
-static const char * invalid_gpuid_hint =
- "A delimiter-free sequence of valid numeric IDs of available GPUs is expected.";
-
-/* The globally shared hwinfo structure. */
+//! The globally shared hwinfo structure
static gmx_hw_info_t *hwinfo_g;
-/* A reference counter for the hwinfo structure */
+//! A reference counter for the hwinfo structure
static int n_hwinfo = 0;
-/* A lock to protect the hwinfo structure */
+//! A lock to protect the hwinfo structure
static tMPI_Thread_mutex_t hw_info_lock = TMPI_THREAD_MUTEX_INITIALIZER;
-#define HOSTNAMELEN 80
-
-/* FW decl. */
-static void set_gpu_ids(gmx_gpu_opt_t *gpu_opt, int nrank, int rank);
-static int gmx_count_gpu_dev_unique(const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt);
-
-gmx_bool gmx_multiple_gpu_per_node_supported()
-{
- return bMultiGpuPerNodeSupported;
-}
-
-gmx_bool gmx_gpu_sharing_supported()
+//! Detect GPUs, if that makes sense to attempt.
+static void gmx_detect_gpus(const gmx::MDLogger &mdlog, const t_commrec *cr)
{
- return bGpuSharingSupported;
-}
-
-static void sprint_gpus(char *sbuf, const gmx_gpu_info_t *gpu_info)
-{
- int i, ndev;
- char stmp[STRLEN];
-
- ndev = gpu_info->n_dev;
-
- sbuf[0] = '\0';
- for (i = 0; i < ndev; i++)
- {
- get_gpu_device_info_string(stmp, gpu_info, i);
- strcat(sbuf, " ");
- strcat(sbuf, stmp);
- if (i < ndev - 1)
- {
- strcat(sbuf, "\n");
- }
- }
-}
-
-static void print_gpu_detection_stats(FILE *fplog,
- const gmx_gpu_info_t *gpu_info,
- const t_commrec *cr)
-{
- char onhost[HOSTNAMELEN+10], stmp[STRLEN];
- int ngpu;
-
- if (!gpu_info->bDetectGPUs)
- {
- /* We skipped the detection, so don't print detection stats */
- return;
- }
-
- ngpu = gpu_info->n_dev;
-
#if GMX_LIB_MPI
- /* We only print the detection on one, of possibly multiple, nodes */
- std::strncpy(onhost, " on host ", 10);
- gmx_gethostname(onhost + 9, HOSTNAMELEN);
-#else
- /* We detect all relevant GPUs */
- std::strncpy(onhost, "", 1);
-#endif
-
- if (ngpu > 0)
- {
- sprint_gpus(stmp, gpu_info);
- md_print_warn(cr, fplog, "%d GPU%s detected%s:\n%s\n",
- ngpu, (ngpu > 1) ? "s" : "", onhost, stmp);
- }
- else
- {
- md_print_warn(cr, fplog, "No GPUs detected%s\n", onhost);
- }
-}
-
-/*! \brief Helper function for reporting GPU usage information
- * in the mdrun log file
- *
- * \param[in] gpu_info Pointer to per-node GPU info struct
- * \param[in] gpu_opt Pointer to per-node GPU options struct
- * \param[in] numPpRanks Number of PP ranks per node
- * \param[in] bPrintHostName Print the hostname in the usage information
- * \return String to write to the log file
- * \throws std::bad_alloc if out of memory */
-static std::string
-makeGpuUsageReport(const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt,
- size_t numPpRanks,
- bool bPrintHostName)
-{
- int ngpu_use = gpu_opt->n_dev_use;
- int ngpu_comp = gpu_info->n_dev_compatible;
- char host[HOSTNAMELEN];
-
- if (bPrintHostName)
- {
- gmx_gethostname(host, HOSTNAMELEN);
- }
-
- /* Issue a note if GPUs are available but not used */
- if (ngpu_comp > 0 && ngpu_use < 1)
- {
- return gmx::formatString("%d compatible GPU%s detected in the system, but none will be used.\n"
- "Consider trying GPU acceleration with the Verlet scheme!\n",
- ngpu_comp, (ngpu_comp > 1) ? "s" : "");
- }
-
- std::string output;
- if (!gpu_opt->bUserSet)
- {
- // gpu_opt->dev_compatible is only populated during auto-selection
- std::string gpuIdsString =
- formatAndJoin(gmx::constArrayRefFromArray(gpu_opt->dev_compatible,
- gpu_opt->n_dev_compatible),
- ",", gmx::StringFormatter("%d"));
- bool bPluralGpus = gpu_opt->n_dev_compatible > 1;
-
- if (bPrintHostName)
- {
- output += gmx::formatString("On host %s ", host);
- }
- output += gmx::formatString("%d compatible GPU%s %s present, with ID%s %s\n",
- gpu_opt->n_dev_compatible,
- bPluralGpus ? "s" : "",
- bPluralGpus ? "are" : "is",
- bPluralGpus ? "s" : "",
- gpuIdsString.c_str());
- }
-
- {
- std::vector<int> gpuIdsInUse;
- for (int i = 0; i < ngpu_use; i++)
- {
- gpuIdsInUse.push_back(get_gpu_device_id(gpu_info, gpu_opt, i));
- }
- std::string gpuIdsString =
- formatAndJoin(gpuIdsInUse, ",", gmx::StringFormatter("%d"));
- int numGpusInUse = gmx_count_gpu_dev_unique(gpu_info, gpu_opt);
- bool bPluralGpus = numGpusInUse > 1;
-
- if (bPrintHostName)
- {
- output += gmx::formatString("On host %s ", host);
- }
- output += gmx::formatString("%d GPU%s %sselected for this run.\n"
- "Mapping of GPU ID%s to the %d PP rank%s in this node: %s\n",
- numGpusInUse, bPluralGpus ? "s" : "",
- gpu_opt->bUserSet ? "user-" : "auto-",
- bPluralGpus ? "s" : "",
- numPpRanks,
- (numPpRanks > 1) ? "s" : "",
- gpuIdsString.c_str());
- }
-
- return output;
-}
-
-/* Give a suitable fatal error or warning if the build configuration
- and runtime CPU do not match. */
-static void
-check_use_of_rdtscp_on_this_cpu(FILE *fplog,
- const t_commrec *cr,
- const gmx::CpuInfo &cpuInfo)
-{
-#ifdef HAVE_RDTSCP
- bool binaryUsesRdtscp = TRUE;
-#else
- bool binaryUsesRdtscp = FALSE;
+ int rank_world;
+ MPI_Comm physicalnode_comm;
#endif
+ int rank_local;
- const char *programName = gmx::getProgramContext().displayName();
-
- if (cpuInfo.supportLevel() < gmx::CpuInfo::SupportLevel::Features)
- {
- if (binaryUsesRdtscp)
- {
- md_print_warn(cr, fplog, "The %s executable was compiled to use the rdtscp CPU instruction. "
- "We cannot detect the features of your current CPU, but will proceed anyway. "
- "If you get a crash, rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option.",
- programName);
- }
- }
- else
- {
- bool cpuHasRdtscp = cpuInfo.feature(gmx::CpuInfo::Feature::X86_Rdtscp);
-
- if (!cpuHasRdtscp && binaryUsesRdtscp)
- {
- gmx_fatal(FARGS, "The %s executable was compiled to use the rdtscp CPU instruction. "
- "However, this is not supported by the current hardware and continuing would lead to a crash. "
- "Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option.",
- programName);
- }
-
- if (cpuHasRdtscp && !binaryUsesRdtscp)
- {
- md_print_warn(cr, fplog, "The current CPU can measure timings more accurately than the code in\n"
- "%s was configured to use. This might affect your simulation\n"
- "speed as accurate timings are needed for load-balancing.\n"
- "Please consider rebuilding %s with the GMX_USE_RDTSCP=ON CMake option.\n",
- programName, programName);
- }
- }
-}
-
-void gmx_check_hw_runconf_consistency(FILE *fplog,
- const gmx_hw_info_t *hwinfo,
- const t_commrec *cr,
- const gmx_hw_opt_t *hw_opt,
- gmx_bool bUseGPU)
-{
- int npppn;
- char th_or_proc[STRLEN], th_or_proc_plural[STRLEN], pernode[STRLEN];
- gmx_bool btMPI, bMPI, bNthreadsAuto, bEmulateGPU;
-
- GMX_RELEASE_ASSERT(hwinfo, "hwinfo must be a non-NULL pointer");
- GMX_RELEASE_ASSERT(cr, "cr must be a non-NULL pointer");
-
- /* Below we only do consistency checks for PP and GPUs,
- * this is irrelevant for PME only nodes, so in that case we return
- * here.
- */
- if (!(cr->duty & DUTY_PP))
+ hwinfo_g->gpu_info.bDetectGPUs =
+ (bGPUBinary && getenv("GMX_DISABLE_GPU_DETECTION") == nullptr);
+ if (!hwinfo_g->gpu_info.bDetectGPUs)
{
return;
}
-#if GMX_THREAD_MPI
- bMPI = FALSE;
- btMPI = TRUE;
- bNthreadsAuto = (hw_opt->nthreads_tmpi < 1);
-#elif GMX_LIB_MPI
- bMPI = TRUE;
- btMPI = FALSE;
- bNthreadsAuto = FALSE;
-#else
- bMPI = FALSE;
- btMPI = FALSE;
- bNthreadsAuto = FALSE;
-#endif
-
- /* GPU emulation detection is done later, but we need here as well
- * -- uncool, but there's no elegant workaround */
- bEmulateGPU = (getenv("GMX_EMULATE_GPU") != NULL);
-
- if (hwinfo->gpu_info.n_dev_compatible > 0)
- {
- std::string gpuUseageReport;
- try
- {
- gpuUseageReport = makeGpuUsageReport(&hwinfo->gpu_info,
- &hw_opt->gpu_opt,
- cr->nrank_pp_intranode,
- bMPI && cr->nnodes > 1);
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-
- /* NOTE: this print is only for and on one physical node */
- md_print_info(cr, fplog, "%s\n", gpuUseageReport.c_str());
- }
-
- /* Need to ensure that we have enough GPUs:
- * - need one GPU per PP node
- * - no GPU oversubscription with tMPI
- * */
- /* number of PP processes per node */
- npppn = cr->nrank_pp_intranode;
-
- pernode[0] = '\0';
- th_or_proc_plural[0] = '\0';
- if (btMPI)
- {
- sprintf(th_or_proc, "thread-MPI thread");
- if (npppn > 1)
- {
- sprintf(th_or_proc_plural, "s");
- }
- }
- else if (bMPI)
- {
- sprintf(th_or_proc, "MPI process");
- if (npppn > 1)
- {
- sprintf(th_or_proc_plural, "es");
- }
- sprintf(pernode, " per node");
- }
- else
- {
- /* neither MPI nor tMPI */
- sprintf(th_or_proc, "process");
- }
-
- if (bUseGPU && hwinfo->gpu_info.n_dev_compatible > 0 &&
- !bEmulateGPU)
- {
- int ngpu_comp, ngpu_use;
- char gpu_comp_plural[2], gpu_use_plural[2];
-
- ngpu_comp = hwinfo->gpu_info.n_dev_compatible;
- ngpu_use = hw_opt->gpu_opt.n_dev_use;
-
- sprintf(gpu_comp_plural, "%s", (ngpu_comp > 1) ? "s" : "");
- sprintf(gpu_use_plural, "%s", (ngpu_use > 1) ? "s" : "");
-
- const char *programName = gmx::getProgramContext().displayName();
-
- /* number of tMPI threads auto-adjusted */
- if (btMPI && bNthreadsAuto)
- {
- if (hw_opt->gpu_opt.bUserSet && npppn < ngpu_use)
- {
- /* The user manually provided more GPUs than threads we
- could automatically start. */
- gmx_fatal(FARGS,
- "%d GPU%s provided, but only %d PP thread-MPI thread%s coud be started.\n"
- "%s requires one PP tread-MPI thread per GPU; use fewer GPUs.",
- ngpu_use, gpu_use_plural,
- npppn, th_or_proc_plural,
- programName);
- }
-
- if (!hw_opt->gpu_opt.bUserSet && npppn < ngpu_comp)
- {
- /* There are more GPUs than tMPI threads; we have
- limited the number GPUs used. */
- md_print_warn(cr, fplog,
- "NOTE: %d GPU%s were detected, but only %d PP thread-MPI thread%s can be started.\n"
- " %s can use one GPU per PP tread-MPI thread, so only %d GPU%s will be used.\n",
- ngpu_comp, gpu_comp_plural,
- npppn, th_or_proc_plural,
- programName, npppn,
- npppn > 1 ? "s" : "");
- }
- }
-
- if (hw_opt->gpu_opt.bUserSet)
- {
- if (ngpu_use != npppn)
- {
- gmx_fatal(FARGS,
- "Incorrect launch configuration: mismatching number of PP %s%s and GPUs%s.\n"
- "%s was started with %d PP %s%s%s, but you provided %d GPU%s.",
- th_or_proc, btMPI ? "s" : "es", pernode,
- programName, npppn, th_or_proc,
- th_or_proc_plural, pernode,
- ngpu_use, gpu_use_plural);
- }
- }
- else
- {
- /* TODO Should we have a gpu_opt->n_dev_supported field? */
- if (ngpu_comp > npppn && gmx_multiple_gpu_per_node_supported())
- {
- md_print_warn(cr, fplog,
- "NOTE: potentially sub-optimal launch configuration, %s started with less\n"
- " PP %s%s%s than GPU%s available.\n"
- " Each PP %s can use only one GPU, %d GPU%s%s will be used.\n",
- programName, th_or_proc,
- th_or_proc_plural, pernode, gpu_comp_plural,
- th_or_proc, npppn, gpu_use_plural, pernode);
- }
-
- if (ngpu_use != npppn)
- {
- /* Avoid duplicate error messages.
- * Unfortunately we can only do this at the physical node
- * level, since the hardware setup and MPI process count
- * might differ between physical nodes.
- */
- if (cr->rank_pp_intranode == 0)
- {
- std::string reasonForLimit;
- if (ngpu_comp > 1 &&
- ngpu_use == 1 &&
- !gmx_multiple_gpu_per_node_supported())
- {
- reasonForLimit = "can be used by ";
- reasonForLimit += getGpuImplementationString();
- reasonForLimit += " in GROMACS";
- }
- else
- {
- reasonForLimit = "was detected";
- }
- gmx_fatal(FARGS,
- "Incorrect launch configuration: mismatching number of PP %s%s and GPUs%s.\n"
- "%s was started with %d PP %s%s%s, but only %d GPU%s %s.",
- th_or_proc, btMPI ? "s" : "es", pernode,
- programName, npppn, th_or_proc,
- th_or_proc_plural, pernode,
- ngpu_use, gpu_use_plural, reasonForLimit.c_str());
- }
- }
- }
-
- {
- int same_count;
-
- same_count = gmx_count_gpu_dev_shared(&hw_opt->gpu_opt);
-
- if (same_count > 0)
- {
- md_print_info(cr, fplog,
- "NOTE: You assigned %s to multiple %s%s.\n",
- same_count > 1 ? "GPUs" : "a GPU", th_or_proc, btMPI ? "s" : "es");
- }
- }
- }
-
-#if GMX_MPI
- if (PAR(cr))
- {
- /* Avoid other ranks to continue after
- inconsistency */
- MPI_Barrier(cr->mpi_comm_mygroup);
- }
-#endif
-
-}
-
-/* Return 0 if none of the GPU (per node) are shared among PP ranks.
- *
- * Sharing GPUs among multiple PP ranks is possible when the user passes
- * GPU IDs. Here we check for sharing and return a non-zero value when
- * this is detected. Note that the return value represents the number of
- * PP rank pairs that share a device.
- */
-int gmx_count_gpu_dev_shared(const gmx_gpu_opt_t *gpu_opt)
-{
- int same_count = 0;
- int ngpu = gpu_opt->n_dev_use;
-
- if (gpu_opt->bUserSet)
- {
- int i, j;
-
- for (i = 0; i < ngpu - 1; i++)
- {
- for (j = i + 1; j < ngpu; j++)
- {
- same_count += (gpu_opt->dev_use[i] ==
- gpu_opt->dev_use[j]);
- }
- }
- }
-
- return same_count;
-}
-
-/* Count and return the number of unique GPUs (per node) selected.
- *
- * As sharing GPUs among multiple PP ranks is possible when the user passes
- * GPU IDs, the number of GPUs user (per node) can be different from the
- * number of GPU IDs selected.
- */
-static int gmx_count_gpu_dev_unique(const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt)
-{
- int i, uniq_count, ngpu;
- int *uniq_ids;
-
- GMX_RELEASE_ASSERT(gpu_info, "gpu_info must be a non-NULL pointer");
- GMX_RELEASE_ASSERT(gpu_opt, "gpu_opt must be a non-NULL pointer");
-
- ngpu = gpu_info->n_dev;
-
- uniq_count = 0;
-
- snew(uniq_ids, ngpu);
-
- /* Each element in uniq_ids will be set to 0 or 1. The n-th element set
- * to 1 indicates that the respective GPU was selected to be used. */
- for (i = 0; i < gpu_opt->n_dev_use; i++)
- {
- int device_id;
-
- device_id = gmx_gpu_sharing_supported() ? get_gpu_device_id(gpu_info, gpu_opt, i) : i;
- uniq_ids[device_id] = 1;
- }
- /* Count the devices used. */
- for (i = 0; i < ngpu; i++)
- {
- uniq_count += uniq_ids[i];
- }
-
- sfree(uniq_ids);
-
- return uniq_count;
-}
-
-static void gmx_detect_gpus(FILE *fplog, const t_commrec *cr)
-{
-#if GMX_LIB_MPI
- int rank_world;
- MPI_Comm physicalnode_comm;
-#endif
- int rank_local;
-
/* Under certain circumstances MPI ranks on the same physical node
* can not simultaneously access the same GPU(s). Therefore we run
* the detection only on one MPI rank per node and broadcast the info.
MPI_Comm_split(MPI_COMM_WORLD, gmx_physicalnode_id_hash(),
rank_world, &physicalnode_comm);
MPI_Comm_rank(physicalnode_comm, &rank_local);
+ GMX_UNUSED_VALUE(cr);
#else
/* Here there should be only one process, check this */
GMX_RELEASE_ASSERT(cr->nnodes == 1 && cr->sim_nodeid == 0, "Only a single (master) process should execute here");
{
sprintf(sbuf, ".");
}
- md_print_warn(cr, fplog,
- "NOTE: Error occurred during GPU detection%s"
- " Can not use GPU acceleration, will fall back to CPU kernels.\n",
- sbuf);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: Error occurred during GPU detection%s"
+ " Can not use GPU acceleration, will fall back to CPU kernels.",
+ sbuf);
}
}
#endif
}
+//! Reduce the locally collected \p hwinfo_g over MPI ranks
static void gmx_collect_hardware_mpi(const gmx::CpuInfo &cpuInfo)
{
const int ncore = hwinfo_g->hardwareTopology->numberOfCores();
* the GPUs affects the hash. Also two identical GPUs won't give
* a gpu_hash of zero after XORing.
*/
- get_gpu_device_info_string(stmp, &hwinfo_g->gpu_info, i);
+ get_gpu_device_info_string(stmp, hwinfo_g->gpu_info, i);
gpu_hash ^= gmx_string_fullhash_func(stmp, gmx_string_hash_init);
}
spinUpCore() noexcept
{
#if defined(HAVE_SYSCONF) && defined(_SC_NPROCESSORS_CONF) && defined(_SC_NPROCESSORS_ONLN)
- // steady_clock is better than system_clock, but unsupported in gcc-4.6.4.
- // For release-2017 we can retire gcc-4.6 support and move to steady_clock.
float dummy = 0.1;
int countConfigured = sysconf(_SC_NPROCESSORS_CONF); // noexcept
- auto start = std::chrono::system_clock::now(); // noexcept
+ auto start = std::chrono::steady_clock::now(); // noexcept
while (sysconf(_SC_NPROCESSORS_ONLN) < countConfigured &&
- std::chrono::system_clock::now() - start < std::chrono::seconds(2))
+ std::chrono::steady_clock::now() - start < std::chrono::seconds(2))
{
for (int i = 1; i < 10000; i++)
{
(defined(THREAD_PTHREADS) || defined(THREAD_WINDOWS))
// Modify this conditional when/if x86 or PowerPC starts to sleep some cores
- if (!isX86 && !isPowerPC)
+ if (c_architecture != Architecture::X86 &&
+ c_architecture != Architecture::PowerPC)
{
int countConfigured = sysconf(_SC_NPROCESSORS_CONF);
std::vector<std::thread> workThreads(countConfigured);
#endif
}
-/*! \brief Sanity check hardware topology and optionally print some notes to log
+/*! \brief Sanity check hardware topology and print some notes to log
*
- * \param fplog Log file pointer. This can be NULL, but the then routine
- * will not do anything.
+ * \param mdlog Logger.
* \param hardwareTopology Reference to hardwareTopology object.
*/
static void
-hardwareTopologyDoubleCheckDetection(FILE gmx_unused *fplog,
- const gmx::HardwareTopology gmx_unused &hardwareTopology)
+hardwareTopologyDoubleCheckDetection(const gmx::MDLogger gmx_unused &mdlog,
+ const gmx::HardwareTopology gmx_unused &hardwareTopology)
{
#if defined HAVE_SYSCONF && defined(_SC_NPROCESSORS_CONF)
- if (fplog == NULL ||
- hardwareTopology.supportLevel() < gmx::HardwareTopology::SupportLevel::LogicalProcessorCount)
+ if (hardwareTopology.supportLevel() < gmx::HardwareTopology::SupportLevel::LogicalProcessorCount)
{
return;
}
*/
if (countConfigured >= 0 && countConfigured != countFromDetection)
{
- fprintf(fplog, "Note: %d CPUs configured, but only %d were detected to be online.\n", countConfigured, countFromDetection);
+ GMX_LOG(mdlog.info).
+ appendTextFormatted("Note: %d CPUs configured, but only %d were detected to be online.\n", countConfigured, countFromDetection);
- if (isX86 && countConfigured == 2*countFromDetection)
+ if (c_architecture == Architecture::X86 &&
+ countConfigured == 2*countFromDetection)
{
- fprintf(fplog, " X86 Hyperthreading is likely disabled; enable it for better performance.\n");
+ GMX_LOG(mdlog.info).
+ appendText(" X86 Hyperthreading is likely disabled; enable it for better performance.");
}
// For PowerPC (likely Power8) it is possible to set SMT to either 2,4, or 8-way hardware threads.
// We only warn if it is completely disabled since default performance drops with SMT8.
- if (isPowerPC && countConfigured == 8*countFromDetection)
+ if (c_architecture == Architecture::PowerPC &&
+ countConfigured == 8*countFromDetection)
{
- fprintf(fplog, " PowerPC SMT is likely disabled; enable SMT2/SMT4 for better performance.\n");
+ GMX_LOG(mdlog.info).
+ appendText(" PowerPC SMT is likely disabled; enable SMT2/SMT4 for better performance.");
}
}
#endif
}
-gmx_hw_info_t *gmx_detect_hardware(FILE *fplog, const t_commrec *cr,
- gmx_bool bDetectGPUs)
+gmx_hw_info_t *gmx_detect_hardware(const gmx::MDLogger &mdlog, const t_commrec *cr)
{
int ret;
// If we detected the topology on this system, double-check that it makes sense
if (hwinfo_g->hardwareTopology->isThisSystem())
{
- hardwareTopologyDoubleCheckDetection(fplog, *(hwinfo_g->hardwareTopology));
+ hardwareTopologyDoubleCheckDetection(mdlog, *(hwinfo_g->hardwareTopology));
}
// TODO: Get rid of this altogether.
/* detect GPUs */
hwinfo_g->gpu_info.n_dev = 0;
hwinfo_g->gpu_info.n_dev_compatible = 0;
- hwinfo_g->gpu_info.gpu_dev = NULL;
-
- /* Run the detection if the binary was compiled with GPU support
- * and we requested detection.
- */
- hwinfo_g->gpu_info.bDetectGPUs =
- (bGPUBinary && bDetectGPUs &&
- getenv("GMX_DISABLE_GPU_DETECTION") == NULL);
- if (hwinfo_g->gpu_info.bDetectGPUs)
- {
- gmx_detect_gpus(fplog, cr);
- }
+ hwinfo_g->gpu_info.gpu_dev = nullptr;
+ gmx_detect_gpus(mdlog, cr);
gmx_collect_hardware_mpi(*hwinfo_g->cpuInfo);
}
/* increase the reference counter */
return hwinfo_g;
}
-static std::string detected_hardware_string(const gmx_hw_info_t *hwinfo,
- bool bFullCpuInfo)
-{
- std::string s;
-
- const gmx::CpuInfo &cpuInfo = *hwinfo_g->cpuInfo;
- const gmx::HardwareTopology &hwTop = *hwinfo->hardwareTopology;
-
- s = gmx::formatString("\n");
- s += gmx::formatString("Running on %d node%s with total",
- hwinfo->nphysicalnode,
- hwinfo->nphysicalnode == 1 ? "" : "s");
- if (hwinfo->ncore_tot > 0)
- {
- s += gmx::formatString(" %d cores,", hwinfo->ncore_tot);
- }
- s += gmx::formatString(" %d logical cores", hwinfo->nhwthread_tot);
- if (hwinfo->gpu_info.bDetectGPUs)
- {
- s += gmx::formatString(", %d compatible GPU%s",
- hwinfo->ngpu_compatible_tot,
- hwinfo->ngpu_compatible_tot == 1 ? "" : "s");
- }
- else if (bGPUBinary)
- {
- s += gmx::formatString(" (GPU detection deactivated)");
- }
- s += gmx::formatString("\n");
-
- if (hwinfo->nphysicalnode > 1)
- {
- /* Print per node hardware feature counts */
- if (hwinfo->ncore_max > 0)
- {
- s += gmx::formatString(" Cores per node: %2d", hwinfo->ncore_min);
- if (hwinfo->ncore_max > hwinfo->ncore_min)
- {
- s += gmx::formatString(" - %2d", hwinfo->ncore_max);
- }
- s += gmx::formatString("\n");
- }
- s += gmx::formatString(" Logical cores per node: %2d", hwinfo->nhwthread_min);
- if (hwinfo->nhwthread_max > hwinfo->nhwthread_min)
- {
- s += gmx::formatString(" - %2d", hwinfo->nhwthread_max);
- }
- s += gmx::formatString("\n");
- if (bGPUBinary)
- {
- s += gmx::formatString(" Compatible GPUs per node: %2d",
- hwinfo->ngpu_compatible_min);
- if (hwinfo->ngpu_compatible_max > hwinfo->ngpu_compatible_min)
- {
- s += gmx::formatString(" - %2d", hwinfo->ngpu_compatible_max);
- }
- s += gmx::formatString("\n");
- if (hwinfo->ngpu_compatible_tot > 0)
- {
- if (hwinfo->bIdenticalGPUs)
- {
- s += gmx::formatString(" All nodes have identical type(s) of GPUs\n");
- }
- else
- {
- /* This message will also appear with identical GPU types
- * when at least one node has no GPU.
- */
- s += gmx::formatString(" Different nodes have different type(s) and/or order of GPUs\n");
- }
- }
- }
- }
-
-#if GMX_LIB_MPI
- char host[HOSTNAMELEN];
- int rank;
-
- gmx_gethostname(host, HOSTNAMELEN);
- MPI_Comm_rank(MPI_COMM_WORLD, &rank);
-
- s += gmx::formatString("Hardware detected on host %s (the node of MPI rank %d):\n",
- host, rank);
-#else
- s += gmx::formatString("Hardware detected:\n");
-#endif
- s += gmx::formatString(" CPU info:\n");
-
- s += gmx::formatString(" Vendor: %s\n", cpuInfo.vendorString().c_str());
-
- s += gmx::formatString(" Brand: %s\n", cpuInfo.brandString().c_str());
-
- if (bFullCpuInfo)
- {
- s += gmx::formatString(" Family: %d Model: %d Stepping: %d\n",
- cpuInfo.family(), cpuInfo.model(), cpuInfo.stepping());
-
- s += gmx::formatString(" Features:");
- for (auto &f : cpuInfo.featureSet())
- {
- s += gmx::formatString(" %s", cpuInfo.featureString(f).c_str());;
- }
- s += gmx::formatString("\n");
- }
-
- s += gmx::formatString(" SIMD instructions most likely to fit this hardware: %s",
- gmx::simdString(static_cast<gmx::SimdType>(hwinfo->simd_suggest_min)).c_str());
-
- if (hwinfo->simd_suggest_max > hwinfo->simd_suggest_min)
- {
- s += gmx::formatString(" - %s", gmx::simdString(static_cast<gmx::SimdType>(hwinfo->simd_suggest_max)).c_str());
- }
- s += gmx::formatString("\n");
-
- s += gmx::formatString(" SIMD instructions selected at GROMACS compile time: %s\n",
- gmx::simdString(gmx::simdCompiled()).c_str());
-
- s += gmx::formatString("\n");
-
- s += gmx::formatString(" Hardware topology: ");
- switch (hwTop.supportLevel())
- {
- case gmx::HardwareTopology::SupportLevel::None:
- s += gmx::formatString("None\n");
- break;
- case gmx::HardwareTopology::SupportLevel::LogicalProcessorCount:
- s += gmx::formatString("Only logical processor count\n");
- break;
- case gmx::HardwareTopology::SupportLevel::Basic:
- s += gmx::formatString("Basic\n");
- break;
- case gmx::HardwareTopology::SupportLevel::Full:
- s += gmx::formatString("Full\n");
- break;
- case gmx::HardwareTopology::SupportLevel::FullWithDevices:
- s += gmx::formatString("Full, with devices\n");
- break;
- }
-
- if (!hwTop.isThisSystem())
- {
- s += gmx::formatString(" NOTE: Hardware topology cached or synthetic, not detected.\n");
- if (char *p = getenv("HWLOC_XMLFILE"))
- {
- s += gmx::formatString(" HWLOC_XMLFILE=%s\n", p);
- }
- }
-
- if (bFullCpuInfo)
- {
- if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::Basic)
- {
- s += gmx::formatString(" Sockets, cores, and logical processors:\n");
-
- for (auto &socket : hwTop.machine().sockets)
- {
- s += gmx::formatString(" Socket %2d:", socket.id);
- for (auto &c : socket.cores)
- {
- s += gmx::formatString(" [");
- for (auto &t : c.hwThreads)
- {
- s += gmx::formatString(" %3d", t.logicalProcessorId);
- }
- s += gmx::formatString("]");
- }
- s += gmx::formatString("\n");
- }
- }
- if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::Full)
- {
- s += gmx::formatString(" Numa nodes:\n");
- for (auto &n : hwTop.machine().numa.nodes)
- {
- s += gmx::formatString(" Node %2d (%" GMX_PRIu64 " bytes mem):", n.id, n.memory);
- for (auto &l : n.logicalProcessorId)
- {
- s += gmx::formatString(" %3d", l);
- }
- s += gmx::formatString("\n");
- }
- s += gmx::formatString(" Latency:\n ");
- for (std::size_t j = 0; j < hwTop.machine().numa.nodes.size(); j++)
- {
- s += gmx::formatString(" %5d", j);
- }
- s += gmx::formatString("\n");
- for (std::size_t i = 0; i < hwTop.machine().numa.nodes.size(); i++)
- {
- s += gmx::formatString(" %5d", i);
- for (std::size_t j = 0; j < hwTop.machine().numa.nodes.size(); j++)
- {
- s += gmx::formatString(" %5.2f", hwTop.machine().numa.relativeLatency[i][j]);
- }
- s += gmx::formatString("\n");
- }
-
-
- s += gmx::formatString(" Caches:\n");
- for (auto &c : hwTop.machine().caches)
- {
- s += gmx::formatString(" L%d: %" GMX_PRIu64 " bytes, linesize %d bytes, assoc. %d, shared %d ways\n",
- c.level, c.size, c.linesize, c.associativity, c.shared);
- }
- }
- if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::FullWithDevices)
- {
- s += gmx::formatString(" PCI devices:\n");
- for (auto &d : hwTop.machine().devices)
- {
- s += gmx::formatString(" %04x:%02x:%02x.%1x Id: %04x:%04x Class: 0x%04x Numa: %d\n",
- d.domain, d.bus, d.dev, d.func, d.vendorId, d.deviceId, d.classId, d.numaNodeId);
- }
- }
- }
-
- if (bGPUBinary && (hwinfo->ngpu_compatible_tot > 0 ||
- hwinfo->gpu_info.n_dev > 0))
- {
- s += gmx::formatString(" GPU info:\n");
- s += gmx::formatString(" Number of GPUs detected: %d\n",
- hwinfo->gpu_info.n_dev);
- if (hwinfo->gpu_info.n_dev > 0)
- {
- char buf[STRLEN];
-
- sprint_gpus(buf, &hwinfo->gpu_info);
- s += gmx::formatString("%s\n", buf);
- }
- }
- return s;
-}
-
-void gmx_print_detected_hardware(FILE *fplog, const t_commrec *cr,
- const gmx_hw_info_t *hwinfo)
-{
- const gmx::CpuInfo &cpuInfo = *hwinfo_g->cpuInfo;
-
- if (fplog != NULL)
- {
- std::string detected;
-
- detected = detected_hardware_string(hwinfo, TRUE);
-
- fprintf(fplog, "%s\n", detected.c_str());
- }
-
- if (MULTIMASTER(cr))
- {
- std::string detected;
-
- detected = detected_hardware_string(hwinfo, FALSE);
-
- fprintf(stderr, "%s\n", detected.c_str());
- }
-
- /* Check the compiled SIMD instruction set against that of the node
- * with the lowest SIMD level support (skip if SIMD detection did not work)
- */
- if (cpuInfo.supportLevel() >= gmx::CpuInfo::SupportLevel::Features)
- {
- gmx::simdCheck(static_cast<gmx::SimdType>(hwinfo->simd_suggest_min), fplog, MULTIMASTER(cr));
- }
-
- /* For RDTSCP we only check on our local node and skip the MPI reduction */
- check_use_of_rdtscp_on_this_cpu(fplog, cr, cpuInfo);
-}
-
-//! \brief Return if any GPU ID (e.g in a user-supplied string) is repeated
-static gmx_bool anyGpuIdIsRepeated(const gmx_gpu_opt_t *gpu_opt)
+bool compatibleGpusFound(const gmx_gpu_info_t &gpu_info)
{
- /* Loop over IDs in the string */
- for (int i = 0; i < gpu_opt->n_dev_use - 1; ++i)
- {
- /* Look for the ID in location i in the following part of the
- string */
- for (int j = i + 1; j < gpu_opt->n_dev_use; ++j)
- {
- if (gpu_opt->dev_use[i] == gpu_opt->dev_use[j])
- {
- /* Same ID found in locations i and j */
- return TRUE;
- }
- }
- }
-
- return FALSE;
-}
-
-void gmx_parse_gpu_ids(gmx_gpu_opt_t *gpu_opt)
-{
- char *env;
-
- if (gpu_opt->gpu_id != NULL && !bGPUBinary)
- {
- gmx_fatal(FARGS, "GPU ID string set, but %s was compiled without GPU support!",
- gmx::getProgramContext().displayName());
- }
-
- env = getenv("GMX_GPU_ID");
- if (env != NULL && gpu_opt->gpu_id != NULL)
- {
- gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
- }
- if (env == NULL)
- {
- env = gpu_opt->gpu_id;
- }
-
- /* parse GPU IDs if the user passed any */
- if (env != NULL)
- {
- /* Parse a "plain" or comma-separated GPU ID string which contains a
- * sequence of digits corresponding to GPU IDs; the order will
- * indicate the process/tMPI thread - GPU assignment. */
- parse_digits_from_string(env, &gpu_opt->n_dev_use, &gpu_opt->dev_use);
-
- if (!gmx_multiple_gpu_per_node_supported() && 1 < gpu_opt->n_dev_use)
- {
- gmx_fatal(FARGS, "The %s implementation only supports using exactly one PP rank per node", getGpuImplementationString());
- }
- if (!gmx_gpu_sharing_supported() && anyGpuIdIsRepeated(gpu_opt))
- {
- gmx_fatal(FARGS, "The %s implementation only supports using exactly one PP rank per GPU", getGpuImplementationString());
- }
- if (gpu_opt->n_dev_use == 0)
- {
- gmx_fatal(FARGS, "Empty GPU ID string encountered.\n%s\n",
- invalid_gpuid_hint);
- }
-
- gpu_opt->bUserSet = TRUE;
- }
-}
-
-void gmx_select_gpu_ids(FILE *fplog, const t_commrec *cr,
- const gmx_gpu_info_t *gpu_info,
- gmx_bool bForceUseGPU,
- gmx_gpu_opt_t *gpu_opt)
-{
- int i;
- char sbuf[STRLEN], stmp[STRLEN];
-
- /* Bail if binary is not compiled with GPU acceleration, but this is either
- * explicitly (-nb gpu) or implicitly (gpu ID passed) requested. */
- if (bForceUseGPU && !bGPUBinary)
- {
- gmx_fatal(FARGS, "GPU acceleration requested, but %s was compiled without GPU support!",
- gmx::getProgramContext().displayName());
- }
-
- if (!(cr->duty & DUTY_PP))
- {
- /* Our rank is not doing PP, we don't use a GPU */
- return;
- }
-
- if (gpu_opt->bUserSet)
- {
- /* Check the GPU IDs passed by the user.
- * (GPU IDs have been parsed by gmx_parse_gpu_ids before)
- */
- int *checkres;
- int res;
-
- snew(checkres, gpu_opt->n_dev_use);
-
- res = check_selected_gpus(checkres, gpu_info, gpu_opt);
-
- if (!res)
- {
- print_gpu_detection_stats(fplog, gpu_info, cr);
-
- sprintf(sbuf, "Some of the requested GPUs do not exist, behave strangely, or are not compatible:\n");
- for (i = 0; i < gpu_opt->n_dev_use; i++)
- {
- if (checkres[i] != egpuCompatible)
- {
- sprintf(stmp, " GPU #%d: %s\n",
- gpu_opt->dev_use[i],
- gpu_detect_res_str[checkres[i]]);
- strcat(sbuf, stmp);
- }
- }
- gmx_fatal(FARGS, "%s", sbuf);
- }
-
- sfree(checkres);
- }
- else if (getenv("GMX_EMULATE_GPU") == NULL)
- {
- pick_compatible_gpus(&hwinfo_g->gpu_info, gpu_opt);
- set_gpu_ids(gpu_opt, cr->nrank_pp_intranode, cr->rank_pp_intranode);
- }
-
- /* If the user asked for a GPU, check whether we have a GPU */
- if (bForceUseGPU && gpu_info->n_dev_compatible == 0)
- {
- gmx_fatal(FARGS, "GPU acceleration requested, but no compatible GPUs were detected.");
- }
-}
-
-/* Select the GPUs we will use. This is an operation local to each physical
- * node. If we have less MPI ranks than GPUs, we will waste some GPUs.
- * nrank and rank are the rank count and id for PP processes in our node.
- */
-static void set_gpu_ids(gmx_gpu_opt_t *gpu_opt, int nrank, int rank)
-{
- GMX_RELEASE_ASSERT(gpu_opt, "Invalid gpu_opt pointer passed");
- GMX_RELEASE_ASSERT(nrank >= 1,
- gmx::formatString("Invalid limit (%d) for the number of GPUs (detected %d compatible GPUs)",
- rank, gpu_opt->n_dev_compatible).c_str());
-
- if (gpu_opt->n_dev_compatible == 0)
- {
- char host[HOSTNAMELEN];
-
- gmx_gethostname(host, HOSTNAMELEN);
- gmx_fatal(FARGS, "A GPU was requested on host %s, but no compatible GPUs were detected. All nodes with PP ranks need to have GPUs. If you intended to use GPU acceleration in a parallel run, you can either avoid using the nodes that don't have GPUs or place PME ranks on these nodes.", host);
- }
-
- int nshare;
-
- nshare = 1;
- if (nrank > gpu_opt->n_dev_compatible)
- {
- if (nrank % gpu_opt->n_dev_compatible == 0)
- {
- nshare = gmx_gpu_sharing_supported() ? nrank/gpu_opt->n_dev_compatible : 1;
- }
- else
- {
- if (rank == 0)
- {
- gmx_fatal(FARGS, "The number of MPI ranks (%d) in a physical node is not a multiple of the number of GPUs (%d). Select a different number of MPI ranks or use the -gpu_id option to manually specify the GPU to be used.",
- nrank, gpu_opt->n_dev_compatible);
- }
-
-#if GMX_MPI
- /* We use a global barrier to prevent ranks from continuing with
- * an invalid setup.
- */
- MPI_Barrier(MPI_COMM_WORLD);
-#endif
- }
- }
-
- /* Here we will waste GPUs when nrank < gpu_opt->n_dev_compatible */
- gpu_opt->n_dev_use = std::min(gpu_opt->n_dev_compatible*nshare, nrank);
- if (!gmx_multiple_gpu_per_node_supported())
- {
- gpu_opt->n_dev_use = std::min(gpu_opt->n_dev_use, 1);
- }
- snew(gpu_opt->dev_use, gpu_opt->n_dev_use);
- for (int i = 0; i != gpu_opt->n_dev_use; ++i)
- {
- /* TODO: improve this implementation: either sort GPUs or remove the weakest here */
- gpu_opt->dev_use[i] = gpu_opt->dev_compatible[i/nshare];
- }
+ return gpu_info.n_dev_compatible > 0;
}
void gmx_hardware_info_free(gmx_hw_info_t *hwinfo)
gmx_fatal(FARGS, "Error unlocking hwinfo mutex: %s", strerror(errno));
}
}
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <string>
+#include <vector>
+
#include "gromacs/utility/basedefinitions.h"
struct gmx_gpu_info_t;
-struct gmx_gpu_opt_t;
struct gmx_hw_info_t;
struct gmx_hw_opt_t;
struct t_commrec;
namespace gmx
{
-
-class HardwareTopology;
-
-} // namespace
-
-/*! \brief Return whether mdrun can use more than one GPU per node
- *
- * The OpenCL implementation cannot use more than one GPU per node,
- * for example. */
-gmx_bool gmx_multiple_gpu_per_node_supported();
-
-/*! \brief Return whether PP ranks can share a GPU
- *
- * The OpenCL implementation cannot share a GPU between ranks, for
- * example. */
-gmx_bool gmx_gpu_sharing_supported();
+class MDLogger;
/*! \brief Run detection, consistency checks, and make available on all ranks.
*
* available on all nodes.
* Caller is responsible for freeing this pointer.
*/
-gmx_hw_info_t *gmx_detect_hardware(FILE *fplog, const t_commrec *cr,
- gmx_bool bDetectGPUs);
-
-/* Print information about the detected hardware to fplog (if != NULL)
- * and to stderr the master rank.
- */
-void gmx_print_detected_hardware(FILE *fplog, const t_commrec *cr,
- const gmx_hw_info_t *hwinfo);
+gmx_hw_info_t *gmx_detect_hardware(const gmx::MDLogger &mdlog,
+ const t_commrec *cr);
+/*! \brief Free the hwinfo structure */
void gmx_hardware_info_free(gmx_hw_info_t *hwinfo);
-void gmx_parse_gpu_ids(gmx_gpu_opt_t *gpu_opt);
-
-void gmx_select_gpu_ids(FILE *fplog, const t_commrec *cr,
- const gmx_gpu_info_t *gpu_info,
- gmx_bool bForceUseGPU,
- gmx_gpu_opt_t *gpu_opt);
-
-/* Check the consistency of hw_opt with hwinfo.
- This function should be called once on each MPI rank. */
-void gmx_check_hw_runconf_consistency(FILE *fplog,
- const gmx_hw_info_t *hwinfo,
- const t_commrec *cr,
- const gmx_hw_opt_t *hw_opt,
- gmx_bool bUseGPU);
-
-/* Check whether a GPU is shared among ranks, and return the number of shared
- gpus
-
- gpu_opt = the gpu options struct
-
- returns: The number of GPUs shared among ranks, or 0 */
-int gmx_count_gpu_dev_shared(const gmx_gpu_opt_t *gpu_opt);
+//! Return whether compatible GPUs were found.
+bool compatibleGpusFound(const gmx_gpu_info_t &gpu_info);
#endif
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "gpu_hw_info.h"
+
+#include "config.h"
+
+/* Note that some of the following arrays must match the "GPU support
+ * enumeration" in src/config.h.cmakein, so that GMX_GPU looks up an
+ * array entry. */
+
+// TODO If/when we unify CUDA and OpenCL support code, this should
+// move to a single place in gpu_utils.
+/* Names of the GPU detection/check results (see e_gpu_detect_res_t in hw_info.h). */
+const char * const gpu_detect_res_str[egpuNR] =
+{
+ "compatible", "inexistent", "incompatible", "insane"
+};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int n_dev_compatible; /* number of compatible GPUs */
};
-/* GPU device selection information -- includes either CUDA or OpenCL devices */
-typedef struct gmx_gpu_opt_t
-{
- char *gpu_id; /* GPU id's to use, each specified as chars */
- gmx_bool bUserSet; /* true if the GPUs in dev_use are manually provided by the user */
-
- int n_dev_compatible; /* number of compatible GPU devices that could be used */
- int *dev_compatible; /* array of compatible GPU device IDs, from which automatic selection occurs */
- int n_dev_use; /* number of GPU devices selected to be used, either by the user or automatically */
- int *dev_use; /* array mapping from PP rank index to GPU device ID; GPU IDs can be listed multiple times when ranks share them */
-} gmx_gpu_opt_t;
-
#ifdef __cplusplus
}
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "hardwareassign.h"
+
+#include "config.h"
+
+#include <cstring>
+
+#include <algorithm>
+#include <string>
+#include <vector>
+
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/hardware/gpu_hw_info.h"
+#include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/sysinfo.h"
+
+#define HOSTNAMELEN 80
+
+namespace gmx
+{
+
+std::vector<int> parseGpuTaskAssignment(const std::string &gpuTaskAssignment)
+{
+ std::vector<int> digits;
+ if (gpuTaskAssignment.empty())
+ {
+ return digits;
+ }
+
+ /* Parse a "plain" or comma-separated GPU ID string which contains
+ * a sequence of digits corresponding to GPU IDs; the order will
+ * indicate the assignment of GPU tasks on this node to GPU
+ * device IDs on this node. */
+ try
+ {
+ digits = parseDigitsFromString(gpuTaskAssignment);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+
+ if (digits.empty())
+ {
+ gmx_fatal(FARGS, "Empty GPU ID string encountered.\n"
+ "An empty, delimiter-free, or comma-separated sequence of valid numeric IDs of available GPUs is required.\n");
+ }
+ return digits;
+}
+
+/*! \brief This function is responsible for the automated mapping the
+ * GPUs to the processes on a single node.
+ *
+ * This selects the GPUs we will use. This is an operation local to each physical node.
+ * If we have less MPI ranks than GPUs, we will waste some GPUs.
+ *
+ * \param[in] compatibleGpus Vector of GPUs that are compatible
+ * \param[in] nrank Number of PP GPU ranks on the node.
+ * \param[in] rank Index of PP GPU rank on the node.
+ *
+ * \returns The assignment of GPU tasks on ranks of this node to GPU devices on this node.
+ */
+static std::vector<int> assign_rank_gpu_ids(const std::vector<int> &compatibleGpus,
+ int nrank, int rank)
+{
+ int numCompatibleGpus = static_cast<int>(compatibleGpus.size());
+ GMX_RELEASE_ASSERT(nrank >= 1,
+ gmx::formatString("Invalid limit (%d) for the number of GPUs (detected %d compatible GPUs)",
+ rank, numCompatibleGpus).c_str());
+
+ if (numCompatibleGpus == 0)
+ {
+ char host[HOSTNAMELEN];
+
+ gmx_gethostname(host, HOSTNAMELEN);
+ gmx_fatal(FARGS, "A GPU was requested on host %s, but no compatible GPUs were detected. All nodes with PP ranks need to have GPUs. If you intended to use GPU acceleration in a parallel run, you can either avoid using the nodes that don't have GPUs or place PME ranks on these nodes.", host);
+ }
+
+ int nshare;
+
+ nshare = 1;
+ if (nrank > numCompatibleGpus)
+ {
+ if (nrank % numCompatibleGpus == 0)
+ {
+ nshare = nrank/numCompatibleGpus;
+ }
+ else
+ {
+ if (rank == 0)
+ {
+ gmx_fatal(FARGS, "The number of MPI ranks (%d) in a physical node is not a multiple of the number of GPUs (%d). Select a different number of MPI ranks or use the -gpu_id option to manually specify the GPU to be used.",
+ nrank, numCompatibleGpus);
+ }
+
+#if GMX_MPI
+ /* We use a global barrier to prevent ranks from continuing with
+ * an invalid setup.
+ */
+ MPI_Barrier(MPI_COMM_WORLD);
+#endif
+ }
+ }
+
+ /* Here we will waste GPUs when nrank < numCompatibleGpus */
+ std::vector<int> taskAssignment;
+ taskAssignment.resize(std::min(numCompatibleGpus*nshare, nrank));
+ for (size_t i = 0; i != taskAssignment.size(); ++i)
+ {
+ /* TODO: improve this implementation: either sort GPUs or remove the weakest here */
+ taskAssignment[i] = compatibleGpus[i/nshare];
+ }
+ return taskAssignment;
+}
+
+/*! \brief Check that all user-selected GPUs are compatible.
+ *
+ * Given the \c userGpuTaskAssignment and \c compatibleGPUs, give a fatal
+ * error if any selected GPUs is not compatible
+ *
+ * The error is given with a suitable descriptive message, which will
+ * have context if this check is done after the hardware detection
+ * results have been reported to the user. However, note that only the
+ * GPUs detected on the master rank are reported, because of the
+ * existing limitations of that reporting.
+ *
+ * \todo Note that the selected GPUs can be different on each rank,
+ * and the IDs of compatible GPUs can be different on each node, so
+ * this routine ought to do communication to determine whether all
+ * ranks are able to proceed. Currently this relies on the MPI runtime
+ * to kill the other processes because GROMACS lacks the appropriate
+ * infrastructure to do a good job of coordinating error messages and
+ * behaviour across MPMD ranks and multiple simulations.
+ *
+ * \param[in] gpu_info GPU information including device description.
+ * \param[in] compatibleGpus Vector of compatible GPUs
+ * \param[in] userGpuTaskAssignment The GPU selection from the user.
+ */
+static void exitUnlessUserGpuTaskAssignmentIsValid(const gmx_gpu_info_t &gpu_info,
+ const std::vector<int> &compatibleGpus,
+ const std::vector<int> &userGpuTaskAssignment)
+{
+ int numIncompatibleGpuIds = 0;
+ std::string message
+ = "Some of the requested GPUs do not exist, behave strangely, or are not compatible:\n";
+
+ for (const auto &gpuId : userGpuTaskAssignment)
+ {
+ if (std::find(compatibleGpus.begin(), compatibleGpus.end(), gpuId) == compatibleGpus.end())
+ {
+ numIncompatibleGpuIds++;
+ message += gmx::formatString(" GPU #%d: %s\n",
+ gpuId,
+ getGpuCompatibilityDescription(gpu_info, gpuId));
+ }
+ }
+
+ if (numIncompatibleGpuIds > 0)
+ {
+ gmx_fatal(FARGS, message.c_str());
+ }
+}
+
+/*! \brief Filter the compatible GPUs
+ *
+ * This function filters gpu_info.gpu_dev for compatible GPUs based
+ * on the previously run compatibility tests.
+ *
+ * \param[in] gpu_info Information detected about GPUs, including compatibility
+ * \return vector of IDs of GPUs already recorded as compatible */
+static std::vector<int> getCompatibleGpus(const gmx_gpu_info_t &gpu_info)
+{
+ // Possible minor over-allocation here, but not important for anything
+ std::vector<int> compatibleGpus;
+ compatibleGpus.reserve(gpu_info.n_dev);
+ for (int i = 0; i < gpu_info.n_dev; i++)
+ {
+ GMX_ASSERT(gpu_info.gpu_dev, "Invalid gpu_info.gpu_dev");
+ if (isGpuCompatible(gpu_info, i))
+ {
+ compatibleGpus.push_back(i);
+ }
+ }
+ return compatibleGpus;
+}
+
+std::vector<int> mapPpRanksToGpus(bool rankCanUseGpu,
+ const t_commrec *cr,
+ const gmx_gpu_info_t &gpu_info,
+ const gmx_hw_opt_t &hw_opt)
+{
+ std::vector<int> taskAssignment;
+
+ if (!rankCanUseGpu)
+ {
+ return taskAssignment;
+ }
+
+ auto compatibleGpus = getCompatibleGpus(gpu_info);
+ if (!hw_opt.gpuIdTaskAssignment.empty())
+ {
+ auto userGpuTaskAssignment = parseGpuTaskAssignment(hw_opt.gpuIdTaskAssignment);
+ exitUnlessUserGpuTaskAssignmentIsValid(gpu_info, compatibleGpus, userGpuTaskAssignment);
+ taskAssignment = userGpuTaskAssignment;
+ }
+ else
+ {
+ taskAssignment = assign_rank_gpu_ids(compatibleGpus, cr->nrank_pp_intranode, cr->rank_pp_intranode);
+ }
+ return taskAssignment;
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_HARDWARE_HARDWAREASSIGN_H
+#define GMX_HARDWARE_HARDWAREASSIGN_H
+
+#include <string>
+#include <vector>
+
+#include "gromacs/utility/basedefinitions.h"
+
+struct gmx_gpu_info_t;
+struct gmx_hw_opt_t;
+struct t_commrec;
+
+namespace gmx
+{
+
+/*! \brief Parse a GPU assignment string into digits
+ *
+ * \param[in] gpuTaskAssignment String like "013" or "0,1,3" typically
+ * supplied by the user to mdrun -gpu_id.
+ *
+ * \returns A vector of integer GPU ids, like {0, 1, 3}.
+ *
+ * \throws std::bad_alloc If out of memory.
+ * InvalidInputError If an invalid character is found (ie not a digit or ',').
+ */
+std::vector<int> parseGpuTaskAssignment(const std::string &gpuTaskAssignment);
+
+/*! \brief Assign PP ranks to valid GPU IDs.
+ *
+ * Will return a validated mapping from PP ranks (ie tasks that can
+ * run on GPUs) to the device IDs of compatible GPUs on their node.
+ * This will be from any non-empty assignment in hw_opt, otherwise a
+ * default automated mapping is generated.
+ *
+ * Note that PME-only ranks have always ignored mdrun -gpu_id, so do
+ * not attempt to validate -gpu_id. They should continue this behaviour
+ * until PME tasks can use GPUs.
+ *
+ * \param[in] rankCanUseGpu Whether this rank can execute a task on a GPU.
+ * \param[in] cr Communication record.
+ * \param[in] gpu_info Information detected about GPUs, including compatibility.
+ * \param[in] hw_opt Parallelisation options, including any user-specified GPU task assignment.
+ *
+ * \returns A valid GPU selection.
+ */
+std::vector<int> mapPpRanksToGpus(bool rankCanUseGpu,
+ const t_commrec *cr,
+ const gmx_gpu_info_t &gpu_info,
+ const gmx_hw_opt_t &hw_opt);
+
+} // namespace
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (depth >= 0)
{
- hwloc_obj_t cache = hwloc_get_next_obj_by_depth(topo, depth, NULL);
- if (cache != NULL)
+ hwloc_obj_t cache = hwloc_get_next_obj_by_depth(topo, depth, nullptr);
+ if (cache != nullptr)
{
std::vector<hwloc_obj_t> hwThreads = getHwLocDescendantsByType(cache, HWLOC_OBJ_PU);
int depth = hwloc_get_type_depth(topo, HWLOC_OBJ_NUMANODE);
const struct hwloc_distances_s * dist = hwloc_get_whole_distance_matrix_by_depth(topo, depth);
- if (dist != NULL && dist->nbobjs == hwlocNumaNodes.size())
+ if (dist != nullptr && dist->nbobjs == hwlocNumaNodes.size())
{
machine->numa.baseLatency = dist->latency_base;
machine->numa.maxRelativeLatency = dist->latency_max;
else
{
// No numa nodes found. Use the entire machine as a numa node.
- const hwloc_obj_t hwlocMachine = hwloc_get_next_obj_by_type(topo, HWLOC_OBJ_MACHINE, NULL);
+ const hwloc_obj_t hwlocMachine = hwloc_get_next_obj_by_type(topo, HWLOC_OBJ_MACHINE, nullptr);
- if (hwlocMachine != NULL)
+ if (hwlocMachine != nullptr)
{
machine->numa.nodes.resize(1);
machine->numa.nodes[0].id = 0;
{
const hwloc_obj_t ancestor = hwloc_get_ancestor_obj_by_type(topo, HWLOC_OBJ_NUMANODE, p);
int numaId;
- if (ancestor != NULL)
+ if (ancestor != nullptr)
{
numaId = ancestor->logical_index;
}
hwloc_topology_set_flags(topo, HWLOC_TOPOLOGY_FLAG_IO_DEVICES);
- if (hwloc_topology_load(topo) != 0 || hwloc_get_root_obj(topo) == NULL)
+ if (hwloc_topology_load(topo) != 0 || hwloc_get_root_obj(topo) == nullptr)
{
hwloc_topology_destroy(topo);
return; // SupportLevel::None.
{
HardwareTopology result;
- // Default values for machine and numa stuff
- result.machine_.logicalProcessorCount = 0;
- result.machine_.numa.baseLatency = 0.0;
- result.machine_.numa.maxRelativeLatency = 0.0;
- result.supportLevel_ = SupportLevel::None;
- result.isThisSystem_ = true;
-
#if GMX_HWLOC
parseHwLoc(&result.machine_, &result.supportLevel_, &result.isThisSystem_);
#endif
return result;
}
+HardwareTopology::Machine::Machine()
+{
+ logicalProcessorCount = 0;
+ numa.baseLatency = 0.0;
+ numa.maxRelativeLatency = 0.0;
+}
+
HardwareTopology::HardwareTopology()
- : supportLevel_(SupportLevel::None)
+ : supportLevel_(SupportLevel::None),
+ machine_(),
+ isThisSystem_(true)
{
}
+HardwareTopology::HardwareTopology(int logicalProcessorCount)
+ : supportLevel_(SupportLevel::None),
+ machine_(),
+ isThisSystem_(true)
+{
+ if (logicalProcessorCount > 0)
+ {
+ machine_.logicalProcessorCount = logicalProcessorCount;
+ supportLevel_ = SupportLevel::LogicalProcessorCount;
+ }
+}
+
int HardwareTopology::numberOfCores() const
{
if (supportLevel() >= SupportLevel::Basic)
*/
struct Machine
{
+ Machine();
+
int logicalProcessorCount; //!< Number of logical processors in system
std::vector<LogicalProcessor> logicalProcessors; //!< Map logical processors to socket/core
std::vector<Socket> sockets; //!< All the sockets in the system
/*! \brief Detects the hardware topology. */
static HardwareTopology detect();
+ /*! \brief Creates a topology with given number of logical cores.
+ *
+ * The support level will be either None or LogicalProcessorCount.
+ *
+ * Intended for testing of code that uses the hardware topology.
+ */
+ explicit HardwareTopology(int logicalProcessorCount);
+
/*! \brief Check what topology information that is available and valid
*
* The amount of hardware topology information that can be detected depends
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_HARDWARE_HWINFO_H
#define GMX_HARDWARE_HWINFO_H
+#include <string>
+
#include "gromacs/hardware/gpu_hw_info.h"
#include "gromacs/utility/basedefinitions.h"
threadaffSEL, threadaffAUTO, threadaffON, threadaffOFF, threadaffNR
};
-/* Threading and GPU options, can be set automatically or by the user */
-typedef struct gmx_hw_opt_t {
- int nthreads_tot; /* Total number of threads requested (TMPI) */
- int nthreads_tmpi; /* Number of TMPI threads requested */
- int nthreads_omp; /* Number of OpenMP threads requested */
- int nthreads_omp_pme; /* As nthreads_omp, but for PME only nodes */
- int thread_affinity; /* Thread affinity switch, see enum above */
- int core_pinning_stride; /* Logical core pinning stride */
- int core_pinning_offset; /* Logical core pinning offset */
-
- gmx_gpu_opt_t gpu_opt; /* The GPU options */
-} gmx_hw_opt_t;
+/*! \internal \brief Threading and GPU options, can be set automatically or by the user
+ *
+ * \todo During mdrunner(), if the user has left any of these values
+ * at their defaults (which tends to mean "choose automatically"),
+ * then those values are over-written with the result of such
+ * automation. This creates problems for the subsequent code in
+ * knowing what was done, why, and reporting correctly to the
+ * user. Find a way to improve this.
+ */
+struct gmx_hw_opt_t
+{
+ //! Total number of threads requested (thread-MPI + OpenMP).
+ int nthreads_tot = 0;
+ //! Number of thread-MPI threads requested.
+ int nthreads_tmpi = 0;
+ //! Number of OpenMP threads requested.
+ int nthreads_omp = 0;
+ //! Number of OpenMP threads to use on PME_only ranks.
+ int nthreads_omp_pme = 0;
+ //! Thread affinity switch, see enum above.
+ int thread_affinity = threadaffSEL;
+ //! Logical core pinning stride.
+ int core_pinning_stride = 0;
+ //! Logical core pinning offset.
+ int core_pinning_offset = 0;
+ //! Empty, or a GPU task-assignment string provided by the user.
+ std::string gpuIdTaskAssignment = "";
+};
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "printhardware.h"
+
+#include "config.h"
+
+#include <cstdlib>
+
+#include <algorithm>
+#include <string>
+#include <vector>
+
+#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/hardware/cpuinfo.h"
+#include "gromacs/hardware/gpu_hw_info.h"
+#include "gromacs/hardware/hardwaretopology.h"
+#include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/simd/support.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/sysinfo.h"
+
+//! Constant used to help minimize preprocessed code
+static const bool bGPUBinary = GMX_GPU != GMX_GPU_NONE;
+
+/*! \brief Return the number of PP rank pairs that share a GPU device between them.
+ *
+ * Sharing GPUs among multiple PP ranks is possible via either user or
+ * automated selection. */
+static int gmx_count_gpu_dev_shared(const std::vector<int> &gpuTaskAssignment,
+ bool userSetGpuIds)
+{
+ int same_count = 0;
+
+ if (userSetGpuIds)
+ {
+ GMX_RELEASE_ASSERT(!gpuTaskAssignment.empty(),
+ "The user cannot choose an empty set of GPU IDs, code is wrong somewhere");
+ size_t ngpu = gpuTaskAssignment.size();
+
+ for (size_t i = 0; i < ngpu - 1; i++)
+ {
+ for (size_t j = i + 1; j < ngpu; j++)
+ {
+ same_count += (gpuTaskAssignment[i] ==
+ gpuTaskAssignment[j]);
+ }
+ }
+ }
+
+ return same_count;
+}
+
+/* Count and return the number of unique GPUs (per node) selected.
+ *
+ * As sharing GPUs among multiple PP ranks is possible, the number of
+ * GPUs used (per node) can be different from the number of GPU IDs
+ * used.
+ */
+static size_t gmx_count_gpu_dev_unique(const std::vector<int> &gpuTaskAssignment)
+{
+ std::set<int> uniqIds;
+ for (const auto &deviceId : gpuTaskAssignment)
+ {
+ uniqIds.insert(deviceId);
+ }
+ return uniqIds.size();
+}
+
+/*! \internal \brief
+ * Returns the GPU information text, one GPU per line.
+ */
+static std::string sprint_gpus(const gmx_gpu_info_t &gpu_info)
+{
+ char stmp[STRLEN];
+ std::vector<std::string> gpuStrings;
+ for (int i = 0; i < gpu_info.n_dev; i++)
+ {
+ get_gpu_device_info_string(stmp, gpu_info, i);
+ gpuStrings.push_back(gmx::formatString(" %s", stmp));
+ }
+ return gmx::joinStrings(gpuStrings, "\n");
+}
+
+void reportGpuUsage(const gmx::MDLogger &mdlog,
+ const gmx_gpu_info_t &gpu_info,
+ bool userSetGpuIds,
+ const std::vector<int> &gpuTaskAssignment,
+ size_t numPpRanks,
+ bool bPrintHostName)
+{
+ if (gpuTaskAssignment.empty())
+ {
+ return;
+ }
+
+ std::string output;
+ {
+ std::string gpuIdsString =
+ formatAndJoin(gpuTaskAssignment, ",", gmx::StringFormatter("%d"));
+ size_t numGpusInUse = gmx_count_gpu_dev_unique(gpuTaskAssignment);
+ bool bPluralGpus = numGpusInUse > 1;
+
+ if (bPrintHostName)
+ {
+ char host[STRLEN];
+ gmx_gethostname(host, STRLEN);
+ output += gmx::formatString("On host %s ", host);
+ }
+ output += gmx::formatString("%zu GPU%s %sselected for this run.\n"
+ "Mapping of GPU ID%s to the %d PP rank%s in this node: %s\n",
+ numGpusInUse, bPluralGpus ? "s" : "",
+ userSetGpuIds ? "user-" : "auto-",
+ bPluralGpus ? "s" : "",
+ numPpRanks,
+ (numPpRanks > 1) ? "s" : "",
+ gpuIdsString.c_str());
+ }
+
+ int same_count = gmx_count_gpu_dev_shared(gpuTaskAssignment, userSetGpuIds);
+
+ if (same_count > 0)
+ {
+ output += gmx::formatString("NOTE: You assigned %s to multiple ranks.\n",
+ same_count > 1 ? "GPU IDs" : "a GPU ID");
+ }
+
+ if (static_cast<size_t>(gpu_info.n_dev_compatible) > numPpRanks)
+ {
+ /* TODO In principle, this warning could be warranted only on
+ * ranks on some nodes, but we lack the infrastructure to do a
+ * good job of reporting that. */
+ output += gmx::formatString("NOTE: potentially sub-optimal launch configuration using fewer\n"
+ " PP ranks on a node than GPUs available on that node.\n");
+ }
+
+ /* NOTE: this print is only for and on one physical node */
+ GMX_LOG(mdlog.warning).appendText(output);
+}
+
+/* Give a suitable fatal error or warning if the build configuration
+ and runtime CPU do not match. */
+static void
+check_use_of_rdtscp_on_this_cpu(const gmx::MDLogger &mdlog,
+ const gmx::CpuInfo &cpuInfo)
+{
+ bool binaryUsesRdtscp = HAVE_RDTSCP;
+
+ const char *programName = gmx::getProgramContext().displayName();
+
+ if (cpuInfo.supportLevel() < gmx::CpuInfo::SupportLevel::Features)
+ {
+ if (binaryUsesRdtscp)
+ {
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "The %s executable was compiled to use the rdtscp CPU instruction. "
+ "We cannot detect the features of your current CPU, but will proceed anyway. "
+ "If you get a crash, rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option.",
+ programName);
+ }
+ }
+ else
+ {
+ bool cpuHasRdtscp = cpuInfo.feature(gmx::CpuInfo::Feature::X86_Rdtscp);
+
+ if (!cpuHasRdtscp && binaryUsesRdtscp)
+ {
+ gmx_fatal(FARGS, "The %s executable was compiled to use the rdtscp CPU instruction. "
+ "However, this is not supported by the current hardware and continuing would lead to a crash. "
+ "Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option.",
+ programName);
+ }
+
+ if (cpuHasRdtscp && !binaryUsesRdtscp)
+ {
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "The current CPU can measure timings more accurately than the code in\n"
+ "%s was configured to use. This might affect your simulation\n"
+ "speed as accurate timings are needed for load-balancing.\n"
+ "Please consider rebuilding %s with the GMX_USE_RDTSCP=ON CMake option.",
+ programName, programName);
+ }
+ }
+}
+
+static std::string detected_hardware_string(const gmx_hw_info_t *hwinfo,
+ bool bFullCpuInfo)
+{
+ std::string s;
+
+ const gmx::CpuInfo &cpuInfo = *hwinfo->cpuInfo;
+ const gmx::HardwareTopology &hwTop = *hwinfo->hardwareTopology;
+
+ s = gmx::formatString("\n");
+ s += gmx::formatString("Running on %d node%s with total",
+ hwinfo->nphysicalnode,
+ hwinfo->nphysicalnode == 1 ? "" : "s");
+ if (hwinfo->ncore_tot > 0)
+ {
+ s += gmx::formatString(" %d cores,", hwinfo->ncore_tot);
+ }
+ s += gmx::formatString(" %d logical cores", hwinfo->nhwthread_tot);
+ if (hwinfo->gpu_info.bDetectGPUs)
+ {
+ s += gmx::formatString(", %d compatible GPU%s",
+ hwinfo->ngpu_compatible_tot,
+ hwinfo->ngpu_compatible_tot == 1 ? "" : "s");
+ }
+ else if (bGPUBinary)
+ {
+ s += gmx::formatString(" (GPU detection deactivated)");
+ }
+ s += gmx::formatString("\n");
+
+ if (hwinfo->nphysicalnode > 1)
+ {
+ /* Print per node hardware feature counts */
+ if (hwinfo->ncore_max > 0)
+ {
+ s += gmx::formatString(" Cores per node: %2d", hwinfo->ncore_min);
+ if (hwinfo->ncore_max > hwinfo->ncore_min)
+ {
+ s += gmx::formatString(" - %2d", hwinfo->ncore_max);
+ }
+ s += gmx::formatString("\n");
+ }
+ s += gmx::formatString(" Logical cores per node: %2d", hwinfo->nhwthread_min);
+ if (hwinfo->nhwthread_max > hwinfo->nhwthread_min)
+ {
+ s += gmx::formatString(" - %2d", hwinfo->nhwthread_max);
+ }
+ s += gmx::formatString("\n");
+ if (bGPUBinary)
+ {
+ s += gmx::formatString(" Compatible GPUs per node: %2d",
+ hwinfo->ngpu_compatible_min);
+ if (hwinfo->ngpu_compatible_max > hwinfo->ngpu_compatible_min)
+ {
+ s += gmx::formatString(" - %2d", hwinfo->ngpu_compatible_max);
+ }
+ s += gmx::formatString("\n");
+ if (hwinfo->ngpu_compatible_tot > 0)
+ {
+ if (hwinfo->bIdenticalGPUs)
+ {
+ s += gmx::formatString(" All nodes have identical type(s) of GPUs\n");
+ }
+ else
+ {
+ /* This message will also appear with identical GPU types
+ * when at least one node has no GPU.
+ */
+ s += gmx::formatString(" Different nodes have different type(s) and/or order of GPUs\n");
+ }
+ }
+ }
+ }
+
+#if GMX_LIB_MPI
+ int rank;
+ char host[STRLEN];
+
+ gmx_gethostname(host, STRLEN);
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+
+ // TODO Use a wrapper around MPI_Get_processor_name instead.
+ s += gmx::formatString("Hardware detected on host %s (the node of MPI rank %d):\n",
+ host, rank);
+#else
+ s += gmx::formatString("Hardware detected:\n");
+#endif
+ s += gmx::formatString(" CPU info:\n");
+
+ s += gmx::formatString(" Vendor: %s\n", cpuInfo.vendorString().c_str());
+
+ s += gmx::formatString(" Brand: %s\n", cpuInfo.brandString().c_str());
+
+ if (bFullCpuInfo)
+ {
+ s += gmx::formatString(" Family: %d Model: %d Stepping: %d\n",
+ cpuInfo.family(), cpuInfo.model(), cpuInfo.stepping());
+
+ s += gmx::formatString(" Features:");
+ for (auto &f : cpuInfo.featureSet())
+ {
+ s += gmx::formatString(" %s", cpuInfo.featureString(f).c_str());;
+ }
+ s += gmx::formatString("\n");
+ }
+
+ s += gmx::formatString(" SIMD instructions most likely to fit this hardware: %s",
+ gmx::simdString(static_cast<gmx::SimdType>(hwinfo->simd_suggest_min)).c_str());
+
+ if (hwinfo->simd_suggest_max > hwinfo->simd_suggest_min)
+ {
+ s += gmx::formatString(" - %s", gmx::simdString(static_cast<gmx::SimdType>(hwinfo->simd_suggest_max)).c_str());
+ }
+ s += gmx::formatString("\n");
+
+ s += gmx::formatString(" SIMD instructions selected at GROMACS compile time: %s\n",
+ gmx::simdString(gmx::simdCompiled()).c_str());
+
+ s += gmx::formatString("\n");
+
+ s += gmx::formatString(" Hardware topology: ");
+ switch (hwTop.supportLevel())
+ {
+ case gmx::HardwareTopology::SupportLevel::None:
+ s += gmx::formatString("None\n");
+ break;
+ case gmx::HardwareTopology::SupportLevel::LogicalProcessorCount:
+ s += gmx::formatString("Only logical processor count\n");
+ break;
+ case gmx::HardwareTopology::SupportLevel::Basic:
+ s += gmx::formatString("Basic\n");
+ break;
+ case gmx::HardwareTopology::SupportLevel::Full:
+ s += gmx::formatString("Full\n");
+ break;
+ case gmx::HardwareTopology::SupportLevel::FullWithDevices:
+ s += gmx::formatString("Full, with devices\n");
+ break;
+ }
+
+ if (!hwTop.isThisSystem())
+ {
+ s += gmx::formatString(" NOTE: Hardware topology cached or synthetic, not detected.\n");
+ if (char *p = std::getenv("HWLOC_XMLFILE"))
+ {
+ s += gmx::formatString(" HWLOC_XMLFILE=%s\n", p);
+ }
+ }
+
+ if (bFullCpuInfo)
+ {
+ if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::Basic)
+ {
+ s += gmx::formatString(" Sockets, cores, and logical processors:\n");
+
+ for (auto &socket : hwTop.machine().sockets)
+ {
+ s += gmx::formatString(" Socket %2d:", socket.id);
+ for (auto &c : socket.cores)
+ {
+ s += gmx::formatString(" [");
+ for (auto &t : c.hwThreads)
+ {
+ s += gmx::formatString(" %3d", t.logicalProcessorId);
+ }
+ s += gmx::formatString("]");
+ }
+ s += gmx::formatString("\n");
+ }
+ }
+ if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::Full)
+ {
+ s += gmx::formatString(" Numa nodes:\n");
+ for (auto &n : hwTop.machine().numa.nodes)
+ {
+ s += gmx::formatString(" Node %2d (%" GMX_PRIu64 " bytes mem):", n.id, n.memory);
+ for (auto &l : n.logicalProcessorId)
+ {
+ s += gmx::formatString(" %3d", l);
+ }
+ s += gmx::formatString("\n");
+ }
+ s += gmx::formatString(" Latency:\n ");
+ for (std::size_t j = 0; j < hwTop.machine().numa.nodes.size(); j++)
+ {
+ s += gmx::formatString(" %5d", j);
+ }
+ s += gmx::formatString("\n");
+ for (std::size_t i = 0; i < hwTop.machine().numa.nodes.size(); i++)
+ {
+ s += gmx::formatString(" %5d", i);
+ for (std::size_t j = 0; j < hwTop.machine().numa.nodes.size(); j++)
+ {
+ s += gmx::formatString(" %5.2f", hwTop.machine().numa.relativeLatency[i][j]);
+ }
+ s += gmx::formatString("\n");
+ }
+
+
+ s += gmx::formatString(" Caches:\n");
+ for (auto &c : hwTop.machine().caches)
+ {
+ s += gmx::formatString(" L%d: %" GMX_PRIu64 " bytes, linesize %d bytes, assoc. %d, shared %d ways\n",
+ c.level, c.size, c.linesize, c.associativity, c.shared);
+ }
+ }
+ if (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::FullWithDevices)
+ {
+ s += gmx::formatString(" PCI devices:\n");
+ for (auto &d : hwTop.machine().devices)
+ {
+ s += gmx::formatString(" %04x:%02x:%02x.%1x Id: %04x:%04x Class: 0x%04x Numa: %d\n",
+ d.domain, d.bus, d.dev, d.func, d.vendorId, d.deviceId, d.classId, d.numaNodeId);
+ }
+ }
+ }
+
+ if (bGPUBinary && (hwinfo->ngpu_compatible_tot > 0 ||
+ hwinfo->gpu_info.n_dev > 0))
+ {
+ s += gmx::formatString(" GPU info:\n");
+ s += gmx::formatString(" Number of GPUs detected: %d\n",
+ hwinfo->gpu_info.n_dev);
+ if (hwinfo->gpu_info.n_dev > 0)
+ {
+ s += sprint_gpus(hwinfo->gpu_info) + "\n";
+ }
+ }
+ return s;
+}
+
+void gmx_print_detected_hardware(FILE *fplog, const t_commrec *cr,
+ const gmx::MDLogger &mdlog,
+ const gmx_hw_info_t *hwinfo)
+{
+ const gmx::CpuInfo &cpuInfo = *hwinfo->cpuInfo;
+
+ if (fplog != nullptr)
+ {
+ std::string detected;
+
+ detected = detected_hardware_string(hwinfo, TRUE);
+
+ fprintf(fplog, "%s\n", detected.c_str());
+ }
+
+ if (MULTIMASTER(cr))
+ {
+ std::string detected;
+
+ detected = detected_hardware_string(hwinfo, FALSE);
+
+ fprintf(stderr, "%s\n", detected.c_str());
+ }
+
+ /* Check the compiled SIMD instruction set against that of the node
+ * with the lowest SIMD level support (skip if SIMD detection did not work)
+ */
+ if (cpuInfo.supportLevel() >= gmx::CpuInfo::SupportLevel::Features)
+ {
+ gmx::simdCheck(static_cast<gmx::SimdType>(hwinfo->simd_suggest_min), fplog, MULTIMASTER(cr));
+ }
+
+ /* For RDTSCP we only check on our local node and skip the MPI reduction */
+ check_use_of_rdtscp_on_this_cpu(mdlog, cpuInfo);
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_HARDWARE_PRINTHARDWARE_H
+#define GMX_HARDWARE_PRINTHARDWARE_H
+
+#include <cstdio>
+
+#include <string>
+#include <vector>
+
+struct gmx_gpu_info_t;
+struct gmx_hw_info_t;
+struct t_commrec;
+
+namespace gmx
+{
+class MDLogger;
+}
+
+/* Print information about the detected hardware to fplog (if != NULL)
+ * and to stderr the master rank.
+ */
+void gmx_print_detected_hardware(FILE *fplog, const t_commrec *cr,
+ const gmx::MDLogger &mdlog,
+ const gmx_hw_info_t *hwinfo);
+
+/*! \brief Log a report on how GPUs are (or could be) being used on
+ * the ranks of the physical node of rank 0 of the simulation.
+ *
+ * \todo It could be useful to report also whether any nodes differed,
+ * and in what way.
+ *
+ * \param[out] mdlog Logging object.
+ * \param[in] gpu_info Information detected about GPUs
+ * \param[in] userSetGpuIds Whether the user selected the GPU ids
+ * \param[in] gpuTaskAssignment The selected GPU IDs.
+ * \param[in] numPpRanks Number of PP ranks per node
+ * \param[in] bPrintHostName Print the hostname in the usage information
+ *
+ * \throws std::bad_alloc if out of memory */
+void reportGpuUsage(const gmx::MDLogger &mdlog,
+ const gmx_gpu_info_t &gpu_info,
+ bool userSetGpuIds,
+ const std::vector<int> &gpuTaskAssignment,
+ size_t numPpRanks,
+ bool bPrintHostName);
+
+#endif
#include "gromacs/imd/imdsocket.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/broadcaststructs.h"
#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/mtop_util.h"
/*! \brief IMD Protocol Version. */
#define IMDVERSION 2
-/*! \brief Broadcast d to all nodes */
-#define block_bc(cr, d) gmx_bcast(sizeof(d), &(d), (cr))
-
-/*! \brief Broadcast nr elements of d to all nodes */
-#define nblock_bc(cr, nr, d) gmx_bcast((nr)*sizeof((d)[0]), (d), (cr))
-
/*! \internal
* \brief
"IMD_PAUSE",
"IMD_TRATE",
"IMD_IOERROR",
- NULL
+ nullptr
};
{
IMDatoms = gmx_mtop_global_atoms(sys);
write_sto_conf_indexed(opt2fn("-imd", nfile, fnm), "IMDgroup", &IMDatoms,
- state->x, state->v, ir->ePBC, state->box, ir->imd->nat, ir->imd->ind);
+ as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), ir->ePBC, state->box, ir->imd->nat, ir->imd->ind);
}
}
/*! \brief Initializes the IMD private data. */
static t_gmx_IMD_setup* imd_create(int imdatoms, int nstimddef, int imdport)
{
- t_gmx_IMD_setup *IMDsetup = NULL;
+ t_gmx_IMD_setup *IMDsetup = nullptr;
snew(IMDsetup, 1);
/* then we reset the IMD step to its default, and reset the connection boolean */
IMDsetup->nstimd_new = IMDsetup->nstimd_def;
- IMDsetup->clientsocket = NULL;
+ IMDsetup->clientsocket = nullptr;
IMDsetup->bConnected = FALSE;
}
*
* Call on master only.
*/
-static FILE *open_imd_out(const char *fn,
- t_gmx_IMD_setup *IMDsetup,
- int nat_total,
- const gmx_output_env_t *oenv,
- unsigned long Flags)
+static FILE *open_imd_out(const char *fn,
+ t_gmx_IMD_setup *IMDsetup,
+ int nat_total,
+ const gmx_output_env_t *oenv,
+ const ContinuationOptions &continuationOptions)
{
FILE *fp;
if (fn && oenv)
{
/* If we append to an existing file, all the header information is already there */
- if (Flags & MD_APPENDFILES)
+ if (continuationOptions.appendFiles)
{
fp = gmx_fio_fopen(fn, "a+");
}
fprintf(stdout, "%s For a log of the IMD pull forces explicitly specify '-if' on the command line.\n"
"%s (Not possible with energy minimization.)\n", IMDstr, IMDstr);
- return NULL;
+ return nullptr;
}
#endif
int nfile,
const t_filenm fnm[],
const gmx_output_env_t *oenv,
- int imdport,
- unsigned long Flags)
+ const MdrunOptions &mdrunOptions)
{
int i;
int nat_total;
return;
}
+ const ImdOptions &options = mdrunOptions.imdOptions;
+
/* It seems we have a .tpr file that defines an IMD group and thus allows IMD sessions.
* Check whether we can actually provide the IMD functionality for this setting: */
if (MASTER(cr))
{
/* Check whether IMD was enabled by one of the command line switches: */
- if ((Flags & MD_IMDWAIT) || (Flags & MD_IMDTERM) || (Flags & MD_IMDPULL))
+ if (options.wait || options.terminatable || options.pull)
{
/* Multiple simulations or replica exchange */
if (MULTISIM(cr))
/* Initialize IMD setup structure. If we read in a pre-IMD .tpr file, imd->nat
* will be zero. For those cases we transfer _all_ atomic positions */
ir->imd->setup = imd_create(ir->imd->nat > 0 ? ir->imd->nat : nat_total,
- defnstimd, imdport);
+ defnstimd, options.port);
IMDsetup = ir->imd->setup;
/* We might need to open an output file for IMD forces data */
if (MASTER(cr))
{
- IMDsetup->outf = open_imd_out(opt2fn("-if", nfile, fnm), ir->imd->setup, nat_total, oenv, Flags);
+ IMDsetup->outf = open_imd_out(opt2fn("-if", nfile, fnm), ir->imd->setup, nat_total, oenv, mdrunOptions.continuationOptions);
}
/* Make sure that we operate with a valid atom index array for the IMD atoms */
snew(IMDsetup->energysendbuf, recsize);
/* Shall we wait for a connection? */
- if (Flags & MD_IMDWAIT)
+ if (options.wait)
{
IMDsetup->bWConnect = TRUE;
fprintf(stderr, "%s Pausing simulation while no IMD connection present (-imdwait).\n", IMDstr);
}
/* Will the IMD clients be able to terminate the simulation? */
- if (Flags & MD_IMDTERM)
+ if (options.terminatable)
{
IMDsetup->bTerminatable = TRUE;
fprintf(stderr, "%s Allow termination of the simulation from IMD client (-imdterm).\n", IMDstr);
}
/* Is pulling from IMD client allowed? */
- if (Flags & MD_IMDPULL)
+ if (options.pull)
{
IMDsetup->bForceActivated = TRUE;
fprintf(stderr, "%s Pulling from IMD remote is enabled (-imdpull).\n", IMDstr);
rvec x[],
t_inputrec *ir,
double t,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle *wcycle)
{
gmx_bool imdstep = FALSE;
t_gmx_IMD_setup *IMDsetup;
void IMD_prep_energies_send_positions(gmx_bool bIMD, gmx_bool bIMDstep,
t_IMD *imd, gmx_enerdata_t *enerd,
gmx_int64_t step, gmx_bool bHaveNewEnergies,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle *wcycle)
{
if (bIMD)
{
return IMDsetup->nstimd;
}
+
void IMD_apply_forces(gmx_bool bIMD, t_IMD *imd, t_commrec *cr, rvec *f,
- gmx_wallcycle_t wcycle)
+ gmx_wallcycle *wcycle)
{
int i, j;
int locndx;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
+#include <cstdio>
+
#include "gromacs/math/vectypes.h"
-#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
+
#if GMX_NATIVE_WINDOWS
#include <Windows.h>
struct gmx_enerdata_t;
struct gmx_mtop_t;
struct gmx_output_env_t;
+struct gmx_wallcycle;
+struct MdrunOptions;
+struct t_commrec;
struct t_filenm;
struct t_gmx_IMD;
struct t_IMD;
struct t_inputrec;
-struct t_state;
+class t_state;
static const char IMDstr[] = "IMD:"; /**< Tag output from the IMD module with this string. */
* \param nfile Number of files.
* \param fnm Struct containing file names etc.
* \param oenv Output options.
- * \param imdport Port to use for IMD connections.
- * \param Flags Flags passed over from main, used to determine
- * whether or not we are appending.
+ * \param mdrunOptions Options for mdrun.
*/
void init_IMD(t_inputrec *ir, t_commrec *cr, gmx_mtop_t *top_global,
FILE *fplog, int defnstimd, rvec x[],
int nfile, const t_filenm fnm[], const gmx_output_env_t *oenv,
- int imdport, unsigned long Flags);
+ const MdrunOptions &mdrunOptions);
/*! \brief IMD required in this time step?
gmx_bool do_IMD(gmx_bool bIMD, gmx_int64_t step, t_commrec *cr,
gmx_bool bNS,
matrix box, rvec x[], t_inputrec *ir, double t,
- gmx_wallcycle_t wcycle);
+ gmx_wallcycle *wcycle);
/*! \brief Get the IMD update frequency.
*/
void IMD_apply_forces(gmx_bool bIMD, t_IMD *imd,
t_commrec *cr, rvec *f,
- gmx_wallcycle_t wcycle);
+ gmx_wallcycle *wcycle);
/*! \brief Copy energies and convert to float from enerdata to the IMD energy record.
void IMD_prep_energies_send_positions(gmx_bool bIMD, gmx_bool bIMDstep,
t_IMD *imd, gmx_enerdata_t *enerd,
gmx_int64_t step, gmx_bool bHaveNewEnergies,
- gmx_wallcycle_t wcycle);
+ gmx_wallcycle *wcycle);
/*! \brief Finalize IMD and do some cleaning up.
*
{
fprintf(stderr, "%s Error in file %s on line %d.\n", IMDstr, file, line);
- if (NULL != msg)
+ if (nullptr != msg)
{
fprintf(stderr, "%s\n", msg);
}
extern IMDSocket* imdsock_create()
{
- IMDSocket *sock = NULL;
+ IMDSocket *sock = nullptr;
#ifdef GMX_IMD
print_IMD_error(ERR_ARGS);
sfree(sock);
- return NULL;
+ return nullptr;
}
else
#endif
{
print_IMD_error(ERR_ARGS);
- return NULL;
+ return nullptr;
}
}
/* is the socket already NULL? */
- if (sock == NULL)
+ if (sock == nullptr)
{
return;
}
int ret = -1;
- if (sock == NULL)
+ if (sock == nullptr)
{
return 1;
}
do
{
/* check the set for read readiness. */
- ret = select(sock->sockfd + 1, &readfds, NULL, NULL, tval);
+ ret = select(sock->sockfd + 1, &readfds, nullptr, nullptr, tval);
/* redo on system interrupt */
}
while (ret < 0 && errno == EINTR);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Make jobz point to the character "V" if eigenvectors
* should be calculated, otherwise "N" (only eigenvalues).
*/
- jobz = (eigenvectors != NULL) ? "V" : "N";
+ jobz = (eigenvectors != nullptr) ? "V" : "N";
/* allocate lapack stuff */
snew(isuppz, 2*n);
}
#endif
- if (eigenvectors != NULL)
+ if (eigenvectors != nullptr)
{
dovec = 1;
}
#if GMX_DOUBLE
F77_FUNC(dseupd, DSEUPD) (&dovec, "A", select, eigenvalues, eigenvectors,
- &n, NULL, "I", &n, "SA", &neig, &abstol,
+ &n, nullptr, "I", &n, "SA", &neig, &abstol,
resid, &ncv, v, &n, iparam, ipntr,
workd, workl, &lworkl, &info);
#else
F77_FUNC(sseupd, SSEUPD) (&dovec, "A", select, eigenvalues, eigenvectors,
- &n, NULL, "I", &n, "SA", &neig, &abstol,
+ &n, nullptr, "I", &n, "SA", &neig, &abstol,
resid, &ncv, v, &n, iparam, ipntr,
workd, workl, &lworkl, &info);
#endif
F77_FUNC(dgemv, DGEMV) ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]],
&c__1, &c_b42, &workd[iwork[9]], &c__1);
}
- else if (*mode == 2)
+ else
{
F77_FUNC(dgemv, DGEMV) ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[10]
], &c__1, &c_b42, &workd[iwork[9]], &c__1);
F77_FUNC(sgemv, SGEMV) ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[8]],
&c__1, &c_b42, &workd[iwork[9]], &c__1);
}
- else if (*mode == 2)
+ else
{
F77_FUNC(sgemv, SGEMV) ("T", n, &iwork[12], &c_b18, &v[v_offset], ldv, &workd[iwork[10]
], &c__1, &c_b42, &workd[iwork[9]], &c__1);
double unfl, sinl, cosr, smin, smax, sinr;
double oldcs;
int oldll;
- double shift, sigmn, oldsn;
+ double shift, sigmn, oldsn = 0.;
int maxit;
double sminl;
double sigmx;
ulp = 2*GMX_DOUBLE_EPS;
rtoli = ulp * 2.;
nb = DSTEBZ_BLOCKSIZE;
+ // cppcheck-suppress knownConditionTrueFalse
if (nb <= 1) {
nb = 0;
}
float unfl, sinl, cosr, smin, smax, sinr;
float oldcs;
int oldll;
- float shift, sigmn, oldsn;
+ float shift, sigmn, oldsn = 0.;
int maxit;
float sminl;
float sigmx;
ulp = 2*GMX_FLOAT_EPS;
rtoli = ulp * 2.;
nb = DSTEBZ_BLOCKSIZE;
+ // cppcheck-suppress knownConditionTrueFalse
if (nb <= 1) {
nb = 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int matrix_invert(FILE *fp, int n, double **a)
{
int i, j, m, lda, *ipiv, lwork, info;
- double **test = NULL, **id, *work;
+ double **test = nullptr, **id, *work;
#ifdef DEBUG_MATRIX
if (fp)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_fatal(FARGS, "Error: Too many iterations in routine JACOBI\n");
}
-int m_inv_gen(real **m, int n, real **minv)
+int m_inv_gen(real *m, int n, real *minv)
{
double **md, **v, *eig, tol, s;
int nzero, i, j, k, nrot;
{
for (j = 0; j < n; j++)
{
- md[i][j] = m[i][j];
+ md[i][j] = m[i*n + j];
}
}
{
s += eig[k]*v[i][k]*v[j][k];
}
- minv[i][j] = s;
+ minv[i*n + j] = s;
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* int *irot = number of jacobi rotations
*/
-int m_inv_gen(real **m, int n, real **minv);
-/* Produces minv, a generalized inverse of m.
+int m_inv_gen(real *m, int n, real *minv);
+/* Produces minv, a generalized inverse of m, both stored as linear arrays.
* Inversion is done via diagonalization,
* eigenvalues smaller than 1e-6 times the average diagonal element
* are assumed to be zero.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
A->ndata[i] = 0;
A->nalloc[i] = 0;
- A->data[i] = NULL;
+ A->data[i] = nullptr;
}
return A;
}
/* Release each row */
for (i = 0; i < A->nrow; i++)
{
- if (A->data[i] != NULL)
+ if (A->data[i] != nullptr)
{
sfree(A->data[i]);
}
if (A->ndata[row] == A->nalloc[row])
{
A->nalloc[row] += 100;
- if (A->data[row] == NULL)
+ if (A->data[row] == nullptr)
{
snew(A->data[row], A->nalloc[row]);
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_install_headers(listed-forces.h)
if (BUILD_TESTING)
-# add_subdirectory(tests)
+ add_subdirectory(tests)
endif()
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return vtot;
}
-real harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
- real *V, real *F)
+static real harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
+ real *V, real *F)
{
const real half = 0.5;
real L1, kk, x0, dx, dx2;
f[aj][m] += f_j[m];
f[ak][m] += f_k[m];
}
- if (g != NULL)
+ if (g != nullptr)
{
copy_ivec(SHIFT_IVEC(g, aj), jt);
}
#endif // GMX_SIMD_HAVE_REAL
-real dopdihs(real cpA, real cpB, real phiA, real phiB, int mult,
- real phi, real lambda, real *V, real *F)
+static real dopdihs(real cpA, real cpB, real phiA, real phiB, int mult,
+ real phi, real lambda, real *V, real *F)
{
real v, dvdlambda, mdphi, v1, sdphi, ddphi;
real L1 = 1.0 - lambda;
* G R O M O S 9 6 F U N C T I O N S
*
***********************************************************/
-real g96harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
- real *V, real *F)
+static real g96harmonic(real kA, real kB, real xA, real xB, real x, real lambda,
+ real *V, real *F)
{
const real half = 0.5;
real L1, kk, x0, dx, dx2;
return vtot;
}
-real g96bond_angle(const rvec xi, const rvec xj, const rvec xk, const t_pbc *pbc,
- rvec r_ij, rvec r_kj,
- int *t1, int *t2)
+static real g96bond_angle(const rvec xi, const rvec xj, const rvec xk, const t_pbc *pbc,
+ rvec r_ij, rvec r_kj,
+ int *t1, int *t2)
/* Return value is the angle between the bonds i-j and j-k */
{
real costh;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_LISTED_FORCES_BONDED_H
#define GMX_LISTED_FORCES_BONDED_H
-#include <stdio.h>
+#include <cstdio>
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/utility/basedefinitions.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-struct gmx_wallcycle;
struct t_graph;
struct t_pbc;
//! \endcond
-#ifdef __cplusplus
-}
-#endif
-
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop, &il, &nmol))
{
- if (nmol > 1 && ir->eDisre != edrEnsemble)
+ if (nmol > 1 && il[F_DISRES].nr > 0 && ir->eDisre != edrEnsemble)
{
gmx_fatal(FARGS, "NMR distance restraints with multiple copies of the same molecule are currently only supported with ensemble averaging. If you just want to restrain distances between atom pairs using a flat-bottomed potential, use a restraint potential (bonds type 10) instead.");
}
dd->Rtav_6 = &(dd->Rt_6[dd->nres]);
ptr = getenv("GMX_DISRE_ENSEMBLE_SIZE");
- if (cr && cr->ms != NULL && ptr != NULL && !bIsREMD)
+ if (cr && cr->ms != nullptr && ptr != nullptr && !bIsREMD)
{
#if GMX_MPI
dd->nsystems = 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
struct gmx_mtop_t;
-struct history_t;
+class history_t;
struct t_commrec;
struct t_inputrec;
struct t_pbc;
-struct t_state;
+class t_state;
/*! \brief
* Initiates *fcd data.
gmx_bool bCalcEnerVir,
gmx_bool bDHDL)
{
- if (!bt->haveBondeds)
- {
- return;
- }
+ assert(bt->haveBondeds);
if (bt->nblock_used > 0)
{
/*! \brief Calculate one element of the list of bonded interactions
for this thread */
-real
+static real
calc_one_bond(int thread,
int ftype, const t_idef *idef,
const rvec x[], rvec4 f[], rvec fshift[],
- t_forcerec *fr,
+ const t_forcerec *fr,
const t_pbc *pbc, const t_graph *g,
gmx_grppairener_t *grpp,
t_nrnb *nrnb,
- real *lambda, real *dvdl,
+ const real *lambda, real *dvdl,
const t_mdatoms *md, t_fcdata *fcd,
gmx_bool bCalcEnerVir,
int *global_atom_index)
v = 0;
}
#endif
- else if (ftype == F_ORIRES)
- {
- if (thread == 0)
- {
- v = interaction_function[ftype].ifunc(nbonds*nat1, iatoms,
- idef->iparams,
- x, f, fshift,
- pbc, g, lambda[efptFTYPE], &(dvdl[efptFTYPE]),
- md, fcd, global_atom_index);
- }
- }
else
{
v = interaction_function[ftype].ifunc(nbn, iatoms+nb0,
(ftype < F_GB12 || ftype > F_GB14);
}
+/*! \brief Compute the bonded part of the listed forces, parallelized over threads
+ */
+static void
+calcBondedForces(const t_idef *idef,
+ const rvec x[],
+ const t_forcerec *fr,
+ const t_pbc *pbc_null,
+ const t_graph *g,
+ gmx_enerdata_t *enerd,
+ t_nrnb *nrnb,
+ const real *lambda,
+ real *dvdl,
+ const t_mdatoms *md,
+ t_fcdata *fcd,
+ gmx_bool bCalcEnerVir,
+ int *global_atom_index)
+{
+ struct bonded_threading_t *bt = fr->bonded_threading;
+
+#pragma omp parallel for num_threads(bt->nthreads) schedule(static)
+ for (int thread = 0; thread < bt->nthreads; thread++)
+ {
+ try
+ {
+ int ftype;
+ real *epot, v;
+ /* thread stuff */
+ rvec4 *ft;
+ rvec *fshift;
+ real *dvdlt;
+ gmx_grppairener_t *grpp;
+
+ zero_thread_output(bt, thread);
+
+ ft = bt->f_t[thread].f;
+
+ if (thread == 0)
+ {
+ fshift = fr->fshift;
+ epot = enerd->term;
+ grpp = &enerd->grpp;
+ dvdlt = dvdl;
+ }
+ else
+ {
+ fshift = bt->f_t[thread].fshift;
+ epot = bt->f_t[thread].ener;
+ grpp = &bt->f_t[thread].grpp;
+ dvdlt = bt->f_t[thread].dvdl;
+ }
+ /* Loop over all bonded force types to calculate the bonded forces */
+ for (ftype = 0; (ftype < F_NRE); ftype++)
+ {
+ if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype))
+ {
+ v = calc_one_bond(thread, ftype, idef, x,
+ ft, fshift, fr, pbc_null, g, grpp,
+ nrnb, lambda, dvdlt,
+ md, fcd, bCalcEnerVir,
+ global_atom_index);
+ epot[ftype] += v;
+ }
+ }
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ }
+}
+
void calc_listed(const t_commrec *cr,
struct gmx_wallcycle *wcycle,
const t_idef *idef,
const struct t_pbc *pbc_full,
const struct t_graph *g,
gmx_enerdata_t *enerd, t_nrnb *nrnb,
- real *lambda,
+ const real *lambda,
const t_mdatoms *md,
t_fcdata *fcd, int *global_atom_index,
int force_flags)
{
struct bonded_threading_t *bt;
gmx_bool bCalcEnerVir;
- int i;
- /* The dummy array is to have a place to store the dhdl at other values
- of lambda, which will be thrown away in the end */
- real dvdl[efptNR];
const t_pbc *pbc_null;
- int thread;
bt = fr->bonded_threading;
bCalcEnerVir = (force_flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY));
- for (i = 0; i < efptNR; i++)
- {
- dvdl[i] = 0.0;
- }
if (fr->bMolPBC)
{
pbc_null = pbc;
}
else
{
- pbc_null = NULL;
- }
-
-#ifdef DEBUG
- if (g && debug)
- {
- p_graph(debug, "Bondage is fun", g);
+ pbc_null = nullptr;
}
-#endif
if ((idef->il[F_POSRES].nr > 0) ||
(idef->il[F_FBPOSRES].nr > 0) ||
/* Do pre force calculation stuff which might require communication */
if (fcd->orires.nr > 0)
{
+ /* This assertion is to ensure we have whole molecules.
+ * Unfortunately we do not have an mdrun state variable that tells
+ * us if molecules in x are not broken over PBC, so we have to make
+ * do with checking graph!=nullptr, which should tell us if we made
+ * molecules whole before calling the current function.
+ */
+ GMX_RELEASE_ASSERT(fr->ePBC == epbcNONE || g != nullptr, "With orientation restraints molecules should be whole");
enerd->term[F_ORIRESDEV] =
calc_orires_dev(cr->ms, idef->il[F_ORIRES].nr,
idef->il[F_ORIRES].iatoms,
wallcycle_sub_stop(wcycle, ewcsRESTRAINTS);
}
- /* TODO: Skip this whole loop with a system/domain without listeds */
- wallcycle_sub_start(wcycle, ewcsLISTED);
-#pragma omp parallel for num_threads(bt->nthreads) schedule(static)
- for (thread = 0; thread < bt->nthreads; thread++)
+ if (bt->haveBondeds)
{
- try
+ wallcycle_sub_start(wcycle, ewcsLISTED);
+ /* The dummy array is to have a place to store the dhdl at other values
+ of lambda, which will be thrown away in the end */
+ real dvdl[efptNR] = {0};
+ calcBondedForces(idef, x, fr, pbc_null, g, enerd, nrnb, lambda, dvdl, md,
+ fcd, bCalcEnerVir, global_atom_index);
+ wallcycle_sub_stop(wcycle, ewcsLISTED);
+
+ wallcycle_sub_start(wcycle, ewcsLISTED_BUF_OPS);
+ reduce_thread_output(fr->natoms_force, f, fr->fshift,
+ enerd->term, &enerd->grpp, dvdl,
+ bt,
+ bCalcEnerVir,
+ force_flags & GMX_FORCE_DHDL);
+
+ if (force_flags & GMX_FORCE_DHDL)
{
- int ftype;
- real *epot, v;
- /* thread stuff */
- rvec4 *ft;
- rvec *fshift;
- real *dvdlt;
- gmx_grppairener_t *grpp;
-
- zero_thread_output(bt, thread);
-
- ft = bt->f_t[thread].f;
-
- if (thread == 0)
- {
- fshift = fr->fshift;
- epot = enerd->term;
- grpp = &enerd->grpp;
- dvdlt = dvdl;
- }
- else
- {
- fshift = bt->f_t[thread].fshift;
- epot = bt->f_t[thread].ener;
- grpp = &bt->f_t[thread].grpp;
- dvdlt = bt->f_t[thread].dvdl;
- }
- /* Loop over all bonded force types to calculate the bonded forces */
- for (ftype = 0; (ftype < F_NRE); ftype++)
+ for (int i = 0; i < efptNR; i++)
{
- if (idef->il[ftype].nr > 0 && ftype_is_bonded_potential(ftype))
- {
- v = calc_one_bond(thread, ftype, idef, x,
- ft, fshift, fr, pbc_null, g, grpp,
- nrnb, lambda, dvdlt,
- md, fcd, bCalcEnerVir,
- global_atom_index);
- epot[ftype] += v;
- }
+ enerd->dvdl_nonlin[i] += dvdl[i];
}
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- }
- wallcycle_sub_stop(wcycle, ewcsLISTED);
-
- wallcycle_sub_start(wcycle, ewcsLISTED_BUF_OPS);
- reduce_thread_output(fr->natoms_force, f, fr->fshift,
- enerd->term, &enerd->grpp, dvdl,
- bt,
- bCalcEnerVir,
- force_flags & GMX_FORCE_DHDL);
- wallcycle_sub_stop(wcycle, ewcsLISTED_BUF_OPS);
-
- /* Remaining code does not have enough flops to bother counting */
- if (force_flags & GMX_FORCE_DHDL)
- {
- for (i = 0; i < efptNR; i++)
- {
- enerd->dvdl_nonlin[i] += dvdl[i];
- }
+ wallcycle_sub_stop(wcycle, ewcsLISTED_BUF_OPS);
}
/* Copy the sum of violations for the distance restraints from fcd */
if (fcd)
{
enerd->term[F_DISRESVIOL] = fcd->disres.sumviol;
-
}
}
t_forcerec *fr,
const struct t_pbc *pbc, const struct t_graph *g,
gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
- real *lambda,
+ const real *lambda,
const t_mdatoms *md,
t_fcdata *fcd,
int *global_atom_index)
}
else
{
- pbc_null = NULL;
+ pbc_null = nullptr;
}
/* Copy the whole idef, so we can modify the contents locally */
const struct t_graph *graph,
gmx_enerdata_t *enerd,
t_nrnb *nrnb,
- real *lambda,
+ const real *lambda,
const t_mdatoms *md,
t_fcdata *fcd,
int *global_atom_index,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_enerdata_t;
struct gmx_grppairener_t;
-struct history_t;
+class history_t;
struct t_commrec;
struct t_fcdata;
struct t_forcerec;
struct t_lambda;
struct t_mdatoms;
struct t_nrnb;
-struct t_state;
+class t_state;
#ifdef __cplusplus
extern "C" {
rvec f[], t_forcerec *fr,
const struct t_pbc *pbc, const struct t_pbc *pbc_full,
const struct t_graph *g,
- gmx_enerdata_t *enerd, t_nrnb *nrnb, real *lambda,
+ gmx_enerdata_t *enerd, t_nrnb *nrnb, const real *lambda,
const t_mdatoms *md,
struct t_fcdata *fcd, int *ddgatindex,
int force_flags);
t_forcerec *fr,
const struct t_pbc *pbc, const struct t_graph *g,
gmx_grppairener_t *grpp, real *epot, t_nrnb *nrnb,
- real *lambda,
+ const real *lambda,
const t_mdatoms *md,
struct t_fcdata *fcd, int *global_atom_index);
const struct t_graph *graph,
gmx_enerdata_t *enerd,
t_nrnb *nrnb,
- real *lambda,
+ const real *lambda,
const t_mdatoms *md,
struct t_fcdata *fcd,
int *global_atom_index,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
int atnr;
- if (global_atom_index == NULL)
+ if (global_atom_index == nullptr)
{
atnr = i + 1;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Note that thread 0 uses the global fshift and energy arrays,
* but to keep the code simple, we initialize all data here.
*/
- bt->f_t[t].f = NULL;
+ bt->f_t[t].f = nullptr;
bt->f_t[t].f_nalloc = 0;
snew(bt->f_t[t].fshift, SHIFTS);
bt->f_t[t].grpp.nener = nenergrp*nenergrp;
}
bt->nblock_used = 0;
- bt->block_index = NULL;
- bt->mask = NULL;
+ bt->block_index = nullptr;
+ bt->mask = nullptr;
bt->block_nalloc = 0;
/* The optimal value after which to switch from uniform to localized
const int max_nthread_uniform = 4;
char * ptr;
- if ((ptr = getenv("GMX_BONDED_NTHREAD_UNIFORM")) != NULL)
+ if ((ptr = getenv("GMX_BONDED_NTHREAD_UNIFORM")) != nullptr)
{
sscanf(ptr, "%d", &bt->bonded_max_nthread_uniform);
- if (fplog != NULL)
+ if (fplog != nullptr)
{
fprintf(fplog, "\nMax threads for uniform bonded distribution set to %d by env.var.\n",
bt->bonded_max_nthread_uniform);
#include "orires.h"
+#include <climits>
#include <cmath>
#include "gromacs/gmxlib/network.h"
const t_commrec *cr, t_oriresdata *od,
t_state *state)
{
- int i, j, d, ex, nmol, *nr_ex;
- double mtot;
- rvec com;
- gmx_mtop_ilistloop_t iloop;
- t_ilist *il;
- gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
- const gmx_multisim_t *ms;
-
od->nr = gmx_mtop_ftype_count(mtop, F_ORIRES);
if (0 == od->nr)
{
od->nr, numFitParams + 1, numFitParams);
}
+ if (ir->bPeriodicMols)
+ {
+ /* Since we apply fitting, we need to make molecules whole and this
+ * can not be done when periodic molecules are present.
+ */
+ gmx_fatal(FARGS, "Orientation restraints can not be applied when periodic molecules are present in the system");
+ }
+
if (PAR(cr))
{
gmx_fatal(FARGS, "Orientation restraints do not work with MPI parallelization. Choose 1 MPI rank, if possible.");
/* Nothing to do */
return;
}
- ms = cr->ms;
od->fc = ir->orires_fc;
od->nex = 0;
- od->S = NULL;
- od->M = NULL;
- od->eig = NULL;
- od->v = NULL;
-
- nr_ex = NULL;
-
- iloop = gmx_mtop_ilistloop_init(mtop);
+ od->S = nullptr;
+ od->M = nullptr;
+ od->eig = nullptr;
+ od->v = nullptr;
+
+ int *nr_ex = nullptr;
+ int typeMin = INT_MAX;
+ int typeMax = 0;
+ gmx_mtop_ilistloop_t iloop = gmx_mtop_ilistloop_init(mtop);
+ t_ilist *il;
+ int nmol;
while (gmx_mtop_ilistloop_next(iloop, &il, &nmol))
{
- for (i = 0; i < il[F_ORIRES].nr; i += 3)
+ if (nmol > 1)
+ {
+ gmx_fatal(FARGS, "Found %d copies of a molecule with orientation restrains while the current code only supports a single copy. If you want to ensemble average, run multiple copies of the system using the multi-sim feature of mdrun.", nmol);
+ }
+
+ for (int i = 0; i < il[F_ORIRES].nr; i += 3)
{
- ex = mtop->ffparams.iparams[il[F_ORIRES].iatoms[i]].orires.ex;
+ int type = il[F_ORIRES].iatoms[i];
+ int ex = mtop->ffparams.iparams[type].orires.ex;
if (ex >= od->nex)
{
srenew(nr_ex, ex+1);
- for (j = od->nex; j < ex+1; j++)
+ for (int j = od->nex; j < ex+1; j++)
{
nr_ex[j] = 0;
}
od->nex = ex+1;
}
+ GMX_ASSERT(nr_ex, "Check for allocated nr_ex to keep the static analyzer happy");
nr_ex[ex]++;
+
+ typeMin = std::min(typeMin, type);
+ typeMax = std::max(typeMax, type);
}
}
+ /* With domain decomposition we use the type index for indexing in global arrays */
+ GMX_RELEASE_ASSERT(typeMax - typeMin + 1 == od->nr, "All orientation restraint parameter entries in the topology should be consecutive");
+ /* Store typeMin so we can index array with the type offset */
+ od->typeMin = typeMin;
+
snew(od->S, od->nex);
/* When not doing time averaging, the instaneous and time averaged data
* are indentical and the pointers can point to the same memory.
*/
snew(od->Dinsl, od->nr);
+
+ const gmx_multisim_t *ms = cr->ms;
if (ms)
{
snew(od->Dins, od->nr);
{
snew(od->otav, od->nr);
}
- snew(od->tmp, od->nex);
- snew(od->TMP, od->nex);
- for (ex = 0; ex < od->nex; ex++)
- {
- snew(od->TMP[ex], 5);
- for (i = 0; i < 5; i++)
- {
- snew(od->TMP[ex][i], 5);
- }
- }
+ snew(od->tmpEq, od->nex);
od->nref = 0;
- for (i = 0; i < mtop->natoms; i++)
+ for (int i = 0; i < mtop->natoms; i++)
{
if (ggrpnr(&mtop->groups, egcORFIT, i) == 0)
{
* Copy it to the other nodes after checking multi compatibility,
* so we are sure the subsystems match before copying.
*/
- clear_rvec(com);
- mtot = 0.0;
- j = 0;
- aloop = gmx_mtop_atomloop_all_init(mtop);
+ rvec com = { 0, 0, 0 };
+ double mtot = 0.0;
+ int j = 0;
+ gmx_mtop_atomloop_all_t aloop = gmx_mtop_atomloop_all_init(mtop);
+ int i = -1;
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
- if (mtop->groups.grpnr[egcORFIT] == NULL ||
+ if (mtop->groups.grpnr[egcORFIT] == nullptr ||
mtop->groups.grpnr[egcORFIT][i] == 0)
{
/* Not correct for free-energy with changing masses */
od->mref[j] = atom->m;
- if (ms == NULL || MASTERSIM(ms))
+ if (ms == nullptr || MASTERSIM(ms))
{
copy_rvec(xref[i], od->xref[j]);
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
com[d] += od->mref[j]*xref[i][d];
}
}
}
svmul(1.0/mtot, com, com);
- if (ms == NULL || MASTERSIM(ms))
+ if (ms == nullptr || MASTERSIM(ms))
{
- for (j = 0; j < od->nref; j++)
+ for (int j = 0; j < od->nref; j++)
{
rvec_dec(od->xref[j], com);
}
}
fprintf(fplog, "Found %d orientation experiments\n", od->nex);
- for (i = 0; i < od->nex; i++)
+ for (int i = 0; i < od->nex; i++)
{
fprintf(fplog, " experiment %d has %d restraints\n", i+1, nr_ex[i]);
}
void diagonalize_orires_tensors(t_oriresdata *od)
{
- int ex, i, j, nrot, ord[DIM], t;
- matrix S, TMP;
-
- if (od->M == NULL)
+ if (od->M == nullptr)
{
snew(od->M, DIM);
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
snew(od->M[i], DIM);
}
snew(od->eig_diag, DIM);
snew(od->v, DIM);
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
snew(od->v[i], DIM);
}
}
- for (ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->nex; ex++)
{
/* Rotate the S tensor back to the reference frame */
+ matrix S, TMP;
mmul(od->R, od->S[ex], TMP);
mtmul(TMP, od->R, S);
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
- for (j = 0; j < DIM; j++)
+ for (int j = 0; j < DIM; j++)
{
od->M[i][j] = S[i][j];
}
}
+ int nrot;
jacobi(od->M, DIM, od->eig_diag, od->v, &nrot);
- for (i = 0; i < DIM; i++)
+ int ord[DIM];
+ for (int i = 0; i < DIM; i++)
{
ord[i] = i;
}
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
- for (j = i+1; j < DIM; j++)
+ for (int j = i+1; j < DIM; j++)
{
if (gmx::square(od->eig_diag[ord[j]]) > gmx::square(od->eig_diag[ord[i]]))
{
- t = ord[i];
+ int t = ord[i];
ord[i] = ord[j];
ord[j] = t;
}
}
}
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
od->eig[ex*12 + i] = od->eig_diag[ord[i]];
}
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
- for (j = 0; j < DIM; j++)
+ for (int j = 0; j < DIM; j++)
{
od->eig[ex*12 + 3 + 3*i + j] = od->v[j][ord[i]];
}
void print_orires_log(FILE *log, t_oriresdata *od)
{
- int ex, i;
real *eig;
diagonalize_orires_tensors(od);
- for (ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->nex; ex++)
{
eig = od->eig + ex*12;
fprintf(log, " Orientation experiment %d:\n", ex+1);
fprintf(log, " order parameter: %g\n", eig[0]);
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
fprintf(log, " eig: %6.3f %6.3f %6.3f %6.3f\n",
(eig[0] != 0) ? eig[i]/eig[0] : eig[i],
const t_mdatoms *md, const rvec x[], const t_pbc *pbc,
t_fcdata *fcd, history_t *hist)
{
- int fa, d, i, j, type, ex, nref;
- real edt, edt_1, invn, pfac, r2, invr, corrfac, weight, wsv2, sw, dev;
- tensor *S, R, TMP;
- rvec5 *Dinsl, *Dins, *Dtav, *rhs;
- real *mref, ***T;
+ int nref;
+ real edt, edt_1, invn, pfac, r2, invr, corrfac, wsv2, sw, dev;
+ OriresMatEq *matEq;
+ real *mref;
double mtot;
rvec *xref, *xtmp, com, r_unrot, r;
t_oriresdata *od;
bTAV = (od->edt != 0);
edt = od->edt;
edt_1 = od->edt_1;
- S = od->S;
- Dinsl = od->Dinsl;
- Dins = od->Dins;
- Dtav = od->Dtav;
- T = od->TMP;
- rhs = od->tmp;
+ matEq = od->tmpEq;
nref = od->nref;
mref = od->mref;
xref = od->xref;
}
clear_rvec(com);
- mtot = 0;
- j = 0;
- for (i = 0; i < md->nr; i++)
+ mtot = 0;
+ int j = 0;
+ for (int i = 0; i < md->nr; i++)
{
if (md->cORF[i] == 0)
{
copy_rvec(x[i], xtmp[j]);
mref[j] = md->massT[i];
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
com[d] += mref[j]*xtmp[j][d];
}
}
}
svmul(1.0/mtot, com, com);
- for (j = 0; j < nref; j++)
+ for (int j = 0; j < nref; j++)
{
rvec_dec(xtmp[j], com);
}
/* Calculate the rotation matrix to rotate x to the reference orientation */
- calc_fit_R(DIM, nref, mref, xref, xtmp, R);
- copy_mat(R, od->R);
+ calc_fit_R(DIM, nref, mref, xref, xtmp, od->R);
- d = 0;
- for (fa = 0; fa < nfa; fa += 3)
+ for (int fa = 0; fa < nfa; fa += 3)
{
- type = forceatoms[fa];
+ const int type = forceatoms[fa];
+ const int restraintIndex = type - od->typeMin;
if (pbc)
{
pbc_dx_aiuc(pbc, x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
{
rvec_sub(x[forceatoms[fa+1]], x[forceatoms[fa+2]], r_unrot);
}
- mvmul(R, r_unrot, r);
+ mvmul(od->R, r_unrot, r);
r2 = norm2(r);
invr = gmx::invsqrt(r2);
/* Calculate the prefactor for the D tensor, this includes the factor 3! */
pfac = ip[type].orires.c*invr*invr*3;
- for (i = 0; i < ip[type].orires.power; i++)
+ for (int i = 0; i < ip[type].orires.power; i++)
{
pfac *= invr;
}
- Dinsl[d][0] = pfac*(2*r[0]*r[0] + r[1]*r[1] - r2);
- Dinsl[d][1] = pfac*(2*r[0]*r[1]);
- Dinsl[d][2] = pfac*(2*r[0]*r[2]);
- Dinsl[d][3] = pfac*(2*r[1]*r[1] + r[0]*r[0] - r2);
- Dinsl[d][4] = pfac*(2*r[1]*r[2]);
+ rvec5 &Dinsl = od->Dinsl[restraintIndex];
+ Dinsl[0] = pfac*(2*r[0]*r[0] + r[1]*r[1] - r2);
+ Dinsl[1] = pfac*(2*r[0]*r[1]);
+ Dinsl[2] = pfac*(2*r[0]*r[2]);
+ Dinsl[3] = pfac*(2*r[1]*r[1] + r[0]*r[0] - r2);
+ Dinsl[4] = pfac*(2*r[1]*r[2]);
if (ms)
{
- for (i = 0; i < 5; i++)
+ for (int i = 0; i < 5; i++)
{
- Dins[d][i] = Dinsl[d][i]*invn;
+ od->Dins[restraintIndex][i] = Dinsl[i]*invn;
}
}
-
- d++;
}
if (ms)
{
- gmx_sum_sim(5*od->nr, Dins[0], ms);
+ gmx_sum_sim(5*od->nr, od->Dins[0], ms);
}
/* Calculate the order tensor S for each experiment via optimization */
- for (ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->nex; ex++)
{
- for (i = 0; i < 5; i++)
+ for (int i = 0; i < 5; i++)
{
- rhs[ex][i] = 0;
- for (j = 0; j <= i; j++)
+ matEq[ex].rhs[i] = 0;
+ for (int j = 0; j <= i; j++)
{
- T[ex][i][j] = 0;
+ matEq[ex].mat[i][j] = 0;
}
}
}
- d = 0;
- for (fa = 0; fa < nfa; fa += 3)
+
+ for (int fa = 0; fa < nfa; fa += 3)
{
+ const int type = forceatoms[fa];
+ const int restraintIndex = type - od->typeMin;
+ rvec5 &Dtav = od->Dtav[restraintIndex];
if (bTAV)
{
/* Here we update Dtav in t_fcdata using the data in history_t.
* Thus the results stay correct when this routine
* is called multiple times.
*/
- for (i = 0; i < 5; i++)
+ for (int i = 0; i < 5; i++)
{
- Dtav[d][i] = edt*hist->orire_Dtav[d*5+i] + edt_1*Dins[d][i];
+ Dtav[i] =
+ edt*hist->orire_Dtav[restraintIndex*5 + i] +
+ edt_1*od->Dins[restraintIndex][i];
}
}
- type = forceatoms[fa];
- ex = ip[type].orires.ex;
- weight = ip[type].orires.kfac;
+ int ex = ip[type].orires.ex;
+ real weight = ip[type].orires.kfac;
/* Calculate the vector rhs and half the matrix T for the 5 equations */
- for (i = 0; i < 5; i++)
+ for (int i = 0; i < 5; i++)
{
- rhs[ex][i] += Dtav[d][i]*ip[type].orires.obs*weight;
- for (j = 0; j <= i; j++)
+ matEq[ex].rhs[i] += Dtav[i]*ip[type].orires.obs*weight;
+ for (int j = 0; j <= i; j++)
{
- T[ex][i][j] += Dtav[d][i]*Dtav[d][j]*weight;
+ matEq[ex].mat[i][j] += Dtav[i]*Dtav[j]*weight;
}
}
- d++;
}
/* Now we have all the data we can calculate S */
- for (ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->nex; ex++)
{
+ OriresMatEq &eq = matEq[ex];
/* Correct corrfac and copy one half of T to the other half */
- for (i = 0; i < 5; i++)
+ for (int i = 0; i < 5; i++)
{
- rhs[ex][i] *= corrfac;
- T[ex][i][i] *= gmx::square(corrfac);
- for (j = 0; j < i; j++)
+ eq.rhs[i] *= corrfac;
+ eq.mat[i][i] *= gmx::square(corrfac);
+ for (int j = 0; j < i; j++)
{
- T[ex][i][j] *= gmx::square(corrfac);
- T[ex][j][i] = T[ex][i][j];
+ eq.mat[i][j] *= gmx::square(corrfac);
+ eq.mat[j][i] = eq.mat[i][j];
}
}
- m_inv_gen(T[ex], 5, T[ex]);
+ m_inv_gen(&eq.mat[0][0], 5, &eq.mat[0][0]);
/* Calculate the orientation tensor S for this experiment */
- S[ex][0][0] = 0;
- S[ex][0][1] = 0;
- S[ex][0][2] = 0;
- S[ex][1][1] = 0;
- S[ex][1][2] = 0;
- for (i = 0; i < 5; i++)
+ matrix &S = od->S[ex];
+ S[0][0] = 0;
+ S[0][1] = 0;
+ S[0][2] = 0;
+ S[1][1] = 0;
+ S[1][2] = 0;
+ for (int i = 0; i < 5; i++)
{
- S[ex][0][0] += 1.5*T[ex][0][i]*rhs[ex][i];
- S[ex][0][1] += 1.5*T[ex][1][i]*rhs[ex][i];
- S[ex][0][2] += 1.5*T[ex][2][i]*rhs[ex][i];
- S[ex][1][1] += 1.5*T[ex][3][i]*rhs[ex][i];
- S[ex][1][2] += 1.5*T[ex][4][i]*rhs[ex][i];
+ S[0][0] += 1.5*eq.mat[0][i]*eq.rhs[i];
+ S[0][1] += 1.5*eq.mat[1][i]*eq.rhs[i];
+ S[0][2] += 1.5*eq.mat[2][i]*eq.rhs[i];
+ S[1][1] += 1.5*eq.mat[3][i]*eq.rhs[i];
+ S[1][2] += 1.5*eq.mat[4][i]*eq.rhs[i];
}
- S[ex][1][0] = S[ex][0][1];
- S[ex][2][0] = S[ex][0][2];
- S[ex][2][1] = S[ex][1][2];
- S[ex][2][2] = -S[ex][0][0] - S[ex][1][1];
+ S[1][0] = S[0][1];
+ S[2][0] = S[0][2];
+ S[2][1] = S[1][2];
+ S[2][2] = -S[0][0] - S[1][1];
}
- wsv2 = 0;
- sw = 0;
+ const matrix *S = od->S;
- d = 0;
- for (fa = 0; fa < nfa; fa += 3)
+ wsv2 = 0;
+ sw = 0;
+
+ for (int fa = 0; fa < nfa; fa += 3)
{
- type = forceatoms[fa];
- ex = ip[type].orires.ex;
+ const int type = forceatoms[fa];
+ const int restraintIndex = type - od->typeMin;
+ const int ex = ip[type].orires.ex;
- od->otav[d] = two_thr*
- corrfac*(S[ex][0][0]*Dtav[d][0] + S[ex][0][1]*Dtav[d][1] +
- S[ex][0][2]*Dtav[d][2] + S[ex][1][1]*Dtav[d][3] +
- S[ex][1][2]*Dtav[d][4]);
+ const rvec5 &Dtav = od->Dtav[restraintIndex];
+ od->otav[restraintIndex] = two_thr*
+ corrfac*(S[ex][0][0]*Dtav[0] + S[ex][0][1]*Dtav[1] +
+ S[ex][0][2]*Dtav[2] + S[ex][1][1]*Dtav[3] +
+ S[ex][1][2]*Dtav[4]);
if (bTAV)
{
- od->oins[d] = two_thr*(S[ex][0][0]*Dins[d][0] + S[ex][0][1]*Dins[d][1] +
- S[ex][0][2]*Dins[d][2] + S[ex][1][1]*Dins[d][3] +
- S[ex][1][2]*Dins[d][4]);
+ const rvec5 &Dins = od->Dins[restraintIndex];
+ od->oins[restraintIndex] = two_thr*
+ (S[ex][0][0]*Dins[0] + S[ex][0][1]*Dins[1] +
+ S[ex][0][2]*Dins[2] + S[ex][1][1]*Dins[3] +
+ S[ex][1][2]*Dins[4]);
}
if (ms)
{
/* When ensemble averaging is used recalculate the local orientation
* for output to the energy file.
*/
- od->oinsl[d] = two_thr*
- (S[ex][0][0]*Dinsl[d][0] + S[ex][0][1]*Dinsl[d][1] +
- S[ex][0][2]*Dinsl[d][2] + S[ex][1][1]*Dinsl[d][3] +
- S[ex][1][2]*Dinsl[d][4]);
+ const rvec5 &Dinsl = od->Dinsl[restraintIndex];
+ od->oinsl[restraintIndex] = two_thr*
+ (S[ex][0][0]*Dinsl[0] + S[ex][0][1]*Dinsl[1] +
+ S[ex][0][2]*Dinsl[2] + S[ex][1][1]*Dinsl[3] +
+ S[ex][1][2]*Dinsl[4]);
}
- dev = od->otav[d] - ip[type].orires.obs;
+ dev = od->otav[restraintIndex] - ip[type].orires.obs;
wsv2 += ip[type].orires.kfac*gmx::square(dev);
sw += ip[type].orires.kfac;
-
- d++;
}
od->rmsdev = std::sqrt(wsv2/sw);
/* Rotate the S matrices back, so we get the correct grad(tr(S D)) */
- for (ex = 0; ex < od->nex; ex++)
+ for (int ex = 0; ex < od->nex; ex++)
{
- tmmul(R, S[ex], TMP);
- mmul(TMP, R, S[ex]);
+ matrix RS;
+ tmmul(od->R, od->S[ex], RS);
+ mmul(RS, od->R, od->S[ex]);
}
return od->rmsdev;
const t_mdatoms gmx_unused *md, t_fcdata *fcd,
int gmx_unused *global_atom_index)
{
- int ai, aj;
- int fa, d, i, type, ex, power, ki = CENTRAL;
+ int ex, power, ki = CENTRAL;
ivec dt;
real r2, invr, invr2, fc, smooth_fc, dev, devins, pfac;
rvec r, Sr, fij;
smooth_fc *= (1.0 - od->exp_min_t_tau);
}
- d = 0;
- for (fa = 0; fa < nfa; fa += 3)
+ for (int fa = 0; fa < nfa; fa += 3)
{
- type = forceatoms[fa];
- ai = forceatoms[fa+1];
- aj = forceatoms[fa+2];
+ const int type = forceatoms[fa];
+ const int ai = forceatoms[fa + 1];
+ const int aj = forceatoms[fa + 2];
+ const int restraintIndex = type - od->typeMin;
if (pbc)
{
ki = pbc_dx_aiuc(pbc, x[ai], x[aj], r);
ex = ip[type].orires.ex;
power = ip[type].orires.power;
fc = smooth_fc*ip[type].orires.kfac;
- dev = od->otav[d] - ip[type].orires.obs;
+ dev = od->otav[restraintIndex] - ip[type].orires.obs;
/* NOTE:
* there is no real potential when time averaging is applied
if (bTAV)
{
/* Calculate the force as the sqrt of tav times instantaneous */
- devins = od->oins[d] - ip[type].orires.obs;
+ devins = od->oins[restraintIndex] - ip[type].orires.obs;
if (dev*devins <= 0)
{
dev = 0;
}
pfac = fc*ip[type].orires.c*invr2;
- for (i = 0; i < power; i++)
+ for (int i = 0; i < power; i++)
{
pfac *= invr;
}
mvmul(od->S[ex], r, Sr);
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
fij[i] =
-pfac*dev*(4*Sr[i] - 2*(2+power)*invr2*iprod(Sr, r)*r[i]);
ki = IVEC2IS(dt);
}
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
f[ai][i] += fij[i];
f[aj][i] -= fij[i];
fshift[ki][i] += fij[i];
fshift[CENTRAL][i] -= fij[i];
}
- d++;
}
}
void update_orires_history(t_fcdata *fcd, history_t *hist)
{
- t_oriresdata *od;
- int pair, i;
+ t_oriresdata *od = &(fcd->orires);
- od = &(fcd->orires);
if (od->edt != 0)
{
/* Copy the new time averages that have been calculated
* in calc_orires_dev.
*/
hist->orire_initf = od->exp_min_t_tau;
- for (pair = 0; pair < od->nr; pair++)
+ for (int pair = 0; pair < od->nr; pair++)
{
- for (i = 0; i < 5; i++)
+ for (int i = 0; i < 5; i++)
{
hist->orire_Dtav[pair*5+i] = od->Dtav[pair][i];
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_mtop_t;
struct gmx_multisim_t;
-struct history_t;
+class history_t;
struct t_inputrec;
struct t_pbc;
struct t_commrec;
struct t_fcdata;
struct t_oriresdata;
-struct t_state;
+class t_state;
/*! \brief
* Decides whether orientation restraints can work, and initializes
}
/*! \brief Compute the energy and force for a single pair interaction */
-real
+static real
evaluate_single(real r2, real tabscale, real *vftab, real tableStride,
real qq, real c6, real c12, real *velec, real *vvdw)
{
}
/*! \brief Compute the energy and force for a single pair interaction under FEP */
-real
+static real
free_energy_evaluate_single(real r2, real sc_r_power, real alpha_coul,
real alpha_vdw, real tabscale, real *vftab, real tableStride,
real qqA, real c6A, real c12A, real qqB,
const t_iatom iatoms[], const t_iparams iparams[],
const rvec x[], rvec4 f[], rvec fshift[],
const struct t_pbc *pbc, const struct t_graph *g,
- real *lambda, real *dvdl,
+ const real *lambda, real *dvdl,
const t_mdatoms *md,
const t_forcerec *fr, gmx_grppairener_t *grppener,
int *global_atom_index)
energygrp_vdw = grppener->ener[egLJSR];
break;
default:
- energygrp_elec = NULL; /* Keep compiler happy */
- energygrp_vdw = NULL; /* Keep compiler happy */
+ energygrp_elec = nullptr; /* Keep compiler happy */
+ energygrp_vdw = nullptr; /* Keep compiler happy */
gmx_fatal(FARGS, "Unknown function type %d in do_nonbonded14", ftype);
break;
}
const t_iatom iatoms[], const t_iparams iparams[],
const rvec x[], rvec4 f[], rvec fshift[],
const struct t_pbc *pbc, const struct t_graph *g,
- real *lambda, real *dvdl,
+ const real *lambda, real *dvdl,
const t_mdatoms *md,
const t_forcerec *fr,
gmx_bool bCalcEnergyAndVirial, gmx_grppairener_t *grppener,
t_pbc pbc_no;
const t_pbc *pbc_nonnull;
- if (pbc != NULL)
+ if (pbc != nullptr)
{
pbc_nonnull = pbc;
}
else
{
- set_pbc(&pbc_no, epbcNONE, NULL);
+ set_pbc(&pbc_no, epbcNONE, nullptr);
pbc_nonnull = &pbc_no;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
do_pairs(int ftype, int nbonds, const t_iatom iatoms[], const t_iparams iparams[],
const rvec x[], rvec4 f[], rvec fshift[],
const struct t_pbc *pbc, const struct t_graph *g,
- real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr,
+ const real *lambda, real *dvdl, const t_mdatoms *md, const t_forcerec *fr,
gmx_bool bCalcEnergyAndVirial, gmx_grppairener_t *grppener,
int *global_atom_index);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
rvec comA_sc, comB_sc, rdist, dpdl, dx;
gmx_bool bForceValid = TRUE;
- if ((f == NULL) || (vir_diag == NULL)) /* should both be null together! */
+ if ((f == nullptr) || (vir_diag == nullptr)) /* should both be null together! */
{
bForceValid = FALSE;
}
const struct t_pbc *pbc,
const rvec x[],
gmx_enerdata_t *enerd,
- real *lambda,
+ const real *lambda,
t_forcerec *fr)
{
real v, dvdl;
dvdl = 0;
v = posres(idef->il[F_POSRES].nr, idef->il[F_POSRES].iatoms,
idef->iparams_posres,
- x, fr->f_novirsum, fr->vir_diag_posres,
- fr->ePBC == epbcNONE ? NULL : pbc,
+ x, as_rvec_array(fr->f_novirsum->data()), fr->vir_diag_posres,
+ fr->ePBC == epbcNONE ? nullptr : pbc,
lambda[efptRESTRAINT], &dvdl,
fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
enerd->term[F_POSRES] += v;
const struct t_pbc *pbc,
const rvec x[],
gmx_enerdata_t *enerd,
- real *lambda,
+ const real *lambda,
t_forcerec *fr)
{
real v;
lambda_dum = (i == 0 ? lambda[efptRESTRAINT] : fepvals->all_lambda[efptRESTRAINT][i-1]);
v = posres(idef->il[F_POSRES].nr, idef->il[F_POSRES].iatoms,
idef->iparams_posres,
- x, NULL, NULL,
- fr->ePBC == epbcNONE ? NULL : pbc, lambda_dum, &dvdl_dum,
+ x, nullptr, nullptr,
+ fr->ePBC == epbcNONE ? nullptr : pbc, lambda_dum, &dvdl_dum,
fr->rc_scaling, fr->ePBC, fr->posres_com, fr->posres_comB);
enerd->enerpart_lambda[i] += v;
}
v = fbposres(idef->il[F_FBPOSRES].nr, idef->il[F_FBPOSRES].iatoms,
idef->iparams_fbposres,
- x, fr->f_novirsum, fr->vir_diag_posres,
- fr->ePBC == epbcNONE ? NULL : pbc,
+ x, as_rvec_array(fr->f_novirsum->data()), fr->vir_diag_posres,
+ fr->ePBC == epbcNONE ? nullptr : pbc,
fr->rc_scaling, fr->ePBC, fr->posres_com);
enerd->term[F_FBPOSRES] += v;
inc_nrnb(nrnb, eNR_FBPOSRES, idef->il[F_FBPOSRES].nr/2);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const struct t_pbc *pbc,
const rvec x[],
gmx_enerdata_t *enerd,
- real *lambda,
+ const real *lambda,
t_forcerec *fr);
/*! \brief Helper function that wraps calls to posres for free-energy
const struct t_pbc *pbc,
const rvec x[],
gmx_enerdata_t *enerd,
- real *lambda,
+ const real *lambda,
t_forcerec *fr);
/*! \brief Helper function that wraps calls to fbposres for
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2016, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(ListedForcesTest listed-forces-test
+ bonded.cpp)
+
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements test of bonded force routines
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_listed-forces
+ */
+#include "gmxpre.h"
+
+#include "gromacs/listed-forces/bonded.h"
+
+#include <cmath>
+
+#include <memory>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/units.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/testfilemanager.h"
+
+namespace gmx
+{
+namespace
+{
+
+//! Number of atoms used in these tests.
+#define NATOMS 4
+
+class BondedTest : public ::testing::Test
+{
+ protected:
+ rvec x[NATOMS];
+ matrix box;
+ test::TestReferenceData refData_;
+ test::TestReferenceChecker checker_;
+ BondedTest( ) :
+ checker_(refData_.rootChecker())
+ {
+ test::FloatingPointTolerance tolerance(test::relativeToleranceAsFloatingPoint(1.0, 1e-6));
+ checker_.setDefaultTolerance(tolerance);
+ clear_rvecs(NATOMS, x);
+ x[1][2] = 1;
+ x[2][1] = x[2][2] = 1;
+ x[3][0] = x[3][1] = x[3][2] = 1;
+
+ clear_mat(box);
+ box[0][0] = box[1][1] = box[2][2] = 1.5;
+ }
+
+ void testBondAngle(int epbc)
+ {
+ rvec r_ij, r_kj;
+ real cosine_angle, angle;
+ int t1, t2;
+ t_pbc pbc;
+
+ set_pbc(&pbc, epbc, box);
+ angle = bond_angle(x[0], x[1], x[2], &pbc,
+ r_ij, r_kj, &cosine_angle,
+ &t1, &t2);
+ checker_.checkReal(angle, "angle");
+ checker_.checkReal(cosine_angle, "cosine_angle");
+ checker_.checkInteger(t1, "t1");
+ checker_.checkInteger(t2, "t2");
+ }
+
+ void testDihedralAngle(int epbc)
+ {
+ rvec r_ij, r_kj, r_kl, m, n;
+ real cosine_angle, angle;
+ int t1, t2, t3;
+ t_pbc pbc;
+
+ set_pbc(&pbc, epbc, box);
+ angle = dih_angle(x[0], x[1], x[2], x[3], &pbc,
+ r_ij, r_kj, r_kl, m, n, &cosine_angle,
+ &t1, &t2, &t3);
+
+ checker_.checkReal(angle, "angle");
+ checker_.checkReal(cosine_angle, "cosine_angle");
+ checker_.checkInteger(t1, "t1");
+ checker_.checkInteger(t2, "t2");
+ checker_.checkInteger(t3, "t3");
+ }
+
+ void testIfunc(int ftype,
+ const std::vector<t_iatom> &iatoms,
+ const t_iparams iparams[],
+ int epbc)
+ {
+ real lambda = 0;
+ real dvdlambda = 0;
+ rvec4 f[NATOMS];
+ for (int i = 0; i < NATOMS; i++)
+ {
+ for (int j = 0; j < 4; j++)
+ {
+ f[i][j] = 0;
+ }
+ }
+ rvec fshift[N_IVEC];
+ clear_rvecs(N_IVEC, fshift);
+ t_pbc pbc;
+ set_pbc(&pbc, epbc, box);
+ int ddgatindex = 0;
+ real energy = interaction_function[ftype].ifunc(iatoms.size(),
+ iatoms.data(),
+ iparams,
+ x, f, fshift,
+ &pbc,
+ /* const struct t_graph *g */ nullptr,
+ lambda, &dvdlambda,
+ /* const struct t_mdatoms *md */ nullptr,
+ /* struct t_fcdata *fcd */ nullptr,
+ &ddgatindex);
+ checker_.checkReal(energy, interaction_function[ftype].longname);
+ }
+
+};
+
+TEST_F (BondedTest, BondAnglePbcNone)
+{
+ testBondAngle(epbcNONE);
+}
+
+TEST_F (BondedTest, BondAnglePbcXy)
+{
+ testBondAngle(epbcXY);
+}
+
+TEST_F (BondedTest, BondAnglePbcXyz)
+{
+ testBondAngle(epbcXYZ);
+}
+
+TEST_F (BondedTest, DihedralAnglePbcNone)
+{
+ testDihedralAngle(epbcNONE);
+}
+
+TEST_F (BondedTest, DihedralAnglePbcXy)
+{
+ testDihedralAngle(epbcXY);
+}
+
+TEST_F (BondedTest, DihedralAnglePbcXyz)
+{
+ testDihedralAngle(epbcXYZ);
+}
+
+TEST_F (BondedTest, IfuncBondsPbcNo)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 0, 1, 2, 0, 2, 3 };
+ t_iparams iparams;
+ iparams.harmonic.rA = iparams.harmonic.rB = 0.8;
+ iparams.harmonic.krA = iparams.harmonic.krB = 50;
+ testIfunc(F_BONDS, iatoms, &iparams, epbcNONE);
+}
+
+TEST_F (BondedTest, IfuncBondsPbcXy)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 0, 1, 2, 0, 2, 3 };
+ t_iparams iparams;
+ iparams.harmonic.rA = iparams.harmonic.rB = 0.8;
+ iparams.harmonic.krA = iparams.harmonic.krB = 50;
+ testIfunc(F_BONDS, iatoms, &iparams, epbcXY);
+}
+
+TEST_F (BondedTest, IfuncBondsPbcXyz)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 0, 1, 2, 0, 2, 3 };
+ t_iparams iparams;
+ iparams.harmonic.rA = iparams.harmonic.rB = 0.8;
+ iparams.harmonic.krA = iparams.harmonic.krB = 50;
+ testIfunc(F_BONDS, iatoms, &iparams, epbcXYZ);
+}
+
+TEST_F (BondedTest, IfuncAnglesPbcNo)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 2, 0, 1, 2, 3 };
+ t_iparams iparams;
+ real k = 50;
+ iparams.harmonic.rA = iparams.harmonic.rB = 100;
+ iparams.harmonic.krA = iparams.harmonic.krB = k;
+ testIfunc(F_ANGLES, iatoms, &iparams, epbcNONE);
+}
+
+TEST_F (BondedTest, IfuncAnglesPbcXy)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 2, 0, 1, 2, 3 };
+ t_iparams iparams;
+ real k = 50;
+ iparams.harmonic.rA = iparams.harmonic.rB = 100;
+ iparams.harmonic.krA = iparams.harmonic.krB = k;
+ testIfunc(F_ANGLES, iatoms, &iparams, epbcXY);
+}
+
+TEST_F (BondedTest, IfuncAnglesPbcXYZ)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 2, 0, 1, 2, 3 };
+ t_iparams iparams;
+ real k = 50;
+ iparams.harmonic.rA = iparams.harmonic.rB = 100;
+ iparams.harmonic.krA = iparams.harmonic.krB = k;
+ testIfunc(F_ANGLES, iatoms, &iparams, epbcXYZ);
+}
+
+TEST_F (BondedTest, IfuncProperDihedralsPbcNo)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 2, 3 };
+ t_iparams iparams;
+ iparams.pdihs.phiA = iparams.pdihs.phiB = -100;
+ iparams.pdihs.cpA = iparams.pdihs.cpB = 10;
+ iparams.pdihs.mult = 1;
+ testIfunc(F_PDIHS, iatoms, &iparams, epbcNONE);
+}
+
+TEST_F (BondedTest, IfuncProperDihedralsPbcXy)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 2, 3 };
+ t_iparams iparams;
+ iparams.pdihs.phiA = iparams.pdihs.phiB = -100;
+ iparams.pdihs.cpA = iparams.pdihs.cpB = 10;
+ iparams.pdihs.mult = 1;
+ testIfunc(F_PDIHS, iatoms, &iparams, epbcXY);
+}
+
+TEST_F (BondedTest, IfuncProperDihedralsPbcXyz)
+{
+ std::vector<t_iatom> iatoms = { 0, 0, 1, 2, 3 };
+ t_iparams iparams;
+ iparams.pdihs.phiA = iparams.pdihs.phiB = -100;
+ iparams.pdihs.cpA = iparams.pdihs.cpB = 10;
+ iparams.pdihs.mult = 1;
+ testIfunc(F_PDIHS, iatoms, &iparams, epbcXYZ);
+}
+
+}
+
+}
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="angle">1.5707964</Real>
+ <Real Name="cosine_angle">0</Real>
+ <Int Name="t1">22</Int>
+ <Int Name="t2">22</Int>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="angle">1.5707964</Real>
+ <Real Name="cosine_angle">0</Real>
+ <Int Name="t1">22</Int>
+ <Int Name="t2">17</Int>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="angle">1.5707964</Real>
+ <Real Name="cosine_angle">0</Real>
+ <Int Name="t1">37</Int>
+ <Int Name="t2">17</Int>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="angle">-1.5707964</Real>
+ <Real Name="cosine_angle">-1</Real>
+ <Int Name="t1">22</Int>
+ <Int Name="t2">22</Int>
+ <Int Name="t3">22</Int>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="angle">-1.5707964</Real>
+ <Real Name="cosine_angle">-1</Real>
+ <Int Name="t1">22</Int>
+ <Int Name="t2">17</Int>
+ <Int Name="t3">23</Int>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="angle">1.5707964</Real>
+ <Real Name="cosine_angle">1</Real>
+ <Int Name="t1">37</Int>
+ <Int Name="t2">17</Int>
+ <Int Name="t3">23</Int>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Angle">1.5230865</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Angle">1.5230865</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Angle">1.5230865</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Bond">2.9999995</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Bond">5.5</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Bond">6.75</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Proper Dih.">19.848078</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Proper Dih.">19.848078</Real>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Real Name="Proper Dih.">0.1519227</Real>
+</ReferenceData>
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
utilities.h
vec.h
vectypes.h
+ paddedvector.h
)
if (BUILD_TESTING)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real rmsdev(int natoms, real mass[], rvec x[], rvec xp[])
{
- return calc_similar_ind(FALSE, natoms, NULL, mass, x, xp);
+ return calc_similar_ind(FALSE, natoms, nullptr, mass, x, xp);
}
real rhodev_ind(int nind, int index[], real mass[], rvec x[], rvec xp[])
real rhodev(int natoms, real mass[], rvec x[], rvec xp[])
{
- return calc_similar_ind(TRUE, natoms, NULL, mass, x, xp);
+ return calc_similar_ind(TRUE, natoms, nullptr, mass, x, xp);
}
void calc_fit_R(int ndim, int natoms, real *w_rls, const rvec *xp, rvec *x, matrix R)
}
tm = 0.0;
clear_rvec(xcm);
- if (ind_cm != NULL)
+ if (ind_cm != nullptr)
{
for (i = 0; i < ncm; i++)
{
xcm[m] /= tm;
}
- if (ind_reset != NULL)
+ if (ind_reset != nullptr)
{
for (i = 0; i < nreset; i++)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return d;
}
-static t_complex rcexp(real r)
+static inline t_complex rcexp(real r)
{
t_complex c;
}
-static t_complex cadd(t_complex a, t_complex b)
+static inline t_complex cadd(t_complex a, t_complex b)
{
t_complex c;
return c;
}
-static t_complex csub(t_complex a, t_complex b)
+static inline t_complex csub(t_complex a, t_complex b)
{
t_complex c;
return d;
}
-static real cabs2(t_complex c)
+static inline real cabs2(t_complex c)
{
real abs2;
abs2 = (c.re*c.re)+(c.im*c.im);
return abs2;
}
-
-
-static t_complex cdiv(t_complex teller, t_complex noemer)
+static inline t_complex cdiv(t_complex teller, t_complex noemer)
{
t_complex res, anoemer;
return rcmul(1.0/anoemer.re, res);
}
+
+inline bool operator==(const t_complex &lhs, const t_complex &rhs){ return (lhs.re == rhs.re) && (lhs.im == rhs.im); }
+inline bool operator!=(const t_complex &lhs, const t_complex &rhs){ return !(lhs == rhs); }
+
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::PaddedRVecVector
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inpublicapi
+ * \ingroup module_math
+ */
+#ifndef GMX_MATH_PADDEDVECTOR_H
+#define GMX_MATH_PADDEDVECTOR_H
+
+#include <vector>
+
+#include "gromacs/math/vectypes.h"
+
+namespace gmx
+{
+
+/*! \brief Temporary definition of a type usable for SIMD-style loads of RVec quantities.
+ *
+ * \todo This vector is not padded yet, padding will be added soon */
+using PaddedRVecVector = std::vector<gmx::RVec>;
+
+} // namespace gmx
+
+// TODO This is a hack to avoid littering gmx:: all over code that is
+// almost all destined to move into the gmx namespace at some point.
+// An alternative would be about 20 files with using statements.
+using gmx::PaddedRVecVector;
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST(RVecTest, CanBeStoredInVector)
{
std::vector<RVec> v;
- v.push_back(RVec(1, 2, 3));
+ v.emplace_back(1, 2, 3);
v.resize(2);
EXPECT_EQ(1, v[0][XX]);
EXPECT_EQ(2, v[0][YY]);
{
std::vector<RVec> v;
rvec x = { 1, 2, 3 };
- v.push_back(x);
+ v.emplace_back(x);
EXPECT_EQ(1, v[0][XX]);
EXPECT_EQ(2, v[0][YY]);
EXPECT_EQ(3, v[0][ZZ]);
TEST(RVecTest, ConvertsImplicitlyTo_rvec)
{
std::vector<RVec> v;
- v.push_back(RVec(1, 2, 3));
+ v.emplace_back(1, 2, 3);
rvec x;
copy_rvec(v[0], x);
EXPECT_EQ(1, x[XX]);
TEST(RVecTest, WorksAsMutable_rvec)
{
std::vector<RVec> v;
- v.push_back(RVec(1, 2, 3));
+ v.emplace_back(1, 2, 3);
rvec x = {2, 3, 4};
copy_rvec(x, v[0]);
EXPECT_EQ(2, v[0][XX]);
TEST(RVecTest, WorksAs_rvec_Array)
{
std::vector<RVec> v;
- v.push_back(RVec(1, 2, 3));
- v.push_back(RVec(2, 3, 4));
+ v.emplace_back(1, 2, 3);
+ v.emplace_back(2, 3, 4);
const rvec *r = as_rvec_array(v.data());
EXPECT_EQ(1, r[0][XX]);
EXPECT_EQ(2, r[0][YY]);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return eg2c_names[unit];
}
- return NULL;
+ return nullptr;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define M_2_SQRTPI 1.128379167095513
#endif
+/*! \brief Enum to select safe or highly unsafe (faster) math functions.
+ *
+ * Normally all the Gromacs math functions should apply reasonable care with
+ * input arguments. While we do not necessarily adhere strictly to IEEE
+ * (in particular not for arguments that might result in NaN, inf, etc.), the
+ * functions should return reasonable values or e.g. clamp results to zero.
+ *
+ * However, in a few cases where we are extremely performance-sensitive it
+ * makes sense to forego these checks too in cases where we know the exact
+ * properties if the input data, and we really need to save every cycle we can.
+ *
+ * This class is typically used as a template parameter to such calls to enable
+ * the caller to select the level of aggressiveness. We should always use the
+ * safe alternative as the default value, and document carefully what might
+ * happen with the unsafe alternative.
+ */
+enum class MathOptimization
+{
+ Safe, //!< Don't do unsafe optimizations. This should always be default.
+ Unsafe //!< Allow optimizations that can be VERY dangerous for general code.
+};
+
/*! \brief Check if two numbers are within a tolerance
*
* This routine checks if the relative difference between two numbers is
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "veccompare.h"
+
+#include <cmath>
+#include <cstdio>
+
+#include "gromacs/utility/compare.h"
+
+void cmp_rvec(FILE *fp, const char *s, int index, const rvec i1, const rvec i2, real ftol, real abstol)
+{
+ if (!equal_real(i1[XX], i2[XX], ftol, abstol) ||
+ !equal_real(i1[YY], i2[YY], ftol, abstol) ||
+ !equal_real(i1[ZZ], i2[ZZ], ftol, abstol))
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%5d] (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
+ s, index, i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
+ }
+ else
+ {
+ fprintf(fp, "%s (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
+ s, i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
+ }
+ }
+}
+
+void cmp_ivec(FILE *fp, const char *s, int index, const ivec i1, const ivec i2)
+{
+ if ((i1[XX] != i2[XX]) || (i1[YY] != i2[YY]) || (i1[ZZ] != i2[ZZ]))
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%5d] (%8d,%8d,%8d - %8d,%8d,%8d)\n", s, index,
+ i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
+ }
+ else
+ {
+ fprintf(fp, "%s (%8d,%8d,%8d - %8d,%8d,%8d)\n", s,
+ i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
+ }
+ }
+}
+
+static void cmp_rvecs_rmstol(FILE *fp, const char *title, int n, const rvec x1[], const rvec x2[],
+ real ftol, real abstol)
+{
+ int i, m;
+ double rms;
+
+ /* For a vector you are usally not interested in a relative difference
+ * on a component that is very small compared to the other components.
+ * Therefore we do the relative comparision relative to the RMS component.
+ */
+ rms = 0.0;
+ for (i = 0; (i < n); i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ rms += x1[i][m]*x1[i][m] + x2[i][m]*x2[i][m];
+ }
+ }
+ rms = sqrt(rms/(2*n*DIM));
+
+ /* Convert the relative tolerance into an absolute tolerance */
+ if (ftol*rms < abstol)
+ {
+ abstol = ftol*rms;
+ }
+
+ /* And now do the actual comparision */
+ for (i = 0; (i < n); i++)
+ {
+ cmp_rvec(fp, title, i, x1[i], x2[i], 0.0, abstol);
+ }
+}
+
+void cmp_rvecs(FILE *fp, const char *title, int n, const rvec x1[], const rvec x2[],
+ gmx_bool bRMSD, real ftol, real abstol)
+{
+ int i, m;
+ double d, ssd;
+
+ if (bRMSD)
+ {
+ ssd = 0;
+ for (i = 0; (i < n); i++)
+ {
+ for (m = 0; m < DIM; m++)
+ {
+ d = x1[i][m] - x2[i][m];
+ ssd += d*d;
+ }
+ }
+ fprintf(fp, "%s RMSD %g\n", title, std::sqrt(ssd/n));
+ }
+ else
+ {
+ cmp_rvecs_rmstol(fp, title, n, x1, x2, ftol, abstol);
+ }
+}
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#ifndef GMX_MATH_VECCOMPARE_H
+#define GMX_MATH_VECCOMPARE_H
-#ifndef GMX_TOOLS_COMPARE_H
-#define GMX_TOOLS_COMPARE_H
+#include <cstdio>
-struct gmx_output_env_t;
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
-/* Routines for comparing data structures from non-trajectory binary
- file formats (e.g. as used by gmx check). */
+void cmp_rvec(FILE *fp, const char *s, int index, const rvec i1, const rvec i2, real ftol, real abstol);
-void
-comp_tpx(const char *fn1, const char *fn2, gmx_bool bRMSD, real ftol, real abstol);
-/* Compare two binary run input files */
+void cmp_ivec(FILE *fp, const char *s, int index, const ivec i1, const ivec i2);
-void comp_tpx_a_and_b_states(const char *fn, real ftol, real abstol);
-/* Compare two A and B states of a free-energy run input file. */
-
-void
-comp_trx(const gmx_output_env_t *oenv, const char *fn1, const char *fn2,
- gmx_bool bRMSD, real ftol, real abstol);
-/* Compare two binary trajectory files */
-
-void
-comp_enx(const char *fn1, const char *fn2, real ftol, real abstol,
- const char *lastener);
-/* Compare two binary energy files */
+void cmp_rvecs(FILE *fp, const char *title, int n, const rvec x1[], const rvec x2[],
+ gmx_bool bRMSD, real ftol, real abstol);
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include "gromacs/math/vec.h"
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/txtdump.h"
void pr_ivec(FILE *fp, int indent, const char *title, const int vec[], int n, gmx_bool bShowNumbers)
}
}
-void pr_rvec(FILE *fp, int indent, const char *title, const real vec[], int n, gmx_bool bShowNumbers)
+template <typename T>
+static void printRealVector(FILE *fp, int indent, const char *title, const T vec[], int n, gmx_bool bShowNumbers)
{
- int i;
-
if (available(fp, vec, indent, title))
{
indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
pr_indent(fp, indent);
fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
}
}
-void pr_dvec(FILE *fp, int indent, const char *title, const double vec[], int n, gmx_bool bShowNumbers)
+void pr_rvec(FILE *fp, int indent, const char *title, const real vec[], int n, gmx_bool bShowNumbers)
{
- int i;
+ printRealVector<real>(fp, indent, title, vec, n, bShowNumbers);
+}
- if (available(fp, vec, indent, title))
- {
- indent = pr_title_n(fp, indent, title, n);
- for (i = 0; i < n; i++)
- {
- pr_indent(fp, indent);
- fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
- }
- }
+void pr_fvec(FILE *fp, int indent, const char *title, const float vec[], int n, gmx_bool bShowNumbers)
+{
+ printRealVector<float>(fp, indent, title, vec, n, bShowNumbers);
+}
+
+void pr_dvec(FILE *fp, int indent, const char *title, const double vec[], int n, gmx_bool bShowNumbers)
+{
+ printRealVector<double>(fp, indent, title, vec, n, bShowNumbers);
}
const char *format;
int i, j;
- if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != nullptr)
{
format = flong;
}
const char *format;
int i, j;
- if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != nullptr)
{
format = flong;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void pr_bvec(FILE *fp, int indent, const char *title, const gmx_bool vec[], int n, gmx_bool bShowNnumbers);
void pr_rvec(FILE *fp, int indent, const char *title, const real vec[], int n, gmx_bool bShowNumbers);
void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, const rvec vec[], int n, int dim);
+void pr_fvec(FILE *fp, int indent, const char *title, const float vec[], int n, gmx_bool bShowNumbers);
void pr_dvec(FILE *fp, int indent, const char *title, const double vec[], int n, gmx_bool bShowNumbers);
void pr_rvecs(FILE *fp, int indent, const char *title, const rvec vec[], int n);
void pr_rvecs_len(FILE *fp, int indent, const char *title, const rvec vec[], int n);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
typedef int ivec[DIM];
-typedef int imatrix[DIM][DIM];
-
#ifdef __cplusplus
namespace gmx
return as_vec_array(x);
}
+//! Shorthand for C++ `ivec`-equivalent type.
+typedef BasicVector<int> IVec;
+
} // namespace gmx
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* This file is completely threadsafe - keep it that way! */
#include "gmxpre.h"
+#include "broadcaststructs.h"
+
#include <string.h>
#include "gromacs/gmxlib/network.h"
#include "gromacs/topology/symtab.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/inmemoryserializer.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreeserializer.h"
#include "gromacs/utility/smalloc.h"
-#define block_bc(cr, d) gmx_bcast( sizeof(d), &(d), (cr))
-/* Probably the test for (nr) > 0 in the next macro is only needed
- * on BlueGene(/L), where IBM's MPI_Bcast will segfault after
- * dereferencing a null pointer, even when no data is to be transferred. */
-#define nblock_bc(cr, nr, d) { if ((nr) > 0) {gmx_bcast((nr)*sizeof((d)[0]), (d), (cr)); }}
-#define snew_bc(cr, d, nr) { if (!MASTER(cr)) {snew((d), (nr)); }}
-/* Dirty macro with bAlloc not as an argument */
-#define nblock_abc(cr, nr, d) { if (bAlloc) {snew((d), (nr)); } nblock_bc(cr, (nr), (d)); }
-
static void bc_cstring(const t_commrec *cr, char **s)
{
int size = 0;
- if (MASTER(cr) && *s != NULL)
+ if (MASTER(cr) && *s != nullptr)
{
/* Size of the char buffer is string length + 1 for '\0' */
size = strlen(*s) + 1;
}
nblock_bc(cr, size, *s);
}
- else if (!MASTER(cr) && *s != NULL)
+ else if (!MASTER(cr) && *s != nullptr)
{
sfree(*s);
- *s = NULL;
+ *s = nullptr;
}
}
block_bc(cr, n);
if (n == 0)
{
- groups->grpnr[g] = NULL;
+ groups->grpnr[g] = nullptr;
}
else
{
}
}
+static void bcastPaddedRVecVector(const t_commrec *cr, PaddedRVecVector *v, unsigned int n)
+{
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ (*v).resize(n + 1);
+ nblock_bc(cr, n, as_rvec_array(v->data()));
+}
+
void bcast_state(const t_commrec *cr, t_state *state)
{
int i, nnht, nnhtp;
- gmx_bool bAlloc;
if (!PAR(cr) || (cr->nnodes - cr->npmenodes <= 1))
{
block_bc(cr, state->nnhpres);
block_bc(cr, state->nhchainlength);
block_bc(cr, state->flags);
- if (state->lambda == NULL)
- {
- snew_bc(cr, state->lambda, efptNR)
- }
if (cr->dd)
{
nnht = (state->ngtc)*(state->nhchainlength);
nnhtp = (state->nnhpres)*(state->nhchainlength);
- /* We still need to allocate the arrays in state for non-master
- * ranks, which is done (implicitly via bAlloc) in the dirty,
- * dirty nblock_abc macro. */
- bAlloc = !MASTER(cr);
- if (bAlloc)
- {
- state->nalloc = state->natoms;
- }
for (i = 0; i < estNR; i++)
{
if (state->flags & (1<<i))
{
switch (i)
{
- case estLAMBDA: nblock_bc(cr, efptNR, state->lambda); break;
+ case estLAMBDA: nblock_bc(cr, efptNR, state->lambda.data()); break;
case estFEPSTATE: block_bc(cr, state->fep_state); break;
case estBOX: block_bc(cr, state->box); break;
case estBOX_REL: block_bc(cr, state->box_rel); break;
case estPRES_PREV: block_bc(cr, state->pres_prev); break;
case estSVIR_PREV: block_bc(cr, state->svir_prev); break;
case estFVIR_PREV: block_bc(cr, state->fvir_prev); break;
- case estNH_XI: nblock_abc(cr, nnht, state->nosehoover_xi); break;
- case estNH_VXI: nblock_abc(cr, nnht, state->nosehoover_vxi); break;
- case estNHPRES_XI: nblock_abc(cr, nnhtp, state->nhpres_xi); break;
- case estNHPRES_VXI: nblock_abc(cr, nnhtp, state->nhpres_vxi); break;
- case estTC_INT: nblock_abc(cr, state->ngtc, state->therm_integral); break;
+ case estNH_XI: nblock_abc(cr, nnht, &state->nosehoover_xi); break;
+ case estNH_VXI: nblock_abc(cr, nnht, &state->nosehoover_vxi); break;
+ case estNHPRES_XI: nblock_abc(cr, nnhtp, &state->nhpres_xi); break;
+ case estNHPRES_VXI: nblock_abc(cr, nnhtp, &state->nhpres_vxi); break;
+ case estTHERM_INT: nblock_abc(cr, state->ngtc, &state->therm_integral); break;
+ case estBAROS_INT: block_bc(cr, state->baros_integral); break;
case estVETA: block_bc(cr, state->veta); break;
case estVOL0: block_bc(cr, state->vol0); break;
- case estX: nblock_abc(cr, state->natoms, state->x); break;
- case estV: nblock_abc(cr, state->natoms, state->v); break;
- case estCGP: nblock_abc(cr, state->natoms, state->cg_p); break;
+ case estX: bcastPaddedRVecVector(cr, &state->x, state->natoms); break;
+ case estV: bcastPaddedRVecVector(cr, &state->v, state->natoms); break;
+ case estCGP: bcastPaddedRVecVector(cr, &state->cg_p, state->natoms); break;
case estDISRE_INITF: block_bc(cr, state->hist.disre_initf); break;
case estDISRE_RM3TAV:
block_bc(cr, state->hist.ndisrepairs);
- nblock_abc(cr, state->hist.ndisrepairs, state->hist.disre_rm3tav);
+ nblock_abc(cr, state->hist.ndisrepairs, &state->hist.disre_rm3tav);
break;
case estORIRE_INITF: block_bc(cr, state->hist.orire_initf); break;
case estORIRE_DTAV:
block_bc(cr, state->hist.norire_Dtav);
- nblock_abc(cr, state->hist.norire_Dtav, state->hist.orire_Dtav);
+ nblock_abc(cr, state->hist.norire_Dtav, &state->hist.orire_Dtav);
break;
default:
gmx_fatal(FARGS,
}
}
-static void bc_cosines(const t_commrec *cr, t_cosines *cs)
-{
- block_bc(cr, cs->n);
- snew_bc(cr, cs->a, cs->n);
- snew_bc(cr, cs->phi, cs->n);
- if (cs->n > 0)
- {
- nblock_bc(cr, cs->n, cs->a);
- nblock_bc(cr, cs->n, cs->phi);
- }
-}
-
static void bc_pull_group(const t_commrec *cr, t_pull_group *pgrp)
{
block_bc(cr, *pgrp);
{
if (!MASTER(cr))
{
- pull->coord[c].externalPotentialProvider = NULL;
+ pull->coord[c].externalPotentialProvider = nullptr;
}
if (pull->coord[c].eType == epullEXTERNAL)
{
static void bc_inputrec(const t_commrec *cr, t_inputrec *inputrec)
{
- int i;
-
+ // Note that this overwrites pointers in inputrec, so all pointer fields
+ // Must be initialized separately below.
block_bc(cr, *inputrec);
+ if (SIMMASTER(cr))
+ {
+ gmx::InMemorySerializer serializer;
+ gmx::serializeKeyValueTree(*inputrec->params, &serializer);
+ std::vector<char> buffer = serializer.finishAndGetBuffer();
+ size_t size = buffer.size();
+ block_bc(cr, size);
+ nblock_bc(cr, size, buffer.data());
+ }
+ else
+ {
+ // block_bc() above overwrites the old pointer, so set it to a
+ // reasonable value in case code below throws.
+ // cppcheck-suppress redundantAssignment
+ inputrec->params = nullptr;
+ std::vector<char> buffer;
+ size_t size;
+ block_bc(cr, size);
+ nblock_abc(cr, size, &buffer);
+ gmx::InMemoryDeserializer serializer(buffer);
+ // cppcheck-suppress redundantAssignment
+ inputrec->params = new gmx::KeyValueTreeObject(
+ gmx::deserializeKeyValueTree(&serializer));
+ }
bc_grpopts(cr, &(inputrec->opts));
snew_bc(cr, inputrec->imd, 1);
bc_imd(cr, inputrec->imd);
}
- for (i = 0; (i < DIM); i++)
- {
- bc_cosines(cr, &(inputrec->ex[i]));
- bc_cosines(cr, &(inputrec->et[i]));
- }
if (inputrec->eSwapCoords != eswapNO)
{
snew_bc(cr, inputrec->swap, 1);
static void bc_molblock(const t_commrec *cr, gmx_molblock_t *molb)
{
- block_bc(cr, molb->type);
- block_bc(cr, molb->nmol);
- block_bc(cr, molb->natoms_mol);
- block_bc(cr, molb->nposres_xA);
+ block_bc(cr, *molb);
if (molb->nposres_xA > 0)
{
snew_bc(cr, molb->posres_xA, molb->nposres_xA);
nblock_bc(cr, molb->nposres_xA*DIM, molb->posres_xA[0]);
}
- block_bc(cr, molb->nposres_xB);
if (molb->nposres_xB > 0)
{
snew_bc(cr, molb->posres_xB, molb->nposres_xB);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ *
+ * \brief Convenience wrappers for broadcasting structs.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ *
+ * \inlibraryapi
+ * \ingroup module_mdlib
+ */
+#ifndef GMX_MDLIB_BROADCASTSTRUCTS_H
+#define GMX_MDLIB_BROADCASTSTRUCTS_H
+
+#include <vector>
+
+#include "gromacs/gmxlib/network.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/utility/smalloc.h"
+
+//! Convenience wrapper for gmx_bcast of a single value.
+template <typename T>
+void block_bc(const t_commrec *cr, T &data)
+{
+ gmx_bcast(sizeof(T), static_cast<void *>(&data), cr);
+}
+//! Convenience wrapper for gmx_bcast of a C-style array.
+template <typename T>
+void nblock_bc(const t_commrec *cr, int numElements, T *data)
+{
+ gmx_bcast(numElements * sizeof(T), static_cast<void *>(data), cr);
+}
+//! Convenience wrapper for allocation with snew of vectors that need allocation on non-master ranks.
+template <typename T>
+void snew_bc(const t_commrec *cr, T * &data, int numElements)
+{
+ if (!MASTER(cr))
+ {
+ snew(data, numElements);
+ }
+}
+//! Convenience wrapper for gmx_bcast of a C-style array which needs allocation on non-master ranks.
+template <typename T>
+static void nblock_abc(const t_commrec *cr, int numElements, T **v)
+{
+ snew_bc(cr, v, numElements);
+ nblock_bc(cr, numElements, *v);
+}
+//! Convenience wrapper for gmx_bcast of a std::vector which needs resizing on non-master ranks.
+template <typename T>
+static void nblock_abc(const t_commrec *cr, int numElements, std::vector<T> *v)
+{
+ if (!MASTER(cr))
+ {
+ v->resize(numElements);
+ }
+ gmx_bcast(numElements*sizeof(T), v->data(), cr);
+}
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
-/* Struct for unique atom type for calculating the energy drift.
- * The atom displacement depends on mass and constraints.
- * The energy jump for given distance depend on LJ type and q.
- */
-typedef struct
-{
- real mass; /* mass */
- int type; /* type (used for LJ parameters) */
- real q; /* charge */
- gmx_bool bConstr; /* constrained, if TRUE, use #DOF=2 iso 3 */
- real con_mass; /* mass of heaviest atom connected by constraints */
- real con_len; /* constraint length to the heaviest atom */
-} atom_nonbonded_kinetic_prop_t;
-
/* Struct for unique atom type for calculating the energy drift.
* The atom displacement depends on mass and constraints.
* The energy jump for given distance depend on LJ type and q.
real md3; // -V''' at the cutoff
} pot_derivatives_t;
-void verletbuf_get_list_setup(gmx_bool gmx_unused bSIMD,
- gmx_bool bGPU,
+void verletbuf_get_list_setup(bool makeSimdPairList,
+ bool makeGpuPairList,
verletbuf_list_setup_t *list_setup)
{
/* When calling this function we often don't know which kernel type we
* of size 1, 2 or 4, so for 4x8 or 8x8 we use the estimate for 4x4.
*/
- if (bGPU)
+ if (makeGpuPairList)
{
- /* The CUDA kernels split the j-clusters in two halves */
+ /* The GPU kernels split the j-clusters in two halves */
list_setup->cluster_size_i = nbnxn_kernel_to_cluster_i_size(nbnxnk8x8x8_GPU);
list_setup->cluster_size_j = nbnxn_kernel_to_cluster_j_size(nbnxnk8x8x8_GPU)/2;
}
kernel_type = nbnxnk4x4_PlainC;
-#if GMX_SIMD
- if (bSIMD)
+ if (GMX_SIMD && makeSimdPairList)
{
#ifdef GMX_NBNXN_SIMD_2XNN
/* We use the smallest cluster size to be on the safe side */
kernel_type = nbnxnk4xN_SIMD_4xN;
#endif
}
-#endif
list_setup->cluster_size_i = nbnxn_kernel_to_cluster_i_size(kernel_type);
list_setup->cluster_size_j = nbnxn_kernel_to_cluster_j_size(kernel_type);
real *vsite_m;
int n_nonlin_vsite_mol;
- att = NULL;
+ att = nullptr;
natt = 0;
- if (n_nonlin_vsite != NULL)
+ if (n_nonlin_vsite != nullptr)
{
*n_nonlin_vsite = 0;
}
&mtop->ffparams,
vsite_m,
&n_nonlin_vsite_mol);
- if (n_nonlin_vsite != NULL)
+ if (n_nonlin_vsite != nullptr)
{
*n_nonlin_vsite += nmol*n_nonlin_vsite_mol;
}
* into account. If an atom has multiple constraints, this will result in
* an overestimate of the displacement, which gives a larger drift and buffer.
*/
-static void constrained_atom_sigma2(real kT_fac,
- const atom_nonbonded_kinetic_prop_t *prop,
- real *sigma2_2d,
- real *sigma2_3d)
+void constrained_atom_sigma2(real kT_fac,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ real *sigma2_2d,
+ real *sigma2_3d)
{
- real sigma2_rot;
- real com_dist;
- real sigma2_rel;
- real scale;
-
/* Here we decompose the motion of a constrained atom into two
* components: rotation around the COM and translation of the COM.
*/
- /* Determine the variance for the displacement of the rotational mode */
- sigma2_rot = kT_fac/(prop->mass*(prop->mass + prop->con_mass)/prop->con_mass);
+ /* Determine the variance of the arc length for the two rotational DOFs */
+ real massFraction = prop->con_mass/(prop->mass + prop->con_mass);
+ real sigma2_rot = kT_fac*massFraction/prop->mass;
/* The distance from the atom to the COM, i.e. the rotational arm */
- com_dist = prop->con_len*prop->con_mass/(prop->mass + prop->con_mass);
+ real comDistance = prop->con_len*massFraction;
/* The variance relative to the arm */
- sigma2_rel = sigma2_rot/(com_dist*com_dist);
- /* At 6 the scaling formula has slope 0,
- * so we keep sigma2_2d constant after that.
+ real sigma2_rel = sigma2_rot/gmx::square(comDistance);
+
+ /* For sigma2_rel << 1 we don't notice the rotational effect and
+ * we have a normal, Gaussian displacement distribution.
+ * For larger sigma2_rel the displacement is much less, in fact it can
+ * not exceed 2*comDistance. We can calculate MSD/arm^2 as:
+ * integral_x=0-inf distance2(x) x/sigma2_rel exp(-x^2/(2 sigma2_rel)) dx
+ * where x is angular displacement and distance2(x) is the distance^2
+ * between points at angle 0 and x:
+ * distance2(x) = (sin(x) - sin(0))^2 + (cos(x) - cos(0))^2
+ * The limiting value of this MSD is 2, which is also the value for
+ * a uniform rotation distribution that would be reached at long time.
+ * The maximum is 2.5695 at sigma2_rel = 4.5119.
+ * We approximate this integral with a rational polynomial with
+ * coefficients from a Taylor expansion. This approximation is an
+ * overestimate for all values of sigma2_rel. Its maximum value
+ * of 2.6491 is reached at sigma2_rel = sqrt(45/2) = 4.7434.
+ * We keep the approximation constant after that.
+ * We use this approximate MSD as the variance for a Gaussian distribution.
+ *
+ * NOTE: For any sensible buffer tolerance this will result in a (large)
+ * overestimate of the buffer size, since the Gaussian has a long tail,
+ * whereas the actual distribution can not reach values larger than 2.
*/
- if (sigma2_rel < 6)
- {
- /* A constrained atom rotates around the atom it is constrained to.
- * This results in a smaller linear displacement than for a free atom.
- * For a perfectly circular displacement, this lowers the displacement
- * by: 1/arcsin(arc_length)
- * and arcsin(x) = 1 + x^2/6 + ...
- * For sigma2_rel<<1 the displacement distribution is erfc
- * (exact formula is provided below). For larger sigma, it is clear
- * that the displacement can't be larger than 2*com_dist.
- * It turns out that the distribution becomes nearly uniform.
- * For intermediate sigma2_rel, scaling down sigma with the third
- * order expansion of arcsin with argument sigma_rel turns out
- * to give a very good approximation of the distribution and variance.
- * Even for larger values, the variance is only slightly overestimated.
- * Note that the most relevant displacements are in the long tail.
- * This rotation approximation always overestimates the tail (which
- * runs to infinity, whereas it should be <= 2*com_dist).
- * Thus we always overestimate the drift and the buffer size.
- */
- scale = 1/(1 + sigma2_rel/6);
- *sigma2_2d = sigma2_rot*scale*scale;
- }
- else
- {
- /* sigma_2d is set to the maximum given by the scaling above.
- * For large sigma2 the real displacement distribution is close
- * to uniform over -2*con_len to 2*com_dist.
- * Our erfc with sigma_2d=sqrt(1.5)*com_dist (which means the sigma
- * of the erfc output distribution is con_dist) overestimates
- * the variance and additionally has a long tail. This means
- * we have a (safe) overestimation of the drift.
- */
- *sigma2_2d = 1.5*com_dist*com_dist;
- }
+ /* Coeffients obtained from a Taylor expansion */
+ const real a = 1.0/3.0;
+ const real b = 2.0/45.0;
+
+ /* Our approximation is constant after sigma2_rel = 1/sqrt(b) */
+ sigma2_rel = std::min(sigma2_rel, 1/std::sqrt(b));
+
+ /* Compute the approximate sigma^2 for 2D motion due to the rotation */
+ *sigma2_2d = gmx::square(comDistance)*
+ sigma2_rel/(1 + a*sigma2_rel + b*gmx::square(sigma2_rel));
/* The constrained atom also moves (in 3D) with the COM of both atoms */
- *sigma2_3d = kT_fac/(prop->mass + prop->con_mass);
+ *sigma2_3d = kT_fac/(prop->mass + prop->con_mass);
}
static void get_atom_sigma2(real kT_fac,
void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
const t_inputrec *ir,
+ int nstlist,
+ int list_lifetime,
real reference_temperature,
const verletbuf_list_setup_t *list_setup,
int *n_nonlin_vsite,
real particle_distance;
real nb_clust_frac_pairs_not_in_list_at_cutoff;
- verletbuf_atomtype_t *att = NULL;
+ verletbuf_atomtype_t *att = nullptr;
int natt = -1, i;
real elfac;
real kT_fac, mass_min;
resolution = 0.001;
env = getenv("GMX_VERLET_BUFFER_RES");
- if (env != NULL)
+ if (env != nullptr)
{
sscanf(env, "%lf", &resolution);
}
}
/* Determine the variance of the atomic displacement
- * over nstlist-1 steps: kT_fac
+ * over list_lifetime steps: kT_fac
* For inertial dynamics (not Brownian dynamics) the mass factor
* is not included in kT_fac, it is added later.
*/
* should be negligible (unless nstlist is extremely large, which
* you wouldn't do anyhow).
*/
- kT_fac = 2*BOLTZ*reference_temperature*(ir->nstlist-1)*ir->delta_t;
+ kT_fac = 2*BOLTZ*reference_temperature*list_lifetime*ir->delta_t;
if (ir->bd_fric > 0)
{
/* This is directly sigma^2 of the displacement */
}
else
{
- kT_fac = BOLTZ*reference_temperature*gmx::square((ir->nstlist-1)*ir->delta_t);
+ kT_fac = BOLTZ*reference_temperature*gmx::square(list_lifetime*ir->delta_t);
}
mass_min = att[0].prop.mass;
drift *= nb_clust_frac_pairs_not_in_list_at_cutoff;
/* Convert the drift to drift per unit time per atom */
- drift /= ir->nstlist*ir->delta_t*mtop->natoms;
+ drift /= nstlist*ir->delta_t*mtop->natoms;
if (debug)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Sets the pair-list setup assumed for the current Gromacs configuration.
* The setup with smallest cluster sizes is return, such that the Verlet
* buffer size estimated with this setup will be conservative.
- * bSIMD tells if to take into account SIMD, when supported.
- * bGPU tells to estimate for GPU kernels (bSIMD is ignored with bGPU=TRUE)
+ * makeSimdPairList tells if to take into account SIMD, when supported.
+ * makeGpuPairList tells to estimate for GPU kernels (makeSimdPairList is ignored with makeGpuPairList==true)
*/
-void verletbuf_get_list_setup(gmx_bool bSIMD,
- gmx_bool bGPU,
+void verletbuf_get_list_setup(bool makeSimdPairList,
+ bool makeGpuPairList,
verletbuf_list_setup_t *list_setup);
/* Calculate the non-bonded pair-list buffer size for the Verlet list
* based on the particle masses, temperature, LJ types, charges
* and constraints as well as the non-bonded force behavior at the cut-off.
+ * The pair list update frequency and the list lifetime, which is nstlist-1
+ * for normal pair-list buffering, are passed separately, as in some cases
+ * we want an estimate for different values than the ones set in the inputrec.
* If reference_temperature < 0, the maximum coupling temperature will be used.
* The target is a maximum energy drift of ir->verletbuf_tol.
* Returns the number of non-linear virtual sites. For these it's difficult
*/
void calc_verlet_buffer_size(const gmx_mtop_t *mtop, real boxvol,
const t_inputrec *ir,
+ int nstlist,
+ int list_lifetime,
real reference_temperature,
const verletbuf_list_setup_t *list_setup,
int *n_nonlin_vsite,
real *rlist);
+/* Struct for unique atom type for calculating the energy drift.
+ * The atom displacement depends on mass and constraints.
+ * The energy jump for given distance depend on LJ type and q.
+ */
+struct atom_nonbonded_kinetic_prop_t
+{
+ real mass; /* mass */
+ int type; /* type (used for LJ parameters) */
+ real q; /* charge */
+ gmx_bool bConstr; /* constrained, if TRUE, use #DOF=2 iso 3 */
+ real con_mass; /* mass of heaviest atom connected by constraints */
+ real con_len; /* constraint length to the heaviest atom */
+};
+
+/* This function computes two components of the estimate of the variance
+ * in the displacement of one atom in a system of two constrained atoms.
+ * Returns in sigma2_2d the variance due to rotation of the constrained
+ * atom around the atom to which it constrained.
+ * Returns in sigma2_3d the variance due to displacement of the COM
+ * of the whole system of the two constrained atoms.
+ *
+ * Only exposed here for testing purposes.
+ */
+void constrained_atom_sigma2(real kT_fac,
+ const atom_nonbonded_kinetic_prop_t *prop,
+ real *sigma2_2d,
+ real *sigma2_3d);
+
#ifdef __cplusplus
}
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int b, i, j;
real mvb, im1, im2, tmp0, tmp1, tmp2;
- if (invmass != NULL)
+ if (invmass != nullptr)
{
for (b = 0; b < ncons; b++)
{
int bi, b, i, j;
real mvb, im1, im2, tmp0, tmp1, tmp2;
- if (invmass != NULL)
+ if (invmass != nullptr)
{
for (bi = 0; bi < ncons; bi++)
{
* so we pass invmass=NULL, which results in the use of 1 for all atoms.
*/
lincs_update_atoms(lincsd, th, 1.0, sol, r,
- (econq != econqForce) ? invmass : NULL, fp);
+ (econq != econqForce) ? invmass : nullptr, fp);
if (bCalcDHDL)
{
#endif // GMX_SIMD_HAVE_REAL
/* Determine the distances and right-hand side for the next iteration */
-static void calc_dist_iter(int b0,
- int b1,
- const int * bla,
- const rvec * gmx_restrict xp,
- const real * gmx_restrict bllen,
- const real * gmx_restrict blc,
- const t_pbc * pbc,
- real wfac,
- real * gmx_restrict rhs,
- real * gmx_restrict sol,
- gmx_bool * bWarn)
+gmx_unused static void calc_dist_iter(
+ int b0,
+ int b1,
+ const int * bla,
+ const rvec * gmx_restrict xp,
+ const real * gmx_restrict bllen,
+ const real * gmx_restrict blc,
+ const t_pbc * pbc,
+ real wfac,
+ real * gmx_restrict rhs,
+ real * gmx_restrict sol,
+ gmx_bool * bWarn)
{
int b;
/* Communicate the corrected non-local coordinates */
if (DOMAINDECOMP(cr))
{
- dd_move_x_constraints(cr->dd, box, xp, NULL, FALSE);
+ dd_move_x_constraints(cr->dd, box, xp, nullptr, FALSE);
}
}
#pragma omp barrier
}
/* nit*ncons*(37+9*nrec) flops */
- if (v != NULL)
+ if (v != nullptr)
{
/* Update the velocities */
lincs_update_atoms(lincsd, th, invdt, mlambda, r, invmass, v);
/* 16 ncons flops */
}
- if (nlocat != NULL && (bCalcDHDL || bCalcVir))
+ if (nlocat != nullptr && (bCalcDHDL || bCalcVir))
{
if (lincsd->bTaskDep)
{
}
/* Sets the elements in the LINCS matrix */
-void set_lincs_matrix(struct gmx_lincsdata *li, real *invmass, real lambda)
+static void set_lincs_matrix(struct gmx_lincsdata *li, real *invmass, real lambda)
{
int i;
const real invsqrt2 = 0.7071067811865475244;
done_blocka(&at2con);
- if (cr->dd == NULL)
+ if (cr->dd == nullptr)
{
/* Since the matrix is static, we should free some memory */
li->ncc_alloc = li->ncc;
srenew(li->tmpncc, li->ncc_alloc);
}
- if (DOMAINDECOMP(cr) && dd_constraints_nlocalatoms(cr->dd) != NULL)
+ if (DOMAINDECOMP(cr) && dd_constraints_nlocalatoms(cr->dd) != nullptr)
{
int *nlocat_dd;
}
else
{
- li->nlocat = NULL;
+ li->nlocat = nullptr;
}
if (debug)
r2 = norm2(dx);
len = r2*gmx::invsqrt(r2);
d = std::abs(len/bllen[b]-1);
- if (d > ma && (nlocat == NULL || nlocat[b]))
+ if (d > ma && (nlocat == nullptr || nlocat[b]))
{
ma = d;
im = b;
}
- if (nlocat == NULL)
+ if (nlocat == nullptr)
{
ssd2 += d*d;
count++;
* We can also easily check if any constraint length is changed,
* if not dH/dlambda=0 and we can also set the boolean to FALSE.
*/
- bCalcDHDL = (ir->efep != efepNO && dvdlambda != NULL);
+ bCalcDHDL = (ir->efep != efepNO && dvdlambda != nullptr);
- if (lincsd->nc == 0 && cr->dd == NULL)
+ if (lincsd->nc == 0 && cr->dd == nullptr)
{
if (bLog || bEner)
{
if (lincsd->ncg_flex)
{
/* Set the flexible constraint lengths to the old lengths */
- if (pbc != NULL)
+ if (pbc != nullptr)
{
for (i = 0; i < lincsd->nc; i++)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
for (i = 0; i < natoms; i++)
{
- if (groups->grpnr[egcCompressedX] == NULL || groups->grpnr[egcCompressedX][i] == 0)
+ if (groups->grpnr[egcCompressedX] == nullptr || groups->grpnr[egcCompressedX][i] == 0)
{
nxtcatoms++;
}
}
}
}
- if (ir->pull != NULL)
+ if (ir->pull != nullptr)
{
cio += div_nsteps(nsteps, ir->pull->nstxout)*20; /* roughly 20 chars per line */
cio += div_nsteps(nsteps, ir->pull->nstfout)*20; /* roughly 20 chars per line */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/invblock.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
FILE *out;
int dd_ac0 = 0, dd_ac1 = 0, i, ii, resnr;
gmx_domdec_t *dd;
- char *anm, *resnm;
+ const char *anm, *resnm;
- dd = NULL;
+ dd = nullptr;
if (DOMAINDECOMP(cr))
{
dd = cr->dd;
fprintf(out, "TITLE %s\n", title);
gmx_write_pdb_box(out, -1, box);
+ int molb = 0;
for (i = start; i < start+homenr; i++)
{
- if (dd != NULL)
+ if (dd != nullptr)
{
if (i >= dd->nat_home && i < dd_ac0)
{
{
ii = i;
}
- gmx_mtop_atominfo_global(mtop, ii, &anm, &resnr, &resnm);
+ mtopGetAtomAndResidueName(mtop, ii, &molb, &anm, &resnr, &resnm, nullptr);
gmx_fprintf_pdb_atomline(out, epdbATOM, ii+1, anm, ' ', resnm, ' ', resnr, ' ',
10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ], 1.0, 0.0, "");
}
lambda += delta_step*ir->fepvals->delta_lambda;
}
- if (vir != NULL)
+ if (vir != nullptr)
{
clear_mat(vir_r_m_dr);
}
* For constraints there is both forward and backward communication.
*/
if (ir->ePBC != epbcNONE &&
- (cr->dd || bMolPBC) && !(cr->dd && cr->dd->constraint_comm == NULL))
+ (cr->dd || bMolPBC) && !(cr->dd && cr->dd->constraint_comm == nullptr))
{
/* With pbc=screw the screw has been changed to a shift
* by the constraint coordinate communication routine,
}
else
{
- pbc_null = NULL;
+ pbc_null = nullptr;
}
/* Communicate the coordinates required for the non-local constraints
{
dd_move_x_constraints(cr->dd, box, x, xprime, econq == econqCoord);
- if (v != NULL)
+ if (v != nullptr)
{
/* We need to initialize the non-local components of v.
* We never actually use these values, but we do increment them,
}
}
- if (constr->lincsd != NULL)
+ if (constr->lincsd != nullptr)
{
bOK = constrain_lincs(fplog, bLog, bEner, ir, step, constr->lincsd, md, cr,
x, xprime, min_proj,
box, pbc_null, lambda, dvdlambda,
- invdt, v, vir != NULL, vir_r_m_dr,
+ invdt, v, vir != nullptr, vir_r_m_dr,
econq, nrnb,
constr->maxwarn, &constr->warncount_lincs);
if (!bOK && constr->maxwarn < INT_MAX)
{
- if (fplog != NULL)
+ if (fplog != nullptr)
{
fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
econstr_names[econtLINCS], gmx_step_str(step, buf));
md->invmass, constr->nblocks, constr->sblock,
idef, ir, x, xprime, nrnb,
constr->lagr, lambda, dvdlambda,
- invdt, v, vir != NULL, vir_r_m_dr,
+ invdt, v, vir != nullptr, vir_r_m_dr,
constr->maxwarn < INT_MAX, econq);
break;
case (econqVeloc):
md->invmass, constr->nblocks, constr->sblock,
idef, ir, x, min_proj, nrnb,
constr->lagr, lambda, dvdlambda,
- invdt, NULL, vir != NULL, vir_r_m_dr,
+ invdt, nullptr, vir != nullptr, vir_r_m_dr,
constr->maxwarn < INT_MAX, econq);
break;
default:
if (!bOK && constr->maxwarn < INT_MAX)
{
- if (fplog != NULL)
+ if (fplog != nullptr)
{
fprintf(fplog, "Constraint error in algorithm %s at step %s\n",
econstr_names[econtSHAKE], gmx_step_str(step, buf));
nth, th,
pbc_null,
x[0], xprime[0],
- invdt, v ? v[0] : NULL,
- vir != NULL,
+ invdt, v ? v[0] : nullptr,
+ vir != nullptr,
th == 0 ? vir_r_m_dr : constr->vir_r_m_dr_th[th],
th == 0 ? &bSettleErrorHasOccurred : &constr->bSettleErrorHasOccurred[th]);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
inc_nrnb(nrnb, eNR_SETTLE, nsettle);
- if (v != NULL)
+ if (v != nullptr)
{
inc_nrnb(nrnb, eNR_CONSTR_V, nsettle*3);
}
- if (vir != NULL)
+ if (vir != nullptr)
{
inc_nrnb(nrnb, eNR_CONSTR_VIR, nsettle*3);
}
{
int calcvir_atom_end;
- if (vir == NULL)
+ if (vir == nullptr)
{
calcvir_atom_end = 0;
}
gmx_incons("Unknown constraint quantity for settle");
}
- if (vir != NULL)
+ if (vir != nullptr)
{
/* Reduce the virial contributions over the threads */
for (int th = 1; th < nth; th++)
}
}
- if (vir != NULL)
+ if (vir != nullptr)
{
/* The normal uses of constrain() pass step_scaling = 1.0.
* The call to constrain() for SD1 that passes step_scaling =
}
if (constr->ed && delta_step > 0)
{
- /* apply the essential dynamcs constraints here */
+ /* apply the essential dynamics constraints here */
do_edsam(ir, step, cr, xprime, v, box, constr->ed);
}
}
}
else
{
- return NULL;
+ return nullptr;
}
}
ncons = idef->il[F_CONSTR].nr/3;
init_blocka(&sblocks);
- gen_sblocks(NULL, 0, md->homenr, idef, &sblocks, FALSE);
+ gen_sblocks(nullptr, 0, md->homenr, idef, &sblocks, FALSE);
/*
bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
gmx_constr_t init_constraints(FILE *fplog,
const gmx_mtop_t *mtop, const t_inputrec *ir,
- gmx_edsam_t ed, t_state *state,
+ bool doEssentialDynamics,
t_commrec *cr)
{
int nconstraints =
int nsettles =
gmx_mtop_ftype_count(mtop, F_SETTLE);
- GMX_RELEASE_ASSERT(!ir->bPull || ir->pull_work != NULL, "init_constraints called with COM pulling before/without initializing the pull code");
+ GMX_RELEASE_ASSERT(!ir->bPull || ir->pull_work != nullptr, "init_constraints called with COM pulling before/without initializing the pull code");
if (nconstraints + nsettles == 0 &&
!(ir->bPull && pull_have_constraint(ir->pull_work)) &&
- ed == NULL)
+ !doEssentialDynamics)
{
- return NULL;
+ return nullptr;
}
struct gmx_constr *constr;
/* Allocate thread-local work arrays */
int nthreads = gmx_omp_nthreads_get(emntSETTLE);
- if (nthreads > 1 && constr->vir_r_m_dr_th == NULL)
+ if (nthreads > 1 && constr->vir_r_m_dr_th == nullptr)
{
snew(constr->vir_r_m_dr_th, nthreads);
snew(constr->bSettleErrorHasOccurred, nthreads);
constr->warncount_lincs = 0;
constr->warncount_settle = 0;
- /* Initialize the essential dynamics sampling.
- * Put the pointer to the ED struct in constr */
- constr->ed = ed;
- if (ed != NULL || state->edsamstate.nED > 0)
- {
- init_edsam(mtop, ir, cr, ed, state->x, state->box, &state->edsamstate);
- }
-
- constr->warn_mtop = mtop;
+ constr->warn_mtop = mtop;
return constr;
}
+/* Put a pointer to the essential dynamics constraints into the constr struct */
+void saveEdsamPointer(gmx_constr_t constr, gmx_edsam_t ed)
+{
+ constr->ed = ed;
+}
+
const t_blocka *atom2constraints_moltype(gmx_constr_t constr)
{
return constr->at2con_mt;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MBLIB_CONSTR_H
#define GMX_MBLIB_CONSTR_H
-#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#endif
struct t_pbc;
-struct t_state;
+class t_state;
enum
{
gmx_settledata_t settle_init(const gmx_mtop_t *mtop);
/* Initializes and returns a structure with SETTLE parameters */
+void settle_free(gmx_settledata_t settled);
+
void settle_set_constraints(gmx_settledata_t settled,
const t_ilist *il_settle,
const t_mdatoms *mdatoms);
gmx_constr_t init_constraints(FILE *log,
const gmx_mtop_t *mtop, const t_inputrec *ir,
- gmx_edsam_t ed, t_state *state,
+ bool doEssentialDynamics,
struct t_commrec *cr);
/* Initialize constraints stuff */
+void saveEdsamPointer(gmx_constr_t constr,
+ struct gmx_edsam *ed);
+/* Put a pointer to the essential dynamics constraints into the constr struct */
+
void set_constraints(gmx_constr_t constr,
gmx_localtop_t *top,
const t_inputrec *ir,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
+#include "gromacs/mdlib/expanded.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/boxutilities.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/gammadistribution.h"
static const double sy_const_5[] = { 0.2967324292201065, 0.2967324292201065, -0.186929716880426, 0.2967324292201065, 0.2967324292201065 };
static const double* sy_const[] = {
- NULL,
+ nullptr,
sy_const_1,
- NULL,
+ nullptr,
sy_const_3,
- NULL,
+ nullptr,
sy_const_5
};
/* if scalefac is NULL, we are doing the NHC of the barostat */
bBarostat = FALSE;
- if (scalefac == NULL)
+ if (scalefac == nullptr)
{
bBarostat = TRUE;
}
}
}
+/*! \brief Sets 1/mass for Parrinello-Rahman in wInv; NOTE: PRESFAC is not included, so not in GROMACS units! */
+static void calcParrinelloRahmanInvMass(const t_inputrec *ir, const matrix box,
+ tensor wInv)
+{
+ real maxBoxLength;
+
+ /* TODO: See if we can make the mass independent of the box size */
+ maxBoxLength = std::max(box[XX][XX], box[YY][YY]);
+ maxBoxLength = std::max(maxBoxLength, box[ZZ][ZZ]);
+
+ for (int d = 0; d < DIM; d++)
+ {
+ for (int n = 0; n < DIM; n++)
+ {
+ wInv[d][n] = (4*M_PI*M_PI*ir->compress[d][n])/(3*ir->tau_p*ir->tau_p*maxBoxLength);
+ }
+ }
+}
+
void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
- t_inputrec *ir, real dt, tensor pres,
+ const t_inputrec *ir, real dt, const tensor pres,
tensor box, tensor box_rel, tensor boxv,
tensor M, matrix mu, gmx_bool bFirstStep)
{
* b = vol/W inv(box') * (P-ref_P) (=h')
*/
- int d, n;
- tensor winv;
real vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
- real atot, arel, change, maxchange, xy_pressure;
+ real atot, arel, change;
tensor invbox, pdiff, t1, t2;
- real maxl;
-
gmx::invertBoxMatrix(box, invbox);
if (!bFirstStep)
* The pressure and compressibility always occur as a product,
* therefore the pressure unit drops out.
*/
- maxl = std::max(box[XX][XX], box[YY][YY]);
- maxl = std::max(maxl, box[ZZ][ZZ]);
- for (d = 0; d < DIM; d++)
- {
- for (n = 0; n < DIM; n++)
- {
- winv[d][n] =
- (4*M_PI*M_PI*ir->compress[d][n])/(3*ir->tau_p*ir->tau_p*maxl);
- }
- }
+ tensor winv;
+ calcParrinelloRahmanInvMass(ir, box, winv);
m_sub(pres, ir->ref_p, pdiff);
* pressure correction here? On the other hand we don't scale the
* box momentarily, but change accelerations, so it might not be crucial.
*/
- xy_pressure = 0.5*(pres[XX][XX]+pres[YY][YY]);
- for (d = 0; d < ZZ; d++)
+ real xy_pressure = 0.5*(pres[XX][XX]+pres[YY][YY]);
+ for (int d = 0; d < ZZ; d++)
{
pdiff[d][d] = (xy_pressure-(pres[ZZ][ZZ]-ir->ref_p[d][d]/box[d][d]));
}
/* Move the off-diagonal elements of the 'force' to one side to ensure
* that we obey the box constraints.
*/
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
- for (n = 0; n < d; n++)
+ for (int n = 0; n < d; n++)
{
t1[d][n] += t1[n][d];
t1[n][d] = 0;
switch (ir->epct)
{
case epctANISOTROPIC:
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
- for (n = 0; n <= d; n++)
+ for (int n = 0; n <= d; n++)
{
t1[d][n] *= winv[d][n]*vol;
}
arel = atot/(3*vol);
/* set all RELATIVE box accelerations equal, and maintain total V
* change speed */
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
- for (n = 0; n <= d; n++)
+ for (int n = 0; n <= d; n++)
{
t1[d][n] = winv[0][0]*vol*arel*box[d][n];
}
arel = atot/(2*box[XX][XX]*box[YY][YY]);
/* set RELATIVE XY box accelerations equal, and maintain total V
* change speed. Dont change the third box vector accelerations */
- for (d = 0; d < ZZ; d++)
+ for (int d = 0; d < ZZ; d++)
{
- for (n = 0; n <= d; n++)
+ for (int n = 0; n <= d; n++)
{
t1[d][n] = winv[d][n]*vol*arel*box[d][n];
}
}
- for (n = 0; n < DIM; n++)
+ for (int n = 0; n < DIM; n++)
{
- t1[ZZ][n] *= winv[d][n]*vol;
+ t1[ZZ][n] *= winv[ZZ][n]*vol;
}
break;
default:
break;
}
- maxchange = 0;
- for (d = 0; d < DIM; d++)
+ real maxchange = 0;
+ for (int d = 0; d < DIM; d++)
{
- for (n = 0; n <= d; n++)
+ for (int n = 0; n <= d; n++)
{
boxv[d][n] += dt*t1[d][n];
mtmul(t2, invbox, M);
/* Determine the scaling matrix mu for the coordinates */
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
- for (n = 0; n <= d; n++)
+ for (int n = 0; n <= d; n++)
{
t1[d][n] = box[d][n] + dt*boxv[d][n];
}
}
void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
- t_inputrec *ir, real dt, tensor pres, matrix box,
- matrix mu)
+ const t_inputrec *ir, real dt,
+ const tensor pres, const matrix box,
+ const matrix force_vir, const matrix constraint_vir,
+ matrix mu, double *baros_integral)
{
int d, n;
real scalar_pressure, xy_pressure, p_corr_z;
mu[XX][ZZ] = 0;
mu[YY][ZZ] = 0;
+ /* Keep track of the work the barostat applies on the system.
+ * Without constraints force_vir tells us how Epot changes when scaling.
+ * With constraints constraint_vir gives us the constraint contribution
+ * to both Epot and Ekin. Although we are not scaling velocities, scaling
+ * the coordinates leads to scaling of distances involved in constraints.
+ * This in turn changes the angular momentum (even if the constrained
+ * distances are corrected at the next step). The kinetic component
+ * of the constraint virial captures the angular momentum change.
+ */
+ for (int d = 0; d < DIM; d++)
+ {
+ for (int n = 0; n <= d; n++)
+ {
+ *baros_integral -= 2*(mu[d][n] - (n == d ? 1 : 0))*(force_vir[d][n] + constraint_vir[d][n]);
+ }
+ }
+
if (debug)
{
pr_rvecs(debug, 0, "PC: pres ", pres, 3);
}
}
-void berendsen_pscale(t_inputrec *ir, matrix mu,
+void berendsen_pscale(const t_inputrec *ir, const matrix mu,
matrix box, matrix box_rel,
int start, int nr_atoms,
- rvec x[], unsigned short cFREEZE[],
+ rvec x[], const unsigned short cFREEZE[],
t_nrnb *nrnb)
{
ivec *nFreeze = ir->opts.nFreeze;
// Trivial OpenMP region that does not throw
int g;
- if (cFREEZE == NULL)
+ if (cFREEZE == nullptr)
{
g = 0;
}
inc_nrnb(nrnb, eNR_PCOUPL, nr_atoms);
}
-void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt)
+void berendsen_tcoupl(const t_inputrec *ir, const gmx_ekindata_t *ekind, real dt,
+ std::vector<double> &therm_integral)
{
- t_grpopts *opts;
- int i;
- real T, reft = 0, lll;
-
- opts = &ir->opts;
+ const t_grpopts *opts = &ir->opts;
- for (i = 0; (i < opts->ngtc); i++)
+ for (int i = 0; (i < opts->ngtc); i++)
{
+ real Ek, T;
+
if (ir->eI == eiVV)
{
- T = ekind->tcstat[i].T;
+ Ek = trace(ekind->tcstat[i].ekinf);
+ T = ekind->tcstat[i].T;
}
else
{
- T = ekind->tcstat[i].Th;
+ Ek = trace(ekind->tcstat[i].ekinh);
+ T = ekind->tcstat[i].Th;
}
if ((opts->tau_t[i] > 0) && (T > 0.0))
{
- reft = std::max<real>(0, opts->ref_t[i]);
- lll = std::sqrt(1.0 + (dt/opts->tau_t[i])*(reft/T-1.0));
+ real reft = std::max<real>(0, opts->ref_t[i]);
+ real lll = std::sqrt(1.0 + (dt/opts->tau_t[i])*(reft/T-1.0));
ekind->tcstat[i].lambda = std::max<real>(std::min<real>(lll, 1.25), 0.8);
}
else
ekind->tcstat[i].lambda = 1.0;
}
+ /* Keep track of the amount of energy we are adding to the system */
+ therm_integral[i] -= (gmx::square(ekind->tcstat[i].lambda) - 1)*Ek;
+
if (debug)
{
fprintf(debug, "TC: group %d: T: %g, Lambda: %g\n",
void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac)
{
- const int *gatindex = (DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ const int *gatindex = (DOMAINDECOMP(cr) ? cr->dd->gatindex : nullptr);
int i;
int gc = 0;
gmx::ThreeFry2x64<0> rng(ir->andersen_seed, gmx::RandomDomain::Thermostat);
}
}
-t_state *init_bufstate(const t_state *template_state)
-{
- t_state *state;
- int nc = template_state->nhchainlength;
- snew(state, 1);
- snew(state->nosehoover_xi, nc*template_state->ngtc);
- snew(state->nosehoover_vxi, nc*template_state->ngtc);
- snew(state->therm_integral, template_state->ngtc);
- snew(state->nhpres_xi, nc*template_state->nnhpres);
- snew(state->nhpres_vxi, nc*template_state->nnhpres);
-
- return state;
-}
-
-void destroy_bufstate(t_state *state)
-{
- sfree(state->x);
- sfree(state->v);
- sfree(state->nosehoover_xi);
- sfree(state->nosehoover_vxi);
- sfree(state->therm_integral);
- sfree(state->nhpres_xi);
- sfree(state->nhpres_vxi);
- sfree(state);
-}
-
void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
gmx_enerdata_t *enerd, t_state *state,
tensor vir, t_mdatoms *md,
break;
case etrtBARONHC:
case etrtBARONHC2:
- NHC_trotter(opts, state->nnhpres, ekind, dt, state->nhpres_xi,
- state->nhpres_vxi, NULL, &(state->veta), MassQ, FALSE);
+ NHC_trotter(opts, state->nnhpres, ekind, dt, state->nhpres_xi.data(),
+ state->nhpres_vxi.data(), nullptr, &(state->veta), MassQ, FALSE);
break;
case etrtNHC:
case etrtNHC2:
- NHC_trotter(opts, opts->ngtc, ekind, dt, state->nosehoover_xi,
- state->nosehoover_vxi, scalefac, NULL, MassQ, (ir->eI == eiVV));
+ NHC_trotter(opts, opts->ngtc, ekind, dt, state->nosehoover_xi.data(),
+ state->nosehoover_vxi.data(), scalefac, nullptr, MassQ, (ir->eI == eiVV));
/* need to rescale the kinetic energies and velocities here. Could
scale the velocities later, but we need them scaled in order to
produce the correct outputs, so we'll scale them here. */
return trotter_seq;
}
-real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ)
+static real energyNoseHoover(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ)
{
- int i, j;
- real nd, ndj;
- real ener_npt, reft, kT;
- double *ivxi, *ixi;
- double *iQinv;
- real vol;
- int nh = state->nhchainlength;
-
- ener_npt = 0;
+ real energy = 0;
- /* now we compute the contribution of the pressure to the conserved quantity*/
+ int nh = state->nhchainlength;
- if (ir->epc == epcMTTK)
+ for (int i = 0; i < ir->opts.ngtc; i++)
{
- /* find the volume, and the kinetic energy of the volume */
+ const double *ixi = &state->nosehoover_xi[i*nh];
+ const double *ivxi = &state->nosehoover_vxi[i*nh];
+ const double *iQinv = &(MassQ->Qinv[i*nh]);
- switch (ir->epct)
- {
-
- case epctISOTROPIC:
- /* contribution from the pressure momenenta */
- ener_npt += 0.5*gmx::square(state->veta)/MassQ->Winv;
+ int nd = ir->opts.nrdf[i];
+ real reft = std::max<real>(ir->opts.ref_t[i], 0);
+ real kT = BOLTZ * reft;
- /* contribution from the PV term */
- vol = det(state->box);
- ener_npt += vol*trace(ir->ref_p)/(DIM*PRESFAC);
+ if (nd > 0.0)
+ {
+ if (inputrecNvtTrotter(ir))
+ {
+ /* contribution from the thermal momenta of the NH chain */
+ for (int j = 0; j < nh; j++)
+ {
+ if (iQinv[j] > 0)
+ {
+ energy += 0.5*gmx::square(ivxi[j])/iQinv[j];
+ /* contribution from the thermal variable of the NH chain */
+ int ndj;
+ if (j == 0)
+ {
+ ndj = nd;
+ }
+ else
+ {
+ ndj = 1.0;
+ }
+ energy += ndj*ixi[j]*kT;
+ }
+ }
+ }
+ else /* Other non Trotter temperature NH control -- no chains yet. */
+ {
+ energy += 0.5*BOLTZ*nd*gmx::square(ivxi[0])/iQinv[0];
+ energy += nd*ixi[0]*kT;
+ }
+ }
+ }
- break;
- case epctANISOTROPIC:
+ return energy;
+}
- break;
+/* Returns the energy from the barostat thermostat chain */
+static real energyPressureMTTK(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ)
+{
+ real energy = 0;
- case epctSURFACETENSION:
+ int nh = state->nhchainlength;
- break;
- case epctSEMIISOTROPIC:
+ for (int i = 0; i < state->nnhpres; i++)
+ {
+ /* note -- assumes only one degree of freedom that is thermostatted in barostat */
+ real reft = std::max<real>(ir->opts.ref_t[0], 0.0); /* using 'System' temperature */
+ real kT = BOLTZ * reft;
- break;
- default:
- break;
+ for (int j = 0; j < nh; j++)
+ {
+ double iQinv = MassQ->QPinv[i*nh + j];
+ if (iQinv > 0)
+ {
+ energy += 0.5*gmx::square(state->nhpres_vxi[i*nh + j]/iQinv);
+ /* contribution from the thermal variable of the NH chain */
+ energy += state->nhpres_xi[i*nh + j]*kT;
+ }
+ if (debug)
+ {
+ fprintf(debug, "P-T-group: %10d Chain %4d ThermV: %15.8f ThermX: %15.8f", i, j, state->nhpres_vxi[i*nh + j], state->nhpres_xi[i*nh + j]);
+ }
}
}
- if (inputrecNptTrotter(ir) || inputrecNphTrotter(ir))
+ return energy;
+}
+
+/* Returns the energy accumulated by the V-rescale or Berendsen thermostat */
+static real energyVrescale(const t_inputrec *ir, const t_state *state)
+{
+ real energy = 0;
+ for (int i = 0; i < ir->opts.ngtc; i++)
{
- /* add the energy from the barostat thermostat chain */
- for (i = 0; i < state->nnhpres; i++)
- {
+ energy += state->therm_integral[i];
+ }
- /* note -- assumes only one degree of freedom that is thermostatted in barostat */
- ivxi = &state->nhpres_vxi[i*nh];
- ixi = &state->nhpres_xi[i*nh];
- iQinv = &(MassQ->QPinv[i*nh]);
- reft = std::max<real>(ir->opts.ref_t[0], 0.0); /* using 'System' temperature */
- kT = BOLTZ * reft;
+ return energy;
+}
- for (j = 0; j < nh; j++)
- {
- if (iQinv[j] > 0)
- {
- ener_npt += 0.5*gmx::square(ivxi[j])/iQinv[j];
- /* contribution from the thermal variable of the NH chain */
- ener_npt += ixi[j]*kT;
- }
- if (debug)
- {
- fprintf(debug, "P-T-group: %10d Chain %4d ThermV: %15.8f ThermX: %15.8f", i, j, ivxi[j], ixi[j]);
- }
- }
- }
- }
+real NPT_energy(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ)
+{
+ real energyNPT = 0;
- if (ir->etc)
+ if (ir->epc != epcNO)
{
- for (i = 0; i < ir->opts.ngtc; i++)
- {
- ixi = &state->nosehoover_xi[i*nh];
- ivxi = &state->nosehoover_vxi[i*nh];
- iQinv = &(MassQ->Qinv[i*nh]);
+ /* Compute the contribution of the pressure to the conserved quantity*/
- nd = ir->opts.nrdf[i];
- reft = std::max<real>(ir->opts.ref_t[i], 0);
- kT = BOLTZ * reft;
+ real vol = det(state->box);
- if (nd > 0.0)
+ switch (ir->epc)
+ {
+ case epcPARRINELLORAHMAN:
{
- if (inputrecNvtTrotter(ir))
+ /* contribution from the pressure momenta */
+ tensor invMass;
+ calcParrinelloRahmanInvMass(ir, state->box, invMass);
+ for (int d = 0; d < DIM; d++)
{
- /* contribution from the thermal momenta of the NH chain */
- for (j = 0; j < nh; j++)
+ for (int n = 0; n <= d; n++)
{
- if (iQinv[j] > 0)
+ if (invMass[d][n] > 0)
{
- ener_npt += 0.5*gmx::square(ivxi[j])/iQinv[j];
- /* contribution from the thermal variable of the NH chain */
- if (j == 0)
- {
- ndj = nd;
- }
- else
- {
- ndj = 1.0;
- }
- ener_npt += ndj*ixi[j]*kT;
+ energyNPT += 0.5*gmx::square(state->boxv[d][n])/(invMass[d][n]*PRESFAC);
}
}
}
- else /* Other non Trotter temperature NH control -- no chains yet. */
+
+ /* Contribution from the PV term.
+ * Not that with non-zero off-diagonal reference pressures,
+ * i.e. applied shear stresses, there are additional terms.
+ * We don't support this here, since that requires keeping
+ * track of unwrapped box diagonal elements. This case is
+ * excluded in integratorHasConservedEnergyQuantity().
+ */
+ energyNPT += vol*trace(ir->ref_p)/(DIM*PRESFAC);
+ break;
+ }
+ case epcMTTK:
+ /* contribution from the pressure momenta */
+ energyNPT += 0.5*gmx::square(state->veta)/MassQ->Winv;
+
+ /* contribution from the PV term */
+ energyNPT += vol*trace(ir->ref_p)/(DIM*PRESFAC);
+
+ if (ir->epc == epcMTTK)
{
- ener_npt += 0.5*BOLTZ*nd*gmx::square(ivxi[0])/iQinv[0];
- ener_npt += nd*ixi[0]*kT;
+ /* contribution from the MTTK chain */
+ energyNPT += energyPressureMTTK(ir, state, MassQ);
}
- }
+ break;
+ case epcBERENDSEN:
+ energyNPT += state->baros_integral;
+ break;
+ default:
+ GMX_RELEASE_ASSERT(false, "Conserved energy quantity for pressure coupling is not handled. A case should be added with either the conserved quantity added or nothing added and an exclusion added to integratorHasConservedEnergyQuantity().");
}
}
- return ener_npt;
+
+ switch (ir->etc)
+ {
+ case etcNO:
+ break;
+ case etcVRESCALE:
+ case etcBERENDSEN:
+ energyNPT += energyVrescale(ir, state);
+ break;
+ case etcNOSEHOOVER:
+ energyNPT += energyNoseHoover(ir, state, MassQ);
+ break;
+ case etcANDERSEN:
+ case etcANDERSENMASSIVE:
+ // Not supported, excluded in integratorHasConservedEnergyQuantity()
+ break;
+ default:
+ GMX_RELEASE_ASSERT(false, "Conserved energy quantity for temperature coupling is not handled. A case should be added with either the conserved quantity added or nothing added and an exclusion added to integratorHasConservedEnergyQuantity().");
+ }
+
+ return energyNPT;
}
}
}
-real vrescale_energy(t_grpopts *opts, double therm_integral[])
-{
- int i;
- real ener;
-
- ener = 0;
- for (i = 0; i < opts->ngtc; i++)
- {
- ener += therm_integral[i];
- }
-
- return ener;
-}
-
void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
int start, int end, rvec v[])
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
} t_gmx_settledata;
-static void init_proj_matrix(settleparam_t *p,
- real invmO, real invmH, real dOH, real dHH)
+static void init_proj_matrix(real invmO, real invmH, real dOH, real dHH,
+ matrix inverseCouplingMatrix)
{
- real imOn, imHn;
- matrix mat;
-
- p->imO = invmO;
- p->imH = invmH;
- /* We normalize the inverse masses with imO for the matrix inversion.
+ /* We normalize the inverse masses with invmO for the matrix inversion.
* so we can keep using masses of almost zero for frozen particles,
* without running out of the float range in invertMatrix.
*/
- imOn = 1;
- imHn = p->imH/p->imO;
+ double invmORelative = 1.0;
+ double invmHRelative = invmH/static_cast<double>(invmO);
+ double distanceRatio = dHH/static_cast<double>(dOH);
/* Construct the constraint coupling matrix */
- mat[0][0] = imOn + imHn;
- mat[0][1] = imOn*(1 - 0.5*dHH*dHH/(dOH*dOH));
- mat[0][2] = imHn*0.5*dHH/dOH;
+ matrix mat;
+ mat[0][0] = invmORelative + invmHRelative;
+ mat[0][1] = invmORelative*(1.0 - 0.5*gmx::square(distanceRatio));
+ mat[0][2] = invmHRelative*0.5*distanceRatio;
mat[1][1] = mat[0][0];
mat[1][2] = mat[0][2];
- mat[2][2] = imHn + imHn;
+ mat[2][2] = invmHRelative + invmHRelative;
mat[1][0] = mat[0][1];
mat[2][0] = mat[0][2];
mat[2][1] = mat[1][2];
- gmx::invertMatrix(mat, p->invmat);
+ invertMatrix(mat, inverseCouplingMatrix);
- msmul(p->invmat, 1/p->imO, p->invmat);
-
- p->invdOH = 1/dOH;
- p->invdHH = 1/dHH;
+ msmul(inverseCouplingMatrix, 1/invmO, inverseCouplingMatrix);
}
static void settleparam_init(settleparam_t *p,
real mO, real mH, real invmO, real invmH,
real dOH, real dHH)
{
+ /* We calculate parameters in double precision to minimize errors.
+ * The velocity correction applied during SETTLE coordinate constraining
+ * introduces a systematic error of approximately 1 bit per atom,
+ * depending on what the compiler does with the code.
+ */
double wohh;
p->mO = mO;
p->wh = mH/wohh;
p->dOH = dOH;
p->dHH = dHH;
- p->rc = dHH/2.0;
- p->ra = 2.0*mH*sqrt(dOH*dOH - p->rc*p->rc)/wohh;
- p->rb = sqrt(dOH*dOH - p->rc*p->rc) - p->ra;
+ double rc = dHH/2.0;
+ double ra = 2.0*mH*std::sqrt(dOH*dOH - rc*rc)/wohh;
+ p->rb = std::sqrt(dOH*dOH - rc*rc) - ra;
+ p->rc = rc;
+ p->ra = ra;
p->irc2 = 1.0/dHH;
- /* For projection: connection matrix inversion */
- init_proj_matrix(p, invmO, invmH, dOH, dHH);
+ /* For projection: inverse masses and coupling matrix inversion */
+ p->imO = invmO;
+ p->imH = invmH;
+
+ p->invdOH = 1.0/dOH;
+ p->invdHH = 1.0/dHH;
+
+ init_proj_matrix(invmO, invmH, dOH, dHH, p->invmat);
if (debug)
{
real dHH = mtop->ffparams.iparams[settle_type].settle.dhh;
settleparam_init(&settled->mass1, 1.0, 1.0, 1.0, 1.0, dOH, dHH);
- settled->ow1 = NULL;
- settled->hw2 = NULL;
- settled->hw3 = NULL;
- settled->virfac = NULL;
+ settled->ow1 = nullptr;
+ settled->hw2 = nullptr;
+ settled->hw3 = nullptr;
+ settled->virfac = nullptr;
settled->nalloc = 0;
/* Without SIMD configured, this bool is not used */
- settled->bUseSimd = (getenv("GMX_DISABLE_SIMD_KERNELS") == NULL);
+ settled->bUseSimd = (getenv("GMX_DISABLE_SIMD_KERNELS") == nullptr);
return settled;
}
+void settle_free(gmx_settledata_t settled)
+{
+ sfree_aligned(settled->ow1);
+ sfree_aligned(settled->hw2);
+ sfree_aligned(settled->hw3);
+ sfree_aligned(settled->virfac);
+ sfree(settled);
+}
+
void settle_set_constraints(gmx_settledata_t settled,
const t_ilist *il_settle,
const t_mdatoms *mdatoms)
hw2 = iatoms[i*nral1 + 2];
hw3 = iatoms[i*nral1 + 3];
- if (pbc == NULL)
+ if (pbc == nullptr)
{
rvec_sub(x[ow1], x[hw2], roh2);
rvec_sub(x[ow1], x[hw3], roh3);
int settleStart = ((numSettlePacks* thread + nthread - 1)/nthread)*packSize;
int settleEnd = ((numSettlePacks*(thread + 1) + nthread - 1)/nthread)*packSize;
- if (v != NULL)
+ if (v != nullptr)
{
if (!bCalcVirial)
{
pbc,
x, xprime,
invdt, v,
- NULL,
+ nullptr,
bErrorHasOccurred);
}
else
pbc,
x, xprime,
invdt, v,
- NULL,
+ nullptr,
bErrorHasOccurred);
}
else
t_pbc pbcNo;
const t_pbc *pbcNonNull;
- if (pbc != NULL)
+ if (pbc != nullptr)
{
pbcNonNull = pbc;
}
else
{
- set_pbc(&pbcNo, epbcNONE, NULL);
+ set_pbc(&pbcNo, epbcNONE, nullptr);
pbcNonNull = &pbcNo;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
eb->e_sim[i].eav = 0;
eb->e_sim[i].esum = 0;
eb->enm[i].name = gmx_strdup(enm[i-index]);
- if (unit != NULL)
+ if (unit != nullptr)
{
eb->enm[i].unit = gmx_strdup(unit);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "expanded.h"
+
#include <stdio.h>
#include <cmath>
#include "gromacs/mdlib/calcmu.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/force.h"
-#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformrealdistribution.h"
#include "gromacs/timing/wallcycle.h"
/* Eventually should contain all the functions needed to initialize expanded ensemble
before the md loop starts */
-extern void init_expanded_ensemble(gmx_bool bStateFromCP, t_inputrec *ir, df_history_t *dfhist)
+void init_expanded_ensemble(gmx_bool bStateFromCP, t_inputrec *ir, df_history_t *dfhist)
{
if (!bStateFromCP)
{
sfree(nene);
}
-real do_logsum(int N, real *a_n)
-{
-
- /* RETURN VALUE */
- /* log(\sum_{i=0}^(N-1) exp[a_n]) */
- real maxarg;
- real sum;
- int i;
- real logsum;
- /* compute maximum argument to exp(.) */
-
- maxarg = a_n[0];
- for (i = 1; i < N; i++)
- {
- maxarg = std::max(maxarg, a_n[i]);
- }
-
- /* compute sum of exp(a_n - maxarg) */
- sum = 0.0;
- for (i = 0; i < N; i++)
- {
- sum = sum + std::exp(a_n[i] - maxarg);
- }
-
- /* compute log sum */
- logsum = std::log(sum) + maxarg;
- return logsum;
-}
-
-int FindMinimum(real *min_metric, int N)
+static int FindMinimum(real *min_metric, int N)
{
real min_val;
}
/* print out the weights to the log, along with current state */
-extern void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
- int fep_state, int frequency, gmx_int64_t step)
+void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
+ int fep_state, int frequency, gmx_int64_t step)
{
int nlim, i, ifep, jfep;
real dw, dg, dv, Tprint;
gmx_bool bSimTemp = FALSE;
nlim = fep->n_lambda;
- if (simtemp != NULL)
+ if (simtemp != nullptr)
{
bSimTemp = TRUE;
}
}
}
-extern int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
- t_state *state, t_extmass *MassQ, int fep_state, df_history_t *dfhist,
- gmx_int64_t step,
- rvec *v, t_mdatoms *mdatoms)
+int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
+ t_state *state, t_extmass *MassQ, int fep_state, df_history_t *dfhist,
+ gmx_int64_t step,
+ rvec *v, t_mdatoms *mdatoms)
/* Note that the state variable is only needed for simulated tempering, not
Hamiltonian expanded ensemble. May be able to remove it after integrator refactoring. */
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MDLIB_EXPANDED_H
+#define GMX_MDLIB_EXPANDED_H
+
+#include <stdio.h>
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+
+struct df_history_t;
+struct gmx_enerdata_t;
+struct t_expanded;
+struct t_extmass;
+struct t_inputrec;
+struct t_lambda;
+struct t_mdatoms;
+struct t_simtemp;
+class t_state;
+
+void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
+
+void init_expanded_ensemble(gmx_bool bStateFromCP, t_inputrec *ir, df_history_t *dfhist);
+
+int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
+ t_state *state, t_extmass *MassQ, int fep_state, df_history_t *dfhist,
+ gmx_int64_t step,
+ rvec *v, t_mdatoms *mdatoms);
+
+void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
+ int fep_state, int frequency, gmx_int64_t step);
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
do_force_listed(wcycle, box, ir->fepvals, cr,
idef, (const rvec *) x, hist, f, fr,
&pbc, graph, enerd, nrnb, lambda, md, fcd,
- DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL,
+ DOMAINDECOMP(cr) ? cr->dd->gatindex : nullptr,
flags);
where();
excl, x, bSB ? boxs : box, mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
- fr->f_novirsum, *vir_q, *vir_lj,
+ as_rvec_array(fr->f_novirsum->data()),
+ *vir_q, *vir_lj,
Vcorrt_q, Vcorrt_lj,
lambda[efptCOUL], lambda[efptVDW],
dvdlt_q, dvdlt_lj);
if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
{
pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;
- if (EEL_PME(fr->eeltype))
- {
- pme_flags |= GMX_PME_DO_COULOMB;
- }
- if (EVDW_PME(fr->vdwtype))
- {
- pme_flags |= GMX_PME_DO_LJ;
- }
+
if (flags & GMX_FORCE_FORCES)
{
pme_flags |= GMX_PME_CALC_F;
/* We don't calculate f, but we do want the potential */
pme_flags |= GMX_PME_CALC_POT;
}
+
+ /* With domain decomposition we close the CPU side load
+ * balancing region here, because PME does global
+ * communication that acts as a global barrier.
+ */
+ if (DOMAINDECOMP(cr))
+ {
+ ddCloseBalanceRegionCpu(cr->dd);
+ }
+
wallcycle_start(wcycle, ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
0, md->homenr - fr->n_tpi,
- x, fr->f_novirsum,
+ x,
+ as_rvec_array(fr->f_novirsum->data()),
md->chargeA, md->chargeB,
md->sqrt_c6A, md->sqrt_c6B,
md->sigmaA, md->sigmaB,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb, wcycle,
- fr->vir_el_recip, fr->ewaldcoeff_q,
- fr->vir_lj_recip, fr->ewaldcoeff_lj,
+ fr->vir_el_recip, fr->vir_lj_recip,
&Vlr_q, &Vlr_lj,
lambda[efptCOUL], lambda[efptVDW],
&dvdl_long_range_q, &dvdl_long_range_lj, pme_flags);
if (!EEL_PME(fr->eeltype) && EEL_PME_EWALD(fr->eeltype))
{
- Vlr_q = do_ewald(ir, x, fr->f_novirsum,
+ Vlr_q = do_ewald(ir, x, as_rvec_array(fr->f_novirsum->data()),
md->chargeA, md->chargeB,
box_size, cr, md->homenr,
fr->vir_el_recip, fr->ewaldcoeff_q,
}
}
-void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals)
+void sum_dhdl(gmx_enerdata_t *enerd, gmx::ConstArrayRef<real> lambda, t_lambda *fepvals)
{
- int i, j, index;
+ int index;
double dlam;
enerd->dvdl_lin[efptVDW] += enerd->term[F_DVDL_VDW]; /* include dispersion correction */
enerd->term[F_DVDL] = 0.0;
- for (i = 0; i < efptNR; i++)
+ for (int i = 0; i < efptNR; i++)
{
if (fepvals->separate_dvdl[i])
{
}
enerd->term[F_DVDL_CONSTR] = 0;
- for (i = 0; i < fepvals->n_lambda; i++)
+ for (int i = 0; i < fepvals->n_lambda; i++)
{
/* note we are iterating over fepvals here!
For the current lam, dlam = 0 automatically,
current lambda, because the contributions to the current
lambda are automatically zeroed */
- for (j = 0; j < efptNR; j++)
+ for (size_t j = 0; j < lambda.size(); j++)
{
/* Note that this loop is over all dhdl components, not just the separated ones */
- dlam = (fepvals->all_lambda[j][i]-lambda[j]);
+ dlam = (fepvals->all_lambda[j][i] - lambda[j]);
enerd->enerpart_lambda[i+1] += dlam*enerd->dvdl_lin[j];
if (debug)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_FORCE_H
#define GMX_MDLIB_FORCE_H
+#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/arrayref.h"
+struct gmx_device_info_t;
struct gmx_edsam;
struct gmx_gpu_info_t;
struct gmx_groups_t;
struct gmx_vsite_t;
-struct history_t;
+class history_t;
struct nonbonded_verlet_t;
struct t_blocka;
struct t_commrec;
struct t_nrnb;
struct t_pbc;
+namespace gmx
+{
+class MDLogger;
+}
+
void calc_vir(int nxf, rvec x[], rvec f[], tensor vir,
gmx_bool bScrewPBC, matrix box);
/* Calculate virial for nxf atoms, and add it to vir */
* and fp (if !=NULL) on the master node.
*/
-
-gmx_bool nbnxn_gpu_acceleration_supported(FILE *fplog,
- const t_commrec *cr,
- const t_inputrec *ir,
- gmx_bool bRerunMD);
-/* Return if GPU acceleration is supported with the given settings.
- *
- * If the return value is FALSE and fplog/cr != NULL, prints a fallback
- * message to fplog/stderr.
- */
-
-gmx_bool nbnxn_simd_supported(FILE *fplog,
- const t_commrec *cr,
- const t_inputrec *ir);
+gmx_bool nbnxn_simd_supported(const gmx::MDLogger &mdlog,
+ const t_inputrec *ir);
/* Return if CPU SIMD support exists for the given inputrec
* If the return value is FALSE and fplog/cr != NULL, prints a fallback
* message to fplog/stderr.
void sum_epot(gmx_grppairener_t *grpp, real *epot);
/* Locally sum the non-bonded potential energy terms */
-void sum_dhdl(gmx_enerdata_t *enerd, real *lambda, t_lambda *fepvals);
+void sum_dhdl(gmx_enerdata_t *enerd, gmx::ConstArrayRef<real> lambda, t_lambda *fepvals);
/* Sum the free energy contributions */
/* Compute the average C6 and C12 params for LJ corrections */
gmx_int64_t step, struct t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_localtop_t *top,
gmx_groups_t *groups,
- matrix box, rvec x[], history_t *hist,
- rvec f[],
+ matrix box, PaddedRVecVector *coordinates, history_t *hist,
+ PaddedRVecVector *force,
tensor vir_force,
t_mdatoms *mdatoms,
gmx_enerdata_t *enerd, t_fcdata *fcd,
- real *lambda, struct t_graph *graph,
+ gmx::ArrayRef<real> lambda, t_graph *graph,
t_forcerec *fr,
gmx_vsite_t *vsite, rvec mu_tot,
- double t, FILE *field, struct gmx_edsam *ed,
+ double t, struct gmx_edsam *ed,
gmx_bool bBornRadii,
- int flags);
+ int flags,
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion);
/* Communicate coordinates (if parallel).
* Do neighbor searching (if necessary).
void free_gpu_resources(const t_forcerec *fr,
const t_commrec *cr,
- const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt);
+ const gmx_device_info_t *deviceInfo);
#endif
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
#include "gromacs/fileio/filetypes.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
#include "gromacs/mdlib/nbnxn_search.h"
#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/mdlib/nbnxn_tuning.h"
#include "gromacs/mdlib/nbnxn_util.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/group.h"
+#include "gromacs/mdtypes/iforceprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/strconvert.h"
#include "nbnxn_gpu_jit_support.h"
const char *egrp_nm[egNR+1] = {
"Coul-SR", "LJ-SR", "Buck-SR",
- "Coul-14", "LJ-14", NULL
+ "Coul-14", "LJ-14", nullptr
};
t_forcerec *mk_forcerec(void)
/* Check if we are doing QM on this group */
qm = FALSE;
- if (qm_grpnr != NULL)
+ if (qm_grpnr != nullptr)
{
for (j = j0; j < j1 && !qm; j++)
{
}
n_solvent_parameters = 0;
- solvent_parameters = NULL;
+ solvent_parameters = nullptr;
/* Allocate temporary array for solvent type */
snew(cg_sp, mtop->nmolblock);
{
check_solvent_cg(molt, cg_mol, nmol,
mtop->groups.grpnr[egcQMMM] ?
- mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
+ mtop->groups.grpnr[egcQMMM]+at_offset+am : nullptr,
&mtop->groups.grps[egcQMMM],
fr,
&n_solvent_parameters, &solvent_parameters,
}
sfree(cg_sp);
- if (bestsol != esolNO && fp != NULL)
+ if (bestsol != esolNO && fp != nullptr)
{
fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
esol_names[bestsol],
{
bId = FALSE;
}
- if (mtop->groups.grpnr[egcQMMM] != NULL)
+ if (mtop->groups.grpnr[egcQMMM] != nullptr)
{
for (ai = a0; ai < a1; ai++)
{
{
if (fr->eeltype == eelGRF)
{
- calc_rffac(NULL, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
+ calc_rffac(nullptr, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
fr->rcoulomb, fr->temp, fr->zsquare, box,
&fr->kappa, &fr->k_rf, &fr->c_rf);
}
int ntp, *typecount;
gmx_bool bBHAM;
real *nbfp;
- real *nbfp_comb = NULL;
+ real *nbfp_comb = nullptr;
ntp = fr->ntype;
bBHAM = fr->bBHAM;
sfree(nbfp_comb);
}
- if (fplog != NULL)
+ if (fplog != nullptr)
{
if (fr->eDispCorr == edispcAllEner ||
fr->eDispCorr == edispcAllEnerPres)
char buf[STRLEN];
int i, j;
- if (tabfn == NULL)
+ if (tabfn == nullptr)
{
if (debug)
{
int ncount, *count;
bondedtable_t *tab;
- tab = NULL;
+ tab = nullptr;
ncount = 0;
- count = NULL;
+ count = nullptr;
count_tables(ftype1, ftype2, mtop, &ncount, &count);
// Are there any relevant tabulated bond interactions?
if (fr->bF_NoVirSum)
{
- fr->f_novirsum_n = natoms_f_novirsum;
- if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
- {
- fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
- srenew(fr->f_novirsum_alloc, fr->f_novirsum_nalloc);
- }
- }
- else
- {
- fr->f_novirsum_n = 0;
+ /* TODO: remove this + 1 when padding is properly implemented */
+ fr->forceBufferNoVirialSummation->resize(natoms_f_novirsum + 1);
}
}
(ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
ir->gb_algorithm == egbHCT ||
ir->gb_algorithm == egbOBC))) &&
- getenv("GMX_NO_ALLVSALL") == NULL
+ getenv("GMX_NO_ALLVSALL") == nullptr
);
if (bAllvsAll && ir->opts.ngener > 1)
if (bPrintNote)
{
- if (MASTER(cr))
- {
- fprintf(stderr, "\n%s\n", note);
- }
- if (fp != NULL)
+ if (fp != nullptr)
{
fprintf(fp, "\n%s\n", note);
}
}
-gmx_bool nbnxn_gpu_acceleration_supported(FILE *fplog,
- const t_commrec *cr,
- const t_inputrec *ir,
- gmx_bool bRerunMD)
-{
- if (bRerunMD && ir->opts.ngener > 1)
- {
- /* Rerun execution time is dominated by I/O and pair search,
- * so GPUs are not very useful, plus they do not support more
- * than one energy group. If the user requested GPUs
- * explicitly, a fatal error is given later. With non-reruns,
- * we fall back to a single whole-of system energy group
- * (which runs much faster than a multiple-energy-groups
- * implementation would), and issue a note in the .log
- * file. Users can re-run if they want the information. */
- md_print_warn(cr, fplog, "Rerun with energy groups is not implemented for GPUs, falling back to the CPU\n");
- return FALSE;
- }
-
- return TRUE;
-}
-
-gmx_bool nbnxn_simd_supported(FILE *fplog,
- const t_commrec *cr,
- const t_inputrec *ir)
+gmx_bool nbnxn_simd_supported(const gmx::MDLogger &mdlog,
+ const t_inputrec *ir)
{
if (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB)
{
/* LJ PME with LB combination rule does 7 mesh operations.
* This so slow that we don't compile SIMD non-bonded kernels
* for that. */
- md_print_warn(cr, fplog, "LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels, falling back to plain C kernels\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels, falling back to plain C kernels");
return FALSE;
}
#endif /* GMX_NBNXN_SIMD_2XNN && GMX_NBNXN_SIMD_4XN */
- if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
+ if (getenv("GMX_NBNXN_SIMD_4XN") != nullptr)
{
#ifdef GMX_NBNXN_SIMD_4XN
*kernel_type = nbnxnk4xN_SIMD_4xN;
gmx_fatal(FARGS, "SIMD 4xN kernels requested, but GROMACS has been compiled without support for these kernels");
#endif
}
- if (getenv("GMX_NBNXN_SIMD_2XNN") != NULL)
+ if (getenv("GMX_NBNXN_SIMD_2XNN") != nullptr)
{
#ifdef GMX_NBNXN_SIMD_2XNN
*kernel_type = nbnxnk4xN_SIMD_2xNN;
* With FMA analytical is sometimes faster for a width if 4 as well.
* On BlueGene/Q, this is faster regardless of precision.
* In single precision, this is faster on Bulldozer.
+ * On Skylake table is faster in single and double. TODO: Test 5xxx series.
*/
-#if GMX_SIMD_REAL_WIDTH >= 8 || \
- (GMX_SIMD_REAL_WIDTH >= 4 && GMX_SIMD_HAVE_FMA && !GMX_DOUBLE) || GMX_SIMD_IBM_QPX
+#if ((GMX_SIMD_REAL_WIDTH >= 8 || (GMX_SIMD_REAL_WIDTH >= 4 && GMX_SIMD_HAVE_FMA && !GMX_DOUBLE)) \
+ && !GMX_SIMD_X86_AVX_512) || GMX_SIMD_IBM_QPX
*ewald_excl = ewaldexclAnalytical;
#endif
- if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
+ if (getenv("GMX_NBNXN_EWALD_TABLE") != nullptr)
{
*ewald_excl = ewaldexclTable;
}
- if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
+ if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != nullptr)
{
*ewald_excl = ewaldexclAnalytical;
}
const char *lookup_nbnxn_kernel_name(int kernel_type)
{
- const char *returnvalue = NULL;
+ const char *returnvalue = nullptr;
switch (kernel_type)
{
case nbnxnkNotSet:
case nbnxnkNR:
default:
gmx_fatal(FARGS, "Illegal kernel type selected");
- returnvalue = NULL;
+ returnvalue = nullptr;
break;
}
return returnvalue;
};
static void pick_nbnxn_kernel(FILE *fp,
- const t_commrec *cr,
+ const gmx::MDLogger &mdlog,
gmx_bool use_simd_kernels,
gmx_bool bUseGPU,
- gmx_bool bEmulateGPU,
+ EmulateGpuNonbonded emulateGpu,
const t_inputrec *ir,
int *kernel_type,
int *ewald_excl,
*kernel_type = nbnxnkNotSet;
*ewald_excl = ewaldexclTable;
- if (bEmulateGPU)
+ if (emulateGpu == EmulateGpuNonbonded::Yes)
{
*kernel_type = nbnxnk8x8x8_PlainC;
if (bDoNonbonded)
{
- md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("Emulating a GPU run on the CPU (slow)");
}
}
else if (bUseGPU)
if (*kernel_type == nbnxnkNotSet)
{
if (use_simd_kernels &&
- nbnxn_simd_supported(fp, cr, ir))
+ nbnxn_simd_supported(mdlog, ir))
{
pick_nbnxn_kernel_cpu(ir, kernel_type, ewald_excl);
}
}
}
- if (bDoNonbonded && fp != NULL)
+ if (bDoNonbonded && fp != nullptr)
{
fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
lookup_nbnxn_kernel_name(*kernel_type),
if (nbnxnk4x4_PlainC == *kernel_type ||
nbnxnk8x8x8_PlainC == *kernel_type)
{
- md_print_warn(cr, fp,
- "WARNING: Using the slow %s kernels. This should\n"
- "not happen during routine usage on supported platforms.\n\n",
- lookup_nbnxn_kernel_name(*kernel_type));
- }
- }
-}
-
-static void pick_nbnxn_resources(FILE *fp,
- const t_commrec *cr,
- const gmx_hw_info_t *hwinfo,
- gmx_bool bDoNonbonded,
- gmx_bool *bUseGPU,
- gmx_bool *bEmulateGPU,
- const gmx_gpu_opt_t *gpu_opt)
-{
- gmx_bool bEmulateGPUEnvVarSet;
- char gpu_err_str[STRLEN];
-
- *bUseGPU = FALSE;
-
- bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
-
- /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
- * GPUs (currently) only handle non-bonded calculations, we will
- * automatically switch to emulation if non-bonded calculations are
- * turned off via GMX_NO_NONBONDED - this is the simple and elegant
- * way to turn off GPU initialization, data movement, and cleanup.
- *
- * GPU emulation can be useful to assess the performance one can expect by
- * adding GPU(s) to the machine. The conditional below allows this even
- * if mdrun is compiled without GPU acceleration support.
- * Note that you should freezing the system as otherwise it will explode.
- */
- *bEmulateGPU = (bEmulateGPUEnvVarSet ||
- (!bDoNonbonded && gpu_opt->n_dev_use > 0));
-
- /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
- */
- if (gpu_opt->n_dev_use > 0 && !(*bEmulateGPU))
- {
- /* Each PP node will use the intra-node id-th device from the
- * list of detected/selected GPUs. */
- if (!init_gpu(fp, cr->rank_pp_intranode, gpu_err_str,
- &hwinfo->gpu_info, gpu_opt))
- {
- /* At this point the init should never fail as we made sure that
- * we have all the GPUs we need. If it still does, we'll bail. */
- /* TODO the decorating of gpu_err_str is nicer if it
- happens inside init_gpu. Out here, the decorating with
- the MPI rank makes sense. */
- gmx_fatal(FARGS, "On rank %d failed to initialize GPU #%d: %s",
- cr->nodeid,
- get_gpu_device_id(&hwinfo->gpu_info, gpu_opt,
- cr->rank_pp_intranode),
- gpu_err_str);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "WARNING: Using the slow %s kernels. This should\n"
+ "not happen during routine usage on supported platforms.",
+ lookup_nbnxn_kernel_name(*kernel_type));
}
-
- /* Here we actually turn on hardware GPU acceleration */
- *bUseGPU = TRUE;
}
}
{
init_ewald_f_table(ic, rtab);
- if (fp != NULL)
+ if (fp != nullptr)
{
fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1/ic->tabq_scale, ic->tabq_size);
snew_aligned(ic->tabq_coul_F, 16, 32);
snew_aligned(ic->tabq_coul_V, 16, 32);
- ic->rlist = fr->rlist;
-
/* Lennard-Jones */
ic->vdwtype = fr->vdwtype;
ic->vdw_modifier = fr->vdw_modifier;
}
}
- if (fp != NULL)
+ if (fp != nullptr)
{
real dispersion_shift;
*interaction_const = ic;
}
+/* TODO deviceInfo should be logically const, but currently
+ * init_gpu modifies it to set up NVML support. This could
+ * happen during the detection phase, and deviceInfo could
+ * the become const. */
static void init_nb_verlet(FILE *fp,
+ const gmx::MDLogger &mdlog,
nonbonded_verlet_t **nb_verlet,
gmx_bool bFEP_NonBonded,
const t_inputrec *ir,
const t_forcerec *fr,
const t_commrec *cr,
- const char *nbpu_opt)
+ const char *nbpu_opt,
+ gmx_device_info_t *deviceInfo,
+ const gmx_mtop_t *mtop,
+ matrix box)
{
nonbonded_verlet_t *nbv;
int i;
char *env;
- gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
+ gmx_bool bHybridGPURun = FALSE;
nbnxn_alloc_t *nb_alloc;
nbnxn_free_t *nb_free;
- snew(nbv, 1);
+ nbv = new nonbonded_verlet_t();
+
+ nbv->emulateGpu = ((getenv("GMX_EMULATE_GPU") != nullptr) ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
+ nbv->bUseGPU = deviceInfo != nullptr;
- pick_nbnxn_resources(fp, cr, fr->hwinfo,
- fr->bNonbonded,
- &nbv->bUseGPU,
- &bEmulateGPU,
- fr->gpu_opt);
+ GMX_RELEASE_ASSERT(!(nbv->emulateGpu == EmulateGpuNonbonded::Yes && nbv->bUseGPU), "When GPU emulation is active, there cannot be a GPU assignment");
+
+ if (nbv->bUseGPU)
+ {
+ /* Use the assigned GPU. */
+ init_gpu(mdlog, cr->nodeid, deviceInfo);
+ }
- nbv->nbs = NULL;
+ nbv->nbs = nullptr;
nbv->min_ci_balanced = 0;
nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
for (i = 0; i < nbv->ngrp; i++)
{
nbv->grp[i].nbl_lists.nnbl = 0;
- nbv->grp[i].nbat = NULL;
+ nbv->grp[i].nbat = nullptr;
nbv->grp[i].kernel_type = nbnxnkNotSet;
if (i == 0) /* local */
{
- pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
- nbv->bUseGPU, bEmulateGPU, ir,
+ pick_nbnxn_kernel(fp, mdlog, fr->use_simd_kernels,
+ nbv->bUseGPU, nbv->emulateGpu, ir,
&nbv->grp[i].kernel_type,
&nbv->grp[i].ewald_excl,
fr->bNonbonded);
}
else /* non-local */
{
- if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
+ if (nbpu_opt != nullptr && strcmp(nbpu_opt, "gpu_cpu") == 0)
{
/* Use GPU for local, select a CPU kernel for non-local */
- pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
- FALSE, FALSE, ir,
+ pick_nbnxn_kernel(fp, mdlog, fr->use_simd_kernels,
+ FALSE, EmulateGpuNonbonded::No, ir,
&nbv->grp[i].kernel_type,
&nbv->grp[i].ewald_excl,
fr->bNonbonded);
}
}
+ nbv->listParams = std::unique_ptr<NbnxnListParameters>(new NbnxnListParameters(ir->rlist));
+ setupDynamicPairlistPruning(fp, ir, mtop, box, nbv->bUseGPU, fr->ic,
+ nbv->listParams.get());
+
nbnxn_init_search(&nbv->nbs,
- DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
- DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
+ DOMAINDECOMP(cr) ? &cr->dd->nc : nullptr,
+ DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : nullptr,
bFEP_NonBonded,
gmx_omp_nthreads_get(emntPairsearch));
if (fr->vdwtype == evdwCUT &&
(fr->vdw_modifier == eintmodNONE ||
fr->vdw_modifier == eintmodPOTSHIFT) &&
- getenv("GMX_NO_LJ_COMB_RULE") == NULL)
+ getenv("GMX_NO_LJ_COMB_RULE") == nullptr)
{
/* Plain LJ cut-off: we can optimize with combination rules */
enbnxninitcombrule = enbnxninitcombruleDETECT;
/* init the NxN GPU data; the last argument tells whether we'll have
* both local and non-local NB calculation on GPU */
nbnxn_gpu_init(&nbv->gpu_nbv,
- &fr->hwinfo->gpu_info,
- fr->gpu_opt,
+ deviceInfo,
fr->ic,
+ nbv->listParams.get(),
nbv->grp,
- cr->rank_pp_intranode,
cr->nodeid,
(nbv->ngrp > 1) && !bHybridGPURun);
}
#endif /* GMX_THREAD_MPI */
- if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
+ if ((env = getenv("GMX_NB_MIN_CI")) != nullptr)
{
char *end;
gmx_bool usingGpu(nonbonded_verlet_t *nbv)
{
- return nbv != NULL && nbv->bUseGPU;
+ return nbv != nullptr && nbv->bUseGPU;
}
-void init_forcerec(FILE *fp,
- t_forcerec *fr,
- t_fcdata *fcd,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop,
- const t_commrec *cr,
- matrix box,
- const char *tabfn,
- const char *tabpfn,
- const t_filenm *tabbfnm,
- const char *nbpu_opt,
- gmx_bool bNoSolvOpt,
- real print_force)
+void init_forcerec(FILE *fp,
+ const gmx::MDLogger &mdlog,
+ t_forcerec *fr,
+ t_fcdata *fcd,
+ const t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ const t_commrec *cr,
+ matrix box,
+ const char *tabfn,
+ const char *tabpfn,
+ const t_filenm *tabbfnm,
+ const char *nbpu_opt,
+ gmx_device_info_t *deviceInfo,
+ gmx_bool bNoSolvOpt,
+ real print_force)
{
int i, m, negp_pp, negptable, egi, egj;
real rtab;
gmx_bool bFEP_NonBonded;
int *nm_ind, egp_flags;
- if (fr->hwinfo == NULL)
- {
- /* Detect hardware, gather information.
- * In mdrun, hwinfo has already been set before calling init_forcerec.
- * Here we ignore GPUs, as tools will not use them anyhow.
- */
- fr->hwinfo = gmx_detect_hardware(fp, cr, FALSE);
- }
-
/* By default we turn SIMD kernels on, but it might be turned off further down... */
fr->use_simd_kernels = TRUE;
fr->sc_sigma6_def = gmx::power6(ir->fepvals->sc_sigma);
env = getenv("GMX_SCSIGMA_MIN");
- if (env != NULL)
+ if (env != nullptr)
{
dbl = 0;
sscanf(env, "%20lf", &dbl);
}
fr->bNonbonded = TRUE;
- if (getenv("GMX_NO_NONBONDED") != NULL)
+ if (getenv("GMX_NO_NONBONDED") != nullptr)
{
/* turn off non-bonded calculations */
fr->bNonbonded = FALSE;
- md_print_warn(cr, fp,
- "Found environment variable GMX_NO_NONBONDED.\n"
- "Disabling nonbonded calculations.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "Found environment variable GMX_NO_NONBONDED.\n"
+ "Disabling nonbonded calculations.");
}
bGenericKernelOnly = FALSE;
* can be used with water optimization, and disable it if that is not the case.
*/
- if (getenv("GMX_NB_GENERIC") != NULL)
+ if (getenv("GMX_NB_GENERIC") != nullptr)
{
- if (fp != NULL)
+ if (fp != nullptr)
{
fprintf(fp,
"Found environment variable GMX_NB_GENERIC.\n"
bNoSolvOpt = TRUE;
}
- if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
+ if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr) )
{
fr->use_simd_kernels = FALSE;
- if (fp != NULL)
+ if (fp != nullptr)
{
fprintf(fp,
"\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
/* Check if we can/should do all-vs-all kernels */
- fr->bAllvsAll = can_use_allvsall(ir, FALSE, NULL, NULL);
- fr->AllvsAll_work = NULL;
- fr->AllvsAll_workgb = NULL;
+ fr->bAllvsAll = can_use_allvsall(ir, FALSE, nullptr, nullptr);
+ fr->AllvsAll_work = nullptr;
+ fr->AllvsAll_workgb = nullptr;
/* All-vs-all kernels have not been implemented in 4.6 and later.
* See Redmine #1249. */
if (fr->bAllvsAll)
{
fr->bAllvsAll = FALSE;
- if (fp != NULL)
+ if (fp != nullptr)
{
fprintf(fp,
"\nYour simulation settings would have triggered the efficient all-vs-all\n"
{
fprintf(stderr, "\n%s\n", note);
}
- if (fp != NULL)
+ if (fp != nullptr)
{
fprintf(fp, "\n%s\n", note);
}
+
+ if (GMX_TARGET_BGQ)
+ {
+ GMX_LOG(mdlog.warning).asParagraph()
+ .appendText("There is no SIMD implementation of the group scheme kernels on "
+ "BlueGene/Q. You will observe better performance from using the "
+ "Verlet cut-off scheme.");
+ }
}
/* Determine if we will do PBC for distances in bonded interactions */
}
else
{
- fr->bMolPBC = TRUE;
+ /* Not making molecules whole is faster in most cases,
+ * but With orientation restraints we need whole molecules.
+ */
+ fr->bMolPBC = (fcd->orires.nr == 0);
- if (getenv("GMX_USE_GRAPH") != NULL)
+ if (getenv("GMX_USE_GRAPH") != nullptr)
{
fr->bMolPBC = FALSE;
if (fp)
{
- md_print_warn(cr, fp, "GMX_USE_GRAPH is set, using the graph for bonded interactions\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("GMX_USE_GRAPH is set, using the graph for bonded interactions");
}
if (mtop->bIntermolecularInteractions)
{
- md_print_warn(cr, fp, "WARNING: Molecules linked by intermolecular interactions have to reside in the same periodic image, otherwise artifacts will occur!\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("WARNING: Molecules linked by intermolecular interactions have to reside in the same periodic image, otherwise artifacts will occur!");
}
}
+ GMX_RELEASE_ASSERT(fr->bMolPBC || !mtop->bIntermolecularInteractions, "We need to use PBC within molecules with inter-molecular interactions");
+
if (bSHAKE && fr->bMolPBC)
{
gmx_fatal(FARGS, "SHAKE is not properly supported with intermolecular interactions. For short simulations where linked molecules remain in the same periodic image, the environment variable GMX_USE_GRAPH can be used to override this check.\n");
fr->bcoultab = FALSE;
}
+ /* This now calculates sum for q and C6 */
+ set_chargesum(fp, fr, mtop);
+
/* Tables are used for direct ewald sum */
if (fr->bEwald)
{
if (ir->ewald_geometry == eewg3DC)
{
+ bool haveNetCharge = (fabs(fr->qsum[0]) > 1e-4 ||
+ fabs(fr->qsum[1]) > 1e-4);
if (fp)
{
- fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
+ fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry%s.\n",
+ haveNetCharge ? " and net charge" : "");
}
please_cite(fp, "In-Chul99a");
+ if (haveNetCharge)
+ {
+ please_cite(fp, "Ballenegger2009");
+ }
}
}
fr->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
}
fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype) ||
+ fr->forceProviders->hasForcesWithoutVirialContribution() ||
gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
- gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
- inputrecElecField(ir)
- );
+ gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0);
+
+ if (fr->bF_NoVirSum)
+ {
+ fr->forceBufferNoVirialSummation = new PaddedRVecVector;
+ }
if (fr->cutoff_scheme == ecutsGROUP &&
ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
fr->cg_nalloc = ncg_mtop(mtop);
srenew(fr->cg_cm, fr->cg_nalloc);
}
- if (fr->shift_vec == NULL)
+ if (fr->shift_vec == nullptr)
{
snew(fr->shift_vec, SHIFTS);
}
- if (fr->fshift == NULL)
+ if (fr->fshift == nullptr)
{
snew(fr->fshift, SHIFTS);
}
- if (fr->nbfp == NULL)
+ if (fr->nbfp == nullptr)
{
fr->ntype = mtop->ffparams.atnr;
fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
&fr->kappa, &fr->k_rf, &fr->c_rf);
}
- /*This now calculates sum for q and c6*/
- set_chargesum(fp, fr, mtop);
-
/* Construct tables for the group scheme. A little unnecessary to
* make both vdw and coul tables sometimes, but what the
* heck. Note that both cutoff schemes construct Ewald tables in
/* make tables for ordinary interactions */
if (bSomeNormalNbListsAreInUse)
{
- make_nbf_tables(fp, fr, rtab, tabfn, NULL, NULL, &fr->nblists[0]);
+ make_nbf_tables(fp, fr, rtab, tabfn, nullptr, nullptr, &fr->nblists[0]);
m = 1;
}
else
&fr->bExcl_IntraCGAll_InterCGNone);
if (DOMAINDECOMP(cr))
{
- fr->cginfo = NULL;
+ fr->cginfo = nullptr;
}
else
{
GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw, "With Verlet lists and no PME rcoulomb and rvdw should be identical");
}
- init_nb_verlet(fp, &fr->nbv, bFEP_NonBonded, ir, fr, cr, nbpu_opt);
+ init_nb_verlet(fp, mdlog, &fr->nbv, bFEP_NonBonded, ir, fr,
+ cr, nbpu_opt, deviceInfo,
+ mtop, box);
}
if (ir->eDispCorr != edispcNO)
* in this run because the PME ranks have no knowledge of whether GPUs
* are used or not, but all ranks need to enter the barrier below.
*/
-void free_gpu_resources(const t_forcerec *fr,
- const t_commrec *cr,
- const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt)
+void free_gpu_resources(const t_forcerec *fr,
+ const t_commrec *cr,
+ const gmx_device_info_t *deviceInfo)
{
gmx_bool bIsPPrankUsingGPU;
char gpu_err_str[STRLEN];
nbnxn_gpu_free(fr->nbv->gpu_nbv);
/* stop the GPU profiler (only CUDA) */
stopGpuProfiler();
+ }
- /* With tMPI we need to wait for all ranks to finish deallocation before
- * destroying the CUDA context in free_gpu() as some tMPI ranks may be sharing
- * GPU and context.
- *
- * This is not a concern in OpenCL where we use one context per rank which
- * is freed in nbnxn_gpu_free().
- *
- * Note: as only PP ranks need to free GPU resources, so it is safe to
- * not call the barrier on PME ranks.
- */
+ /* With tMPI we need to wait for all ranks to finish deallocation before
+ * destroying the CUDA context in free_gpu() as some tMPI ranks may be sharing
+ * GPU and context.
+ *
+ * This is not a concern in OpenCL where we use one context per rank which
+ * is freed in nbnxn_gpu_free().
+ *
+ * Note: it is safe to not call the barrier on the ranks which do not use GPU,
+ * but it is easier and more futureproof to call it on the whole node.
+ */
#if GMX_THREAD_MPI
- if (PAR(cr))
- {
- gmx_barrier(cr);
- }
+ if (PAR(cr) || MULTISIM(cr))
+ {
+ gmx_barrier_physical_node(cr);
+ }
#endif /* GMX_THREAD_MPI */
+ if (bIsPPrankUsingGPU)
+ {
/* uninitialize GPU (by destroying the context) */
- if (!free_cuda_gpu(cr->rank_pp_intranode, gpu_err_str, gpu_info, gpu_opt))
+ if (!free_cuda_gpu(deviceInfo, gpu_err_str))
{
gmx_warning("On rank %d failed to free GPU #%d: %s",
cr->nodeid, get_current_cuda_gpu_device_id(), gpu_err_str);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/timing/wallcycle.h"
+struct gmx_device_info_t;
struct t_commrec;
struct t_fcdata;
struct t_filenm;
+namespace gmx
+{
+class MDLogger;
+}
+
/*! \brief Create a new forcerec structure */
t_forcerec *mk_forcerec(void);
*
* The Force rec struct must be created with mk_forcerec.
* \param[in] fplog File for printing
+ * \param[in] mdlog File for printing
* \param[out] fr The forcerec
* \param[in] fcd Force constant data
* \param[in] ir Inputrec structure
* \param[in] tabpfn Table potential file for pair interactions
* \param[in] tabbfnm Table potential files for bonded interactions
* \param[in] nbpu_opt Nonbonded Processing Unit (GPU/CPU etc.)
+ * \param[in] deviceInfo Info about GPU device to use for short-ranged work
* \param[in] bNoSolvOpt Do not use solvent optimization
* \param[in] print_force Print forces for atoms with force >= print_force
*/
void init_forcerec(FILE *fplog,
+ const gmx::MDLogger &mdlog,
t_forcerec *fr,
t_fcdata *fcd,
const t_inputrec *ir,
const char *tabpfn,
const t_filenm *tabbfnm,
const char *nbpu_opt,
+ gmx_device_info_t *deviceInfo,
gmx_bool bNoSolvOpt,
real print_force);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nl->maxnrj = 0;
nl->nri = 0;
nl->nrj = 0;
- nl->iinr = NULL;
- nl->gid = NULL;
- nl->shift = NULL;
- nl->jindex = NULL;
- nl->jjnr = NULL;
+ nl->iinr = nullptr;
+ nl->gid = nullptr;
+ nl->shift = nullptr;
+ nl->jindex = nullptr;
+ nl->jjnr = nullptr;
/*nl->nltype = nltype;*/
srenew(nl->iinr, nl->maxnri);
snew(fr->invsqrta, natoms);
snew(fr->dvda, natoms);
- fr->dadx = NULL;
- fr->dadx_rawptr = NULL;
+ fr->dadx = nullptr;
+ fr->dadx_rawptr = nullptr;
fr->nalloc_dadx = 0;
- born->gpol_still_work = NULL;
- born->gpol_hct_work = NULL;
+ born->gpol_still_work = nullptr;
+ born->gpol_hct_work = nullptr;
/* snew(born->asurf,natoms); */
/* snew(born->dasurf,natoms); */
int cnt;
int ndadx;
- if (fr->bAllvsAll && fr->dadx == NULL)
+ if (fr->bAllvsAll && fr->dadx == nullptr)
{
/* We might need up to 8 atoms of padding before and after,
* and another 4 units to guarantee SSE alignment.
return vctot;
}
-real calc_gb_selfcorrections(t_commrec *cr, int natoms,
- real *charge, gmx_genborn_t *born, real *dvda, double facel)
+static real calc_gb_selfcorrections(t_commrec *cr, int natoms,
+ real *charge, gmx_genborn_t *born, real *dvda, double facel)
{
int i, ai, at0, at1;
real rai, e, derb, q, q2, fi, rai_inv, vtot;
}
-real calc_gb_nonpolar(t_commrec *cr, t_forcerec *fr, int natoms, gmx_genborn_t *born, gmx_localtop_t *top,
- real *dvda, t_mdatoms *md)
+static real calc_gb_nonpolar(t_commrec *cr, t_forcerec *fr, int natoms, gmx_genborn_t *born, gmx_localtop_t *top,
+ real *dvda, t_mdatoms *md)
{
int ai, i, at0, at1;
real e, es, rai, term, probe, tmp, factor;
-real calc_gb_chainrule(int natoms, t_nblist *nl, real *dadx, real *dvda, rvec x[], rvec t[], rvec fshift[],
- rvec shift_vec[], int gb_algorithm, gmx_genborn_t *born)
+static real calc_gb_chainrule(int natoms, t_nblist *nl, real *dadx, real *dvda, rvec x[], rvec t[], rvec fshift[],
+ rvec shift_vec[], int gb_algorithm, gmx_genborn_t *born)
{
int i, k, n, ai, aj, nj0, nj1, n0, n1;
int shift;
}
else
{
- pbc_null = NULL;
+ pbc_null = nullptr;
}
if (sa_algorithm == esaAPPROX)
srenew(lists->list, lists->list_nalloc);
for (i = lists->nlist; i < lists->list_nalloc; i++)
{
- lists->list[i].aj = NULL;
+ lists->list[i].aj = nullptr;
lists->list[i].aj_nalloc = 0;
}
aj = il->iatoms[ind+2];
int shift = CENTRAL;
- if (g != NULL)
+ if (g != nullptr)
{
rvec_sub(x[ai], x[aj], dx);
ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), dt);
t_pbc pbc;
struct gbtmpnbls *nls;
- gbtmpnbl_t *list = NULL;
+ gbtmpnbl_t *list = nullptr;
set_pbc(&pbc, fr->ePBC, box);
nls = born->nblist_work;
void make_local_gb(const t_commrec *cr, gmx_genborn_t *born, int gb_algorithm)
{
int i, at0, at1;
- gmx_domdec_t *dd = NULL;
+ gmx_domdec_t *dd = nullptr;
if (DOMAINDECOMP(cr))
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2009, The GROMACS Development Team.
- * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
aadata = *((gmx_allvsallgb2_data_t **)work);
- if (aadata == NULL)
+ if (aadata == nullptr)
{
genborn_allvsall_setup(&aadata, top->idef.il, mdatoms->nr,
FALSE, FALSE, TRUE);
aadata = *((gmx_allvsallgb2_data_t **)work);
- if (aadata == NULL)
+ if (aadata == nullptr)
{
genborn_allvsall_setup(&aadata, top->idef.il, mdatoms->nr,
TRUE, TRUE, TRUE);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdlib>
#include <cstring>
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/programcontext.h"
/** Structure with the number of threads for each OpenMP multi-threaded
* The "group" scheme supports OpenMP only in PME and in thise case all but
* the PME nthread values default to 1.
*/
-static void pick_module_nthreads(FILE *fplog, int m,
- gmx_bool bSimMaster,
+static void pick_module_nthreads(const gmx::MDLogger &mdlog, int m,
gmx_bool bFullOmpSupport,
gmx_bool bSepPME)
{
char *env;
int nth;
- char sbuf[STRLEN];
const bool bOMP = GMX_OPENMP;
}
/* check the environment variable */
- if ((env = getenv(modth_env_var[m])) != NULL)
+ if ((env = getenv(modth_env_var[m])) != nullptr)
{
sscanf(env, "%d", &nth);
+ // cppcheck-suppress knownConditionTrueFalse
if (!bOMP)
{
gmx_warning("%s=%d is set, but %s is compiled without OpenMP!",
/* with the verlet codepath, when any GMX_*_NUM_THREADS env var is set,
* OMP_NUM_THREADS also has to be set */
- if (bFullOmpSupport && getenv("OMP_NUM_THREADS") == NULL)
+ if (bFullOmpSupport && getenv("OMP_NUM_THREADS") == nullptr)
{
gmx_warning("%s=%d is set, the default number of threads also "
"needs to be set with OMP_NUM_THREADS!",
/* only babble if we are really overriding with a different value */
if ((bSepPME && m == emntPME && nth != modth.gnth_pme) || (nth != modth.gnth))
{
- sprintf(sbuf, "%s=%d set, overriding the default number of %s threads",
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "%s=%d set, overriding the default number of %s threads",
modth_env_var[m], nth, mod_name[m]);
- if (bSimMaster)
- {
- fprintf(stderr, "\n%s\n", sbuf);
- }
- if (fplog)
- {
- fprintf(fplog, "%s\n", sbuf);
- }
}
}
else
GMX_RELEASE_ASSERT(nthreads_omp, "nthreads_omp must be a non-NULL pointer");
- if ((env = getenv("OMP_NUM_THREADS")) != NULL)
+ if ((env = getenv("OMP_NUM_THREADS")) != nullptr)
{
int nt_omp;
/*! \brief Helper function for parsing various input about the number
of OpenMP threads to use in various modules and deciding what to
do about it. */
-static void manage_number_of_openmp_threads(FILE *fplog,
- const t_commrec *cr,
- bool bOMP,
- int nthreads_hw_avail,
- int omp_nthreads_req,
- int omp_nthreads_pme_req,
- gmx_bool gmx_unused bThisNodePMEOnly,
- gmx_bool bFullOmpSupport,
- int nppn,
- gmx_bool bSepPME)
+static void manage_number_of_openmp_threads(const gmx::MDLogger &mdlog,
+ const t_commrec *cr,
+ bool bOMP,
+ int nthreads_hw_avail,
+ int omp_nthreads_req,
+ int omp_nthreads_pme_req,
+ gmx_bool gmx_unused bThisNodePMEOnly,
+ gmx_bool bFullOmpSupport,
+ int nppn,
+ gmx_bool bSepPME)
{
int nth;
char *env;
{
return;
}
+#else
+ GMX_UNUSED_VALUE(cr);
#endif
if (modth.initialized)
* - 1
*/
nth = 1;
- if ((env = getenv("OMP_NUM_THREADS")) != NULL)
+ if ((env = getenv("OMP_NUM_THREADS")) != nullptr)
{
if (!bOMP && (std::strncmp(env, "1", 1) != 0))
{
/* now set the per-module values */
modth.nth[emntDefault] = modth.gnth;
- pick_module_nthreads(fplog, emntDomdec, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntPairsearch, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntNonbonded, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntBonded, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntPME, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntUpdate, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntVSITE, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntLINCS, SIMMASTER(cr), bFullOmpSupport, bSepPME);
- pick_module_nthreads(fplog, emntSETTLE, SIMMASTER(cr), bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntDomdec, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntPairsearch, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntNonbonded, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntBonded, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntPME, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntUpdate, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntVSITE, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntLINCS, bFullOmpSupport, bSepPME);
+ pick_module_nthreads(mdlog, emntSETTLE, bFullOmpSupport, bSepPME);
/* set the number of threads globally */
if (bOMP)
/*! \brief Report on the OpenMP settings that will be used */
static void
-reportOpenmpSettings(FILE *fplog,
- const t_commrec *cr,
- gmx_bool bOMP,
- gmx_bool bFullOmpSupport,
- gmx_bool bSepPME)
+reportOpenmpSettings(const gmx::MDLogger &mdlog,
+ const t_commrec *cr,
+ gmx_bool bOMP,
+ gmx_bool bFullOmpSupport,
+ gmx_bool bSepPME)
{
#if GMX_THREAD_MPI
const char *mpi_str = "per tMPI thread";
{
if (nth_max == nth_min)
{
- md_print_info(cr, fplog, "Using %d OpenMP thread%s %s\n",
- nth_min, nth_min > 1 ? "s" : "",
- cr->nnodes > 1 ? mpi_str : "");
+ GMX_LOG(mdlog.warning).appendTextFormatted(
+ "Using %d OpenMP thread%s %s",
+ nth_min, nth_min > 1 ? "s" : "",
+ cr->nnodes > 1 ? mpi_str : "");
}
else
{
- md_print_info(cr, fplog, "Using %d - %d OpenMP threads %s\n",
- nth_min, nth_max, mpi_str);
+ GMX_LOG(mdlog.warning).appendTextFormatted(
+ "Using %d - %d OpenMP threads %s",
+ nth_min, nth_max, mpi_str);
}
}
if (bSepPME && (nth_pme_min != nth_min || nth_pme_max != nth_max))
{
if (nth_pme_max == nth_pme_min)
{
- md_print_info(cr, fplog, "Using %d OpenMP thread%s %s for PME\n",
- nth_pme_min, nth_pme_min > 1 ? "s" : "",
- cr->nnodes > 1 ? mpi_str : "");
+ GMX_LOG(mdlog.warning).appendTextFormatted(
+ "Using %d OpenMP thread%s %s for PME",
+ nth_pme_min, nth_pme_min > 1 ? "s" : "",
+ cr->nnodes > 1 ? mpi_str : "");
}
else
{
- md_print_info(cr, fplog, "Using %d - %d OpenMP threads %s for PME\n",
- nth_pme_min, nth_pme_max, mpi_str);
+ GMX_LOG(mdlog.warning).appendTextFormatted(
+ "Using %d - %d OpenMP threads %s for PME",
+ nth_pme_min, nth_pme_max, mpi_str);
}
}
- md_print_info(cr, fplog, "\n");
+ GMX_LOG(mdlog.warning);
}
/*! \brief Detect and warn about oversubscription of cores.
*
* \todo Enable this for separate PME nodes as well! */
static void
-issueOversubscriptionWarning(FILE *fplog,
- const t_commrec *cr,
- int nthreads_hw_avail,
- int nppn,
- gmx_bool bSepPME)
+issueOversubscriptionWarning(const gmx::MDLogger &mdlog,
+ const t_commrec *cr,
+ int nthreads_hw_avail,
+ int nppn,
+ gmx_bool bSepPME)
{
char sbuf[STRLEN], sbuf1[STRLEN], sbuf2[STRLEN];
#endif
}
#endif
- md_print_warn(cr, fplog,
- "WARNING: %sversubscribing the available %d logical CPU cores%s with %d %s.\n"
- " This will cause considerable performance loss!",
- sbuf2, nthreads_hw_avail, sbuf1, nppn*modth.gnth, sbuf);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "WARNING: %sversubscribing the available %d logical CPU cores%s with %d %s.\n"
+ " This will cause considerable performance loss!",
+ sbuf2, nthreads_hw_avail, sbuf1, nppn*modth.gnth, sbuf);
}
}
-void gmx_omp_nthreads_init(FILE *fplog, t_commrec *cr,
+void gmx_omp_nthreads_init(const gmx::MDLogger &mdlog, t_commrec *cr,
int nthreads_hw_avail,
int omp_nthreads_req,
int omp_nthreads_pme_req,
bSepPME = ( (cr->duty & DUTY_PP) && !(cr->duty & DUTY_PME)) ||
(!(cr->duty & DUTY_PP) && (cr->duty & DUTY_PME));
- manage_number_of_openmp_threads(fplog, cr, bOMP,
+ manage_number_of_openmp_threads(mdlog, cr, bOMP,
nthreads_hw_avail,
omp_nthreads_req, omp_nthreads_pme_req,
bThisNodePMEOnly, bFullOmpSupport,
}
#endif
- reportOpenmpSettings(fplog, cr, bOMP, bFullOmpSupport, bSepPME);
- issueOversubscriptionWarning(fplog, cr, nthreads_hw_avail, nppn, bSepPME);
+ reportOpenmpSettings(mdlog, cr, bOMP, bFullOmpSupport, bSepPME);
+ issueOversubscriptionWarning(mdlog, cr, nthreads_hw_avail, nppn, bSepPME);
}
int gmx_omp_nthreads_get(int mod)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_commrec;
+namespace gmx
+{
+class MDLogger;
+}
+
/** Enum values corresponding to multithreaded algorithmic modules. */
typedef enum module_nth
{
* It is compatible with tMPI, thread-safety is ensured (for the features
* available with tMPI).
* This function should caled only once during the initialization of mdrun. */
-void gmx_omp_nthreads_init(FILE *fplog, t_commrec *cr,
+void gmx_omp_nthreads_init(const gmx::MDLogger &fplog, t_commrec *cr,
int nthreads_hw_avail,
int omp_nthreads_req,
int omp_nthreads_pme_req,
* the reduction in computional cost due to parallelization. This routine
* returns 1 when the overhead is expected to be higher than the gain.
*/
-static int gmx_omp_nthreads_get_simple_rvec_task(int mod, int nrvec)
+static inline int gmx_omp_nthreads_get_simple_rvec_task(int mod, int nrvec)
{
/* There can be a relatively large overhead to an OpenMP parallel for loop.
* This overhead increases, slowly, with the numbe of threads used.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "groupcoord.h"
-#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
/* Save the atoms index in the local atom numbers array */
(*anrs_loc)[localnr] = ii;
- if (coll_ind != NULL)
+ if (coll_ind != nullptr)
{
/* Keep track of where this local atom belongs in the collective index array.
* This is needed when reducing the local arrays to a collective/global array
* The rest of the code is for making the group whole again in case atoms changed
* their PBC representation / crossed a box boundary. We only do that if the
* shifts array is allocated. */
- if (NULL != shifts)
+ if (nullptr != shifts)
{
/* To make the group whole, start with a whole group and each
* step move the assembled positions at closest distance to the positions
clear_dvec(dsumvec);
/* Loop over all atoms and add their weighted position vectors */
- if (weight != NULL)
+ if (weight != nullptr)
{
for (i = 0; i < nat; i++)
{
weight_sum = get_sum_of_positions(x, weight, nr, dcenter);
- if (weight != NULL)
+ if (weight != nullptr)
{
denom = weight_sum; /* Divide by the sum of weight */
}
weight_sum = buf[3];
}
- if (weight_loc != NULL)
+ if (weight_loc != nullptr)
{
denom = 1.0/weight_sum; /* Divide by the sum of weight to get center of mass e.g. */
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/mdtypes/state.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
+class energyhistory_t;
struct gmx_mtop_t;
struct gmx_membed_t;
struct gmx_output_env_t;
+struct MdrunOptions;
+struct ObservablesHistory;
+struct ReplicaExchangeParameters;
struct t_commrec;
struct t_filenm;
struct t_inputrec;
+class t_state;
namespace gmx
{
+
+class IMDOutputProvider;
+class MDLogger;
+
/*! \brief Integrator algorithm implementation.
*
* \param[in] fplog Log file for output
* \param[in] cr Communication record
+ * \param[in] mdlog Log writer for important output
* \param[in] nfile Number of files
* \param[in] fnm Filename structure array
* \param[in] oenv Output information
- * \param[in] bVerbose Verbose output or not
- * \param[in] nstglobalcomm How often global communication is done
+ * \param[in] mdrunOptions Options for mdrun
* \param[in] vsite Virtual site information
* \param[in] constr Constraint information
- * \param[in] stepout How often we writen to the console
+ * \param[in] outputProvider Additional output provider
* \param[in] inputrec Input record with mdp options
* \param[in] top_global Molecular topology for the whole system
* \param[in] fcd Force and constraint data
* \param[in] state_global The state (x, v, f, box etc.) of the whole system
+ * \param[in] observablesHistory The observables statistics history
* \param[in] mdatoms Structure containing atom information
* \param[in] nrnb Accounting for floating point operations
* \param[in] wcycle Wall cycle timing information
- * \param[in] ed Essential dynamics sampling information
* \param[in] fr Force record with cut-off information and more
- * \param[in] repl_ex_nst How often we do replica exchange (in steps)
- * \param[in] repl_ex_nex How many replicas we have
- * \param[in] repl_ex_seed The seed for Monte Carlo swaps
+ * \param[in] replExParams Parameters for the replica exchange algorithm
* \param[in] membed Membrane embedding data structure
- * \param[in] cpt_period How often to checkpoint the simulation
- * \param[in] max_hours Maximume length of the simulation (wall time)
- * \param[in] imdport Interactive MD port (socket)
- * \param[in] Flags Flags to control mdrun
* \param[in] walltime_accounting More timing information
*/
-typedef double integrator_t (FILE *fplog, t_commrec *cr,
+typedef double integrator_t (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
+ ObservablesHistory *observablesHistory,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ const ReplicaExchangeParameters &replExParams,
gmx_membed_t gmx_unused * membed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
gmx_walltime_accounting_t walltime_accounting);
} // namespace gmx
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int *ibuf, p;
gmx_bool bCompatible;
- if (NULL != log && !bQuiet)
+ if (nullptr != log && !bQuiet)
{
fprintf(log, "Multi-checking %s ... ", name);
}
- if (ms == NULL)
+ if (ms == nullptr)
{
gmx_fatal(FARGS,
"check_multi_int called with a NULL communication pointer");
if (bCompatible)
{
- if (NULL != log && !bQuiet)
+ if (nullptr != log && !bQuiet)
{
fprintf(log, "OK\n");
}
}
else
{
- if (NULL != log)
+ if (nullptr != log)
{
fprintf(log, "\n%s is not equal for all subsystems\n", name);
for (p = 0; p < ms->nsim; p++)
int p;
gmx_bool bCompatible;
- if (NULL != log && !bQuiet)
+ if (nullptr != log && !bQuiet)
{
fprintf(log, "Multi-checking %s ... ", name);
}
- if (ms == NULL)
+ if (ms == nullptr)
{
gmx_fatal(FARGS,
"check_multi_int called with a NULL communication pointer");
if (bCompatible)
{
- if (NULL != log && !bQuiet)
+ if (nullptr != log && !bQuiet)
{
fprintf(log, "OK\n");
}
{
// TODO Part of this error message would also be good to go to
// stderr (from one rank of one sim only)
- if (NULL != log)
+ if (nullptr != log)
{
fprintf(log, "\n%s is not equal for all subsystems\n", name);
for (p = 0; p < ms->nsim; p++)
{
if (fp)
{
- gmx_fatal_set_log_file(NULL);
+ gmx_fatal_set_log_file(nullptr);
gmx_fio_fclose(fp);
}
}
#include <algorithm>
#include "gromacs/domdec/domdec.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/math/vec.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
return nmin;
}
-void copy_coupling_state(t_state *statea, t_state *stateb,
- gmx_ekindata_t *ekinda, gmx_ekindata_t *ekindb, t_grpopts* opts)
-{
-
- /* MRS note -- might be able to get rid of some of the arguments. Look over it when it's all debugged */
-
- int i, j, nc;
-
- /* Make sure we have enough space for x and v */
- if (statea->nalloc > stateb->nalloc)
- {
- stateb->nalloc = statea->nalloc;
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries.
- */
- srenew(stateb->x, stateb->nalloc + 1);
- srenew(stateb->v, stateb->nalloc + 1);
- }
-
- stateb->natoms = statea->natoms;
- stateb->ngtc = statea->ngtc;
- stateb->nnhpres = statea->nnhpres;
- stateb->veta = statea->veta;
- if (ekinda)
- {
- copy_mat(ekinda->ekin, ekindb->ekin);
- for (i = 0; i < stateb->ngtc; i++)
- {
- ekindb->tcstat[i].T = ekinda->tcstat[i].T;
- ekindb->tcstat[i].Th = ekinda->tcstat[i].Th;
- copy_mat(ekinda->tcstat[i].ekinh, ekindb->tcstat[i].ekinh);
- copy_mat(ekinda->tcstat[i].ekinf, ekindb->tcstat[i].ekinf);
- ekindb->tcstat[i].ekinscalef_nhc = ekinda->tcstat[i].ekinscalef_nhc;
- ekindb->tcstat[i].ekinscaleh_nhc = ekinda->tcstat[i].ekinscaleh_nhc;
- ekindb->tcstat[i].vscale_nhc = ekinda->tcstat[i].vscale_nhc;
- }
- }
- copy_rvecn(statea->x, stateb->x, 0, stateb->natoms);
- copy_rvecn(statea->v, stateb->v, 0, stateb->natoms);
- copy_mat(statea->box, stateb->box);
- copy_mat(statea->box_rel, stateb->box_rel);
- copy_mat(statea->boxv, stateb->boxv);
-
- for (i = 0; i < stateb->ngtc; i++)
- {
- nc = i*opts->nhchainlength;
- for (j = 0; j < opts->nhchainlength; j++)
- {
- stateb->nosehoover_xi[nc+j] = statea->nosehoover_xi[nc+j];
- stateb->nosehoover_vxi[nc+j] = statea->nosehoover_vxi[nc+j];
- }
- }
- if (stateb->nhpres_xi != NULL)
- {
- for (i = 0; i < stateb->nnhpres; i++)
- {
- nc = i*opts->nhchainlength;
- for (j = 0; j < opts->nhchainlength; j++)
- {
- stateb->nhpres_xi[nc+j] = statea->nhpres_xi[nc+j];
- stateb->nhpres_vxi[nc+j] = statea->nhpres_vxi[nc+j];
- }
- }
- }
-}
-
-real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state, t_extmass *MassQ)
-{
- real quantity = 0;
- switch (ir->etc)
- {
- case etcNO:
- break;
- case etcBERENDSEN:
- break;
- case etcNOSEHOOVER:
- quantity = NPT_energy(ir, state, MassQ);
- break;
- case etcVRESCALE:
- quantity = vrescale_energy(&(ir->opts), state->therm_integral);
- break;
- default:
- break;
- }
- return quantity;
-}
-
/* TODO Specialize this routine into init-time and loop-time versions?
e.g. bReadEkin is only true when restoring from checkpoint */
void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_inputrec *ir,
t_state *state, t_mdatoms *mdatoms,
t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
- tensor pres, rvec mu_tot, gmx_constr_t constr,
+ tensor pres, rvec mu_tot, struct gmx_constr *constr,
gmx::SimulationSignaller *signalCoordinator,
matrix box, int *totalNumberOfBondedInteractions,
gmx_bool *bSumEkinhOld, int flags)
if (bStopCM)
{
calc_vcm_grp(0, mdatoms->homenr, mdatoms,
- state->x, state->v, vcm);
+ as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), vcm);
}
if (bTemp || bStopCM || bPres || bEner || bConstrain)
{
wallcycle_start(wcycle, ewcMoveE);
global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
- ir, ekind, constr, bStopCM ? vcm : NULL,
+ ir, ekind, constr, bStopCM ? vcm : nullptr,
signalBuffer.size(), signalBuffer.data(),
totalNumberOfBondedInteractions,
*bSumEkinhOld, flags);
{
correct_ekin(debug,
0, mdatoms->homenr,
- state->v, vcm->group_p[0],
+ as_rvec_array(state->v.data()), vcm->group_p[0],
mdatoms->massT, mdatoms->tmass, ekind->ekin);
}
{
check_cm_grp(fplog, vcm, ir, 1);
do_stopcm_grp(0, mdatoms->homenr, mdatoms->cVCM,
- state->x, state->v, vcm);
+ as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), vcm);
inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
}
}
}
-void check_nst_param(FILE *fplog, t_commrec *cr,
- const char *desc_nst, int nst,
- const char *desc_p, int *p)
+/* check whether an 'nst'-style parameter p is a multiple of nst, and
+ set it to be one if not, with a warning. */
+static void check_nst_param(const gmx::MDLogger &mdlog,
+ const char *desc_nst, int nst,
+ const char *desc_p, int *p)
{
if (*p > 0 && *p % nst != 0)
{
/* Round up to the next multiple of nst */
*p = ((*p)/nst + 1)*nst;
- md_print_warn(cr, fplog,
- "NOTE: %s changes %s to %d\n", desc_nst, desc_p, *p);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: %s changes %s to %d", desc_nst, desc_p, *p);
}
}
return nst;
}
-int check_nstglobalcomm(FILE *fplog, t_commrec *cr,
- int nstglobalcomm, t_inputrec *ir)
+int check_nstglobalcomm(const gmx::MDLogger &mdlog, int nstglobalcomm, t_inputrec *ir)
{
if (!EI_DYNAMICS(ir->eI))
{
nstglobalcomm > ir->nstlist && nstglobalcomm % ir->nstlist != 0)
{
nstglobalcomm = (nstglobalcomm / ir->nstlist)*ir->nstlist;
- md_print_warn(cr, fplog, "WARNING: nstglobalcomm is larger than nstlist, but not a multiple, setting it to %d\n", nstglobalcomm);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "WARNING: nstglobalcomm is larger than nstlist, but not a multiple, setting it to %d",
+ nstglobalcomm);
}
if (ir->nstcalcenergy > 0)
{
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstcalcenergy", &ir->nstcalcenergy);
}
if (ir->etc != etcNO && ir->nsttcouple > 0)
{
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nsttcouple", &ir->nsttcouple);
}
if (ir->epc != epcNO && ir->nstpcouple > 0)
{
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstpcouple", &ir->nstpcouple);
}
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstenergy", &ir->nstenergy);
- check_nst_param(fplog, cr, "-gcom", nstglobalcomm,
+ check_nst_param(mdlog, "-gcom", nstglobalcomm,
"nstlog", &ir->nstlog);
}
if (ir->comm_mode != ecmNO && ir->nstcomm < nstglobalcomm)
{
- md_print_warn(cr, fplog, "WARNING: Changing nstcomm from %d to %d\n",
- ir->nstcomm, nstglobalcomm);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "WARNING: Changing nstcomm from %d to %d",
+ ir->nstcomm, nstglobalcomm);
ir->nstcomm = nstglobalcomm;
}
- if (fplog)
- {
- fprintf(fplog, "Intra-simulation communication will occur every %d steps.\n", nstglobalcomm);
- }
+ GMX_LOG(mdlog.info).appendTextFormatted(
+ "Intra-simulation communication will occur every %d steps.\n", nstglobalcomm);
return nstglobalcomm;
}
}
+// TODO Most of this logic seems to belong in the respective modules
void set_state_entries(t_state *state, const t_inputrec *ir)
{
/* The entries in the state in the tpx file might not correspond
state->flags |= (1<<estFEPSTATE);
}
state->flags |= (1<<estX);
- if (state->lambda == NULL)
- {
- snew(state->lambda, efptNR);
- }
- if (state->x == NULL)
- {
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries.
- */
- snew(state->x, state->nalloc + 1);
- }
+ GMX_RELEASE_ASSERT(state->x.size() >= static_cast<unsigned int>(state->natoms), "We should start a run with an initialized state->x");
if (EI_DYNAMICS(ir->eI))
{
state->flags |= (1<<estV);
- if (state->v == NULL)
- {
- snew(state->v, state->nalloc + 1);
- }
- }
- if (ir->eI == eiCG)
- {
- state->flags |= (1<<estCGP);
- if (state->cg_p == NULL)
- {
- /* cg_p is not stored in the tpx file, so we need to allocate it */
- snew(state->cg_p, state->nalloc + 1);
- }
}
state->nnhpres = 0;
if ((ir->epc == epcPARRINELLORAHMAN) || (ir->epc == epcMTTK))
{
state->flags |= (1<<estBOXV);
+ state->flags |= (1<<estPRES_PREV);
}
- if (ir->epc != epcNO)
+ if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
{
- if (inputrecNptTrotter(ir) || (inputrecNphTrotter(ir)))
- {
- state->nnhpres = 1;
- state->flags |= (1<<estNHPRES_XI);
- state->flags |= (1<<estNHPRES_VXI);
- state->flags |= (1<<estSVIR_PREV);
- state->flags |= (1<<estFVIR_PREV);
- state->flags |= (1<<estVETA);
- state->flags |= (1<<estVOL0);
- }
- else
- {
- state->flags |= (1<<estPRES_PREV);
- }
+ state->nnhpres = 1;
+ state->flags |= (1<<estNHPRES_XI);
+ state->flags |= (1<<estNHPRES_VXI);
+ state->flags |= (1<<estSVIR_PREV);
+ state->flags |= (1<<estFVIR_PREV);
+ state->flags |= (1<<estVETA);
+ state->flags |= (1<<estVOL0);
+ }
+ if (ir->epc == epcBERENDSEN)
+ {
+ state->flags |= (1<<estBAROS_INT);
}
}
state->flags |= (1<<estNH_VXI);
}
- if (ir->etc == etcVRESCALE)
+ if (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)
{
- state->flags |= (1<<estTC_INT);
+ state->flags |= (1<<estTHERM_INT);
}
init_gtc_state(state, state->ngtc, state->nnhpres, ir->opts.nhchainlength); /* allocate the space for nose-hoover chains */
init_ekinstate(&state->ekinstate, ir);
- snew(state->enerhist, 1);
- init_energyhistory(state->enerhist);
- init_df_history(&state->dfhist, ir->fepvals->n_lambda);
- state->swapstate.eSwapCoords = ir->eSwapCoords;
+
+ if (ir->bExpanded)
+ {
+ snew(state->dfhist, 1);
+ init_df_history(state->dfhist, ir->fepvals->n_lambda);
+ }
}
struct t_grpopts;
struct t_lambda;
struct t_nrnb;
-struct t_state;
+class t_state;
struct t_trxframe;
namespace gmx
{
-
+class MDLogger;
class SimulationSignaller;
-
}
/* Define a number of flags to better control the information
/*! \brief Return the number of steps that will take place between
* intra-simulation communications, given the constraints of the
* inputrec and the value of mdrun -gcom. */
-int check_nstglobalcomm(FILE *fplog,
- t_commrec *cr,
- int nstglobalcomm,
- t_inputrec *ir);
-
-/* check whether an 'nst'-style parameter p is a multiple of nst, and
- set it to be one if not, with a warning. */
-void check_nst_param(FILE *fplog, t_commrec *cr,
- const char *desc_nst, int nst,
- const char *desc_p, int *p);
+int check_nstglobalcomm(const gmx::MDLogger &mdlog,
+ int nstglobalcomm,
+ t_inputrec *ir);
/*! \brief Return true if the \p value is equal across the set of multi-simulations
*
void rerun_parallel_comm(t_commrec *cr, t_trxframe *fr,
gmx_bool *bLastStep);
-/* get the conserved energy associated with the ensemble type*/
-real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
- t_extmass *MassQ);
-
/* set the lambda values at each step of mdrun when they change */
void set_current_lambdas(gmx_int64_t step, t_lambda *fepvals, gmx_bool bRerunMD,
t_trxframe *rerun_fr, t_state *state_global, t_state *state, double lam0[]);
int multisim_min(const gmx_multisim_t *ms, int nmin, int n);
/* Set an appropriate value for n across the whole multi-simulation */
-void copy_coupling_state(t_state *statea, t_state *stateb,
- gmx_ekindata_t *ekinda, gmx_ekindata_t *ekindb, t_grpopts* opts);
-/* Copy stuff from state A to state B */
-
void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_inputrec *ir,
t_forcerec *fr, gmx_ekindata_t *ekind,
t_state *state, t_mdatoms *mdatoms,
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
t_mdatoms *init_mdatoms(FILE *fp, const gmx_mtop_t *mtop, gmx_bool bFreeEnergy)
{
- int a;
- double tmA, tmB;
- t_atom *atom;
- t_mdatoms *md;
- gmx_mtop_atomloop_all_t aloop;
-
+ t_mdatoms *md;
snew(md, 1);
md->nenergrp = mtop->groups.grps[egcENER].nr;
- md->bVCMgrps = FALSE;
- tmA = 0.0;
- tmB = 0.0;
+ md->bVCMgrps = (mtop->groups.grps[egcVCM].nr > 1);
+
+ /* Determine the total system mass and perturbed atom counts */
+ double totalMassA = 0.0;
+ double totalMassB = 0.0;
- aloop = gmx_mtop_atomloop_all_init(mtop);
- while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
+ gmx_mtop_atomloop_block_t aloop = gmx_mtop_atomloop_block_init(mtop);
+ const t_atom *atom;
+ int nmol;
+ while (gmx_mtop_atomloop_block_next(aloop, &atom, &nmol))
{
- if (ggrpnr(&mtop->groups, egcVCM, a) > 0)
- {
- md->bVCMgrps = TRUE;
- }
+ totalMassA += nmol*atom->m;
+ totalMassB += nmol*atom->mB;
if (bFreeEnergy && PERTURBED(*atom))
{
md->nPerturbed++;
if (atom->mB != atom->m)
{
- md->nMassPerturbed++;
+ md->nMassPerturbed += nmol;
}
if (atom->qB != atom->q)
{
- md->nChargePerturbed++;
+ md->nChargePerturbed += nmol;
}
if (atom->typeB != atom->type)
{
- md->nTypePerturbed++;
+ md->nTypePerturbed += nmol;
}
}
-
- tmA += atom->m;
- tmB += atom->mB;
}
- md->tmassA = tmA;
- md->tmassB = tmB;
+ md->tmassA = totalMassA;
+ md->tmassB = totalMassB;
if (bFreeEnergy && fp)
{
t_mdatoms *md)
{
gmx_bool bLJPME;
- gmx_mtop_atomlookup_t alook;
- int i;
const t_grpopts *opts;
const gmx_groups_t *groups;
int nthreads gmx_unused;
groups = &mtop->groups;
- /* Index==NULL indicates no DD (unless we have a DD node with no
- * atoms), so also check for homenr. This should be
- * signaled properly with an extra parameter or nindex==-1.
- */
- if (index == NULL && (homenr > 0))
+ /* nindex>=0 indicates DD where we use an index */
+ if (nindex >= 0)
{
- md->nr = mtop->natoms;
+ md->nr = nindex;
}
else
{
- md->nr = nindex;
+ md->nr = mtop->natoms;
}
if (md->nr > md->nalloc)
}
srenew(md->massT, md->nalloc);
srenew(md->invmass, md->nalloc);
+ srenew(md->invMassPerDim, md->nalloc);
srenew(md->chargeA, md->nalloc);
srenew(md->typeA, md->nalloc);
if (md->nPerturbed)
* Therefore, when adding code, the user should use something like:
* gprnrU1 = (md->cU1==NULL ? 0 : md->cU1[localatindex])
*/
- if (mtop->groups.grpnr[egcUser1] != NULL)
+ if (mtop->groups.grpnr[egcUser1] != nullptr)
{
srenew(md->cU1, md->nalloc);
}
- if (mtop->groups.grpnr[egcUser2] != NULL)
+ if (mtop->groups.grpnr[egcUser2] != nullptr)
{
srenew(md->cU2, md->nalloc);
}
}
}
- alook = gmx_mtop_atomlookup_init(mtop);
+ int molb = 0;
// cppcheck-suppress unreadVariable
nthreads = gmx_omp_nthreads_get(emntDefault);
-#pragma omp parallel for num_threads(nthreads) schedule(static)
- for (i = 0; i < md->nr; i++)
+#pragma omp parallel for num_threads(nthreads) schedule(static) firstprivate(molb)
+ for (int i = 0; i < md->nr; i++)
{
try
{
int g, ag;
real mA, mB, fac;
real c6, c12;
- t_atom *atom;
- if (index == NULL)
+ if (index == nullptr)
{
ag = i;
}
else
{
- ag = index[i];
+ ag = index[i];
}
- gmx_mtop_atomnr_to_atom(alook, ag, &atom);
+ const t_atom &atom = mtopGetAtomParameters(mtop, ag, &molb);
if (md->cFREEZE)
{
{
/* The friction coefficient is mass/tau_t */
fac = ir->delta_t/opts->tau_t[md->cTC ? groups->grpnr[egcTC][ag] : 0];
- mA = 0.5*atom->m*fac;
- mB = 0.5*atom->mB*fac;
+ mA = 0.5*atom.m*fac;
+ mB = 0.5*atom.mB*fac;
}
}
else
{
- mA = atom->m;
- mB = atom->mB;
+ mA = atom.m;
+ mB = atom.mB;
}
if (md->nMassPerturbed)
{
md->massB[i] = mB;
}
md->massT[i] = mA;
+
if (mA == 0.0)
{
- md->invmass[i] = 0;
+ md->invmass[i] = 0;
+ md->invMassPerDim[i][XX] = 0;
+ md->invMassPerDim[i][YY] = 0;
+ md->invMassPerDim[i][ZZ] = 0;
}
else if (md->cFREEZE)
{
*/
md->invmass[i] = 1.0/mA;
}
+ for (int d = 0; d < DIM; d++)
+ {
+ md->invMassPerDim[i][d] = (opts->nFreeze[g][d] ? 0 : 1.0/mA);
+ }
}
else
{
- md->invmass[i] = 1.0/mA;
+ md->invmass[i] = 1.0/mA;
+ for (int d = 0; d < DIM; d++)
+ {
+ md->invMassPerDim[i][d] = 1.0/mA;
+ }
}
- md->chargeA[i] = atom->q;
- md->typeA[i] = atom->type;
+
+ md->chargeA[i] = atom.q;
+ md->typeA[i] = atom.type;
if (bLJPME)
{
- c6 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c6;
- c12 = mtop->ffparams.iparams[atom->type*(mtop->ffparams.atnr+1)].lj.c12;
+ c6 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom.type*(mtop->ffparams.atnr+1)].lj.c12;
md->sqrt_c6A[i] = sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
}
if (md->nPerturbed)
{
- md->bPerturbed[i] = PERTURBED(*atom);
- md->chargeB[i] = atom->qB;
- md->typeB[i] = atom->typeB;
+ md->bPerturbed[i] = PERTURBED(atom);
+ md->chargeB[i] = atom.qB;
+ md->typeB[i] = atom.typeB;
if (bLJPME)
{
- c6 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c6;
- c12 = mtop->ffparams.iparams[atom->typeB*(mtop->ffparams.atnr+1)].lj.c12;
+ c6 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c6;
+ c12 = mtop->ffparams.iparams[atom.typeB*(mtop->ffparams.atnr+1)].lj.c12;
md->sqrt_c6B[i] = sqrt(c6);
if (c6 == 0.0 || c12 == 0)
{
md->sigma3B[i] = 1/(md->sigmaB[i]*md->sigmaB[i]*md->sigmaB[i]);
}
}
- md->ptype[i] = atom->ptype;
+ md->ptype[i] = atom.ptype;
if (md->cTC)
{
md->cTC[i] = groups->grpnr[egcTC][ag];
if (ir->bQMMM)
{
- if (groups->grpnr[egcQMMM] == 0 ||
+ if (groups->grpnr[egcQMMM] == nullptr ||
groups->grpnr[egcQMMM][ag] < groups->grps[egcQMMM].nr-1)
{
md->bQM[i] = TRUE;
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
- gmx_mtop_atomlookup_destroy(alook);
-
md->homenr = homenr;
+ /* We set mass, invmass, invMassPerDim and tmass for lambda=0.
+ * For free-energy runs, these should be updated using update_mdatoms().
+ */
+ md->tmass = md->tmassA;
md->lambda = 0;
}
void update_mdatoms(t_mdatoms *md, real lambda)
{
- int al, end;
- real L1 = 1.0-lambda;
-
- end = md->nr;
-
- if (md->nMassPerturbed)
+ if (md->nMassPerturbed && lambda != md->lambda)
{
- for (al = 0; (al < end); al++)
+ real L1 = 1 - lambda;
+
+ /* Update masses of perturbed atoms for the change in lambda */
+ // cppcheck-suppress unreadVariable
+ int gmx_unused nthreads = gmx_omp_nthreads_get(emntDefault);
+#pragma omp parallel for num_threads(nthreads) schedule(static)
+ for (int i = 0; i < md->nr; i++)
{
- if (md->bPerturbed[al])
+ if (md->bPerturbed[i])
{
- md->massT[al] = L1*md->massA[al]+ lambda*md->massB[al];
- if (md->invmass[al] > 1.1*ALMOST_ZERO)
+ md->massT[i] = L1*md->massA[i] + lambda*md->massB[i];
+ /* Atoms with invmass 0 or ALMOST_ZERO are massless or frozen
+ * and their invmass does not depend on lambda.
+ */
+ if (md->invmass[i] > 1.1*ALMOST_ZERO)
{
- md->invmass[al] = 1.0/md->massT[al];
+ md->invmass[i] = 1.0/md->massT[i];
+ for (int d = 0; d < DIM; d++)
+ {
+ if (md->invMassPerDim[i][d] > 1.1*ALMOST_ZERO)
+ {
+ md->invMassPerDim[i][d] = md->invmass[i];
+ }
+ }
}
}
}
- md->tmass = L1*md->tmassA + lambda*md->tmassB;
- }
- else
- {
- md->tmass = md->tmassA;
+
+ /* Update the system mass for the change in lambda */
+ md->tmass = L1*md->tmassA + lambda*md->tmassB;
}
+
md->lambda = lambda;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_mdatoms *md);
/* This routine copies the atoms->atom struct into md.
* If index!=NULL only the indexed atoms are copied.
+ * For the masses the A-state (lambda=0) mass is used.
+ * Sets md->lambda = 0.
+ * In free-energy runs, update_mdatoms() should be called after atoms2md()
+ * to set the masses corresponding to the value of lambda at each step.
*/
void update_mdatoms(t_mdatoms *md, real lambda);
-/* (Re)set all the mass parameters */
+/* When necessary, sets all the mass parameters to values corresponding
+ * to the free-energy parameter lambda.
+ * Sets md->lambda = lambda.
+ */
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/topology/mtop_util.h"
{
md->nCrmsd = 1;
}
- md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
+ md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != nullptr);
}
else
{
}
else if (i == F_ECONSERVED)
{
- md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
- (ir->epc == epcNO || ir->epc == epcMTTK));
+ md->bEner[i] = (integratorHasConservedEnergyQuantity(ir));
}
else
{
/* Pass NULL for unit to let get_ebin_space determine the units
* for interaction_function[i].longname
*/
- md->ie = get_ebin_space(md->ebin, md->f_nre, ener_nm, NULL);
+ md->ie = get_ebin_space(md->ebin, md->f_nre, ener_nm, nullptr);
if (md->nCrmsd)
{
/* This should be called directly after the call for md->ie,
do_enxnms(fp_ene, &md->ebin->nener, &md->ebin->enm);
}
- md->print_grpnms = NULL;
+ md->print_grpnms = nullptr;
/* check whether we're going to write dh histograms */
- md->dhc = NULL;
+ md->dhc = nullptr;
if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
{
/* Currently dh histograms are only written with dynamics */
mde_delta_h_coll_init(md->dhc, ir);
}
- md->fp_dhdl = NULL;
+ md->fp_dhdl = nullptr;
snew(md->dE, ir->fepvals->n_lambda);
}
else
{
/* zero for simulated tempering */
md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];
- if (md->temperatures != NULL)
+ if (md->temperatures != nullptr)
{
/* MRS: is this right, given the way we have defined the exchange probabilities? */
/* is this even useful to have at all? */
if (md->nE > 1)
{
- if (md->print_grpnms == NULL)
+ if (md->print_grpnms == nullptr)
{
snew(md->print_grpnms, md->nE);
n = 0;
}
-void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin)
+void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin)
{
- int i;
+ const t_ebin * const ebin = mdebin->ebin;
- enerhist->nsteps = mdebin->ebin->nsteps;
- enerhist->nsum = mdebin->ebin->nsum;
- enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
- enerhist->nsum_sim = mdebin->ebin->nsum_sim;
- enerhist->nener = mdebin->ebin->nener;
+ enerhist->nsteps = ebin->nsteps;
+ enerhist->nsum = ebin->nsum;
+ enerhist->nsteps_sim = ebin->nsteps_sim;
+ enerhist->nsum_sim = ebin->nsum_sim;
- if (mdebin->ebin->nsum > 0)
+ if (ebin->nsum > 0)
{
- /* Check if we need to allocate first */
- if (enerhist->ener_ave == NULL)
- {
- snew(enerhist->ener_ave, enerhist->nener);
- snew(enerhist->ener_sum, enerhist->nener);
- }
+ /* This will only actually resize the first time */
+ enerhist->ener_ave.resize(ebin->nener);
+ enerhist->ener_sum.resize(ebin->nener);
- for (i = 0; i < enerhist->nener; i++)
+ for (int i = 0; i < ebin->nener; i++)
{
- enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
- enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
+ enerhist->ener_ave[i] = ebin->e[i].eav;
+ enerhist->ener_sum[i] = ebin->e[i].esum;
}
}
- if (mdebin->ebin->nsum_sim > 0)
+ if (ebin->nsum_sim > 0)
{
- /* Check if we need to allocate first */
- if (enerhist->ener_sum_sim == NULL)
- {
- snew(enerhist->ener_sum_sim, enerhist->nener);
- }
+ /* This will only actually resize the first time */
+ enerhist->ener_sum_sim.resize(ebin->nener);
- for (i = 0; i < enerhist->nener; i++)
+ for (int i = 0; i < ebin->nener; i++)
{
- enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
+ enerhist->ener_sum_sim[i] = ebin->e_sim[i].esum;
}
}
if (mdebin->dhc)
}
}
-void restore_energyhistory_from_state(t_mdebin * mdebin,
- energyhistory_t * enerhist)
+void restore_energyhistory_from_state(t_mdebin * mdebin,
+ const energyhistory_t * enerhist)
{
- int i;
+ unsigned int nener = static_cast<unsigned int>(mdebin->ebin->nener);
- if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
- mdebin->ebin->nener != enerhist->nener)
+ if ((enerhist->nsum > 0 && nener != enerhist->ener_sum.size()) ||
+ (enerhist->nsum_sim > 0 && nener != enerhist->ener_sum_sim.size()))
{
- gmx_fatal(FARGS, "Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
- mdebin->ebin->nener, enerhist->nener);
+ gmx_fatal(FARGS, "Mismatch between number of energies in run input (%d) and checkpoint file (%u or %u).",
+ nener, enerhist->ener_sum.size(), enerhist->ener_sum_sim.size());
}
mdebin->ebin->nsteps = enerhist->nsteps;
mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
mdebin->ebin->nsum_sim = enerhist->nsum_sim;
- for (i = 0; i < mdebin->ebin->nener; i++)
+ for (int i = 0; i < mdebin->ebin->nener; i++)
{
mdebin->ebin->e[i].eav =
(enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
}
if (mdebin->dhc)
{
- mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);
+ mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist->deltaHForeignLambdas.get());
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/enxio.h"
#include "gromacs/mdlib/ebin.h"
#include "gromacs/mdtypes/forcerec.h"
-#include "gromacs/mdtypes/state.h"
+class energyhistory_t;
struct gmx_constr;
struct gmx_ekindata_t;
struct gmx_mtop_t;
struct t_fcdata;
struct t_grpopts;
struct t_lambda;
+class t_state;
/* The functions & data structures here determine the content for outputting
the .edr file; the file format and actual writing is done with functions
/* Between .edr writes, the averages are history dependent,
and that history needs to be retained in checkpoints.
- These functions set/read the energyhistory_t structure
+ These functions set/read the energyhistory_t class
that is written to checkpoints in checkpoint.c */
-/* Set the energyhistory_t data structure from a mdebin structure */
-void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin);
+/* Set the energyhistory_t data from a mdebin structure */
+void update_energyhistory(energyhistory_t * enerhist, const t_mdebin * mdebin);
-/* Read the energyhistory_t data structure to a mdebin structure*/
-void restore_energyhistory_from_state(t_mdebin * mdebin,
- energyhistory_t * enerhist);
+/* Read the energyhistory_t data to a mdebin structure*/
+void restore_energyhistory_from_state(t_mdebin * mdebin,
+ const energyhistory_t * enerhist);
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <math.h>
#include <string.h>
+#include <cassert>
+
#include "gromacs/fileio/enxio.h"
#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
/* reset the delta_h list to prepare it for new values */
dh->type = type;
dh->derivative = derivative;
- dh->lambda = lambda;
dh->nlambda = nlambda;
snew(dh->lambda, nlambda);
for (i = 0; i < nlambda; i++)
{
+ assert(lambda);
dh->lambda[i] = lambda[i];
}
dh->ndhmax = ndhmax+2;
for (i = 0; i < 2; i++)
{
- dh->bin[i] = NULL;
+ dh->bin[i] = nullptr;
}
snew(dh->dh, dh->ndhmax);
}
-void mde_delta_h_handle_block(t_mde_delta_h *dh, t_enxblock *blk)
+static void mde_delta_h_handle_block(t_mde_delta_h *dh, t_enxblock *blk)
{
/* first check which type we should use: histogram or raw data */
if (dh->nhist == 0)
{
blk->sub[2].nr = 0;
blk->sub[2].type = xdr_datatype_float;
- blk->sub[2].fval = NULL;
+ blk->sub[2].fval = nullptr;
}
}
else
else
{
/* don't allocate the meta-data subblocks for lambda vectors */
- dhc->native_lambda_vec = NULL;
+ dhc->native_lambda_vec = nullptr;
dhc->n_lambda_vec = 0;
- dhc->native_lambda_components = 0;
+ dhc->native_lambda_components = nullptr;
dhc->lambda_index = -1;
}
/* allocate metadata subblocks */
/* now decide which data to write out */
dhc->nlambda = 0;
dhc->ndhdl = 0;
- dhc->dh_expanded = NULL;
- dhc->dh_energy = NULL;
- dhc->dh_pv = NULL;
+ dhc->dh_expanded = nullptr;
+ dhc->dh_energy = nullptr;
+ dhc->dh_pv = nullptr;
/* total number of raw data point collections in the sample */
dhc->ndh = 0;
dhc->dh_expanded = dhc->dh+n;
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
- dhbtEXPANDED, 0, 0, NULL);
+ dhbtEXPANDED, 0, 0, nullptr);
n++;
}
if (bEnergy)
dhc->dh_energy = dhc->dh+n;
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
- dhbtEN, 0, 0, NULL);
+ dhbtEN, 0, 0, nullptr);
n++;
}
/* add the dhdl's */
dhc->dh_pv = dhc->dh+n;
mde_delta_h_init(dhc->dh+n, ir->fepvals->dh_hist_size,
ir->fepvals->dh_hist_spacing, ndhmax,
- dhbtPV, 0, 0, NULL);
+ dhbtPV, 0, 0, nullptr);
n++;
}
}
{
mde_delta_h_add_dh(dhc->dh_du+i, foreign_dU[i]);
}
- if (dhc->dh_pv != NULL)
+ if (dhc->dh_pv != nullptr)
{
mde_delta_h_add_dh(dhc->dh_pv, pV);
}
- if (dhc->dh_energy != NULL)
+ if (dhc->dh_energy != nullptr)
{
mde_delta_h_add_dh(dhc->dh_energy, energy);
}
- if (dhc->dh_expanded != NULL)
+ if (dhc->dh_expanded != nullptr)
{
mde_delta_h_add_dh(dhc->dh_expanded, fep_state);
}
/* only allocate lambda vector component blocks if they must be written out
for backward compatibility */
- if (dhc->native_lambda_components != NULL)
+ if (dhc->native_lambda_components != nullptr)
{
add_subblocks_enxblock(blk, 2);
}
dhc->subblock_d[3] = dhc->start_lambda; /* old-style lambda at starttime */
dhc->subblock_d[4] = dhc->delta_lambda; /* lambda diff. between samples */
/* set the lambda vector components if they exist */
- if (dhc->native_lambda_components != NULL)
+ if (dhc->native_lambda_components != nullptr)
{
for (i = 0; i < dhc->n_lambda_vec; i++)
{
blk->sub[0].type = xdr_datatype_double;
blk->sub[0].dval = dhc->subblock_d;
- if (dhc->native_lambda_components != NULL)
+ if (dhc->native_lambda_components != nullptr)
{
dhc->subblock_i[0] = dhc->lambda_index;
/* set the lambda vector component IDs if they exist */
}
/* set the energyhistory variables to save state */
-void mde_delta_h_coll_update_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist)
+void mde_delta_h_coll_update_energyhistory(const t_mde_delta_h_coll *dhc,
+ energyhistory_t *enerhist)
{
- int i;
- if (!enerhist->dht)
+ if (enerhist->deltaHForeignLambdas == nullptr)
{
- snew(enerhist->dht, 1);
- snew(enerhist->dht->ndh, dhc->ndh);
- snew(enerhist->dht->dh, dhc->ndh);
- enerhist->dht->nndh = dhc->ndh;
+ enerhist->deltaHForeignLambdas.reset(new delta_h_history_t);
+ enerhist->deltaHForeignLambdas->dh.resize(dhc->ndh);
}
- else
- {
- if (enerhist->dht->nndh != dhc->ndh)
- {
- gmx_incons("energy history number of delta_h histograms != inputrec's number");
- }
- }
- for (i = 0; i < dhc->ndh; i++)
+
+ delta_h_history_t * const deltaH = enerhist->deltaHForeignLambdas.get();
+
+ GMX_RELEASE_ASSERT(deltaH->dh.size() == static_cast<size_t>(dhc->ndh), "energy history number of delta_h histograms should match inputrec's number");
+
+ for (int i = 0; i < dhc->ndh; i++)
{
- enerhist->dht->dh[i] = dhc->dh[i].dh;
- enerhist->dht->ndh[i] = dhc->dh[i].ndh;
+ std::vector<real> &dh = deltaH->dh[i];
+ dh.resize(dhc->dh[i].ndh);
+ std::copy(dh.begin(), dh.end(), dhc->dh[i].dh);
}
- enerhist->dht->start_time = dhc->start_time;
- enerhist->dht->start_lambda = dhc->start_lambda;
+ deltaH->start_time = dhc->start_time;
+ deltaH->start_lambda = dhc->start_lambda;
}
/* restore the variables from an energyhistory */
-void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist)
+void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll *dhc,
+ const delta_h_history_t *deltaH)
{
- int i;
- unsigned int j;
-
- if (!dhc)
- {
- gmx_incons("No delta_h histograms found");
- }
- if (!enerhist->dht)
- {
- gmx_incons("No delta_h histograms found in energy history");
- }
- if (enerhist->dht->nndh != dhc->ndh)
- {
- gmx_incons("energy history number of delta_h histograms != inputrec's number");
- }
+ GMX_RELEASE_ASSERT(dhc, "Should have delta_h histograms");
+ GMX_RELEASE_ASSERT(deltaH, "Should have delta_h histograms in energy history");
+ GMX_RELEASE_ASSERT(deltaH->dh.size() == static_cast<size_t>(dhc->ndh), "energy history number of delta_h histograms should match inputrec's number");
- for (i = 0; i < enerhist->dht->nndh; i++)
+ for (unsigned int i = 0; i < deltaH->dh.size(); i++)
{
- dhc->dh[i].ndh = enerhist->dht->ndh[i];
- for (j = 0; j < dhc->dh[i].ndh; j++)
+ dhc->dh[i].ndh = deltaH->dh[i].size();
+ for (unsigned int j = 0; j < dhc->dh[i].ndh; j++)
{
- dhc->dh[i].dh[j] = enerhist->dht->dh[i][j];
+ dhc->dh[i].dh[j] = deltaH->dh[i][j];
}
}
- dhc->start_time = enerhist->dht->start_time;
- if (enerhist->dht->start_lambda_set)
+ dhc->start_time = deltaH->start_time;
+ if (deltaH->start_lambda_set)
{
- dhc->start_lambda = enerhist->dht->start_lambda;
+ dhc->start_lambda = deltaH->start_lambda;
}
if (dhc->dh[0].ndh > 0)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/mdebin.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
/* The functions & data structures here describe writing
energy differences (or their histogram )for use with g_bar */
+class delta_h_history_t;
+
/* Data for one foreign lambda, or derivative. */
typedef struct
{
/* set the energyhistory variables to save state */
-void mde_delta_h_coll_update_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist);
+void mde_delta_h_coll_update_energyhistory(const t_mde_delta_h_coll *dhc,
+ energyhistory_t *enerhist);
/* restore the variables from an energyhistory */
-void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll *dhc,
- energyhistory_t *enerhist);
-
-
-#ifdef __cplusplus
-}
-#endif
+void mde_delta_h_coll_restore_energyhistory(t_mde_delta_h_coll *dhc,
+ const delta_h_history_t *deltaH);
#endif /* _mdebin_bar_h */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/trajectory_writing.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/imdoutputprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
struct gmx_mdoutf {
- t_fileio *fp_trn;
- t_fileio *fp_xtc;
- tng_trajectory_t tng;
- tng_trajectory_t tng_low_prec;
- int x_compression_precision; /* only used by XTC output */
- ener_file_t fp_ene;
- const char *fn_cpt;
- gmx_bool bKeepAndNumCPT;
- int eIntegrator;
- gmx_bool bExpanded;
- int elamstats;
- int simulation_part;
- FILE *fp_dhdl;
- FILE *fp_field;
- int natoms_global;
- int natoms_x_compressed;
- gmx_groups_t *groups; /* for compressed position writing */
- gmx_wallcycle_t wcycle;
- rvec *f_global;
+ t_fileio *fp_trn;
+ t_fileio *fp_xtc;
+ tng_trajectory_t tng;
+ tng_trajectory_t tng_low_prec;
+ int x_compression_precision; /* only used by XTC output */
+ ener_file_t fp_ene;
+ const char *fn_cpt;
+ gmx_bool bKeepAndNumCPT;
+ int eIntegrator;
+ gmx_bool bExpanded;
+ int elamstats;
+ int simulation_part;
+ FILE *fp_dhdl;
+ int natoms_global;
+ int natoms_x_compressed;
+ gmx_groups_t *groups; /* for compressed position writing */
+ gmx_wallcycle_t wcycle;
+ rvec *f_global;
+ gmx::IMDOutputProvider *outputProvider;
};
gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
- int mdrun_flags, const t_commrec *cr,
+ const MdrunOptions &mdrunOptions,
+ const t_commrec *cr,
+ gmx::IMDOutputProvider *outputProvider,
const t_inputrec *ir, gmx_mtop_t *top_global,
const gmx_output_env_t *oenv, gmx_wallcycle_t wcycle)
{
snew(of, 1);
- of->fp_trn = NULL;
- of->fp_ene = NULL;
- of->fp_xtc = NULL;
- of->tng = NULL;
- of->tng_low_prec = NULL;
- of->fp_dhdl = NULL;
- of->fp_field = NULL;
+ of->fp_trn = nullptr;
+ of->fp_ene = nullptr;
+ of->fp_xtc = nullptr;
+ of->tng = nullptr;
+ of->tng_low_prec = nullptr;
+ of->fp_dhdl = nullptr;
of->eIntegrator = ir->eI;
of->bExpanded = ir->bExpanded;
of->simulation_part = ir->simulation_part;
of->x_compression_precision = static_cast<int>(ir->x_compression_precision);
of->wcycle = wcycle;
- of->f_global = NULL;
+ of->f_global = nullptr;
+ of->outputProvider = outputProvider;
if (MASTER(cr))
{
- bAppendFiles = (mdrun_flags & MD_APPENDFILES);
+ bAppendFiles = mdrunOptions.continuationOptions.appendFiles;
- of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
+ of->bKeepAndNumCPT = mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles;
filemode = bAppendFiles ? appendMode : writeMode;
}
}
- if (opt2bSet("-field", nfile, fnm) &&
- (ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
- {
- if (bAppendFiles)
- {
- of->fp_field = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
- filemode);
- }
- else
- {
- of->fp_field = xvgropen(opt2fn("-field", nfile, fnm),
- "Applied electric field", "Time (ps)",
- "E (V/nm)", oenv);
- }
- }
+ outputProvider->initOutput(fplog, nfile, fnm, bAppendFiles, oenv);
/* Set up atom counts so they can be passed to actual
trajectory-writing routines later. Also, XTC writing needs
return of;
}
-FILE *mdoutf_get_fp_field(gmx_mdoutf_t of)
-{
- return of->fp_field;
-}
-
ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of)
{
return of->fp_ene;
gmx_mtop_t *top_global,
gmx_int64_t step, double t,
t_state *state_local, t_state *state_global,
- rvec *f_local)
+ ObservablesHistory *observablesHistory,
+ PaddedRVecVector *f_local)
{
- rvec *local_v;
- rvec *global_v;
rvec *f_global;
- /* MRS -- defining these variables is to manage the difference
- * between half step and full step velocities, but there must be a better way . . . */
-
- local_v = state_local->v;
- global_v = state_global->v;
-
if (DOMAINDECOMP(cr))
{
if (mdof_flags & MDOF_CPT)
{
if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
{
- dd_collect_vec(cr->dd, state_local, state_local->x,
- state_global->x);
+ dd_collect_vec(cr->dd, state_local, &state_local->x,
+ &state_global->x);
}
if (mdof_flags & MDOF_V)
{
- dd_collect_vec(cr->dd, state_local, local_v,
- global_v);
+ dd_collect_vec(cr->dd, state_local, &state_local->v,
+ &state_global->v);
}
}
f_global = of->f_global;
}
else
{
- if (mdof_flags & MDOF_CPT)
- {
- /* All pointers in state_local are equal to state_global,
- * but we need to copy the non-pointer entries.
- */
- state_global->lambda = state_local->lambda;
- state_global->veta = state_local->veta;
- state_global->vol0 = state_local->vol0;
- copy_mat(state_local->box, state_global->box);
- copy_mat(state_local->boxv, state_global->boxv);
- copy_mat(state_local->svir_prev, state_global->svir_prev);
- copy_mat(state_local->fvir_prev, state_global->fvir_prev);
- copy_mat(state_local->pres_prev, state_global->pres_prev);
- }
- f_global = f_local;
+ /* We have the whole state locally: copy the local state pointer */
+ state_global = state_local;
+
+ f_global = as_rvec_array(f_local->data());
}
if (MASTER(cr))
DOMAINDECOMP(cr) ? cr->dd->nc : one_ivec,
DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes,
of->eIntegrator, of->simulation_part,
- of->bExpanded, of->elamstats, step, t, state_global);
+ of->bExpanded, of->elamstats, step, t,
+ state_global, observablesHistory);
}
if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
{
+ const rvec *x = (mdof_flags & MDOF_X) ? as_rvec_array(state_global->x.data()) : nullptr;
+ const rvec *v = (mdof_flags & MDOF_V) ? as_rvec_array(state_global->v.data()) : nullptr;
+ const rvec *f = (mdof_flags & MDOF_F) ? f_global : nullptr;
+
if (of->fp_trn)
{
gmx_trr_write_frame(of->fp_trn, step, t, state_local->lambda[efptFEP],
state_local->box, top_global->natoms,
- (mdof_flags & MDOF_X) ? state_global->x : NULL,
- (mdof_flags & MDOF_V) ? global_v : NULL,
- (mdof_flags & MDOF_F) ? f_global : NULL);
+ x, v, f);
if (gmx_fio_flush(of->fp_trn) != 0)
{
gmx_file("Cannot write trajectory; maybe you are out of disk space?");
gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
state_local->box,
top_global->natoms,
- (mdof_flags & MDOF_X) ? state_global->x : NULL,
- (mdof_flags & MDOF_V) ? global_v : NULL,
- (mdof_flags & MDOF_F) ? f_global : NULL);
+ x, v, f);
}
/* If only a TNG file is open for compressed coordinate output (no uncompressed
coordinate output) also write forces and velocities to it. */
gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, state_local->lambda[efptFEP],
state_local->box,
top_global->natoms,
- (mdof_flags & MDOF_X) ? state_global->x : NULL,
- (mdof_flags & MDOF_V) ? global_v : NULL,
- (mdof_flags & MDOF_F) ? f_global : NULL);
+ x, v, f);
}
}
if (mdof_flags & MDOF_X_COMPRESSED)
{
- rvec *xxtc = NULL;
+ rvec *xxtc = nullptr;
if (of->natoms_x_compressed == of->natoms_global)
{
/* We are writing the positions of all of the atoms to
the compressed output */
- xxtc = state_global->x;
+ xxtc = as_rvec_array(state_global->x.data());
}
else
{
state_local->box,
of->natoms_x_compressed,
xxtc,
- NULL,
- NULL);
+ nullptr,
+ nullptr);
if (of->natoms_x_compressed != of->natoms_global)
{
sfree(xxtc);
void done_mdoutf(gmx_mdoutf_t of)
{
- if (of->fp_ene != NULL)
+ if (of->fp_ene != nullptr)
{
close_enx(of->fp_ene);
}
{
gmx_trr_close(of->fp_trn);
}
- if (of->fp_dhdl != NULL)
+ if (of->fp_dhdl != nullptr)
{
gmx_fio_fclose(of->fp_dhdl);
}
- if (of->fp_field != NULL)
- {
- /* This is opened sometimes with xvgropen, sometimes with
- * gmx_fio_fopen, so we use the least common denominator for closing.
- */
- gmx_fio_fclose(of->fp_field);
- }
- if (of->f_global != NULL)
+ of->outputProvider->finishOutput();
+ if (of->f_global != nullptr)
{
sfree(of->f_global);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
#include "gromacs/fileio/enxio.h"
+#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/basedefinitions.h"
+class energyhistory_t;
struct gmx_mtop_t;
struct gmx_output_env_t;
+struct MdrunOptions;
+struct ObservablesHistory;
struct t_commrec;
struct t_filenm;
struct t_inputrec;
+namespace gmx
+{
+class IMDOutputProvider;
+}
+
typedef struct gmx_mdoutf *gmx_mdoutf_t;
/*! \brief Allocate and initialize object to manager trajectory writing output
gmx_mdoutf_t init_mdoutf(FILE *fplog,
int nfile,
const t_filenm fnm[],
- int mdrun_flags,
+ const MdrunOptions &mdrunOptions,
const t_commrec *cr,
+ gmx::IMDOutputProvider *outputProvider,
const t_inputrec *ir,
gmx_mtop_t *mtop,
const gmx_output_env_t *oenv,
gmx_wallcycle_t wcycle);
-/*! \brief Getter for file pointer */
-FILE *mdoutf_get_fp_field(gmx_mdoutf_t of);
-
/*! \brief Getter for file pointer */
ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of);
*
* Writes data to trn, xtc and/or checkpoint. What is written is
* determined by the mdof_flags defined below. Data is collected to
- * the master node only when necessary.
+ * the master node only when necessary. Without domain decomposition
+ * only data from state_local is used and state_global is ignored.
*/
void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
gmx_mdoutf_t of,
gmx_mtop_t *top_global,
gmx_int64_t step, double t,
t_state *state_local, t_state *state_global,
- rvec *f_local);
+ ObservablesHistory *observablesHistory,
+ PaddedRVecVector *f_local);
#define MDOF_X (1<<0)
#define MDOF_V (1<<1)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+
+/*! \libinternal \file
+ *
+ * \brief This file declares types and functions for initializing an MD run
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \inlibraryapi
+ */
+
#ifndef GMX_MDLIB_MDRUN_H
#define GMX_MDLIB_MDRUN_H
-#include <stdio.h>
-#include <time.h>
-
#include "gromacs/timing/wallcycle.h"
-struct df_history_t;
-struct gmx_constr;
-struct gmx_edsam;
-struct gmx_enerdata_t;
struct gmx_mtop_t;
struct t_commrec;
-struct t_expanded;
-struct t_extmass;
struct t_inputrec;
-struct t_lambda;
-struct t_mdatoms;
-struct t_simtemp;
-struct t_state;
-
-#define MD_POLARISE (1<<2)
-#define MD_RERUN (1<<4)
-#define MD_RERUN_VSITE (1<<5)
-#define MD_DDBONDCHECK (1<<10)
-#define MD_DDBONDCOMM (1<<11)
-#define MD_CONFOUT (1<<12)
-#define MD_REPRODUCIBLE (1<<13)
-#define MD_APPENDFILES (1<<15)
-#define MD_APPENDFILESSET (1<<21)
-#define MD_KEEPANDNUMCPT (1<<16)
-#define MD_READ_EKIN (1<<17)
-#define MD_STARTFROMCPT (1<<18)
-#define MD_RESETCOUNTERSHALFWAY (1<<19)
-#define MD_TUNEPME (1<<20)
-#define MD_NTOMPSET (1<<21)
-#define MD_IMDWAIT (1<<23)
-#define MD_IMDTERM (1<<24)
-#define MD_IMDPULL (1<<25)
-
-/* The options for the domain decomposition MPI task ordering */
-enum {
- ddrankorderSEL, ddrankorderINTERLEAVE, ddrankorderPP_PME, ddrankorderCARTESIAN, ddrankorderNR
+class t_state;
+
+//! \internal \brief Options and settings for continuing from checkpoint
+struct ContinuationOptions
+{
+ //! \brief Constructor
+ ContinuationOptions() :
+ appendFiles(false),
+ appendFilesOptionSet(false),
+ startedFromCheckpoint(false),
+ haveReadEkin(false)
+ {
+ }
+
+ //! True if we are continuing from a checkpoint and should append output files
+ bool appendFiles;
+ //! True if the -append option was explicitly set by the user (either to true of false
+ bool appendFilesOptionSet;
+ //! True if we started from a checkpoint file
+ bool startedFromCheckpoint;
+ //! True if we read the kinetic energy from checkpoint file
+ bool haveReadEkin;
};
-void init_npt_masses(t_inputrec *ir, t_state *state, t_extmass *MassQ, gmx_bool bInit);
+//! \internal \brief Options for writing checkpoint files
+struct CheckpointOptions
+{
+ //! \brief Constructor
+ CheckpointOptions() :
+ keepAndNumberCheckpointFiles(FALSE),
+ period(15)
+ {
+ }
-void init_expanded_ensemble(gmx_bool bStateFromCP, t_inputrec *ir, df_history_t *dfhist);
+ //! True means keep all checkpoint file and add the step number to the name
+ gmx_bool keepAndNumberCheckpointFiles;
+ //! The period in minutes for writing checkpoint files
+ real period;
+};
-int ExpandedEnsembleDynamics(FILE *log, t_inputrec *ir, gmx_enerdata_t *enerd,
- t_state *state, t_extmass *MassQ, int fep_state, df_history_t *dfhist,
- gmx_int64_t step,
- rvec *v, t_mdatoms *mdatoms);
+//! \internal \brief Options for timing (parts of) mdrun
+struct TimingOptions
+{
+ //! \brief Constructor
+ TimingOptions() :
+ resetStep(-1),
+ resetHalfway(FALSE)
+ {
+ }
-void PrintFreeEnergyInfoToFile(FILE *outfile, t_lambda *fep, t_expanded *expand, t_simtemp *simtemp, df_history_t *dfhist,
- int fep_state, int frequency, gmx_int64_t step);
+ //! Reset timers at the start of this MD step, -1 means do not reset
+ int resetStep;
+ //! If true, reset timers half-way the run
+ gmx_bool resetHalfway;
+};
+
+//! \internal \brief Options for IMD
+struct ImdOptions
+{
+ //! Constructor
+ ImdOptions() :
+ port(8888),
+ wait(FALSE),
+ terminatable(FALSE),
+ pull(FALSE)
+ {
+ }
+
+ //! IMD listening port
+ int port;
+ //! If true, pause the simulation while no IMD client is connected
+ gmx_bool wait;
+ //! If true, allow termination of the simulation from IMD client
+ gmx_bool terminatable;
+ //! If true, allow COM pulling in the simulation from IMD client
+ gmx_bool pull;
+};
-/* Allocate and initialize node-local state entries. */
+//! \internal \brief Collection of all options of mdrun that are not processed separately
+struct MdrunOptions
+{
+ //! \brief Constructor
+ MdrunOptions() :
+ rerun(FALSE),
+ rerunConstructVsites(FALSE),
+ globalCommunicationInterval(-1),
+ reproducible(FALSE),
+ writeConfout(TRUE),
+ continuationOptions(),
+ checkpointOptions(),
+ numStepsCommandline(-2),
+ maximumHoursToRun(-1),
+ timingOptions(),
+ tunePme(TRUE),
+ ntompOptionIsSet(FALSE),
+ imdOptions(),
+ verbose(FALSE),
+ verboseStepPrintInterval(100)
+ {
+ }
+
+ //! Re-compute energies, and possibly forces, for frames from an input tracjectory
+ gmx_bool rerun;
+ //! Re-construct virual sites durin a rerun simulation
+ gmx_bool rerunConstructVsites;
+ //! Request to do global communication at this interval in steps, -1 is determine from inputrec
+ int globalCommunicationInterval;
+ //! Try to make the simulation binary reproducible
+ gmx_bool reproducible;
+ //! Write confout.gro at the end of the run
+ gmx_bool writeConfout;
+ //! Options for continuing a simulation from a checkpoint file
+ ContinuationOptions continuationOptions;
+ //! Options for checkpointing th simulation
+ CheckpointOptions checkpointOptions;
+ //! Number of steps to run, -2 is use inputrec, -1 is infinite
+ gmx_int64_t numStepsCommandline;
+ //! Maximum duration of this simulation in wall-clock hours, -1 is no limit
+ real maximumHoursToRun;
+ //! Options for timing the run
+ TimingOptions timingOptions;
+ //! If true and supported, will tune the PP-PME load balance
+ gmx_bool tunePme;
+ //! True if the user explicitly set the -ntomp command line option
+ gmx_bool ntompOptionIsSet;
+ //! Options for IMD
+ ImdOptions imdOptions;
+ //! Increase the verbosity level in the logging and/or stdout/stderr
+ gmx_bool verbose;
+ //! If verbose=true, print remaining runtime at this step interval
+ int verboseStepPrintInterval;
+};
+
+//! \brief Allocate and initialize node-local state entries
void set_state_entries(t_state *state, const t_inputrec *ir);
-/* Broadcast the data for a simulation, and allocate node-specific settings */
+//! \brief Broadcast inputrec and mtop and allocate node-specific settings
void init_parallel(t_commrec *cr, t_inputrec *inputrec,
gmx_mtop_t *mtop);
+//! \brief Broadcasts state from the master to all ranks in cr->mpi_comm_mygroup
void bcast_state(const t_commrec *cr, t_state *state);
-/* Broadcasts state from the master to all nodes in cr->mpi_comm_mygroup.
- */
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "mdsetup.h"
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/listed-forces/manage-threading.h"
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/shellfc.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
+
+/* TODO: Add a routine that collects the initial setup of the algorithms.
+ *
+ * The final solution should be an MD algorithm base class with methods
+ * for initialization and atom-data setup.
+ */
+
+void mdAlgorithmsSetupAtomData(t_commrec *cr,
+ const t_inputrec *ir,
+ const gmx_mtop_t *top_global,
+ gmx_localtop_t *top,
+ t_forcerec *fr,
+ t_graph **graph,
+ t_mdatoms *mdatoms,
+ gmx_vsite_t *vsite,
+ gmx_shellfc_t *shellfc)
+{
+ bool usingDomDec = DOMAINDECOMP(cr);
+
+ int numAtomIndex, numHomeAtoms;
+ int *atomIndex;
+
+ if (usingDomDec)
+ {
+ numAtomIndex = dd_natoms_mdatoms(cr->dd);
+ atomIndex = cr->dd->gatindex;
+ numHomeAtoms = cr->dd->nat_home;
+ }
+ else
+ {
+ numAtomIndex = -1;
+ atomIndex = nullptr;
+ numHomeAtoms = top_global->natoms;
+ }
+ atoms2md(top_global, ir, numAtomIndex, atomIndex, numHomeAtoms, mdatoms);
+
+ if (usingDomDec)
+ {
+ dd_sort_local_top(cr->dd, mdatoms, top);
+ }
+ else
+ {
+ /* Currently gmx_generate_local_top allocates and returns a pointer.
+ * We should implement a more elegant solution.
+ */
+ gmx_localtop_t *tmpTop;
+
+ tmpTop = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
+ *top = *tmpTop;
+ sfree(tmpTop);
+ }
+
+ if (vsite)
+ {
+ if (usingDomDec)
+ {
+ /* The vsites were already assigned by the domdec topology code.
+ * We only need to do the thread division here.
+ */
+ split_vsites_over_threads(top->idef.il, top->idef.iparams,
+ mdatoms, FALSE, vsite);
+ }
+ else
+ {
+ set_vsite_top(vsite, top, mdatoms, cr);
+ }
+ }
+
+ if (!usingDomDec && ir->ePBC != epbcNONE && !fr->bMolPBC)
+ {
+ GMX_ASSERT(graph != NULL, "We use a graph with PBC (no periodic mols) and without DD");
+
+ *graph = mk_graph(nullptr, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
+ }
+ else if (graph != nullptr)
+ {
+ *graph = nullptr;
+ }
+
+ /* Note that with DD only flexible constraints, not shells, are supported
+ * and these don't require setup in make_local_shells().
+ */
+ if (!usingDomDec && shellfc)
+ {
+ make_local_shells(cr, mdatoms, shellfc);
+ }
+
+ setup_bonded_threading(fr, &top->idef);
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MDLIB_MDSETUP_H
+#define GMX_MDLIB_MDSETUP_H
+
+#include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/shellfc.h"
+#include "gromacs/mdlib/vsite.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/forcerec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/topology/topology.h"
+
+/*! \brief Sets atom data for several MD algorithms
+ *
+ * Most MD algorithms require two different setup calls:
+ * one for initialization and parameter setting and one for atom data setup.
+ * This routine sets the atom data for the (locally available) atoms.
+ * This is called at the start of serial runs and during domain decomposition.
+ *
+ * \param[in] cr Communication record
+ * \param[in] ir Input parameter record
+ * \param[in] top_global The global topology
+ * \param[in,out] top The local topology
+ * \param[in,out] fr The force calculation parameter/data record
+ * \param[out] graph The molecular graph, can be NULL
+ * \param[out] mdatoms The MD atom data
+ * \param[in,out] vsite The virtual site data, can be NULL
+ * \param[in,out] shellfc The shell/flexible-constraint data, can be NULL
+ */
+void mdAlgorithmsSetupAtomData(t_commrec *cr,
+ const t_inputrec *ir,
+ const gmx_mtop_t *top_global,
+ gmx_localtop_t *top,
+ t_forcerec *fr,
+ t_graph **graph,
+ t_mdatoms *mdatoms,
+ gmx_vsite_t *vsite,
+ gmx_shellfc_t *shellfc);
+
+#endif
#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/mtxio.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/imd/imd.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/shellfc.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
//! Utility structure for manipulating states during EM
typedef struct {
//! Copy of the global state
- t_state s;
+ t_state s;
//! Force array
- rvec *f;
+ PaddedRVecVector f;
//! Potential energy
- real epot;
+ real epot;
//! Norm of the force
- real fnorm;
+ real fnorm;
//! Maximum force
- real fmax;
+ real fmax;
//! Direction
- int a_fmax;
+ int a_fmax;
} em_state_t;
-//! Initiate em_state_t structure and return pointer to it
-static em_state_t *init_em_state()
-{
- em_state_t *ems;
-
- snew(ems, 1);
-
- /* does this need to be here? Should the array be declared differently (staticaly)in the state definition? */
- snew(ems->s.lambda, efptNR);
-
- return ems;
-}
-
//! Print the EM starting conditions
static void print_em_start(FILE *fplog,
t_commrec *cr,
//! Print message about convergence of the EM
static void print_converged(FILE *fp, const char *alg, real ftol,
gmx_int64_t count, gmx_bool bDone, gmx_int64_t nsteps,
- real epot, real fmax, int nfmax, real fnorm)
+ const em_state_t *ems, double sqrtNumAtoms)
{
char buf[STEPSTRSIZE];
}
#if GMX_DOUBLE
- fprintf(fp, "Potential Energy = %21.14e\n", epot);
- fprintf(fp, "Maximum force = %21.14e on atom %d\n", fmax, nfmax+1);
- fprintf(fp, "Norm of force = %21.14e\n", fnorm);
+ fprintf(fp, "Potential Energy = %21.14e\n", ems->epot);
+ fprintf(fp, "Maximum force = %21.14e on atom %d\n", ems->fmax, ems->a_fmax + 1);
+ fprintf(fp, "Norm of force = %21.14e\n", ems->fnorm/sqrtNumAtoms);
#else
- fprintf(fp, "Potential Energy = %14.7e\n", epot);
- fprintf(fp, "Maximum force = %14.7e on atom %d\n", fmax, nfmax+1);
- fprintf(fp, "Norm of force = %14.7e\n", fnorm);
+ fprintf(fp, "Potential Energy = %14.7e\n", ems->epot);
+ fprintf(fp, "Maximum force = %14.7e on atom %d\n", ems->fmax, ems->a_fmax + 1);
+ fprintf(fp, "Norm of force = %14.7e\n", ems->fnorm/sqrtNumAtoms);
#endif
}
//! Compute the norm and max of the force array in parallel
static void get_f_norm_max(t_commrec *cr,
- t_grpopts *opts, t_mdatoms *mdatoms, rvec *f,
+ t_grpopts *opts, t_mdatoms *mdatoms, const rvec *f,
real *fnorm, real *fmax, int *a_fmax)
{
double fnorm2, *sum;
t_grpopts *opts, t_mdatoms *mdatoms,
em_state_t *ems)
{
- get_f_norm_max(cr, opts, mdatoms, ems->f, &ems->fnorm, &ems->fmax, &ems->a_fmax);
+ get_f_norm_max(cr, opts, mdatoms, as_rvec_array(ems->f.data()),
+ &ems->fnorm, &ems->fmax, &ems->a_fmax);
}
//! Initialize the energy minimization
-void init_em(FILE *fplog, const char *title,
- t_commrec *cr, t_inputrec *ir,
- t_state *state_global, gmx_mtop_t *top_global,
- em_state_t *ems, gmx_localtop_t **top,
- rvec **f,
- t_nrnb *nrnb, rvec mu_tot,
- t_forcerec *fr, gmx_enerdata_t **enerd,
- t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int nfile, const t_filenm fnm[],
- gmx_mdoutf_t *outf, t_mdebin **mdebin,
- int imdport, unsigned long gmx_unused Flags,
- gmx_wallcycle_t wcycle)
+static void init_em(FILE *fplog, const char *title,
+ t_commrec *cr, gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *ir,
+ const MdrunOptions &mdrunOptions,
+ t_state *state_global, gmx_mtop_t *top_global,
+ em_state_t *ems, gmx_localtop_t **top,
+ t_nrnb *nrnb, rvec mu_tot,
+ t_forcerec *fr, gmx_enerdata_t **enerd,
+ t_graph **graph, t_mdatoms *mdatoms, gmx_global_stat_t *gstat,
+ gmx_vsite_t *vsite, gmx_constr_t constr, gmx_shellfc_t **shellfc,
+ int nfile, const t_filenm fnm[],
+ gmx_mdoutf_t *outf, t_mdebin **mdebin,
+ gmx_wallcycle_t wcycle)
{
- int i;
real dvdl_constr;
if (fplog)
state_global->ngtc = 0;
/* Initialize lambda variables */
- initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, NULL);
+ initialize_lambdas(fplog, ir, &(state_global->fep_state), state_global->lambda, nullptr);
init_nrnb(nrnb);
/* Interactive molecular dynamics */
- init_IMD(ir, cr, top_global, fplog, 1, state_global->x,
- nfile, fnm, NULL, imdport, Flags);
+ init_IMD(ir, cr, top_global, fplog, 1, as_rvec_array(state_global->x.data()),
+ nfile, fnm, nullptr, mdrunOptions);
+
+ if (ir->eI == eiNM)
+ {
+ GMX_ASSERT(shellfc != NULL, "With NM we always support shells");
+
+ *shellfc = init_shell_flexcon(stdout,
+ top_global,
+ n_flexible_constraints(constr),
+ ir->nstcalcenergy,
+ DOMAINDECOMP(cr));
+ }
+ else
+ {
+ GMX_ASSERT(EI_ENERGY_MINIMIZATION(ir->eI), "This else currently only handles energy minimizers, consider if your algorithm needs shell/flexible-constraint support");
+
+ /* With energy minimization, shells and flexible constraints are
+ * automatically minimized when treated like normal DOFS.
+ */
+ if (shellfc != nullptr)
+ {
+ *shellfc = nullptr;
+ }
+ }
if (DOMAINDECOMP(cr))
{
dd_init_local_state(cr->dd, state_global, &ems->s);
- *f = NULL;
-
/* Distribute the charge groups over the nodes from the master node */
dd_partition_system(fplog, ir->init_step, cr, TRUE, 1,
state_global, top_global, ir,
&ems->s, &ems->f, mdatoms, *top,
fr, vsite, constr,
- nrnb, NULL, FALSE);
+ nrnb, nullptr, FALSE);
dd_store_state(cr->dd, &ems->s);
- *graph = NULL;
+ *graph = nullptr;
}
else
{
- snew(*f, top_global->natoms);
-
+ state_change_natoms(state_global, state_global->natoms);
/* Just copy the state */
ems->s = *state_global;
+ state_change_natoms(&ems->s, ems->s.natoms);
/* We need to allocate one element extra, since we might use
* (unaligned) 4-wide SIMD loads to access rvec entries.
*/
- snew(ems->s.x, ems->s.nalloc + 1);
- snew(ems->f, ems->s.nalloc+1);
- snew(ems->s.v, ems->s.nalloc+1);
- for (i = 0; i < state_global->natoms; i++)
- {
- copy_rvec(state_global->x[i], ems->s.x[i]);
- }
- copy_mat(state_global->box, ems->s.box);
-
- *top = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
-
- setup_bonded_threading(fr, &(*top)->idef);
-
- if (ir->ePBC != epbcNONE && !fr->bMolPBC)
- {
- *graph = mk_graph(fplog, &((*top)->idef), 0, top_global->natoms, FALSE, FALSE);
- }
- else
- {
- *graph = NULL;
- }
+ ems->f.resize(ems->s.natoms + 1);
- atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
+ snew(*top, 1);
+ mdAlgorithmsSetupAtomData(cr, ir, top_global, *top, fr,
+ graph, mdatoms,
+ vsite, shellfc ? *shellfc : nullptr);
if (vsite)
{
{
/* Constrain the starting coordinates */
dvdl_constr = 0;
- constrain(PAR(cr) ? NULL : fplog, TRUE, TRUE, constr, &(*top)->idef,
+ constrain(PAR(cr) ? nullptr : fplog, TRUE, TRUE, constr, &(*top)->idef,
ir, cr, -1, 0, 1.0, mdatoms,
- ems->s.x, ems->s.x, NULL, fr->bMolPBC, ems->s.box,
+ as_rvec_array(ems->s.x.data()),
+ as_rvec_array(ems->s.x.data()),
+ nullptr,
+ fr->bMolPBC, ems->s.box,
ems->s.lambda[efptFEP], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
+ nullptr, nullptr, nrnb, econqCoord);
}
}
}
else
{
- *gstat = NULL;
+ *gstat = nullptr;
}
- *outf = init_mdoutf(fplog, nfile, fnm, 0, cr, ir, top_global, NULL, wcycle);
+ *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, top_global, nullptr, wcycle);
snew(*enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
*enerd);
- if (mdebin != NULL)
+ if (mdebin != nullptr)
{
/* Init bin for energy stuff */
- *mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, NULL);
+ *mdebin = init_mdebin(mdoutf_get_fp_ene(*outf), top_global, ir, nullptr);
}
clear_rvec(mu_tot);
}
//! Swap two different EM states during minimization
-static void swap_em_state(em_state_t *ems1, em_state_t *ems2)
+static void swap_em_state(em_state_t **ems1, em_state_t **ems2)
{
- em_state_t tmp;
+ em_state_t *tmp;
tmp = *ems1;
*ems1 = *ems2;
*ems2 = tmp;
}
-//! Copy coordinate from an EM state to a "normal" state structure
-static void copy_em_coords(em_state_t *ems, t_state *state)
-{
- int i;
-
- for (i = 0; (i < state->natoms); i++)
- {
- copy_rvec(ems->s.x[i], state->x[i]);
- }
-}
-
//! Save the EM trajectory
static void write_em_traj(FILE *fplog, t_commrec *cr,
gmx_mdoutf_t outf,
gmx_mtop_t *top_global,
t_inputrec *ir, gmx_int64_t step,
em_state_t *state,
- t_state *state_global)
+ t_state *state_global,
+ ObservablesHistory *observablesHistory)
{
- int mdof_flags;
- gmx_bool bIMDout = FALSE;
-
-
- /* Shall we do IMD output? */
- if (ir->bIMD)
- {
- bIMDout = do_per_step(step, IMD_get_step(ir->imd->setup));
- }
-
- if ((bX || bF || bIMDout || confout != NULL) && !DOMAINDECOMP(cr))
- {
- copy_em_coords(state, state_global);
- }
+ int mdof_flags = 0;
- mdof_flags = 0;
if (bX)
{
mdof_flags |= MDOF_X;
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
top_global, step, (double)step,
- &state->s, state_global, state->f);
+ &state->s, state_global, observablesHistory,
+ &state->f);
- if (confout != NULL && MASTER(cr))
+ if (confout != nullptr && MASTER(cr))
{
+ GMX_RELEASE_ASSERT(bX, "The code below assumes that (with domain decomposition), x is collected to state_global in the call above.");
+ /* With domain decomposition the call above collected the state->s.x
+ * into state_global->x. Without DD we copy the local state pointer.
+ */
+ if (!DOMAINDECOMP(cr))
+ {
+ state_global = &state->s;
+ }
+
if (ir->ePBC != epbcNONE && !ir->bPeriodicMols && DOMAINDECOMP(cr))
{
/* Make molecules whole only for confout writing */
- do_pbc_mtop(fplog, ir->ePBC, state_global->box, top_global,
- state_global->x);
+ do_pbc_mtop(fplog, ir->ePBC, state->s.box, top_global,
+ as_rvec_array(state_global->x.data()));
}
write_sto_conf_mtop(confout,
*top_global->name, top_global,
- state_global->x, NULL, ir->ePBC, state_global->box);
+ as_rvec_array(state_global->x.data()), nullptr, ir->ePBC, state->s.box);
}
}
// \returns true when the step succeeded, false when a constraint error occurred
static bool do_em_step(t_commrec *cr, t_inputrec *ir, t_mdatoms *md,
gmx_bool bMolPBC,
- em_state_t *ems1, real a, rvec *f, em_state_t *ems2,
+ em_state_t *ems1, real a, const PaddedRVecVector *force,
+ em_state_t *ems2,
gmx_constr_t constr, gmx_localtop_t *top,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_int64_t count)
s2->flags = s1->flags;
- if (s2->nalloc != s1->nalloc)
+ if (s2->natoms != s1->natoms)
{
- s2->nalloc = s1->nalloc;
+ state_change_natoms(s2, s1->natoms);
/* We need to allocate one element extra, since we might use
* (unaligned) 4-wide SIMD loads to access rvec entries.
*/
- srenew(s2->x, s1->nalloc + 1);
- srenew(ems2->f, s1->nalloc);
- if (s2->flags & (1<<estCGP))
- {
- srenew(s2->cg_p, s1->nalloc + 1);
- }
+ ems2->f.resize(s2->natoms + 1);
+ }
+ if (DOMAINDECOMP(cr) && s2->cg_gl.size() != s1->cg_gl.size())
+ {
+ s2->cg_gl.resize(s1->cg_gl.size());
}
- s2->natoms = s1->natoms;
copy_mat(s1->box, s2->box);
/* Copy free energy state */
- for (int i = 0; i < efptNR; i++)
- {
- s2->lambda[i] = s1->lambda[i];
- }
+ s2->lambda = s1->lambda;
copy_mat(s1->box, s2->box);
start = 0;
nthreads = gmx_omp_nthreads_get(emntUpdate);
#pragma omp parallel num_threads(nthreads)
{
- rvec *x1 = s1->x;
- rvec *x2 = s2->x;
+ const rvec *x1 = as_rvec_array(s1->x.data());
+ rvec *x2 = as_rvec_array(s2->x.data());
+ const rvec *f = as_rvec_array(force->data());
- int gf = 0;
+ int gf = 0;
#pragma omp for schedule(static) nowait
for (int i = start; i < end; i++)
{
if (s2->flags & (1<<estCGP))
{
/* Copy the CG p vector */
- rvec *p1 = s1->cg_p;
- rvec *p2 = s2->cg_p;
+ const rvec *p1 = as_rvec_array(s1->cg_p.data());
+ rvec *p2 = as_rvec_array(s2->cg_p.data());
#pragma omp for schedule(static) nowait
for (int i = start; i < end; i++)
{
if (DOMAINDECOMP(cr))
{
s2->ddp_count = s1->ddp_count;
- if (s2->cg_gl_nalloc < s1->cg_gl_nalloc)
- {
-#pragma omp barrier
- s2->cg_gl_nalloc = s1->cg_gl_nalloc;
- try
- {
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries.
- */
- srenew(s2->cg_gl, s2->cg_gl_nalloc + 1);
- }
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
-#pragma omp barrier
- }
- s2->ncg_gl = s1->ncg_gl;
+
+ /* OpenMP does not supported unsigned loop variables */
#pragma omp for schedule(static) nowait
- for (int i = 0; i < s2->ncg_gl; i++)
+ for (int i = 0; i < static_cast<int>(s2->cg_gl.size()); i++)
{
s2->cg_gl[i] = s1->cg_gl[i];
}
wallcycle_start(wcycle, ewcCONSTR);
dvdl_constr = 0;
validStep =
- constrain(NULL, TRUE, TRUE, constr, &top->idef,
+ constrain(nullptr, TRUE, TRUE, constr, &top->idef,
ir, cr, count, 0, 1.0, md,
- s1->x, s2->x, NULL, bMolPBC, s2->box,
+ as_rvec_array(s1->x.data()), as_rvec_array(s2->x.data()),
+ nullptr, bMolPBC, s2->box,
s2->lambda[efptBONDED], &dvdl_constr,
- NULL, NULL, nrnb, econqCoord);
+ nullptr, nullptr, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
// We should move this check to the different minimizers
{
/* Repartition the domain decomposition */
dd_partition_system(fplog, step, cr, FALSE, 1,
- NULL, top_global, ir,
+ nullptr, top_global, ir,
&ems->s, &ems->f,
mdatoms, top, fr, vsite, constr,
nrnb, wcycle, FALSE);
if (vsite)
{
- construct_vsites(vsite, ems->s.x, 1, NULL,
+ construct_vsites(vsite, as_rvec_array(ems->s.x.data()), 1, nullptr,
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, ems->s.box);
}
*/
do_force(fplog, cr, inputrec,
count, nrnb, wcycle, top, &top_global->groups,
- ems->s.box, ems->s.x, &ems->s.hist,
- ems->f, force_vir, mdatoms, enerd, fcd,
- ems->s.lambda, graph, fr, vsite, mu_tot, t, NULL, NULL, TRUE,
+ ems->s.box, &ems->s.x, &ems->s.hist,
+ &ems->f, force_vir, mdatoms, enerd, fcd,
+ ems->s.lambda, graph, fr, vsite, mu_tot, t, nullptr, TRUE,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
- (bNS ? GMX_FORCE_NS : 0));
+ (bNS ? GMX_FORCE_NS : 0),
+ DOMAINDECOMP(cr) ?
+ DdOpenBalanceRegionBeforeForceComputation::yes :
+ DdOpenBalanceRegionBeforeForceComputation::no,
+ DOMAINDECOMP(cr) ?
+ DdCloseBalanceRegionAfterForceComputation::yes :
+ DdCloseBalanceRegionAfterForceComputation::no);
/* Clear the unused shake virial and pressure */
clear_mat(shake_vir);
wallcycle_start(wcycle, ewcMoveE);
global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
- inputrec, NULL, NULL, NULL, 1, &terminate,
- NULL, FALSE,
+ inputrec, nullptr, nullptr, nullptr, 1, &terminate,
+ nullptr, FALSE,
CGLO_ENERGY |
CGLO_PRESSURE |
CGLO_CONSTRAINT);
/* Project out the constraint components of the force */
wallcycle_start(wcycle, ewcCONSTR);
dvdl_constr = 0;
- constrain(NULL, FALSE, FALSE, constr, &top->idef,
+ rvec *f_rvec = as_rvec_array(ems->f.data());
+ constrain(nullptr, FALSE, FALSE, constr, &top->idef,
inputrec, cr, count, 0, 1.0, mdatoms,
- ems->s.x, ems->f, ems->f, fr->bMolPBC, ems->s.box,
+ as_rvec_array(ems->s.x.data()), f_rvec, f_rvec,
+ fr->bMolPBC, ems->s.box,
ems->s.lambda[efptBONDED], &dvdl_constr,
- NULL, &shake_vir, nrnb, econqForceDispl);
+ nullptr, &shake_vir, nrnb, econqForceDispl);
enerd->term[F_DVDL_CONSTR] += dvdl_constr;
m_add(force_vir, shake_vir, vir);
wallcycle_stop(wcycle, ewcCONSTR);
gmx_mtop_t *top_global,
em_state_t *s_min, em_state_t *s_b)
{
- rvec *fm, *fb, *fmg;
t_block *cgs_gl;
int ncg, *cg_gl, *index, c, cg, i, a0, a1, a, gf, m;
double partsum;
fprintf(debug, "Doing reorder_partsum\n");
}
- fm = s_min->f;
- fb = s_b->f;
+ const rvec *fm = as_rvec_array(s_min->f.data());
+ const rvec *fb = as_rvec_array(s_b->f.data());
cgs_gl = dd_charge_groups_global(cr->dd);
index = cgs_gl->index;
* This conflicts with the spirit of domain decomposition,
* but to fully optimize this a much more complicated algorithm is required.
*/
+ rvec *fmg;
snew(fmg, top_global->natoms);
- ncg = s_min->s.ncg_gl;
- cg_gl = s_min->s.cg_gl;
+ ncg = s_min->s.cg_gl.size();
+ cg_gl = s_min->s.cg_gl.data();
i = 0;
for (c = 0; c < ncg; c++)
{
gmx_sum(top_global->natoms*3, fmg[0], cr);
/* Now we will determine the part of the sum for the cgs in state s_b */
- ncg = s_b->s.ncg_gl;
- cg_gl = s_b->s.cg_gl;
+ ncg = s_b->s.cg_gl.size();
+ cg_gl = s_b->s.cg_gl.data();
partsum = 0;
i = 0;
gf = 0;
gmx_mtop_t *top_global,
em_state_t *s_min, em_state_t *s_b)
{
- rvec *fm, *fb;
double sum;
- int gf, i, m;
/* This is just the classical Polak-Ribiere calculation of beta;
* it looks a bit complicated since we take freeze groups into account,
(s_min->s.ddp_count == cr->dd->ddp_count &&
s_b->s.ddp_count == cr->dd->ddp_count))
{
- fm = s_min->f;
- fb = s_b->f;
- sum = 0;
- gf = 0;
+ const rvec *fm = as_rvec_array(s_min->f.data());
+ const rvec *fb = as_rvec_array(s_b->f.data());
+ sum = 0;
+ int gf = 0;
/* This part of code can be incorrect with DD,
* since the atom ordering in s_b and s_min might differ.
*/
- for (i = 0; i < mdatoms->homenr; i++)
+ for (int i = 0; i < mdatoms->homenr; i++)
{
if (mdatoms->cFREEZE)
{
gf = mdatoms->cFREEZE[i];
}
- for (m = 0; m < DIM; m++)
+ for (int m = 0; m < DIM; m++)
{
if (!opts->nFreeze[gf][m])
{
{
/*! \brief Do conjugate gradients minimization
- \copydoc integrator_t (FILE *fplog, t_commrec *cr,
+ \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed,
t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ const ReplicaExchangeParameters &replExParams,
gmx_membed_t gmx_unused *membed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
gmx_walltime_accounting_t walltime_accounting)
*/
-double do_cg(FILE *fplog, t_commrec *cr,
+double do_cg(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
- int gmx_unused nstglobalcomm,
+ const gmx_output_env_t gmx_unused *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
+ ObservablesHistory *observablesHistory,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
const char *CG = "Polak-Ribiere Conjugate Gradients";
- em_state_t *s_min, *s_a, *s_b, *s_c;
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
- rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
- rvec *p, *sf;
- double gpa, gpb, gpc, tmp, minstep;
- real fnormn;
+ double tmp, minstep;
real stepsize;
real a, b, c, beta = 0.0;
real epot_repl = 0;
tensor vir, pres;
int number_steps, neval = 0, nstcg = inputrec->nstcgsteep;
gmx_mdoutf_t outf;
- int i, m, gf, step, nminstep;
+ int m, step, nminstep;
step = 0;
- s_min = init_em_state();
- s_a = init_em_state();
- s_b = init_em_state();
- s_c = init_em_state();
+ // Ensure the extra per-atom state array gets allocated
+ state_global->flags |= (1<<estCGP);
+
+ /* Create 4 states on the stack and extract pointers that we will swap */
+ em_state_t s0 {}, s1 {}, s2 {}, s3 {};
+ em_state_t *s_min = &s0;
+ em_state_t *s_a = &s1;
+ em_state_t *s_b = &s2;
+ em_state_t *s_c = &s3;
/* Init em and store the local state in s_min */
- init_em(fplog, CG, cr, inputrec,
- state_global, top_global, s_min, &top, &f,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+ init_em(fplog, CG, cr, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, s_min, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat,
+ vsite, constr, nullptr,
+ nfile, fnm, &outf, &mdebin, wcycle);
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, CG);
/* Copy stuff to the energy bin for easy printing etc. */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
print_ebin_header(fplog, step, step);
print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
*/
/* Calculate the new direction in p, and the gradient in this direction, gpa */
- p = s_min->s.cg_p;
- sf = s_min->f;
- gpa = 0;
- gf = 0;
- for (i = 0; i < mdatoms->homenr; i++)
+ rvec *pm = as_rvec_array(s_min->s.cg_p.data());
+ const rvec *sfm = as_rvec_array(s_min->f.data());
+ double gpa = 0;
+ int gf = 0;
+ for (int i = 0; i < mdatoms->homenr; i++)
{
if (mdatoms->cFREEZE)
{
{
if (!inputrec->opts.nFreeze[gf][m])
{
- p[i][m] = sf[i][m] + beta*p[i][m];
- gpa -= p[i][m]*sf[i][m];
+ pm[i][m] = sfm[i][m] + beta*pm[i][m];
+ gpa -= pm[i][m]*sfm[i][m];
/* f is negative gradient, thus the sign */
}
else
{
- p[i][m] = 0;
+ pm[i][m] = 0;
}
}
}
}
/* Calculate the norm of the search vector */
- get_f_norm_max(cr, &(inputrec->opts), mdatoms, p, &pnorm, NULL, NULL);
+ get_f_norm_max(cr, &(inputrec->opts), mdatoms, pm, &pnorm, nullptr, nullptr);
/* Just in case stepsize reaches zero due to numerical precision... */
if (stepsize <= 0)
* relative change in coordinate is smaller than precision
*/
minstep = 0;
- for (i = 0; i < mdatoms->homenr; i++)
+ for (int i = 0; i < mdatoms->homenr; i++)
{
for (m = 0; m < DIM; m++)
{
{
tmp = 1.0;
}
- tmp = p[i][m]/tmp;
+ tmp = pm[i][m]/tmp;
minstep += tmp*tmp;
}
}
do_x = do_per_step(step, inputrec->nstxout);
do_f = do_per_step(step, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
+ write_em_traj(fplog, cr, outf, do_x, do_f, nullptr,
top_global, inputrec, step,
- s_min, state_global);
+ s_min, state_global, observablesHistory);
/* Take a step downhill.
* In theory, we should minimize the function along this direction.
}
/* Take a trial step (new coords in s_c) */
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, c, s_min->s.cg_p, s_c,
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, c, &s_min->s.cg_p, s_c,
constr, top, nrnb, wcycle, -1);
neval++;
mu_tot, enerd, vir, pres, -1, FALSE);
/* Calc derivative along line */
- p = s_c->s.cg_p;
- sf = s_c->f;
- gpc = 0;
- for (i = 0; i < mdatoms->homenr; i++)
+ const rvec *pc = as_rvec_array(s_c->s.cg_p.data());
+ const rvec *sfc = as_rvec_array(s_c->f.data());
+ double gpc = 0;
+ for (int i = 0; i < mdatoms->homenr; i++)
{
for (m = 0; m < DIM; m++)
{
- gpc -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
+ gpc -= pc[i][m]*sfc[i][m]; /* f is negative gradient, thus the sign */
}
}
/* Sum the gradient along the line across CPUs */
*
* If we already found a lower value we just skip this step and continue to the update.
*/
+ double gpb;
if (!foundlower)
{
nminstep = 0;
}
/* Take a trial step to this new point - new coords in s_b */
- do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, b, s_min->s.cg_p, s_b,
+ do_em_step(cr, inputrec, mdatoms, fr->bMolPBC, s_min, b, &s_min->s.cg_p, s_b,
constr, top, nrnb, wcycle, -1);
neval++;
/* p does not change within a step, but since the domain decomposition
* might change, we have to use cg_p of s_b here.
*/
- p = s_b->s.cg_p;
- sf = s_b->f;
- gpb = 0;
- for (i = 0; i < mdatoms->homenr; i++)
+ const rvec *pb = as_rvec_array(s_b->s.cg_p.data());
+ const rvec *sfb = as_rvec_array(s_b->f.data());
+ gpb = 0;
+ for (int i = 0; i < mdatoms->homenr; i++)
{
for (m = 0; m < DIM; m++)
{
- gpb -= p[i][m]*sf[i][m]; /* f is negative gradient, thus the sign */
+ gpb -= pb[i][m]*sfb[i][m]; /* f is negative gradient, thus the sign */
}
}
/* Sum the gradient along the line across CPUs */
if (gpb > 0)
{
/* Replace c endpoint with b */
- swap_em_state(s_b, s_c);
+ swap_em_state(&s_b, &s_c);
c = b;
gpc = gpb;
}
else
{
/* Replace a endpoint with b */
- swap_em_state(s_b, s_a);
+ swap_em_state(&s_b, &s_a);
a = b;
gpa = gpb;
}
fprintf(debug, "CGE: C (%f) is lower than A (%f), moving C to B\n",
s_c->epot, s_a->epot);
}
- swap_em_state(s_b, s_c);
+ swap_em_state(&s_b, &s_c);
gpb = gpc;
}
else
fprintf(debug, "CGE: A (%f) is lower than C (%f), moving A to B\n",
s_a->epot, s_c->epot);
}
- swap_em_state(s_b, s_a);
+ swap_em_state(&s_b, &s_a);
gpb = gpa;
}
fprintf(debug, "CGE: Found a lower energy %f, moving C to B\n",
s_c->epot);
}
- swap_em_state(s_b, s_c);
+ swap_em_state(&s_b, &s_c);
gpb = gpc;
}
/* update positions */
- swap_em_state(s_min, s_b);
+ swap_em_state(&s_min, &s_b);
gpa = gpb;
/* Print it if necessary */
if (MASTER(cr))
{
- if (bVerbose)
+ if (mdrunOptions.verbose)
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
mdatoms->tmass, enerd, &s_min->s, inputrec->fepvals, inputrec->expandedvals, s_min->s.box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
do_log = do_per_step(step, inputrec->nstlog);
do_ene = do_per_step(step, inputrec->nstenergy);
print_ebin_header(fplog, step, step);
}
print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : NULL, step, step, eprNORMAL,
+ do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
/* Send energies and positions to the IMD client if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
+ if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
{
IMD_send_positions(inputrec->imd);
}
{
/* Write final energy file entries */
print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : NULL, step, step, eprNORMAL,
+ !do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
}
write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
top_global, inputrec, step,
- s_min, state_global);
+ s_min, state_global, observablesHistory);
if (MASTER(cr))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fnormn = s_min->fnorm/sqrtNumAtoms;
print_converged(stderr, CG, inputrec->em_tol, step, converged, number_steps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+ s_min, sqrtNumAtoms);
print_converged(fplog, CG, inputrec->em_tol, step, converged, number_steps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+ s_min, sqrtNumAtoms);
fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
}
/*! \brief Do L-BFGS conjugate gradients minimization
- \copydoc integrator_t (FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout,
- t_inputrec *inputrec,
- gmx_mtop_t *top_global, t_fcdata *fcd,
- t_state *state_global,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
- t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
- gmx_walltime_accounting_t walltime_accounting)
+ \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,
+ t_forcerec *fr,
+ const ReplicaExchangeParameters &replExParams,
+ gmx_membed_t gmx_unused *membed,
+ gmx_walltime_accounting_t walltime_accounting)
*/
-double do_lbfgs(FILE *fplog, t_commrec *cr,
+double do_lbfgs(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
- int gmx_unused nstglobalcomm,
+ const gmx_output_env_t gmx_unused *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
+ ObservablesHistory *observablesHistory,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
static const char *LBFGS = "Low-Memory BFGS Minimizer";
em_state_t ems;
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
- rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
int ncorr, nmaxcorr, point, cp, neval, nminstep;
double stepsize, step_taken, gpa, gpb, gpc, tmp, minstep;
- real *rho, *alpha, *ff, *xx, *p, *s, *lastx, *lastf, **dx, **dg;
- real *xa, *xb, *xc, *fa, *fb, *fc, *xtmp, *ftmp;
+ real *rho, *alpha, *p, *s, **dx, **dg;
real a, b, c, maxdelta, delta;
- real diag, Epot0, Epot, EpotA, EpotB, EpotC;
+ real diag, Epot0;
real dgdx, dgdg, sq, yr, beta;
t_mdebin *mdebin;
gmx_bool converged;
rvec mu_tot;
- real fnorm, fmax;
gmx_bool do_log, do_ene, do_x, do_f, foundlower, *frozen;
tensor vir, pres;
int start, end, number_steps;
gmx_mdoutf_t outf;
- int i, k, m, n, nfmax, gf, step;
+ int i, k, m, n, gf, step;
int mdof_flags;
if (PAR(cr))
gmx_fatal(FARGS, "Cannot do parallel L-BFGS Minimization - yet.\n");
}
- if (NULL != constr)
+ if (nullptr != constr)
{
gmx_fatal(FARGS, "The combination of constraints and L-BFGS minimization is not implemented. Either do not use constraints, or use another minimizer (e.g. steepest descent).");
}
n = 3*state_global->natoms;
nmaxcorr = inputrec->nbfgscorr;
- /* Allocate memory */
- /* Use pointers to real so we dont have to loop over both atoms and
- * dimensions all the time...
- * x/f are allocated as rvec *, so make new x0/f0 pointers-to-real
- * that point to the same memory.
- */
- snew(xa, n);
- snew(xb, n);
- snew(xc, n);
- snew(fa, n);
- snew(fb, n);
- snew(fc, n);
snew(frozen, n);
snew(p, n);
- snew(lastx, n);
- snew(lastf, n);
snew(rho, nmaxcorr);
snew(alpha, nmaxcorr);
neval = 0;
/* Init em */
- init_em(fplog, LBFGS, cr, inputrec,
- state_global, top_global, &ems, &top, &f,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
- /* Do_lbfgs is not completely updated like do_steep and do_cg,
- * so we free some memory again.
- */
- sfree(ems.s.x);
- sfree(ems.f);
-
- xx = (real *)state_global->x;
- ff = (real *)f;
+ init_em(fplog, LBFGS, cr, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, &ems, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat,
+ vsite, constr, nullptr,
+ nfile, fnm, &outf, &mdebin, wcycle);
start = 0;
end = mdatoms->homenr;
+ /* We need 4 working states */
+ em_state_t s0 {}, s1 {}, s2 {}, s3 {};
+ em_state_t *sa = &s0;
+ em_state_t *sb = &s1;
+ em_state_t *sc = &s2;
+ em_state_t *last = &s3;
+ /* Initialize by copying the state from ems (we could skip x and f here) */
+ *sa = ems;
+ *sb = ems;
+ *sc = ems;
+
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, LBFGS);
if (vsite)
{
- construct_vsites(vsite, state_global->x, 1, NULL,
+ construct_vsites(vsite, as_rvec_array(state_global->x.data()), 1, nullptr,
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, state_global->box);
}
* We do not unshift, so molecules are always whole
*/
neval++;
- ems.s.x = state_global->x;
- ems.f = f;
evaluate_energy(fplog, cr,
top_global, &ems, top,
inputrec, nrnb, wcycle, gstat,
/* Copy stuff to the energy bin for easy printing etc. */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
mdatoms->tmass, enerd, state_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
print_ebin_header(fplog, step, step);
print_ebin(mdoutf_get_fp_ene(outf), TRUE, FALSE, FALSE, fplog, step, step, eprNORMAL,
}
where();
- /* This is the starting energy */
- Epot = enerd->term[F_EPOT];
-
- fnorm = ems.fnorm;
- fmax = ems.fmax;
- nfmax = ems.a_fmax;
-
/* Set the initial step.
* since it will be multiplied by the non-normalized search direction
* vector (force vector the first time), we scale it by the
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "Using %d BFGS correction steps.\n\n", nmaxcorr);
- fprintf(stderr, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(stderr, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
+ fprintf(stderr, " F-max = %12.5e on atom %d\n", ems.fmax, ems.a_fmax + 1);
+ fprintf(stderr, " F-Norm = %12.5e\n", ems.fnorm/sqrtNumAtoms);
fprintf(stderr, "\n");
/* and copy to the log file too... */
fprintf(fplog, "Using %d BFGS correction steps.\n\n", nmaxcorr);
- fprintf(fplog, " F-max = %12.5e on atom %d\n", fmax, nfmax+1);
- fprintf(fplog, " F-Norm = %12.5e\n", fnorm/sqrtNumAtoms);
+ fprintf(fplog, " F-max = %12.5e on atom %d\n", ems.fmax, ems.a_fmax + 1);
+ fprintf(fplog, " F-Norm = %12.5e\n", ems.fnorm/sqrtNumAtoms);
fprintf(fplog, "\n");
}
point = 0;
// Set initial search direction to the force (-gradient), or 0 for frozen particles.
+ real *fInit = static_cast<real *>(as_rvec_array(ems.f.data())[0]);
for (i = 0; i < n; i++)
{
if (!frozen[i])
{
- dx[point][i] = ff[i]; /* Initial search direction */
+ dx[point][i] = fInit[i]; /* Initial search direction */
}
else
{
// (the main efficiency in the algorithm comes from changing directions), but
// we still need an initial value, so estimate it as the inverse of the norm
// so we take small steps where the potential fluctuates a lot.
- stepsize = 1.0/fnorm;
+ stepsize = 1.0/ems.fnorm;
/* Start the loop over BFGS steps.
* Each successful step is counted, and we continue until
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags,
- top_global, step, (real)step, state_global, state_global, f);
+ top_global, step, (real)step, &ems.s, state_global, observablesHistory, &ems.f);
/* Do the linesearching in the direction dx[point][0..(n-1)] */
/* make s a pointer to current search direction - point=0 first time we get here */
s = dx[point];
+ real *xx = static_cast<real *>(as_rvec_array(ems.s.x.data())[0]);
+ real *ff = static_cast<real *>(as_rvec_array(ems.f.data())[0]);
+
// calculate line gradient in position A
for (gpa = 0, i = 0; i < n; i++)
{
}
// Before taking any steps along the line, store the old position
- for (i = 0; i < n; i++)
- {
- lastx[i] = xx[i];
- lastf[i] = ff[i];
- }
- Epot0 = Epot;
+ *last = ems;
+ real *lastx = static_cast<real *>(as_rvec_array(last->s.x.data())[0]);
+ real *lastf = static_cast<real *>(as_rvec_array(last->f.data())[0]);
+ Epot0 = ems.epot;
- for (i = 0; i < n; i++)
- {
- xa[i] = xx[i];
- }
+ *sa = ems;
/* Take a step downhill.
* In theory, we should find the actual minimum of the function in this
// State "A" is the first position along the line.
// reference position along line is initially zero
- EpotA = Epot0;
a = 0.0;
// Check stepsize first. We do not allow displacements
while (maxdelta > inputrec->em_stepsize);
// Take a trial step and move the coordinate array xc[] to position C
+ real *xc = static_cast<real *>(as_rvec_array(sc->s.x.data())[0]);
for (i = 0; i < n; i++)
{
xc[i] = lastx[i] + c*s[i];
neval++;
// Calculate energy for the trial step in position C
- ems.s.x = (rvec *)xc;
- ems.f = (rvec *)fc;
evaluate_energy(fplog, cr,
- top_global, &ems, top,
+ top_global, sc, top,
inputrec, nrnb, wcycle, gstat,
vsite, constr, fcd, graph, mdatoms, fr,
mu_tot, enerd, vir, pres, step, FALSE);
- EpotC = ems.epot;
// Calc line gradient in position C
+ real *fc = static_cast<real *>(as_rvec_array(sc->f.data())[0]);
for (gpc = 0, i = 0; i < n; i++)
{
gpc -= s[i]*fc[i]; /* f is negative gradient, thus the sign */
// This is the max amount of increase in energy we tolerate.
// By allowing VERY small changes (close to numerical precision) we
// frequently find even better (lower) final energies.
- tmp = sqrt(GMX_REAL_EPS)*fabs(EpotA);
+ tmp = sqrt(GMX_REAL_EPS)*fabs(sa->epot);
// Accept the step if the energy is lower in the new position C (compared to A),
// or if it is not significantly higher and the line derivative is still negative.
- if (EpotC < EpotA || (gpc < 0 && EpotC < (EpotA+tmp)))
+ if (sc->epot < sa->epot || (gpc < 0 && sc->epot < (sa->epot + tmp)))
{
// Great, we found a better energy. We no longer try to alter the
// stepsize, but simply accept this new better position. The we select a new
// to take smaller steps along a line. Set fnorm based on the new C position,
// which will be used to update the stepsize to 1/fnorm further down.
foundlower = TRUE;
- fnorm = ems.fnorm;
}
else
{
// I also have a safeguard for potentially really pathological functions so we never
// take more than 20 steps before we give up.
// If we already found a lower value we just skip this step and continue to the update.
- nminstep = 0;
+ real fnorm = 0;
+ nminstep = 0;
do
{
// Select a new trial point B in the interval [A,C].
}
// Take a trial step to point B
+ real *xb = static_cast<real *>(as_rvec_array(sb->s.x.data())[0]);
for (i = 0; i < n; i++)
{
xb[i] = lastx[i] + b*s[i];
neval++;
// Calculate energy for the trial step in point B
- ems.s.x = (rvec *)xb;
- ems.f = (rvec *)fb;
evaluate_energy(fplog, cr,
- top_global, &ems, top,
+ top_global, sb, top,
inputrec, nrnb, wcycle, gstat,
vsite, constr, fcd, graph, mdatoms, fr,
mu_tot, enerd, vir, pres, step, FALSE);
- EpotB = ems.epot;
- fnorm = ems.fnorm;
+ fnorm = sb->fnorm;
// Calculate gradient in point B
+ real *fb = static_cast<real *>(as_rvec_array(sb->f.data())[0]);
for (gpb = 0, i = 0; i < n; i++)
{
gpb -= s[i]*fb[i]; /* f is negative gradient, thus the sign */
if (gpb > 0)
{
/* Replace c endpoint with b */
- EpotC = EpotB;
- c = b;
- gpc = gpb;
- /* swap coord pointers b/c */
- xtmp = xb;
- ftmp = fb;
- xb = xc;
- fb = fc;
- xc = xtmp;
- fc = ftmp;
+ c = b;
+ /* swap states b and c */
+ swap_em_state(&sb, &sc);
}
else
{
/* Replace a endpoint with b */
- EpotA = EpotB;
- a = b;
- gpa = gpb;
- /* swap coord pointers a/b */
- xtmp = xb;
- ftmp = fb;
- xb = xa;
- fb = fa;
- xa = xtmp;
- fa = ftmp;
+ a = b;
+ /* swap states a and b */
+ swap_em_state(&sa, &sb);
}
/*
*/
nminstep++;
}
- while ((EpotB > EpotA || EpotB > EpotC) && (nminstep < 20));
+ while ((sb->epot > sa->epot || sb->epot > sc->epot) && (nminstep < 20));
- if (fabs(EpotB-Epot0) < GMX_REAL_EPS || nminstep >= 20)
+ if (fabs(sb->epot - Epot0) < GMX_REAL_EPS || nminstep >= 20)
{
/* OK. We couldn't find a significantly lower energy.
* If ncorr==0 this was steepest descent, and then we give up.
/* Select min energy state of A & C, put the best in xx/ff/Epot
*/
- if (EpotC < EpotA)
+ if (sc->epot < sa->epot)
{
- Epot = EpotC;
/* Use state C */
- for (i = 0; i < n; i++)
- {
- xx[i] = xc[i];
- ff[i] = fc[i];
- }
+ ems = *sc;
step_taken = c;
}
else
{
- Epot = EpotA;
/* Use state A */
- for (i = 0; i < n; i++)
- {
- xx[i] = xa[i];
- ff[i] = fa[i];
- }
+ ems = *sa;
step_taken = a;
}
else
{
/* found lower */
- Epot = EpotC;
/* Use state C */
- for (i = 0; i < n; i++)
- {
- xx[i] = xc[i];
- ff[i] = fc[i];
- }
+ ems = *sc;
step_taken = c;
}
}
}
- /* Test whether the convergence criterion is met */
- get_f_norm_max(cr, &(inputrec->opts), mdatoms, f, &fnorm, &fmax, &nfmax);
-
/* Print it if necessary */
if (MASTER(cr))
{
- if (bVerbose)
+ if (mdrunOptions.verbose)
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
fprintf(stderr, "\rStep %d, Epot=%12.6e, Fnorm=%9.3e, Fmax=%9.3e (atom %d)\n",
- step, Epot, fnorm/sqrtNumAtoms, fmax, nfmax+1);
+ step, ems.epot, ems.fnorm/sqrtNumAtoms, ems.fmax, ems.a_fmax + 1);
fflush(stderr);
}
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)step,
mdatoms->tmass, enerd, state_global, inputrec->fepvals, inputrec->expandedvals, state_global->box,
- NULL, NULL, vir, pres, NULL, mu_tot, constr);
+ nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
do_log = do_per_step(step, inputrec->nstlog);
do_ene = do_per_step(step, inputrec->nstenergy);
if (do_log)
print_ebin_header(fplog, step, step);
}
print_ebin(mdoutf_get_fp_ene(outf), do_ene, FALSE, FALSE,
- do_log ? fplog : NULL, step, step, eprNORMAL,
+ do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
/* Send x and E to IMD client, if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
+ if (do_IMD(inputrec->bIMD, step, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
{
IMD_send_positions(inputrec->imd);
}
// Reset stepsize in we are doing more iterations
- stepsize = 1.0/fnorm;
+ stepsize = 1.0/ems.fnorm;
/* Stop when the maximum force lies below tolerance.
* If we have reached machine precision, converged is already set to true.
*/
- converged = converged || (fmax < inputrec->em_tol);
+ converged = converged || (ems.fmax < inputrec->em_tol);
} /* End of the loop */
step--; /* we never took that last step in this case */
}
- if (fmax > inputrec->em_tol)
+ if (ems.fmax > inputrec->em_tol)
{
if (MASTER(cr))
{
if (!do_ene || !do_log) /* Write final energy file entries */
{
print_ebin(mdoutf_get_fp_ene(outf), !do_ene, FALSE, FALSE,
- !do_log ? fplog : NULL, step, step, eprNORMAL,
+ !do_log ? fplog : nullptr, step, step, eprNORMAL,
mdebin, fcd, &(top_global->groups), &(inputrec->opts));
}
do_f = !do_per_step(step, inputrec->nstfout);
write_em_traj(fplog, cr, outf, do_x, do_f, ftp2fn(efSTO, nfile, fnm),
top_global, inputrec, step,
- &ems, state_global);
+ &ems, state_global, observablesHistory);
if (MASTER(cr))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
print_converged(stderr, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
+ number_steps, &ems, sqrtNumAtoms);
print_converged(fplog, LBFGS, inputrec->em_tol, step, converged,
- number_steps, Epot, fmax, nfmax, fnorm/sqrtNumAtoms);
+ number_steps, &ems, sqrtNumAtoms);
fprintf(fplog, "\nPerformed %d energy evaluations in total.\n", neval);
}
} /* That's all folks */
/*! \brief Do steepest descents minimization
- \copydoc integrator_t (FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout,
- t_inputrec *inputrec,
- gmx_mtop_t *top_global, t_fcdata *fcd,
- t_state *state_global,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
- t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
- gmx_walltime_accounting_t walltime_accounting)
+ \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,
+ t_forcerec *fr,
+ const ReplicaExchangeParameters &replExParams,
+ gmx_walltime_accounting_t walltime_accounting)
*/
-double do_steep(FILE *fplog, t_commrec *cr,
+double do_steep(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
- int gmx_unused nstglobalcomm,
+ const gmx_output_env_t gmx_unused *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
+ ObservablesHistory *observablesHistory,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
const char *SD = "Steepest Descents";
- em_state_t *s_min, *s_try;
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
- rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
real stepsize;
- real ustep, fnormn;
+ real ustep;
gmx_mdoutf_t outf;
t_mdebin *mdebin;
gmx_bool bDone, bAbort, do_x, do_f;
int count = 0;
int steps_accepted = 0;
- s_min = init_em_state();
- s_try = init_em_state();
+ /* Create 2 states on the stack and extract pointers that we will swap */
+ em_state_t s0 {}, s1 {};
+ em_state_t *s_min = &s0;
+ em_state_t *s_try = &s1;
/* Init em and store the local state in s_try */
- init_em(fplog, SD, cr, inputrec,
- state_global, top_global, s_try, &top, &f,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, &mdebin, imdport, Flags, wcycle);
+ init_em(fplog, SD, cr, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, s_try, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat,
+ vsite, constr, nullptr,
+ nfile, fnm, &outf, &mdebin, wcycle);
/* Print to log file */
print_em_start(fplog, cr, walltime_accounting, wcycle, SD);
{
validStep =
do_em_step(cr, inputrec, mdatoms, fr->bMolPBC,
- s_min, stepsize, s_min->f, s_try,
+ s_min, stepsize, &s_min->f, s_try,
constr, top, nrnb, wcycle, count);
}
/* Print it if necessary */
if (MASTER(cr))
{
- if (bVerbose)
+ if (mdrunOptions.verbose)
{
fprintf(stderr, "Step=%5d, Dmax= %6.1e nm, Epot= %12.5e Fmax= %11.5e, atom= %d%c",
count, ustep, s_try->epot, s_try->fmax, s_try->a_fmax+1,
/* Store the new (lower) energies */
upd_mdebin(mdebin, FALSE, FALSE, (double)count,
mdatoms->tmass, enerd, &s_try->s, inputrec->fepvals, inputrec->expandedvals,
- s_try->s.box, NULL, NULL, vir, pres, NULL, mu_tot, constr);
+ s_try->s.box, nullptr, nullptr, vir, pres, nullptr, mu_tot, constr);
/* Prepare IMD energy record, if bIMD is TRUE. */
IMD_fill_energy_record(inputrec->bIMD, inputrec->imd, enerd, count, TRUE);
/* Copy the arrays for force, positions and energy */
/* The 'Min' array always holds the coords and forces of the minimal
sampled energy */
- swap_em_state(s_min, s_try);
+ swap_em_state(&s_min, &s_try);
if (count > 0)
{
ustep *= 1.2;
/* Write to trn, if necessary */
do_x = do_per_step(steps_accepted, inputrec->nstxout);
do_f = do_per_step(steps_accepted, inputrec->nstfout);
- write_em_traj(fplog, cr, outf, do_x, do_f, NULL,
+ write_em_traj(fplog, cr, outf, do_x, do_f, nullptr,
top_global, inputrec, count,
- s_min, state_global);
+ s_min, state_global, observablesHistory);
}
else
{
{
if (MASTER(cr))
{
- warn_step(stderr, inputrec->em_tol, count == nsteps, constr != NULL);
- warn_step(fplog, inputrec->em_tol, count == nsteps, constr != NULL);
+ warn_step(stderr, inputrec->em_tol, count == nsteps, constr != nullptr);
+ warn_step(fplog, inputrec->em_tol, count == nsteps, constr != nullptr);
}
bAbort = TRUE;
}
/* Send IMD energies and positions, if bIMD is TRUE. */
- if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box, state_global->x, inputrec, 0, wcycle) && MASTER(cr))
+ if (do_IMD(inputrec->bIMD, count, cr, TRUE, state_global->box, as_rvec_array(state_global->x.data()), inputrec, 0, wcycle) && MASTER(cr))
{
IMD_send_positions(inputrec->imd);
}
}
write_em_traj(fplog, cr, outf, TRUE, inputrec->nstfout, ftp2fn(efSTO, nfile, fnm),
top_global, inputrec, count,
- s_min, state_global);
+ s_min, state_global, observablesHistory);
if (MASTER(cr))
{
double sqrtNumAtoms = sqrt(static_cast<double>(state_global->natoms));
- fnormn = s_min->fnorm/sqrtNumAtoms;
print_converged(stderr, SD, inputrec->em_tol, count, bDone, nsteps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+ s_min, sqrtNumAtoms);
print_converged(fplog, SD, inputrec->em_tol, count, bDone, nsteps,
- s_min->epot, s_min->fmax, s_min->a_fmax, fnormn);
+ s_min, sqrtNumAtoms);
}
finish_em(cr, outf, walltime_accounting, wcycle);
} /* That's all folks */
/*! \brief Do normal modes analysis
- \copydoc integrator_t (FILE *fplog, t_commrec *cr,
- int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
- gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout,
- t_inputrec *inputrec,
- gmx_mtop_t *top_global, t_fcdata *fcd,
- t_state *state_global,
- t_mdatoms *mdatoms,
- t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
- t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
- gmx_walltime_accounting_t walltime_accounting)
+ \copydoc integrator_t(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
+ gmx_vsite_t *vsite, gmx_constr_t constr,
+ gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *inputrec,
+ gmx_mtop_t *top_global, t_fcdata *fcd,
+ t_state *state_global,
+ t_mdatoms *mdatoms,
+ t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_edsam_t ed,
+ t_forcerec *fr,
+ const ReplicaExchangeParameters &replExParams,
+ gmx_walltime_accounting_t walltime_accounting)
*/
-double do_nm(FILE *fplog, t_commrec *cr,
+double do_nm(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t gmx_unused *oenv, gmx_bool bVerbose,
- int gmx_unused nstglobalcomm,
+ const gmx_output_env_t gmx_unused *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int gmx_unused stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
+ ObservablesHistory gmx_unused *observablesHistory,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int imdport,
- unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
const char *NM = "Normal Mode Analysis";
int nnodes, node;
gmx_localtop_t *top;
gmx_enerdata_t *enerd;
- rvec *f;
gmx_global_stat_t gstat;
t_graph *graph;
tensor vir, pres;
rvec *fneg, *dfdx;
gmx_bool bSparse; /* use sparse matrix storage format */
size_t sz;
- gmx_sparsematrix_t * sparse_matrix = NULL;
- real * full_matrix = NULL;
- em_state_t * state_work;
+ gmx_sparsematrix_t * sparse_matrix = nullptr;
+ real * full_matrix = nullptr;
/* added with respect to mdrun */
int row, col;
real x_min;
bool bIsMaster = MASTER(cr);
- if (constr != NULL)
+ if (constr != nullptr)
{
gmx_fatal(FARGS, "Constraints present with Normal Mode Analysis, this combination is not supported");
}
- state_work = init_em_state();
+ gmx_shellfc_t *shellfc;
- /* Init em and store the local state in state_minimum */
- init_em(fplog, NM, cr, inputrec,
- state_global, top_global, state_work, &top,
- &f,
- nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat, vsite, constr,
- nfile, fnm, &outf, NULL, imdport, Flags, wcycle);
+ em_state_t state_work {};
- gmx_shellfc_t *shellfc = init_shell_flexcon(stdout,
- top_global,
- n_flexible_constraints(constr),
- inputrec->nstcalcenergy,
- DOMAINDECOMP(cr));
+ /* Init em and store the local state in state_minimum */
+ init_em(fplog, NM, cr, outputProvider, inputrec, mdrunOptions,
+ state_global, top_global, &state_work, &top,
+ nrnb, mu_tot, fr, &enerd, &graph, mdatoms, &gstat,
+ vsite, constr, &shellfc,
+ nfile, fnm, &outf, nullptr, wcycle);
- if (shellfc)
- {
- make_local_shells(cr, mdatoms, shellfc);
- }
std::vector<size_t> atom_index = get_atom_index(top_global);
snew(fneg, atom_index.size());
snew(dfdx, atom_index.size());
*/
if (EEL_FULL(fr->eeltype) || fr->rlist == 0.0)
{
- md_print_info(cr, fplog, "Non-cutoff electrostatics used, forcing full Hessian format.\n");
+ GMX_LOG(mdlog.warning).appendText("Non-cutoff electrostatics used, forcing full Hessian format.");
bSparse = FALSE;
}
else if (atom_index.size() < 1000)
{
- md_print_info(cr, fplog, "Small system size (N=%d), using full Hessian format.\n", atom_index.size());
+ GMX_LOG(mdlog.warning).appendTextFormatted("Small system size (N=%d), using full Hessian format.",
+ atom_index.size());
bSparse = FALSE;
}
else
{
- md_print_info(cr, fplog, "Using compressed symmetric sparse Hessian format.\n");
+ GMX_LOG(mdlog.warning).appendText("Using compressed symmetric sparse Hessian format.");
bSparse = TRUE;
}
/* Make evaluate_energy do a single node force calculation */
cr->nnodes = 1;
evaluate_energy(fplog, cr,
- top_global, state_work, top,
+ top_global, &state_work, top,
inputrec, nrnb, wcycle, gstat,
vsite, constr, fcd, graph, mdatoms, fr,
mu_tot, enerd, vir, pres, -1, TRUE);
cr->nnodes = nnodes;
/* if forces are not small, warn user */
- get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, state_work);
+ get_state_f_norm_max(cr, &(inputrec->opts), mdatoms, &state_work);
- md_print_info(cr, fplog, "Maximum force:%12.5e\n", state_work->fmax);
- if (state_work->fmax > 1.0e-3)
+ GMX_LOG(mdlog.warning).appendTextFormatted("Maximum force:%12.5e", state_work.fmax);
+ if (state_work.fmax > 1.0e-3)
{
- md_print_info(cr, fplog,
- "The force is probably not small enough to "
- "ensure that you are at a minimum.\n"
- "Be aware that negative eigenvalues may occur\n"
- "when the resulting matrix is diagonalized.\n\n");
+ GMX_LOG(mdlog.warning).appendText(
+ "The force is probably not small enough to "
+ "ensure that you are at a minimum.\n"
+ "Be aware that negative eigenvalues may occur\n"
+ "when the resulting matrix is diagonalized.");
}
/***********************************************************
int force_flags = GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES;
double t = 0;
- x_min = state_work->s.x[atom][d];
+ x_min = state_work.s.x[atom][d];
for (unsigned int dx = 0; (dx < 2); dx++)
{
if (dx == 0)
{
- state_work->s.x[atom][d] = x_min - der_range;
+ state_work.s.x[atom][d] = x_min - der_range;
}
else
{
- state_work->s.x[atom][d] = x_min + der_range;
+ state_work.s.x[atom][d] = x_min + der_range;
}
/* Make evaluate_energy do a single node force calculation */
if (shellfc)
{
/* Now is the time to relax the shells */
- (void) relax_shell_flexcon(fplog, cr, bVerbose, step,
+ (void) relax_shell_flexcon(fplog, cr, mdrunOptions.verbose, step,
inputrec, bNS, force_flags,
top,
constr, enerd, fcd,
- &state_work->s, state_work->f, vir, mdatoms,
+ &state_work.s, &state_work.f, vir, mdatoms,
nrnb, wcycle, graph, &top_global->groups,
shellfc, fr, bBornRadii, t, mu_tot,
- vsite, NULL);
+ vsite,
+ DdOpenBalanceRegionBeforeForceComputation::no,
+ DdCloseBalanceRegionAfterForceComputation::no);
bNS = false;
step++;
}
else
{
evaluate_energy(fplog, cr,
- top_global, state_work, top,
+ top_global, &state_work, top,
inputrec, nrnb, wcycle, gstat,
vsite, constr, fcd, graph, mdatoms, fr,
mu_tot, enerd, vir, pres, atom*2+dx, FALSE);
{
for (size_t i = 0; i < atom_index.size(); i++)
{
- copy_rvec(state_work->f[atom_index[i]], fneg[i]);
+ copy_rvec(state_work.f[atom_index[i]], fneg[i]);
}
}
}
/* x is restored to original */
- state_work->s.x[atom][d] = x_min;
+ state_work.s.x[atom][d] = x_min;
for (size_t j = 0; j < atom_index.size(); j++)
{
for (size_t k = 0; (k < DIM); k++)
{
dfdx[j][k] =
- -(state_work->f[atom_index[j]][k] - fneg[j][k])/(2*der_range);
+ -(state_work.f[atom_index[j]][k] - fneg[j][k])/(2*der_range);
}
}
}
}
- if (bVerbose && fplog)
+ if (mdrunOptions.verbose && fplog)
{
fflush(fplog);
}
}
/* write progress */
- if (bIsMaster && bVerbose)
+ if (bIsMaster && mdrunOptions.verbose)
{
fprintf(stderr, "\rFinished step %d out of %d",
static_cast<int>(std::min(atom+nnodes, atom_index.size())),
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
+// FIXME: remove the "__" prefix in front of the group def when we move the
+// nonbonded code into separate dir.
+
+/*! \libinternal \defgroup __module_nb_verlet Short-range non-bonded interaction module
+ * \ingroup group_mdrun
+ *
+ * \brief Computes forces and energies for short-range pair-interactions
+ * based on the Verlet algorithm. The algorithm uses pair-lists generated
+ * at fixed intervals as well as various flavors of pair interaction kernels
+ * implemented for a wide range of CPU and GPU architectures.
+ *
+ * The module includes support for flavors of Coulomb and Lennard-Jones interaction
+ * treatment implemented for a large range of SIMD instruction sets for CPU
+ * architectures as well as in CUDA and OpenCL for GPU architectures.
+ * Additionally there is a reference CPU non-SIMD and a reference CPU
+ * for GPU pair-list setup interaction kernel.
+ *
+ * The implementation of the kernels is based on the cluster non-bonded algorithm
+ * which in the code is referred to as the NxN algorithms ("nbnxn_" prefix);
+ * for details of the algorithm see DOI:10.1016/j.cpc.2013.06.003.
+ *
+ * Algorithmically, the non-bonded computation has two different modes:
+ * A "classical" mode: generate a list every nstlist steps containing at least
+ * all atom pairs up to a distance of rlistOuter and compute pair interactions
+ * for all pairs that are within the interaction cut-off.
+ * A "dynamic pruning" mode: generate an "outer-list" up to cut-off rlistOuter
+ * every nstlist steps and prune the outer-list using a cut-off of rlistInner
+ * every nstlistPrune steps to obtain a, smaller, "inner-list". This
+ * results in fewer interaction computations and allows for a larger nstlist.
+ * On a GPU, this dynamic pruning is performed in a rolling fashion, pruning
+ * only a sub-part of the list each (second) step. This way it can often
+ * overlap with integration and constraints on the CPU.
+ * Currently a simple heuristic determines which mode will be used.
+ *
+ * TODO: add a summary list and brief descriptions of the different submodules:
+ * search, CPU kernels, GPU glue code + kernels.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Szilárd Páll <pall.szilard@gmail.com>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \author Anca Hamuraru <anca@streamcomputing.eu>
+ * \author Teemu Virolainen <teemu@streamcomputing.eu>
+ * \author Dimitrios Karkoulis <dimitris.karkoulis@gmail.com>
+ *
+ * TODO: add more authors!
+ */
+
+/*! \libinternal \file
+ *
+ * \brief This file contains the public interface of the non-bonded Verlet module
+ * that implements the NxN cluster non-bonded algorithm to efficiently compute
+ * pair forces.
+ *
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \author Szilárd Páll <pall.szilard@gmail.com>
+ *
+ * \inlibraryapi
+ * \ingroup __module_nb_verlet
+ */
+
+
#ifndef NB_VERLET_H
#define NB_VERLET_H
+#include <memory>
+
#include "gromacs/mdlib/nbnxn_gpu_types.h"
#include "gromacs/mdlib/nbnxn_pairlist.h"
+//! Help pass GPU-emulation parameters with type safety.
+enum class EmulateGpuNonbonded : bool
+{
+ //! Do not emulate GPUs.
+ No,
+ //! Do emulate GPUs.
+ Yes
+};
+
#ifdef __cplusplus
extern "C" {
#endif
-/** Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
+/*! \brief Nonbonded NxN kernel types: plain C, CPU SIMD, GPU, GPU emulation */
typedef enum
{
nbnxnkNotSet = 0,
nbnxnkNR
} nbnxn_kernel_type;
-/** Return a string indentifying the kernel type */
+/*! \brief Return a string identifying the kernel type.
+ *
+ * \param [in] kernel_type nonbonded kernel types, takes values from the nbnxn_kernel_type enum
+ * \returns a string identifying the kernel corresponding to the type passed as argument
+ */
const char *lookup_nbnxn_kernel_name(int kernel_type);
+/*! \brief Ewald exclusion types */
enum {
ewaldexclTable, ewaldexclAnalytical
};
-/* Atom locality indicator: local, non-local, all, used for calls to:
- gridding, pair-search, force calculation, x/f buffer operations */
+/*! \brief Atom locality indicator: local, non-local, all.
+ *
+ * Used for calls to:
+ * gridding, pair-search, force calculation, x/f buffer operations
+ * */
enum {
eatLocal = 0, eatNonlocal = 1, eatAll
};
+/*! \brief Tests for local atom range */
#define LOCAL_A(x) ((x) == eatLocal)
+/*! \brief Tests for non-local atom range */
#define NONLOCAL_A(x) ((x) == eatNonlocal)
+/*! \brief Tests for either local or non-local atom range */
#define LOCAL_OR_NONLOCAL_A(x) (LOCAL_A(x) || NONLOCAL_A(x))
-/* Interaction locality indicator (used in pair-list search/calculations):
- - local interactions require local atom data and affect local output only;
- - non-local interactions require both local and non-local atom data and
- affect both local- and non-local output. */
+/*! \brief Interaction locality indicator
+ *
+ * Used in pair-list search/calculations in the following manner:
+ * - local interactions require local atom data and affect local output only;
+ * - non-local interactions require both local and non-local atom data and
+ * affect both local- and non-local output.
+ */
enum {
eintLocal = 0, eintNonlocal = 1
};
+/*! \brief Tests for local interaction indicator */
#define LOCAL_I(x) ((x) == eintLocal)
+/*! \brief Tests for non-local interaction indicator */
#define NONLOCAL_I(x) ((x) == eintNonlocal)
+/*! \brief Flag to tell the nonbonded kernels whether to clear the force output buffers */
enum {
enbvClearFNo, enbvClearFYes
};
+/*! \libinternal
+ * \brief Non-bonded interaction group data structure. */
typedef struct nonbonded_verlet_group_t {
- nbnxn_pairlist_set_t nbl_lists; /* pair list(s) */
- nbnxn_atomdata_t *nbat; /* atom data */
- int kernel_type; /* non-bonded kernel - see enum above */
- int ewald_excl; /* Ewald exclusion - see enum above */
+ nbnxn_pairlist_set_t nbl_lists; /**< pair list(s) */
+ nbnxn_atomdata_t *nbat; /**< atom data */
+ int kernel_type; /**< non-bonded kernel - see enum above */
+ int ewald_excl; /**< Ewald exclusion - see enum above */
} nonbonded_verlet_group_t;
-/* non-bonded data structure with Verlet-type cut-off */
+/*! \libinternal
+ * \brief Top-level non-bonded data structure for the Verlet-type cut-off scheme. */
typedef struct nonbonded_verlet_t {
- nbnxn_search_t nbs; /* n vs n atom pair searching data */
- int ngrp; /* number of interaction groups */
- nonbonded_verlet_group_t grp[2]; /* local and non-local interaction group */
-
- gmx_bool bUseGPU; /* TRUE when GPU acceleration is used */
- gmx_nbnxn_gpu_t *gpu_nbv; /* pointer to GPU nb verlet data */
- int min_ci_balanced; /* pair list balancing parameter
- used for the 8x8x8 GPU kernels */
+ std::unique_ptr<NbnxnListParameters> listParams; /**< Parameters for the search and list pruning setup */
+ nbnxn_search_t nbs; /**< n vs n atom pair searching data */
+ int ngrp; /**< number of interaction groups */
+ nonbonded_verlet_group_t grp[2]; /**< local and non-local interaction group */
+
+ gmx_bool bUseGPU; /**< TRUE when non-bonded interactions are computed on a physical GPU */
+ EmulateGpuNonbonded emulateGpu; /**< true when non-bonded interactions are computed on the CPU using GPU-style pair lists */
+ gmx_nbnxn_gpu_t *gpu_nbv; /**< pointer to GPU nb verlet data */
+ int min_ci_balanced; /**< pair list balancing parameter
+ used for the 8x8x8 GPU kernels */
} nonbonded_verlet_t;
/*! \brief Getter for bUseGPU */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "nbnxn_atomdata.h"
-#include "config.h"
-
#include <assert.h>
#include <stdlib.h>
#include <string.h>
ma(&ptr_new, nbytes_new);
- if (nbytes_new > 0 && ptr_new == NULL)
+ if (nbytes_new > 0 && ptr_new == nullptr)
{
gmx_fatal(FARGS, "Allocation of %d bytes failed", nbytes_new);
}
}
memcpy(ptr_new, *ptr, nbytes_copy);
}
- if (*ptr != NULL)
+ if (*ptr != nullptr)
{
mf(*ptr);
}
int nenergrp, int stride,
nbnxn_alloc_t *ma)
{
- out->f = NULL;
+ out->f = nullptr;
ma((void **)&out->fshift, SHIFTS*DIM*sizeof(*out->fshift));
out->nV = nenergrp*nenergrp;
ma((void **)&out->Vvdw, out->nV*sizeof(*out->Vvdw));
}
}
-static void clear_nbat_real(int na, int nbatFormat, real *xnb, int a0)
-{
- int j, c;
-
- switch (nbatFormat)
- {
- case nbatXYZ:
- for (int a = 0; a < na; a++)
- {
- for (int d = 0; d < DIM; d++)
- {
- xnb[(a0+a)*STRIDE_XYZ+d] = 0;
- }
- }
- break;
- case nbatXYZQ:
- for (int a = 0; a < na; a++)
- {
- for (int d = 0; d < DIM; d++)
- {
- xnb[(a0+a)*STRIDE_XYZQ+d] = 0;
- }
- }
- break;
- case nbatX4:
- j = atom_to_x_index<c_packX4>(a0);
- c = a0 & (c_packX4 - 1);
- for (int a = 0; a < na; a++)
- {
- xnb[j+XX*c_packX4] = 0;
- xnb[j+YY*c_packX4] = 0;
- xnb[j+ZZ*c_packX4] = 0;
- j++;
- c++;
- if (c == c_packX4)
- {
- j += (DIM-1)*c_packX4;
- c = 0;
- }
- }
- break;
- case nbatX8:
- j = atom_to_x_index<c_packX8>(a0);
- c = a0 & (c_packX8-1);
- for (int a = 0; a < na; a++)
- {
- xnb[j+XX*c_packX8] = 0;
- xnb[j+YY*c_packX8] = 0;
- xnb[j+ZZ*c_packX8] = 0;
- j++;
- c++;
- if (c == c_packX8)
- {
- j += (DIM-1)*c_packX8;
- c = 0;
- }
- }
- break;
- }
-}
-
void copy_rvec_to_nbat_real(const int *a, int na, int na_round,
const rvec *x, int nbatFormat,
real *xnb, int a0)
char *ptr;
gmx_bool simple, bCombGeom, bCombLB, bSIMD;
- if (alloc == NULL)
+ if (alloc == nullptr)
{
nbat->alloc = nbnxn_alloc_aligned;
}
{
nbat->alloc = alloc;
}
- if (free == NULL)
+ if (free == nullptr)
{
nbat->free = nbnxn_free_aligned;
}
*/
tol = 1e-5;
ptr = getenv("GMX_LJCOMB_TOL");
- if (ptr != NULL)
+ if (ptr != nullptr)
{
double dbl;
set_lj_parameter_data(nbat, bSIMD);
nbat->natoms = 0;
- nbat->type = NULL;
- nbat->lj_comb = NULL;
+ nbat->type = nullptr;
+ nbat->lj_comb = nullptr;
if (simple)
{
int pack_x;
nbat->XFormat = nbatXYZQ;
nbat->FFormat = nbatXYZ;
}
- nbat->q = NULL;
+ nbat->q = nullptr;
nbat->nenergrp = n_energygroups;
if (!simple)
{
/* Energy groups not supported yet for super-sub lists */
- if (n_energygroups > 1 && fp != NULL)
+ if (n_energygroups > 1 && fp != nullptr)
{
fprintf(fp, "\nNOTE: With GPUs, reporting energy group contributions is not supported\n\n");
}
{
nbat->neg_2log++;
}
- nbat->energrp = NULL;
+ nbat->energrp = nullptr;
nbat->alloc((void **)&nbat->shift_vec, SHIFTS*sizeof(*nbat->shift_vec));
nbat->xstride = (nbat->XFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
nbat->fstride = (nbat->FFormat == nbatXYZQ ? STRIDE_XYZQ : DIM);
- nbat->x = NULL;
+ nbat->x = nullptr;
#if GMX_SIMD
if (simple)
nbat->nenergrp, 1<<nbat->neg_2log,
nbat->alloc);
}
- nbat->buffer_flags.flag = NULL;
+ nbat->buffer_flags.flag = nullptr;
nbat->buffer_flags.flag_nalloc = 0;
nth = gmx_omp_nthreads_get(emntNonbonded);
ptr = getenv("GMX_USE_TREEREDUCE");
- if (ptr != NULL)
+ if (ptr != nullptr)
{
- nbat->bUseTreeReduce = strtol(ptr, 0, 10);
+ nbat->bUseTreeReduce = strtol(ptr, nullptr, 10);
}
#if defined __MIC__
else if (nth > 8) /*on the CPU we currently don't benefit even at 32*/
}
}
-static void
+gmx_unused static void
nbnxn_atomdata_reduce_reals(real * gmx_restrict dest,
gmx_bool bDestSet,
real ** gmx_restrict src,
}
}
-static void
+gmx_unused static void
nbnxn_atomdata_reduce_reals_simd(real gmx_unused * gmx_restrict dest,
gmx_bool gmx_unused bDestSet,
real gmx_unused ** gmx_restrict src,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef _nbnxn_atomdata_h
#define _nbnxn_atomdata_h
+#include <cstdio>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/utility/basedefinitions.h"
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
nbnxn_cuda_kernel_F_noprune.cu
nbnxn_cuda_kernel_F_prune.cu
nbnxn_cuda_kernel_VF_noprune.cu
- nbnxn_cuda_kernel_VF_prune.cu)
+ nbnxn_cuda_kernel_VF_prune.cu
+ nbnxn_cuda_kernel_pruneonly.cu)
endif()
file(GLOB NBNXN_CUDA_SOURCES
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
+#include "nbnxn_cuda.h"
+
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "nbnxn_cuda_types.h"
+/*
+ * Texture references are created at compile-time and need to be declared
+ * at file scope as global variables (see http://docs.nvidia.com/cuda/cuda-c-programming-guide/index.html#texture-reference-api).
+ * The texture references below are used in two translation units;
+ * we declare them here along the kernels that use them (when compiling legacy Fermi kernels),
+ * and provide getters (see below) used by the data_mgmt module where the
+ * textures are bound/unbound.
+ * (In principle we could do it the other way arond, but that would likely require
+ * device linking and we'd rather avoid technical hurdles.)
+ */
/*! Texture reference for LJ C6/C12 parameters; bound to cu_nbparam_t.nbfp */
texture<float, 1, cudaReadModeElementType> nbfp_texref;
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
#undef CALC_ENERGIES
#undef PRUNE_NBL
+
+/* Prune-only kernels */
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_pruneonly.cuh"
#undef FUNCTION_DECLARATION_ONLY
/* Now generate the function definitions if we are using a single compilation unit. */
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_F_prune.cu"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_VF_noprune.cu"
#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_VF_prune.cu"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_pruneonly.cu"
#else
/* Prevent compilation in multiple compilation unit mode for CC 2.x. Although we have
* build-time checks to prevent this, the user could manually tweaks nvcc flags
#endif /* GMX_CUDA_NB_SINGLE_COMPILATION_UNIT */
-
/*! Nonbonded kernel function pointer type */
typedef void (*nbnxn_cu_kfunc_ptr_t)(const cu_atomdata_t,
const cu_nbparam_t,
/*! Returns the number of blocks to be used for the nonbonded GPU kernel. */
-static inline int calc_nb_kernel_nblock(int nwork_units, gmx_device_info_t *dinfo)
+static inline int calc_nb_kernel_nblock(int nwork_units, const gmx_device_info_t *dinfo)
{
int max_grid_x_size;
int evdwtype,
bool bDoEne,
bool bDoPrune,
- struct gmx_device_info_t gmx_unused *devInfo)
+ const gmx_device_info_t gmx_unused *devInfo)
{
nbnxn_cu_kfunc_ptr_t res;
return res;
}
-/*! Calculates the amount of shared memory required by the CUDA kernel in use. */
-static inline int calc_shmem_required(const int num_threads_z, gmx_device_info_t gmx_unused *dinfo, const cu_nbparam_t *nbp)
+/*! \brief Calculates the amount of shared memory required by the nonbonded kernel in use. */
+static inline int calc_shmem_required_nonbonded(const int num_threads_z, const gmx_device_info_t gmx_unused *dinfo, const cu_nbparam_t *nbp)
{
int shmem;
call is taken care of later in this function. */
if (iloc == eintNonlocal && plist->nsci == 0)
{
+ plist->haveFreshList = false;
+
return;
}
CU_RET_ERR(stat, "cudaEventRecord failed");
}
+ if (nbp->useDynamicPruning && plist->haveFreshList)
+ {
+ /* Prunes for rlistOuter and rlistInner, sets plist->haveFreshList=false
+ (TODO: ATM that's the way the timing accounting can distinguish between
+ separate prune kernel and combined force+prune, maybe we need a better way?).
+ */
+ nbnxn_gpu_launch_kernel_pruneonly(nb, iloc, 1);
+ }
+
if (plist->nsci == 0)
{
/* Don't launch an empty local kernel (not allowed with CUDA) */
nb_kernel = select_nbnxn_kernel(nbp->eeltype,
nbp->vdwtype,
bCalcEner,
- plist->bDoPrune || always_prune,
+ (plist->haveFreshList && !nb->timers->didPrune[iloc]) || always_prune,
nb->dev_info);
/* Kernel launch config:
nblock = calc_nb_kernel_nblock(plist->nsci, nb->dev_info);
dim_block = dim3(c_clSize, c_clSize, num_threads_z);
dim_grid = dim3(nblock, 1, 1);
- shmem = calc_shmem_required(num_threads_z, nb->dev_info, nbp);
+ shmem = calc_shmem_required_nonbonded(num_threads_z, nb->dev_info, nbp);
if (debug)
{
- fprintf(debug, "GPU launch configuration:\n\tThread block: %dx%dx%d\n\t"
- "\tGrid: %dx%d\n\t#Super-clusters/clusters: %d/%d (%d)\n"
+ fprintf(debug, "Non-bonded GPU launch configuration:\n\tThread block: %ux%ux%u\n\t"
+ "\tGrid: %ux%u\n\t#Super-clusters/clusters: %d/%d (%d)\n"
"\tShMem: %d\n",
dim_block.x, dim_block.y, dim_block.z,
dim_grid.x, dim_grid.y, plist->nsci*c_numClPerSupercl,
#endif
}
+/*! Calculates the amount of shared memory required by the CUDA kernel in use. */
+static inline int calc_shmem_required_prune(const int num_threads_z)
+{
+ int shmem;
+
+ /* i-atom x in shared memory */
+ shmem = c_numClPerSupercl * c_clSize * sizeof(float4);
+ /* cj in shared memory, for each warp separately */
+ shmem += num_threads_z * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize * sizeof(int);
+
+ return shmem;
+}
+
+void nbnxn_gpu_launch_kernel_pruneonly(gmx_nbnxn_cuda_t *nb,
+ int iloc,
+ int numParts)
+{
+ cudaError_t stat;
+
+ cu_atomdata_t *adat = nb->atdat;
+ cu_nbparam_t *nbp = nb->nbparam;
+ cu_plist_t *plist = nb->plist[iloc];
+ cu_timers_t *t = nb->timers;
+ cudaStream_t stream = nb->stream[iloc];
+
+ bool bDoTime = nb->bDoTime;
+
+ if (plist->haveFreshList)
+ {
+ GMX_ASSERT(numParts == 1, "With first pruning we expect 1 part");
+
+ /* Set rollingPruningNumParts to signal that it is not set */
+ plist->rollingPruningNumParts = 0;
+ plist->rollingPruningPart = 0;
+ }
+ else
+ {
+ if (plist->rollingPruningNumParts == 0)
+ {
+ plist->rollingPruningNumParts = numParts;
+ }
+ else
+ {
+ GMX_ASSERT(numParts == plist->rollingPruningNumParts, "It is not allowed to change numParts in between list generation steps");
+ }
+ }
+
+ /* Use a local variable for part and update in plist, so we can return here
+ * without duplicating the part increment code.
+ */
+ int part = plist->rollingPruningPart;
+
+ plist->rollingPruningPart++;
+ if (plist->rollingPruningPart >= plist->rollingPruningNumParts)
+ {
+ plist->rollingPruningPart = 0;
+ }
+
+ /* Compute the number of list entries to prune in this pass */
+ int numSciInPart = (plist->nsci - part)/numParts;
+
+ /* Don't launch the kernel if there is no work to do (not allowed with CUDA) */
+ if (numSciInPart <= 0)
+ {
+ plist->haveFreshList = false;
+
+ return;
+ }
+
+ cudaEvent_t startEvent, stopEvent;
+ if (bDoTime)
+ {
+ startEvent = (plist->haveFreshList ? t->start_prune_k[iloc] : t->start_rollingPrune_k[iloc]);
+ stopEvent = (plist->haveFreshList ? t->stop_prune_k[iloc] : t->stop_rollingPrune_k[iloc]);
+ }
+
+ /* beginning of timed prune calculation section */
+ if (bDoTime)
+ {
+ stat = cudaEventRecord(startEvent, stream);
+ CU_RET_ERR(stat, "cudaEventRecord failed");
+ }
+
+ /* Kernel launch config:
+ * - The thread block dimensions match the size of i-clusters, j-clusters,
+ * and j-cluster concurrency, in x, y, and z, respectively.
+ * - The 1D block-grid contains as many blocks as super-clusters.
+ */
+ int num_threads_z = c_cudaPruneKernelJ4Concurrency;
+ int nblock = calc_nb_kernel_nblock(numSciInPart, nb->dev_info);
+ dim3 dim_block = dim3(c_clSize, c_clSize, num_threads_z);
+ dim3 dim_grid = dim3(nblock, 1, 1);
+ int shmem = calc_shmem_required_prune(num_threads_z);
+
+ if (debug)
+ {
+ fprintf(debug, "Pruning GPU kernel launch configuration:\n\tThread block: %dx%dx%d\n\t"
+ "\tGrid: %dx%d\n\t#Super-clusters/clusters: %d/%d (%d)\n"
+ "\tShMem: %d\n",
+ dim_block.x, dim_block.y, dim_block.z,
+ dim_grid.x, dim_grid.y, numSciInPart*c_numClPerSupercl,
+ c_numClPerSupercl, plist->na_c,
+ shmem);
+ }
+
+ if (bUseCudaLaunchKernel)
+ {
+ gmx_unused void* kernel_args[5];
+ kernel_args[0] = adat;
+ kernel_args[1] = nbp;
+ kernel_args[2] = plist;
+ kernel_args[3] = &numParts;
+ kernel_args[4] = ∂
+
+#if GMX_CUDA_VERSION >= 7000
+ if (plist->haveFreshList)
+ {
+ cudaLaunchKernel((void *)nbnxn_kernel_prune_cuda<true>, dim_grid, dim_block, kernel_args, shmem, stream);
+ }
+ else
+ {
+ cudaLaunchKernel((void *)nbnxn_kernel_prune_cuda<false>, dim_grid, dim_block, kernel_args, shmem, stream);
+ }
+#endif
+ }
+ else
+ {
+ if (plist->haveFreshList)
+ {
+ nbnxn_kernel_prune_cuda<true><<< dim_grid, dim_block, shmem, stream>>> (*adat, *nbp, *plist, numParts, part);
+ }
+ else
+ {
+ nbnxn_kernel_prune_cuda<false><<< dim_grid, dim_block, shmem, stream>>> (*adat, *nbp, *plist, numParts, part);
+ }
+ }
+ CU_LAUNCH_ERR("k_pruneonly");
+
+ /* TODO: consider a more elegant way to track which kernel has been called
+ (combined or separate 1st pass prune, rolling prune). */
+ if (plist->haveFreshList)
+ {
+ plist->haveFreshList = false;
+ /* Mark that pruning has been done */
+ nb->timers->didPrune[iloc] = true;
+ }
+ else
+ {
+ /* Mark that rolling pruning has been done */
+ nb->timers->didRollingPrune[iloc] = true;
+ }
+
+ if (bDoTime)
+ {
+ stat = cudaEventRecord(stopEvent, stream);
+ CU_RET_ERR(stat, "cudaEventRecord failed");
+ }
+
+#if (defined(WIN32) || defined( _WIN32 ))
+ /* Windows: force flushing WDDM queue */
+ stat = cudaStreamQuery(stream);
+#endif
+}
+
void nbnxn_gpu_launch_cpyback(gmx_nbnxn_cuda_t *nb,
const nbnxn_atomdata_t *nbatom,
int flags,
}
}
+/*! \brief Count pruning kernel time if either kernel has been triggered
+ *
+ * We do the accounting for either of the two pruning kernel flavors:
+ * - 1st pass prune: ran during the current step (prior to the force kernel);
+ * - rolling prune: ran at the end of the previous step (prior to the current step H2D xq);
+ *
+ * Note that the resetting of cu_timers_t::didPrune and cu_timers_t::didRollingPrune should happen
+ * after calling this function.
+ *
+ * \param[in] timers structs with CUDA timer objects
+ * \param[inout] timings GPU task timing data
+ * \param[in] iloc interaction locality
+ */
+static void countPruneKernelTime(const cu_timers_t *timers,
+ gmx_wallclock_gpu_t *timings,
+ const int iloc)
+{
+ // We might have not done any pruning (e.g. if we skipped with empty domains).
+ if (!timers->didPrune[iloc] && !timers->didRollingPrune[iloc])
+ {
+ return;
+ }
+
+ if (timers->didPrune[iloc])
+ {
+ timings->pruneTime.c++;
+ timings->pruneTime.t += cu_event_elapsed(timers->start_prune_k[iloc],
+ timers->stop_prune_k[iloc]);
+ }
+ if (timers->didRollingPrune[iloc])
+ {
+ timings->dynamicPruneTime.c++;
+ timings->dynamicPruneTime.t += cu_event_elapsed(timers->start_rollingPrune_k[iloc],
+ timers->stop_rollingPrune_k[iloc]);
+ }
+}
+
void nbnxn_gpu_wait_for_gpu(gmx_nbnxn_cuda_t *nb,
int flags, int aloc,
real *e_lj, real *e_el, rvec *fshift)
/* turn energy calculation always on/off (for debugging/testing only) */
bCalcEner = (bCalcEner || always_ener) && !never_ener;
- /* Launch wait/update timers & counters, unless doing the non-local phase
- when there is not actually work to do. This is consistent with
- nbnxn_cuda_launch_kernel.
+ /* Launch wait/update timers & counters and do reduction into staging buffers
+ BUT skip it when during the non-local phase there was actually no work to do.
+ This is consistent with nbnxn_gpu_launch_kernel.
NOTE: if timing with multiple GPUs (streams) becomes possible, the
counters could end up being inconsistent due to not being incremented
on some of the nodes! */
- if (iloc == eintNonlocal && nb->plist[iloc]->nsci == 0)
+ if (!(iloc == eintNonlocal && nb->plist[iloc]->nsci == 0))
{
- return;
- }
-
- stat = cudaStreamSynchronize(nb->stream[iloc]);
- CU_RET_ERR(stat, "cudaStreamSynchronize failed in cu_blockwait_nb");
+ stat = cudaStreamSynchronize(nb->stream[iloc]);
+ CU_RET_ERR(stat, "cudaStreamSynchronize failed in cu_blockwait_nb");
- /* timing data accumulation */
- if (nb->bDoTime)
- {
- /* only increase counter once (at local F wait) */
- if (LOCAL_I(iloc))
+ /* timing data accumulation */
+ if (nb->bDoTime)
{
- timings->nb_c++;
- timings->ktime[plist->bDoPrune ? 1 : 0][bCalcEner ? 1 : 0].c += 1;
- }
-
- /* kernel timings */
- timings->ktime[plist->bDoPrune ? 1 : 0][bCalcEner ? 1 : 0].t +=
- cu_event_elapsed(timers->start_nb_k[iloc], timers->stop_nb_k[iloc]);
-
- /* X/q H2D and F D2H timings */
- timings->nb_h2d_t += cu_event_elapsed(timers->start_nb_h2d[iloc],
- timers->stop_nb_h2d[iloc]);
- timings->nb_d2h_t += cu_event_elapsed(timers->start_nb_d2h[iloc],
- timers->stop_nb_d2h[iloc]);
-
- /* only count atdat and pair-list H2D at pair-search step */
- if (plist->bDoPrune)
- {
- /* atdat transfer timing (add only once, at local F wait) */
- if (LOCAL_A(aloc))
+ /* only increase counter once (at local F wait) */
+ if (LOCAL_I(iloc))
{
- timings->pl_h2d_c++;
- timings->pl_h2d_t += cu_event_elapsed(timers->start_atdat,
- timers->stop_atdat);
+ timings->nb_c++;
+ timings->ktime[plist->haveFreshList ? 1 : 0][bCalcEner ? 1 : 0].c += 1;
}
- timings->pl_h2d_t += cu_event_elapsed(timers->start_pl_h2d[iloc],
- timers->stop_pl_h2d[iloc]);
+ /* kernel timings */
+ timings->ktime[plist->haveFreshList ? 1 : 0][bCalcEner ? 1 : 0].t +=
+ cu_event_elapsed(timers->start_nb_k[iloc], timers->stop_nb_k[iloc]);
+
+ /* X/q H2D and F D2H timings */
+ timings->nb_h2d_t += cu_event_elapsed(timers->start_nb_h2d[iloc],
+ timers->stop_nb_h2d[iloc]);
+ timings->nb_d2h_t += cu_event_elapsed(timers->start_nb_d2h[iloc],
+ timers->stop_nb_d2h[iloc]);
+
+ /* Count the pruning kernel times for both cases:1st pass (at search step)
+ and rolling pruning (if called at the previous step).
+ We do the accounting here as this is the only sync point where we
+ know (without checking or additional sync-ing) that prune tasks in
+ in the current stream have completed (having just blocking-waited
+ for the force D2H). */
+ countPruneKernelTime(timers, timings, iloc);
+
+ /* only count atdat and pair-list H2D at pair-search step */
+ if (timers->didPairlistH2D[iloc])
+ {
+ /* atdat transfer timing (add only once, at local F wait) */
+ if (LOCAL_A(aloc))
+ {
+ timings->pl_h2d_c++;
+ timings->pl_h2d_t += cu_event_elapsed(timers->start_atdat,
+ timers->stop_atdat);
+ }
+
+ timings->pl_h2d_t += cu_event_elapsed(timers->start_pl_h2d[iloc],
+ timers->stop_pl_h2d[iloc]);
+
+ /* Clear the timing flag for the next step */
+ timers->didPairlistH2D[iloc] = false;
+ }
}
- }
- /* add up energies and shift forces (only once at local F wait) */
- if (LOCAL_I(iloc))
- {
- if (bCalcEner)
+ /* add up energies and shift forces (only once at local F wait) */
+ if (LOCAL_I(iloc))
{
- *e_lj += *nbst.e_lj;
- *e_el += *nbst.e_el;
- }
+ if (bCalcEner)
+ {
+ *e_lj += *nbst.e_lj;
+ *e_el += *nbst.e_el;
+ }
- if (bCalcFshift)
- {
- for (int i = 0; i < SHIFTS; i++)
+ if (bCalcFshift)
{
- fshift[i][0] += nbst.fshift[i].x;
- fshift[i][1] += nbst.fshift[i].y;
- fshift[i][2] += nbst.fshift[i].z;
+ for (int i = 0; i < SHIFTS; i++)
+ {
+ fshift[i][0] += nbst.fshift[i].x;
+ fshift[i][1] += nbst.fshift[i].y;
+ fshift[i][2] += nbst.fshift[i].z;
+ }
}
}
}
- /* turn off pruning (doesn't matter if this is pair-search step or not) */
- plist->bDoPrune = false;
+ /* Always reset both pruning flags (doesn't hurt doing it even when timing is off). */
+ timers->didPrune[iloc] = timers->didRollingPrune[iloc] = false;
+
+ /* Turn off initial list pruning (doesn't hurt if this is not pair-search step). */
+ plist->haveFreshList = false;
}
-/*! Return the reference to the nbfp texture. */
const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_nbfp_texref()
{
+ assert(!c_disableCudaTextures);
return nbfp_texref;
}
-/*! Return the reference to the nbfp_comb texture. */
const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_nbfp_comb_texref()
{
+ assert(!c_disableCudaTextures);
return nbfp_comb_texref;
}
-/*! Return the reference to the coulomb_tab. */
const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_coulomb_tab_texref()
{
+ assert(!c_disableCudaTextures);
return coulomb_tab_texref;
}
-/*! Set up the cache configuration for the non-bonded kernels,
- */
-void nbnxn_cuda_set_cacheconfig(gmx_device_info_t *devinfo)
+void nbnxn_cuda_set_cacheconfig(const gmx_device_info_t *devinfo)
{
cudaError_t stat;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares nbnxn cuda cache and texture helper functions
+ */
+#ifndef GMX_MDLIB_NBNXN_CUDA_NBNXN_CUDA_H
+#define GMX_MDLIB_NBNXN_CUDA_NBNXN_CUDA_H
+
+#include "nbnxn_cuda_types.h"
+
+//! Set up the cache configuration for the non-bonded kernels.
+void nbnxn_cuda_set_cacheconfig(const gmx_device_info_t *devinfo);
+//! Return the reference to the nbfp texture.
+const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_nbfp_texref();
+//! Return the reference to the nbfp_comb texture.
+const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_nbfp_comb_texref();
+//! Return the reference to the coulomb_tab.
+const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_coulomb_tab_texref();
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <assert.h>
#include <stdarg.h>
#include <stdio.h>
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/gpu_utils/pmalloc_cuda.h"
-#include "gromacs/hardware/detecthardware.h"
#include "gromacs/hardware/gpu_hw_info.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
+#include "nbnxn_cuda.h"
#include "nbnxn_cuda_types.h"
static bool bUseCudaEventBlockingSync = false; /* makes the CPU thread block */
*/
static unsigned int gpu_min_ci_balanced_factor = 44;
-/* Functions from nbnxn_cuda.cu */
-extern void nbnxn_cuda_set_cacheconfig(gmx_device_info_t *devinfo);
-extern const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_nbfp_texref();
-extern const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_nbfp_comb_texref();
-extern const struct texture<float, 1, cudaReadModeElementType> &nbnxn_cuda_get_coulomb_tab_texref();
-
-
/* Fw. decl. */
static void nbnxn_cuda_clear_e_fshift(gmx_nbnxn_cuda_t *nb);
*/
static bool use_texobj(const gmx_device_info_t *dev_info)
{
+ assert(!c_disableCudaTextures);
/* Only device CC >= 3.0 (Kepler and later) support texture objects */
return (dev_info->prop.major >= 3);
}
void *devPtr,
size_t sizeInBytes)
{
+ assert(!c_disableCudaTextures);
+
cudaError_t stat;
cudaResourceDesc rd;
cudaTextureDesc td;
const void *devPtr,
size_t sizeInBytes)
{
+ assert(!c_disableCudaTextures);
+
cudaError_t stat;
cudaChannelFormatDesc cd;
nbp->coulomb_tab_size = ic->tabq_size;
nbp->coulomb_tab_scale = ic->tabq_scale;
- if (use_texobj(dev_info))
- {
- setup1DFloatTexture(nbp->coulomb_tab_texobj, nbp->coulomb_tab,
- nbp->coulomb_tab_size*sizeof(*nbp->coulomb_tab));
- }
- else
+ if (!c_disableCudaTextures)
{
- setup1DFloatTexture(&nbnxn_cuda_get_coulomb_tab_texref(), nbp->coulomb_tab,
- nbp->coulomb_tab_size*sizeof(*nbp->coulomb_tab));
+ if (use_texobj(dev_info))
+ {
+ setup1DFloatTexture(nbp->coulomb_tab_texobj, nbp->coulomb_tab,
+ nbp->coulomb_tab_size*sizeof(*nbp->coulomb_tab));
+ }
+ else
+ {
+ setup1DFloatTexture(&nbnxn_cuda_get_coulomb_tab_texref(), nbp->coulomb_tab,
+ nbp->coulomb_tab_size*sizeof(*nbp->coulomb_tab));
+ }
}
}
/*! Copies all parameters related to the cut-off from ic to nbp */
static void set_cutoff_parameters(cu_nbparam_t *nbp,
- const interaction_const_t *ic)
+ const interaction_const_t *ic,
+ const NbnxnListParameters *listParams)
{
- nbp->ewald_beta = ic->ewaldcoeff_q;
- nbp->sh_ewald = ic->sh_ewald;
- nbp->epsfac = ic->epsfac;
- nbp->two_k_rf = 2.0 * ic->k_rf;
- nbp->c_rf = ic->c_rf;
- nbp->rvdw_sq = ic->rvdw * ic->rvdw;
- nbp->rcoulomb_sq = ic->rcoulomb * ic->rcoulomb;
- nbp->rlist_sq = ic->rlist * ic->rlist;
-
- nbp->sh_lj_ewald = ic->sh_lj_ewald;
- nbp->ewaldcoeff_lj = ic->ewaldcoeff_lj;
-
- nbp->rvdw_switch = ic->rvdw_switch;
- nbp->dispersion_shift = ic->dispersion_shift;
- nbp->repulsion_shift = ic->repulsion_shift;
- nbp->vdw_switch = ic->vdw_switch;
+ nbp->ewald_beta = ic->ewaldcoeff_q;
+ nbp->sh_ewald = ic->sh_ewald;
+ nbp->epsfac = ic->epsfac;
+ nbp->two_k_rf = 2.0 * ic->k_rf;
+ nbp->c_rf = ic->c_rf;
+ nbp->rvdw_sq = ic->rvdw * ic->rvdw;
+ nbp->rcoulomb_sq = ic->rcoulomb * ic->rcoulomb;
+ nbp->rlistOuter_sq = listParams->rlistOuter * listParams->rlistOuter;
+ nbp->rlistInner_sq = listParams->rlistInner * listParams->rlistInner;
+ nbp->useDynamicPruning = listParams->useDynamicPruning;
+
+ nbp->sh_lj_ewald = ic->sh_lj_ewald;
+ nbp->ewaldcoeff_lj = ic->ewaldcoeff_lj;
+
+ nbp->rvdw_switch = ic->rvdw_switch;
+ nbp->dispersion_shift = ic->dispersion_shift;
+ nbp->repulsion_shift = ic->repulsion_shift;
+ nbp->vdw_switch = ic->vdw_switch;
}
/*! \brief Initialize LJ parameter lookup table.
CU_RET_ERR(stat, "cudaMalloc failed in initParamLookupTable");
cu_copy_H2D(devPtr, (void *)hostPtr, sizeInBytes);
- if (use_texobj(devInfo))
- {
- setup1DFloatTexture(texObj, devPtr, sizeInBytes);
- }
- else
+ if (!c_disableCudaTextures)
{
- setup1DFloatTexture(texRef, devPtr, sizeInBytes);
+ if (use_texobj(devInfo))
+ {
+ setup1DFloatTexture(texObj, devPtr, sizeInBytes);
+ }
+ else
+ {
+ setup1DFloatTexture(texRef, devPtr, sizeInBytes);
+ }
}
}
/*! Initializes the nonbonded parameter data structure. */
static void init_nbparam(cu_nbparam_t *nbp,
const interaction_const_t *ic,
+ const NbnxnListParameters *listParams,
const nbnxn_atomdata_t *nbat,
const gmx_device_info_t *dev_info)
{
ntypes = nbat->ntype;
- set_cutoff_parameters(nbp, ic);
+ set_cutoff_parameters(nbp, ic, listParams);
/* The kernel code supports LJ combination rules (geometric and LB) for
* all kernel types, but we only generate useful combination rule kernels.
/*! Re-generate the GPU Ewald force table, resets rlist, and update the
* electrostatic type switching to twin cut-off (or back) if needed. */
void nbnxn_gpu_pme_loadbal_update_param(const nonbonded_verlet_t *nbv,
- const interaction_const_t *ic)
+ const interaction_const_t *ic,
+ const NbnxnListParameters *listParams)
{
if (!nbv || nbv->grp[0].kernel_type != nbnxnk8x8x8_GPU)
{
gmx_nbnxn_cuda_t *nb = nbv->gpu_nbv;
cu_nbparam_t *nbp = nb->nbparam;
- set_cutoff_parameters(nbp, ic);
+ set_cutoff_parameters(nbp, ic, listParams);
nbp->eeltype = pick_ewald_kernel_type(ic->rcoulomb != ic->rvdw,
nb->dev_info);
{
/* initialize to NULL pointers to data that is not allocated here and will
need reallocation in nbnxn_gpu_init_pairlist */
- pl->sci = NULL;
- pl->cj4 = NULL;
- pl->excl = NULL;
+ pl->sci = NULL;
+ pl->cj4 = NULL;
+ pl->imask = NULL;
+ pl->excl = NULL;
/* size -1 indicates that the respective array hasn't been initialized yet */
- pl->na_c = -1;
- pl->nsci = -1;
- pl->sci_nalloc = -1;
- pl->ncj4 = -1;
- pl->cj4_nalloc = -1;
- pl->nexcl = -1;
- pl->excl_nalloc = -1;
- pl->bDoPrune = false;
+ pl->na_c = -1;
+ pl->nsci = -1;
+ pl->sci_nalloc = -1;
+ pl->ncj4 = -1;
+ pl->cj4_nalloc = -1;
+ pl->nimask = -1;
+ pl->imask_nalloc = -1;
+ pl->nexcl = -1;
+ pl->excl_nalloc = -1;
+ pl->haveFreshList = false;
}
/*! Initializes the timer data structure. */
stat = cudaEventCreateWithFlags(&(t->stop_nb_k[i]), eventflags);
CU_RET_ERR(stat, "cudaEventCreate on stop_nb_k failed");
+ stat = cudaEventCreateWithFlags(&(t->start_prune_k[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on start_prune_k failed");
+ stat = cudaEventCreateWithFlags(&(t->stop_prune_k[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on stop_prune_k failed");
+
+ stat = cudaEventCreateWithFlags(&(t->start_rollingPrune_k[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on start_rollingPrune_k failed");
+ stat = cudaEventCreateWithFlags(&(t->stop_rollingPrune_k[i]), eventflags);
+ CU_RET_ERR(stat, "cudaEventCreate on stop_rollingPrune_k failed");
stat = cudaEventCreateWithFlags(&(t->start_pl_h2d[i]), eventflags);
CU_RET_ERR(stat, "cudaEventCreate on start_pl_h2d failed");
CU_RET_ERR(stat, "cudaEventCreate on start_nb_d2h failed");
stat = cudaEventCreateWithFlags(&(t->stop_nb_d2h[i]), eventflags);
CU_RET_ERR(stat, "cudaEventCreate on stop_nb_d2h failed");
+
+ t->didPairlistH2D[i] = false;
+ t->didPrune[i] = false;
+ t->didRollingPrune[i] = false;
}
}
t->ktime[i][j].c = 0;
}
}
+ t->pruneTime.c = 0;
+ t->pruneTime.t = 0.0;
+ t->dynamicPruneTime.c = 0;
+ t->dynamicPruneTime.t = 0.0;
}
/*! Initializes simulation constant data. */
static void nbnxn_cuda_init_const(gmx_nbnxn_cuda_t *nb,
const interaction_const_t *ic,
+ const NbnxnListParameters *listParams,
const nonbonded_verlet_group_t *nbv_group)
{
init_atomdata_first(nb->atdat, nbv_group[0].nbat->ntype);
- init_nbparam(nb->nbparam, ic, nbv_group[0].nbat, nb->dev_info);
+ init_nbparam(nb->nbparam, ic, listParams, nbv_group[0].nbat, nb->dev_info);
/* clear energy and shift force outputs */
nbnxn_cuda_clear_e_fshift(nb);
}
void nbnxn_gpu_init(gmx_nbnxn_cuda_t **p_nb,
- const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt,
+ const gmx_device_info_t *deviceInfo,
const interaction_const_t *ic,
+ const NbnxnListParameters *listParams,
nonbonded_verlet_group_t *nbv_grp,
- int my_gpu_index,
int /*rank*/,
gmx_bool bLocalAndNonlocal)
{
cudaError_t stat;
gmx_nbnxn_cuda_t *nb;
- assert(gpu_info);
-
if (p_nb == NULL)
{
return;
init_plist(nb->plist[eintLocal]);
/* set device info, just point it to the right GPU among the detected ones */
- nb->dev_info = &gpu_info->gpu_dev[get_gpu_device_id(gpu_info, gpu_opt, my_gpu_index)];
+ nb->dev_info = deviceInfo;
/* local/non-local GPU streams */
stat = cudaStreamCreate(&nb->stream[eintLocal]);
{
init_plist(nb->plist[eintNonlocal]);
- /* CUDA stream priority available in the CUDA RT 5.5 API.
- * Note that the device we're running on does not have to support
+ /* Note that the device we're running on does not have to support
* priorities, because we are querying the priority range which in this
* case will be a single value.
*/
-#if GMX_CUDA_VERSION >= 5050
- {
- int highest_priority;
- stat = cudaDeviceGetStreamPriorityRange(NULL, &highest_priority);
- CU_RET_ERR(stat, "cudaDeviceGetStreamPriorityRange failed");
-
- stat = cudaStreamCreateWithPriority(&nb->stream[eintNonlocal],
- cudaStreamDefault,
- highest_priority);
- CU_RET_ERR(stat, "cudaStreamCreateWithPriority on stream[eintNonlocal] failed");
- }
-#else
- stat = cudaStreamCreate(&nb->stream[eintNonlocal]);
- CU_RET_ERR(stat, "cudaStreamCreate on stream[eintNonlocal] failed");
-#endif
+ int highest_priority;
+ stat = cudaDeviceGetStreamPriorityRange(NULL, &highest_priority);
+ CU_RET_ERR(stat, "cudaDeviceGetStreamPriorityRange failed");
+
+ stat = cudaStreamCreateWithPriority(&nb->stream[eintNonlocal],
+ cudaStreamDefault,
+ highest_priority);
+ CU_RET_ERR(stat, "cudaStreamCreateWithPriority on stream[eintNonlocal] failed");
}
/* init events for sychronization (timing disabled for performance reasons!) */
/* pick L1 cache configuration */
nbnxn_cuda_set_cacheconfig(nb->dev_info);
- nbnxn_cuda_init_const(nb, ic, nbv_grp);
+ nbnxn_cuda_init_const(nb, ic, listParams, nbv_grp);
*p_nb = nb;
{
stat = cudaEventRecord(nb->timers->start_pl_h2d[iloc], stream);
CU_RET_ERR(stat, "cudaEventRecord failed");
+ nb->timers->didPairlistH2D[iloc] = true;
}
cu_realloc_buffered((void **)&d_plist->sci, h_plist->sci, sizeof(*d_plist->sci),
h_plist->ncj4,
stream, true);
+ /* this call only allocates space on the device (no data is transferred) */
+ cu_realloc_buffered((void **)&d_plist->imask, NULL, sizeof(*d_plist->imask),
+ &d_plist->nimask, &d_plist->imask_nalloc,
+ h_plist->ncj4*c_nbnxnGpuClusterpairSplit,
+ stream, true);
+
cu_realloc_buffered((void **)&d_plist->excl, h_plist->excl, sizeof(*d_plist->excl),
&d_plist->nexcl, &d_plist->excl_nalloc,
h_plist->nexcl,
CU_RET_ERR(stat, "cudaEventRecord failed");
}
- /* need to prune the pair list during the next step */
- d_plist->bDoPrune = true;
+ /* the next use of thist list we be the first one, so we need to prune */
+ d_plist->haveFreshList = true;
}
void nbnxn_gpu_upload_shiftvec(gmx_nbnxn_cuda_t *nb,
if (nbparam->eeltype == eelCuEWALD_TAB || nbparam->eeltype == eelCuEWALD_TAB_TWIN)
{
- /* Only device CC >= 3.0 (Kepler and later) support texture objects */
- if (use_texobj(dev_info))
- {
- stat = cudaDestroyTextureObject(nbparam->coulomb_tab_texobj);
- CU_RET_ERR(stat, "cudaDestroyTextureObject on coulomb_tab_texobj failed");
- }
- else
+ if (!c_disableCudaTextures)
{
- GMX_UNUSED_VALUE(dev_info);
- stat = cudaUnbindTexture(nbnxn_cuda_get_coulomb_tab_texref());
- CU_RET_ERR(stat, "cudaUnbindTexture on coulomb_tab_texref failed");
+ /* Only device CC >= 3.0 (Kepler and later) support texture objects */
+ if (use_texobj(dev_info))
+ {
+ stat = cudaDestroyTextureObject(nbparam->coulomb_tab_texobj);
+ CU_RET_ERR(stat, "cudaDestroyTextureObject on coulomb_tab_texobj failed");
+ }
+ else
+ {
+ GMX_UNUSED_VALUE(dev_info);
+ stat = cudaUnbindTexture(nbnxn_cuda_get_coulomb_tab_texref());
+ CU_RET_ERR(stat, "cudaUnbindTexture on coulomb_tab_texref failed");
+ }
}
cu_free_buffered(nbparam->coulomb_tab, &nbparam->coulomb_tab_size);
}
stat = cudaEventDestroy(timers->stop_nb_k[i]);
CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_nb_k");
+ stat = cudaEventDestroy(timers->start_prune_k[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_prune_k");
+ stat = cudaEventDestroy(timers->stop_prune_k[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_prune_k");
+
+ stat = cudaEventDestroy(timers->start_rollingPrune_k[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_rollingPrune_k");
+ stat = cudaEventDestroy(timers->stop_rollingPrune_k[i]);
+ CU_RET_ERR(stat, "cudaEventDestroy failed on timers->stop_rollingPrune_k");
+
stat = cudaEventDestroy(timers->start_pl_h2d[i]);
CU_RET_ERR(stat, "cudaEventDestroy failed on timers->start_pl_h2d");
stat = cudaEventDestroy(timers->stop_pl_h2d[i]);
if (!useLjCombRule(nb->nbparam))
{
- /* Only device CC >= 3.0 (Kepler and later) support texture objects */
- if (use_texobj(nb->dev_info))
+ if (!c_disableCudaTextures)
{
- stat = cudaDestroyTextureObject(nbparam->nbfp_texobj);
- CU_RET_ERR(stat, "cudaDestroyTextureObject on nbfp_texobj failed");
- }
- else
- {
- stat = cudaUnbindTexture(nbnxn_cuda_get_nbfp_texref());
- CU_RET_ERR(stat, "cudaUnbindTexture on nbfp_texref failed");
+ /* Only device CC >= 3.0 (Kepler and later) support texture objects */
+ if (use_texobj(nb->dev_info))
+ {
+ stat = cudaDestroyTextureObject(nbparam->nbfp_texobj);
+ CU_RET_ERR(stat, "cudaDestroyTextureObject on nbfp_texobj failed");
+ }
+ else
+ {
+ stat = cudaUnbindTexture(nbnxn_cuda_get_nbfp_texref());
+ CU_RET_ERR(stat, "cudaUnbindTexture on nbfp_texref failed");
+ }
}
cu_free_buffered(nbparam->nbfp);
}
if (nbparam->vdwtype == evdwCuEWALDGEOM || nbparam->vdwtype == evdwCuEWALDLB)
{
- /* Only device CC >= 3.0 (Kepler and later) support texture objects */
- if (use_texobj(nb->dev_info))
- {
- stat = cudaDestroyTextureObject(nbparam->nbfp_comb_texobj);
- CU_RET_ERR(stat, "cudaDestroyTextureObject on nbfp_comb_texobj failed");
- }
- else
+ if (!c_disableCudaTextures)
{
- stat = cudaUnbindTexture(nbnxn_cuda_get_nbfp_comb_texref());
- CU_RET_ERR(stat, "cudaUnbindTexture on nbfp_comb_texref failed");
+ /* Only device CC >= 3.0 (Kepler and later) support texture objects */
+ if (use_texobj(nb->dev_info))
+ {
+ stat = cudaDestroyTextureObject(nbparam->nbfp_comb_texobj);
+ CU_RET_ERR(stat, "cudaDestroyTextureObject on nbfp_comb_texobj failed");
+ }
+ else
+ {
+ stat = cudaUnbindTexture(nbnxn_cuda_get_nbfp_comb_texref());
+ CU_RET_ERR(stat, "cudaUnbindTexture on nbfp_comb_texref failed");
+ }
}
cu_free_buffered(nbparam->nbfp_comb);
}
cu_free_buffered(plist->sci, &plist->nsci, &plist->sci_nalloc);
cu_free_buffered(plist->cj4, &plist->ncj4, &plist->cj4_nalloc);
+ cu_free_buffered(plist->imask, &plist->nimask, &plist->imask_nalloc);
cu_free_buffered(plist->excl, &plist->nexcl, &plist->excl_nalloc);
if (nb->bUseTwoStreams)
{
cu_free_buffered(plist_nl->sci, &plist_nl->nsci, &plist_nl->sci_nalloc);
cu_free_buffered(plist_nl->cj4, &plist_nl->ncj4, &plist_nl->cj4_nalloc);
+ cu_free_buffered(plist_nl->imask, &plist_nl->nimask, &plist_nl->imask_nalloc);
cu_free_buffered(plist_nl->excl, &plist_nl->nexcl, &plist->excl_nalloc);
}
}
}
-void cu_synchstream_atdat(gmx_nbnxn_cuda_t *nb, int iloc)
-{
- cudaError_t stat;
- cudaStream_t stream = nb->stream[iloc];
-
- stat = cudaStreamWaitEvent(stream, nb->timers->stop_atdat, 0);
- CU_RET_ERR(stat, "cudaStreamWaitEvent failed");
-}
-
gmx_wallclock_gpu_t * nbnxn_gpu_get_timings(gmx_nbnxn_cuda_t *nb)
{
return (nb != NULL && nb->bDoTime) ? nb->timings : NULL;
*/
#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
+#include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
#include "gromacs/math/utilities.h"
#include "gromacs/pbcutil/ishift.h"
/* Note that floating-point constants in CUDA code should be suffixed
* code that is in double precision.
*/
-#if GMX_PTX_ARCH < 300
-#error "nbnxn_cuda_kernel.cuh included with GMX_PTX_ARCH < 300"
+#if GMX_PTX_ARCH < 300 && GMX_PTX_ARCH != 0
+#error "nbnxn_cuda_kernel.cuh included with GMX_PTX_ARCH < 300 or host pass"
#endif
#if defined EL_EWALD_ANA || defined EL_EWALD_TAB
Kernel launch parameters:
- #blocks = #pair lists, blockId = pair list Id
- #threads = NTHREAD_Z * c_clSize^2
- - shmem = see nbnxn_cuda.cu:calc_shmem_required()
+ - shmem = see nbnxn_cuda.cu:calc_shmem_required_nonbonded()
Each thread calculates an i force-component taking one pair of i-j atoms.
*/
#ifdef EL_RF
float two_k_rf = nbparam.two_k_rf;
#endif
-#ifdef EL_EWALD_TAB
- float coulomb_tab_scale = nbparam.coulomb_tab_scale;
-#endif
#ifdef EL_EWALD_ANA
float beta2 = nbparam.ewald_beta*nbparam.ewald_beta;
float beta3 = nbparam.ewald_beta*nbparam.ewald_beta*nbparam.ewald_beta;
#endif
#ifdef PRUNE_NBL
- float rlist_sq = nbparam.rlist_sq;
+ float rlist_sq = nbparam.rlistOuter_sq;
#endif
#ifdef CALC_ENERGIES
ci = sci * c_numClPerSupercl + tidxj;
ai = ci * c_clSize + tidxi;
- xqbuf = xq[ai] + shift_vec[nb_sci.shift];
+ float *shiftptr = (float *)&shift_vec[nb_sci.shift];
+ xqbuf = xq[ai] + make_float4(LDG(shiftptr), LDG(shiftptr + 1), LDG(shiftptr + 2), 0.0f);
xqbuf.w *= nbparam.epsfac;
xqib[tidxj * c_clSize + tidxi] = xqbuf;
#endif
#ifdef LJ_EWALD
+ #if DISABLE_CUDA_TEXTURES
+ E_lj += LDG(&nbparam.nbfp[atom_types[(sci*c_numClPerSupercl + i)*c_clSize + tidxi]*(ntypes + 1)*2]);
+ #else
E_lj += tex1Dfetch<float>(nbparam.nbfp_texobj, atom_types[(sci*c_numClPerSupercl + i)*c_clSize + tidxi]*(ntypes + 1)*2);
+ #endif
#endif
}
#endif /* CALC_ENERGIES */
+#ifdef EXCLUSION_FORCES
+ const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
+#endif
+
int j4LoopStart = cij4_start + tidxz;
/* loop over the j clusters = seen by any of the atoms in the current super-cluster */
for (j4 = j4LoopStart; j4 < cij4_end; j4 += NTHREAD_Z)
#endif
{
/* Pre-load cj into shared memory on both warps separately */
- if ((tidxj == 0 || tidxj == 4) && tidxi < c_nbnxnGpuJgroupSize)
+ if ((tidxj == 0 | tidxj == 4) & (tidxi < c_nbnxnGpuJgroupSize))
{
cjs[tidxi + tidxj * c_nbnxnGpuJgroupSize/c_splitClSize] = pl_cj4[j4].cj[tidxi];
}
/* cutoff & exclusion check */
#ifdef EXCLUSION_FORCES
- if (r2 < rcoulomb_sq *
- (nb_sci.shift != CENTRAL || ci != cj || tidxj > tidxi))
+ if ((r2 < rcoulomb_sq) * (nonSelfInteraction | (ci != cj)))
#else
- if (r2 < rcoulomb_sq * int_bit)
+ if ((r2 < rcoulomb_sq) * int_bit)
#endif
{
/* load the rest of the i-atom parameters */
#ifndef LJ_COMB
/* LJ 6*C6 and 12*C12 */
typei = atib[i * c_clSize + tidxi];
- c6 = tex1Dfetch<float>(nbparam.nbfp_texobj, 2 * (ntypes * typei + typej));
- c12 = tex1Dfetch<float>(nbparam.nbfp_texobj, 2 * (ntypes * typei + typej) + 1);
+ fetch_nbfp_c6_c12(c6, c12, nbparam, ntypes * typei + typej);
#else
ljcp_i = ljcpib[i * c_clSize + tidxi];
#ifdef LJ_COMB_GEOM
#ifdef LJ_POT_SWITCH
#ifdef CALC_ENERGIES
- calculate_potential_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F_E(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#else
- calculate_potential_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#endif /* CALC_ENERGIES */
#endif /* LJ_POT_SWITCH */
F_invr += qi * qj_f * (int_bit*inv_r2*inv_r + pmecorrF(beta2*r2)*beta3);
#elif defined EL_EWALD_TAB
F_invr += qi * qj_f * (int_bit*inv_r2 -
- interpolate_coulomb_force_r(nbparam.coulomb_tab_texobj, r2 * inv_r, coulomb_tab_scale)) * inv_r;
+ interpolate_coulomb_force_r(nbparam, r2 * inv_r)) * inv_r;
#endif /* EL_EWALD_ANA/TAB */
#ifdef CALC_ENERGIES
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
+#include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
#include "gromacs/math/utilities.h"
#include "gromacs/pbcutil/ishift.h"
/* Note that floating-point constants in CUDA code should be suffixed
Kernel launch parameters:
- #blocks = #pair lists, blockId = pair list Id
- #threads = c_clSize^2
- - shmem = see nbnxn_cuda.cu:calc_shmem_required()
+ - shmem = see nbnxn_cuda.cu:calc_shmem_required_nonbonded()
Each thread calculates an i force-component taking one pair of i-j atoms.
*/
#ifdef EL_RF
float two_k_rf = nbparam.two_k_rf;
#endif
-#ifdef EL_EWALD_TAB
- float coulomb_tab_scale = nbparam.coulomb_tab_scale;
-#endif
#ifdef EL_EWALD_ANA
float beta2 = nbparam.ewald_beta*nbparam.ewald_beta;
float beta3 = nbparam.ewald_beta*nbparam.ewald_beta*nbparam.ewald_beta;
#endif
#ifdef PRUNE_NBL
- float rlist_sq = nbparam.rlist_sq;
+ float rlistOuter_sq = nbparam.rlistOuter_sq;
#endif
#ifdef CALC_ENERGIES
#endif
#ifdef LJ_EWALD
+ #if DISABLE_CUDA_TEXTURES
+ E_lj += LDG(&nbparam.nbfp[atom_types[(sci*c_numClPerSupercl + i)*c_clSize + tidxi]*(ntypes + 1)*2]);
+ #else
E_lj += tex1Dfetch(nbfp_texref, atom_types[(sci*c_numClPerSupercl + i)*c_clSize + tidxi]*(ntypes + 1)*2);
+ #endif
#endif
}
#endif /* CALC_ENERGIES */
+#ifdef EXCLUSION_FORCES
+ const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
+#endif
+
/* loop over the j clusters = seen by any of the atoms in the current super-cluster */
for (j4 = cij4_start; j4 < cij4_end; j4++)
{
#endif
{
/* Pre-load cj into shared memory on both warps separately */
- if ((tidxj == 0 || tidxj == 4) && tidxi < c_nbnxnGpuJgroupSize)
+ if ((tidxj == 0 | tidxj == 4) & (tidxi < c_nbnxnGpuJgroupSize))
{
cjs[tidxi + tidxj * c_nbnxnGpuJgroupSize/c_splitClSize] = pl_cj4[j4].cj[tidxi];
}
/* If _none_ of the atoms pairs are in cutoff range,
the bit corresponding to the current
cluster-pair in imask gets set to 0. */
- if (!__any(r2 < rlist_sq))
+ if (!__any(r2 < rlistOuter_sq))
{
imask &= ~mask_ji;
}
/* cutoff & exclusion check */
#ifdef EXCLUSION_FORCES
- if (r2 < rcoulomb_sq *
- (nb_sci.shift != CENTRAL || ci != cj || tidxj > tidxi))
+ if ((r2 < rcoulomb_sq) * (nonSelfInteraction | (ci != cj)))
#else
- if (r2 < rcoulomb_sq * int_bit)
+ if ((r2 < rcoulomb_sq) * int_bit)
#endif
{
/* load the rest of the i-atom parameters */
#ifndef LJ_COMB
/* LJ 6*C6 and 12*C12 */
typei = atom_types[ai];
- c6 = tex1Dfetch(nbfp_texref, 2 * (ntypes * typei + typej));
- c12 = tex1Dfetch(nbfp_texref, 2 * (ntypes * typei + typej) + 1);
+ fetch_nbfp_c6_c12(c6, c12, nbparam, ntypes * typei + typej);
#else
ljcp_i = lj_comb[ai];
#ifdef LJ_COMB_GEOM
#ifdef LJ_POT_SWITCH
#ifdef CALC_ENERGIES
- calculate_potential_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F_E(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#else
- calculate_potential_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#endif /* CALC_ENERGIES */
#endif /* LJ_POT_SWITCH */
#ifdef VDW_CUTOFF_CHECK
/* Separate VDW cut-off check to enable twin-range cut-offs
- * (rvdw < rcoulomb <= rlist)
+ * (rvdw < rcoulomb <= rlistOuter)
*/
vdw_in_range = (r2 < rvdw_sq) ? 1.0f : 0.0f;
F_invr *= vdw_in_range;
F_invr += qi * qj_f * (int_bit*inv_r2*inv_r + pmecorrF(beta2*r2)*beta3);
#elif defined EL_EWALD_TAB
F_invr += qi * qj_f * (int_bit*inv_r2 -
- interpolate_coulomb_force_r(r2 * inv_r, coulomb_tab_scale)) * inv_r;
+ interpolate_coulomb_force_r(nbparam, r2 * inv_r)) * inv_r;
#endif /* EL_EWALD_ANA/TAB */
#ifdef CALC_ENERGIES
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "nbnxn_cuda_kernel_pruneonly.cuh"
+
+#ifndef FUNCTION_DECLARATION_ONLY
+/* Instantiate external template functions */
+template __global__ void nbnxn_kernel_prune_cuda<false>(const cu_atomdata_t, const cu_nbparam_t, const cu_plist_t, int, int);
+template __global__ void nbnxn_kernel_prune_cuda<true>(const cu_atomdata_t, const cu_nbparam_t, const cu_plist_t, int, int);
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * CUDA non-bonded prune-only kernel.
+ *
+ * Unlike the non-bonded interaction kernels, this is not preprocessor-generated,
+ * the two flavors achieved by templating.
+ *
+ * \author Szilárd Páll <pall.szilard@gmail.com>
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_mdlib
+ */
+#include "gmxpre.h"
+
+#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
+#include "gromacs/math/utilities.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh"
+#include "gromacs/pbcutil/ishift.h"
+
+#include "nbnxn_cuda_types.h"
+
+/* Note that floating-point constants in CUDA code should be suffixed
+ * with f (e.g. 0.5f), to stop the compiler producing intermediate
+ * code that is in double precision.
+ */
+
+/**@{*/
+/*! \brief Compute capability dependent definition of kernel launch configuration parameters.
+ *
+ * Kernel launch bounds for different compute capabilities. The value of NTHREAD_Z
+ * represents the j-concurrency, hence it determines the number of threads per block.
+ * It is chosen such that 100% occupancy is maintained (on Maxwell and later for any NTHREAD_Z,
+ * requires >=4 warp/block, NTHREAD_Z>=2 on Kepler).
+ *
+ * Hence, values NTHREAD_Z >= 2 trade inter- for intra-block parallelism
+ * which has the advantage of lowering the overhead of starting up a block, filling shmem
+ * and registers, etc. Ideally we'd want to expose as much intra-block work as possible
+ * As we also split lists to cater for the block-parallelization needed by the register-
+ * limited non-bonded kernels, for very short j-loops large NTHREAD_Z will cause slowdown
+ * as it leads to intra-block warp imbalance. Ideally, we'd want to auto-tune the choice
+ * of NTHREAD_Z, but for now we instead pick a reasonable tradeoff-value.
+ *
+ * Note that given the above input size tradeoffs and that performance depends on
+ * additional factors including GPU arch, #SM's, we'll accept performance tradeoffs
+ * of using a fixed NTHREAD_Z=4. The following outliers have been observed:
+ * - up to 25% faster (rolling) prune kernels with NTHREAD_Z=8 in the regime where lists
+ * are not split (much), but the rolling chunks are small;
+ * - with large inputs NTHREAD_Z=1 is 2-3% faster (on CC>=5.0)
+ */
+#define NTHREAD_Z (GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY)
+#define THREADS_PER_BLOCK (c_clSize*c_clSize*NTHREAD_Z)
+// we want 100% occupancy, so max threads/block
+#define MIN_BLOCKS_PER_MP (GMX_CUDA_MAX_THREADS_PER_MP/THREADS_PER_BLOCK)
+/**@}*/
+
+/*! \brief Nonbonded list pruning kernel.
+ *
+ * The \p haveFreshList template parameter defines the two flavors of the kernel; when
+ * true a new list from immediately after pair-list generation is pruned using rlistOuter,
+ * the pruned masks are stored in a separate buffer and the outer-list is pruned
+ * using the rlistInner distance; when false only the pruning with rlistInner is performed.
+ *
+ * Kernel launch parameters:
+ * - #blocks = #pair lists, blockId = pair list Id
+ * - #threads = NTHREAD_Z * c_clSize^2
+ * - shmem = see nbnxn_cuda.cu:calc_shmem_required_prune()
+ *
+ * Each thread calculates an i-j atom distance..
+ */
+template <bool haveFreshList>
+__launch_bounds__(THREADS_PER_BLOCK, MIN_BLOCKS_PER_MP)
+__global__ void nbnxn_kernel_prune_cuda(const cu_atomdata_t atdat,
+ const cu_nbparam_t nbparam,
+ const cu_plist_t plist,
+ int numParts,
+ int part)
+#ifdef FUNCTION_DECLARATION_ONLY
+; /* Only do function declaration, omit the function body. */
+#else
+{
+
+ /* convenience variables */
+ const nbnxn_sci_t *pl_sci = plist.sci;
+ nbnxn_cj4_t *pl_cj4 = plist.cj4;
+ const float4 *xq = atdat.xq;
+ const float3 *shift_vec = atdat.shift_vec;
+
+ float rlistOuter_sq = nbparam.rlistOuter_sq;
+ float rlistInner_sq = nbparam.rlistInner_sq;
+
+ /* thread/block/warp id-s */
+ unsigned int tidxi = threadIdx.x;
+ unsigned int tidxj = threadIdx.y;
+#if NTHREAD_Z == 1
+ unsigned int tidxz = 0;
+#else
+ unsigned int tidxz = threadIdx.z;
+#endif
+ unsigned int bidx = blockIdx.x;
+ unsigned int widx = (threadIdx.y * c_clSize) / warp_size; /* warp index */
+
+ /* shmem buffer for i x pre-loading */
+ extern __shared__ float4 xib[];
+
+ /* shmem buffer for cj, for each warp separately */
+ int *cjs = ((int *)(xib + c_numClPerSupercl * c_clSize)) + tidxz * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize;
+
+ nbnxn_sci_t nb_sci = pl_sci[bidx*numParts + part]; /* my i super-cluster's index = sciOffset + current bidx * numParts + part */
+ int sci = nb_sci.sci; /* super-cluster */
+ int cij4_start = nb_sci.cj4_ind_start; /* first ...*/
+ int cij4_end = nb_sci.cj4_ind_end; /* and last index of j clusters */
+
+ if (tidxz == 0)
+ {
+ /* Pre-load i-atom x and q into shared memory */
+ int ci = sci * c_numClPerSupercl + tidxj;
+ int ai = ci * c_clSize + tidxi;
+
+ /* We don't need q, but using float4 in shmem avoids bank conflicts.
+ (but it also wastes L2 bandwidth). */
+ float4 tmp = xq[ai];
+ float4 xi = tmp + shift_vec[nb_sci.shift];
+ xib[tidxj * c_clSize + tidxi] = xi;
+ }
+ __syncthreads();
+
+ /* loop over the j clusters = seen by any of the atoms in the current super-cluster */
+ for (int j4 = cij4_start + tidxz; j4 < cij4_end; j4 += NTHREAD_Z)
+ {
+ unsigned int imaskFull, imaskCheck, imaskNew;
+
+ if (haveFreshList)
+ {
+ /* Read the mask from the list transferred from the CPU */
+ imaskFull = pl_cj4[j4].imei[widx].imask;
+ /* We attempt to prune all pairs present in the original list */
+ imaskCheck = imaskFull;
+ imaskNew = 0;
+ }
+ else
+ {
+ /* Read the mask from the "warp-pruned" by rlistOuter mask array */
+ imaskFull = plist.imask[j4*c_nbnxnGpuClusterpairSplit + widx];
+ /* Read the old rolling pruned mask, use as a base for new */
+ imaskNew = pl_cj4[j4].imei[widx].imask;
+ /* We only need to check pairs with different mask */
+ imaskCheck = (imaskNew ^ imaskFull);
+ }
+
+ if (imaskCheck)
+ {
+ /* Pre-load cj into shared memory on both warps separately */
+ if ((tidxj == 0 || tidxj == 4) && tidxi < c_nbnxnGpuJgroupSize)
+ {
+ cjs[tidxi + tidxj * c_nbnxnGpuJgroupSize/c_splitClSize] = pl_cj4[j4].cj[tidxi];
+ }
+
+#pragma unroll 4
+ for (int jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
+ {
+ if (imaskCheck & (superClInteractionMask << (jm * c_numClPerSupercl)))
+ {
+ unsigned int mask_ji = (1U << (jm * c_numClPerSupercl));
+
+ int cj = cjs[jm + (tidxj & 4) * c_nbnxnGpuJgroupSize/c_splitClSize];
+ int aj = cj * c_clSize + tidxj;
+
+ /* load j atom data */
+ float4 tmp = xq[aj];
+ float3 xj = make_float3(tmp.x, tmp.y, tmp.z);
+
+#pragma unroll 8
+ for (int i = 0; i < c_numClPerSupercl; i++)
+ {
+ if (imaskCheck & mask_ji)
+ {
+ /* load i-cluster coordinates from shmem */
+ float4 xi = xib[i * c_clSize + tidxi];
+
+
+ /* distance between i and j atoms */
+ float3 rv = make_float3(xi.x, xi.y, xi.z) - xj;
+ float r2 = norm2(rv);
+
+ /* If _none_ of the atoms pairs are in rlistOuter
+ range, the bit corresponding to the current
+ cluster-pair in imask gets set to 0. */
+ if (haveFreshList && !__any(r2 < rlistOuter_sq))
+ {
+ imaskFull &= ~mask_ji;
+ }
+ /* If any atom pair is within range, set the bit
+ corresponding to the current cluster-pair. */
+ if (__any(r2 < rlistInner_sq))
+ {
+ imaskNew |= mask_ji;
+ }
+ }
+
+ /* shift the mask bit by 1 */
+ mask_ji += mask_ji;
+ }
+ }
+ }
+
+ if (haveFreshList)
+ {
+ /* copy the list pruned to rlistOuter to a separate buffer */
+ plist.imask[j4*c_nbnxnGpuClusterpairSplit + widx] = imaskFull;
+ }
+ /* update the imask with only the pairs up to rlistInner */
+ plist.cj4[j4].imei[widx].imask = imaskNew;
+ }
+ }
+}
+#endif /* FUNCTION_DECLARATION_ONLY */
+
+#undef NTHREAD_Z
+#undef MIN_BLOCKS_PER_MP
+#undef THREADS_PER_BLOCK
* \author Szilárd Páll <pall.szilard@gmail.com>
* \ingroup module_mdlib
*/
-#include "config.h"
-
#include <assert.h>
/* Note that floating-point constants in CUDA code should be suffixed
* with f (e.g. 0.5f), to stop the compiler producing intermediate
* code that is in double precision.
*/
-#include "config.h"
#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
+#include "gromacs/gpu_utils/cuda_kernel_utils.cuh"
#include "gromacs/gpu_utils/vectype_ops.cuh"
#include "nbnxn_cuda_types.h"
#ifndef NBNXN_CUDA_KERNEL_UTILS_CUH
#define NBNXN_CUDA_KERNEL_UTILS_CUH
-/* Use texture objects if supported by the target hardware. */
-#if GMX_PTX_ARCH >= 300
+/* Use texture objects if supported by the target hardware (and in host pass). */
+#if GMX_PTX_ARCH >= 300 || GMX_PTX_ARCH == 0
/* Note: convenience macro, needs to be undef-ed at the end of the file. */
#define USE_TEXOBJ
#endif
static const int c_splitClSize = c_clSize/c_nbnxnGpuClusterpairSplit;
/*! \brief Stride in the force accumualation buffer */
static const int c_fbufStride = c_clSizeSq;
+/*! \brief i-cluster interaction mask for a super-cluster with all c_numClPerSupercl=8 bits set */
+static const unsigned superClInteractionMask = ((1U << c_numClPerSupercl) - 1U);
static const float c_oneSixth = 0.16666667f;
static const float c_oneTwelveth = 0.08333333f;
-/* With multiple compilation units this ensures that texture refs are available
- in the the kernels' compilation units. */
-#if !GMX_CUDA_NB_SINGLE_COMPILATION_UNIT
-/*! Texture reference for LJ C6/C12 parameters; bound to cu_nbparam_t.nbfp */
-extern texture<float, 1, cudaReadModeElementType> nbfp_texref;
-
-/*! Texture reference for LJ-PME parameters; bound to cu_nbparam_t.nbfp_comb */
-extern texture<float, 1, cudaReadModeElementType> nbfp_comb_texref;
-
-/*! Texture reference for Ewald coulomb force table; bound to cu_nbparam_t.coulomb_tab */
-extern texture<float, 1, cudaReadModeElementType> coulomb_tab_texref;
-#endif /* GMX_CUDA_NB_SINGLE_COMPILATION_UNIT */
/*! Convert LJ sigma,epsilon parameters to C6,C12. */
static __forceinline__ __device__
/*! Apply potential switch, force-only version. */
static __forceinline__ __device__
void calculate_potential_switch_F(const cu_nbparam_t nbparam,
- float c6,
- float c12,
float inv_r,
float r2,
float *F_invr,
/*! Apply potential switch, force + energy version. */
static __forceinline__ __device__
void calculate_potential_switch_F_E(const cu_nbparam_t nbparam,
- float c6,
- float c12,
float inv_r,
float r2,
float *F_invr,
*E_lj *= sw;
}
+
+/*! \brief Fetch C6 grid contribution coefficients and return the product of these.
+ *
+ * Depending on what is supported, it fetches parameters either
+ * using direct load, texture objects, or texrefs.
+ */
+static __forceinline__ __device__
+float calculate_lj_ewald_c6grid(const cu_nbparam_t nbparam,
+ int typei,
+ int typej)
+{
+#if DISABLE_CUDA_TEXTURES
+ return LDG(&nbparam.nbfp_comb[2*typei]) * LDG(&nbparam.nbfp_comb[2*typej]);
+#else
+#ifdef USE_TEXOBJ
+ return tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typei) * tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typej);
+#else
+ return tex1Dfetch(nbfp_comb_texref, 2*typei) * tex1Dfetch(nbfp_comb_texref, 2*typej);
+#endif /* USE_TEXOBJ */
+#endif /* DISABLE_CUDA_TEXTURES */
+}
+
+
/*! Calculate LJ-PME grid force contribution with
* geometric combination rule.
*/
{
float c6grid, inv_r6_nm, cr2, expmcr2, poly;
-#ifdef USE_TEXOBJ
- c6grid = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typei) * tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typej);
-#else
- c6grid = tex1Dfetch(nbfp_comb_texref, 2*typei) * tex1Dfetch(nbfp_comb_texref, 2*typej);
-#endif /* USE_TEXOBJ */
+ c6grid = calculate_lj_ewald_c6grid(nbparam, typei, typej);
/* Recalculate inv_r6 without exclusion mask */
inv_r6_nm = inv_r2*inv_r2*inv_r2;
*F_invr += c6grid*(inv_r6_nm - expmcr2*(inv_r6_nm*poly + lje_coeff6_6))*inv_r2;
}
+
/*! Calculate LJ-PME grid force + energy contribution with
* geometric combination rule.
*/
{
float c6grid, inv_r6_nm, cr2, expmcr2, poly, sh_mask;
-#ifdef USE_TEXOBJ
- c6grid = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typei) * tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typej);
-#else
- c6grid = tex1Dfetch(nbfp_comb_texref, 2*typei) * tex1Dfetch(nbfp_comb_texref, 2*typej);
-#endif /* USE_TEXOBJ */
+ c6grid = calculate_lj_ewald_c6grid(nbparam, typei, typej);
/* Recalculate inv_r6 without exclusion mask */
inv_r6_nm = inv_r2*inv_r2*inv_r2;
*E_lj += c_oneSixth*c6grid*(inv_r6_nm*(1.0f - expmcr2*poly) + sh_mask);
}
+/*! Fetch per-type LJ parameters.
+ *
+ * Depending on what is supported, it fetches parameters either
+ * using direct load, texture objects, or texrefs.
+ */
+static __forceinline__ __device__
+float2 fetch_nbfp_comb_c6_c12(const cu_nbparam_t nbparam,
+ int type)
+{
+ float2 c6c12;
+#if DISABLE_CUDA_TEXTURES
+ /* Force an 8-byte fetch to save a memory instruction. */
+ float2 *nbfp_comb = (float2 *)nbparam.nbfp_comb;
+ c6c12 = LDG(&nbfp_comb[type]);
+#else
+ /* NOTE: as we always do 8-byte aligned loads, we could
+ fetch float2 here too just as above. */
+#ifdef USE_TEXOBJ
+ c6c12.x = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*type);
+ c6c12.y = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*type + 1);
+#else
+ c6c12.x = tex1Dfetch(nbfp_comb_texref, 2*type);
+ c6c12.y = tex1Dfetch(nbfp_comb_texref, 2*type + 1);
+#endif /* USE_TEXOBJ */
+#endif /* DISABLE_CUDA_TEXTURES */
+
+ return c6c12;
+}
+
+
/*! Calculate LJ-PME grid force + energy contribution (if E_lj != NULL) with
* Lorentz-Berthelot combination rule.
* We use a single F+E kernel with conditional because the performance impact
float sigma, sigma2, epsilon;
/* sigma and epsilon are scaled to give 6*C6 */
-#ifdef USE_TEXOBJ
- sigma = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typei ) + tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typej );
- epsilon = tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typei + 1) * tex1Dfetch<float>(nbparam.nbfp_comb_texobj, 2*typej + 1);
-#else
- sigma = tex1Dfetch(nbfp_comb_texref, 2*typei ) + tex1Dfetch(nbfp_comb_texref, 2*typej );
- epsilon = tex1Dfetch(nbfp_comb_texref, 2*typei + 1) * tex1Dfetch(nbfp_comb_texref, 2*typej + 1);
-#endif /* USE_TEXOBJ */
+ float2 c6c12_i = fetch_nbfp_comb_c6_c12(nbparam, typei);
+ float2 c6c12_j = fetch_nbfp_comb_c6_c12(nbparam, typej);
+
+ sigma = c6c12_i.x + c6c12_j.x;
+ epsilon = c6c12_i.y * c6c12_j.y;
+
sigma2 = sigma*sigma;
c6grid = epsilon*sigma2*sigma2*sigma2;
}
}
-/*! Interpolate Ewald coulomb force using the table through the tex_nbfp texture.
- * Original idea: from the OpenMM project
+
+/*! Fetch two consecutive values from the Ewald correction F*r table.
+ *
+ * Depending on what is supported, it fetches parameters either
+ * using direct load, texture objects, or texrefs.
*/
static __forceinline__ __device__
-float interpolate_coulomb_force_r(float r, float scale)
+float2 fetch_coulomb_force_r(const cu_nbparam_t nbparam,
+ int index)
{
- float normalized = scale * r;
- int index = (int) normalized;
- float fract2 = normalized - index;
- float fract1 = 1.0f - fract2;
+ float2 d;
+
+#if DISABLE_CUDA_TEXTURES
+ /* Can't do 8-byte fetch because some of the addresses will be misaligned. */
+ d.x = LDG(&nbparam.coulomb_tab[index]);
+ d.y = LDG(&nbparam.coulomb_tab[index + 1]);
+#else
+#ifdef USE_TEXOBJ
+ d.x = tex1Dfetch<float>(nbparam.coulomb_tab_texobj, index);
+ d.y = tex1Dfetch<float>(nbparam.coulomb_tab_texobj, index + 1);
+#else
+ d.x = tex1Dfetch(coulomb_tab_texref, index);
+ d.y = tex1Dfetch(coulomb_tab_texref, index + 1);
+#endif // USE_TEXOBJ
+#endif // DISABLE_CUDA_TEXTURES
- return fract1 * tex1Dfetch(coulomb_tab_texref, index)
- + fract2 * tex1Dfetch(coulomb_tab_texref, index + 1);
+ return d;
}
+/*! Linear interpolation using exactly two FMA operations.
+ *
+ * Implements numeric equivalent of: (1-t)*d0 + t*d1
+ * Note that CUDA does not have fnms, otherwise we'd use
+ * fma(t, d1, fnms(t, d0, d0)
+ * but input modifiers are designed for this and are fast.
+ */
+template <typename T>
+__forceinline__ __host__ __device__
+T lerp(T d0, T d1, T t)
+{
+ return fma(t, d1, fma(-t, d0, d0));
+}
+
+/*! Interpolate Ewald coulomb force correction using the F*r table.
+ */
static __forceinline__ __device__
-float interpolate_coulomb_force_r(cudaTextureObject_t texobj_coulomb_tab,
- float r, float scale)
+float interpolate_coulomb_force_r(const cu_nbparam_t nbparam,
+ float r)
{
- float normalized = scale * r;
- int index = (int) normalized;
- float fract2 = normalized - index;
- float fract1 = 1.0f - fract2;
+ float normalized = nbparam.coulomb_tab_scale * r;
+ int index = (int) normalized;
+ float fraction = normalized - index;
+
+ float2 d01 = fetch_coulomb_force_r(nbparam, index);
- return fract1 * tex1Dfetch<float>(texobj_coulomb_tab, index) +
- fract2 * tex1Dfetch<float>(texobj_coulomb_tab, index + 1);
+ return lerp(d01.x, d01.y, fraction);
}
+/*! Fetch C6 and C12 from the parameter table.
+ *
+ * Depending on what is supported, it fetches parameters either
+ * using direct load, texture objects, or texrefs.
+ */
+static __forceinline__ __device__
+void fetch_nbfp_c6_c12(float &c6,
+ float &c12,
+ const cu_nbparam_t nbparam,
+ int baseIndex)
+{
+#if DISABLE_CUDA_TEXTURES
+ /* Force an 8-byte fetch to save a memory instruction. */
+ float2 *nbfp = (float2 *)nbparam.nbfp;
+ float2 c6c12;
+ c6c12 = LDG(&nbfp[baseIndex]);
+ c6 = c6c12.x;
+ c12 = c6c12.y;
+#else
+ /* NOTE: as we always do 8-byte aligned loads, we could
+ fetch float2 here too just as above. */
+#ifdef USE_TEXOBJ
+ c6 = tex1Dfetch<float>(nbparam.nbfp_texobj, 2*baseIndex);
+ c12 = tex1Dfetch<float>(nbparam.nbfp_texobj, 2*baseIndex + 1);
+#else
+ c6 = tex1Dfetch(nbfp_texref, 2*baseIndex);
+ c12 = tex1Dfetch(nbfp_texref, 2*baseIndex + 1);
+#endif
+#endif // DISABLE_CUDA_TEXTURES
+}
+
+
/*! Calculate analytical Ewald correction term. */
static __forceinline__ __device__
float pmecorrF(float z2)
/*! Final j-force reduction; this implementation only with power of two
* array sizes and with sm >= 3.0
*/
-#if GMX_PTX_ARCH >= 300
+#if GMX_PTX_ARCH >= 300 || GMX_PTX_ARCH == 0
static __forceinline__ __device__
void reduce_force_j_warp_shfl(float3 f, float3 *fout,
int tidxi, int aidx,
/*! Final i-force reduction; this implementation works only with power of two
* array sizes and with sm >= 3.0
*/
-#if GMX_PTX_ARCH >= 300
+#if GMX_PTX_ARCH >= 300 || GMX_PTX_ARCH == 0
static __forceinline__ __device__
void reduce_force_i_warp_shfl(float3 fin, float3 *fout,
float *fshift_buf, bool bCalcFshift,
/*! Energy reduction; this implementation works only with power of two
* array sizes and with sm >= 3.0
*/
-#if GMX_PTX_ARCH >= 300
+#if GMX_PTX_ARCH >= 300 || GMX_PTX_ARCH == 0
static __forceinline__ __device__
void reduce_energy_warp_shfl(float E_lj, float E_el,
float *e_lj, float *e_el,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \ingroup module_mdlib
*/
-#if GMX_PTX_ARCH >= 300
+/* Use the standard non-Fermi kernel in host pass too (to avoid texref API calls). */
+#if GMX_PTX_ARCH >= 300 || GMX_PTX_ARCH == 0
#define FLAVOR_LEVEL_GENERATOR "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh"
#else
#define FLAVOR_LEVEL_GENERATOR "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_fermi.cuh"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2012, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef NBNXN_CUDA_TYPES_H
#define NBNXN_CUDA_TYPES_H
+#include "gromacs/gpu_utils/cuda_arch_utils.cuh"
#include "gromacs/gpu_utils/cudautils.cuh"
#include "gromacs/mdlib/nbnxn_consts.h"
#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/timing/gpu_timing.h"
+/*! \brief Macro definining default for the prune kernel's j4 processing concurrency.
+ *
+ * The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override.
+ */
+#ifndef GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY 4
+#endif
+/*! \brief Default for the prune kernel's j4 processing concurrency.
+ *
+ * Initialized using the #GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro which allows compile-time override.
+ */
+const int c_cudaPruneKernelJ4Concurrency = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY;
+
/* TODO: consider moving this to kernel_utils */
/* Convenience defines */
/*! \brief number of clusters per supercluster. */
/*! \brief cluster size = number of atoms per cluster. */
static const int c_clSize = c_nbnxnGpuClusterSize;
+/*! \brief True if the use of texture fetch in the CUDA kernels is disabled. */
+static const bool c_disableCudaTextures = DISABLE_CUDA_TEXTURES;
+
+
#ifdef __cplusplus
extern "C" {
#endif
struct cu_nbparam
{
- int eeltype; /**< type of electrostatics, takes values from #eelCu */
- int vdwtype; /**< type of VdW impl., takes values from #evdwCu */
+ int eeltype; /**< type of electrostatics, takes values from #eelCu */
+ int vdwtype; /**< type of VdW impl., takes values from #evdwCu */
- float epsfac; /**< charge multiplication factor */
- float c_rf; /**< Reaction-field/plain cutoff electrostatics const. */
- float two_k_rf; /**< Reaction-field electrostatics constant */
- float ewald_beta; /**< Ewald/PME parameter */
- float sh_ewald; /**< Ewald/PME correction term substracted from the direct-space potential */
- float sh_lj_ewald; /**< LJ-Ewald/PME correction term added to the correction potential */
- float ewaldcoeff_lj; /**< LJ-Ewald/PME coefficient */
+ float epsfac; /**< charge multiplication factor */
+ float c_rf; /**< Reaction-field/plain cutoff electrostatics const. */
+ float two_k_rf; /**< Reaction-field electrostatics constant */
+ float ewald_beta; /**< Ewald/PME parameter */
+ float sh_ewald; /**< Ewald/PME correction term substracted from the direct-space potential */
+ float sh_lj_ewald; /**< LJ-Ewald/PME correction term added to the correction potential */
+ float ewaldcoeff_lj; /**< LJ-Ewald/PME coefficient */
- float rcoulomb_sq; /**< Coulomb cut-off squared */
+ float rcoulomb_sq; /**< Coulomb cut-off squared */
- float rvdw_sq; /**< VdW cut-off squared */
- float rvdw_switch; /**< VdW switched cut-off */
- float rlist_sq; /**< pair-list cut-off squared */
+ float rvdw_sq; /**< VdW cut-off squared */
+ float rvdw_switch; /**< VdW switched cut-off */
+ float rlistOuter_sq; /**< Full, outer pair-list cut-off squared */
+ float rlistInner_sq; /**< Inner, dynamic pruned pair-list cut-off squared */
+ bool useDynamicPruning; /**< True if we use dynamic pair-list pruning */
- shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
- shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
- switch_consts_t vdw_switch; /**< VdW switch constants */
+ shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
+ shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
+ switch_consts_t vdw_switch; /**< VdW switch constants */
/* LJ non-bonded parameters - accessed through texture memory */
float *nbfp; /**< nonbonded parameter table with C6/C12 pairs per atom type-pair, 2*ntype^2 elements */
*/
struct cu_plist
{
- int na_c; /**< number of atoms per cluster */
-
- int nsci; /**< size of sci, # of i clusters in the list */
- int sci_nalloc; /**< allocation size of sci */
- nbnxn_sci_t *sci; /**< list of i-cluster ("super-clusters") */
-
- int ncj4; /**< total # of 4*j clusters */
- int cj4_nalloc; /**< allocation size of cj4 */
- nbnxn_cj4_t *cj4; /**< 4*j cluster list, contains j cluster number
- and index into the i cluster list */
- nbnxn_excl_t *excl; /**< atom interaction bits */
- int nexcl; /**< count for excl */
- int excl_nalloc; /**< allocation size of excl */
-
- bool bDoPrune; /**< true if pair-list pruning needs to be
- done during the current step */
+ int na_c; /**< number of atoms per cluster */
+
+ int nsci; /**< size of sci, # of i clusters in the list */
+ int sci_nalloc; /**< allocation size of sci */
+ nbnxn_sci_t *sci; /**< list of i-cluster ("super-clusters") */
+
+ int ncj4; /**< total # of 4*j clusters */
+ int cj4_nalloc; /**< allocation size of cj4 */
+ nbnxn_cj4_t *cj4; /**< 4*j cluster list, contains j cluster number
+ and index into the i cluster list */
+ int nimask; /**< # of 4*j clusters * # of warps */
+ int imask_nalloc; /**< allocation size of imask */
+ unsigned int *imask; /**< imask for 2 warps for each 4*j cluster group */
+ nbnxn_excl_t *excl; /**< atom interaction bits */
+ int nexcl; /**< count for excl */
+ int excl_nalloc; /**< allocation size of excl */
+
+ /* parameter+variables for normal and rolling pruning */
+ bool haveFreshList; /**< true after search, indictes that initial pruning with outer prunning is needed */
+ int rollingPruningNumParts; /**< the number of parts/steps over which one cyle of roling pruning takes places */
+ int rollingPruningPart; /**< the next part to which the roling pruning needs to be applied */
};
/** \internal
*/
struct cu_timers
{
- cudaEvent_t start_atdat; /**< start event for atom data transfer (every PS step) */
- cudaEvent_t stop_atdat; /**< stop event for atom data transfer (every PS step) */
- cudaEvent_t start_nb_h2d[2]; /**< start events for x/q H2D transfers (l/nl, every step) */
- cudaEvent_t stop_nb_h2d[2]; /**< stop events for x/q H2D transfers (l/nl, every step) */
- cudaEvent_t start_nb_d2h[2]; /**< start events for f D2H transfer (l/nl, every step) */
- cudaEvent_t stop_nb_d2h[2]; /**< stop events for f D2H transfer (l/nl, every step) */
- cudaEvent_t start_pl_h2d[2]; /**< start events for pair-list H2D transfers (l/nl, every PS step) */
- cudaEvent_t stop_pl_h2d[2]; /**< start events for pair-list H2D transfers (l/nl, every PS step) */
- cudaEvent_t start_nb_k[2]; /**< start event for non-bonded kernels (l/nl, every step) */
- cudaEvent_t stop_nb_k[2]; /**< stop event non-bonded kernels (l/nl, every step) */
+ cudaEvent_t start_atdat; /**< start event for atom data transfer (every PS step) */
+ cudaEvent_t stop_atdat; /**< stop event for atom data transfer (every PS step) */
+ cudaEvent_t start_nb_h2d[2]; /**< start events for x/q H2D transfers (l/nl, every step) */
+ cudaEvent_t stop_nb_h2d[2]; /**< stop events for x/q H2D transfers (l/nl, every step) */
+ cudaEvent_t start_nb_d2h[2]; /**< start events for f D2H transfer (l/nl, every step) */
+ cudaEvent_t stop_nb_d2h[2]; /**< stop events for f D2H transfer (l/nl, every step) */
+ cudaEvent_t start_pl_h2d[2]; /**< start events for pair-list H2D transfers (l/nl, every PS step) */
+ cudaEvent_t stop_pl_h2d[2]; /**< start events for pair-list H2D transfers (l/nl, every PS step) */
+ bool didPairlistH2D[2]; /**< true when a pair-list transfer has been done at this step */
+ cudaEvent_t start_nb_k[2]; /**< start event for non-bonded kernels (l/nl, every step) */
+ cudaEvent_t stop_nb_k[2]; /**< stop event non-bonded kernels (l/nl, every step) */
+ cudaEvent_t start_prune_k[2]; /**< start event for the 1st pass list pruning kernel (l/nl, every PS step) */
+ cudaEvent_t stop_prune_k[2]; /**< stop event for the 1st pass list pruning kernel (l/nl, every PS step) */
+ bool didPrune[2]; /**< true when we timed pruning and the timings need to be accounted for */
+ cudaEvent_t start_rollingPrune_k[2]; /**< start event for rolling pruning kernels (l/nl, frequency depends on chunk size) */
+ cudaEvent_t stop_rollingPrune_k[2]; /**< stop event for rolling pruning kernels (l/nl, frequency depends on chunk size) */
+ bool didRollingPrune[2]; /**< true when we timed rolling pruning (at the previous step) and the timings need to be accounted for */
};
/** \internal
*/
struct gmx_nbnxn_cuda_t
{
- struct gmx_device_info_t *dev_info; /**< CUDA device information */
+ const gmx_device_info_t *dev_info; /**< CUDA device information */
bool bUseTwoStreams; /**< true if doing both local/non-local NB work on GPU */
cu_atomdata_t *atdat; /**< atom data */
cu_nbparam_t *nbparam; /**< parameters required for the non-bonded calc. */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int gmx_unused flags,
int gmx_unused iloc) GPU_FUNC_TERM
+/*! \brief
+ * Launch asynchronously the nonbonded prune-only kernel.
+ *
+ * The local and non-local list pruning are launched in their separate streams.
+ *
+ * Notes for future scheduling tuning:
+ * Currently we schedule the dynamic pruning between two MD steps *after* both local and
+ * nonlocal force D2H transfers completed. We could launch already after the cpyback
+ * is launched, but we want to avoid prune kernels (especially in the non-local
+ * high prio-stream) competing with nonbonded work.
+ *
+ * However, this is not ideal as this schedule does not expose the available
+ * concurrency. The dynamic pruning kernel:
+ * - should be allowed to overlap with any task other than force compute, including
+ * transfers (F D2H and the next step's x H2D as well as force clearing).
+ * - we'd prefer to avoid competition with non-bonded force kernels belonging
+ * to the same rank and ideally other ranks too.
+ *
+ * In the most general case, the former would require scheduling pruning in a separate
+ * stream and adding additional event sync points to ensure that force kernels read
+ * consistent pair list data. This would lead to some overhead (due to extra
+ * cudaStreamWaitEvent calls, 3-5 us/call) which we might be able to live with.
+ * The gains from additional overlap might not be significant as long as
+ * update+constraints anyway takes longer than pruning, but there will still
+ * be use-cases where more overlap may help (e.g. multiple ranks per GPU,
+ * no/hbonds only constraints).
+ * The above second point is harder to address given that multiple ranks will often
+ * share a GPU. Ranks that complete their nonbondeds sooner can schedule pruning earlier
+ * and without a third priority level it is difficult to avoid some interference of
+ * prune kernels with force tasks (in particular preemption of low-prio local force task).
+ *
+ * \param [inout] nb GPU nonbonded data.
+ * \param [in] iloc Interaction locality flag.
+ * \param [in] numParts Number of parts the pair list is split into in the rolling kernel.
+ */
+GPU_FUNC_QUALIFIER
+void nbnxn_gpu_launch_kernel_pruneonly(gmx_nbnxn_gpu_t gmx_unused *nb,
+ int gmx_unused iloc,
+ int gmx_unused numParts) GPU_FUNC_TERM
+
/*! \brief
* Launch asynchronously the download of nonbonded forces from the GPU
* (and energies/shift forces if required).
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct nonbonded_verlet_group_t;
struct nbnxn_pairlist_t;
struct nbnxn_atomdata_t;
+struct NbnxnListParameters;
struct gmx_wallclock_gpu_t;
struct gmx_gpu_info_t;
-struct gmx_gpu_opt_t;
/** Initializes the data structures related to GPU nonbonded calculations. */
GPU_FUNC_QUALIFIER
void nbnxn_gpu_init(gmx_nbnxn_gpu_t gmx_unused **p_nb,
- const struct gmx_gpu_info_t gmx_unused *gpu_info,
- const struct gmx_gpu_opt_t gmx_unused *gpu_opt,
+ const gmx_device_info_t gmx_unused *deviceInfo,
const interaction_const_t gmx_unused *ic,
+ const NbnxnListParameters gmx_unused *listParams,
nonbonded_verlet_group_t gmx_unused *nbv_grp,
- int gmx_unused my_gpu_index,
int gmx_unused rank,
/* true if both local and non-local are done on GPU */
gmx_bool gmx_unused bLocalAndNonlocal) GPU_FUNC_TERM
*/
GPU_FUNC_QUALIFIER
void nbnxn_gpu_pme_loadbal_update_param(const struct nonbonded_verlet_t gmx_unused *nbv,
- const interaction_const_t gmx_unused *ic) GPU_FUNC_TERM
+ const interaction_const_t gmx_unused *ic,
+ const NbnxnListParameters gmx_unused *listParams) GPU_FUNC_TERM
/** Uploads shift vector to the GPU if the box is dynamic (otherwise just returns). */
GPU_FUNC_QUALIFIER
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static void nbnxn_grid_init(nbnxn_grid_t * grid)
{
- grid->cxy_na = NULL;
- grid->cxy_ind = NULL;
+ grid->cxy_na = nullptr;
+ grid->cxy_ind = nullptr;
grid->cxy_nalloc = 0;
- grid->bb = NULL;
- grid->bbj = NULL;
+ grid->bb = nullptr;
+ grid->bbj = nullptr;
grid->nc_nalloc = 0;
}
}
/* Packed coordinates, bb order xyz0 */
-static void calc_bounding_box_x_x4_halves(int na, const real *x,
- nbnxn_bb_t *bb, nbnxn_bb_t *bbj)
+gmx_unused static void calc_bounding_box_x_x4_halves(int na, const real *x,
+ nbnxn_bb_t *bb, nbnxn_bb_t *bbj)
{
// TODO: During SIMDv2 transition only some archs use namespace (remove when done)
using namespace gmx;
fill_cell(nbs, grid, nbat,
ash_c, ash_c+na_c, atinfo, x,
- NULL);
+ nullptr);
/* This copy to bbcz is not really necessary.
* But it allows to use the same grid search code
/* Home zone */
for (int i = n0; i < n1; i++)
{
- if (move == NULL || move[i] >= 0)
+ if (move == nullptr || move[i] >= 0)
{
/* We need to be careful with rounding,
* particles might be a few bits outside the local zone.
}
}
-static void init_buffer_flags(nbnxn_buffer_flags_t *flags,
- int natoms)
-{
- flags->nflag = (natoms + NBNXN_BUFFERFLAG_SIZE - 1)/NBNXN_BUFFERFLAG_SIZE;
- if (flags->nflag > flags->flag_nalloc)
- {
- flags->flag_nalloc = over_alloc_large(flags->nflag);
- srenew(flags->flag, flags->flag_nalloc);
- }
- for (int b = 0; b < flags->nflag; b++)
- {
- bitmask_clear(&(flags->flag[b]));
- }
-}
-
/* Sets up a grid and puts the atoms on the grid.
* This function only operates on one domain of the domain decompostion.
* Note that without domain decomposition there is only one domain.
c1[d] = zones->size[zone].bb_x1[d];
}
- nbnxn_put_on_grid(nbs, nbs->ePBC, NULL,
+ nbnxn_put_on_grid(nbs, nbs->ePBC, nullptr,
zone, c0, c1,
zones->cg_range[zone],
zones->cg_range[zone+1],
-1,
atinfo,
x,
- 0, NULL,
+ 0, nullptr,
nb_kernel_type,
nbat);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int stride, const real *x,
nbnxn_list_work_t *work);
-static gmx_icell_set_x_t icell_set_x_simple;
-#if GMX_SIMD
-static gmx_icell_set_x_t icell_set_x_simple_simd_4xn;
-static gmx_icell_set_x_t icell_set_x_simple_simd_2xnn;
-#endif
-static gmx_icell_set_x_t icell_set_x_supersub;
-
/* Local cycle count struct for profiling */
typedef struct {
int count;
} nbnxn_search_t_t;
-static void nbs_cycle_start(nbnxn_cycle_t *cc)
+static inline void nbs_cycle_start(nbnxn_cycle_t *cc)
{
cc->start = gmx_cycles_read();
}
-static void nbs_cycle_stop(nbnxn_cycle_t *cc)
+static inline void nbs_cycle_stop(nbnxn_cycle_t *cc)
{
cc->c += gmx_cycles_read() - cc->start;
cc->count++;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ *
+ * \brief
+ * Declares the nbnxn pair interaction kernel function types and kind counts, also declares utility functions used in nbnxn_kernel.cpp.
+ *
+ * \author Berk Hess <hess@kth.se>
+ */
+
#ifndef _nbnxn_kernel_common_h
#define _nbnxn_kernel_common_h
#include "gromacs/math/vectypes.h"
+/* nbnxn_atomdata_t and nbnxn_pairlist_t could be forward declared, but that requires modifications in all SIMD kernel files */
+#include "gromacs/mdlib/nbnxn_atomdata.h"
#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
+struct interaction_const_t;
-/* Clear the force buffer f. Either the whole buffer or only the parts
- * used by the current thread when nbat->bUseBufferFlags is set.
+/*! \brief Pair-interaction kernel type that also calculates energies.
+ */
+typedef void (nbk_func_ener)(const nbnxn_pairlist_t *nbl,
+ const nbnxn_atomdata_t *nbat,
+ const interaction_const_t *ic,
+ rvec *shift_vec,
+ real *f,
+ real *fshift,
+ real *Vvdw,
+ real *Vc);
+
+/*! \brief Pointer to \p nbk_func_ener.
+ */
+typedef nbk_func_ener *p_nbk_func_ener;
+
+/*! \brief Pair-interaction kernel type that does not calculates energies.
+ */
+typedef void (nbk_func_noener)(const nbnxn_pairlist_t *nbl,
+ const nbnxn_atomdata_t *nbat,
+ const interaction_const_t *ic,
+ rvec *shift_vec,
+ real *f,
+ real *fshift);
+
+/*! \brief Pointer to \p nbk_func_noener.
+ */
+typedef nbk_func_noener *p_nbk_func_noener;
+
+/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
+ */
+enum {
+ coulktRF, coulktTAB, coulktTAB_TWIN, coulktEWALD, coulktEWALD_TWIN, coulktNR
+};
+
+/*! \brief Kinds of Van der Waals treatments in SIMD Verlet kernels
+ *
+ * The \p LJCUT_COMB refers to the LJ combination rule for the short range.
+ * The \p EWALDCOMB refers to the combination rule for the grid part.
+ * \p vdwktNR is the number of VdW treatments for the SIMD kernels.
+ * \p vdwktNR_ref is the number of VdW treatments for the C reference kernels.
+ * These two numbers differ, because currently only the reference kernels
+ * support LB combination rules for the LJ-Ewald grid part.
+ */
+enum {
+ vdwktLJCUT_COMBGEOM, vdwktLJCUT_COMBLB, vdwktLJCUT_COMBNONE, vdwktLJFORCESWITCH, vdwktLJPOTSWITCH, vdwktLJEWALDCOMBGEOM, vdwktLJEWALDCOMBLB, vdwktNR = vdwktLJEWALDCOMBLB, vdwktNR_ref
+};
+
+/*! \brief Clears the force buffer.
+ *
+ * Either the whole buffer is cleared or only the parts used
+ * by the current thread when nbat->bUseBufferFlags is set.
* In the latter case output_index is the task/thread list/buffer index.
*/
void
clear_f(const nbnxn_atomdata_t *nbat, int output_index, real *f);
-/* Clear the shift forces */
+/*! \brief Clears the shift forces.
+ */
void
clear_fshift(real *fshift);
-/* Reduce the collected energy terms over the pair-lists/threads */
+/*! \brief Reduces the collected energy terms over the pair-lists/threads.
+ */
void
reduce_energies_over_lists(const nbnxn_atomdata_t *nbat,
int nlist,
real *Vvdw,
real *Vc);
-#if 0
-{
-#endif
-#ifdef __cplusplus
-}
-#endif
-
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_cpu.h"
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/force_flags.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
+
+#include "nbnxn_kernel_common.h"
+#define INCLUDE_KERNELFUNCTION_TABLES
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
+#ifdef GMX_NBNXN_SIMD_2XNN
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
+#endif
+#ifdef GMX_NBNXN_SIMD_4XN
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
+#endif
+#undef INCLUDE_FUNCTION_TABLES
+
+/*! \brief Clears the energy group output buffers
+ *
+ * \param[in,out] out nbnxn kernel output struct
+ */
+static void clearGroupEnergies(nbnxn_atomdata_output_t *out)
+{
+ for (int i = 0; i < out->nV; i++)
+ {
+ out->Vvdw[i] = 0;
+ out->Vc[i] = 0;
+ }
+
+ for (int i = 0; i < out->nVS; i++)
+ {
+ out->VSvdw[i] = 0;
+ }
+ for (int i = 0; i < out->nVS; i++)
+ {
+ out->VSc[i] = 0;
+ }
+}
+
+/*! \brief Reduce the group-pair energy buffers produced by a SIMD kernel
+ * to single terms in the output buffers.
+ *
+ * The SIMD kernels produce a large number of energy buffer in SIMD registers
+ * to avoid scattered reads and writes.
+ *
+ * \tparam unrollj The unroll size for j-particles in the SIMD kernel
+ * \param[in] numGroups The number of energy groups
+ * \param[in] numGroups_2log Log2 of numGroups, rounded up
+ * \param[in] vVdwSimd SIMD Van der Waals energy buffers
+ * \param[in] vCoulombSimd SIMD Coulomb energy buffers
+ * \param[in,out] vVdw Van der Waals energy output buffer
+ * \param[in,out] vCoulomb Coulomb energy output buffer
+ */
+template <int unrollj> static void
+reduceGroupEnergySimdBuffers(int numGroups,
+ int numGroups_2log,
+ const real * gmx_restrict vVdwSimd,
+ const real * gmx_restrict vCoulombSimd,
+ real * gmx_restrict vVdw,
+ real * gmx_restrict vCoulomb)
+{
+ // cppcheck-suppress duplicateExpression
+ const int unrollj_half = unrollj/2;
+ /* Energies are stored in SIMD registers with size 2^numGroups_2log */
+ const int numGroupsStorage = (1 << numGroups_2log);
+
+ /* The size of the SIMD energy group buffer array is:
+ * numGroups*numGroups*numGroupsStorage*unrollj_half*simd_width
+ */
+ for (int i = 0; i < numGroups; i++)
+ {
+ for (int j1 = 0; j1 < numGroups; j1++)
+ {
+ for (int j0 = 0; j0 < numGroups; j0++)
+ {
+ int c = ((i*numGroups + j1)*numGroupsStorage + j0)*unrollj_half*unrollj;
+ for (int s = 0; s < unrollj_half; s++)
+ {
+ vVdw [i*numGroups + j0] += vVdwSimd [c + 0];
+ vVdw [i*numGroups + j1] += vVdwSimd [c + 1];
+ vCoulomb[i*numGroups + j0] += vCoulombSimd[c + 0];
+ vCoulomb[i*numGroups + j1] += vCoulombSimd[c + 1];
+ c += unrollj + 2;
+ }
+ }
+ }
+ }
+}
+
+void
+nbnxn_kernel_cpu(nonbonded_verlet_group_t *nbvg,
+ const interaction_const_t *ic,
+ rvec *shiftVectors,
+ int forceFlags,
+ int clearF,
+ real *fshift,
+ real *vCoulomb,
+ real *vVdw)
+{
+ const nbnxn_atomdata_t *nbat = nbvg->nbat;
+
+ int coulkt;
+ if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
+ {
+ coulkt = coulktRF;
+ }
+ else
+ {
+ if (nbvg->ewald_excl == ewaldexclTable)
+ {
+ if (ic->rcoulomb == ic->rvdw)
+ {
+ coulkt = coulktTAB;
+ }
+ else
+ {
+ coulkt = coulktTAB_TWIN;
+ }
+ }
+ else
+ {
+ if (ic->rcoulomb == ic->rvdw)
+ {
+ coulkt = coulktEWALD;
+ }
+ else
+ {
+ coulkt = coulktEWALD_TWIN;
+ }
+ }
+ }
+
+ int vdwkt = 0;
+ if (ic->vdwtype == evdwCUT)
+ {
+ switch (ic->vdw_modifier)
+ {
+ case eintmodNONE:
+ case eintmodPOTSHIFT:
+ switch (nbat->comb_rule)
+ {
+ case ljcrGEOM: vdwkt = vdwktLJCUT_COMBGEOM; break;
+ case ljcrLB: vdwkt = vdwktLJCUT_COMBLB; break;
+ case ljcrNONE: vdwkt = vdwktLJCUT_COMBNONE; break;
+ default:
+ GMX_RELEASE_ASSERT(false, "Unknown combination rule");
+ }
+ break;
+ case eintmodFORCESWITCH:
+ vdwkt = vdwktLJFORCESWITCH;
+ break;
+ case eintmodPOTSWITCH:
+ vdwkt = vdwktLJPOTSWITCH;
+ break;
+ default:
+ GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction modifier");
+ }
+ }
+ else if (ic->vdwtype == evdwPME)
+ {
+ if (ic->ljpme_comb_rule == eljpmeGEOM)
+ {
+ vdwkt = vdwktLJEWALDCOMBGEOM;
+ }
+ else
+ {
+ vdwkt = vdwktLJEWALDCOMBLB;
+ /* At setup we (should have) selected the C reference kernel */
+ GMX_RELEASE_ASSERT(nbvg->kernel_type == nbnxnk4x4_PlainC, "Only the C reference nbnxn SIMD kernel supports LJ-PME with LB combination rules");
+ }
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(false, "Unsupported VdW interaction type");
+ }
+
+ int nnbl = nbvg->nbl_lists.nnbl;
+ nbnxn_pairlist_t **nbl = nbvg->nbl_lists.nbl;
+
+ GMX_ASSERT(nbl[0]->nci >= 0, "nci<0, which signals an invalid pair-list");
+
+ // cppcheck-suppress unreadVariable
+ int gmx_unused nthreads = gmx_omp_nthreads_get(emntNonbonded);
+#pragma omp parallel for schedule(static) num_threads(nthreads)
+ for (int nb = 0; nb < nnbl; nb++)
+ {
+ // Presently, the kernels do not call C++ code that can throw,
+ // so no need for a try/catch pair in this OpenMP region.
+ nbnxn_atomdata_output_t *out = &nbat->out[nb];
+
+ if (clearF == enbvClearFYes)
+ {
+ clear_f(nbat, nb, out->f);
+ }
+
+ real *fshift_p;
+ if ((forceFlags & GMX_FORCE_VIRIAL) && nnbl == 1)
+ {
+ fshift_p = fshift;
+ }
+ else
+ {
+ fshift_p = out->fshift;
+
+ if (clearF == enbvClearFYes)
+ {
+ clear_fshift(fshift_p);
+ }
+ }
+
+ if (!(forceFlags & GMX_FORCE_ENERGY))
+ {
+ /* Don't calculate energies */
+ switch (nbvg->kernel_type)
+ {
+ case nbnxnk4x4_PlainC:
+ nbnxn_kernel_noener_ref[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p);
+ break;
+#ifdef GMX_NBNXN_SIMD_2XNN
+ case nbnxnk4xN_SIMD_2xNN:
+ nbnxn_kernel_noener_simd_2xnn[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p);
+ break;
+#endif
+#ifdef GMX_NBNXN_SIMD_4XN
+ case nbnxnk4xN_SIMD_4xN:
+ nbnxn_kernel_noener_simd_4xn[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p);
+ break;
+#endif
+ default:
+ GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
+ }
+ }
+ else if (out->nV == 1)
+ {
+ /* A single energy group (pair) */
+ out->Vvdw[0] = 0;
+ out->Vc[0] = 0;
+
+ switch (nbvg->kernel_type)
+ {
+ case nbnxnk4x4_PlainC:
+ nbnxn_kernel_ener_ref[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p,
+ out->Vvdw,
+ out->Vc);
+ break;
+#ifdef GMX_NBNXN_SIMD_2XNN
+ case nbnxnk4xN_SIMD_2xNN:
+ nbnxn_kernel_ener_simd_2xnn[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p,
+ out->Vvdw,
+ out->Vc);
+ break;
+#endif
+#ifdef GMX_NBNXN_SIMD_4XN
+ case nbnxnk4xN_SIMD_4xN:
+ nbnxn_kernel_ener_simd_4xn[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p,
+ out->Vvdw,
+ out->Vc);
+ break;
+#endif
+ default:
+ GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
+ }
+ }
+ else
+ {
+ /* Calculate energy group contributions */
+ clearGroupEnergies(out);
+
+ int unrollj = 0;
+
+ switch (nbvg->kernel_type)
+ {
+ case nbnxnk4x4_PlainC:
+ unrollj = NBNXN_CPU_CLUSTER_I_SIZE;
+ nbnxn_kernel_energrp_ref[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p,
+ out->Vvdw,
+ out->Vc);
+ break;
+#ifdef GMX_NBNXN_SIMD_2XNN
+ case nbnxnk4xN_SIMD_2xNN:
+ unrollj = GMX_SIMD_REAL_WIDTH/2;
+ nbnxn_kernel_energrp_simd_2xnn[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p,
+ out->VSvdw,
+ out->VSc);
+ break;
+#endif
+#ifdef GMX_NBNXN_SIMD_4XN
+ case nbnxnk4xN_SIMD_4xN:
+ unrollj = GMX_SIMD_REAL_WIDTH;
+ nbnxn_kernel_energrp_simd_4xn[coulkt][vdwkt](nbl[nb], nbat,
+ ic,
+ shiftVectors,
+ out->f,
+ fshift_p,
+ out->VSvdw,
+ out->VSc);
+ break;
+#endif
+ default:
+ GMX_RELEASE_ASSERT(false, "Unsupported kernel architecture");
+ }
+
+ if (nbvg->kernel_type != nbnxnk4x4_PlainC)
+ {
+ switch (unrollj)
+ {
+ case 2:
+ reduceGroupEnergySimdBuffers<2>(nbat->nenergrp,
+ nbat->neg_2log,
+ out->VSvdw, out->VSc,
+ out->Vvdw, out->Vc);
+ break;
+ case 4:
+ reduceGroupEnergySimdBuffers<4>(nbat->nenergrp,
+ nbat->neg_2log,
+ out->VSvdw, out->VSc,
+ out->Vvdw, out->Vc);
+ break;
+ case 8:
+ reduceGroupEnergySimdBuffers<8>(nbat->nenergrp,
+ nbat->neg_2log,
+ out->VSvdw, out->VSc,
+ out->Vvdw, out->Vc);
+ break;
+ default:
+ GMX_RELEASE_ASSERT(false, "Unsupported j-unroll size");
+ }
+ }
+ }
+ }
+
+ if (forceFlags & GMX_FORCE_ENERGY)
+ {
+ reduce_energies_over_lists(nbat, nnbl, vVdw, vCoulomb);
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ *
+ * \brief
+ * Declares the nbnxn pair interaction kernel dispatcher.
+ *
+ * \author Berk Hess <hess@kth.se>
+ */
+
+#ifndef _nbnxn_kernel_cpu_h
+#define _nbnxn_kernel_cpu_h
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
+
+struct interaction_const_t;
+struct nonbonded_verlet_group_t;
+
+/*! \brief Dispatches the non-bonded N versus M atom cluster CPU kernels.
+ *
+ * OpenMP parallelization is performed within this function.
+ * Energy reduction, but not force and shift force reduction, is performed
+ * within this function.
+ *
+ * \param[in,out] nbvg The group (local/non-local) to compute interaction for
+ * \param[in] ic Non-bonded interaction constants
+ * \param[in] shiftVectors The PBC shift vectors
+ * \param[in] forceFlags Flags that tell what to compute
+ * \param[in] clearF Enum that tells if to clear the force output buffer
+ * \param[out] fshift Shift force output buffer
+ * \param[out] vCoulomb Output buffer for Coulomb energies
+ * \param[out] vVdw Output buffer for Van der Waals energies
+ */
+void
+nbnxn_kernel_cpu(nonbonded_verlet_group_t *nbvg,
+ const interaction_const_t *ic,
+ rvec *shiftVectors,
+ int forceFlags,
+ int clearF,
+ real *fshift,
+ real *vCoulomb,
+ real *vVdw);
+
+#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# are:
#
# A single header file that declares all the kernel functions for
-# this nbnxn kernel structure type, including the function that does
-# the dispatch via the function pointer table.
-#
-# A single C kernel dispatcher file that defines the function that
-# decides at run time which kernel to call.
+# this nbnxn kernel structure type and a function pointer table.
#
# Many C kernel files, each defining a single kernel function. These
# functions can take a noticeable time to compile, and should tend
},
}
-KernelDispatcherTemplate = read_kernel_template("nbnxn_kernel_simd_template.cpp.pre")
KernelsHeaderTemplate = read_kernel_template("nbnxn_kernel_simd_template.h.pre")
-# For each Verlet kernel type, write three kinds of files:
-# a header file defining the functions for all the kernels,
-# a code file containing the kernel function lookup table and
-# the kernel dispatcher function
+# For each Verlet kernel type, write two kinds of files:
+# a header file defining the functions for all the kernels and
+# the kernel function lookup table
# for each kernel, a file defining the single C function for that kernel
for type in VerletKernelTypeDict:
DirName = "../simd_{0}".format(type)
with open('{0}/{1}'.format(DirName,KernelsHeaderFileName),'w') as fp:
fp.write(FileHeader.format(type))
fp.write(KernelsHeaderTemplate
- .format(KernelsName,
- " " * (len(KernelsName) + 1),
- KernelDeclarations))
-
- # Write the file defining the kernel dispatcher
- # function for this type
- with open('{0}/{1}'.format(DirName,"{0}.cpp".format(KernelsName,type)),'w') as fp:
- fp.write(FileHeader.format(type))
- fp.write(KernelDispatcherTemplate
- .format(VerletKernelTypeDict[type]['Define'],
- VerletKernelTypeDict[type]['WidthSetup'],
- VerletKernelTypeDict[type]['WidthCheck'],
- VerletKernelTypeDict[type]['UnrollSize'],
- KernelsHeaderFileName,
- KernelsName,
- ' ' * (len(KernelsName)+1),
+ .format(KernelDeclarations,
+ type,
KernelFunctionLookupTable['F'],
KernelFunctionLookupTable['VF'],
- KernelFunctionLookupTable['VgrpF'],
- )
+ KernelFunctionLookupTable['VgrpF'])
)
sys.exit()
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_simd.h"
-#include "gromacs/mdtypes/interaction_const.h"
-#include "gromacs/mdtypes/md_enums.h"
-
-#ifdef {0}
-
-{1}#include "gromacs/simd/vector_operations.h"
-
-{2}
-#define GMX_SIMD_J_UNROLL_SIZE {3}
-#include "{4}"
-
-#include "gromacs/mdlib/force_flags.h"
-#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
-#include "gromacs/simd/simd.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/real.h"
-
-/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
- */
-enum {{
- coulktRF, coulktTAB, coulktTAB_TWIN, coulktEWALD, coulktEWALD_TWIN, coulktNR
-}};
-
-/*! \brief Kinds of Van der Waals treatments in SIMD Verlet kernels
- */
-enum {{
- vdwktLJCUT_COMBGEOM, vdwktLJCUT_COMBLB, vdwktLJCUT_COMBNONE, vdwktLJFORCESWITCH, vdwktLJPOTSWITCH, vdwktLJEWALDCOMBGEOM, vdwktNR
-}};
-
-/* Declare and define the kernel function pointer lookup tables.
- * The minor index of the array goes over both the LJ combination rules,
- * which is only supported by plain cut-off, and the LJ switch/PME functions.
- */
-static p_nbk_func_noener p_nbk_noener[coulktNR][vdwktNR] =
-{7}
-static p_nbk_func_ener p_nbk_ener[coulktNR][vdwktNR] =
-{8}
-static p_nbk_func_ener p_nbk_energrp[coulktNR][vdwktNR] =
-{9}
-
-static void
-reduce_group_energies(int ng, int ng_2log,
- const real *VSvdw, const real *VSc,
- real *Vvdw, real *Vc)
-{{
- const int unrollj = GMX_SIMD_REAL_WIDTH/GMX_SIMD_J_UNROLL_SIZE;
- const int unrollj_half = unrollj/2;
- int ng_p2, i, j, j0, j1, c, s;
-
- ng_p2 = (1<<ng_2log);
-
- /* The size of the x86 SIMD energy group buffer array is:
- * ng*ng*ng_p2*unrollj_half*simd_width
- */
- for (i = 0; i < ng; i++)
- {{
- for (j = 0; j < ng; j++)
- {{
- Vvdw[i*ng+j] = 0;
- Vc[i*ng+j] = 0;
- }}
-
- for (j1 = 0; j1 < ng; j1++)
- {{
- for (j0 = 0; j0 < ng; j0++)
- {{
- c = ((i*ng + j1)*ng_p2 + j0)*unrollj_half*unrollj;
- for (s = 0; s < unrollj_half; s++)
- {{
- Vvdw[i*ng+j0] += VSvdw[c+0];
- Vvdw[i*ng+j1] += VSvdw[c+1];
- Vc [i*ng+j0] += VSc [c+0];
- Vc [i*ng+j1] += VSc [c+1];
- c += unrollj + 2;
- }}
- }}
- }}
- }}
-}}
-
-#else /* {0} */
-
-#include "gromacs/utility/fatalerror.h"
-
-#endif /* {0} */
-
-void
-{5}(nbnxn_pairlist_set_t gmx_unused *nbl_list,
-{6}const nbnxn_atomdata_t gmx_unused *nbat,
-{6}const interaction_const_t gmx_unused *ic,
-{6}int gmx_unused ewald_excl,
-{6}rvec gmx_unused *shift_vec,
-{6}int gmx_unused force_flags,
-{6}int gmx_unused clearF,
-{6}real gmx_unused *fshift,
-{6}real gmx_unused *Vc,
-{6}real gmx_unused *Vvdw)
-#ifdef {0}
-{{
- int nnbl;
- nbnxn_pairlist_t **nbl;
- int coulkt, vdwkt = 0;
- int nb, nthreads;
-
- nnbl = nbl_list->nnbl;
- nbl = nbl_list->nbl;
-
- if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
- {{
- coulkt = coulktRF;
- }}
- else
- {{
- if (ewald_excl == ewaldexclTable)
- {{
- if (ic->rcoulomb == ic->rvdw)
- {{
- coulkt = coulktTAB;
- }}
- else
- {{
- coulkt = coulktTAB_TWIN;
- }}
- }}
- else
- {{
- if (ic->rcoulomb == ic->rvdw)
- {{
- coulkt = coulktEWALD;
- }}
- else
- {{
- coulkt = coulktEWALD_TWIN;
- }}
- }}
- }}
-
- if (ic->vdwtype == evdwCUT)
- {{
- switch (ic->vdw_modifier)
- {{
- case eintmodNONE:
- case eintmodPOTSHIFT:
- switch (nbat->comb_rule)
- {{
- case ljcrGEOM: vdwkt = vdwktLJCUT_COMBGEOM; break;
- case ljcrLB: vdwkt = vdwktLJCUT_COMBLB; break;
- case ljcrNONE: vdwkt = vdwktLJCUT_COMBNONE; break;
- default: gmx_incons("Unknown combination rule");
- }}
- break;
- case eintmodFORCESWITCH:
- vdwkt = vdwktLJFORCESWITCH;
- break;
- case eintmodPOTSWITCH:
- vdwkt = vdwktLJPOTSWITCH;
- break;
- default:
- gmx_incons("Unsupported VdW interaction modifier");
- }}
- }}
- else if (ic->vdwtype == evdwPME)
- {{
- if (ic->ljpme_comb_rule == eljpmeLB)
- {{
- gmx_incons("The nbnxn SIMD kernels don't support LJ-PME with LB");
- }}
- vdwkt = vdwktLJEWALDCOMBGEOM;
- }}
- else
- {{
- gmx_incons("Unsupported VdW interaction type");
- }}
- // cppcheck-suppress unreadVariable
- nthreads = gmx_omp_nthreads_get(emntNonbonded);
-#pragma omp parallel for schedule(static) num_threads(nthreads)
- for (nb = 0; nb < nnbl; nb++)
- {{
- // Presently, the kernels do not call C++ code that can throw, so
- // no need for a try/catch pair in this OpenMP region.
- nbnxn_atomdata_output_t *out;
- real *fshift_p;
-
- out = &nbat->out[nb];
-
- if (clearF == enbvClearFYes)
- {{
- clear_f(nbat, nb, out->f);
- }}
-
- if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
- {{
- fshift_p = fshift;
- }}
- else
- {{
- fshift_p = out->fshift;
-
- if (clearF == enbvClearFYes)
- {{
- clear_fshift(fshift_p);
- }}
- }}
-
- if (!(force_flags & GMX_FORCE_ENERGY))
- {{
- /* Don't calculate energies */
- p_nbk_noener[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p);
- }}
- else if (out->nV == 1)
- {{
- /* No energy groups */
- out->Vvdw[0] = 0;
- out->Vc[0] = 0;
-
- p_nbk_ener[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->Vvdw,
- out->Vc);
- }}
- else
- {{
- /* Calculate energy group contributions */
- int i;
-
- for (i = 0; i < out->nVS; i++)
- {{
- out->VSvdw[i] = 0;
- }}
- for (i = 0; i < out->nVS; i++)
- {{
- out->VSc[i] = 0;
- }}
-
- p_nbk_energrp[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->VSvdw,
- out->VSc);
-
- reduce_group_energies(nbat->nenergrp, nbat->neg_2log,
- out->VSvdw, out->VSc,
- out->Vvdw, out->Vc);
- }}
- }}
-
- if (force_flags & GMX_FORCE_ENERGY)
- {{
- reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
- }}
-}}
-#else
-{{
- gmx_incons("{5} called when such kernels "
- " are not enabled.");
-}}
-#endif
-#undef GMX_SIMD_J_UNROLL_SIZE
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
-#include "gromacs/mdtypes/interaction_const.h"
-#include "gromacs/utility/real.h"
-/*! \brief Run-time dispatcher for nbnxn kernel functions. */
-void
-{0}(nbnxn_pairlist_set_t *nbl_list,
-{1}const nbnxn_atomdata_t *nbat,
-{1}const interaction_const_t *ic,
-{1}int ewald_excl,
-{1}rvec *shift_vec,
-{1}int force_flags,
-{1}int clearF,
-{1}real *fshift,
-{1}real *Vc,
-{1}real *Vvdw);
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
-/* Need an #include guard so that sim_util.c can include all
- * such files. */
-#ifndef _nbnxn_kernel_simd_include_h
-#define _nbnxn_kernel_simd_include_h
-/*! \brief Typedefs for declaring kernel functions. */
-typedef void (nbk_func_ener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift,
- real *Vvdw,
- real *Vc);
-typedef nbk_func_ener *p_nbk_func_ener;
+/* Declare all the different kernel functions.
+ */
+{0}
-typedef void (nbk_func_noener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift);
-typedef nbk_func_noener *p_nbk_func_noener;
-#endif
+#ifdef INCLUDE_KERNELFUNCTION_TABLES
+/* Declare and define the kernel function pointer lookup tables.
+ * The minor index of the array goes over both the LJ combination rules,
+ * which is only supported by plain cut-off, and the LJ switch/PME functions.
+ */
+p_nbk_func_noener nbnxn_kernel_noener_simd_{1}[coulktNR][vdwktNR] =
{2}
+p_nbk_func_ener nbnxn_kernel_ener_simd_{1}[coulktNR][vdwktNR] =
+{3}
+p_nbk_func_ener nbnxn_kernel_energrp_simd_{1}[coulktNR][vdwktNR] =
+{4}
+
+#endif /* INCLUDE_KERNELFUNCTION_TABLES */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_consts.h"
-#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/fatalerror.h"
+#include "nbnxn_kernel_common.h"
+
static const int c_numClPerSupercl = c_nbnxnGpuNumClusterPerSupercluster;
static const int c_clSize = c_nbnxnGpuClusterSize;
const real *x;
gmx_bool bEner;
gmx_bool bEwald;
- const real *Ftab = NULL;
+ const real *Ftab = nullptr;
real rcut2, rvdw2, rlist2;
int ntype;
real facel;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_prune.h"
+
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/utility/gmxassert.h"
+
+#include "nbnxn_kernel_ref_prune.h"
+#include "simd_2xnn/nbnxn_kernel_simd_2xnn_prune.h"
+#include "simd_4xn/nbnxn_kernel_simd_4xn_prune.h"
+
+
+void nbnxn_kernel_cpu_prune(nonbonded_verlet_group_t *nbvg,
+ const rvec *shift_vec,
+ real rlistInner)
+{
+ nbnxn_pairlist_set_t *nbl_lists = &nbvg->nbl_lists;
+ const nbnxn_atomdata_t *nbat = nbvg->nbat;
+
+ GMX_ASSERT(nbl_lists->nbl[0]->nciOuter >= 0, "nciOuter<0, which signals an invalid pair-list");
+
+ // cppcheck-suppress unreadVariable
+ int gmx_unused nthreads = gmx_omp_nthreads_get(emntNonbonded);
+#pragma omp parallel for schedule(static) num_threads(nthreads)
+ for (int i = 0; i < nbl_lists->nnbl; i++)
+ {
+ nbnxn_pairlist_t *nbl = nbl_lists->nbl[i];
+
+ switch (nbvg->kernel_type)
+ {
+ case nbnxnk4xN_SIMD_4xN:
+ nbnxn_kernel_prune_4xn(nbl, nbat, shift_vec, rlistInner);
+ break;
+ case nbnxnk4xN_SIMD_2xNN:
+ nbnxn_kernel_prune_2xnn(nbl, nbat, shift_vec, rlistInner);
+ break;
+ case nbnxnk4x4_PlainC:
+ nbnxn_kernel_prune_ref(nbl, nbat, shift_vec, rlistInner);
+ break;
+ default:
+ GMX_RELEASE_ASSERT(false, "kernel type not handled (yet)");
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ *
+ * \brief
+ * Declares the pair-list pruning kernel wrapper function.
+ *
+ * The wrapper function internally performs the OpenMP parallelization
+ * and calls the selected kernel flavor (different SIMD types / C reference).
+ *
+ * \author Berk Hess <hess@kth.se>
+ */
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/real.h"
+
+struct nonbonded_verlet_group_t;
+
+/*! \brief Prune all pair-lists in the set with distance \p rlistInner
+ *
+ * For all pair-lists in the set takes the outer list and prunes out
+ * pairs beyond \p rlistInner and writes the result to a list that is
+ * to be consumed by the non-bonded kernel.
+ */
+void nbnxn_kernel_cpu_prune(nonbonded_verlet_group_t *nbvg,
+ const rvec *shift_vec,
+ real rlistInner);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_consts.h"
-#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
-/*! \brief Typedefs for declaring lookup tables of kernel functions.
- */
-
-typedef void (*p_nbk_func_noener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift);
-
-typedef void (*p_nbk_func_ener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift,
- real *Vvdw,
- real *Vc);
/* Analytical reaction-field kernels */
#define CALC_COUL_RF
#undef LJ_EWALD
#undef VDW_CUTOFF_CHECK
#undef CALC_COUL_TAB
-
-
-enum {
- coultRF, coultTAB, coultTAB_TWIN, coultNR
-};
-
-enum {
- vdwtCUT, vdwtFSWITCH, vdwtPSWITCH, vdwtEWALDGEOM, vdwtEWALDLB, vdwtNR
-};
-
-p_nbk_func_noener p_nbk_c_noener[coultNR][vdwtNR] =
-{
- { nbnxn_kernel_ElecRF_VdwLJ_F_ref, nbnxn_kernel_ElecRF_VdwLJFsw_F_ref, nbnxn_kernel_ElecRF_VdwLJPsw_F_ref, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref },
- { nbnxn_kernel_ElecQSTab_VdwLJ_F_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref, nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref }
-};
-
-p_nbk_func_ener p_nbk_c_ener[coultNR][vdwtNR] =
-{
- { nbnxn_kernel_ElecRF_VdwLJ_VF_ref, nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref, nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref },
- { nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref }
-};
-
-p_nbk_func_ener p_nbk_c_energrp[coultNR][vdwtNR] =
-{
- { nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref, nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref },
- { nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref, nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref },
- { nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref, nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref }
-};
-
-void
-nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- int force_flags,
- int clearF,
- real *fshift,
- real *Vc,
- real *Vvdw)
-{
- int nnbl;
- nbnxn_pairlist_t **nbl;
- int coult;
- int vdwt;
- int nb;
- int nthreads gmx_unused;
-
- nnbl = nbl_list->nnbl;
- nbl = nbl_list->nbl;
-
- if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
- {
- coult = coultRF;
- }
- else
- {
- if (ic->rcoulomb == ic->rvdw)
- {
- coult = coultTAB;
- }
- else
- {
- coult = coultTAB_TWIN;
- }
- }
-
- if (ic->vdwtype == evdwCUT)
- {
- switch (ic->vdw_modifier)
- {
- case eintmodPOTSHIFT:
- case eintmodNONE:
- vdwt = vdwtCUT;
- break;
- case eintmodFORCESWITCH:
- vdwt = vdwtFSWITCH;
- break;
- case eintmodPOTSWITCH:
- vdwt = vdwtPSWITCH;
- break;
- default:
- gmx_incons("Unsupported VdW modifier");
- break;
- }
- }
- else if (ic->vdwtype == evdwPME)
- {
- if (ic->ljpme_comb_rule == ljcrGEOM)
- {
- assert(nbat->comb_rule == ljcrGEOM);
- vdwt = vdwtEWALDGEOM;
- }
- else
- {
- assert(nbat->comb_rule == ljcrLB);
- vdwt = vdwtEWALDLB;
- }
- }
- else
- {
- gmx_incons("Unsupported vdwtype in nbnxn reference kernel");
- }
-
- // cppcheck-suppress unreadVariable
- nthreads = gmx_omp_nthreads_get(emntNonbonded);
-#pragma omp parallel for schedule(static) num_threads(nthreads)
- for (nb = 0; nb < nnbl; nb++)
- {
- // Presently, the kernels do not call C++ code that can throw, so
- // no need for a try/catch pair in this OpenMP region.
- nbnxn_atomdata_output_t *out;
- real *fshift_p;
-
- out = &nbat->out[nb];
-
- if (clearF == enbvClearFYes)
- {
- clear_f(nbat, nb, out->f);
- }
-
- if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
- {
- fshift_p = fshift;
- }
- else
- {
- fshift_p = out->fshift;
-
- if (clearF == enbvClearFYes)
- {
- clear_fshift(fshift_p);
- }
- }
-
- if (!(force_flags & GMX_FORCE_ENERGY))
- {
- /* Don't calculate energies */
- p_nbk_c_noener[coult][vdwt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p);
- }
- else if (out->nV == 1)
- {
- /* No energy groups */
- out->Vvdw[0] = 0;
- out->Vc[0] = 0;
-
- p_nbk_c_ener[coult][vdwt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->Vvdw,
- out->Vc);
- }
- else
- {
- /* Calculate energy group contributions */
- int i;
-
- for (i = 0; i < out->nV; i++)
- {
- out->Vvdw[i] = 0;
- }
- for (i = 0; i < out->nV; i++)
- {
- out->Vc[i] = 0;
- }
-
- p_nbk_c_energrp[coult][vdwt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->Vvdw,
- out->Vc);
- }
- }
-
- if (force_flags & GMX_FORCE_ENERGY)
- {
- reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
- }
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef _nbnxn_kernel_ref_h
-#define _nbnxn_kernel_ref_h
+#include "nbnxn_kernel_common.h"
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
-#include "gromacs/mdtypes/forcerec.h"
-#include "gromacs/utility/real.h"
+/* Declare all the different kernel functions.
+ */
+nbk_func_noener nbnxn_kernel_ElecRF_VdwLJ_F_ref;
+nbk_func_noener nbnxn_kernel_ElecRF_VdwLJFsw_F_ref;
+nbk_func_noener nbnxn_kernel_ElecRF_VdwLJPsw_F_ref;
+nbk_func_noener nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref;
+nbk_func_noener nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTab_VdwLJ_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref;
+nbk_func_noener nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref;
+
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJ_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref;
+
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref;
+nbk_func_ener nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref;
-#ifdef __cplusplus
-extern "C" {
-#endif
+#ifdef INCLUDE_KERNELFUNCTION_TABLES
+
+/* Declare and define the kernel function pointer lookup tables.
+ * The minor index of the array goes over both the LJ combination rules,
+ * which is only supported by plain cut-off, and the LJ switch/PME functions.
+ * For the C reference kernels, unlike the SIMD kernels, there is not much
+ * advantage in using combination rules, so we (re-)use the same kernel.
+ */
+p_nbk_func_noener nbnxn_kernel_noener_ref[coulktNR][vdwktNR_ref] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJ_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombLB_F_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_F_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_F_ref
+ }
+};
-/* Wrapper call for the non-bonded n vs n reference kernels */
-void
-nbnxn_kernel_ref(const nbnxn_pairlist_set_t *nbl_list,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- int force_flags,
- int clearF,
- real *fshift,
- real *Vc,
- real *Vvdw);
+p_nbk_func_ener nbnxn_kernel_ener_ref[coulktNR][vdwktNR_ref] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombLB_VF_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VF_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VF_ref
+ }
+};
-#ifdef __cplusplus
-}
-#endif
+p_nbk_func_ener nbnxn_kernel_energrp_ref[coulktNR][vdwktNR_ref] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_ref,
+ nbnxn_kernel_ElecRF_VdwLJEwCombLB_VgrpF_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_ref,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombLB_VgrpF_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPsw_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_ref,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombLB_VgrpF_ref
+ }
+};
-#endif
+#endif /* INCLUDE_KERNELFUNCTION_TABLES */
{
real skipmask_rvdw;
- skipmask_rvdw = (rsq < rvdw2);
+ skipmask_rvdw = (rsq < rvdw2) ? 1.0 : 0.0;
frLJ *= skipmask_rvdw;
#ifdef CALC_ENERGIES
VLJ *= skipmask_rvdw;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#error "No VdW type defined"
#endif
-static void
+void
#ifndef CALC_ENERGIES
NBK_FUNC_NAME(_F)
#else
const nbnxn_atomdata_t *nbat,
const interaction_const_t *ic,
rvec *shift_vec,
- real *f
-#ifdef CALC_SHIFTFORCES
- ,
- real *fshift
-#endif
+ real *f,
+ real gmx_unused *fshift
#ifdef CALC_ENERGIES
,
real *Vvdw,
}
}
#ifdef CALC_SHIFTFORCES
- if (fshift != NULL)
+ if (fshift != nullptr)
{
/* Add i forces to shifted force list */
for (i = 0; i < UNROLLI; i++)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_ref_prune.h"
+
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/utility/gmxassert.h"
+
+
+/* Prune a single nbnxn_pairlist_t entry with distance rlistInner */
+void
+nbnxn_kernel_prune_ref(nbnxn_pairlist_t * nbl,
+ const nbnxn_atomdata_t * nbat,
+ const rvec * gmx_restrict shift_vec,
+ real rlistInner)
+{
+ const nbnxn_ci_t * gmx_restrict ciOuter = nbl->ciOuter;
+ nbnxn_ci_t * gmx_restrict ciInner = nbl->ci;
+
+ const nbnxn_cj_t * gmx_restrict cjOuter = nbl->cjOuter;
+ nbnxn_cj_t * gmx_restrict cjInner = nbl->cj;
+
+ const real * gmx_restrict shiftvec = shift_vec[0];
+ const real * gmx_restrict x = nbat->x;
+
+ const real rlist2 = rlistInner*rlistInner;
+
+ /* Use compile time constants to speed up the code */
+ constexpr int c_xStride = 3;
+ GMX_ASSERT(c_xStride == nbat->xstride, "xStride should match nbat->xstride");
+ constexpr int c_xiStride = 3;
+
+ constexpr int c_iUnroll = NBNXN_CPU_CLUSTER_I_SIZE;
+ constexpr int c_jUnroll = NBNXN_CPU_CLUSTER_I_SIZE;
+
+ /* Initialize the new list as empty and add pairs that are in range */
+ int nciInner = 0;
+ int ncjInner = 0;
+ for (int ciIndex = 0; ciIndex < nbl->nciOuter; ciIndex++)
+ {
+ const nbnxn_ci_t * gmx_restrict ciEntry = &ciOuter[ciIndex];
+
+ /* Copy the original list entry to the pruned entry */
+ ciInner[nciInner].ci = ciEntry->ci;
+ ciInner[nciInner].shift = ciEntry->shift;
+ ciInner[nciInner].cj_ind_start = ncjInner;
+
+ /* Extract shift data */
+ int ish = (ciEntry->shift & NBNXN_CI_SHIFT);
+ int ci = ciEntry->ci;
+
+ /* Load i atom coordinates */
+ real xi[c_iUnroll*c_xiStride];
+ for (int i = 0; i < c_iUnroll; i++)
+ {
+ for (int d = 0; d < DIM; d++)
+ {
+ xi[i*c_xiStride + d] = x[(ci*c_iUnroll + i)*c_xStride + d] + shiftvec[ish*DIM + d];
+ }
+ }
+
+ for (int cjind = ciEntry->cj_ind_start; cjind < ciEntry->cj_ind_end; cjind++)
+ {
+ /* j-cluster index */
+ int cj = cjOuter[cjind].cj;
+
+ bool isInRange = false;
+ for (int i = 0; i < c_iUnroll && !isInRange; i++)
+ {
+ for (int j = 0; j < c_jUnroll; j++)
+ {
+ int aj = cj*c_jUnroll + j;
+
+ real dx = xi[i*c_xiStride + XX] - x[aj*c_xStride + XX];
+ real dy = xi[i*c_xiStride + YY] - x[aj*c_xStride + YY];
+ real dz = xi[i*c_xiStride + ZZ] - x[aj*c_xStride + ZZ];
+
+ real rsq = dx*dx + dy*dy + dz*dz;
+
+ if (rsq < rlist2)
+ {
+ isInRange = true;
+ }
+ }
+ }
+
+ if (isInRange)
+ {
+ /* This cluster is in range, put it in the pruned list */
+ cjInner[ncjInner++] = cjOuter[cjind];
+ }
+ }
+
+ /* Check if there are any j's in the list, if so, add the i-entry */
+ if (ncjInner > ciInner[nciInner].cj_ind_start)
+ {
+ ciInner[nciInner].cj_ind_end = ncjInner;
+ nciInner++;
+ }
+ }
+
+ nbl->nci = nciInner;
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief
+ * Declares the C reference pruning only kernel.
+ *
+ * \author Berk Hess <hess@kth.se>
+ */
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct nbnxn_atomdata_t;
+struct nbnxn_pairlist_t;
+
+/*! \brief Prune a single nbnxn_pairlist_t entry with distance \p rlistInner
+ *
+ * Reads a cluster pairlist \p nbl->ciOuter, \p nbl->cjOuter and writes
+ * all cluster pairs within \p rlistInner to \p nbl->ci, \p nbl->cj.
+ */
+void
+nbnxn_kernel_prune_ref(nbnxn_pairlist_t * nbl,
+ const nbnxn_atomdata_t * nbat,
+ const rvec * gmx_restrict shift_vec,
+ real rlistInner);
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the Verlet kernel generator for
- * kernel type 2xnn.
- */
-
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_simd.h"
-#include "gromacs/mdtypes/interaction_const.h"
-#include "gromacs/mdtypes/md_enums.h"
-
-#ifdef GMX_NBNXN_SIMD_2XNN
-
-/* Include the full-width SIMD macros */
-#include "gromacs/simd/vector_operations.h"
-
-#if !(GMX_SIMD_REAL_WIDTH == 8 || GMX_SIMD_REAL_WIDTH == 16)
-#error "unsupported SIMD width"
-#endif
-
-#define GMX_SIMD_J_UNROLL_SIZE 2
-#include "nbnxn_kernel_simd_2xnn.h"
-
-#include "gromacs/mdlib/force_flags.h"
-#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
-#include "gromacs/simd/simd.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/real.h"
-
-/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
- */
-enum {
- coulktRF, coulktTAB, coulktTAB_TWIN, coulktEWALD, coulktEWALD_TWIN, coulktNR
-};
-
-/*! \brief Kinds of Van der Waals treatments in SIMD Verlet kernels
- */
-enum {
- vdwktLJCUT_COMBGEOM, vdwktLJCUT_COMBLB, vdwktLJCUT_COMBNONE, vdwktLJFORCESWITCH, vdwktLJPOTSWITCH, vdwktLJEWALDCOMBGEOM, vdwktNR
-};
-
-/* Declare and define the kernel function pointer lookup tables.
- * The minor index of the array goes over both the LJ combination rules,
- * which is only supported by plain cut-off, and the LJ switch/PME functions.
- */
-static p_nbk_func_noener p_nbk_noener[coulktNR][vdwktNR] =
-{
- {
- nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn,
- nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn,
- nbnxn_kernel_ElecRF_VdwLJ_F_2xnn,
- nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn,
- nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn,
- },
- {
- nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn,
- },
- {
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn,
- },
- {
- nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn,
- nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn,
- nbnxn_kernel_ElecEw_VdwLJ_F_2xnn,
- nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn,
- nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn,
- nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn,
- },
- {
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn,
- },
-};
-
-static p_nbk_func_ener p_nbk_ener[coulktNR][vdwktNR] =
-{
- {
- nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn,
- },
- {
- nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn,
- },
- {
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn,
- },
- {
- nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn,
- },
- {
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn,
- },
-};
-
-static p_nbk_func_ener p_nbk_energrp[coulktNR][vdwktNR] =
-{
- {
- nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn,
- },
- {
- nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn,
- },
- {
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn,
- },
- {
- nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn,
- nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn,
- },
- {
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn,
- },
-};
-
-
-static void
-reduce_group_energies(int ng, int ng_2log,
- const real *VSvdw, const real *VSc,
- real *Vvdw, real *Vc)
-{
- const int unrollj = GMX_SIMD_REAL_WIDTH/GMX_SIMD_J_UNROLL_SIZE;
- const int unrollj_half = unrollj/2;
- int ng_p2, i, j, j0, j1, c, s;
-
- ng_p2 = (1<<ng_2log);
-
- /* The size of the x86 SIMD energy group buffer array is:
- * ng*ng*ng_p2*unrollj_half*simd_width
- */
- for (i = 0; i < ng; i++)
- {
- for (j = 0; j < ng; j++)
- {
- Vvdw[i*ng+j] = 0;
- Vc[i*ng+j] = 0;
- }
-
- for (j1 = 0; j1 < ng; j1++)
- {
- for (j0 = 0; j0 < ng; j0++)
- {
- c = ((i*ng + j1)*ng_p2 + j0)*unrollj_half*unrollj;
- for (s = 0; s < unrollj_half; s++)
- {
- Vvdw[i*ng+j0] += VSvdw[c+0];
- Vvdw[i*ng+j1] += VSvdw[c+1];
- Vc [i*ng+j0] += VSc [c+0];
- Vc [i*ng+j1] += VSc [c+1];
- c += unrollj + 2;
- }
- }
- }
- }
-}
-
-#else /* GMX_NBNXN_SIMD_2XNN */
-
-#include "gromacs/utility/fatalerror.h"
-
-#endif /* GMX_NBNXN_SIMD_2XNN */
-
-void
-nbnxn_kernel_simd_2xnn(nbnxn_pairlist_set_t gmx_unused *nbl_list,
- const nbnxn_atomdata_t gmx_unused *nbat,
- const interaction_const_t gmx_unused *ic,
- int gmx_unused ewald_excl,
- rvec gmx_unused *shift_vec,
- int gmx_unused force_flags,
- int gmx_unused clearF,
- real gmx_unused *fshift,
- real gmx_unused *Vc,
- real gmx_unused *Vvdw)
-#ifdef GMX_NBNXN_SIMD_2XNN
-{
- int nnbl;
- nbnxn_pairlist_t **nbl;
- int coulkt, vdwkt = 0;
- int nb, nthreads gmx_unused;
-
- nnbl = nbl_list->nnbl;
- nbl = nbl_list->nbl;
-
- if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
- {
- coulkt = coulktRF;
- }
- else
- {
- if (ewald_excl == ewaldexclTable)
- {
- if (ic->rcoulomb == ic->rvdw)
- {
- coulkt = coulktTAB;
- }
- else
- {
- coulkt = coulktTAB_TWIN;
- }
- }
- else
- {
- if (ic->rcoulomb == ic->rvdw)
- {
- coulkt = coulktEWALD;
- }
- else
- {
- coulkt = coulktEWALD_TWIN;
- }
- }
- }
-
- if (ic->vdwtype == evdwCUT)
- {
- switch (ic->vdw_modifier)
- {
- case eintmodNONE:
- case eintmodPOTSHIFT:
- switch (nbat->comb_rule)
- {
- case ljcrGEOM: vdwkt = vdwktLJCUT_COMBGEOM; break;
- case ljcrLB: vdwkt = vdwktLJCUT_COMBLB; break;
- case ljcrNONE: vdwkt = vdwktLJCUT_COMBNONE; break;
- default: gmx_incons("Unknown combination rule");
- }
- break;
- case eintmodFORCESWITCH:
- vdwkt = vdwktLJFORCESWITCH;
- break;
- case eintmodPOTSWITCH:
- vdwkt = vdwktLJPOTSWITCH;
- break;
- default:
- gmx_incons("Unsupported VdW interaction modifier");
- }
- }
- else if (ic->vdwtype == evdwPME)
- {
- if (ic->ljpme_comb_rule == eljpmeLB)
- {
- gmx_incons("The nbnxn SIMD kernels don't support LJ-PME with LB");
- }
- vdwkt = vdwktLJEWALDCOMBGEOM;
- }
- else
- {
- gmx_incons("Unsupported VdW interaction type");
- }
- // cppcheck-suppress unreadVariable
- nthreads = gmx_omp_nthreads_get(emntNonbonded);
-#pragma omp parallel for schedule(static) num_threads(nthreads)
- for (nb = 0; nb < nnbl; nb++)
- {
- // Presently, the kernels do not call C++ code that can throw, so
- // no need for a try/catch pair in this OpenMP region.
- nbnxn_atomdata_output_t *out;
- real *fshift_p;
-
- out = &nbat->out[nb];
-
- if (clearF == enbvClearFYes)
- {
- clear_f(nbat, nb, out->f);
- }
-
- if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
- {
- fshift_p = fshift;
- }
- else
- {
- fshift_p = out->fshift;
-
- if (clearF == enbvClearFYes)
- {
- clear_fshift(fshift_p);
- }
- }
-
- if (!(force_flags & GMX_FORCE_ENERGY))
- {
- /* Don't calculate energies */
- p_nbk_noener[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p);
- }
- else if (out->nV == 1)
- {
- /* No energy groups */
- out->Vvdw[0] = 0;
- out->Vc[0] = 0;
-
- p_nbk_ener[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->Vvdw,
- out->Vc);
- }
- else
- {
- /* Calculate energy group contributions */
- int i;
-
- for (i = 0; i < out->nVS; i++)
- {
- out->VSvdw[i] = 0;
- }
- for (i = 0; i < out->nVS; i++)
- {
- out->VSc[i] = 0;
- }
-
- p_nbk_energrp[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->VSvdw,
- out->VSc);
-
- reduce_group_energies(nbat->nenergrp, nbat->neg_2log,
- out->VSvdw, out->VSc,
- out->Vvdw, out->Vc);
- }
- }
-
- if (force_flags & GMX_FORCE_ENERGY)
- {
- reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
- }
-}
-#else
-{
- gmx_incons("nbnxn_kernel_simd_2xnn called when such kernels "
- " are not enabled.");
-}
-#endif
-#undef GMX_SIMD_J_UNROLL_SIZE
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* kernel type 2xnn.
*/
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
-#include "gromacs/mdtypes/interaction_const.h"
-#include "gromacs/utility/real.h"
-/*! \brief Run-time dispatcher for nbnxn kernel functions. */
-void
-nbnxn_kernel_simd_2xnn(nbnxn_pairlist_set_t *nbl_list,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- int ewald_excl,
- rvec *shift_vec,
- int force_flags,
- int clearF,
- real *fshift,
- real *Vc,
- real *Vvdw);
-
-/* Need an #include guard so that sim_util.c can include all
- * such files. */
-#ifndef _nbnxn_kernel_simd_include_h
-#define _nbnxn_kernel_simd_include_h
-/*! \brief Typedefs for declaring kernel functions. */
-typedef void (nbk_func_ener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift,
- real *Vvdw,
- real *Vc);
-typedef nbk_func_ener *p_nbk_func_ener;
-
-typedef void (nbk_func_noener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift);
-typedef nbk_func_noener *p_nbk_func_noener;
-#endif
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+/* Declare all the different kernel functions.
+ */
nbk_func_ener nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn;
nbk_func_ener nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn;
nbk_func_ener nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn;
nbk_func_noener nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn;
nbk_func_noener nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn;
nbk_func_noener nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn;
+
+
+
+#ifdef INCLUDE_KERNELFUNCTION_TABLES
+
+/* Declare and define the kernel function pointer lookup tables.
+ * The minor index of the array goes over both the LJ combination rules,
+ * which is only supported by plain cut-off, and the LJ switch/PME functions.
+ */
+p_nbk_func_noener nbnxn_kernel_noener_simd_2xnn[coulktNR][vdwktNR] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_F_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_F_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJ_F_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJFSw_F_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJPSw_F_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJ_F_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJFSw_F_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJPSw_F_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_F_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_F_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJ_F_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJFSw_F_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJPSw_F_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_2xnn,
+ },
+};
+
+p_nbk_func_ener nbnxn_kernel_ener_simd_2xnn[coulktNR][vdwktNR] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_VF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJ_VF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJFSw_VF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJPSw_VF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_VF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJ_VF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJFSw_VF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJPSw_VF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_2xnn,
+ },
+};
+
+p_nbk_func_ener nbnxn_kernel_energrp_simd_2xnn[coulktNR][vdwktNR] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJ_VgrpF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJ_VgrpF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_2xnn,
+ },
+ {
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_2xnn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_2xnn,
+ },
+};
+
+
+#endif /* INCLUDE_KERNELFUNCTION_TABLES */
#ifndef HALF_LJ
cr2_S2 = lje_c2_S * selectByMask(rsq_S2, wco_vdw_S2);
#endif
- expmcr2_S0 = exp( -cr2_S0);
+ // Unsafe version of our exp() should be fine, since these arguments should never
+ // be smaller than -127 for any reasonable choice of cutoff or ewald coefficients.
+ expmcr2_S0 = exp<MathOptimization::Unsafe>( -cr2_S0);
#ifndef HALF_LJ
- expmcr2_S2 = exp( -cr2_S2);
+ expmcr2_S2 = exp<MathOptimization::Unsafe>( -cr2_S2);
#endif
/* 1 + cr2 + 1/2*cr2^2 */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_simd_2xnn_prune.h"
+
+#include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/utility/gmxassert.h"
+
+#ifdef GMX_NBNXN_SIMD_2XNN
+#define GMX_SIMD_J_UNROLL_SIZE 2
+#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn_common.h"
+#endif
+
+/* Prune a single nbnxn_pairtlist_t entry with distance rlistInner */
+void
+nbnxn_kernel_prune_2xnn(nbnxn_pairlist_t * nbl,
+ const nbnxn_atomdata_t * nbat,
+ const rvec * gmx_restrict shift_vec,
+ real rlistInner)
+{
+#ifdef GMX_NBNXN_SIMD_2XNN
+ const nbnxn_ci_t * gmx_restrict ciOuter = nbl->ciOuter;
+ nbnxn_ci_t * gmx_restrict ciInner = nbl->ci;
+
+ const nbnxn_cj_t * gmx_restrict cjOuter = nbl->cjOuter;
+ nbnxn_cj_t * gmx_restrict cjInner = nbl->cj;
+
+ const real * gmx_restrict shiftvec = shift_vec[0];
+ const real * gmx_restrict x = nbat->x;
+
+ const SimdReal rlist2_S(rlistInner*rlistInner);
+
+ /* Initialize the new list as empty and add pairs that are in range */
+ int nciInner = 0;
+ int ncjInner = 0;
+ for (int i = 0; i < nbl->nciOuter; i++)
+ {
+ const nbnxn_ci_t * gmx_restrict ciEntry = &ciOuter[i];
+
+ /* Copy the original list entry to the pruned entry */
+ ciInner[nciInner].ci = ciEntry->ci;
+ ciInner[nciInner].shift = ciEntry->shift;
+ ciInner[nciInner].cj_ind_start = ncjInner;
+
+ /* Extract shift data */
+ int ish = (ciEntry->shift & NBNXN_CI_SHIFT);
+ int ish3 = ish*3;
+ int ci = ciEntry->ci;
+
+ SimdReal shX_S = SimdReal(shiftvec[ish3 ]);
+ SimdReal shY_S = SimdReal(shiftvec[ish3 + 1]);
+ SimdReal shZ_S = SimdReal(shiftvec[ish3 + 2]);
+
+#if UNROLLJ <= 4
+ int sci = ci*STRIDE;
+ int scix = sci*DIM;
+#else
+ int sci = (ci >> 1)*STRIDE;
+ int scix = sci*DIM + (ci & 1)*(STRIDE >> 1);
+ sci += (ci & 1)*(STRIDE >> 1);
+#endif
+
+ /* Load i atom data */
+ int sciy = scix + STRIDE;
+ int sciz = sciy + STRIDE;
+ SimdReal ix_S0 = load1DualHsimd(x + scix ) + shX_S;
+ SimdReal ix_S2 = load1DualHsimd(x + scix + 2) + shX_S;
+ SimdReal iy_S0 = load1DualHsimd(x + sciy ) + shY_S;
+ SimdReal iy_S2 = load1DualHsimd(x + sciy + 2) + shY_S;
+ SimdReal iz_S0 = load1DualHsimd(x + sciz ) + shZ_S;
+ SimdReal iz_S2 = load1DualHsimd(x + sciz + 2) + shZ_S;
+
+ for (int cjind = ciEntry->cj_ind_start; cjind < ciEntry->cj_ind_end; cjind++)
+ {
+ /* j-cluster index */
+ int cj = cjOuter[cjind].cj;
+
+ /* Atom indices (of the first atom in the cluster) */
+ int aj = cj*UNROLLJ;
+#if UNROLLJ == STRIDE
+ int ajx = aj*DIM;
+#else
+ int ajx = (cj >> 1)*DIM*STRIDE + (cj & 1)*UNROLLJ;
+#endif
+ int ajy = ajx + STRIDE;
+ int ajz = ajy + STRIDE;
+
+ /* load j atom coordinates */
+ SimdReal jx_S = loadDuplicateHsimd(x + ajx);
+ SimdReal jy_S = loadDuplicateHsimd(x + ajy);
+ SimdReal jz_S = loadDuplicateHsimd(x + ajz);
+
+ /* Calculate distance */
+ SimdReal dx_S0 = ix_S0 - jx_S;
+ SimdReal dy_S0 = iy_S0 - jy_S;
+ SimdReal dz_S0 = iz_S0 - jz_S;
+ SimdReal dx_S2 = ix_S2 - jx_S;
+ SimdReal dy_S2 = iy_S2 - jy_S;
+ SimdReal dz_S2 = iz_S2 - jz_S;
+
+ /* rsq = dx*dx+dy*dy+dz*dz */
+ SimdReal rsq_S0 = norm2(dx_S0, dy_S0, dz_S0);
+ SimdReal rsq_S2 = norm2(dx_S2, dy_S2, dz_S2);
+
+ /* Do the cut-off check */
+ SimdBool wco_S0 = (rsq_S0 < rlist2_S);
+ SimdBool wco_S2 = (rsq_S2 < rlist2_S);
+
+ wco_S0 = wco_S0 || wco_S2;
+
+ /* Putting the assignment inside the conditional is slower */
+ cjInner[ncjInner] = cjOuter[cjind];
+ if (anyTrue(wco_S0))
+ {
+ ncjInner++;
+ }
+ }
+
+ if (ncjInner > ciInner[nciInner].cj_ind_start)
+ {
+ ciInner[nciInner].cj_ind_end = ncjInner;
+ nciInner++;
+ }
+ }
+
+ nbl->nci = nciInner;
+
+#else /* GMX_NBNXN_SIMD_2XNN */
+
+ GMX_RELEASE_ASSERT(false, "2xNN kernel called without 2xNN support");
+
+ GMX_UNUSED_VALUE(nbl);
+ GMX_UNUSED_VALUE(nbat);
+ GMX_UNUSED_VALUE(shift_vec);
+ GMX_UNUSED_VALUE(rlistInner);
+
+#endif /* GMX_NBNXN_SIMD_2XNN */
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief
+ * Declares the SIMD 2xNN pruning only kernel.
+ *
+ * \author Berk Hess <hess@kth.se>
+ */
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct nbnxn_atomdata_t;
+struct nbnxn_pairlist_t;
+
+/*! \brief Prune a single nbnxn_pairlist_t entry with distance \p rlistInner
+ *
+ * Reads a cluster pairlist \p nbl->ciOuter, \p nbl->cjOuter and writes
+ * all cluster pairs within \p rlistInner to \p nbl->ci, \p nbl->cj.
+ */
+void
+nbnxn_kernel_prune_2xnn(nbnxn_pairlist_t * nbl,
+ const nbnxn_atomdata_t * nbat,
+ const rvec * gmx_restrict shift_vec,
+ real rlistInner);
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*
- * Note: this file was generated by the Verlet kernel generator for
- * kernel type 4xn.
- */
-
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_simd.h"
-#include "gromacs/mdtypes/interaction_const.h"
-#include "gromacs/mdtypes/md_enums.h"
-
-#ifdef GMX_NBNXN_SIMD_4XN
-
-#include "gromacs/simd/vector_operations.h"
-
-#if !(GMX_SIMD_REAL_WIDTH == 2 || GMX_SIMD_REAL_WIDTH == 4 || GMX_SIMD_REAL_WIDTH == 8)
-#error "unsupported SIMD width"
-#endif
-
-#define GMX_SIMD_J_UNROLL_SIZE 1
-#include "nbnxn_kernel_simd_4xn.h"
-
-#include "gromacs/mdlib/force_flags.h"
-#include "gromacs/mdlib/gmx_omp_nthreads.h"
-#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
-#include "gromacs/simd/simd.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/real.h"
-
-/*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
- */
-enum {
- coulktRF, coulktTAB, coulktTAB_TWIN, coulktEWALD, coulktEWALD_TWIN, coulktNR
-};
-
-/*! \brief Kinds of Van der Waals treatments in SIMD Verlet kernels
- */
-enum {
- vdwktLJCUT_COMBGEOM, vdwktLJCUT_COMBLB, vdwktLJCUT_COMBNONE, vdwktLJFORCESWITCH, vdwktLJPOTSWITCH, vdwktLJEWALDCOMBGEOM, vdwktNR
-};
-
-/* Declare and define the kernel function pointer lookup tables.
- * The minor index of the array goes over both the LJ combination rules,
- * which is only supported by plain cut-off, and the LJ switch/PME functions.
- */
-static p_nbk_func_noener p_nbk_noener[coulktNR][vdwktNR] =
-{
- {
- nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn,
- nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn,
- nbnxn_kernel_ElecRF_VdwLJ_F_4xn,
- nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn,
- nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn,
- },
- {
- nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn,
- },
- {
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn,
- },
- {
- nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn,
- nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn,
- nbnxn_kernel_ElecEw_VdwLJ_F_4xn,
- nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn,
- nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn,
- nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn,
- },
- {
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn,
- },
-};
-
-static p_nbk_func_ener p_nbk_ener[coulktNR][vdwktNR] =
-{
- {
- nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn,
- nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn,
- nbnxn_kernel_ElecRF_VdwLJ_VF_4xn,
- nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn,
- nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn,
- },
- {
- nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn,
- },
- {
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn,
- },
- {
- nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn,
- nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn,
- nbnxn_kernel_ElecEw_VdwLJ_VF_4xn,
- nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn,
- nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn,
- nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn,
- },
- {
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn,
- },
-};
-
-static p_nbk_func_ener p_nbk_energrp[coulktNR][vdwktNR] =
-{
- {
- nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn,
- nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn,
- nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn,
- nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn,
- nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn,
- nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn,
- },
- {
- nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn,
- nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn,
- },
- {
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn,
- nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn,
- },
- {
- nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn,
- nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn,
- nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn,
- nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn,
- nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn,
- nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn,
- },
- {
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn,
- nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn,
- },
-};
-
-
-static void
-reduce_group_energies(int ng, int ng_2log,
- const real *VSvdw, const real *VSc,
- real *Vvdw, real *Vc)
-{
- const int unrollj = GMX_SIMD_REAL_WIDTH/GMX_SIMD_J_UNROLL_SIZE;
- const int unrollj_half = unrollj/2;
- int ng_p2, i, j, j0, j1, c, s;
-
- ng_p2 = (1<<ng_2log);
-
- /* The size of the x86 SIMD energy group buffer array is:
- * ng*ng*ng_p2*unrollj_half*simd_width
- */
- for (i = 0; i < ng; i++)
- {
- for (j = 0; j < ng; j++)
- {
- Vvdw[i*ng+j] = 0;
- Vc[i*ng+j] = 0;
- }
-
- for (j1 = 0; j1 < ng; j1++)
- {
- for (j0 = 0; j0 < ng; j0++)
- {
- c = ((i*ng + j1)*ng_p2 + j0)*unrollj_half*unrollj;
- for (s = 0; s < unrollj_half; s++)
- {
- Vvdw[i*ng+j0] += VSvdw[c+0];
- Vvdw[i*ng+j1] += VSvdw[c+1];
- Vc [i*ng+j0] += VSc [c+0];
- Vc [i*ng+j1] += VSc [c+1];
- c += unrollj + 2;
- }
- }
- }
- }
-}
-
-#else /* GMX_NBNXN_SIMD_4XN */
-
-#include "gromacs/utility/fatalerror.h"
-
-#endif /* GMX_NBNXN_SIMD_4XN */
-
-void
-nbnxn_kernel_simd_4xn(nbnxn_pairlist_set_t gmx_unused *nbl_list,
- const nbnxn_atomdata_t gmx_unused *nbat,
- const interaction_const_t gmx_unused *ic,
- int gmx_unused ewald_excl,
- rvec gmx_unused *shift_vec,
- int gmx_unused force_flags,
- int gmx_unused clearF,
- real gmx_unused *fshift,
- real gmx_unused *Vc,
- real gmx_unused *Vvdw)
-#ifdef GMX_NBNXN_SIMD_4XN
-{
- int nnbl;
- nbnxn_pairlist_t **nbl;
- int coulkt, vdwkt = 0;
- int nb, nthreads gmx_unused;
-
- nnbl = nbl_list->nnbl;
- nbl = nbl_list->nbl;
-
- if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
- {
- coulkt = coulktRF;
- }
- else
- {
- if (ewald_excl == ewaldexclTable)
- {
- if (ic->rcoulomb == ic->rvdw)
- {
- coulkt = coulktTAB;
- }
- else
- {
- coulkt = coulktTAB_TWIN;
- }
- }
- else
- {
- if (ic->rcoulomb == ic->rvdw)
- {
- coulkt = coulktEWALD;
- }
- else
- {
- coulkt = coulktEWALD_TWIN;
- }
- }
- }
-
- if (ic->vdwtype == evdwCUT)
- {
- switch (ic->vdw_modifier)
- {
- case eintmodNONE:
- case eintmodPOTSHIFT:
- switch (nbat->comb_rule)
- {
- case ljcrGEOM: vdwkt = vdwktLJCUT_COMBGEOM; break;
- case ljcrLB: vdwkt = vdwktLJCUT_COMBLB; break;
- case ljcrNONE: vdwkt = vdwktLJCUT_COMBNONE; break;
- default: gmx_incons("Unknown combination rule");
- }
- break;
- case eintmodFORCESWITCH:
- vdwkt = vdwktLJFORCESWITCH;
- break;
- case eintmodPOTSWITCH:
- vdwkt = vdwktLJPOTSWITCH;
- break;
- default:
- gmx_incons("Unsupported VdW interaction modifier");
- }
- }
- else if (ic->vdwtype == evdwPME)
- {
- if (ic->ljpme_comb_rule == eljpmeLB)
- {
- gmx_incons("The nbnxn SIMD kernels don't support LJ-PME with LB");
- }
- vdwkt = vdwktLJEWALDCOMBGEOM;
- }
- else
- {
- gmx_incons("Unsupported VdW interaction type");
- }
- // cppcheck-suppress unreadVariable
- nthreads = gmx_omp_nthreads_get(emntNonbonded);
-#pragma omp parallel for schedule(static) num_threads(nthreads)
- for (nb = 0; nb < nnbl; nb++)
- {
- // Presently, the kernels do not call C++ code that can throw, so
- // no need for a try/catch pair in this OpenMP region.
- nbnxn_atomdata_output_t *out;
- real *fshift_p;
-
- out = &nbat->out[nb];
-
- if (clearF == enbvClearFYes)
- {
- clear_f(nbat, nb, out->f);
- }
-
- if ((force_flags & GMX_FORCE_VIRIAL) && nnbl == 1)
- {
- fshift_p = fshift;
- }
- else
- {
- fshift_p = out->fshift;
-
- if (clearF == enbvClearFYes)
- {
- clear_fshift(fshift_p);
- }
- }
-
- if (!(force_flags & GMX_FORCE_ENERGY))
- {
- /* Don't calculate energies */
- p_nbk_noener[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p);
- }
- else if (out->nV == 1)
- {
- /* No energy groups */
- out->Vvdw[0] = 0;
- out->Vc[0] = 0;
-
- p_nbk_ener[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->Vvdw,
- out->Vc);
- }
- else
- {
- /* Calculate energy group contributions */
- int i;
-
- for (i = 0; i < out->nVS; i++)
- {
- out->VSvdw[i] = 0;
- }
- for (i = 0; i < out->nVS; i++)
- {
- out->VSc[i] = 0;
- }
-
- p_nbk_energrp[coulkt][vdwkt](nbl[nb], nbat,
- ic,
- shift_vec,
- out->f,
- fshift_p,
- out->VSvdw,
- out->VSc);
-
- reduce_group_energies(nbat->nenergrp, nbat->neg_2log,
- out->VSvdw, out->VSc,
- out->Vvdw, out->Vc);
- }
- }
-
- if (force_flags & GMX_FORCE_ENERGY)
- {
- reduce_energies_over_lists(nbat, nnbl, Vvdw, Vc);
- }
-}
-#else
-{
- gmx_incons("nbnxn_kernel_simd_4xn called when such kernels "
- " are not enabled.");
-}
-#endif
-#undef GMX_SIMD_J_UNROLL_SIZE
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* kernel type 4xn.
*/
-#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
-#include "gromacs/mdtypes/interaction_const.h"
-#include "gromacs/utility/real.h"
-/*! \brief Run-time dispatcher for nbnxn kernel functions. */
-void
-nbnxn_kernel_simd_4xn(nbnxn_pairlist_set_t *nbl_list,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- int ewald_excl,
- rvec *shift_vec,
- int force_flags,
- int clearF,
- real *fshift,
- real *Vc,
- real *Vvdw);
-
-/* Need an #include guard so that sim_util.c can include all
- * such files. */
-#ifndef _nbnxn_kernel_simd_include_h
-#define _nbnxn_kernel_simd_include_h
-/*! \brief Typedefs for declaring kernel functions. */
-typedef void (nbk_func_ener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift,
- real *Vvdw,
- real *Vc);
-typedef nbk_func_ener *p_nbk_func_ener;
-
-typedef void (nbk_func_noener)(const nbnxn_pairlist_t *nbl,
- const nbnxn_atomdata_t *nbat,
- const interaction_const_t *ic,
- rvec *shift_vec,
- real *f,
- real *fshift);
-typedef nbk_func_noener *p_nbk_func_noener;
-#endif
+#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_common.h"
+/* Declare all the different kernel functions.
+ */
nbk_func_ener nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn;
nbk_func_ener nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn;
nbk_func_ener nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn;
nbk_func_noener nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn;
nbk_func_noener nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn;
nbk_func_noener nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn;
+
+
+
+#ifdef INCLUDE_KERNELFUNCTION_TABLES
+
+/* Declare and define the kernel function pointer lookup tables.
+ * The minor index of the array goes over both the LJ combination rules,
+ * which is only supported by plain cut-off, and the LJ switch/PME functions.
+ */
+p_nbk_func_noener nbnxn_kernel_noener_simd_4xn[coulktNR][vdwktNR] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_F_4xn,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_F_4xn,
+ nbnxn_kernel_ElecRF_VdwLJ_F_4xn,
+ nbnxn_kernel_ElecRF_VdwLJFSw_F_4xn,
+ nbnxn_kernel_ElecRF_VdwLJPSw_F_4xn,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_F_4xn,
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJCombGeom_F_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJCombLB_F_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJ_F_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJFSw_F_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJPSw_F_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_F_4xn,
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_F_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_F_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_F_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_F_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_F_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_F_4xn,
+ },
+ {
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_F_4xn,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_F_4xn,
+ nbnxn_kernel_ElecEw_VdwLJ_F_4xn,
+ nbnxn_kernel_ElecEw_VdwLJFSw_F_4xn,
+ nbnxn_kernel_ElecEw_VdwLJPSw_F_4xn,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_F_4xn,
+ },
+ {
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_F_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_F_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJ_F_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_F_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_F_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_F_4xn,
+ },
+};
+
+p_nbk_func_ener nbnxn_kernel_ener_simd_4xn[coulktNR][vdwktNR] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_VF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_VF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJ_VF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJFSw_VF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJPSw_VF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJCombLB_VF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJFSw_VF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJPSw_VF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_VF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_VF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJ_VF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJFSw_VF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJPSw_VF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_4xn,
+ },
+};
+
+p_nbk_func_ener nbnxn_kernel_energrp_simd_4xn[coulktNR][vdwktNR] =
+{
+ {
+ nbnxn_kernel_ElecRF_VdwLJCombGeom_VgrpF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJCombLB_VgrpF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJ_VgrpF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJFSw_VgrpF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJPSw_VgrpF_4xn,
+ nbnxn_kernel_ElecRF_VdwLJEwCombGeom_VgrpF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecQSTab_VdwLJCombGeom_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJCombLB_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJ_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJFSw_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJPSw_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTab_VdwLJEwCombGeom_VgrpF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombGeom_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJCombLB_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJ_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJFSw_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJPSw_VgrpF_4xn,
+ nbnxn_kernel_ElecQSTabTwinCut_VdwLJEwCombGeom_VgrpF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecEw_VdwLJCombGeom_VgrpF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJCombLB_VgrpF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJ_VgrpF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJFSw_VgrpF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJPSw_VgrpF_4xn,
+ nbnxn_kernel_ElecEw_VdwLJEwCombGeom_VgrpF_4xn,
+ },
+ {
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VgrpF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VgrpF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJ_VgrpF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJFSw_VgrpF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJPSw_VgrpF_4xn,
+ nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VgrpF_4xn,
+ },
+};
+
+
+#endif /* INCLUDE_KERNELFUNCTION_TABLES */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
cr2_S2 = lje_c2_S * selectByMask(rsq_S2, wco_vdw_S2);
cr2_S3 = lje_c2_S * selectByMask(rsq_S3, wco_vdw_S3);
#endif
- expmcr2_S0 = exp( -cr2_S0 );
- expmcr2_S1 = exp( -cr2_S1 );
+ // Unsafe version of our exp() should be fine, since these arguments should never
+ // be smaller than -127 for any reasonable choice of cutoff or ewald coefficients.
+ expmcr2_S0 = exp<MathOptimization::Unsafe>( -cr2_S0 );
+ expmcr2_S1 = exp<MathOptimization::Unsafe>( -cr2_S1 );
#ifndef HALF_LJ
- expmcr2_S2 = exp( -cr2_S2 );
- expmcr2_S3 = exp( -cr2_S3 );
+ expmcr2_S2 = exp<MathOptimization::Unsafe>( -cr2_S2 );
+ expmcr2_S3 = exp<MathOptimization::Unsafe>( -cr2_S3 );
#endif
/* 1 + cr2 + 1/2*cr2^2 */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#else
const real *nbfp0 = nbfp_ptr + type[sci ]*nbat->ntype*c_simdBestPairAlignment;
const real *nbfp1 = nbfp_ptr + type[sci+1]*nbat->ntype*c_simdBestPairAlignment;
- const real *nbfp2 = NULL, *nbfp3 = NULL;
+ const real *nbfp2 = nullptr, *nbfp3 = nullptr;
if (!half_LJ)
{
nbfp2 = nbfp_ptr + type[sci+2]*nbat->ntype*c_simdBestPairAlignment;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#include "gmxpre.h"
+
+#include "nbnxn_kernel_simd_4xn_prune.h"
+
+#include "gromacs/mdlib/nbnxn_pairlist.h"
+#include "gromacs/mdlib/nbnxn_simd.h"
+#include "gromacs/utility/gmxassert.h"
+
+#ifdef GMX_NBNXN_SIMD_4XN
+#define GMX_SIMD_J_UNROLL_SIZE 1
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn_common.h"
+#endif
+
+/* Prune a single nbnxn_pairtlist_t entry with distance rlistInner */
+void
+nbnxn_kernel_prune_4xn(nbnxn_pairlist_t * nbl,
+ const nbnxn_atomdata_t * nbat,
+ const rvec * gmx_restrict shift_vec,
+ real rlistInner)
+{
+#ifdef GMX_NBNXN_SIMD_4XN
+ const nbnxn_ci_t * gmx_restrict ciOuter = nbl->ciOuter;
+ nbnxn_ci_t * gmx_restrict ciInner = nbl->ci;
+
+ const nbnxn_cj_t * gmx_restrict cjOuter = nbl->cjOuter;
+ nbnxn_cj_t * gmx_restrict cjInner = nbl->cj;
+
+ const real * gmx_restrict shiftvec = shift_vec[0];
+ const real * gmx_restrict x = nbat->x;
+
+ const SimdReal rlist2_S(rlistInner*rlistInner);
+
+ /* Initialize the new list as empty and add pairs that are in range */
+ int nciInner = 0;
+ int ncjInner = 0;
+ for (int i = 0; i < nbl->nciOuter; i++)
+ {
+ const nbnxn_ci_t * gmx_restrict ciEntry = &ciOuter[i];
+
+ /* Copy the original list entry to the pruned entry */
+ ciInner[nciInner].ci = ciEntry->ci;
+ ciInner[nciInner].shift = ciEntry->shift;
+ ciInner[nciInner].cj_ind_start = ncjInner;
+
+ /* Extract shift data */
+ int ish = (ciEntry->shift & NBNXN_CI_SHIFT);
+ int ish3 = ish*3;
+ int ci = ciEntry->ci;
+
+ SimdReal shX_S = SimdReal(shiftvec[ish3 ]);
+ SimdReal shY_S = SimdReal(shiftvec[ish3 + 1]);
+ SimdReal shZ_S = SimdReal(shiftvec[ish3 + 2]);
+
+#if UNROLLJ <= 4
+ int sci = ci*STRIDE;
+ int scix = sci*DIM;
+#else
+ int sci = (ci >> 1)*STRIDE;
+ int scix = sci*DIM + (ci & 1)*(STRIDE >> 1);
+ sci += (ci & 1)*(STRIDE >> 1);
+#endif
+
+ /* Load i atom data */
+ int sciy = scix + STRIDE;
+ int sciz = sciy + STRIDE;
+ SimdReal ix_S0 = SimdReal(x[scix ]) + shX_S;
+ SimdReal ix_S1 = SimdReal(x[scix + 1]) + shX_S;
+ SimdReal ix_S2 = SimdReal(x[scix + 2]) + shX_S;
+ SimdReal ix_S3 = SimdReal(x[scix + 3]) + shX_S;
+ SimdReal iy_S0 = SimdReal(x[sciy ]) + shY_S;
+ SimdReal iy_S1 = SimdReal(x[sciy + 1]) + shY_S;
+ SimdReal iy_S2 = SimdReal(x[sciy + 2]) + shY_S;
+ SimdReal iy_S3 = SimdReal(x[sciy + 3]) + shY_S;
+ SimdReal iz_S0 = SimdReal(x[sciz ]) + shZ_S;
+ SimdReal iz_S1 = SimdReal(x[sciz + 1]) + shZ_S;
+ SimdReal iz_S2 = SimdReal(x[sciz + 2]) + shZ_S;
+ SimdReal iz_S3 = SimdReal(x[sciz + 3]) + shZ_S;
+
+ for (int cjind = ciEntry->cj_ind_start; cjind < ciEntry->cj_ind_end; cjind++)
+ {
+ /* j-cluster index */
+ int cj = cjOuter[cjind].cj;
+
+ /* Atom indices (of the first atom in the cluster) */
+ int aj = cj*UNROLLJ;
+#if UNROLLJ == STRIDE
+ int ajx = aj*DIM;
+#else
+ int ajx = (cj >> 1)*DIM*STRIDE + (cj & 1)*UNROLLJ;
+#endif
+ int ajy = ajx + STRIDE;
+ int ajz = ajy + STRIDE;
+
+ /* load j atom coordinates */
+ SimdReal jx_S = load(x + ajx);
+ SimdReal jy_S = load(x + ajy);
+ SimdReal jz_S = load(x + ajz);
+
+ /* Calculate distance */
+ SimdReal dx_S0 = ix_S0 - jx_S;
+ SimdReal dy_S0 = iy_S0 - jy_S;
+ SimdReal dz_S0 = iz_S0 - jz_S;
+ SimdReal dx_S1 = ix_S1 - jx_S;
+ SimdReal dy_S1 = iy_S1 - jy_S;
+ SimdReal dz_S1 = iz_S1 - jz_S;
+ SimdReal dx_S2 = ix_S2 - jx_S;
+ SimdReal dy_S2 = iy_S2 - jy_S;
+ SimdReal dz_S2 = iz_S2 - jz_S;
+ SimdReal dx_S3 = ix_S3 - jx_S;
+ SimdReal dy_S3 = iy_S3 - jy_S;
+ SimdReal dz_S3 = iz_S3 - jz_S;
+
+ /* rsq = dx*dx+dy*dy+dz*dz */
+ SimdReal rsq_S0 = norm2(dx_S0, dy_S0, dz_S0);
+ SimdReal rsq_S1 = norm2(dx_S1, dy_S1, dz_S1);
+ SimdReal rsq_S2 = norm2(dx_S2, dy_S2, dz_S2);
+ SimdReal rsq_S3 = norm2(dx_S3, dy_S3, dz_S3);
+
+ /* Do the cut-off check */
+ SimdBool wco_S0 = (rsq_S0 < rlist2_S);
+ SimdBool wco_S1 = (rsq_S1 < rlist2_S);
+ SimdBool wco_S2 = (rsq_S2 < rlist2_S);
+ SimdBool wco_S3 = (rsq_S3 < rlist2_S);
+
+ wco_S0 = wco_S0 || wco_S1;
+ wco_S2 = wco_S2 || wco_S3;
+ wco_S0 = wco_S0 || wco_S2;
+
+ /* Putting the assignment inside the conditional is slower */
+ cjInner[ncjInner] = cjOuter[cjind];
+ if (anyTrue(wco_S0))
+ {
+ ncjInner++;
+ }
+ }
+
+ if (ncjInner > ciInner[nciInner].cj_ind_start)
+ {
+ ciInner[nciInner].cj_ind_end = ncjInner;
+ nciInner++;
+ }
+ }
+
+ nbl->nci = nciInner;
+
+#else /* GMX_NBNXN_SIMD_4XN */
+
+ GMX_RELEASE_ASSERT(false, "4xN kernel called without 4xN support");
+
+ GMX_UNUSED_VALUE(nbl);
+ GMX_UNUSED_VALUE(nbat);
+ GMX_UNUSED_VALUE(shift_vec);
+ GMX_UNUSED_VALUE(rlistInner);
+
+#endif /* GMX_NBNXN_SIMD_4XN */
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief
+ * Declares the SIMD 4xN pruning only kernel.
+ *
+ * \author Berk Hess <hess@kth.se>
+ */
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+struct nbnxn_atomdata_t;
+struct nbnxn_pairlist_t;
+
+/*! \brief Prune a single nbnxn_pairlist_t entry with distance \p rlistInner
+ *
+ * Reads a cluster pairlist \p nbl->ciOuter, \p nbl->cjOuter and writes
+ * all cluster pairs within \p rlistInner to \p nbl->ci, \p nbl->cj.
+ */
+void
+nbnxn_kernel_prune_4xn(nbnxn_pairlist_t * nbl,
+ const nbnxn_atomdata_t * nbat,
+ const rvec * gmx_restrict shift_vec,
+ real rlistInner);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \author Dimitrios Karkoulis <dimitris.karkoulis@gmail.com>
* \author Szilárd Páll <pall.szilard@gmail.com>
* \ingroup module_mdlib
+ *
+ * TODO (psz):
+ * - Add a static const cl_uint c_pruneKernelWorkDim / c_nbnxnKernelWorkDim = 3;
+ * - Rework the copying of OCL data structures done before every invocation of both
+ * nb and prune kernels (using fillin_ocl_structures); also consider at the same
+ * time calling clSetKernelArg only on the updated parameters (if tracking changed
+ * parameters is feasible);
+ * - Consider using the event_wait_list argument to clEnqueueNDRangeKernel to mark
+ * dependencies on the kernel launched: e.g. the non-local nb kernel's dependency
+ * on the misc_ops_and_local_H2D_done event could be better expressed this way.
+ *
+ * - Consider extracting common sections of the OpenCL and CUDA nbnxn logic, e.g:
+ * - in nbnxn_gpu_launch_kernel_pruneonly() the pre- and post-kernel launch logic
+ * is identical in the two implementations, so a 3-way split might allow sharing
+ * code;
+ * -
+ *
*/
#include "gmxpre.h"
-#include "config.h"
-
#include <assert.h>
#include <stdlib.h>
#include <limits>
#endif
+#include "thread_mpi/atomic.h"
+
#include "gromacs/gpu_utils/oclutils.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_consts.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
-#include "gromacs/timing/gpu_timing.h"
-
-#ifdef TMPI_ATOMICS
-#include "thread_mpi/atomic.h"
-#endif
-
#include "gromacs/mdlib/nbnxn_gpu.h"
#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/timing/gpu_timing.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
/*! \brief Validates the input global work size parameter.
*/
-static inline void validate_global_work_size(size_t *global_work_size, int work_dim, gmx_device_info_t *dinfo)
+static inline void validate_global_work_size(size_t *global_work_size, int work_dim, const gmx_device_info_t *dinfo)
{
cl_uint device_size_t_size_bits;
cl_uint host_size_t_size_bits;
{ "nbnxn_kernel_ElecEwTwinCut_VdwLJ_VF_prune_opencl", "nbnxn_kernel_ElecEwTwinCut_VdwLJCombGeom_VF_prune_opencl", "nbnxn_kernel_ElecEwTwinCut_VdwLJCombLB_VF_prune_opencl", "nbnxn_kernel_ElecEwTwinCut_VdwLJFsw_VF_prune_opencl", "nbnxn_kernel_ElecEwTwinCut_VdwLJPsw_VF_prune_opencl", "nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombGeom_VF_prune_opencl", "nbnxn_kernel_ElecEwTwinCut_VdwLJEwCombLB_VF_prune_opencl" }
};
+/*! \brief Return a pointer to the prune kernel version to be executed at the current invocation.
+ *
+ * \param[in] kernel_pruneonly array of prune kernel objects
+ * \param[in] firstPrunePass true if the first pruning pass is being executed
+ */
+static inline cl_kernel selectPruneKernel(cl_kernel kernel_pruneonly[],
+ bool firstPrunePass)
+{
+ cl_kernel *kernelPtr;
+
+ if (firstPrunePass)
+ {
+ kernelPtr = &(kernel_pruneonly[epruneFirst]);
+ }
+ else
+ {
+ kernelPtr = &(kernel_pruneonly[epruneRolling]);
+ }
+ // TODO: consider creating the prune kernel object here to avoid a
+ // clCreateKernel for the rolling prune kernel if this is not needed.
+ return *kernelPtr;
+}
/*! \brief Return a pointer to the kernel version to be executed at the current step.
* OpenCL kernel objects are cached in nb. If the requested kernel is not
return *kernel_ptr;
}
-/*! \brief Calculates the amount of shared memory required by the OpenCL kernel in use.
+/*! \brief Calculates the amount of shared memory required by the nonbonded kernel in use.
*/
-static inline int calc_shmem_required(int vdwType,
- bool bPrefetchLjParam)
+static inline int calc_shmem_required_nonbonded(int vdwType,
+ bool bPrefetchLjParam)
{
int shmem;
* The device can't use the same data structures as the host for two main reasons:
* - OpenCL restrictions (pointers are not accepted inside data structures)
* - some host side fields are not needed for the OpenCL kernels.
+ *
+ * This function is called before the launch of both nbnxn and prune kernels.
*/
static void fillin_ocl_structures(cl_nbparam_t *nbp,
cl_nbparam_params_t *nbparams_params)
nbparams_params->ewald_beta = nbp->ewald_beta;
nbparams_params->rcoulomb_sq = nbp->rcoulomb_sq;
nbparams_params->repulsion_shift = nbp->repulsion_shift;
- nbparams_params->rlist_sq = nbp->rlist_sq;
+ nbparams_params->rlistOuter_sq = nbp->rlistOuter_sq;
nbparams_params->rvdw_sq = nbp->rvdw_sq;
+ nbparams_params->rlistInner_sq = nbp->rlistInner_sq;
nbparams_params->rvdw_switch = nbp->rvdw_switch;
nbparams_params->sh_ewald = nbp->sh_ewald;
nbparams_params->sh_lj_ewald = nbp->sh_lj_ewald;
nbparams_params->vdw_switch = nbp->vdw_switch;
}
-/*! \brief Waits for the commands associated with the input event to finish.
- * Then it releases the event and sets it to 0.
- * Don't use this function when more than one wait will be issued for the event.
- */
-void wait_ocl_event(cl_event *ocl_event)
-{
- cl_int gmx_unused cl_error;
-
- /* Blocking wait for the event */
- cl_error = clWaitForEvents(1, ocl_event);
- assert(CL_SUCCESS == cl_error);
-
- /* Release event and reset it to 0 */
- cl_error = clReleaseEvent(*ocl_event);
- assert(CL_SUCCESS == cl_error);
- *ocl_event = 0;
-}
-
/*! \brief Enqueues a wait for event completion.
*
* Then it releases the event and sets it to 0.
* Don't use this function when more than one wait will be issued for the event.
* Equivalent to Cuda Stream Sync. */
-void sync_ocl_event(cl_command_queue stream, cl_event *ocl_event)
+static void sync_ocl_event(cl_command_queue stream, cl_event *ocl_event)
{
cl_int gmx_unused cl_error;
* The function returns 0.0 if the input event, *ocl_event, is 0.
* Don't use this function when more than one wait will be issued for the event.
*/
-double ocl_event_elapsed_ms(cl_event *ocl_event)
+static double ocl_event_elapsed_ms(cl_event *ocl_event)
{
cl_int gmx_unused cl_error;
cl_ulong start_ns, end_ns;
call is taken care of later in this function. */
if (iloc == eintNonlocal && plist->nsci == 0)
{
+ plist->haveFreshList = false;
+
return;
}
}
}
+ if (nbp->useDynamicPruning && plist->haveFreshList)
+ {
+ /* Prunes for rlistOuter and rlistInner, sets plist->haveFreshList=false
+ (that's the way the timing accounting can distinguish between
+ separate prune kernel and combined force+prune).
+ */
+ nbnxn_gpu_launch_kernel_pruneonly(nb, iloc, 1);
+ }
+
if (plist->nsci == 0)
{
/* Don't launch an empty local kernel (is not allowed with OpenCL).
nbp->eeltype,
nbp->vdwtype,
bCalcEner,
- plist->bDoPrune || always_prune);
+ (plist->haveFreshList && !nb->timers->didPrune[iloc]) || always_prune);
/* kernel launch config */
local_work_size[0] = c_clSize;
validate_global_work_size(global_work_size, 3, nb->dev_info);
- shmem = calc_shmem_required(nbp->vdwtype, nb->bPrefetchLjParam);
+ shmem = calc_shmem_required_nonbonded(nbp->vdwtype, nb->bPrefetchLjParam);
#ifdef DEBUG_OCL
{
#endif
if (debug)
{
- fprintf(debug, "GPU launch configuration:\n\tLocal work size: %dx%dx%d\n\t"
+ fprintf(debug, "Non-bonded GPU launch configuration:\n\tLocal work size: %dx%dx%d\n\t"
"Global work size : %dx%d\n\t#Super-clusters/clusters: %d/%d (%d)\n",
(int)(local_work_size[0]), (int)(local_work_size[1]), (int)(local_work_size[2]),
(int)(global_work_size[0]), (int)(global_work_size[1]), plist->nsci*c_numClPerSupercl,
}
#endif
}
+
+
+/*! \brief Calculates the amount of shared memory required by the prune kernel.
+ *
+ * Note that for the sake of simplicity we use the CUDA terminology "shared memory"
+ * for OpenCL local memory.
+ *
+ * \param[in] num_threads_z cj4 concurrency equal to the number of threads/work items in the 3-rd dimension.
+ * \returns the amount of local memory in bytes required by the pruning kernel
+ */
+static inline int calc_shmem_required_prune(const int num_threads_z)
+{
+ int shmem;
+
+ /* i-atom x in shared memory (for convenience we load all 4 components including q) */
+ shmem = c_numClPerSupercl * c_clSize * sizeof(float)*4;
+ /* cj in shared memory, for each warp separately */
+ shmem += num_threads_z * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize * sizeof(int);
+ /* Warp vote, requires one uint per warp/32 threads per block. */
+ shmem += sizeof(cl_uint) * 2*num_threads_z;
+
+ return shmem;
+}
+
+void nbnxn_gpu_launch_kernel_pruneonly(gmx_nbnxn_gpu_t *nb,
+ int iloc,
+ int numParts)
+{
+ cl_int cl_error;
+
+ cl_atomdata_t *adat = nb->atdat;
+ cl_nbparam_t *nbp = nb->nbparam;
+ cl_plist_t *plist = nb->plist[iloc];
+ cl_timers_t *t = nb->timers;
+ cl_command_queue stream = nb->stream[iloc];
+ bool bDoTime = nb->bDoTime;
+
+ if (plist->haveFreshList)
+ {
+ GMX_ASSERT(numParts == 1, "With first pruning we expect 1 part");
+
+ /* Set rollingPruningNumParts to signal that it is not set */
+ plist->rollingPruningNumParts = 0;
+ plist->rollingPruningPart = 0;
+ }
+ else
+ {
+ if (plist->rollingPruningNumParts == 0)
+ {
+ plist->rollingPruningNumParts = numParts;
+ }
+ else
+ {
+ GMX_ASSERT(numParts == plist->rollingPruningNumParts, "It is not allowed to change numParts in between list generation steps");
+ }
+ }
+
+ /* Use a local variable for part and update in plist, so we can return here
+ * without duplicating the part increment code.
+ */
+ int part = plist->rollingPruningPart;
+
+ plist->rollingPruningPart++;
+ if (plist->rollingPruningPart >= plist->rollingPruningNumParts)
+ {
+ plist->rollingPruningPart = 0;
+ }
+
+ /* Compute the number of list entries to prune in this pass */
+ int numSciInPart = (plist->nsci - part)/numParts;
+
+ /* Don't launch the kernel if there is no work to do. */
+ if (numSciInPart <= 0)
+ {
+ plist->haveFreshList = false;
+
+ return;
+ }
+
+ /* Kernel launch config:
+ * - The thread block dimensions match the size of i-clusters, j-clusters,
+ * and j-cluster concurrency, in x, y, and z, respectively.
+ * - The 1D block-grid contains as many blocks as super-clusters.
+ */
+ int num_threads_z = getOclPruneKernelJ4Concurrency(nb->dev_info->vendor_e);
+ cl_kernel pruneKernel = selectPruneKernel(nb->kernel_pruneonly, plist->haveFreshList);
+
+ /* kernel launch config */
+ size_t local_work_size[3], global_work_size[3];
+ local_work_size[0] = c_clSize;
+ local_work_size[1] = c_clSize;
+ local_work_size[2] = num_threads_z;
+
+ global_work_size[0] = numSciInPart * local_work_size[0];
+ global_work_size[1] = 1 * local_work_size[1];
+ global_work_size[2] = 1 * local_work_size[2];
+
+ validate_global_work_size(global_work_size, 3, nb->dev_info);
+
+ int shmem = calc_shmem_required_prune(num_threads_z);
+
+ if (debug)
+ {
+ fprintf(debug, "Pruning GPU kernel launch configuration:\n\tLocal work size: %dx%dx%d\n\t"
+ "\tGlobal work size: %dx%d\n\t#Super-clusters/clusters: %d/%d (%d)\n"
+ "\tShMem: %d\n",
+ (int)(local_work_size[0]), (int)(local_work_size[1]), (int)(local_work_size[2]),
+ (int)(global_work_size[0]), (int)(global_work_size[1]), plist->nsci*c_numClPerSupercl,
+ c_numClPerSupercl, plist->na_c, shmem);
+ }
+
+ cl_nbparam_params_t nbparams_params;
+ fillin_ocl_structures(nbp, &nbparams_params);
+
+ cl_uint arg_no = 0;
+ cl_error = CL_SUCCESS;
+
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(nbparams_params), &(nbparams_params));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(cl_mem), &(adat->xq));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(cl_mem), &(adat->shift_vec));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(cl_mem), &(plist->sci));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(cl_mem), &(plist->cj4));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(cl_mem), &(plist->imask));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(int), &(numParts));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, sizeof(int), &(part));
+ cl_error |= clSetKernelArg(pruneKernel, arg_no++, shmem, nullptr);
+ assert(cl_error == CL_SUCCESS);
+
+ cl_event *pruneEventPtr = nullptr;
+ if (bDoTime)
+ {
+ pruneEventPtr = plist->haveFreshList ? &t->prune_k[iloc] : &t->rollingPrune_k[iloc];
+ }
+
+ cl_error = clEnqueueNDRangeKernel(stream, pruneKernel, 3,
+ nullptr, global_work_size, local_work_size,
+ 0, nullptr, pruneEventPtr);
+ GMX_RELEASE_ASSERT(CL_SUCCESS == cl_error, ocl_get_error_string(cl_error).c_str());
+
+ if (plist->haveFreshList)
+ {
+ plist->haveFreshList = false;
+ /* Mark that pruning has been done */
+ nb->timers->didPrune[iloc] = true;
+ }
+ else
+ {
+ /* Mark that rolling pruning has been done */
+ nb->timers->didRollingPrune[iloc] = true;
+ }
+}
+
/*! \brief
* Launch asynchronously the download of nonbonded forces from the GPU
* (and energies/shift forces if required).
}
}
+/*! \brief Count pruning kernel time if either kernel has been triggered
+ *
+ * We do the accounting for either of the two pruning kernel flavors:
+ * - 1st pass prune: ran during the current step (prior to the force kernel);
+ * - rolling prune: ran at the end of the previous step (prior to the current step H2D xq);
+ *
+ * Note that the resetting of cu_timers_t::didPrune and cu_timers_t::didRollingPrune should happen
+ * after calling this function.
+ *
+ * \param[inout] timers structs with OCL timer objects
+ * \param[inout] timings GPU task timing data
+ * \param[in] iloc interaction locality
+ */
+static void countPruneKernelTime(cl_timers_t *timers,
+ gmx_wallclock_gpu_t *timings,
+ const int iloc)
+{
+ // We might have not done any pruning (e.g. if we skipped with empty domains).
+ if (!timers->didPrune[iloc] && !timers->didRollingPrune[iloc])
+ {
+ return;
+ }
+
+ if (timers->didPrune[iloc])
+ {
+ timings->pruneTime.c++;
+ timings->pruneTime.t += ocl_event_elapsed_ms(&timers->prune_k[iloc]);
+ }
+
+ if (timers->didRollingPrune[iloc])
+ {
+ timings->dynamicPruneTime.c++;
+ timings->dynamicPruneTime.t += ocl_event_elapsed_ms(&timers->rollingPrune_k[iloc]);
+ }
+}
+
/*! \brief
* Wait for the asynchronously launched nonbonded calculations and data
* transfers to finish.
{
/* NOTE: only implemented for single-precision at this time */
cl_int gmx_unused cl_error;
- int i, iloc = -1;
+ int iloc = -1;
/* determine interaction locality from atom locality */
if (LOCAL_A(aloc))
/* turn energy calculation always on/off (for debugging/testing only) */
bCalcEner = (bCalcEner || always_ener) && !never_ener;
- /* Launch wait/update timers & counters, unless doing the non-local phase
- when there is not actually work to do. This is consistent with
- nbnxn_gpu_launch_kernel.
+ /* Launch wait/update timers & counters and do reduction into staging buffers
+ BUT skip it when during the non-local phase there was actually no work to do.
+ This is consistent with nbnxn_gpu_launch_kernel.
NOTE: if timing with multiple GPUs (streams) becomes possible, the
counters could end up being inconsistent due to not being incremented
on some of the nodes! */
- if (iloc == eintNonlocal && nb->plist[iloc]->nsci == 0)
+ if (!(iloc == eintNonlocal && nb->plist[iloc]->nsci == 0))
{
- return;
- }
-
- /* Actual sync point. Waits for everything to be finished in the command queue. TODO: Find out if a more fine grained solution is needed */
- cl_error = clFinish(nb->stream[iloc]);
- assert(CL_SUCCESS == cl_error);
+ /* Actual sync point. Waits for everything to be finished in the command queue. TODO: Find out if a more fine grained solution is needed */
+ cl_error = clFinish(nb->stream[iloc]);
+ assert(CL_SUCCESS == cl_error);
- /* timing data accumulation */
- if (nb->bDoTime)
- {
- /* only increase counter once (at local F wait) */
- if (LOCAL_I(iloc))
+ /* timing data accumulation */
+ if (nb->bDoTime)
{
- timings->nb_c++;
- timings->ktime[plist->bDoPrune ? 1 : 0][bCalcEner ? 1 : 0].c += 1;
- }
+ /* only increase counter once (at local F wait) */
+ if (LOCAL_I(iloc))
+ {
+ timings->nb_c++;
+ timings->ktime[plist->haveFreshList ? 1 : 0][bCalcEner ? 1 : 0].c += 1;
+ }
- /* kernel timings */
+ /* kernel timings */
- timings->ktime[plist->bDoPrune ? 1 : 0][bCalcEner ? 1 : 0].t +=
- ocl_event_elapsed_ms(timers->nb_k + iloc);
+ timings->ktime[plist->haveFreshList ? 1 : 0][bCalcEner ? 1 : 0].t +=
+ ocl_event_elapsed_ms(timers->nb_k + iloc);
- /* X/q H2D and F D2H timings */
- timings->nb_h2d_t += ocl_event_elapsed_ms(timers->nb_h2d + iloc);
- timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_f + iloc);
- timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_fshift + iloc);
- timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_e_el + iloc);
- timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_e_lj + iloc);
+ /* X/q H2D and F D2H timings */
+ timings->nb_h2d_t += ocl_event_elapsed_ms(timers->nb_h2d + iloc);
+ timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_f + iloc);
+ timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_fshift + iloc);
+ timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_e_el + iloc);
+ timings->nb_d2h_t += ocl_event_elapsed_ms(timers->nb_d2h_e_lj + iloc);
- /* only count atdat and pair-list H2D at pair-search step */
- if (plist->bDoPrune)
- {
- /* atdat transfer timing (add only once, at local F wait) */
- if (LOCAL_A(aloc))
+ /* Count the pruning kernel times for both cases:1st pass (at search step)
+ and rolling pruning (if called at the previous step).
+ We do the accounting here as this is the only sync point where we
+ know (without checking or additional sync-ing) that prune tasks in
+ in the current stream have completed (having just blocking-waited
+ for the force D2H). */
+ countPruneKernelTime(timers, timings, iloc);
+
+ /* only count atdat and pair-list H2D at pair-search step */
+ if (timers->didPairlistH2D[iloc])
{
- timings->pl_h2d_c++;
- timings->pl_h2d_t += ocl_event_elapsed_ms(&(timers->atdat));
- }
+ /* atdat transfer timing (add only once, at local F wait) */
+ if (LOCAL_A(aloc))
+ {
+ timings->pl_h2d_c++;
+ timings->pl_h2d_t += ocl_event_elapsed_ms(&(timers->atdat));
+ }
- timings->pl_h2d_t +=
- ocl_event_elapsed_ms(timers->pl_h2d_sci + iloc) +
- ocl_event_elapsed_ms(timers->pl_h2d_cj4 + iloc) +
- ocl_event_elapsed_ms(timers->pl_h2d_excl + iloc);
+ timings->pl_h2d_t +=
+ ocl_event_elapsed_ms(timers->pl_h2d_sci + iloc) +
+ ocl_event_elapsed_ms(timers->pl_h2d_cj4 + iloc) +
+ ocl_event_elapsed_ms(timers->pl_h2d_excl + iloc);
+ /* Clear the timing flag for the next step */
+ timers->didPairlistH2D[iloc] = false;
+ }
}
- }
- /* add up energies and shift forces (only once at local F wait) */
- if (LOCAL_I(iloc))
- {
- if (bCalcEner)
+ /* add up energies and shift forces (only once at local F wait) */
+ if (LOCAL_I(iloc))
{
- *e_lj += *nbst.e_lj;
- *e_el += *nbst.e_el;
- }
+ if (bCalcEner)
+ {
+ *e_lj += *nbst.e_lj;
+ *e_el += *nbst.e_el;
+ }
- if (bCalcFshift)
- {
- for (i = 0; i < SHIFTS; i++)
+ if (bCalcFshift)
{
- fshift[i][0] += (nbst.fshift)[i][0];
- fshift[i][1] += (nbst.fshift)[i][1];
- fshift[i][2] += (nbst.fshift)[i][2];
+ for (int i = 0; i < SHIFTS; i++)
+ {
+ fshift[i][0] += (nbst.fshift)[i][0];
+ fshift[i][1] += (nbst.fshift)[i][1];
+ fshift[i][2] += (nbst.fshift)[i][2];
+ }
}
}
}
- /* turn off pruning (doesn't matter if this is pair-search step or not) */
- plist->bDoPrune = false;
+ /* Always reset both pruning flags (doesn't hurt doing it even when timing is off). */
+ timers->didPrune[iloc] = timers->didRollingPrune[iloc] = false;
+ /* Turn off initial list pruning (doesn't hurt if this is not pair-search step). */
+ plist->haveFreshList = false;
}
/*! \brief Selects the Ewald kernel type, analytical or tabulated, single or twin cut-off. */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/gpu_utils/oclutils.h"
-#include "gromacs/hardware/detecthardware.h"
#include "gromacs/hardware/gpu_hw_info.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdlib/force_flags.h"
*
* If the pointers to the size variables are NULL no resetting happens.
*/
-void ocl_free_buffered(cl_mem d_ptr, int *n, int *nalloc)
+static void ocl_free_buffered(cl_mem d_ptr, int *n, int *nalloc)
{
cl_int gmx_unused cl_error;
* for this operation or to query profiling information.
* OpenCL equivalent of cu_realloc_buffered.
*/
-void ocl_realloc_buffered(cl_mem *d_dest, void *h_src,
- size_t type_size,
- int *curr_size, int *curr_alloc_size,
- int req_size,
- cl_context context,
- cl_command_queue s,
- bool bAsync = true,
- cl_event *copy_event = NULL)
+static void ocl_realloc_buffered(cl_mem *d_dest, void *h_src,
+ size_t type_size,
+ int *curr_size, int *curr_alloc_size,
+ int req_size,
+ cl_context context,
+ cl_command_queue s,
+ bool bAsync = true,
+ cl_event *copy_event = NULL)
{
if (d_dest == NULL || req_size < 0)
{
/*! \brief Copies all parameters related to the cut-off from ic to nbp
*/
static void set_cutoff_parameters(cl_nbparam_t *nbp,
- const interaction_const_t *ic)
+ const interaction_const_t *ic,
+ const NbnxnListParameters *listParams)
{
- nbp->ewald_beta = ic->ewaldcoeff_q;
- nbp->sh_ewald = ic->sh_ewald;
- nbp->epsfac = ic->epsfac;
- nbp->two_k_rf = 2.0 * ic->k_rf;
- nbp->c_rf = ic->c_rf;
- nbp->rvdw_sq = ic->rvdw * ic->rvdw;
- nbp->rcoulomb_sq = ic->rcoulomb * ic->rcoulomb;
- nbp->rlist_sq = ic->rlist * ic->rlist;
-
- nbp->sh_lj_ewald = ic->sh_lj_ewald;
- nbp->ewaldcoeff_lj = ic->ewaldcoeff_lj;
-
- nbp->rvdw_switch = ic->rvdw_switch;
- nbp->dispersion_shift = ic->dispersion_shift;
- nbp->repulsion_shift = ic->repulsion_shift;
- nbp->vdw_switch = ic->vdw_switch;
+ nbp->ewald_beta = ic->ewaldcoeff_q;
+ nbp->sh_ewald = ic->sh_ewald;
+ nbp->epsfac = ic->epsfac;
+ nbp->two_k_rf = 2.0 * ic->k_rf;
+ nbp->c_rf = ic->c_rf;
+ nbp->rvdw_sq = ic->rvdw * ic->rvdw;
+ nbp->rcoulomb_sq = ic->rcoulomb * ic->rcoulomb;
+ nbp->rlistOuter_sq = listParams->rlistOuter * listParams->rlistOuter;
+ nbp->rlistInner_sq = listParams->rlistInner * listParams->rlistInner;
+ nbp->useDynamicPruning = listParams->useDynamicPruning;
+
+ nbp->sh_lj_ewald = ic->sh_lj_ewald;
+ nbp->ewaldcoeff_lj = ic->ewaldcoeff_lj;
+
+ nbp->rvdw_switch = ic->rvdw_switch;
+ nbp->dispersion_shift = ic->dispersion_shift;
+ nbp->repulsion_shift = ic->repulsion_shift;
+ nbp->vdw_switch = ic->vdw_switch;
}
/*! \brief Returns the kinds of electrostatics and Vdw OpenCL
*/
static void init_nbparam(cl_nbparam_t *nbp,
const interaction_const_t *ic,
+ const NbnxnListParameters *listParams,
const nbnxn_atomdata_t *nbat,
const gmx_device_runtime_data_t *runData)
{
ntypes = nbat->ntype;
- set_cutoff_parameters(nbp, ic);
+ set_cutoff_parameters(nbp, ic, listParams);
map_interaction_types_to_gpu_kernel_flavors(ic,
nbat->comb_rule,
//! This function is documented in the header file
void nbnxn_gpu_pme_loadbal_update_param(const nonbonded_verlet_t *nbv,
- const interaction_const_t *ic)
+ const interaction_const_t *ic,
+ const NbnxnListParameters *listParams)
{
if (!nbv || nbv->grp[0].kernel_type != nbnxnk8x8x8_GPU)
{
gmx_nbnxn_ocl_t *nb = nbv->gpu_nbv;
cl_nbparam_t *nbp = nb->nbparam;
- set_cutoff_parameters(nbp, ic);
+ set_cutoff_parameters(nbp, ic, listParams);
nbp->eeltype = nbnxn_gpu_pick_ewald_kernel_type(ic->rcoulomb != ic->rvdw);
need reallocation in nbnxn_gpu_init_pairlist */
pl->sci = NULL;
pl->cj4 = NULL;
+ pl->imask = NULL;
pl->excl = NULL;
/* size -1 indicates that the respective array hasn't been initialized yet */
- pl->na_c = -1;
- pl->nsci = -1;
- pl->sci_nalloc = -1;
- pl->ncj4 = -1;
- pl->cj4_nalloc = -1;
- pl->nexcl = -1;
- pl->excl_nalloc = -1;
- pl->bDoPrune = false;
+ pl->na_c = -1;
+ pl->nsci = -1;
+ pl->sci_nalloc = -1;
+ pl->ncj4 = -1;
+ pl->cj4_nalloc = -1;
+ pl->nimask = -1;
+ pl->imask_nalloc = -1;
+ pl->nexcl = -1;
+ pl->excl_nalloc = -1;
+ pl->haveFreshList = false;
}
/*! \brief Initializes the timer data structure.
*/
-static void init_timers(cl_timers_t gmx_unused *t, bool gmx_unused bUseTwoStreams)
+static void init_timers(cl_timers_t *t,
+ bool bUseTwoStreams)
{
- /* Nothing to initialize for OpenCL */
+ for (int i = 0; i <= (bUseTwoStreams ? 1 : 0); i++)
+ {
+ t->didPairlistH2D[i] = false;
+ t->didPrune[i] = false;
+ t->didRollingPrune[i] = false;
+ }
}
/*! \brief Initializes the timings data structure.
t->ktime[i][j].c = 0;
}
}
+
+ t->pruneTime.c = 0;
+ t->pruneTime.t = 0.0;
+ t->dynamicPruneTime.c = 0;
+ t->dynamicPruneTime.t = 0.0;
}
/*! \brief Creates context for OpenCL GPU given by \p mygpu
{
/* Init to 0 main kernel arrays */
/* They will be later on initialized in select_nbnxn_kernel */
+ // TODO: consider always creating all variants of the kernels here so that there is no
+ // need for late call to clCreateKernel -- if that gives any advantage?
memset(nb->kernel_ener_noprune_ptr, 0, sizeof(nb->kernel_ener_noprune_ptr));
memset(nb->kernel_ener_prune_ptr, 0, sizeof(nb->kernel_ener_prune_ptr));
memset(nb->kernel_noener_noprune_ptr, 0, sizeof(nb->kernel_noener_noprune_ptr));
memset(nb->kernel_noener_prune_ptr, 0, sizeof(nb->kernel_noener_prune_ptr));
+ /* Init pruning kernels
+ *
+ * TODO: we could avoid creating kernels if dynamic pruning is turned off,
+ * but ATM that depends on force flags not passed into the initialization.
+ */
+ nb->kernel_pruneonly[epruneFirst] = nbnxn_gpu_create_kernel(nb, "nbnxn_kernel_prune_opencl");
+ nb->kernel_pruneonly[epruneRolling] = nbnxn_gpu_create_kernel(nb, "nbnxn_kernel_prune_rolling_opencl");
+
/* Init auxiliary kernels */
nb->kernel_memset_f = nbnxn_gpu_create_kernel(nb, "memset_f");
nb->kernel_memset_f2 = nbnxn_gpu_create_kernel(nb, "memset_f2");
*/
static void nbnxn_ocl_init_const(gmx_nbnxn_ocl_t *nb,
const interaction_const_t *ic,
+ const NbnxnListParameters *listParams,
const nonbonded_verlet_group_t *nbv_group)
{
init_atomdata_first(nb->atdat, nbv_group[0].nbat->ntype, nb->dev_rundata);
- init_nbparam(nb->nbparam, ic, nbv_group[0].nbat, nb->dev_rundata);
+ init_nbparam(nb->nbparam, ic, listParams, nbv_group[0].nbat, nb->dev_rundata);
}
//! This function is documented in the header file
void nbnxn_gpu_init(gmx_nbnxn_ocl_t **p_nb,
- const gmx_gpu_info_t *gpu_info,
- const gmx_gpu_opt_t *gpu_opt,
+ const gmx_device_info_t *deviceInfo,
const interaction_const_t *ic,
+ const NbnxnListParameters *listParams,
nonbonded_verlet_group_t *nbv_grp,
- int my_gpu_index,
int rank,
gmx_bool bLocalAndNonlocal)
{
cl_int cl_error;
cl_command_queue_properties queue_properties;
- assert(gpu_info);
- assert(gpu_opt);
assert(ic);
if (p_nb == NULL)
snew(nb->timings, 1);
/* set device info, just point it to the right GPU among the detected ones */
- nb->dev_info = gpu_info->gpu_dev + gpu_opt->dev_use[my_gpu_index];
+ nb->dev_info = deviceInfo;
snew(nb->dev_rundata, 1);
/* init to NULL the debug buffer */
init_timings(nb->timings);
}
- nbnxn_ocl_init_const(nb, ic, nbv_grp);
+ nbnxn_ocl_init_const(nb, ic, listParams, nbv_grp);
/* Enable LJ param manual prefetch for AMD or if we request through env. var.
* TODO: decide about NVIDIA
}
}
+ if (nb->bDoTime)
+ {
+ nb->timers->didPairlistH2D[iloc] = true;
+ }
+
ocl_realloc_buffered(&d_plist->sci, h_plist->sci, sizeof(nbnxn_sci_t),
&d_plist->nsci, &d_plist->sci_nalloc,
h_plist->nsci,
nb->dev_rundata->context,
stream, true, &(nb->timers->pl_h2d_cj4[iloc]));
+ /* this call only allocates space on the device (no data is transferred) */
+ ocl_realloc_buffered(&d_plist->imask, NULL, sizeof(unsigned int),
+ &d_plist->nimask, &d_plist->imask_nalloc,
+ h_plist->ncj4*c_nbnxnGpuClusterpairSplit,
+ nb->dev_rundata->context,
+ stream, true, &(nb->timers->pl_h2d_imask[iloc]));
+
ocl_realloc_buffered(&d_plist->excl, h_plist->excl, sizeof(nbnxn_excl_t),
&d_plist->nexcl, &d_plist->excl_nalloc,
h_plist->nexcl,
stream, true, &(nb->timers->pl_h2d_excl[iloc]));
/* need to prune the pair list during the next step */
- d_plist->bDoPrune = true;
+ d_plist->haveFreshList = true;
}
//! This function is documented in the header file
}
/*! \brief Releases an OpenCL kernel pointer */
-void free_kernel(cl_kernel *kernel_ptr)
+static void free_kernel(cl_kernel *kernel_ptr)
{
cl_int gmx_unused cl_error;
}
/*! \brief Releases a list of OpenCL kernel pointers */
-void free_kernels(cl_kernel *kernels, int count)
+static void free_kernels(cl_kernel *kernels, int count)
{
int i;
/* Free plist */
free_ocl_buffer(&(nb->plist[eintLocal]->sci));
free_ocl_buffer(&(nb->plist[eintLocal]->cj4));
+ free_ocl_buffer(&(nb->plist[eintLocal]->imask));
free_ocl_buffer(&(nb->plist[eintLocal]->excl));
sfree(nb->plist[eintLocal]);
if (nb->bUseTwoStreams)
{
free_ocl_buffer(&(nb->plist[eintNonlocal]->sci));
free_ocl_buffer(&(nb->plist[eintNonlocal]->cj4));
+ free_ocl_buffer(&(nb->plist[eintNonlocal]->imask));
free_ocl_buffer(&(nb->plist[eintNonlocal]->excl));
sfree(nb->plist[eintNonlocal]);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* files outside the nbnxn_ocl as macros, to avoid including those files
* in the JIT compilation that happens at runtime.
*/
+
extraDefines += gmx::formatString(
- " -DCENTRAL=%d -DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=%d -DNBNXN_GPU_CLUSTER_SIZE=%d -DNBNXN_GPU_JGROUP_SIZE=%d -DNBNXN_MIN_RSQ=%s %s",
- CENTRAL, /* Defined in ishift.h */
- c_nbnxnGpuNumClusterPerSupercluster, /* Defined in nbnxn_pairlist.h */
- c_nbnxnGpuClusterSize, /* Defined in nbnxn_pairlist.h */
- c_nbnxnGpuJgroupSize, /* Defined in nbnxn_pairlist.h */
- STRINGIFY_MACRO(NBNXN_MIN_RSQ) /* Defined in nbnxn_consts.h */
- /* NBNXN_MIN_RSQ passed as string to avoid
- floating point representation problems with sprintf */
+ " -DCENTRAL=%d "
+ "-DNBNXN_GPU_NCLUSTER_PER_SUPERCLUSTER=%d -DNBNXN_GPU_CLUSTER_SIZE=%d -DNBNXN_GPU_JGROUP_SIZE=%d "
+ "-DGMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY=%d "
+ "-DNBNXN_MIN_RSQ=%s %s",
+ CENTRAL, /* Defined in ishift.h */
+ c_nbnxnGpuNumClusterPerSupercluster, /* Defined in nbnxn_pairlist.h */
+ c_nbnxnGpuClusterSize, /* Defined in nbnxn_pairlist.h */
+ c_nbnxnGpuJgroupSize, /* Defined in nbnxn_pairlist.h */
+ getOclPruneKernelJ4Concurrency(nb->dev_info->vendor_e), /* In nbnxn_ocl_types.h */
+ STRINGIFY_MACRO(NBNXN_MIN_RSQ) /* Defined in nbnxn_consts.h */
+ /* NBNXN_MIN_RSQ passed as string to avoid
+ floating point representation problems with sprintf */
, (nb->bPrefetchLjParam) ? "-DIATYPE_SHMEM" : ""
);
-
try
{
/* TODO when we have a proper MPI-aware logging module,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
float beta3 = nbparam->ewald_beta*nbparam->ewald_beta*nbparam->ewald_beta;
#endif
#ifdef PRUNE_NBL
- float rlist_sq = nbparam->rlist_sq;
+ float rlist_sq = nbparam->rlistOuter_sq;
#endif
#ifdef CALC_ENERGIES
#endif /* CALC_ENERGIES */
+#ifdef EXCLUSION_FORCES
+ const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
+#endif
+
/* loop over the j clusters = seen by any of the atoms in the current super-cluster */
for (j4 = cij4_start; j4 < cij4_end; j4++)
{
#endif
{
/* Pre-load cj into shared memory on both warps separately */
- if ((tidxj == 0 || tidxj == 4) && tidxi < NBNXN_GPU_JGROUP_SIZE)
+ if ((tidxj == 0 | tidxj == 4) & (tidxi < NBNXN_GPU_JGROUP_SIZE))
{
cjs[tidxi + tidxj * NBNXN_GPU_JGROUP_SIZE / 4] = pl_cj4[j4].cj[tidxi];
}
/* cutoff & exclusion check */
#ifdef EXCLUSION_FORCES
- if (r2 < rcoulomb_sq *
- (nb_sci.shift != CENTRAL || ci != cj || tidxj > tidxi))
+ if ((r2 < rcoulomb_sq) * (nonSelfInteraction | (ci != cj)))
#else
- if (r2 < rcoulomb_sq * int_bit)
+ if ((r2 < rcoulomb_sq) * int_bit)
#endif
{
/* load the rest of the i-atom parameters */
#ifdef LJ_POT_SWITCH
#ifdef CALC_ENERGIES
- calculate_potential_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F_E(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#else
- calculate_potential_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#endif /* CALC_ENERGIES */
#endif /* LJ_POT_SWITCH */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
float beta3 = nbparam->ewald_beta*nbparam->ewald_beta*nbparam->ewald_beta;
#endif
#ifdef PRUNE_NBL
- float rlist_sq = nbparam->rlist_sq;
+ float rlist_sq = nbparam->rlistOuter_sq;
#endif
#ifdef CALC_ENERGIES
#endif /* CALC_ENERGIES */
+#ifdef EXCLUSION_FORCES
+ const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
+#endif
+
/* loop over the j clusters = seen by any of the atoms in the current super-cluster */
for (j4 = cij4_start; j4 < cij4_end; j4++)
{
#endif
{
/* Pre-load cj into shared memory on both warps separately */
- if ((tidxj == 0 || tidxj == 4) && tidxi < NBNXN_GPU_JGROUP_SIZE)
+ if ((tidxj == 0 | tidxj == 4) & (tidxi < NBNXN_GPU_JGROUP_SIZE))
{
cjs[tidxi + tidxj * NBNXN_GPU_JGROUP_SIZE / 4] = pl_cj4[j4].cj[tidxi];
}
/* cutoff & exclusion check */
#ifdef EXCLUSION_FORCES
- if (r2 < rcoulomb_sq *
- (nb_sci.shift != CENTRAL || ci != cj || tidxj > tidxi))
+ if ((r2 < rcoulomb_sq) * (nonSelfInteraction | (ci != cj)))
#else
- if (r2 < rcoulomb_sq * int_bit)
+ if ((r2 < rcoulomb_sq) * int_bit)
#endif
{
/* load the rest of the i-atom parameters */
#ifdef LJ_POT_SWITCH
#ifdef CALC_ENERGIES
- calculate_potential_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F_E(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#else
- calculate_potential_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#endif /* CALC_ENERGIES */
#endif /* LJ_POT_SWITCH */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
float beta3 = nbparam->ewald_beta*nbparam->ewald_beta*nbparam->ewald_beta;
#endif
#ifdef PRUNE_NBL
- float rlist_sq = nbparam->rlist_sq;
+ float rlist_sq = nbparam->rlistOuter_sq;
#endif
#ifdef CALC_ENERGIES
#endif /* CALC_ENERGIES */
+#ifdef EXCLUSION_FORCES
+ const int nonSelfInteraction = !(nb_sci.shift == CENTRAL & tidxj <= tidxi);
+#endif
+
/* loop over the j clusters = seen by any of the atoms in the current super-cluster */
for (j4 = cij4_start; j4 < cij4_end; j4++)
{
#endif
{
/* Pre-load cj into shared memory on both warps separately */
- if ((tidxj == 0 || tidxj == 4) && tidxi < NBNXN_GPU_JGROUP_SIZE)
+ if ((tidxj == 0 | tidxj == 4) & (tidxi < NBNXN_GPU_JGROUP_SIZE))
{
cjs[tidxi + tidxj * NBNXN_GPU_JGROUP_SIZE / 4] = pl_cj4[j4].cj[tidxi];
}
/* cutoff & exclusion check */
#ifdef EXCLUSION_FORCES
- if (r2 < rcoulomb_sq *
- (nb_sci.shift != CENTRAL || ci != cj || tidxj > tidxi))
+ if ((r2 < rcoulomb_sq) * (nonSelfInteraction | (ci != cj)))
#else
- if (r2 < rcoulomb_sq * int_bit)
+ if ((r2 < rcoulomb_sq) * int_bit)
#endif
{
/* load the rest of the i-atom parameters */
#ifdef LJ_POT_SWITCH
#ifdef CALC_ENERGIES
- calculate_potential_switch_F_E(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F_E(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#else
- calculate_potential_switch_F(nbparam, c6, c12, inv_r, r2, &F_invr, &E_lj_p);
+ calculate_potential_switch_F(nbparam, inv_r, r2, &F_invr, &E_lj_p);
#endif /* CALC_ENERGIES */
#endif /* LJ_POT_SWITCH */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief OpenCL pruning kernel.
+ *
+ * OpenCL 1.2 support is expected; tested on AMD GCN and NVIDIA CC >3.0.
+ *
+ * \author Szilárd Páll <pall.szilard@gmail.com>
+ * \ingroup module_mdlib
+ */
+
+#include "nbnxn_ocl_kernel_utils.clh"
+
+/* Note: the AMD compiler testing was done with (fglrx 15.12) performs best with wg
+ * size 256 (this is an artificial compiler limitation). The compiler is also
+ * sensitive to tidx/widx declaration and warp_any initialization.
+ * With the current tweaks the regular prune kenel achieves 90%, the rolling 100%
+ * occupancy with both Fiji and Hawaii.
+ * TODO: if the wg size limit is removed in an upcoming AMD compiler the NTHREAD_Z=4
+ * should be revisited.
+ *
+ */
+#define NTHREAD_Z GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+
+#if !defined _AMD_SOURCE_ && ! defined _NVIDIA_SOURCE_
+ #error "The pruning kernel has not been tested on arch with execution width <32."
+#endif
+
+__attribute__((reqd_work_group_size(CL_SIZE, CL_SIZE, NTHREAD_Z)))
+#ifdef HAVE_FRESH_LIST
+ __kernel void nbnxn_kernel_prune_opencl
+#else
+ __kernel void nbnxn_kernel_prune_rolling_opencl
+#endif
+(
+ cl_nbparam_params_t nbparam_params,
+ const __global float4 *restrict xq,
+ const __global float *restrict shift_vec,
+ const __global nbnxn_sci_t *pl_sci,
+ __global nbnxn_cj4_t *pl_cj4,
+#if !defined HAVE_FRESH_LIST
+ const
+#endif
+ __global unsigned int *restrict prePrunedImask,
+ int numParts,
+ int part,
+ __local float4 *xib
+)
+{
+ /* convenience variables */
+ cl_nbparam_params_t *nbparam = &nbparam_params;
+
+ float rlistOuter_sq = nbparam->rlistOuter_sq;
+ float rlistInner_sq = nbparam->rlistInner_sq;
+
+ /* thread/block/warp id-s */
+ unsigned int tidxi = get_local_id(0);
+ unsigned int tidxj = get_local_id(1);
+ unsigned int tidx = get_local_id(1) * get_local_size(0) + get_local_id(0);
+#if NTHREAD_Z == 1
+ unsigned int tidxz = 0;
+#else
+ unsigned int tidxz = get_local_id(2);
+#endif
+ unsigned int bidx = get_group_id(0);
+ unsigned int widx = tidx / WARP_SIZE;
+
+#ifdef HAVE_FRESH_LIST
+ const bool haveFreshList = true;
+#else
+ const bool haveFreshList = false;
+#endif
+
+ // TODO move these consts to utils and unify their use with the nonbonded kernels
+ const int c_numClPerSupercl = NCL_PER_SUPERCL;
+ const int c_clSize = CL_SIZE;
+ const int c_nbnxnGpuJgroupSize = NBNXN_GPU_JGROUP_SIZE;
+
+ // TODO pass this value at compile-time as a macro
+ const int c_nbnxnGpuClusterpairSplit = 2;
+ const int c_splitClSize = c_clSize/c_nbnxnGpuClusterpairSplit;
+
+ /*! i-cluster interaction mask for a super-cluster with all c_numClPerSupercl=8 bits set */
+ const unsigned superClInteractionMask = ((1U << c_numClPerSupercl) - 1U);
+
+ /* shmem buffer for i cj pre-loading */
+ #define LOCAL_OFFSET xib + c_numClPerSupercl * c_clSize
+ __local int *cjs = (((__local int *)(LOCAL_OFFSET)) + tidxz * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize);
+ #undef LOCAL_OFFSET
+ /* Offset calculated using xib because cjs depends on on tidxz! */
+ #define LOCAL_OFFSET (((__local int *)(xib + c_numClPerSupercl * c_clSize)) + (NTHREAD_Z * c_nbnxnGpuClusterpairSplit * c_nbnxnGpuJgroupSize))
+
+ /* Local buffer used to implement __any warp vote function from CUDA.
+ volatile is used to avoid compiler optimizations for AMD builds. */
+ volatile __local uint *warp_any = (__local uint*)(LOCAL_OFFSET);
+ #undef LOCAL_OFFSET
+
+ unsigned int warpVoteSlot = NTHREAD_Z*tidxz + widx;
+ /* Initialise warp vote.*/
+ if(tidx == 0 || tidx == 32)
+ {
+ warp_any[warpVoteSlot] = 0;
+ }
+
+ nbnxn_sci_t nb_sci = pl_sci[bidx*numParts + part]; /* my i super-cluster's index = sciOffset + current bidx * numParts + part */
+ int sci = nb_sci.sci; /* super-cluster */
+ int cij4_start = nb_sci.cj4_ind_start; /* first ...*/
+ int cij4_end = nb_sci.cj4_ind_end; /* and last index of j clusters */
+
+ if (tidxz == 0)
+ {
+ /* Pre-load i-atom x and q into shared memory */
+ int ci = sci * c_numClPerSupercl + tidxj;
+ int ai = ci * c_clSize + tidxi;
+
+ /* We don't need q, but using float4 in shmem avoids bank conflicts */
+ float4 tmp = xq[ai];
+ float4 xi = tmp + (float4)(shift_vec[3 * nb_sci.shift], shift_vec[3 * nb_sci.shift + 1], shift_vec[3 * nb_sci.shift + 2], 0.0f);
+ xib[tidxj * c_clSize + tidxi] = xi;
+ }
+ barrier(CLK_LOCAL_MEM_FENCE);
+
+
+ /* loop over the j clusters = seen by any of the atoms in the current super-cluster */
+ for (int j4 = cij4_start + tidxz; j4 < cij4_end; j4 += NTHREAD_Z)
+ {
+ unsigned int imaskFull, imaskCheck, imaskNew;
+
+ if (haveFreshList)
+ {
+ /* Read the mask from the list transferred from the CPU */
+ imaskFull = pl_cj4[j4].imei[widx].imask;
+ /* We attempt to prune all pairs present in the original list */
+ imaskCheck = imaskFull;
+ imaskNew = 0;
+ }
+ else
+ {
+ /* Read the mask from the "warp-pruned" by rlistOuter mask array */
+ imaskFull = prePrunedImask[j4*c_nbnxnGpuClusterpairSplit + widx];
+ /* Read the old rolling pruned mask, use as a base for new */
+ imaskNew = pl_cj4[j4].imei[widx].imask;
+ /* We only need to check pairs with different mask */
+ imaskCheck = (imaskNew ^ imaskFull);
+ }
+
+ if (imaskCheck)
+ {
+ /* Pre-load cj into shared memory on both warps separately */
+ if ((tidxj == 0 | tidxj == 4) & (tidxi < c_nbnxnGpuJgroupSize))
+ {
+ cjs[tidxi + tidxj * c_nbnxnGpuJgroupSize/c_splitClSize] = pl_cj4[j4].cj[tidxi];
+ }
+
+#pragma unroll 4
+ for (int jm = 0; jm < c_nbnxnGpuJgroupSize; jm++)
+ {
+ if (imaskCheck & (superClInteractionMask << (jm * c_numClPerSupercl)))
+ {
+ unsigned int mask_ji = (1U << (jm * c_numClPerSupercl));
+
+ int cj = cjs[jm + (tidxj & 4) * c_nbnxnGpuJgroupSize/c_splitClSize];
+ int aj = cj * c_clSize + tidxj;
+
+ /* load j atom data */
+ float4 tmp = xq[aj];
+ float3 xj = (float3)(tmp.xyz);
+
+#pragma unroll 8
+ for (int i = 0; i < c_numClPerSupercl; i++)
+ {
+ if (imaskCheck & mask_ji)
+ {
+ /* load i-cluster coordinates from shmem */
+ float4 xi = xib[i * c_clSize + tidxi];
+
+ /* distance between i and j atoms */
+ float3 rv = (float3)(xi.xyz) - xj;
+ float r2 = norm2(rv);
+
+ if (haveFreshList)
+ {
+ /* If _none_ of the atoms pairs are in cutoff range,
+ the bit corresponding to the current
+ cluster-pair in imask gets set to 0. */
+ if (r2 < rlistOuter_sq)
+ {
+ warp_any[warpVoteSlot] = 1;
+ }
+ if (!warp_any[warpVoteSlot])
+ {
+ imaskFull &= ~mask_ji;
+ }
+ warp_any[warpVoteSlot] = 0;
+ }
+ /* If any atom pair is within range, set the bit
+ corresponding to the current cluster-pair. */
+ if (r2 < rlistInner_sq)
+ {
+ warp_any[warpVoteSlot] = 1;
+ }
+ if (warp_any[warpVoteSlot])
+ {
+ imaskNew |= mask_ji;
+ }
+ warp_any[warpVoteSlot] = 0;
+ }
+
+ /* shift the mask bit by 1 */
+ mask_ji += mask_ji;
+ }
+ }
+ }
+
+#ifdef HAVE_FRESH_LIST
+ {
+ /* copy the list pruned to rlistOuter to a separate buffer */
+ prePrunedImask[j4*c_nbnxnGpuClusterpairSplit + widx] = imaskFull;
+ }
+#endif
+ /* update the imask with only the pairs up to rlistInner */
+ pl_cj4[j4].imei[widx].imask = imaskNew;
+ }
+ }
+}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
float rvdw_sq; /**< VdW cut-off squared */
float rvdw_switch; /**< VdW switched cut-off */
- float rlist_sq; /**< pair-list cut-off squared */
+ float rlistOuter_sq; /**< Full, outer pair-list cut-off squared */
+ float rlistInner_sq; /**< Inner, dynamic pruned pair-list cut-off squared XXX: this is only needed in the pruning kernels, but for now we also pass it to the nonbondeds */
shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
/*! Apply potential switch, force-only version. */
__INLINE__ __device__
void calculate_potential_switch_F(cl_nbparam_params_t *nbparam,
- float c6,
- float c12,
float inv_r,
float r2,
float *F_invr,
/*! Apply potential switch, force + energy version. */
__INLINE__ __device__
void calculate_potential_switch_F_E(cl_nbparam_params_t *nbparam,
- float c6,
- float c12,
float inv_r,
float r2,
float *F_invr,
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
#define __IN_OPENCL_KERNEL__
/* Auxiliary kernels */
}
}
+/* Generate pruning kernels. */
+#define HAVE_FRESH_LIST 1
+#include "nbnxn_ocl_kernel_pruneonly.clh"
+#undef HAVE_FRESH_LIST
+#include "nbnxn_ocl_kernel_pruneonly.clh"
+
#if defined GMX_OCL_FASTGEN
#define FLAVOR_LEVEL_GENERATOR "nbnxn_ocl_kernels_fastgen.clh"
#elif defined GMX_OCL_FASTGEN_ADD_TWINCUT
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Data types used internally in the nbnxn_ocl module.
*
* \author Anca Hamuraru <anca@streamcomputing.eu>
+ * \author Szilárd Páll <pszilard@kth.se>
* \ingroup module_mdlib
*/
# include <CL/opencl.h>
#endif
+#include "gromacs/gpu_utils/oclutils.h"
#include "gromacs/mdlib/nbnxn_pairlist.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/utility/real.h"
//! Define 1/sqrt(pi)
#define M_FLOAT_1_SQRTPI 0.564189583547756f
+/*! \brief Macros defining platform-dependent defaults for the prune kernel's j4 processing concurrency.
+ *
+ * The GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY macro allows compile-time override.
+ */
+/*! @{ */
+#ifndef GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_AMD 4
+#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_NVIDIA 4
+#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_DEFAULT 4
+#else
+#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_AMD GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_NVIDIA GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+#define GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_DEFAULT GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY
+#endif
+/*! @} */
+/*! \brief Constants for platform-dependent defaults for the prune kernel's j4 processing concurrency.
+ *
+ * Initialized using macros that can be overridden at compile-time (using #GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY).
+ */
+/*! @{ */
+const int c_oclPruneKernelJ4ConcurrencyAMD = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_AMD;
+const int c_oclPruneKernelJ4ConcurrencyNVIDIA = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_NVIDIA;
+const int c_oclPruneKernelJ4ConcurrencyDefault = GMX_NBNXN_PRUNE_KERNEL_J4_CONCURRENCY_DEFAULT;
+/*! @} */
+
+/*! \brief Returns the j4 processing concurrency parameter for the vendor \p vendorId
+ * \param vendorId takes values from #ocl_vendor_id_t.
+ */
+static inline int getOclPruneKernelJ4Concurrency(int vendorId)
+{
+ assert(vendorId < OCL_VENDOR_UNKNOWN);
+ switch (vendorId)
+ {
+ case OCL_VENDOR_AMD: return c_oclPruneKernelJ4ConcurrencyAMD; break;
+ case OCL_VENDOR_NVIDIA: return c_oclPruneKernelJ4ConcurrencyNVIDIA; break;
+ default: return c_oclPruneKernelJ4ConcurrencyDefault; break;
+ }
+}
+
#ifdef __cplusplus
extern "C" {
evdwOclCUT, evdwOclCUTCOMBGEOM, evdwOclCUTCOMBLB, evdwOclFSWITCH, evdwOclPSWITCH, evdwOclEWALDGEOM, evdwOclEWALDLB, evdwOclNR
};
+/*! \brief Pruning kernel flavors.
+ *
+ * The values correspond to the first call of the pruning post-list generation
+ * and the rolling pruning, respectively.
+ */
+enum ePruneKind {
+ epruneFirst, epruneRolling, ePruneNR
+};
+
/*! \internal
* \brief Staging area for temporary data downloaded from the GPU.
*
typedef struct cl_nbparam
{
- int eeltype; /**< type of electrostatics, takes values from #eelOcl */
- int vdwtype; /**< type of VdW impl., takes values from #evdwOcl */
+ int eeltype; /**< type of electrostatics, takes values from #eelOcl */
+ int vdwtype; /**< type of VdW impl., takes values from #evdwOcl */
- float epsfac; /**< charge multiplication factor */
- float c_rf; /**< Reaction-field/plain cutoff electrostatics const. */
- float two_k_rf; /**< Reaction-field electrostatics constant */
- float ewald_beta; /**< Ewald/PME parameter */
- float sh_ewald; /**< Ewald/PME correction term substracted from the direct-space potential */
- float sh_lj_ewald; /**< LJ-Ewald/PME correction term added to the correction potential */
- float ewaldcoeff_lj; /**< LJ-Ewald/PME coefficient */
+ float epsfac; /**< charge multiplication factor */
+ float c_rf; /**< Reaction-field/plain cutoff electrostatics const. */
+ float two_k_rf; /**< Reaction-field electrostatics constant */
+ float ewald_beta; /**< Ewald/PME parameter */
+ float sh_ewald; /**< Ewald/PME correction term substracted from the direct-space potential */
+ float sh_lj_ewald; /**< LJ-Ewald/PME correction term added to the correction potential */
+ float ewaldcoeff_lj; /**< LJ-Ewald/PME coefficient */
- float rcoulomb_sq; /**< Coulomb cut-off squared */
+ float rcoulomb_sq; /**< Coulomb cut-off squared */
- float rvdw_sq; /**< VdW cut-off squared */
- float rvdw_switch; /**< VdW switched cut-off */
- float rlist_sq; /**< pair-list cut-off squared */
+ float rvdw_sq; /**< VdW cut-off squared */
+ float rvdw_switch; /**< VdW switched cut-off */
+ float rlistOuter_sq; /**< Full, outer pair-list cut-off squared */
+ float rlistInner_sq; /**< Inner, dynamic pruned pair-list cut-off squared */
+ bool useDynamicPruning; /**< True if we use dynamic pair-list pruning */
- shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
- shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
- switch_consts_t vdw_switch; /**< VdW switch constants */
+ shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
+ shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
+ switch_consts_t vdw_switch; /**< VdW switch constants */
/* LJ non-bonded parameters - accessed through texture memory */
cl_mem nbfp_climg2d; /**< nonbonded parameter table with C6/C12 pairs per atom type-pair, 2*ntype^2 elements */
float rvdw_sq; /**< VdW cut-off squared */
float rvdw_switch; /**< VdW switched cut-off */
- float rlist_sq; /**< pair-list cut-off squared */
+ float rlistOuter_sq; /**< Full, outer pair-list cut-off squared */
+ float rlistInner_sq; /**< Inner, dynamic pruned pair-list cut-off squared */
shift_consts_t dispersion_shift; /**< VdW shift dispersion constants */
shift_consts_t repulsion_shift; /**< VdW shift repulsion constants */
*/
typedef struct cl_plist
{
- int na_c; /**< number of atoms per cluster */
-
- int nsci; /**< size of sci, # of i clusters in the list */
- int sci_nalloc; /**< allocation size of sci */
- cl_mem sci; /**< list of i-cluster ("super-clusters").
- It contains elements of type nbnxn_sci_t */
-
- int ncj4; /**< total # of 4*j clusters */
- int cj4_nalloc; /**< allocation size of cj4 */
- cl_mem cj4; /**< 4*j cluster list, contains j cluster number and
- index into the i cluster list.
- It contains elements of type nbnxn_cj4_t */
- cl_mem excl; /**< atom interaction bits
- It contains elements of type nbnxn_excl_t */
- int nexcl; /**< count for excl */
- int excl_nalloc; /**< allocation size of excl */
-
- cl_bool bDoPrune; /**< true if pair-list pruning needs to be
- done during the current step */
+ int na_c; /**< number of atoms per cluster */
+
+ int nsci; /**< size of sci, # of i clusters in the list */
+ int sci_nalloc; /**< allocation size of sci */
+ cl_mem sci; /**< list of i-cluster ("super-clusters").
+ It contains elements of type nbnxn_sci_t */
+
+ int ncj4; /**< total # of 4*j clusters */
+ int cj4_nalloc; /**< allocation size of cj4 */
+ cl_mem cj4; /**< 4*j cluster list, contains j cluster number and
+ index into the i cluster list.
+ It contains elements of type nbnxn_cj4_t */
+ int nimask; /**< # of 4*j clusters * # of warps */
+ int imask_nalloc; /**< allocation size of imask */
+ cl_mem imask; /**< imask for 2 warps for each 4*j cluster group */
+ cl_mem excl; /**< atom interaction bits
+ It contains elements of type nbnxn_excl_t */
+ int nexcl; /**< count for excl */
+ int excl_nalloc; /**< allocation size of excl */
+
+ /* parameter+variables for normal and rolling pruning */
+ bool haveFreshList; /**< true after search, indictes that initial pruning with outer prunning is needed */
+ int rollingPruningNumParts; /**< the number of parts/steps over which one cyle of roling pruning takes places */
+ int rollingPruningPart; /**< the next part to which the roling pruning needs to be applied */
}cl_plist_t;
*/
typedef struct cl_timers
{
- cl_event atdat; /**< event for atom data transfer (every PS step) */
+ cl_event atdat; /**< event for atom data transfer (every PS step) */
+
+ cl_event nb_h2d[2]; /**< events for x/q H2D transfers (l/nl, every step) */
- cl_event nb_h2d[2]; /**< events for x/q H2D transfers (l/nl, every step) */
+ cl_event nb_d2h_f[2]; /**< events for f D2H transfer (l/nl, every step) */
+ cl_event nb_d2h_fshift[2]; /**< events for fshift D2H transfer (l/nl, every step) */
+ cl_event nb_d2h_e_el[2]; /**< events for e_el D2H transfer (l/nl, every step) */
+ cl_event nb_d2h_e_lj[2]; /**< events for e_lj D2H transfer (l/nl, every step) */
- cl_event nb_d2h_f[2]; /**< events for f D2H transfer (l/nl, every step) */
- cl_event nb_d2h_fshift[2]; /**< events for fshift D2H transfer (l/nl, every step) */
- cl_event nb_d2h_e_el[2]; /**< events for e_el D2H transfer (l/nl, every step) */
- cl_event nb_d2h_e_lj[2]; /**< events for e_lj D2H transfer (l/nl, every step) */
+ cl_event pl_h2d_sci[2]; /**< events for pair-list sci H2D transfers (l/nl, every PS step) */
+ cl_event pl_h2d_cj4[2]; /**< events for pair-list cj4 H2D transfers (l/nl, every PS step) */
+ cl_event pl_h2d_excl[2]; /**< events for pair-list excl H2D transfers (l/nl, every PS step)*/
+ cl_event pl_h2d_imask[2]; /**< events for pair-list imask H2D transfers (l/nl, every PS step)*/
- cl_event pl_h2d_sci[2]; /**< events for pair-list sci H2D transfers (l/nl, every PS step) */
- cl_event pl_h2d_cj4[2]; /**< events for pair-list cj4 H2D transfers (l/nl, every PS step) */
- cl_event pl_h2d_excl[2]; /**< events for pair-list excl H2D transfers (l/nl, every PS step)*/
+ cl_event nb_k[2]; /**< event for non-bonded kernels (l/nl, every step) */
- cl_event nb_k[2]; /**< event for non-bonded kernels (l/nl, every step) */
+ bool didPairlistH2D[2]; /**< tells if we timed a pair-list transfer */
+ cl_event prune_k[2]; /**< event for pruning kernel (every prune step) */
+ bool didPrune[2]; /**< tells uf we timed pruning this (or previous step for rolling) and that the timings need to be accounted for */
+ cl_event rollingPrune_k[2]; /**< event for rolling pruning kernel (every prune step) */
+ bool didRollingPrune[2]; /**< tells uf we timed pruning this (or previous step for rolling) and that the timings need to be accounted for */
} cl_timers_t;
/*! \internal
*/
struct gmx_nbnxn_ocl_t
{
- struct gmx_device_info_t *dev_info; /**< OpenCL device information */
+ const gmx_device_info_t *dev_info; /**< OpenCL device information */
struct gmx_device_runtime_data_t *dev_rundata; /**< OpenCL runtime data (context, kernels) */
/**< Pointers to non-bonded kernel functions
cl_kernel kernel_noener_prune_ptr[eelOclNR][evdwOclNR];
cl_kernel kernel_ener_prune_ptr[eelOclNR][evdwOclNR];
///@}
+ cl_kernel kernel_pruneonly[ePruneNR]; /**< prune kernels, ePruneKind defined the kernel kinds */
- bool bPrefetchLjParam; /**< true if prefetching fg i-atom LJ parameters should be used in the kernels */
+ bool bPrefetchLjParam; /**< true if prefetching fg i-atom LJ parameters should be used in the kernels */
/**< auxiliary kernels implementing memset-like functions */
///@{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstddef>
-#include "thread_mpi/atomic.h"
-
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/bitmask.h"
#include "gromacs/utility/real.h"
+struct tMPI_Atomic;
+
+/*! \cond INTERNAL */
+
+/*! \brief The setup for generating and pruning the nbnxn pair list.
+ *
+ * Without dynamic pruning rlistOuter=rlistInner.
+ */
+struct NbnxnListParameters
+{
+ /*! \brief Constructor producing a struct with dynamic pruning disabled
+ */
+ NbnxnListParameters(real rlist) :
+ useDynamicPruning(false),
+ nstlistPrune(-1),
+ rlistOuter(rlist),
+ rlistInner(rlist),
+ numRollingParts(1)
+ {
+ }
+
+ bool useDynamicPruning; //!< Are we using dynamic pair-list pruning
+ int nstlistPrune; //!< Pair-list dynamic pruning interval
+ real rlistOuter; //!< Cut-off of the larger, outer pair-list
+ real rlistInner; //!< Cut-off of the smaller, inner pair-list
+ int numRollingParts; //!< The number parts to divide the pair-list into for rolling pruning, a value of 1 gives no rolling pruning
+};
+
+/*! \endcond */
+
/* With GPU kernels the i and j cluster size is 8 atoms */
static const int c_nbnxnGpuClusterSize = 8;
int na_sc; /* The number of atoms per super cluster */
real rlist; /* The radius for constructing the list */
int nci; /* The number of i-clusters in the list */
+ int nciOuter; /* The number of i-clusters in the outer, unpruned list, -1 when invalid */
nbnxn_ci_t *ci; /* The i-cluster list, size nci */
- int ci_nalloc; /* The allocation size of ci */
+ nbnxn_ci_t *ciOuter; /* The outer, unpruned i-cluster list, size nciOuter(=-1 when invalid) */
+ int ci_nalloc; /* The allocation size of ci/ciOuter */
int nsci; /* The number of i-super-clusters in the list */
nbnxn_sci_t *sci; /* The i-super-cluster list */
int sci_nalloc; /* The allocation size of sci */
int ncj; /* The number of j-clusters in the list */
nbnxn_cj_t *cj; /* The j-cluster list, size ncj */
- int cj_nalloc; /* The allocation size of cj */
+ nbnxn_cj_t *cjOuter; /* The outer, unpruned j-cluster list, size ncj */
+ int cj_nalloc; /* The allocation size of cj/cj0 */
int ncjInUse; /* The number of j-clusters that are used by ci entries in this list, will be <= ncj */
int ncj4; /* The total number of 4*j clusters */
} nbnxn_pairlist_t;
typedef struct {
- int nnbl; /* number of lists */
- nbnxn_pairlist_t **nbl; /* lists */
- nbnxn_pairlist_t **nbl_work; /* work space for rebalancing lists */
- gmx_bool bCombined; /* TRUE if lists get combined into one (the 1st) */
- gmx_bool bSimple; /* TRUE if the list of of type "simple"
- (na_sc=na_s, no super-clusters used) */
- int natpair_ljq; /* Total number of atom pairs for LJ+Q kernel */
- int natpair_lj; /* Total number of atom pairs for LJ kernel */
- int natpair_q; /* Total number of atom pairs for Q kernel */
- t_nblist **nbl_fep;
+ int nnbl; /* number of lists */
+ nbnxn_pairlist_t **nbl; /* lists */
+ nbnxn_pairlist_t **nbl_work; /* work space for rebalancing lists */
+ gmx_bool bCombined; /* TRUE if lists get combined into one (the 1st) */
+ gmx_bool bSimple; /* TRUE if the list of of type "simple"
+ (na_sc=na_s, no super-clusters used) */
+ int natpair_ljq; /* Total number of atom pairs for LJ+Q kernel */
+ int natpair_lj; /* Total number of atom pairs for LJ kernel */
+ int natpair_q; /* Total number of atom pairs for Q kernel */
+ t_nblist **nbl_fep; /* List of free-energy atom pair interactions */
+ gmx_int64_t outerListCreationStep; /* Step at which the outer list was created */
} nbnxn_pairlist_set_t;
enum {
gmx_bool bUseBufferFlags; /* Use the flags or operate on all atoms */
nbnxn_buffer_flags_t buffer_flags; /* Flags for buffer zeroing+reduc. */
gmx_bool bUseTreeReduce; /* Use tree for force reduction */
- tMPI_Atomic_t *syncStep; /* Synchronization step for tree reduce */
+ tMPI_Atomic *syncStep; /* Synchronization step for tree reduce */
} nbnxn_atomdata_t;
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* This leads to more conditionals than shifting forward.
* We do this to get more balanced pair lists.
*/
-static const bool pbc_shift_backward = true;
+constexpr bool c_pbcShiftBackward = true;
static void nbs_cycle_clear(nbnxn_cycle_t *cc)
fprintf(fp, "\n");
}
-static gmx_inline int ci_to_cj(int ci, int na_cj_2log)
+gmx_unused static gmx_inline int ci_to_cj(int ci, int na_cj_2log)
{
switch (na_cj_2log)
{
nl->maxnrj = 0;
nl->nri = 0;
nl->nrj = 0;
- nl->iinr = NULL;
- nl->gid = NULL;
- nl->shift = NULL;
- nl->jindex = NULL;
- nl->jjnr = NULL;
- nl->excl_fep = NULL;
+ nl->iinr = nullptr;
+ nl->gid = nullptr;
+ nl->shift = nullptr;
+ nl->jindex = nullptr;
+ nl->jjnr = nullptr;
+ nl->excl_fep = nullptr;
}
nbs->bFEP = bFEP;
- nbs->DomDec = (n_dd_cells != NULL);
+ nbs->DomDec = (n_dd_cells != nullptr);
clear_ivec(nbs->dd_dim);
ngrid = 1;
nbnxn_grids_init(nbs, ngrid);
- nbs->cell = NULL;
+ nbs->cell = nullptr;
nbs->cell_nalloc = 0;
- nbs->a = NULL;
+ nbs->a = nullptr;
nbs->a_nalloc = 0;
nbs->nthread_max = nthread_max;
snew(nbs->work, nbs->nthread_max);
for (int t = 0; t < nbs->nthread_max; t++)
{
- nbs->work[t].cxy_na = NULL;
+ nbs->work[t].cxy_na = nullptr;
nbs->work[t].cxy_na_nalloc = 0;
- nbs->work[t].sort_work = NULL;
+ nbs->work[t].sort_work = nullptr;
nbs->work[t].sort_work_nalloc = 0;
snew(nbs->work[t].nbl_fep, 1);
}
/* Initialize detailed nbsearch cycle counting */
- nbs->print_cycles = (getenv("GMX_NBNXN_CYCLE") != 0);
+ nbs->print_cycles = (getenv("GMX_NBNXN_CYCLE") != nullptr);
nbs->search_count = 0;
nbs_cycle_clear(nbs->cc);
for (int t = 0; t < nbs->nthread_max; t++)
}
/* Reference code calculating the distance^2 between two bounding boxes */
-static float box_dist2(float bx0, float bx1, float by0,
+/*
+ static float box_dist2(float bx0, float bx1, float by0,
float by1, float bz0, float bz1,
const nbnxn_bb_t *bb)
-{
+ {
float d2;
float dl, dh, dm, dm0;
d2 += dm0*dm0;
return d2;
-}
+ }
+ */
/* Plain C code calculating the distance^2 between two bounding boxes */
static float subc_bb_dist2(int si, const nbnxn_bb_t *bb_i_ci,
#endif /* NBNXN_SEARCH_BB_SIMD4 */
-/* Returns if any atom pair from two clusters is within distance sqrt(rl2) */
+/* Returns if any atom pair from two clusters is within distance sqrt(rlist2) */
static gmx_inline gmx_bool
clusterpair_in_range(const nbnxn_list_work_t *work,
int si,
int csj, int stride, const real *x_j,
- real rl2)
+ real rlist2)
{
#if !GMX_SIMD4_HAVE_REAL
real d2 = gmx::square(x_i[i0 ] - x_j[j0 ]) + gmx::square(x_i[i0+1] - x_j[j0+1]) + gmx::square(x_i[i0+2] - x_j[j0+2]);
- if (d2 < rl2)
+ if (d2 < rlist2)
{
return TRUE;
}
*/
assert(c_nbnxnGpuClusterSize == 8);
- Simd4Real rc2_S = Simd4Real(rl2);
+ Simd4Real rc2_S = Simd4Real(rlist2);
const real *x_i = work->x_ci_simd;
}
}
-/* Ensures there is enough space for ncell extra j-cells in the list */
+/* Ensures there is enough space for maxNumExtraClusters extra j-clusters in the list */
static void check_cell_list_space_simple(nbnxn_pairlist_t *nbl,
- int ncell)
+ int maxNumExtraClusters)
{
int cj_max;
- cj_max = nbl->ncj + ncell;
+ cj_max = nbl->ncj + maxNumExtraClusters;
if (cj_max > nbl->cj_nalloc)
{
nbl->ncj*sizeof(*nbl->cj),
nbl->cj_nalloc*sizeof(*nbl->cj),
nbl->alloc, nbl->free);
+
+ nbnxn_realloc_void((void **)&nbl->cjOuter,
+ nbl->ncj*sizeof(*nbl->cjOuter),
+ nbl->cj_nalloc*sizeof(*nbl->cjOuter),
+ nbl->alloc, nbl->free);
}
}
nbnxn_alloc_t *alloc,
nbnxn_free_t *free)
{
- if (alloc == NULL)
+ if (alloc == nullptr)
{
nbl->alloc = nbnxn_alloc_aligned;
}
{
nbl->alloc = alloc;
}
- if (free == NULL)
+ if (free == nullptr)
{
nbl->free = nbnxn_free_aligned;
}
nbl->na_ci = 0;
nbl->na_cj = 0;
nbl->nci = 0;
- nbl->ci = NULL;
+ nbl->ci = nullptr;
nbl->ci_nalloc = 0;
nbl->nsci = 0;
- nbl->sci = NULL;
+ nbl->sci = nullptr;
nbl->sci_nalloc = 0;
nbl->ncj = 0;
nbl->ncjInUse = 0;
- nbl->cj = NULL;
+ nbl->cj = nullptr;
nbl->cj_nalloc = 0;
nbl->ncj4 = 0;
/* We need one element extra in sj, so alloc initially with 1 */
nbl->cj4_nalloc = 0;
- nbl->cj4 = NULL;
+ nbl->cj4 = nullptr;
nbl->nci_tot = 0;
if (!nbl->bSimple)
GMX_ASSERT(sizeof(nbl->cj4[0].imei[0].imask)*8 >= c_nbnxnGpuJgroupSize*c_gpuNumClusterPerCell, "The i super-cluster cluster interaction mask does not contain a sufficient number of bits");
GMX_ASSERT(sizeof(nbl->excl[0])*8 >= c_nbnxnGpuJgroupSize*c_gpuNumClusterPerCell, "The GPU exclusion mask does not contain a sufficient number of bits");
- nbl->excl = NULL;
+ nbl->excl = nullptr;
nbl->excl_nalloc = 0;
nbl->nexcl = 0;
check_excl_space(nbl, 1);
#endif
snew_aligned(nbl->work->d2, c_gpuNumClusterPerCell, NBNXN_SEARCH_BB_MEM_ALIGN);
- nbl->work->sort = NULL;
+ nbl->work->sort = nullptr;
nbl->work->sort_nalloc = 0;
- nbl->work->sci_sort = NULL;
+ nbl->work->sci_sort = nullptr;
nbl->work->sci_sort_nalloc = 0;
}
}
else
{
- nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, NULL, NULL);
+ nbnxn_init_pairlist(nbl_list->nbl[i], nbl_list->bSimple, nullptr, nullptr);
if (bSimple && nbl_list->nnbl > 1)
{
snew(nbl_list->nbl_work[i], 1);
- nbnxn_init_pairlist(nbl_list->nbl_work[i], nbl_list->bSimple, NULL, NULL);
+ nbnxn_init_pairlist(nbl_list->nbl_work[i], nbl_list->bSimple, nullptr, nullptr);
}
}
}
/* Returns a diagonal or off-diagonal interaction mask for cj-size=2 */
-static unsigned int get_imask_simd_j2(gmx_bool rdiag, int ci, int cj)
+gmx_unused static unsigned int get_imask_simd_j2(gmx_bool rdiag, int ci, int cj)
{
return (rdiag && ci*2 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_0 :
(rdiag && ci*2+1 == cj ? NBNXN_INTERACTION_MASK_DIAG_J2_1 :
}
/* Returns a diagonal or off-diagonal interaction mask for cj-size=4 */
-static unsigned int get_imask_simd_j4(gmx_bool rdiag, int ci, int cj)
+gmx_unused static unsigned int get_imask_simd_j4(gmx_bool rdiag, int ci, int cj)
{
return (rdiag && ci == cj ? NBNXN_INTERACTION_MASK_DIAG : NBNXN_INTERACTION_MASK_ALL);
}
/* Returns a diagonal or off-diagonal interaction mask for cj-size=8 */
-static unsigned int get_imask_simd_j8(gmx_bool rdiag, int ci, int cj)
+gmx_unused static unsigned int get_imask_simd_j8(gmx_bool rdiag, int ci, int cj)
{
return (rdiag && ci == cj*2 ? NBNXN_INTERACTION_MASK_DIAG_J8_0 :
(rdiag && ci == cj*2+1 ? NBNXN_INTERACTION_MASK_DIAG_J8_1 :
#endif
#endif
-/* Plain C code for making a pair list of cell ci vs cell cjf-cjl.
- * Checks bounding box distances and possibly atom pair distances.
+/* Plain C code for checking and adding cluster-pairs to the list.
+ *
+ * \param[in] gridj The j-grid
+ * \param[in,out] nbl The pair-list to store the cluster pairs in
+ * \param[in] icluster The index of the i-cluster
+ * \param[in] jclusterFirst The first cluster in the j-range
+ * \param[in] jclusterLast The last cluster in the j-range
+ * \param[in] excludeSubDiagonal Exclude atom pairs with i-index > j-index
+ * \param[in] x_j Coordinates for the j-atom, in xyz format
+ * \param[in] rlist2 The squared list cut-off
+ * \param[in] rbb2 The squared cut-off for putting cluster-pairs in the list based on bounding box distance only
+ * \param[in,out] numDistanceChecks The number of distance checks performed
*/
-static void make_cluster_list_simple(const nbnxn_grid_t *gridj,
- nbnxn_pairlist_t *nbl,
- int ci, int cjf, int cjl,
- gmx_bool remove_sub_diag,
- const real *x_j,
- real rl2, float rbb2,
- int *ndistc)
+static void
+makeClusterListSimple(const nbnxn_grid_t * gridj,
+ nbnxn_pairlist_t * nbl,
+ int icluster,
+ int jclusterFirst,
+ int jclusterLast,
+ bool excludeSubDiagonal,
+ const real * gmx_restrict x_j,
+ real rlist2,
+ float rbb2,
+ int * gmx_restrict numDistanceChecks)
{
- const nbnxn_bb_t *bb_ci;
- const real *x_ci;
+ const nbnxn_bb_t * gmx_restrict bb_ci = nbl->work->bb_ci;
+ const real * gmx_restrict x_ci = nbl->work->x_ci;
- gmx_bool InRange;
- real d2;
- int cjf_gl, cjl_gl;
-
- bb_ci = nbl->work->bb_ci;
- x_ci = nbl->work->x_ci;
+ gmx_bool InRange;
InRange = FALSE;
- while (!InRange && cjf <= cjl)
+ while (!InRange && jclusterFirst <= jclusterLast)
{
- d2 = subc_bb_dist2(0, bb_ci, cjf, gridj->bb);
- *ndistc += 2;
+ real d2 = subc_bb_dist2(0, bb_ci, jclusterFirst, gridj->bb);
+ *numDistanceChecks += 2;
/* Check if the distance is within the distance where
* we use only the bounding box distance rbb,
{
InRange = TRUE;
}
- else if (d2 < rl2)
+ else if (d2 < rlist2)
{
- cjf_gl = gridj->cell0 + cjf;
+ int cjf_gl = gridj->cell0 + jclusterFirst;
for (int i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE && !InRange; i++)
{
for (int j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE; j++)
InRange = InRange ||
(gmx::square(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+XX]) +
gmx::square(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+YY]) +
- gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rl2);
+ gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjf_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rlist2);
}
}
- *ndistc += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
+ *numDistanceChecks += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
}
if (!InRange)
{
- cjf++;
+ jclusterFirst++;
}
}
if (!InRange)
}
InRange = FALSE;
- while (!InRange && cjl > cjf)
+ while (!InRange && jclusterLast > jclusterFirst)
{
- d2 = subc_bb_dist2(0, bb_ci, cjl, gridj->bb);
- *ndistc += 2;
+ real d2 = subc_bb_dist2(0, bb_ci, jclusterLast, gridj->bb);
+ *numDistanceChecks += 2;
/* Check if the distance is within the distance where
* we use only the bounding box distance rbb,
{
InRange = TRUE;
}
- else if (d2 < rl2)
+ else if (d2 < rlist2)
{
- cjl_gl = gridj->cell0 + cjl;
+ int cjl_gl = gridj->cell0 + jclusterLast;
for (int i = 0; i < NBNXN_CPU_CLUSTER_I_SIZE && !InRange; i++)
{
for (int j = 0; j < NBNXN_CPU_CLUSTER_I_SIZE; j++)
InRange = InRange ||
(gmx::square(x_ci[i*STRIDE_XYZ+XX] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+XX]) +
gmx::square(x_ci[i*STRIDE_XYZ+YY] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+YY]) +
- gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rl2);
+ gmx::square(x_ci[i*STRIDE_XYZ+ZZ] - x_j[(cjl_gl*NBNXN_CPU_CLUSTER_I_SIZE+j)*STRIDE_XYZ+ZZ]) < rlist2);
}
}
- *ndistc += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
+ *numDistanceChecks += NBNXN_CPU_CLUSTER_I_SIZE*NBNXN_CPU_CLUSTER_I_SIZE;
}
if (!InRange)
{
- cjl--;
+ jclusterLast--;
}
}
- if (cjf <= cjl)
+ if (jclusterFirst <= jclusterLast)
{
- for (int cj = cjf; cj <= cjl; cj++)
+ for (int jcluster = jclusterFirst; jcluster <= jclusterLast; jcluster++)
{
/* Store cj and the interaction mask */
- nbl->cj[nbl->ncj].cj = gridj->cell0 + cj;
- nbl->cj[nbl->ncj].excl = get_imask(remove_sub_diag, ci, cj);
+ nbl->cj[nbl->ncj].cj = gridj->cell0 + jcluster;
+ nbl->cj[nbl->ncj].excl = get_imask(excludeSubDiagonal, icluster, jcluster);
nbl->ncj++;
}
/* Increase the closing index in i super-cell list */
int sci, int scj,
gmx_bool sci_equals_scj,
int stride, const real *x,
- real rl2, float rbb2,
- int *ndistc)
+ real rlist2, float rbb2,
+ int *numDistanceChecks)
{
nbnxn_list_work_t *work = nbl->work;
/* Determine all ci1 bb distances in one call with SIMD4 */
subc_bb_dist2_simd4_xxxx(gridj->pbb+(cj>>STRIDE_PBB_2LOG)*NNBSBB_XXXX+(cj & (STRIDE_PBB-1)),
ci1, pbb_ci, d2l);
- *ndistc += c_nbnxnGpuClusterSize*2;
+ *numDistanceChecks += c_nbnxnGpuClusterSize*2;
#endif
int npair = 0;
#if !NBNXN_BBXXXX
/* Determine the bb distance between ci and cj */
- d2l[ci] = subc_bb_dist2(ci, bb_ci, cj, gridj->bb);
- *ndistc += 2;
+ d2l[ci] = subc_bb_dist2(ci, bb_ci, cj, gridj->bb);
+ *numDistanceChecks += 2;
#endif
float d2 = d2l[ci];
* or within the cut-off and there is at least one atom pair
* within the cut-off. This check is very costly.
*/
- *ndistc += c_nbnxnGpuClusterSize*c_nbnxnGpuClusterSize;
+ *numDistanceChecks += c_nbnxnGpuClusterSize*c_nbnxnGpuClusterSize;
if (d2 < rbb2 ||
- (d2 < rl2 &&
- clusterpair_in_range(work, ci, cj_gl, stride, x, rl2)))
+ (d2 < rlist2 &&
+ clusterpair_in_range(work, ci, cj_gl, stride, x, rlist2)))
#else
/* Check if the distance between the two bounding boxes
* in within the pair-list cut-off.
*/
- if (d2 < rl2)
+ if (d2 < rlist2)
#endif
{
/* Flag this i-subcell to be taken into account */
* within the cut-off, so we could get rid of it.
*/
if (npair == 1 && d2l[ci_last] >= rbb2 &&
- !clusterpair_in_range(work, ci_last, cj_gl, stride, x, rl2))
+ !clusterpair_in_range(work, ci_last, cj_gl, stride, x, rlist2))
{
imask &= ~(1U << (cj_offset*c_gpuNumClusterPerCell + ci_last));
npair--;
nbl->nci*sizeof(*nbl->ci),
nbl->ci_nalloc*sizeof(*nbl->ci),
nbl->alloc, nbl->free);
+
+ nbnxn_realloc_void((void **)&nbl->ciOuter,
+ nbl->nci*sizeof(*nbl->ciOuter),
+ nbl->ci_nalloc*sizeof(*nbl->ciOuter),
+ nbl->alloc, nbl->free);
}
/* Reallocate the super-cell sci list for at least n entries */
nbl->ncjInUse = 0;
nbl->ncj4 = 0;
nbl->nci_tot = 0;
+ nbl->nciOuter = -1;
nbl->nexcl = 1;
nbl->work->ncj_noq = 0;
{
nl->nri = 0;
nl->nrj = 0;
- if (nl->jindex == NULL)
+ if (nl->jindex == nullptr)
{
snew(nl->jindex, 1);
}
#endif
/* Sets a super-cell and sub cell bounding boxes, including PBC shift */
-static void set_icell_bb_supersub(const nbnxn_bb_t *bb, int ci,
- real shx, real shy, real shz,
- nbnxn_bb_t *bb_ci)
+gmx_unused static void set_icell_bb_supersub(const nbnxn_bb_t *bb, int ci,
+ real shx, real shy, real shz,
+ nbnxn_bb_t *bb_ci)
{
for (int i = 0; i < c_gpuNumClusterPerCell; i++)
{
{
int na_cj_2log;
matrix box;
- real rl2, rl_fep2 = 0;
+ real rlist2, rl_fep2 = 0;
float rbb2;
int ci_b, ci, ci_x, ci_y, ci_xy, cj;
ivec shp;
int shift;
real shx, shy, shz;
int conv_i, cell0_i;
- const nbnxn_bb_t *bb_i = NULL;
+ const nbnxn_bb_t *bb_i = nullptr;
#if NBNXN_BBXXXX
- const float *pbb_i = NULL;
+ const float *pbb_i = nullptr;
#endif
const float *bbcz_i, *bbcz_j;
const int *flags_i;
real bz1_frac;
real d2cx, d2z, d2z_cx, d2z_cy, d2zx, d2zxy, d2xy;
int cxf, cxl, cyf, cyf_x, cyl;
- int c0, c1, cs, cf, cl;
- int ndistc;
- int ncpcheck;
+ int numDistanceChecks;
int gridi_flag_shift = 0, gridj_flag_shift = 0;
- gmx_bitmask_t *gridj_flag = NULL;
+ gmx_bitmask_t *gridj_flag = nullptr;
int ncj_old_i, ncj_old_j;
nbs_cycle_start(&work->cc[enbsCCsearch]);
copy_mat(nbs->box, box);
- rl2 = nbl->rlist*nbl->rlist;
+ rlist2 = nbl->rlist*nbl->rlist;
if (nbs->bFEP && !nbl->bSimple)
{
else
{
if (d == XX &&
- box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < std::sqrt(rl2))
+ box[XX][XX] - fabs(box[YY][XX]) - fabs(box[ZZ][XX]) < std::sqrt(rlist2))
{
shp[d] = 2;
}
gridi->nc, gridi->nc/(double)(gridi->ncx*gridi->ncy), ci_block);
}
- ndistc = 0;
- ncpcheck = 0;
+ numDistanceChecks = 0;
/* Initially ci_b and ci to 1 before where we want them to start,
* as they will both be incremented in next_ci.
{
d2cx = gmx::square(gridj->c0[XX] - bx1);
- if (d2cx >= rl2)
+ if (d2cx >= rlist2)
{
continue;
}
d2z_cx = d2z + d2cx;
- if (d2z_cx >= rl2)
+ if (d2z_cx >= rlist2)
{
continue;
}
get_cell_range(by0, by1,
gridj->ncy, gridj->c0[YY], gridj->sy, gridj->inv_sy,
- d2z_cx, rl2,
+ d2z_cx, rlist2,
&cyf, &cyl);
if (cyf > cyl)
{
shift = XYZ2IS(tx, ty, tz);
- if (pbc_shift_backward && gridi == gridj && shift > CENTRAL)
+ if (c_pbcShiftBackward && gridi == gridj && shift > CENTRAL)
{
continue;
}
get_cell_range(bx0, bx1,
gridj->ncx, gridj->c0[XX], gridj->sx, gridj->inv_sx,
- d2z_cy, rl2,
+ d2z_cy, rlist2,
&cxf, &cxl);
if (cxf > cxl)
new_sci_entry(nbl, cell0_i+ci, shift);
}
- if ((!pbc_shift_backward || (shift == CENTRAL &&
+ if ((!c_pbcShiftBackward || (shift == CENTRAL &&
gridi == gridj)) &&
cxf < ci_x)
{
if (gridi == gridj &&
cx == 0 &&
- (!pbc_shift_backward || shift == CENTRAL) &&
+ (!c_pbcShiftBackward || shift == CENTRAL) &&
cyf < ci_y)
{
/* Leave the pairs with i > j.
for (int cy = cyf_x; cy <= cyl; cy++)
{
- c0 = gridj->cxy_ind[cx*gridj->ncy+cy];
- c1 = gridj->cxy_ind[cx*gridj->ncy+cy+1];
-
- if (pbc_shift_backward &&
- gridi == gridj &&
- shift == CENTRAL && c0 < ci)
- {
- c0 = ci;
- }
+ const int columnStart = gridj->cxy_ind[cx*gridj->ncy + cy];
+ const int columnEnd = gridj->cxy_ind[cx*gridj->ncy + cy + 1];
d2zxy = d2zx;
if (gridj->c0[YY] + cy*gridj->sy > by1)
{
d2zxy += gmx::square(gridj->c0[YY] + (cy+1)*gridj->sy - by0);
}
- if (c1 > c0 && d2zxy < rl2)
+ if (columnStart < columnEnd && d2zxy < rlist2)
{
- cs = c0 + static_cast<int>(bz1_frac*(c1 - c0));
- if (cs >= c1)
+ /* To improve efficiency in the common case
+ * of a homogeneous particle distribution,
+ * we estimate the index of the middle cell
+ * in range (midCell). We search down and up
+ * starting from this index.
+ *
+ * Note that the bbcz_j array contains bounds
+ * for i-clusters, thus for clusters of 4 atoms.
+ * For the common case where the j-cluster size
+ * is 8, we could step with a stride of 2,
+ * but we do not do this because it would
+ * complicate this code even more.
+ */
+ int midCell = columnStart + static_cast<int>(bz1_frac*(columnEnd - columnStart));
+ if (midCell >= columnEnd)
{
- cs = c1 - 1;
+ midCell = columnEnd - 1;
}
d2xy = d2zxy - d2z;
/* Find the lowest cell that can possibly
* be within range.
+ * Check if we hit the bottom of the grid,
+ * if the j-cell is below the i-cell and if so,
+ * if it is within range.
*/
- cf = cs;
- while (cf > c0 &&
- (bbcz_j[cf*NNBSBB_D+1] >= bz0 ||
- d2xy + gmx::square(bbcz_j[cf*NNBSBB_D+1] - bz0) < rl2))
+ int downTestCell = midCell;
+ while (downTestCell >= columnStart &&
+ (bbcz_j[downTestCell*NNBSBB_D + 1] >= bz0 ||
+ d2xy + gmx::square(bbcz_j[downTestCell*NNBSBB_D + 1] - bz0) < rlist2))
{
- cf--;
+ downTestCell--;
}
+ int firstCell = downTestCell + 1;
/* Find the highest cell that can possibly
* be within range.
+ * Check if we hit the top of the grid,
+ * if the j-cell is above the i-cell and if so,
+ * if it is within range.
*/
- cl = cs;
- while (cl < c1-1 &&
- (bbcz_j[cl*NNBSBB_D] <= bz1 ||
- d2xy + gmx::square(bbcz_j[cl*NNBSBB_D] - bz1) < rl2))
+ int upTestCell = midCell + 1;
+ while (upTestCell < columnEnd &&
+ (bbcz_j[upTestCell*NNBSBB_D] <= bz1 ||
+ d2xy + gmx::square(bbcz_j[upTestCell*NNBSBB_D] - bz1) < rlist2))
{
- cl++;
+ upTestCell++;
}
+ int lastCell = upTestCell - 1;
-#ifdef NBNXN_REFCODE
+#define NBNXN_REFCODE 0
+#if NBNXN_REFCODE
{
/* Simple reference code, for debugging,
* overrides the more complex code above.
*/
- cf = c1;
- cl = -1;
- for (int k = c0; k < c1; k++)
+ firstCell = columnEnd;
+ lastCell = -1;
+ for (int k = columnStart; k < columnEnd; k++)
{
- if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
- k < cf)
+ if (d2xy + gmx::square(bbcz_j[k*NNBSBB_D + 1] - bz0) < rlist2 &&
+ k < firstCell)
{
- cf = k;
+ firstCell = k;
}
- if (box_dist2(bx0, bx1, by0, by1, bz0, bz1, bb+k) < rl2 &&
- k > cl)
+ if (d2xy + gmx::square(bbcz_j[k*NNBSBB_D] - bz1) < rlist2 &&
+ k > lastCell)
{
- cl = k;
+ lastCell = k;
}
}
}
/* We want each atom/cell pair only once,
* only use cj >= ci.
*/
- if (!pbc_shift_backward || shift == CENTRAL)
+ if (!c_pbcShiftBackward || shift == CENTRAL)
{
- cf = std::max(cf, ci);
+ firstCell = std::max(firstCell, ci);
}
}
- if (cf <= cl)
+ if (firstCell <= lastCell)
{
+ GMX_ASSERT(firstCell >= columnStart && lastCell < columnEnd, "The range should reside within the current grid column");
+
/* For f buffer flags with simple lists */
ncj_old_j = nbl->ncj;
+ if (nbl->bSimple)
+ {
+ /* We have a maximum of 2 j-clusters
+ * per i-cluster sized cell.
+ */
+ check_cell_list_space_simple(nbl, 2*(lastCell - firstCell + 1));
+ }
+ else
+ {
+ check_cell_list_space_supersub(nbl, lastCell - firstCell + 1);
+ }
+
switch (nb_kernel_type)
{
case nbnxnk4x4_PlainC:
- check_cell_list_space_simple(nbl, cl-cf+1);
-
- make_cluster_list_simple(gridj,
- nbl, ci, cf, cl,
- (gridi == gridj && shift == CENTRAL),
- nbat->x,
- rl2, rbb2,
- &ndistc);
+ makeClusterListSimple(gridj,
+ nbl, ci, firstCell, lastCell,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rlist2, rbb2,
+ &numDistanceChecks);
break;
#ifdef GMX_NBNXN_SIMD_4XN
case nbnxnk4xN_SIMD_4xN:
- check_cell_list_space_simple(nbl, ci_to_cj_simd_4xn(cl - cf) + 2);
- make_cluster_list_simd_4xn(gridj,
- nbl, ci, cf, cl,
- (gridi == gridj && shift == CENTRAL),
- nbat->x,
- rl2, rbb2,
- &ndistc);
+ makeClusterListSimd4xn(gridj,
+ nbl, ci, firstCell, lastCell,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rlist2, rbb2,
+ &numDistanceChecks);
break;
#endif
#ifdef GMX_NBNXN_SIMD_2XNN
case nbnxnk4xN_SIMD_2xNN:
- check_cell_list_space_simple(nbl, ci_to_cj_simd_2xnn(cl - cf) + 2);
- make_cluster_list_simd_2xnn(gridj,
- nbl, ci, cf, cl,
- (gridi == gridj && shift == CENTRAL),
- nbat->x,
- rl2, rbb2,
- &ndistc);
+ makeClusterListSimd2xnn(gridj,
+ nbl, ci, firstCell, lastCell,
+ (gridi == gridj && shift == CENTRAL),
+ nbat->x,
+ rlist2, rbb2,
+ &numDistanceChecks);
break;
#endif
case nbnxnk8x8x8_PlainC:
case nbnxnk8x8x8_GPU:
- check_cell_list_space_supersub(nbl, cl-cf+1);
- for (cj = cf; cj <= cl; cj++)
+ for (cj = firstCell; cj <= lastCell; cj++)
{
make_cluster_list_supersub(gridi, gridj,
nbl, ci, cj,
(gridi == gridj && shift == CENTRAL && ci == cj),
nbat->xstride, nbat->x,
- rl2, rbb2,
- &ndistc);
+ rlist2, rbb2,
+ &numDistanceChecks);
}
break;
}
- ncpcheck += cl - cf + 1;
if (bFBufferFlag && nbl->ncj > ncj_old_j)
{
}
}
- work->ndistc = ndistc;
+ work->ndistc = numDistanceChecks;
nbs_cycle_stop(&work->cc[enbsCCsearch]);
if (debug)
{
- fprintf(debug, "number of distance checks %d\n", ndistc);
- fprintf(debug, "ncpcheck %s %d\n", gridi == gridj ? "local" : "non-local",
- ncpcheck);
+ fprintf(debug, "number of distance checks %d\n", numDistanceChecks);
if (nbl->bSimple)
{
balance_fep_lists(nbs, nbl_list);
}
+ /* This is a fresh list, so not pruned, stored using ci and nci.
+ * ciOuter and nciOuter are invalid at this point.
+ */
+ GMX_ASSERT(nbl_list->nbl[0]->nciOuter == -1, "nciOuter should have been set to -1 to signal that it is invalid");
+
/* Special performance logging stuff (env.var. GMX_NBNXN_CYCLE) */
if (LOCAL_I(iloc))
{
}
}
}
+
+void nbnxnPrepareListForDynamicPruning(nbnxn_pairlist_set_t *listSet)
+{
+ /* TODO: Restructure the lists so we have actual outer and inner
+ * list objects so we can set a single pointer instead of
+ * swapping several pointers.
+ */
+
+ for (int i = 0; i < listSet->nnbl; i++)
+ {
+ /* The search produced a list in ci/cj.
+ * Swap the list pointers so we get the outer list is ciOuter,cjOuter
+ * and we can prune that to get an inner list in ci/cj.
+ */
+ nbnxn_pairlist_t *list = listSet->nbl[i];
+ list->nciOuter = list->nci;
+
+ nbnxn_ci_t *ciTmp = list->ciOuter;
+ list->ciOuter = list->ci;
+ list->ci = ciTmp;
+
+ nbnxn_cj_t *cjTmp = list->cjOuter;
+ list->cjOuter = list->cj;
+ list->cj = cjTmp;
+
+ /* Signal that this inner list is currently invalid */
+ list->nci = -1;
+ }
+}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int nb_kernel_type,
t_nrnb *nrnb);
+/*! \brief Prepare the list-set produced by the search for dynamic pruning
+ *
+ * \param[in,out] listSet The list-set to prepare for dynamic pruning.
+ */
+void nbnxnPrepareListForDynamicPruning(nbnxn_pairlist_set_t *listSet);
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
store(x_ci_simd + 5*GMX_SIMD_REAL_WIDTH, load1DualHsimd(x + ia + 2*STRIDE_S + 2) + SimdReal(shz) );
}
-/* SIMD code for making a pair list of cell ci vs cell cjf-cjl
- * for coordinates in packed format.
+/* SIMD code for checking and adding cluster-pairs to the list using coordinates in packed format.
+ *
* Checks bouding box distances and possibly atom pair distances.
* This is an accelerated version of make_cluster_list_simple.
+ *
+ * \param[in] gridj The j-grid
+ * \param[in,out] nbl The pair-list to store the cluster pairs in
+ * \param[in] icluster The index of the i-cluster
+ * \param[in] firstCell The first cluster in the j-range, using i-cluster size indexing
+ * \param[in] lastCell The last cluster in the j-range, using i-cluster size indexing
+ * \param[in] excludeSubDiagonal Exclude atom pairs with i-index > j-index
+ * \param[in] x_j Coordinates for the j-atom, in SIMD packed format
+ * \param[in] rlist2 The squared list cut-off
+ * \param[in] rbb2 The squared cut-off for putting cluster-pairs in the list based on bounding box distance only
+ * \param[in,out] numDistanceChecks The number of distance checks performed
*/
static gmx_inline void
-make_cluster_list_simd_2xnn(const nbnxn_grid_t *gridj,
- nbnxn_pairlist_t *nbl,
- int ci, int cjf, int cjl,
- gmx_bool remove_sub_diag,
- const real *x_j,
- real rl2, float rbb2,
- int *ndistc)
+makeClusterListSimd2xnn(const nbnxn_grid_t * gridj,
+ nbnxn_pairlist_t * nbl,
+ int icluster,
+ int firstCell,
+ int lastCell,
+ bool excludeSubDiagonal,
+ const real * gmx_restrict x_j,
+ real rlist2,
+ float rbb2,
+ int * gmx_restrict numDistanceChecks)
{
- const real *x_ci_simd;
- const nbnxn_bb_t *bb_ci;
+ const real * gmx_restrict x_ci_simd = nbl->work->x_ci_simd;
+ const nbnxn_bb_t * gmx_restrict bb_ci = nbl->work->bb_ci;
SimdReal jx_S, jy_S, jz_S;
gmx_bool InRange;
float d2;
- int xind_f, xind_l, cj;
-
- cjf = ci_to_cj_simd_2xnn(cjf);
- cjl = ci_to_cj_simd_2xnn(cjl + 1) - 1;
-
- x_ci_simd = nbl->work->x_ci_simd;
+ int xind_f, xind_l;
- bb_ci = nbl->work->bb_ci;
+ int jclusterFirst = ci_to_cj_simd_2xnn(firstCell);
+ int jclusterLast = ci_to_cj_simd_2xnn(lastCell);
+ GMX_ASSERT(jclusterLast >= jclusterFirst, "We should have a non-empty j-cluster range, since the calling code should have ensured a non-empty cell range");
- rc2_S = SimdReal(rl2);
+ rc2_S = SimdReal(rlist2);
InRange = FALSE;
- while (!InRange && cjf <= cjl)
+ while (!InRange && jclusterFirst <= jclusterLast)
{
#ifdef NBNXN_SEARCH_BB_SIMD4
- d2 = subc_bb_dist2_simd4(0, bb_ci, cjf, gridj->bbj);
+ d2 = subc_bb_dist2_simd4(0, bb_ci, jclusterFirst, gridj->bbj);
#else
- d2 = subc_bb_dist2(0, bb_ci, cjf, gridj->bbj);
+ d2 = subc_bb_dist2(0, bb_ci, jclusterFirst, gridj->bbj);
#endif
- *ndistc += 2;
+ *numDistanceChecks += 2;
/* Check if the distance is within the distance where
* we use only the bounding box distance rbb,
{
InRange = TRUE;
}
- else if (d2 < rl2)
+ else if (d2 < rlist2)
{
- xind_f = x_ind_cj_simd_2xnn(ci_to_cj_simd_2xnn(gridj->cell0) + cjf);
+ xind_f = x_ind_cj_simd_2xnn(ci_to_cj_simd_2xnn(gridj->cell0) + jclusterFirst);
- jx_S = loadDuplicateHsimd(x_j+xind_f+0*STRIDE_S);
- jy_S = loadDuplicateHsimd(x_j+xind_f+1*STRIDE_S);
- jz_S = loadDuplicateHsimd(x_j+xind_f+2*STRIDE_S);
+ jx_S = loadDuplicateHsimd(x_j + xind_f + 0*STRIDE_S);
+ jy_S = loadDuplicateHsimd(x_j + xind_f + 1*STRIDE_S);
+ jz_S = loadDuplicateHsimd(x_j + xind_f + 2*STRIDE_S);
/* Calculate distance */
dx_S0 = load(x_ci_simd + 0*GMX_SIMD_REAL_WIDTH) - jx_S;
InRange = anyTrue(wco_any_S);
- *ndistc += 2*GMX_SIMD_REAL_WIDTH;
+ *numDistanceChecks += 2*GMX_SIMD_REAL_WIDTH;
}
if (!InRange)
{
- cjf++;
+ jclusterFirst++;
}
}
if (!InRange)
}
InRange = FALSE;
- while (!InRange && cjl > cjf)
+ while (!InRange && jclusterLast > jclusterFirst)
{
#ifdef NBNXN_SEARCH_BB_SIMD4
- d2 = subc_bb_dist2_simd4(0, bb_ci, cjl, gridj->bbj);
+ d2 = subc_bb_dist2_simd4(0, bb_ci, jclusterLast, gridj->bbj);
#else
- d2 = subc_bb_dist2(0, bb_ci, cjl, gridj->bbj);
+ d2 = subc_bb_dist2(0, bb_ci, jclusterLast, gridj->bbj);
#endif
- *ndistc += 2;
+ *numDistanceChecks += 2;
/* Check if the distance is within the distance where
* we use only the bounding box distance rbb,
{
InRange = TRUE;
}
- else if (d2 < rl2)
+ else if (d2 < rlist2)
{
- xind_l = x_ind_cj_simd_2xnn(ci_to_cj_simd_2xnn(gridj->cell0) + cjl);
+ xind_l = x_ind_cj_simd_2xnn(ci_to_cj_simd_2xnn(gridj->cell0) + jclusterLast);
- jx_S = loadDuplicateHsimd(x_j+xind_l+0*STRIDE_S);
- jy_S = loadDuplicateHsimd(x_j+xind_l+1*STRIDE_S);
- jz_S = loadDuplicateHsimd(x_j+xind_l+2*STRIDE_S);
+ jx_S = loadDuplicateHsimd(x_j + xind_l + 0*STRIDE_S);
+ jy_S = loadDuplicateHsimd(x_j + xind_l + 1*STRIDE_S);
+ jz_S = loadDuplicateHsimd(x_j + xind_l + 2*STRIDE_S);
/* Calculate distance */
dx_S0 = load(x_ci_simd + 0*GMX_SIMD_REAL_WIDTH) - jx_S;
InRange = anyTrue(wco_any_S);
- *ndistc += 2*GMX_SIMD_REAL_WIDTH;
+ *numDistanceChecks += 2*GMX_SIMD_REAL_WIDTH;
}
if (!InRange)
{
- cjl--;
+ jclusterLast--;
}
}
- if (cjf <= cjl)
+ if (jclusterFirst <= jclusterLast)
{
- for (cj = cjf; cj <= cjl; cj++)
+ for (int jcluster = jclusterFirst; jcluster <= jclusterLast; jcluster++)
{
/* Store cj and the interaction mask */
- nbl->cj[nbl->ncj].cj = ci_to_cj_simd_2xnn(gridj->cell0) + cj;
- nbl->cj[nbl->ncj].excl = get_imask_simd_2xnn(remove_sub_diag, ci, cj);
+ nbl->cj[nbl->ncj].cj = ci_to_cj_simd_2xnn(gridj->cell0) + jcluster;
+ nbl->cj[nbl->ncj].excl = get_imask_simd_2xnn(excludeSubDiagonal, icluster, jcluster);
nbl->ncj++;
}
/* Increase the closing index in i super-cell list */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
store(x_ci_simd + 11*GMX_SIMD_REAL_WIDTH, SimdReal(x[ia + 2*STRIDE_S + 3] + shz) );
}
-/* SIMD code for making a pair list of cell ci vs cell cjf-cjl
- * for coordinates in packed format.
+/* SIMD code for checking and adding cluster-pairs to the list using coordinates in packed format.
+ *
* Checks bouding box distances and possibly atom pair distances.
* This is an accelerated version of make_cluster_list_simple.
+ *
+ * \param[in] gridj The j-grid
+ * \param[in,out] nbl The pair-list to store the cluster pairs in
+ * \param[in] icluster The index of the i-cluster
+ * \param[in] firstCell The first cluster in the j-range, using i-cluster size indexing
+ * \param[in] lastCell The last cluster in the j-range, using i-cluster size indexing
+ * \param[in] excludeSubDiagonal Exclude atom pairs with i-index > j-index
+ * \param[in] x_j Coordinates for the j-atom, in SIMD packed format
+ * \param[in] rlist2 The squared list cut-off
+ * \param[in] rbb2 The squared cut-off for putting cluster-pairs in the list based on bounding box distance only
+ * \param[in,out] numDistanceChecks The number of distance checks performed
*/
static gmx_inline void
-make_cluster_list_simd_4xn(const nbnxn_grid_t *gridj,
- nbnxn_pairlist_t *nbl,
- int ci, int cjf, int cjl,
- gmx_bool remove_sub_diag,
- const real *x_j,
- real rl2, float rbb2,
- int *ndistc)
+makeClusterListSimd4xn(const nbnxn_grid_t * gridj,
+ nbnxn_pairlist_t * nbl,
+ int icluster,
+ int firstCell,
+ int lastCell,
+ bool excludeSubDiagonal,
+ const real * gmx_restrict x_j,
+ real rlist2,
+ float rbb2,
+ int * gmx_restrict numDistanceChecks)
{
- const real *x_ci_simd = nbl->work->x_ci_simd;
- const nbnxn_bb_t *bb_ci;
+ const real * gmx_restrict x_ci_simd = nbl->work->x_ci_simd;
+ const nbnxn_bb_t * gmx_restrict bb_ci = nbl->work->bb_ci;
SimdReal jx_S, jy_S, jz_S;
gmx_bool InRange;
float d2;
- int xind_f, xind_l, cj;
+ int xind_f, xind_l;
+ /* Convert the j-range from i-cluster size indexing to j-cluster indexing */
/* cppcheck-suppress selfAssignment . selfAssignment for width 4.*/
- cjf = ci_to_cj_simd_4xn(cjf);
- cjl = ci_to_cj_simd_4xn(cjl + 1) - 1;
-
- bb_ci = nbl->work->bb_ci;
+ int jclusterFirst = ci_to_cj_simd_4xn(firstCell);
+#if GMX_SIMD_REAL_WIDTH >= NBNXN_CPU_CLUSTER_I_SIZE
+ int jclusterLast = ci_to_cj_simd_4xn(lastCell);
+#else
+ /* Set the correct last j-cluster with a j-cluster size of 2 */
+ int jclusterLast = ci_to_cj_simd_4xn(lastCell + 1) - 1;
+#endif
+ GMX_ASSERT(jclusterLast >= jclusterFirst, "We should have a non-empty j-cluster range, since the calling code should have ensured a non-empty cell range");
- rc2_S = SimdReal(rl2);
+ rc2_S = SimdReal(rlist2);
InRange = FALSE;
- while (!InRange && cjf <= cjl)
+ while (!InRange && jclusterFirst <= jclusterLast)
{
#ifdef NBNXN_SEARCH_BB_SIMD4
- d2 = subc_bb_dist2_simd4(0, bb_ci, cjf, gridj->bbj);
+ d2 = subc_bb_dist2_simd4(0, bb_ci, jclusterFirst, gridj->bbj);
#else
- d2 = subc_bb_dist2(0, bb_ci, cjf, gridj->bbj);
+ d2 = subc_bb_dist2(0, bb_ci, jclusterFirst, gridj->bbj);
#endif
- *ndistc += 2;
+ *numDistanceChecks += 2;
/* Check if the distance is within the distance where
* we use only the bounding box distance rbb,
{
InRange = TRUE;
}
- else if (d2 < rl2)
+ else if (d2 < rlist2)
{
- xind_f = x_ind_cj_simd_4xn(ci_to_cj_simd_4xn(gridj->cell0) + cjf);
+ xind_f = x_ind_cj_simd_4xn(ci_to_cj_simd_4xn(gridj->cell0) + jclusterFirst);
- jx_S = load(x_j+xind_f+0*STRIDE_S);
- jy_S = load(x_j+xind_f+1*STRIDE_S);
- jz_S = load(x_j+xind_f+2*STRIDE_S);
+ jx_S = load(x_j + xind_f + 0*STRIDE_S);
+ jy_S = load(x_j + xind_f + 1*STRIDE_S);
+ jz_S = load(x_j + xind_f + 2*STRIDE_S);
/* Calculate distance */
InRange = anyTrue(wco_any_S);
- *ndistc += 4*GMX_SIMD_REAL_WIDTH;
+ *numDistanceChecks += 4*GMX_SIMD_REAL_WIDTH;
}
if (!InRange)
{
- cjf++;
+ jclusterFirst++;
}
}
if (!InRange)
}
InRange = FALSE;
- while (!InRange && cjl > cjf)
+ while (!InRange && jclusterLast > jclusterFirst)
{
#ifdef NBNXN_SEARCH_BB_SIMD4
- d2 = subc_bb_dist2_simd4(0, bb_ci, cjl, gridj->bbj);
+ d2 = subc_bb_dist2_simd4(0, bb_ci, jclusterLast, gridj->bbj);
#else
- d2 = subc_bb_dist2(0, bb_ci, cjl, gridj->bbj);
+ d2 = subc_bb_dist2(0, bb_ci, jclusterLast, gridj->bbj);
#endif
- *ndistc += 2;
+ *numDistanceChecks += 2;
/* Check if the distance is within the distance where
* we use only the bounding box distance rbb,
{
InRange = TRUE;
}
- else if (d2 < rl2)
+ else if (d2 < rlist2)
{
- xind_l = x_ind_cj_simd_4xn(ci_to_cj_simd_4xn(gridj->cell0) + cjl);
+ xind_l = x_ind_cj_simd_4xn(ci_to_cj_simd_4xn(gridj->cell0) + jclusterLast);
- jx_S = load(x_j+xind_l+0*STRIDE_S);
- jy_S = load(x_j+xind_l+1*STRIDE_S);
- jz_S = load(x_j+xind_l+2*STRIDE_S);
+ jx_S = load(x_j +xind_l + 0*STRIDE_S);
+ jy_S = load(x_j +xind_l + 1*STRIDE_S);
+ jz_S = load(x_j +xind_l + 2*STRIDE_S);
/* Calculate distance */
dx_S0 = load(x_ci_simd + 0*GMX_SIMD_REAL_WIDTH) - jx_S;
InRange = anyTrue(wco_any_S);
- *ndistc += 4*GMX_SIMD_REAL_WIDTH;
+ *numDistanceChecks += 4*GMX_SIMD_REAL_WIDTH;
}
if (!InRange)
{
- cjl--;
+ jclusterLast--;
}
}
- if (cjf <= cjl)
+ if (jclusterFirst <= jclusterLast)
{
- for (cj = cjf; cj <= cjl; cj++)
+ for (int jcluster = jclusterFirst; jcluster <= jclusterLast; jcluster++)
{
/* Store cj and the interaction mask */
- nbl->cj[nbl->ncj].cj = ci_to_cj_simd_4xn(gridj->cell0) + cj;
- nbl->cj[nbl->ncj].excl = get_imask_simd_4xn(remove_sub_diag, ci, cj);
+ nbl->cj[nbl->ncj].cj = ci_to_cj_simd_4xn(gridj->cell0) + jcluster;
+ nbl->cj[nbl->ncj].excl = get_imask_simd_4xn(excludeSubDiagonal, icluster, jcluster);
nbl->ncj++;
}
/* Increase the closing index in i super-cell list */
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ *
+ * \brief Implements functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup __module_nb_verlet
+ */
+
+#include "gmxpre.h"
+
+#include "nbnxn_tuning.h"
+
+#include <assert.h>
+#include <stdlib.h>
+
+#include <cmath>
+
+#include <algorithm>
+#include <string>
+
+#include "gromacs/domdec/domdec.h"
+#include "gromacs/hardware/cpuinfo.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/calc_verletbuf.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/interaction_const.h"
+#include "gromacs/mdtypes/state.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxassert.h"
+
+/*! \brief Returns if we can (heuristically) change nstlist and rlist
+ *
+ * \param [in] ir The input parameter record
+ */
+static bool supportsDynamicPairlistGenerationInterval(const t_inputrec &ir)
+{
+ return
+ ir.cutoff_scheme == ecutsVERLET &&
+ EI_DYNAMICS(ir.eI) &&
+ !(EI_MD(ir.eI) && ir.etc == etcNO) &&
+ ir.verletbuf_tol > 0;
+}
+
+/*! \brief Cost of non-bonded kernels
+ *
+ * We determine the extra cost of the non-bonded kernels compared to
+ * a reference nstlist value of 10 (which is the default in grompp).
+ */
+static const int nbnxnReferenceNstlist = 10;
+//! The values to try when switching
+const int nstlist_try[] = { 20, 25, 40, 50, 80, 100 };
+//! Number of elements in the neighborsearch list trials.
+#define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
+/* Increase nstlist until the size of the pair-list increased by
+ * \p c_nbnxnListSizeFactor??? or more, but never more than
+ * \p c_nbnxnListSizeFactor??? + \p c_nbnxnListSizeFactorMargin.
+ * Since we have dynamic pair list pruning, the force kernel cost depends
+ * only very weakly on nstlist. It depends strongly on nstlistPrune.
+ * Increasing nstlist mainly affects the cost of the pair search (down due
+ * to lower frequency, up due to larger list) and the list pruning kernel.
+ * We increase nstlist conservatively with regard to kernel performance.
+ * In serial the search cost is not high and thus we don't gain much by
+ * increasing nstlist a lot. In parallel the MPI and CPU-GPU communication
+ * volume as well as the communication buffer preparation and reduction time
+ * increase quickly with rlist and thus nslist. Therefore we should avoid
+ * large nstlist, even if that also reduces the domain decomposition cost.
+ * With GPUs we perform the dynamic pruning in a rolling fashion and this
+ * overlaps with the update on the CPU, which allows even larger nstlist.
+ */
+// CPU: pair-search is a factor ~1.5 slower than the non-bonded kernel.
+//! Target pair-list size increase ratio for CPU
+static const float c_nbnxnListSizeFactorCpu = 1.25;
+// Intel KNL: pair-search is a factor ~2-3 slower than the non-bonded kernel.
+//! Target pair-list size increase ratio for Intel KNL
+static const float c_nbnxnListSizeFactorIntelXeonPhi = 1.4;
+// GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel.
+//! Target pair-list size increase ratio for hybrid CPU-GPU
+static const float c_nbnxnListSizeFactorGPU = 1.4;
+//! Never increase the size of the pair-list more than the factor above plus this margin
+static const float c_nbnxnListSizeFactorMargin = 0.1;
+
+void increaseNstlist(FILE *fp, t_commrec *cr,
+ t_inputrec *ir, int nstlist_cmdline,
+ const gmx_mtop_t *mtop,
+ const matrix box,
+ bool useOrEmulateGpuForNonbondeds,
+ const gmx::CpuInfo &cpuinfo)
+{
+ float listfac_ok, listfac_max;
+ int nstlist_orig, nstlist_prev;
+ verletbuf_list_setup_t ls;
+ real rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
+ real rlist_new, rlist_prev;
+ size_t nstlist_ind = 0;
+ gmx_bool bBox, bDD, bCont;
+ const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
+ const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
+ const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
+ const char *box_err = "Can not increase nstlist because the box is too small";
+ const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
+ char buf[STRLEN];
+
+ if (nstlist_cmdline <= 0)
+ {
+ if (ir->nstlist == 1)
+ {
+ /* The user probably set nstlist=1 for a reason,
+ * don't mess with the settings.
+ */
+ return;
+ }
+
+ if (fp != nullptr && useOrEmulateGpuForNonbondeds && ir->nstlist < nstlist_try[0])
+ {
+ fprintf(fp, nstl_gpu, ir->nstlist);
+ }
+ nstlist_ind = 0;
+ while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
+ {
+ nstlist_ind++;
+ }
+ if (nstlist_ind == NNSTL)
+ {
+ /* There are no larger nstlist value to try */
+ return;
+ }
+ }
+
+ if (EI_MD(ir->eI) && ir->etc == etcNO)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", nve_err);
+ }
+ if (fp != nullptr)
+ {
+ fprintf(fp, "%s\n", nve_err);
+ }
+
+ return;
+ }
+
+ if (ir->verletbuf_tol == 0 && useOrEmulateGpuForNonbondeds)
+ {
+ gmx_fatal(FARGS, "You are using an old tpr file with a GPU, please generate a new tpr file with an up to date version of grompp");
+ }
+
+ if (ir->verletbuf_tol < 0)
+ {
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n", vbd_err);
+ }
+ if (fp != nullptr)
+ {
+ fprintf(fp, "%s\n", vbd_err);
+ }
+
+ return;
+ }
+
+ if (useOrEmulateGpuForNonbondeds)
+ {
+ listfac_ok = c_nbnxnListSizeFactorGPU;
+ }
+ else if (cpuinfo.brandString().find("Xeon Phi") != std::string::npos)
+ {
+ listfac_ok = c_nbnxnListSizeFactorIntelXeonPhi;
+ }
+ else
+ {
+ listfac_ok = c_nbnxnListSizeFactorCpu;
+ }
+ listfac_max = listfac_ok + c_nbnxnListSizeFactorMargin;
+
+ nstlist_orig = ir->nstlist;
+ if (nstlist_cmdline > 0)
+ {
+ if (fp)
+ {
+ sprintf(buf, "Getting nstlist=%d from command line option",
+ nstlist_cmdline);
+ }
+ ir->nstlist = nstlist_cmdline;
+ }
+
+ verletbuf_get_list_setup(TRUE, useOrEmulateGpuForNonbondeds, &ls);
+
+ /* Allow rlist to make the list a given factor larger than the list
+ * would be with the reference value for nstlist (10).
+ */
+ nstlist_prev = ir->nstlist;
+ ir->nstlist = nbnxnReferenceNstlist;
+ calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1,
+ -1, &ls, nullptr, &rlistWithReferenceNstlist);
+ ir->nstlist = nstlist_prev;
+
+ /* Determine the pair list size increase due to zero interactions */
+ rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
+ mtop->natoms/det(box));
+ rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_ok) - rlist_inc;
+ rlist_max = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_max) - rlist_inc;
+ if (debug)
+ {
+ fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
+ rlist_inc, rlist_ok, rlist_max);
+ }
+
+ nstlist_prev = nstlist_orig;
+ rlist_prev = ir->rlist;
+ do
+ {
+ if (nstlist_cmdline <= 0)
+ {
+ ir->nstlist = nstlist_try[nstlist_ind];
+ }
+
+ /* Set the pair-list buffer size in ir */
+ calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1, -1, &ls, nullptr, &rlist_new);
+
+ /* Does rlist fit in the box? */
+ bBox = (gmx::square(rlist_new) < max_cutoff2(ir->ePBC, box));
+ bDD = TRUE;
+ if (bBox && DOMAINDECOMP(cr))
+ {
+ /* Check if rlist fits in the domain decomposition */
+ if (inputrec2nboundeddim(ir) < DIM)
+ {
+ gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
+ }
+ t_state state_tmp;
+ copy_mat(box, state_tmp.box);
+ bDD = change_dd_cutoff(cr, &state_tmp, ir, rlist_new);
+ }
+
+ if (debug)
+ {
+ fprintf(debug, "nstlist %d rlist %.3f bBox %d bDD %d\n",
+ ir->nstlist, rlist_new, bBox, bDD);
+ }
+
+ bCont = FALSE;
+
+ if (nstlist_cmdline <= 0)
+ {
+ if (bBox && bDD && rlist_new <= rlist_max)
+ {
+ /* Increase nstlist */
+ nstlist_prev = ir->nstlist;
+ rlist_prev = rlist_new;
+ bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
+ }
+ else
+ {
+ /* Stick with the previous nstlist */
+ ir->nstlist = nstlist_prev;
+ rlist_new = rlist_prev;
+ bBox = TRUE;
+ bDD = TRUE;
+ }
+ }
+
+ nstlist_ind++;
+ }
+ while (bCont);
+
+ if (!bBox || !bDD)
+ {
+ gmx_warning(!bBox ? box_err : dd_err);
+ if (fp != nullptr)
+ {
+ fprintf(fp, "\n%s\n", bBox ? box_err : dd_err);
+ }
+ ir->nstlist = nstlist_orig;
+ }
+ else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
+ {
+ sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
+ nstlist_orig, ir->nstlist,
+ ir->rlist, rlist_new);
+ if (MASTER(cr))
+ {
+ fprintf(stderr, "%s\n\n", buf);
+ }
+ if (fp != nullptr)
+ {
+ fprintf(fp, "%s\n\n", buf);
+ }
+ ir->rlist = rlist_new;
+ }
+}
+
+/*! \brief The interval in steps at which we perform dynamic, rolling pruning on a GPU.
+ *
+ * Ideally we should auto-tune this value.
+ * Not considering overheads, 1 would be the ideal value. But 2 seems
+ * a reasonable compromise that reduces GPU kernel launch overheads and
+ * also avoids inefficiency on large GPUs when pruning small lists.
+ * Because with domain decomposition we alternate local/non-local pruning
+ * at even/odd steps, which gives a period of 2, this value currenly needs
+ * to be 2, which is indirectly asserted when the GPU pruning is dispatched
+ * during the force evaluation.
+ */
+static const int c_nbnxnGpuRollingListPruningInterval = 2;
+
+/*! \brief The minimum nstlist for dynamic pair list pruning.
+ *
+ * In most cases going lower than 4 will lead to a too high pruning cost.
+ * This value should be a multiple of \p c_nbnxnGpuRollingListPruningInterval
+ */
+static const int c_nbnxnDynamicListPruningMinLifetime = 4;
+
+/*! \brief Set the dynamic pairlist pruning parameters in \p ic
+ *
+ * \param[in] ir The input parameter record
+ * \param[in] mtop The global topology
+ * \param[in] box The unit cell
+ * \param[in] useGpu Tells if we are using a GPU for non-bondeds
+ * \param[in] listSetup The nbnxn pair list setup
+ * \param[in] userSetNstlistPrune The user set ic->nstlistPrune (using an env.var.)
+ * \param[in] ic The nonbonded interactions constants
+ * \param[in,out] listParams The list setup parameters
+ */
+static void
+setDynamicPairlistPruningParameters(const t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ matrix box,
+ gmx_bool useGpu,
+ const verletbuf_list_setup_t &listSetup,
+ bool userSetNstlistPrune,
+ const interaction_const_t *ic,
+ NbnxnListParameters *listParams)
+{
+ /* When nstlistPrune was set by the user, we need to execute one loop
+ * iteration to determine rlistInner.
+ * Otherwise we compute rlistInner and increase nstlist as long as
+ * we have a pairlist buffer of length 0 (i.e. rlistInner == cutoff).
+ */
+ const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
+ int tunedNstlistPrune = listParams->nstlistPrune;
+ do
+ {
+ /* Dynamic pruning on the GPU is performed on the list for
+ * the next step on the coordinates of the current step,
+ * so the list lifetime is nstlistPrune (not the usual nstlist-1).
+ */
+ int listLifetime = tunedNstlistPrune - (useGpu ? 0 : 1);
+ listParams->nstlistPrune = tunedNstlistPrune;
+ calc_verlet_buffer_size(mtop, det(box), ir,
+ tunedNstlistPrune, listLifetime,
+ -1, &listSetup, NULL,
+ &listParams->rlistInner);
+
+ /* On the GPU we apply the dynamic pruning in a rolling fashion
+ * every c_nbnxnGpuRollingListPruningInterval steps,
+ * so keep nstlistPrune a multiple of the interval.
+ */
+ tunedNstlistPrune += useGpu ? c_nbnxnGpuRollingListPruningInterval : 1;
+ }
+ while (!userSetNstlistPrune &&
+ tunedNstlistPrune < ir->nstlist &&
+ listParams->rlistInner == interactionCutoff);
+
+ if (userSetNstlistPrune)
+ {
+ listParams->useDynamicPruning = true;
+ }
+ else
+ {
+ /* Determine the pair list size increase due to zero interactions */
+ real rlistInc = nbnxn_get_rlist_effective_inc(listSetup.cluster_size_j,
+ mtop->natoms/det(box));
+
+ /* Dynamic pruning is only useful when the inner list is smaller than
+ * the outer. The factor 0.99 ensures at least 3% list size reduction.
+ *
+ * With dynamic pruning on the CPU we prune after updating,
+ * so nstlistPrune=nstlist-1 would add useless extra work.
+ * With the GPU there will probably be more overhead than gain
+ * with nstlistPrune=nstlist-1, so we disable dynamic pruning.
+ * Note that in such cases the first sub-condition is likely also false.
+ */
+ listParams->useDynamicPruning =
+ (listParams->rlistInner + rlistInc < 0.99*(listParams->rlistOuter + rlistInc) &&
+ listParams->nstlistPrune < ir->nstlist - 1);
+ }
+
+ if (!listParams->useDynamicPruning)
+ {
+ /* These parameters should not be used, but set them to useful values */
+ listParams->nstlistPrune = -1;
+ listParams->rlistInner = listParams->rlistOuter;
+ }
+}
+
+void setupDynamicPairlistPruning(FILE *fplog,
+ const t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ matrix box,
+ bool useGpu,
+ const interaction_const_t *ic,
+ NbnxnListParameters *listParams)
+{
+ GMX_RELEASE_ASSERT(listParams->rlistOuter > 0, "With the nbnxn setup rlist should be > 0");
+
+ /* Initialize the parameters to no dynamic list pruning */
+ listParams->useDynamicPruning = false;
+
+ if (supportsDynamicPairlistGenerationInterval(*ir) &&
+ getenv("GMX_DISABLE_DYNAMICPRUNING") == NULL)
+ {
+ verletbuf_list_setup_t ls;
+ verletbuf_get_list_setup(TRUE, TRUE, &ls);
+
+ /* Note that nstlistPrune can have any value independently of nstlist.
+ * Actually applying rolling pruning is only useful when
+ * nstlistPrune < nstlist -1
+ */
+ char *env = getenv("GMX_NSTLIST_DYNAMICPRUNING");
+ bool userSetNstlistPrune = (env != NULL);
+
+ if (userSetNstlistPrune)
+ {
+ char *end;
+ listParams->nstlistPrune = strtol(env, &end, 10);
+ if (!end || (*end != 0) ||
+ !(listParams->nstlistPrune > 0 && listParams->nstlistPrune < ir->nstlist))
+ {
+ gmx_fatal(FARGS, "Invalid value passed in GMX_NSTLIST_DYNAMICPRUNING=%s, should be > 0 and < nstlist", env);
+ }
+ }
+ else
+ {
+ static_assert(c_nbnxnDynamicListPruningMinLifetime % c_nbnxnGpuRollingListPruningInterval == 0,
+ "c_nbnxnDynamicListPruningMinLifetime sets the starting value for nstlistPrune, which should be divisible by the rolling pruning interval for efficiency reasons.");
+
+ // TODO: Use auto-tuning to determine nstlistPrune
+ listParams->nstlistPrune = c_nbnxnDynamicListPruningMinLifetime;
+ }
+
+ setDynamicPairlistPruningParameters(ir, mtop, box, useGpu, ls,
+ userSetNstlistPrune, ic,
+ listParams);
+
+ if (listParams->useDynamicPruning && useGpu)
+ {
+ /* Note that we can round down here. This makes the effective
+ * rolling pruning interval slightly shorter than nstlistTune,
+ * thus giving correct results, but a slightly lower efficiency.
+ */
+ GMX_RELEASE_ASSERT(listParams->nstlistPrune >= c_nbnxnGpuRollingListPruningInterval,
+ ( "With dynamic list pruning on GPUs pruning frequency must be at least as large as the rolling pruning interval (" +
+ std::to_string(c_nbnxnGpuRollingListPruningInterval) +
+ ").").c_str() );
+ listParams->numRollingParts = listParams->nstlistPrune/c_nbnxnGpuRollingListPruningInterval;
+ }
+ else
+ {
+ listParams->numRollingParts = 1;
+ }
+
+ if (fplog && listParams->useDynamicPruning)
+ {
+ const real interactionCutoff = std::max(ic->rcoulomb, ic->rvdw);
+ fprintf(fplog,
+ "Using a dual pair-list setup updated with dynamic%s pruning:\n"
+ " outer list: updated every %3d steps, buffer %.3f nm, rlist %.3f nm\n"
+ " inner list: updated every %3d steps, buffer %.3f nm, rlist %.3f nm\n",
+ listParams->numRollingParts > 1 ? ", rolling" : "",
+ ir->nstlist, listParams->rlistOuter - interactionCutoff, listParams->rlistOuter,
+ listParams->nstlistPrune, listParams->rlistInner - interactionCutoff, listParams->rlistInner);
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ *
+ * \brief Declares functions for tuning adjustable parameters for the nbnxn non-bonded search and interaction kernels
+ *
+ * \author Berk Hess <hess@kth.se>
+ *
+ * \inlibraryapi
+ * \ingroup __module_nb_verlet
+ */
+
+#ifndef NBNXN_TUNING_H
+#define NBNXN_TUNING_H
+
+#include <stdio.h>
+
+#include "gromacs/math/vectypes.h"
+
+namespace gmx
+{
+class CpuInfo;
+}
+
+struct gmx_mtop_t;
+struct interaction_const_t;
+struct NbnxnListParameters;
+struct t_commrec;
+struct t_inputrec;
+
+/*! \brief Try to increase nstlist when using the Verlet cut-off scheme
+ *
+ * \param[in,out] fplog Log file
+ * \param[in] cr The communication record
+ * \param[in] ir The input parameter record
+ * \param[in] nstlistOnCmdline The value of nstlist provided on the command line
+ * \param[in] mtop The global topology
+ * \param[in] box The unit cell
+ * \param[in] useOrEmulateGpuForNonbondeds Tells if we are using a GPU for non-bondeds
+ * \param[in] cpuinfo Information about the CPU(s)
+ */
+void increaseNstlist(FILE *fplog, t_commrec *cr,
+ t_inputrec *ir, int nstlistOnCmdline,
+ const gmx_mtop_t *mtop,
+ const matrix box,
+ bool useOrEmulateGpuForNonbondeds,
+ const gmx::CpuInfo &cpuinfo);
+
+/*! \brief Set up the dynamic pairlist pruning
+ *
+ * \param[in,out] fplog Log file
+ * \param[in] ir The input parameter record
+ * \param[in] mtop The global topology
+ * \param[in] box The unit cell
+ * \param[in] useGpu Tells if we are using a GPU for non-bondeds
+ * \param[in] ic The nonbonded interactions constants
+ * \param[in,out] listParams The list setup parameters
+ */
+void setupDynamicPairlistPruning(FILE *fplog,
+ const t_inputrec *ir,
+ const gmx_mtop_t *mtop,
+ matrix box,
+ bool useGpu,
+ const interaction_const_t *ic,
+ NbnxnListParameters *listParams);
+
+#endif /* NBNXN_TUNING_H */
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
nl = nl_sr;
homenr = maxsr;
- if (nl == NULL)
+ if (nl == nullptr)
{
return;
}
nl->maxnrj = 0;
nl->nri = -1;
nl->nrj = 0;
- nl->iinr = NULL;
- nl->gid = NULL;
- nl->shift = NULL;
- nl->jindex = NULL;
- nl->jjnr = NULL;
- nl->excl_fep = NULL;
+ nl->iinr = nullptr;
+ nl->gid = nullptr;
+ nl->shift = nullptr;
+ nl->jindex = nullptr;
+ nl->jjnr = nullptr;
+ nl->excl_fep = nullptr;
reallocate_nblist(nl);
nl->jindex[0] = 0;
type = GMX_NBLIST_INTERACTION_STANDARD;
bElecAndVdwSwitchDiffers = ( (fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw));
- fr->ns->bCGlist = (getenv("GMX_NBLISTCG") != 0);
+ fr->ns->bCGlist = (getenv("GMX_NBLISTCG") != nullptr);
if (!fr->ns->bCGlist)
{
igeometry_def = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
else
{
igeometry_def = GMX_NBLIST_GEOMETRY_CG_CG;
- if (log != NULL)
+ if (log != nullptr)
{
fprintf(log, "\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
}
maxsr_wat, GMX_NBKERNEL_VDW_NONE, eintmodNONE, ielec, ielecmod, igeometry_ww, type, bElecAndVdwSwitchDiffers);
/* Did we get the solvent loops so we can use optimized water kernels? */
- if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == NULL
- || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == NULL
- || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == NULL
- || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == NULL)
+ if (nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf == nullptr
+ || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf == nullptr
+ || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf == nullptr
+ || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf == nullptr)
{
fr->solvent_opt = esolNO;
- if (log != NULL)
+ if (log != nullptr)
{
fprintf(log, "Note: The available nonbonded kernels do not support water optimization - disabling.\n");
}
/* QMMM MM list */
if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
{
- if (NULL == fr->QMMMlist)
+ if (nullptr == fr->QMMMlist)
{
snew(fr->QMMMlist, 1);
}
maxsr, 0, 0, ielec, ielecmod, GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE, GMX_NBLIST_INTERACTION_STANDARD, bElecAndVdwSwitchDiffers);
}
- if (log != NULL)
+ if (log != nullptr)
{
fprintf(log, "\n");
}
t_nblist * vdwc;
t_nblist * vdw;
t_nblist * coul;
- t_nblist * vdwc_free = NULL;
- t_nblist * vdw_free = NULL;
- t_nblist * coul_free = NULL;
- t_nblist * vdwc_ww = NULL;
- t_nblist * coul_ww = NULL;
+ t_nblist * vdwc_free = nullptr;
+ t_nblist * vdw_free = nullptr;
+ t_nblist * coul_free = nullptr;
+ t_nblist * vdwc_ww = nullptr;
+ t_nblist * coul_ww = nullptr;
int i, j, jcg, igid, gid, nbl_ind;
int jj, jj0, jj1, i_atom;
return nns;
}
-void ns_realloc_natoms(gmx_ns_t *ns, int natoms)
+static void ns_realloc_natoms(gmx_ns_t *ns, int natoms)
{
int i;
}
ns->nra_alloc = 0;
- ns->bexcl = NULL;
+ ns->bexcl = nullptr;
if (!DOMAINDECOMP(cr))
{
ns_realloc_natoms(ns, mtop->natoms);
char *ptr = getenv("GMX_DUMP_NL");
if (ptr)
{
- ns->dump_nl = strtol(ptr, NULL, 10);
+ ns->dump_nl = strtol(ptr, nullptr, 10);
if (fplog)
{
fprintf(fplog, "GMX_DUMP_NL = %d", ns->dump_nl);
}
else
{
- dd_zones = NULL;
+ dd_zones = nullptr;
- get_nsgrid_boundaries(grid->nboundeddim, box, NULL, NULL, NULL, NULL,
+ get_nsgrid_boundaries(grid->nboundeddim, box, nullptr, nullptr, nullptr, nullptr,
cgs->nr, fr->cg_cm, grid_x0, grid_x1, &grid_dens);
- grid_first(log, grid, NULL, NULL, box, grid_x0, grid_x1,
+ grid_first(log, grid, nullptr, nullptr, box, grid_x0, grid_x1,
fr->rlist, grid_dens);
}
}
else
{
- fill_grid(NULL, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
+ fill_grid(nullptr, grid, cgs->nr, fr->cg0, fr->hcg, fr->cg_cm);
grid->icg0 = fr->cg0;
grid->icg1 = fr->hcg;
}
/* Set the grid cell index for the test particle only.
* The cell to cg index is not corrected, but that does not matter.
*/
- fill_grid(NULL, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
+ fill_grid(nullptr, ns->grid, fr->hcg, fr->hcg-1, fr->hcg, fr->cg_cm);
}
if (!fr->ns->bCGlist)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
}
-void get_nsgrid_boundaries_vac(real av, real stddev,
- real *bound0, real *bound1,
- real *bdens0, real *bdens1)
+static void get_nsgrid_boundaries_vac(real av, real stddev,
+ real *bound0, real *bound1,
+ real *bdens0, real *bdens1)
{
/* Set the grid to 2 times the standard deviation of
* the charge group centers in both directions.
{
if (d < nboundeddim)
{
- grid_x0[d] = (gr0 != NULL ? (*gr0)[d] : 0);
- grid_x1[d] = (gr1 != NULL ? (*gr1)[d] : box[d][d]);
+ grid_x0[d] = (gr0 != nullptr ? (*gr0)[d] : 0);
+ grid_x1[d] = (gr1 != nullptr ? (*gr1)[d] : box[d][d]);
vol *= (grid_x1[d] - grid_x0[d]);
}
else
{
- if (ddbox == NULL)
+ if (ddbox == nullptr)
{
get_nsgrid_boundaries_vac(av[d], stddev[d],
&grid_x0[d], &grid_x1[d],
bdens1 = grid_x1[d];
}
/* Check for a DD cell not at a lower edge */
- if (dd != NULL && gr0 != NULL && dd->ci[d] > 0)
+ if (dd != nullptr && gr0 != nullptr && dd->ci[d] > 0)
{
grid_x0[d] = (*gr0)[d];
bdens0 = (*gr0)[d];
}
/* Check for a DD cell not at a higher edge */
- if (dd != NULL && gr1 != NULL && dd->ci[d] < dd->nc[d]-1)
+ if (dd != nullptr && gr1 != nullptr && dd->ci[d] < dd->nc[d]-1)
{
grid_x1[d] = (*gr1)[d];
bdens1 = (*gr1)[d];
fprintf(debug, "Filling grid from %d to %d\n", cg0, cg1);
}
- if (dd_zones == NULL)
+ if (dd_zones == nullptr)
{
for (cg = cg0; cg < cg1; cg++)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
fprintf(debug, "nr. of distance calculations in bondeds: C %.1f SIMD %.1f\n", ndtot_c, ndtot_simd);
}
- if (ndistance_c != NULL)
+ if (ndistance_c != nullptr)
{
*ndistance_c = ndtot_c;
}
- if (ndistance_simd != NULL)
+ if (ndistance_simd != nullptr)
{
*ndistance_simd = ndtot_simd;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "qm_orca.h"
+
#include <math.h>
#include <stdio.h>
#include <stdlib.h>
}
-void write_orca_input(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
+static void write_orca_input(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
{
int i;
t_QMMMrec *QMMMrec;
/* here we include the insertion of the additional orca-input */
snew(buf, 200);
- if (addInputFile != NULL)
+ if (addInputFile != nullptr)
{
while (!feof(addInputFile))
{
- if (fgets(buf, 200, addInputFile) != NULL)
+ if (fgets(buf, 200, addInputFile) != nullptr)
{
fputs(buf, out);
}
fclose(out);
} /* write_orca_input */
-real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
- t_QMrec *qm, t_MMrec *mm)
+static real read_orca_output(rvec QMgrad[], rvec MMgrad[], t_forcerec *fr,
+ t_QMrec *qm, t_MMrec *mm)
{
int
i, j, atnum;
{
sprintf(orca_xyzFilename, "%s.xyz", qm->orca_basename);
xyz = fopen(orca_xyzFilename, "r");
- if (fgets(buf, 300, xyz) == NULL)
+ if (fgets(buf, 300, xyz) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
- if (fgets(buf, 300, xyz) == NULL)
+ if (fgets(buf, 300, xyz) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
for (i = 0; i < qm->nrQMatoms; i++)
{
- if (fgets(buf, 300, xyz) == NULL)
+ if (fgets(buf, 300, xyz) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
*/
for (j = 0; j < 7; j++)
{
- if (fgets(buf, 300, engrad) == NULL)
+ if (fgets(buf, 300, engrad) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
}
/* now comes the energy
*/
- if (fgets(buf, 300, engrad) == NULL)
+ if (fgets(buf, 300, engrad) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
*/
for (j = 0; j < 3; j++)
{
- if (fgets(buf, 300, engrad) == NULL)
+ if (fgets(buf, 300, engrad) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
for (i = 0; i < 3*qm->nrQMatoms; i++)
{
k = i/3;
- if (fgets(buf, 300, engrad) == NULL)
+ if (fgets(buf, 300, engrad) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
*/
/* we can skip the first line
*/
- if (fgets(buf, 300, pcgrad) == NULL)
+ if (fgets(buf, 300, pcgrad) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
for (i = 0; i < mm->nrMMatoms; i++)
{
- if (fgets(buf, 300, pcgrad) == NULL)
+ if (fgets(buf, 300, pcgrad) == nullptr)
{
gmx_fatal(FARGS, "Unexpected end of ORCA output");
}
return(QMener);
}
-void do_orca(char *orca_dir, char *basename)
+static void do_orca(char *orca_dir, char *basename)
{
/* make the call to the orca binary through system()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gromacs/mdlib/qmmm.h"
+
+#ifndef GMX_MDLIB_QM_ORCA_H
+#define GMX_MDLIB_QM_ORCA_H
+
+void
+init_orca(t_QMrec *qm);
+
+real
+call_orca(t_forcerec *fr, t_QMrec *qm,
+ t_MMrec *mm, rvec f[], rvec fshift[]);
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/nblist.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/fatalerror.h"
call_gaussian(t_forcerec *fr, t_QMrec *qm, t_MMrec *mm, rvec f[], rvec fshift[]);
#elif GMX_QMMM_ORCA
-/* ORCA interface */
-
-void
-init_orca(t_QMrec *qm);
-
-real
-call_orca(t_forcerec *fr, t_QMrec *qm,
- t_MMrec *mm, rvec f[], rvec fshift[]);
-
+#include "gromacs/mdlib/qm_orca.h"
#endif
} /* struct_comp */
-real call_QMroutine(t_commrec gmx_unused *cr, t_forcerec gmx_unused *fr, t_QMrec gmx_unused *qm,
- t_MMrec gmx_unused *mm, rvec gmx_unused f[], rvec gmx_unused fshift[])
+static real call_QMroutine(t_commrec gmx_unused *cr, t_forcerec gmx_unused *fr, t_QMrec gmx_unused *qm,
+ t_MMrec gmx_unused *mm, rvec gmx_unused f[], rvec gmx_unused fshift[])
{
/* makes a call to the requested QM routine (qm->QMmethod)
* Note that f is actually the gradient, i.e. -f
return (QMener);
}
-void init_QMroutine(t_commrec gmx_unused *cr, t_QMrec gmx_unused *qm, t_MMrec gmx_unused *mm)
+static void init_QMroutine(t_commrec gmx_unused *cr, t_QMrec gmx_unused *qm, t_MMrec gmx_unused *mm)
{
/* makes a call to the requested QM routine (qm->QMmethod)
*/
}
} /* init_QMroutine */
-void update_QMMM_coord(rvec x[], t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
+static void update_QMMM_coord(rvec x[], t_forcerec *fr, t_QMrec *qm, t_MMrec *mm)
{
/* shifts the QM and MM particles into the central box and stores
* these shifted coordinates in the coordinate arrays of the
* Only needed in case of QM/MM optimizations
*/
FILE
- *out = NULL;
+ *out = nullptr;
int
- i, j, k, nrexcl = 0, *excluded = NULL, max_excl = 0;
+ i, j, k, nrexcl = 0, *excluded = nullptr, max_excl = 0;
out = fopen("QMMMexcl.dat", "w");
/* QMMM core routines */
-t_QMrec *mk_QMrec(void)
+static t_QMrec *mk_QMrec(void)
{
t_QMrec *qm;
snew(qm, 1);
return qm;
} /* mk_QMrec */
-t_MMrec *mk_MMrec(void)
+static t_MMrec *mk_MMrec(void)
{
t_MMrec *mm;
snew(mm, 1);
{
/* fills the t_QMrec struct of QM group grpnr
*/
- int i;
- gmx_mtop_atomlookup_t alook;
- t_atom *atom;
-
qm->nrQMatoms = nr;
snew(qm->xQM, nr);
snew(qm->indexQM, nr);
snew(qm->shiftQM, nr); /* the shifts */
- for (i = 0; i < nr; i++)
+ for (int i = 0; i < nr; i++)
{
qm->indexQM[i] = atomarray[i];
}
- alook = gmx_mtop_atomlookup_init(mtop);
-
snew(qm->atomicnumberQM, nr);
- for (i = 0; i < qm->nrQMatoms; i++)
+ int molb = 0;
+ for (int i = 0; i < qm->nrQMatoms; i++)
{
- gmx_mtop_atomnr_to_atom(alook, qm->indexQM[i], &atom);
- qm->nelectrons += mtop->atomtypes.atomnumber[atom->type];
- qm->atomicnumberQM[i] = mtop->atomtypes.atomnumber[atom->type];
+ const t_atom &atom = mtopGetAtomParameters(mtop, qm->indexQM[i], &molb);
+ qm->nelectrons += mtop->atomtypes.atomnumber[atom.type];
+ qm->atomicnumberQM[i] = mtop->atomtypes.atomnumber[atom.type];
}
- gmx_mtop_atomlookup_destroy(alook);
-
qm->QMcharge = ir->opts.QMcharge[grpnr];
qm->multiplicity = ir->opts.QMmult[grpnr];
qm->nelectrons -= ir->opts.QMcharge[grpnr];
} /* init_QMrec */
-t_QMrec *copy_QMrec(t_QMrec *qm)
+static t_QMrec *copy_QMrec(t_QMrec *qm)
{
/* copies the contents of qm into a new t_QMrec struct */
t_QMrec
*/
gmx_groups_t *groups;
- int *qm_arr = NULL, vsite, ai, aj;
+ int *qm_arr = nullptr, vsite, ai, aj;
int qm_max = 0, qm_nr = 0, i, j, jmax, k, l, nrvsite2 = 0;
t_QMMMrec *qr;
t_MMrec *mm;
t_iatom *iatoms;
real c12au, c6au;
gmx_mtop_atomloop_all_t aloop;
- t_atom *atom;
gmx_mtop_ilistloop_all_t iloop;
int a_offset;
t_ilist *ilist_mol;
- gmx_mtop_atomlookup_t alook;
if (ir->cutoff_scheme != ecutsGROUP)
{
{
/* new layer */
aloop = gmx_mtop_atomloop_all_init(mtop);
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
{
if (qm_nr >= qm_max)
/* standard QMMM, all layers are merged together so there is one QM
* subsystem and one MM subsystem.
- * Also we set the charges to zero in the md->charge arrays to prevent
- * the innerloops from doubly counting the electostatic QM MM interaction
+ * Also we set the charges to zero in mtop to prevent the innerloops
+ * from doubly counting the electostatic QM MM interaction
+ * TODO: Consider doing this in grompp instead.
*/
- alook = gmx_mtop_atomlookup_init(mtop);
-
+ int molb = 0;
for (k = 0; k < qm_nr; k++)
{
- gmx_mtop_atomnr_to_atom(alook, qm_arr[k], &atom);
+ int indexInMolecule;
+ mtopGetMolblockIndex(mtop, qm_arr[k], &molb, nullptr, &indexInMolecule);
+ t_atom *atom = &mtop->moltype[mtop->molblock[molb].type].atoms.atom[indexInMolecule];
atom->q = 0.0;
atom->qB = 0.0;
}
{
for (i = 0; i < qm_nr; i++)
{
- gmx_mtop_atomnr_to_atom(alook, qm_arr[i], &atom);
+ const t_atom &atom = mtopGetAtomParameters(mtop, qm_arr[i], &molb);
/* nbfp now includes the 6.0/12.0 derivative prefactors */
- qr->qm[0]->c6[i] = C6(fr->nbfp, mtop->ffparams.atnr, atom->type, atom->type)/c6au/6.0;
- qr->qm[0]->c12[i] = C12(fr->nbfp, mtop->ffparams.atnr, atom->type, atom->type)/c12au/12.0;
+ qr->qm[0]->c6[i] = C6(fr->nbfp, mtop->ffparams.atnr, atom.type, atom.type)/c6au/6.0;
+ qr->qm[0]->c12[i] = C12(fr->nbfp, mtop->ffparams.atnr, atom.type, atom.type)/c12au/12.0;
}
}
*/
for (i = 0; i < qm_nr; i++)
{
- gmx_mtop_atomnr_to_ilist(alook, qm_arr[i], &ilist_mol, &a_offset);
- nrvsite2 = ilist_mol[F_VSITE2].nr;
- iatoms = ilist_mol[F_VSITE2].iatoms;
+ mtopGetMolblockIndex(mtop, qm_arr[i], &molb, nullptr, &a_offset);
+ ilist_mol = mtop->moltype[mtop->molblock[molb].type].ilist;
+ nrvsite2 = ilist_mol[F_VSITE2].nr;
+ iatoms = ilist_mol[F_VSITE2].iatoms;
for (k = 0; k < nrvsite2; k += 4)
{
}
}
- gmx_mtop_atomlookup_destroy(alook);
-
/* MM rec creation */
mm = mk_MMrec();
mm->scalefactor = ir->scalefactor;
int
mm_max = 0, mm_nr = 0, mm_nr_new, i, j, is, k, shift;
t_j_particle
- *mm_j_particles = NULL, *qm_i_particles = NULL;
+ *mm_j_particles = nullptr, *qm_i_particles = nullptr;
t_QMMMrec
*qr;
t_nblist
t_pbc
pbc;
int
- *parallelMMarray = NULL;
+ *parallelMMarray = nullptr;
real
c12au, c6au;
t_QMrec
*qm, *qm2;
t_MMrec
- *mm = NULL;
+ *mm = nullptr;
rvec
- *forces = NULL, *fshift = NULL,
- *forces2 = NULL, *fshift2 = NULL; /* needed for multilayer ONIOM */
+ *forces = nullptr, *fshift = nullptr,
+ *forces2 = nullptr, *fshift2 = nullptr; /* needed for multilayer ONIOM */
int
i, j, k;
/* make a local copy the QMMMrec pointer
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(d, 1);
d->nalloc = 0;
- d->rij = NULL;
- d->half_of_reduced_mass = NULL;
- d->distance_squared_tolerance = NULL;
- d->constraint_distance_squared = NULL;
+ d->rij = nullptr;
+ d->half_of_reduced_mass = nullptr;
+ d->distance_squared_tolerance = nullptr;
+ d->constraint_distance_squared = nullptr;
/* SOR initialization */
d->delta = 0.1;
*nerror = error;
}
-int vec_shakef(FILE *fplog, gmx_shakedata_t shaked,
- real invmass[], int ncon,
- t_iparams ip[], t_iatom *iatom,
- real tol, rvec x[], rvec prime[], real omega,
- gmx_bool bFEP, real lambda, real scaled_lagrange_multiplier[],
- real invdt, rvec *v,
- gmx_bool bCalcVir, tensor vir_r_m_dr, int econq)
+static int vec_shakef(FILE *fplog, gmx_shakedata_t shaked,
+ real invmass[], int ncon,
+ t_iparams ip[], t_iatom *iatom,
+ real tol, rvec x[], rvec prime[], real omega,
+ gmx_bool bFEP, real lambda, real scaled_lagrange_multiplier[],
+ real invdt, rvec *v,
+ gmx_bool bCalcVir, tensor vir_r_m_dr, int econq)
{
rvec *rij;
real *half_of_reduced_mass, *distance_squared_tolerance, *constraint_distance_squared;
i = ia[1];
j = ia[2];
- if ((econq == econqCoord) && v != NULL)
+ if ((econq == econqCoord) && v != nullptr)
{
/* Correct the velocities */
mm = scaled_lagrange_multiplier[ll]*invmass[i]*invdt;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include <array>
+#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/gmxlib/chargegroup.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/cstringutil.h"
} t_shell;
struct gmx_shellfc_t {
+ /* Shell counts, indices, parameters and working data */
int nshell_gl; /* The number of shells in the system */
t_shell *shell_gl; /* All the shells (for DD only) */
int *shell_index_gl; /* Global shell index (for DD only) */
gmx_bool bPredict; /* Predict shell positions */
gmx_bool bRequireInit; /* Require initialization of shell positions */
int nflexcon; /* The number of flexible constraints */
- rvec *x[2]; /* Array for iterative minimization */
- rvec *f[2]; /* Array for iterative minimization */
- int x_nalloc; /* The allocation size of x and f */
+
+ /* Temporary arrays, should be fixed size 2 when fully converted to C++ */
+ PaddedRVecVector *x; /* Array for iterative minimization */
+ PaddedRVecVector *f; /* Array for iterative minimization */
+
+ /* Flexible constraint working data */
rvec *acc_dir; /* Acceleration direction for flexcon */
rvec *x_old; /* Old coordinates for flexcon */
int flex_nalloc; /* The allocation size of acc_dir and x_old */
int i, m, s1, n1, n2, n3;
real dt_1, fudge, tm, m1, m2, m3;
rvec *ptr;
- gmx_mtop_atomlookup_t alook = NULL;
- t_atom *atom;
-
- if (mass == NULL)
- {
- alook = gmx_mtop_atomlookup_init(mtop);
- }
/* We introduce a fudge factor for performance reasons: with this choice
* the initial force on the shells is about a factor of two lower than
dt_1 = fudge*dt;
}
+ int molb = 0;
for (i = 0; (i < ns); i++)
{
s1 = s[i].shell;
else
{
/* Not the correct masses with FE, but it is just a prediction... */
- gmx_mtop_atomnr_to_atom(alook, n1, &atom);
- m1 = atom->m;
- gmx_mtop_atomnr_to_atom(alook, n2, &atom);
- m2 = atom->m;
+ m1 = mtopGetAtomMass(mtop, n1, &molb);
+ m2 = mtopGetAtomMass(mtop, n2, &molb);
}
tm = dt_1/(m1+m2);
for (m = 0; (m < DIM); m++)
else
{
/* Not the correct masses with FE, but it is just a prediction... */
- gmx_mtop_atomnr_to_atom(alook, n1, &atom);
- m1 = atom->m;
- gmx_mtop_atomnr_to_atom(alook, n2, &atom);
- m2 = atom->m;
- gmx_mtop_atomnr_to_atom(alook, n3, &atom);
- m3 = atom->m;
+ m1 = mtopGetAtomMass(mtop, n1, &molb);
+ m2 = mtopGetAtomMass(mtop, n2, &molb);
+ m3 = mtopGetAtomMass(mtop, n3, &molb);
}
tm = dt_1/(m1+m2+m3);
for (m = 0; (m < DIM); m++)
gmx_fatal(FARGS, "Shell %d has %d nuclei!", i, s[i].nnucl);
}
}
-
- if (mass == NULL)
- {
- gmx_mtop_atomlookup_destroy(alook);
- }
}
/*! \brief Count the different particle types in a system
gmx_mtop_atomloop_block_t aloopb = gmx_mtop_atomloop_block_init(mtop);
int nmol;
- t_atom *atom;
+ const t_atom *atom;
while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
{
switch (atom->ptype)
{
gmx_shellfc_t *shfc;
t_shell *shell;
- int *shell_index = NULL, *at2cg;
- t_atom *atom;
+ int *shell_index = nullptr, *at2cg;
+ const t_atom *atom;
int ns, nshell, nsi;
int i, j, type, mb, a_offset, cg, mol, ftype, nra;
if (nshell == 0 && nflexcon == 0)
{
/* We're not doing shells or flexible constraints */
- return NULL;
+ return nullptr;
}
snew(shfc, 1);
+ shfc->x = new PaddedRVecVector[2] {};
+ shfc->f = new PaddedRVecVector[2] {};
shfc->nflexcon = nflexcon;
if (nshell == 0)
shfc->shell_gl = shell;
shfc->shell_index_gl = shell_index;
- shfc->bPredict = (getenv("GMX_NOPREDICT") == NULL);
+ shfc->bPredict = (getenv("GMX_NOPREDICT") == nullptr);
shfc->bRequireInit = FALSE;
if (!shfc->bPredict)
{
}
else
{
- shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != NULL);
+ shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != nullptr);
if (shfc->bRequireInit && fplog)
{
fprintf(fplog, "\nWill always initiate shell positions\n");
{
t_shell *shell;
int a0, a1, *ind, nshell, i;
- gmx_domdec_t *dd = NULL;
+ gmx_domdec_t *dd = nullptr;
if (DOMAINDECOMP(cr))
{
shfc->shell = shell;
}
-static void do_1pos(rvec xnew, rvec xold, rvec f, real step)
+static void do_1pos(rvec xnew, const rvec xold, const rvec f, real step)
{
real xo, yo, zo;
real dx, dy, dz;
xnew[ZZ] = zo+dz;
}
-static void do_1pos3(rvec xnew, rvec xold, rvec f, rvec step)
+static void do_1pos3(rvec xnew, const rvec xold, const rvec f, const rvec step)
{
real xo, yo, zo;
real dx, dy, dz;
xnew[ZZ] = zo+dz;
}
-static void directional_sd(rvec xold[], rvec xnew[], rvec acc_dir[],
- int start, int homenr, real step)
+static void directional_sd(const PaddedRVecVector *xold, PaddedRVecVector *xnew, const rvec acc_dir[],
+ int homenr, real step)
{
- int i;
+ const rvec *xo = as_rvec_array(xold->data());
+ rvec *xn = as_rvec_array(xnew->data());
- for (i = start; i < homenr; i++)
+ for (int i = 0; i < homenr; i++)
{
- do_1pos(xnew[i], xold[i], acc_dir[i], step);
+ do_1pos(xn[i], xo[i], acc_dir[i], step);
}
}
-static void shell_pos_sd(rvec xcur[], rvec xnew[], rvec f[],
+static void shell_pos_sd(const PaddedRVecVector * gmx_restrict xcur,
+ PaddedRVecVector * gmx_restrict xnew,
+ const PaddedRVecVector *f,
int ns, t_shell s[], int count)
{
const real step_scale_min = 0.8,
{
for (d = 0; d < DIM; d++)
{
- dx = xcur[shell][d] - s[i].xold[d];
- df = f[shell][d] - s[i].fold[d];
+ dx = (*xcur)[shell][d] - s[i].xold[d];
+ df = (*f)[shell][d] - s[i].fold[d];
/* -dx/df gets used to generate an interpolated value, but would
* cause a NaN if df were binary-equal to zero. Values close to
* zero won't cause problems (because of the min() and max()), so
#endif
}
}
- copy_rvec(xcur[shell], s[i].xold);
- copy_rvec(f[shell], s[i].fold);
+ copy_rvec((*xcur)[shell], s[i].xold);
+ copy_rvec((*f)[shell], s[i].fold);
- do_1pos3(xnew[shell], xcur[shell], f[shell], s[i].step);
+ do_1pos3((*xnew)[shell], (*xcur)[shell], (*f)[shell], s[i].step);
if (gmx_debug_at)
{
fprintf(debug, "shell[%d] = %d\n", i, shell);
- pr_rvec(debug, 0, "fshell", f[shell], DIM, TRUE);
- pr_rvec(debug, 0, "xold", xcur[shell], DIM, TRUE);
+ pr_rvec(debug, 0, "fshell", (*f)[shell], DIM, TRUE);
+ pr_rvec(debug, 0, "xold", (*xcur)[shell], DIM, TRUE);
pr_rvec(debug, 0, "step", s[i].step, DIM, TRUE);
- pr_rvec(debug, 0, "xnew", xnew[shell], DIM, TRUE);
+ pr_rvec(debug, 0, "xnew", (*xnew)[shell], DIM, TRUE);
}
}
#ifdef PRINT_STEP
}
-static real rms_force(t_commrec *cr, rvec f[], int ns, t_shell s[],
+static real rms_force(t_commrec *cr, const PaddedRVecVector *force, int ns, t_shell s[],
int ndir, real *sf_dir, real *Epot)
{
- int i, shell, ntot;
- double buf[4];
+ double buf[4];
+ const rvec *f = as_rvec_array(force->data());
buf[0] = *sf_dir;
- for (i = 0; i < ns; i++)
+ for (int i = 0; i < ns; i++)
{
- shell = s[i].shell;
- buf[0] += norm2(f[shell]);
+ int shell = s[i].shell;
+ buf[0] += norm2(f[shell]);
}
- ntot = ns;
+ int ntot = ns;
if (PAR(cr))
{
return (ntot ? std::sqrt(buf[0]/ntot) : 0);
}
-static void check_pbc(FILE *fp, rvec x[], int shell)
+static void check_pbc(FILE *fp, PaddedRVecVector x, int shell)
{
int m, now;
{
if (fabs(x[shell][m]-x[now][m]) > 0.3)
{
- pr_rvecs(fp, 0, "SHELL-X", x+now, 5);
+ pr_rvecs(fp, 0, "SHELL-X", as_rvec_array(x.data())+now, 5);
break;
}
}
}
-static void dump_shells(FILE *fp, rvec x[], rvec f[], real ftol, int ns, t_shell s[])
+static void dump_shells(FILE *fp, PaddedRVecVector x, PaddedRVecVector f, real ftol, int ns, t_shell s[])
{
int i, shell;
real ft2, ff2;
static void init_adir(FILE *log, gmx_shellfc_t *shfc,
gmx_constr_t constr, t_idef *idef, t_inputrec *ir,
t_commrec *cr, int dd_ac1,
- gmx_int64_t step, t_mdatoms *md, int start, int end,
+ gmx_int64_t step, t_mdatoms *md, int end,
rvec *x_old, rvec *x_init, rvec *x,
rvec *f, rvec *acc_dir,
gmx_bool bMolPBC, matrix box,
- real *lambda, real *dvdlambda, t_nrnb *nrnb)
+ gmx::ConstArrayRef<real> lambda, real *dvdlambda,
+ t_nrnb *nrnb)
{
rvec *xnold, *xnew;
double dt, w_dt;
}
else
{
- n = end - start;
+ n = end;
}
if (n > shfc->adir_nalloc)
{
dt = ir->delta_t;
/* Does NOT work with freeze or acceleration groups (yet) */
- for (n = start; n < end; n++)
+ for (n = 0; n < end; n++)
{
w_dt = md->invmass[n]*dt;
{
if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
{
- xnold[n-start][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
- xnew[n-start][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
+ xnold[n][d] = x[n][d] - (x_init[n][d] - x_old[n][d]);
+ xnew[n][d] = 2*x[n][d] - x_old[n][d] + f[n][d]*w_dt*dt;
}
else
{
- xnold[n-start][d] = x[n][d];
- xnew[n-start][d] = x[n][d];
+ xnold[n][d] = x[n][d];
+ xnew[n][d] = x[n][d];
}
}
}
constrain(log, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
- x, xnold-start, NULL, bMolPBC, box,
+ x, xnold, nullptr, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- NULL, NULL, nrnb, econqCoord);
+ nullptr, nullptr, nrnb, econqCoord);
constrain(log, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
- x, xnew-start, NULL, bMolPBC, box,
+ x, xnew, nullptr, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- NULL, NULL, nrnb, econqCoord);
+ nullptr, nullptr, nrnb, econqCoord);
- for (n = start; n < end; n++)
+ for (n = 0; n < end; n++)
{
for (d = 0; d < DIM; d++)
{
- xnew[n-start][d] =
- -(2*x[n][d]-xnold[n-start][d]-xnew[n-start][d])/gmx::square(dt)
+ xnew[n][d] =
+ -(2*x[n][d]-xnold[n][d]-xnew[n][d])/gmx::square(dt)
- f[n][d]*md->invmass[n];
}
clear_rvec(acc_dir[n]);
/* Project the acceleration on the old bond directions */
constrain(log, FALSE, FALSE, constr, idef, ir, cr, step, 0, 1.0, md,
- x_old, xnew-start, acc_dir, bMolPBC, box,
+ x_old, xnew, acc_dir, bMolPBC, box,
lambda[efptBONDED], &(dvdlambda[efptBONDED]),
- NULL, NULL, nrnb, econqDeriv_FlexCon);
+ nullptr, nullptr, nrnb, econqDeriv_FlexCon);
}
void relax_shell_flexcon(FILE *fplog, t_commrec *cr, gmx_bool bVerbose,
gmx_localtop_t *top,
gmx_constr_t constr,
gmx_enerdata_t *enerd, t_fcdata *fcd,
- t_state *state, rvec f[],
+ t_state *state, PaddedRVecVector *f,
tensor force_vir,
t_mdatoms *md,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_bool bBornRadii,
double t, rvec mu_tot,
gmx_vsite_t *vsite,
- FILE *fp_field)
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion)
{
int nshell;
t_shell *shell;
t_idef *idef;
- rvec *pos[2], *force[2], *acc_dir = NULL, *x_old = NULL;
+ rvec *acc_dir = nullptr, *x_old = nullptr;
real Epot[2], df[2];
real sf_dir, invdt;
real ftol, dum = 0;
char sbuf[22];
gmx_bool bCont, bInit, bConverged;
int nat, dd_ac0, dd_ac1 = 0, i;
- int start = 0, homenr = md->homenr, end = start+homenr, cg0, cg1;
+ int homenr = md->homenr, end = homenr, cg0, cg1;
int nflexcon, number_steps, d, Min = 0, count = 0;
#define Try (1-Min) /* At start Try = 1 */
nat = state->natoms;
}
- if (nat > shfc->x_nalloc)
+ for (i = 0; (i < 2); i++)
{
- /* Allocate local arrays */
- shfc->x_nalloc = over_alloc_dd(nat);
- for (i = 0; (i < 2); i++)
- {
- srenew(shfc->x[i], shfc->x_nalloc);
- srenew(shfc->f[i], shfc->x_nalloc);
- }
+ shfc->x[i].resize(nat + 1);
+ shfc->f[i].resize(nat + 1);
}
+
+ /* Create pointer that we can swap */
+ PaddedRVecVector *pos[2];
+ PaddedRVecVector *force[2];
for (i = 0; (i < 2); i++)
{
- pos[i] = shfc->x[i];
- force[i] = shfc->f[i];
+ pos[i] = &shfc->x[i];
+ force[i] = &shfc->f[i];
}
if (bDoNS && inputrec->ePBC != epbcNONE && !DOMAINDECOMP(cr))
*/
if (inputrec->cutoff_scheme == ecutsVERLET)
{
- put_atoms_in_box_omp(fr->ePBC, state->box, md->homenr, state->x);
+ put_atoms_in_box_omp(fr->ePBC, state->box, md->homenr, as_rvec_array(state->x.data()));
}
else
{
cg0 = 0;
cg1 = top->cgs.nr;
put_charge_groups_in_box(fplog, cg0, cg1, fr->ePBC, state->box,
- &(top->cgs), state->x, fr->cg_cm);
+ &(top->cgs), as_rvec_array(state->x.data()), fr->cg_cm);
}
if (graph)
{
- mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
+ mk_mshift(fplog, graph, fr->ePBC, state->box, as_rvec_array(state->x.data()));
}
}
/* After this all coordinate arrays will contain whole charge groups */
if (graph)
{
- shift_self(graph, state->box, state->x);
+ shift_self(graph, state->box, as_rvec_array(state->x.data()));
}
if (nflexcon)
for (d = 0; d < DIM; d++)
{
shfc->x_old[i][d] =
- state->x[start+i][d] - state->v[start+i][d]*inputrec->delta_t;
+ state->x[i][d] - state->v[i][d]*inputrec->delta_t;
}
}
}
- /* Do a prediction of the shell positions */
- if (shfc->bPredict && !bCont)
+ /* Do a prediction of the shell positions, when appropriate.
+ * Without velocities (EM, NM, BD) we only do initial prediction.
+ */
+ if (shfc->bPredict && !bCont && (EI_STATE_VELOCITY(inputrec->eI) || bInit))
{
- predict_shells(fplog, state->x, state->v, inputrec->delta_t, nshell, shell,
- md->massT, NULL, bInit);
+ predict_shells(fplog, as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), inputrec->delta_t, nshell, shell,
+ md->massT, nullptr, bInit);
}
/* do_force expected the charge groups to be in the box */
if (graph)
{
- unshift_self(graph, state->box, state->x);
+ unshift_self(graph, state->box, as_rvec_array(state->x.data()));
}
/* Calculate the forces first time around */
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "x b4 do_force", state->x + start, homenr);
+ pr_rvecs(debug, 0, "x b4 do_force", as_rvec_array(state->x.data()), homenr);
}
do_force(fplog, cr, inputrec, mdstep, nrnb, wcycle, top, groups,
- state->box, state->x, &state->hist,
+ state->box, &state->x, &state->hist,
force[Min], force_vir, md, enerd, fcd,
state->lambda, graph,
- fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii,
- (bDoNS ? GMX_FORCE_NS : 0) | force_flags);
+ fr, vsite, mu_tot, t, nullptr, bBornRadii,
+ (bDoNS ? GMX_FORCE_NS : 0) | force_flags,
+ ddOpenBalanceRegion, ddCloseBalanceRegion);
sf_dir = 0;
if (nflexcon)
{
init_adir(fplog, shfc,
- constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
- shfc->x_old-start, state->x, state->x, force[Min],
- shfc->acc_dir-start,
+ constr, idef, inputrec, cr, dd_ac1, mdstep, md, end,
+ shfc->x_old, as_rvec_array(state->x.data()), as_rvec_array(state->x.data()), as_rvec_array(force[Min]->data()),
+ shfc->acc_dir,
fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
- for (i = start; i < end; i++)
+ for (i = 0; i < end; i++)
{
- sf_dir += md->massT[i]*norm2(shfc->acc_dir[i-start]);
+ sf_dir += md->massT[i]*norm2(shfc->acc_dir[i]);
}
}
Epot[Min] = enerd->term[F_EPOT];
- df[Min] = rms_force(cr, shfc->f[Min], nshell, shell, nflexcon, &sf_dir, &Epot[Min]);
+ df[Min] = rms_force(cr, &shfc->f[Min], nshell, shell, nflexcon, &sf_dir, &Epot[Min]);
df[Try] = 0;
if (debug)
{
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "force0", force[Min], md->nr);
+ pr_rvecs(debug, 0, "force0", as_rvec_array(force[Min]->data()), md->nr);
}
if (nshell+nflexcon > 0)
* shell positions are updated, therefore the other particles must
* be set here.
*/
- memcpy(pos[Min], state->x, nat*sizeof(state->x[0]));
- memcpy(pos[Try], state->x, nat*sizeof(state->x[0]));
+ *pos[Min] = state->x;
+ *pos[Try] = state->x;
}
if (bVerbose && MASTER(cr))
{
if (vsite)
{
- construct_vsites(vsite, pos[Min], inputrec->delta_t, state->v,
+ construct_vsites(vsite, as_rvec_array(pos[Min]->data()),
+ inputrec->delta_t, as_rvec_array(state->v.data()),
idef->iparams, idef->il,
fr->ePBC, fr->bMolPBC, cr, state->box);
}
if (nflexcon)
{
init_adir(fplog, shfc,
- constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
- x_old-start, state->x, pos[Min], force[Min], acc_dir-start,
+ constr, idef, inputrec, cr, dd_ac1, mdstep, md, end,
+ x_old, as_rvec_array(state->x.data()), as_rvec_array(pos[Min]->data()), as_rvec_array(force[Min]->data()), acc_dir,
fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
- directional_sd(pos[Min], pos[Try], acc_dir-start, start, end,
- fr->fc_stepsize);
+ directional_sd(pos[Min], pos[Try], acc_dir, end, fr->fc_stepsize);
}
/* New positions, Steepest descent */
/* do_force expected the charge groups to be in the box */
if (graph)
{
- unshift_self(graph, state->box, pos[Try]);
+ unshift_self(graph, state->box, as_rvec_array(pos[Try]->data()));
}
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "RELAX: pos[Min] ", pos[Min] + start, homenr);
- pr_rvecs(debug, 0, "RELAX: pos[Try] ", pos[Try] + start, homenr);
+ pr_rvecs(debug, 0, "RELAX: pos[Min] ", as_rvec_array(pos[Min]->data()), homenr);
+ pr_rvecs(debug, 0, "RELAX: pos[Try] ", as_rvec_array(pos[Try]->data()), homenr);
}
/* Try the new positions */
do_force(fplog, cr, inputrec, 1, nrnb, wcycle,
top, groups, state->box, pos[Try], &state->hist,
force[Try], force_vir,
md, enerd, fcd, state->lambda, graph,
- fr, vsite, mu_tot, t, fp_field, NULL, bBornRadii,
- force_flags);
+ fr, vsite, mu_tot, t, nullptr, bBornRadii,
+ force_flags,
+ ddOpenBalanceRegion, ddCloseBalanceRegion);
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "RELAX: force[Min]", force[Min] + start, homenr);
- pr_rvecs(debug, 0, "RELAX: force[Try]", force[Try] + start, homenr);
+ pr_rvecs(debug, 0, "RELAX: force[Min]", as_rvec_array(force[Min]->data()), homenr);
+ pr_rvecs(debug, 0, "RELAX: force[Try]", as_rvec_array(force[Try]->data()), homenr);
}
sf_dir = 0;
if (nflexcon)
{
init_adir(fplog, shfc,
- constr, idef, inputrec, cr, dd_ac1, mdstep, md, start, end,
- x_old-start, state->x, pos[Try], force[Try], acc_dir-start,
+ constr, idef, inputrec, cr, dd_ac1, mdstep, md, end,
+ x_old, as_rvec_array(state->x.data()), as_rvec_array(pos[Try]->data()), as_rvec_array(force[Try]->data()), acc_dir,
fr->bMolPBC, state->box, state->lambda, &dum, nrnb);
- for (i = start; i < end; i++)
+ for (i = 0; i < end; i++)
{
- sf_dir += md->massT[i]*norm2(acc_dir[i-start]);
+ sf_dir += md->massT[i]*norm2(acc_dir[i]);
}
}
{
if (gmx_debug_at)
{
- pr_rvecs(debug, 0, "F na do_force", force[Try] + start, homenr);
+ pr_rvecs(debug, 0, "F na do_force", as_rvec_array(force[Try]->data()), homenr);
}
if (gmx_debug_at)
{
fprintf(debug, "SHELL ITER %d\n", count);
- dump_shells(debug, pos[Try], force[Try], ftol, nshell, shell);
+ dump_shells(debug, *pos[Try], *force[Try], ftol, nshell, shell);
}
}
{
/* Correct the velocities for the flexible constraints */
invdt = 1/inputrec->delta_t;
- for (i = start; i < end; i++)
+ for (i = 0; i < end; i++)
{
for (d = 0; d < DIM; d++)
{
}
/* Copy back the coordinates and the forces */
- memcpy(state->x, pos[Min], nat*sizeof(state->x[0]));
- memcpy(f, force[Min], nat*sizeof(f[0]));
+ state->x = *pos[Min];
+ *f = *force[Min];
}
void done_shellfc(FILE *fplog, gmx_shellfc_t *shfc, gmx_int64_t numSteps)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include "gromacs/domdec/dlbtiming.h"
+#include "gromacs/math/paddedvector.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/timing/wallcycle.h"
struct t_fcdata;
struct t_graph;
struct t_inputrec;
-struct t_state;
+class t_state;
/* Initialization function, also predicts the initial shell postions.
*/
gmx_localtop_t *top,
gmx_constr *constr,
gmx_enerdata_t *enerd, t_fcdata *fcd,
- t_state *state, rvec f[],
+ t_state *state, PaddedRVecVector *f,
tensor force_vir,
t_mdatoms *md,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_bool bBornRadii,
double t, rvec mu_tot,
gmx_vsite_t *vsite,
- FILE *fp_field);
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion);
/* Print some final output */
void done_shellfc(FILE *fplog, gmx_shellfc_t *shellfc, gmx_int64_t numSteps);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
act.sa_handler = signal_handler;
sigemptyset(&act.sa_mask);
act.sa_flags = SA_RESTART;
- sigaction(signum, &act, NULL);
+ sigaction(signum, &act, nullptr);
#else
signal(signum, signal_handler);
#endif
void signal_handler_install(void)
{
- if (getenv("GMX_NO_TERM") == NULL)
+ if (getenv("GMX_NO_TERM") == nullptr)
{
if (debug)
{
}
gmx_signal(SIGTERM);
}
- if (getenv("GMX_NO_INT") == NULL)
+ if (getenv("GMX_NO_INT") == nullptr)
{
if (debug)
{
gmx_signal(SIGINT);
}
#if HAVE_SIGUSR1
- if (getenv("GMX_NO_USR1") == NULL)
+ if (getenv("GMX_NO_USR1") == nullptr)
{
if (debug)
{
#include <stdio.h>
#include <string.h>
+#include <cstdint>
+
#include <array>
+#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/gmxlib/chargegroup.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
-#include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
-#include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
-#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/iforceprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/wallcyclereporting.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/sysinfo.h"
#include "nbnxn_gpu.h"
+#include "nbnxn_kernels/nbnxn_kernel_cpu.h"
+#include "nbnxn_kernels/nbnxn_kernel_prune.h"
void print_time(FILE *out,
gmx_walltime_accounting_t walltime_accounting,
walltime_accounting_get_start_time_stamp(walltime_accounting));
}
-static void sum_forces(int start, int end, rvec f[], rvec flr[])
+static void sum_forces(rvec f[], const PaddedRVecVector *forceToAdd)
{
- int i;
+ /* TODO: remove this - 1 when padding is properly implemented */
+ int end = forceToAdd->size() - 1;
+ const rvec *fAdd = as_rvec_array(forceToAdd->data());
- if (gmx_debug_at)
- {
- pr_rvecs(debug, 0, "fsr", f+start, end-start);
- pr_rvecs(debug, 0, "flr", flr+start, end-start);
- }
// cppcheck-suppress unreadVariable
int gmx_unused nt = gmx_omp_nthreads_get(emntDefault);
#pragma omp parallel for num_threads(nt) schedule(static)
- for (i = start; i < end; i++)
+ for (int i = 0; i < end; i++)
{
- rvec_inc(f[i], flr[i]);
- }
-}
-
-/*
- * calc_f_el calculates forces due to an electric field.
- *
- * force is kJ mol^-1 nm^-1 = e * kJ mol^-1 nm^-1 / e
- *
- * Et[] contains the parameters for the time dependent
- * part of the field.
- * Ex[] contains the parameters for
- * the spatial dependent part of the field.
- * The function should return the energy due to the electric field
- * (if any) but for now returns 0.
- *
- * WARNING:
- * There can be problems with the virial.
- * Since the field is not self-consistent this is unavoidable.
- * For neutral molecules the virial is correct within this approximation.
- * For neutral systems with many charged molecules the error is small.
- * But for systems with a net charge or a few charged molecules
- * the error can be significant when the field is high.
- * Solution: implement a self-consistent electric field into PME.
- */
-static void calc_f_el(FILE *fp, int start, int homenr,
- real charge[], rvec f[],
- t_cosines Ex[], t_cosines Et[], double t)
-{
- rvec Ext;
- real t0;
- int i, m;
-
- for (m = 0; (m < DIM); m++)
- {
- if (Et[m].n > 0)
- {
- if (Et[m].n == 3)
- {
- t0 = Et[m].a[1];
- Ext[m] = std::cos(Et[m].a[0]*(t-t0))*std::exp(-gmx::square(t-t0)/(2.0*gmx::square(Et[m].a[2])));
- }
- else
- {
- Ext[m] = std::cos(Et[m].a[0]*t);
- }
- }
- else
- {
- Ext[m] = 1.0;
- }
- if (Ex[m].n > 0)
- {
- /* Convert the field strength from V/nm to MD-units */
- Ext[m] *= Ex[m].a[0]*FIELDFAC;
- for (i = start; (i < start+homenr); i++)
- {
- f[i][m] += charge[i]*Ext[m];
- }
- }
- else
- {
- Ext[m] = 0;
- }
- }
- if (fp != NULL)
- {
- fprintf(fp, "%10g %10g %10g %10g #FIELD\n", t,
- Ext[XX]/FIELDFAC, Ext[YY]/FIELDFAC, Ext[ZZ]/FIELDFAC);
+ rvec_inc(f[i], fAdd[i]);
}
}
wallcycle_start(wcycle, ewcPP_PMEWAITRECVF);
dvdl_q = 0;
dvdl_lj = 0;
- gmx_pme_receive_f(cr, fr->f_novirsum, fr->vir_el_recip, &e_q,
+ gmx_pme_receive_f(cr, as_rvec_array(fr->f_novirsum->data()), fr->vir_el_recip, &e_q,
fr->vir_lj_recip, &e_lj, &dvdl_q, &dvdl_lj,
&cycles_seppme);
enerd->term[F_COUL_RECIP] += e_q;
}
static void print_large_forces(FILE *fp, t_mdatoms *md, t_commrec *cr,
- gmx_int64_t step, real pforce, rvec *x, rvec *f)
+ gmx_int64_t step, real forceTolerance,
+ const rvec *x, const rvec *f)
{
- int i;
- real pf2, fn2;
- char buf[STEPSTRSIZE];
-
- pf2 = gmx::square(pforce);
- for (i = 0; i < md->homenr; i++)
+ real force2Tolerance = gmx::square(forceTolerance);
+ std::uintmax_t numNonFinite = 0;
+ for (int i = 0; i < md->homenr; i++)
{
- fn2 = norm2(f[i]);
- /* We also catch NAN, if the compiler does not optimize this away. */
- if (fn2 >= pf2 || fn2 != fn2)
+ real force2 = norm2(f[i]);
+ bool nonFinite = !std::isfinite(force2);
+ if (force2 >= force2Tolerance || nonFinite)
+ {
+ fprintf(fp, "step %" GMX_PRId64 " atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
+ step,
+ ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], std::sqrt(force2));
+ }
+ if (nonFinite)
{
- fprintf(fp, "step %s atom %6d x %8.3f %8.3f %8.3f force %12.5e\n",
- gmx_step_str(step, buf),
- ddglatnr(cr->dd, i), x[i][XX], x[i][YY], x[i][ZZ], std::sqrt(fn2));
+ numNonFinite++;
}
}
+ if (numNonFinite > 0)
+ {
+ /* Note that with MPI this fatal call on one rank might interrupt
+ * the printing on other ranks. But we can only avoid that with
+ * an expensive MPI barrier that we would need at each step.
+ */
+ gmx_fatal(FARGS, "At step %" GMX_PRId64 " detected non-finite forces on %ju atoms", step, numNonFinite);
+ }
}
static void post_process_forces(t_commrec *cr,
* if the constructing atoms aren't local.
*/
wallcycle_start(wcycle, ewcVSITESPREAD);
- spread_vsite_f(vsite, x, fr->f_novirsum, NULL,
+ spread_vsite_f(vsite, x, as_rvec_array(fr->f_novirsum->data()), nullptr,
(flags & GMX_FORCE_VIRIAL), fr->vir_el_recip,
nrnb,
&top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
if (flags & GMX_FORCE_VIRIAL)
{
/* Now add the forces, this is local */
- if (fr->bDomDec)
- {
- sum_forces(0, fr->f_novirsum_n, f, fr->f_novirsum);
- }
- else
- {
- sum_forces(0, mdatoms->homenr,
- f, fr->f_novirsum);
- }
+ sum_forces(f, fr->f_novirsum);
+
if (EEL_FULL(fr->eeltype))
{
/* Add the mesh contribution to the virial */
gmx_enerdata_t *enerd,
int flags, int ilocality,
int clearF,
+ gmx_int64_t step,
t_nrnb *nrnb,
gmx_wallcycle_t wcycle)
{
- int enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
- nonbonded_verlet_group_t *nbvg;
- gmx_bool bUsingGpuKernels;
-
if (!(flags & GMX_FORCE_NONBONDED))
{
/* skip non-bonded calculation */
return;
}
- nbvg = &fr->nbv->grp[ilocality];
+ nonbonded_verlet_t *nbv = fr->nbv;
+ nonbonded_verlet_group_t *nbvg = &nbv->grp[ilocality];
/* GPU kernel launch overhead is already timed separately */
if (fr->cutoff_scheme != ecutsVERLET)
gmx_incons("Invalid cut-off scheme passed!");
}
- bUsingGpuKernels = (nbvg->kernel_type == nbnxnk8x8x8_GPU);
+ bool bUsingGpuKernels = (nbvg->kernel_type == nbnxnk8x8x8_GPU);
if (!bUsingGpuKernels)
{
+ /* When dynamic pair-list pruning is requested, we need to prune
+ * at nstlistPrune steps.
+ */
+ if (nbv->listParams->useDynamicPruning &&
+ (step - nbvg->nbl_lists.outerListCreationStep) % nbv->listParams->nstlistPrune == 0)
+ {
+ /* Prune the pair-list beyond fr->ic->rlistPrune using
+ * the current coordinates of the atoms.
+ */
+ wallcycle_sub_start(wcycle, ewcsNONBONDED_PRUNING);
+ nbnxn_kernel_cpu_prune(nbvg, fr->shift_vec, nbv->listParams->rlistInner);
+ wallcycle_sub_stop(wcycle, ewcsNONBONDED_PRUNING);
+ }
+
wallcycle_sub_start(wcycle, ewcsNONBONDED);
}
+
switch (nbvg->kernel_type)
{
case nbnxnk4x4_PlainC:
- nbnxn_kernel_ref(&nbvg->nbl_lists,
- nbvg->nbat, ic,
+ case nbnxnk4xN_SIMD_4xN:
+ case nbnxnk4xN_SIMD_2xNN:
+ nbnxn_kernel_cpu(nbvg,
+ ic,
fr->shift_vec,
flags,
clearF,
enerd->grpp.ener[egLJSR]);
break;
- case nbnxnk4xN_SIMD_4xN:
- nbnxn_kernel_simd_4xn(&nbvg->nbl_lists,
- nbvg->nbat, ic,
- nbvg->ewald_excl,
- fr->shift_vec,
- flags,
- clearF,
- fr->fshift[0],
- enerd->grpp.ener[egCOULSR],
- fr->bBHAM ?
- enerd->grpp.ener[egBHAMSR] :
- enerd->grpp.ener[egLJSR]);
- break;
- case nbnxnk4xN_SIMD_2xNN:
- nbnxn_kernel_simd_2xnn(&nbvg->nbl_lists,
- nbvg->nbat, ic,
- nbvg->ewald_excl,
- fr->shift_vec,
- flags,
- clearF,
- fr->fshift[0],
- enerd->grpp.ener[egCOULSR],
- fr->bBHAM ?
- enerd->grpp.ener[egBHAMSR] :
- enerd->grpp.ener[egLJSR]);
- break;
-
case nbnxnk8x8x8_GPU:
- nbnxn_gpu_launch_kernel(fr->nbv->gpu_nbv, nbvg->nbat, flags, ilocality);
+ nbnxn_gpu_launch_kernel(nbv->gpu_nbv, nbvg->nbat, flags, ilocality);
break;
case nbnxnk8x8x8_PlainC:
break;
default:
- gmx_incons("Invalid nonbonded kernel type passed!");
+ GMX_RELEASE_ASSERT(false, "Invalid nonbonded kernel type passed!");
}
if (!bUsingGpuKernels)
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
+ int enr_nbnxn_kernel_ljc, enr_nbnxn_kernel_lj;
if (EEL_RF(ic->eeltype) || ic->eeltype == eelCUT)
{
enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_RF;
}
else if ((!bUsingGpuKernels && nbvg->ewald_excl == ewaldexclAnalytical) ||
- (bUsingGpuKernels && nbnxn_gpu_is_kernel_ewald_analytical(fr->nbv->gpu_nbv)))
+ (bUsingGpuKernels && nbnxn_gpu_is_kernel_ewald_analytical(nbv->gpu_nbv)))
{
enr_nbnxn_kernel_ljc = eNR_NBNXN_LJ_EWALD;
}
gmx_bool use_GPU(const nonbonded_verlet_t *nbv)
{
- return nbv != NULL && nbv->bUseGPU;
+ return nbv != nullptr && nbv->bUseGPU;
}
static gmx_inline void clear_rvecs_omp(int n, rvec v[])
}
}
-void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
- t_inputrec *inputrec,
- gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_localtop_t *top,
- gmx_groups_t gmx_unused *groups,
- matrix box, rvec x[], history_t *hist,
- rvec f[],
- tensor vir_force,
- t_mdatoms *mdatoms,
- gmx_enerdata_t *enerd, t_fcdata *fcd,
- real *lambda, t_graph *graph,
- t_forcerec *fr, interaction_const_t *ic,
- gmx_vsite_t *vsite, rvec mu_tot,
- double t, FILE *field, gmx_edsam_t ed,
- gmx_bool bBornRadii,
- int flags)
+static void do_force_cutsVERLET(FILE *fplog, t_commrec *cr,
+ t_inputrec *inputrec,
+ gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_localtop_t *top,
+ gmx_groups_t gmx_unused *groups,
+ matrix box, rvec x[], history_t *hist,
+ PaddedRVecVector *force,
+ tensor vir_force,
+ t_mdatoms *mdatoms,
+ gmx_enerdata_t *enerd, t_fcdata *fcd,
+ real *lambda, t_graph *graph,
+ t_forcerec *fr, interaction_const_t *ic,
+ gmx_vsite_t *vsite, rvec mu_tot,
+ double t, gmx_edsam_t ed,
+ gmx_bool bBornRadii,
+ int flags,
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion)
{
int cg1, i, j;
- int start, homenr;
double mu[2*DIM];
gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM;
gmx_bool bDoForces, bUseGPU, bUseOrEmulGPU;
gmx_bool bDiffKernels = FALSE;
rvec vzero, box_diag;
- float cycles_pme, cycles_force, cycles_wait_gpu;
- /* TODO To avoid loss of precision, float can't be used for a
- * cycle count. Build an object that can do this right and perhaps
- * also be used by gmx_wallcycle_t */
- gmx_cycles_t cycleCountBeforeLocalWorkCompletes = 0;
- nonbonded_verlet_t *nbv;
-
- cycles_force = 0;
+ float cycles_pme, cycles_wait_gpu;
+ nonbonded_verlet_t *nbv = fr->nbv;
+
+ bStateChanged = (flags & GMX_FORCE_STATECHANGED);
+ bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll == FALSE);
+ bFillGrid = (bNS && bStateChanged);
+ bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
+ bDoForces = (flags & GMX_FORCE_FORCES);
+ bUseGPU = fr->nbv->bUseGPU;
+ bUseOrEmulGPU = bUseGPU || (fr->nbv->emulateGpu == EmulateGpuNonbonded::Yes);
+
+ /* At a search step we need to start the first balancing region
+ * somewhere early inside the step after communication during domain
+ * decomposition (and not during the previous step as usual).
+ */
+ if (bNS &&
+ ddOpenBalanceRegion == DdOpenBalanceRegionBeforeForceComputation::yes)
+ {
+ ddOpenBalanceRegionCpu(cr->dd, DdAllowBalanceRegionReopen::yes);
+ }
+
cycles_wait_gpu = 0;
- nbv = fr->nbv;
- start = 0;
- homenr = mdatoms->homenr;
+ const int start = 0;
+ const int homenr = mdatoms->homenr;
clear_mat(vir_force);
cg1--;
}
- bStateChanged = (flags & GMX_FORCE_STATECHANGED);
- bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll == FALSE);
- bFillGrid = (bNS && bStateChanged);
- bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
- bDoForces = (flags & GMX_FORCE_FORCES);
- bUseGPU = fr->nbv->bUseGPU;
- bUseOrEmulGPU = bUseGPU || (nbv->grp[0].kernel_type == nbnxnk8x8x8_PlainC);
-
if (bStateChanged)
{
update_forcerec(fr, box);
* we do not need to worry about shifting.
*/
- int pme_flags = 0;
-
wallcycle_start(wcycle, ewcPP_PMESENDX);
bBS = (inputrec->nwall == 2);
svmul(inputrec->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
}
- if (EEL_PME(fr->eeltype))
- {
- pme_flags |= GMX_PME_DO_COULOMB;
- }
-
- if (EVDW_PME(fr->vdwtype))
- {
- pme_flags |= GMX_PME_DO_LJ;
- }
-
gmx_pme_send_coordinates(cr, bBS ? boxs : box, x,
- mdatoms->nChargePerturbed, mdatoms->nTypePerturbed, lambda[efptCOUL], lambda[efptVDW],
+ lambda[efptCOUL], lambda[efptVDW],
(flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),
- pme_flags, step);
+ step);
wallcycle_stop(wcycle, ewcPP_PMESENDX);
}
nbnxn_put_on_grid(nbv->nbs, fr->ePBC, box,
0, vzero, box_diag,
0, mdatoms->homenr, -1, fr->cginfo, x,
- 0, NULL,
+ 0, nullptr,
nbv->grp[eintLocal].kernel_type,
nbv->grp[eintLocal].nbat);
wallcycle_sub_stop(wcycle, ewcsNBS_GRID_LOCAL);
wallcycle_sub_start(wcycle, ewcsNBS_SEARCH_LOCAL);
nbnxn_make_pairlist(nbv->nbs, nbv->grp[eintLocal].nbat,
&top->excls,
- ic->rlist,
+ nbv->listParams->rlistOuter,
nbv->min_ci_balanced,
&nbv->grp[eintLocal].nbl_lists,
eintLocal,
nbv->grp[eintLocal].kernel_type,
nrnb);
+ nbv->grp[eintLocal].nbl_lists.outerListCreationStep = step;
+ if (nbv->listParams->useDynamicPruning && !bUseGPU)
+ {
+ nbnxnPrepareListForDynamicPruning(&nbv->grp[eintLocal].nbl_lists);
+ }
wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_LOCAL);
if (bUseGPU)
if (bUseGPU)
{
+ if (DOMAINDECOMP(cr))
+ {
+ ddOpenBalanceRegionGpu(cr->dd);
+ }
+
wallcycle_start(wcycle, ewcLAUNCH_GPU_NB);
/* launch local nonbonded F on GPU */
do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFNo,
- nrnb, wcycle);
+ step, nrnb, wcycle);
wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
nbnxn_make_pairlist(nbv->nbs, nbv->grp[eintNonlocal].nbat,
&top->excls,
- ic->rlist,
+ nbv->listParams->rlistOuter,
nbv->min_ci_balanced,
&nbv->grp[eintNonlocal].nbl_lists,
eintNonlocal,
nbv->grp[eintNonlocal].kernel_type,
nrnb);
-
+ nbv->grp[eintNonlocal].nbl_lists.outerListCreationStep = step;
+ if (nbv->listParams->useDynamicPruning && !bUseGPU)
+ {
+ nbnxnPrepareListForDynamicPruning(&nbv->grp[eintNonlocal].nbl_lists);
+ }
wallcycle_sub_stop(wcycle, ewcsNBS_SEARCH_NONLOCAL);
if (nbv->grp[eintNonlocal].kernel_type == nbnxnk8x8x8_GPU)
nbnxn_atomdata_copy_x_to_nbat_x(nbv->nbs, eatNonlocal, FALSE, x,
nbv->grp[eintNonlocal].nbat);
wallcycle_sub_stop(wcycle, ewcsNB_X_BUF_OPS);
- cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
+ wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
}
if (bUseGPU && !bDiffKernels)
wallcycle_start(wcycle, ewcLAUNCH_GPU_NB);
/* launch non-local nonbonded F on GPU */
do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFNo,
- nrnb, wcycle);
- cycles_force += wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
+ step, nrnb, wcycle);
+ wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
}
}
nbnxn_gpu_launch_cpyback(nbv->gpu_nbv, nbv->grp[eintLocal].nbat,
flags, eatLocal);
- cycles_force += wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
+ wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
if (bStateChanged && inputrecNeedMutot(inputrec))
if (PAR(cr))
{
gmx_sumd(2*DIM, mu, cr);
+ ddReopenBalanceRegionCpu(cr->dd);
}
for (i = 0; i < 2; i++)
if (inputrec->bRot)
{
- /* Enforced rotation has its own cycle counter that starts after the collective
- * coordinates have been communicated. It is added to ddCyclF to allow
- * for proper load-balancing */
wallcycle_start(wcycle, ewcROT);
- do_rotation(cr, inputrec, box, x, t, step, wcycle, bNS);
+ do_rotation(cr, inputrec, box, x, t, step, bNS);
wallcycle_stop(wcycle, ewcROT);
}
+ /* Temporary solution until all routines take PaddedRVecVector */
+ rvec *f = as_rvec_array(force->data());
+
/* Start the force cycle counter.
- * This counter is stopped after do_force_lowlevel.
- * No parallel communication should occur while this counter is running,
- * since that will interfere with the dynamic load balancing.
+ * Note that a different counter is used for dynamic load balancing.
*/
wallcycle_start(wcycle, ewcFORCE);
if (bDoForces)
{
if (flags & GMX_FORCE_VIRIAL)
{
- fr->f_novirsum = fr->f_novirsum_alloc;
+ fr->f_novirsum = fr->forceBufferNoVirialSummation;
}
else
{
* a separate array for forces that do not contribute
* to the pressure.
*/
- fr->f_novirsum = f;
+ fr->f_novirsum = force;
}
}
{
if (flags & GMX_FORCE_VIRIAL)
{
- if (fr->bDomDec)
- {
- clear_rvecs_omp(fr->f_novirsum_n, fr->f_novirsum);
- }
- else
- {
- clear_rvecs_omp(homenr, fr->f_novirsum+start);
- }
+ /* TODO: remove this - 1 when padding is properly implemented */
+ clear_rvecs_omp(fr->f_novirsum->size() - 1,
+ as_rvec_array(fr->f_novirsum->data()));
}
}
/* Clear the short- and long-range forces */
if (!bUseOrEmulGPU)
{
- /* Maybe we should move this into do_force_lowlevel */
do_nb_verlet(fr, ic, enerd, flags, eintLocal, enbvClearFYes,
- nrnb, wcycle);
+ step, nrnb, wcycle);
}
if (fr->efep != efepNO)
{
do_nb_verlet(fr, ic, enerd, flags, eintNonlocal,
bDiffKernels ? enbvClearFYes : enbvClearFNo,
- nrnb, wcycle);
+ step, nrnb, wcycle);
}
if (!bUseOrEmulGPU)
* This can be split into a local and a non-local part when overlapping
* communication with calculation with domain decomposition.
*/
- cycles_force += wallcycle_stop(wcycle, ewcFORCE);
+ wallcycle_stop(wcycle, ewcFORCE);
wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
nbnxn_atomdata_add_nbat_f_to_f(nbv->nbs, eatAll, nbv->grp[aloc].nbat, f);
wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
- cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
+ wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
wallcycle_start_nocount(wcycle, ewcFORCE);
/* if there are multiple fshift output buffers reduce them */
inputrec->fepvals, lambda, graph, &(top->excls), fr->mu_tot,
flags, &cycles_pme);
- cycles_force += wallcycle_stop(wcycle, ewcFORCE);
+ wallcycle_stop(wcycle, ewcFORCE);
if (ed)
{
{
if (bUseGPU)
{
- float cycles_tmp;
-
wallcycle_start(wcycle, ewcWAIT_GPU_NB_NL);
nbnxn_gpu_wait_for_gpu(nbv->gpu_nbv,
flags, eatNonlocal,
enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
fr->fshift);
- cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_NL);
- cycles_wait_gpu += cycles_tmp;
- cycles_force += cycles_tmp;
+ cycles_wait_gpu += wallcycle_stop(wcycle, ewcWAIT_GPU_NB_NL);
}
else
{
wallcycle_start_nocount(wcycle, ewcFORCE);
do_nb_verlet(fr, ic, enerd, flags, eintNonlocal, enbvClearFYes,
- nrnb, wcycle);
- cycles_force += wallcycle_stop(wcycle, ewcFORCE);
+ step, nrnb, wcycle);
+ wallcycle_stop(wcycle, ewcFORCE);
}
wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
wallcycle_sub_start(wcycle, ewcsNB_F_BUF_OPS);
nbv->grp[eintNonlocal].nbat, f);
}
wallcycle_sub_stop(wcycle, ewcsNB_F_BUF_OPS);
- cycles_force += wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
+ wallcycle_stop(wcycle, ewcNB_XF_BUF_OPS);
}
}
- if (bDoForces && DOMAINDECOMP(cr))
+ if (DOMAINDECOMP(cr))
{
- if (bUseGPU)
+ /* We are done with the CPU compute.
+ * We will now communicate the non-local forces.
+ * If we use a GPU this will overlap with GPU work, so in that case
+ * we do not close the DD force balancing region here.
+ */
+ if (ddCloseBalanceRegion == DdCloseBalanceRegionAfterForceComputation::yes)
{
- /* We are done with the CPU compute, but the GPU local non-bonded
- * kernel can still be running while we communicate the forces.
- * We start a counter here, so we can, hopefully, time the rest
- * of the GPU kernel execution and data transfer.
- */
- cycleCountBeforeLocalWorkCompletes = gmx_cycles_read();
+ ddCloseBalanceRegionCpu(cr->dd);
+ }
+ if (bDoForces)
+ {
+ wallcycle_start(wcycle, ewcMOVEF);
+ dd_move_f(cr->dd, f, fr->fshift);
+ wallcycle_stop(wcycle, ewcMOVEF);
}
-
- /* Communicate the forces */
- wallcycle_start(wcycle, ewcMOVEF);
- dd_move_f(cr->dd, f, fr->fshift);
- wallcycle_stop(wcycle, ewcMOVEF);
}
if (bUseOrEmulGPU)
/* wait for local forces (or calculate in emulation mode) */
if (bUseGPU)
{
- float cycles_tmp, cycles_wait_est;
/* Measured overhead on CUDA and OpenCL with(out) GPU sharing
* is between 0.5 and 1.5 Mcycles. So 2 MCycles is an overestimate,
* but even with a step of 0.1 ms the difference is less than 1%
flags, eatLocal,
enerd->grpp.ener[egLJSR], enerd->grpp.ener[egCOULSR],
fr->fshift);
- cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
+ float cycles_tmp = wallcycle_stop(wcycle, ewcWAIT_GPU_NB_L);
- if (bDoForces && DOMAINDECOMP(cr))
+ if (ddCloseBalanceRegion == DdCloseBalanceRegionAfterForceComputation::yes)
{
- cycles_wait_est = gmx_cycles_read() - cycleCountBeforeLocalWorkCompletes;
-
- if (cycles_tmp < gpuWaitApiOverheadMargin)
+ DdBalanceRegionWaitedForGpu waitedForGpu = DdBalanceRegionWaitedForGpu::yes;
+ if (bDoForces && cycles_tmp <= gpuWaitApiOverheadMargin)
{
/* We measured few cycles, it could be that the kernel
* and transfer finished earlier and there was no actual
* wait time, only API call overhead.
* Then the actual time could be anywhere between 0 and
- * cycles_wait_est. As a compromise, we use half the time.
+ * cycles_wait_est. We will use half of cycles_wait_est.
*/
- cycles_wait_est *= 0.5f;
+ waitedForGpu = DdBalanceRegionWaitedForGpu::no;
}
+ ddCloseBalanceRegionGpu(cr->dd, cycles_wait_gpu, waitedForGpu);
}
- else
- {
- /* No force communication so we actually timed the wait */
- cycles_wait_est = cycles_tmp;
- }
- /* Even though this is after dd_move_f, the actual task we are
- * waiting for runs asynchronously with dd_move_f and we usually
- * have nothing to balance it with, so we can and should add
- * the time to the force time for load balancing.
- */
- cycles_force += cycles_wait_est;
- cycles_wait_gpu += cycles_wait_est;
/* now clear the GPU outputs while we finish the step on the CPU */
wallcycle_start_nocount(wcycle, ewcLAUNCH_GPU_NB);
nbnxn_gpu_clear_outputs(nbv->gpu_nbv, flags);
+
+ /* Is dynamic pair-list pruning activated? */
+ if (nbv->listParams->useDynamicPruning)
+ {
+ /* We should not launch the rolling pruning kernel at a search
+ * step or just before search steps, since that's useless.
+ * Without domain decomposition we prune at even steps.
+ * With domain decomposition we alternate local and non-local
+ * pruning at even and odd steps.
+ */
+ int numRollingParts = nbv->listParams->numRollingParts;
+ GMX_ASSERT(numRollingParts == nbv->listParams->nstlistPrune/2, "Since we alternate local/non-local at even/odd steps, we need numRollingParts<=nstlistPrune/2 for correctness and == for efficiency");
+ int stepWithCurrentList = step - nbv->grp[eintLocal].nbl_lists.outerListCreationStep;
+ bool stepIsEven = ((stepWithCurrentList & 1) == 0);
+ if (stepWithCurrentList > 0 &&
+ stepWithCurrentList < inputrec->nstlist - 1 &&
+ (stepIsEven || DOMAINDECOMP(cr)))
+ {
+ nbnxn_gpu_launch_kernel_pruneonly(fr->nbv->gpu_nbv,
+ stepIsEven ? eintLocal : eintNonlocal,
+ numRollingParts);
+ }
+ }
wallcycle_stop(wcycle, ewcLAUNCH_GPU_NB);
}
else
wallcycle_start_nocount(wcycle, ewcFORCE);
do_nb_verlet(fr, ic, enerd, flags, eintLocal,
DOMAINDECOMP(cr) ? enbvClearFNo : enbvClearFYes,
- nrnb, wcycle);
+ step, nrnb, wcycle);
wallcycle_stop(wcycle, ewcFORCE);
}
wallcycle_start(wcycle, ewcNB_XF_BUF_OPS);
if (DOMAINDECOMP(cr))
{
dd_force_flop_stop(cr->dd, nrnb);
- if (wcycle)
- {
- dd_cycles_add(cr->dd, cycles_force-cycles_pme, ddCyclF);
- if (bUseGPU)
- {
- dd_cycles_add(cr->dd, cycles_wait_gpu, ddCyclWaitGPU);
- }
- }
}
if (bDoForces)
{
- if (inputrecElecField(inputrec))
+ /* Collect forces from modules */
+ gmx::ArrayRef<gmx::RVec> fNoVirSum;
+ if (fr->bF_NoVirSum)
{
- /* Compute forces due to electric field */
- calc_f_el(MASTER(cr) ? field : NULL,
- start, homenr, mdatoms->chargeA, fr->f_novirsum,
- inputrec->ex, inputrec->et, t);
+ fNoVirSum = *fr->f_novirsum;
}
+ fr->forceProviders->calculateForces(cr, mdatoms, box, t, x, *force, fNoVirSum);
/* If we have NoVirSum forces, but we do not calculate the virial,
* we sum fr->f_novirsum=f later.
if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
{
wallcycle_start(wcycle, ewcVSITESPREAD);
- spread_vsite_f(vsite, x, f, fr->fshift, FALSE, NULL, nrnb,
+ spread_vsite_f(vsite, x, f, fr->fshift, FALSE, nullptr, nrnb,
&top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
wallcycle_stop(wcycle, ewcVSITESPREAD);
}
}
}
-void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
- t_inputrec *inputrec,
- gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_localtop_t *top,
- gmx_groups_t *groups,
- matrix box, rvec x[], history_t *hist,
- rvec f[],
- tensor vir_force,
- t_mdatoms *mdatoms,
- gmx_enerdata_t *enerd, t_fcdata *fcd,
- real *lambda, t_graph *graph,
- t_forcerec *fr, gmx_vsite_t *vsite, rvec mu_tot,
- double t, FILE *field, gmx_edsam_t ed,
- gmx_bool bBornRadii,
- int flags)
+static void do_force_cutsGROUP(FILE *fplog, t_commrec *cr,
+ t_inputrec *inputrec,
+ gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
+ gmx_localtop_t *top,
+ gmx_groups_t *groups,
+ matrix box, rvec x[], history_t *hist,
+ PaddedRVecVector *force,
+ tensor vir_force,
+ t_mdatoms *mdatoms,
+ gmx_enerdata_t *enerd, t_fcdata *fcd,
+ real *lambda, t_graph *graph,
+ t_forcerec *fr, gmx_vsite_t *vsite, rvec mu_tot,
+ double t, gmx_edsam_t ed,
+ gmx_bool bBornRadii,
+ int flags,
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion)
{
int cg0, cg1, i, j;
- int start, homenr;
double mu[2*DIM];
gmx_bool bStateChanged, bNS, bFillGrid, bCalcCGCM;
gmx_bool bDoForces;
- float cycles_pme, cycles_force;
+ float cycles_pme;
- start = 0;
- homenr = mdatoms->homenr;
+ const int start = 0;
+ const int homenr = mdatoms->homenr;
clear_mat(vir_force);
* we do not need to worry about shifting.
*/
- int pme_flags = 0;
-
wallcycle_start(wcycle, ewcPP_PMESENDX);
bBS = (inputrec->nwall == 2);
svmul(inputrec->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
}
- if (EEL_PME(fr->eeltype))
- {
- pme_flags |= GMX_PME_DO_COULOMB;
- }
-
- if (EVDW_PME(fr->vdwtype))
- {
- pme_flags |= GMX_PME_DO_LJ;
- }
-
gmx_pme_send_coordinates(cr, bBS ? boxs : box, x,
- mdatoms->nChargePerturbed, mdatoms->nTypePerturbed, lambda[efptCOUL], lambda[efptVDW],
+ lambda[efptCOUL], lambda[efptVDW],
(flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY)),
- pme_flags, step);
+ step);
wallcycle_stop(wcycle, ewcPP_PMESENDX);
}
wallcycle_start(wcycle, ewcMOVEX);
dd_move_x(cr->dd, box, x);
wallcycle_stop(wcycle, ewcMOVEX);
+ /* No GPU support, no move_x overlap, so reopen the balance region here */
+ if (ddOpenBalanceRegion == DdOpenBalanceRegionBeforeForceComputation::yes)
+ {
+ ddReopenBalanceRegionCpu(cr->dd);
+ }
}
if (inputrecNeedMutot(inputrec))
if (PAR(cr))
{
gmx_sumd(2*DIM, mu, cr);
+ ddReopenBalanceRegionCpu(cr->dd);
}
for (i = 0; i < 2; i++)
{
if (inputrec->bRot)
{
- /* Enforced rotation has its own cycle counter that starts after the collective
- * coordinates have been communicated. It is added to ddCyclF to allow
- * for proper load-balancing */
wallcycle_start(wcycle, ewcROT);
- do_rotation(cr, inputrec, box, x, t, step, wcycle, bNS);
+ do_rotation(cr, inputrec, box, x, t, step, bNS);
wallcycle_stop(wcycle, ewcROT);
}
+ /* Temporary solution until all routines take PaddedRVecVector */
+ rvec *f = as_rvec_array(force->data());
+
/* Start the force cycle counter.
- * This counter is stopped after do_force_lowlevel.
- * No parallel communication should occur while this counter is running,
- * since that will interfere with the dynamic load balancing.
+ * Note that a different counter is used for dynamic load balancing.
*/
wallcycle_start(wcycle, ewcFORCE);
{
if (flags & GMX_FORCE_VIRIAL)
{
- fr->f_novirsum = fr->f_novirsum_alloc;
- if (fr->bDomDec)
- {
- clear_rvecs(fr->f_novirsum_n, fr->f_novirsum);
- }
- else
- {
- clear_rvecs(homenr, fr->f_novirsum+start);
- }
+ fr->f_novirsum = fr->forceBufferNoVirialSummation;
+ /* TODO: remove this - 1 when padding is properly implemented */
+ clear_rvecs(fr->f_novirsum->size() - 1,
+ as_rvec_array(fr->f_novirsum->data()));
}
else
{
* a separate array for forces that do not contribute
* to the pressure.
*/
- fr->f_novirsum = f;
+ fr->f_novirsum = force;
}
}
flags,
&cycles_pme);
- cycles_force = wallcycle_stop(wcycle, ewcFORCE);
-
- if (ed)
- {
- do_flood(cr, inputrec, x, f, ed, box, step, bNS);
- }
+ wallcycle_stop(wcycle, ewcFORCE);
if (DOMAINDECOMP(cr))
{
dd_force_flop_stop(cr->dd, nrnb);
- if (wcycle)
+
+ if (ddCloseBalanceRegion == DdCloseBalanceRegionAfterForceComputation::yes)
{
- dd_cycles_add(cr->dd, cycles_force-cycles_pme, ddCyclF);
+ ddCloseBalanceRegionCpu(cr->dd);
}
}
+ if (ed)
+ {
+ do_flood(cr, inputrec, x, f, ed, box, step, bNS);
+ }
+
if (bDoForces)
{
- if (inputrecElecField(inputrec))
+ /* Collect forces from modules */
+ gmx::ArrayRef<gmx::RVec> fNoVirSum;
+ if (fr->bF_NoVirSum)
{
- /* Compute forces due to electric field */
- calc_f_el(MASTER(cr) ? field : NULL,
- start, homenr, mdatoms->chargeA, fr->f_novirsum,
- inputrec->ex, inputrec->et, t);
+ fNoVirSum = *fr->f_novirsum;
}
+ fr->forceProviders->calculateForces(cr, mdatoms, box, t, x, *force, fNoVirSum);
/* Communicate the forces */
if (DOMAINDECOMP(cr))
if (EEL_FULL(fr->eeltype) && cr->dd->n_intercg_excl &&
(flags & GMX_FORCE_VIRIAL))
{
- dd_move_f(cr->dd, fr->f_novirsum, NULL);
+ dd_move_f(cr->dd, as_rvec_array(fr->f_novirsum->data()), nullptr);
}
wallcycle_stop(wcycle, ewcMOVEF);
}
if (vsite && !(fr->bF_NoVirSum && !(flags & GMX_FORCE_VIRIAL)))
{
wallcycle_start(wcycle, ewcVSITESPREAD);
- spread_vsite_f(vsite, x, f, fr->fshift, FALSE, NULL, nrnb,
+ spread_vsite_f(vsite, x, f, fr->fshift, FALSE, nullptr, nrnb,
&top->idef, fr->ePBC, fr->bMolPBC, graph, box, cr);
wallcycle_stop(wcycle, ewcVSITESPREAD);
}
gmx_int64_t step, t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_localtop_t *top,
gmx_groups_t *groups,
- matrix box, rvec x[], history_t *hist,
- rvec f[],
+ matrix box, PaddedRVecVector *coordinates, history_t *hist,
+ PaddedRVecVector *force,
tensor vir_force,
t_mdatoms *mdatoms,
gmx_enerdata_t *enerd, t_fcdata *fcd,
- real *lambda, t_graph *graph,
+ gmx::ArrayRef<real> lambda, t_graph *graph,
t_forcerec *fr,
gmx_vsite_t *vsite, rvec mu_tot,
- double t, FILE *field, gmx_edsam_t ed,
+ double t, gmx_edsam_t ed,
gmx_bool bBornRadii,
- int flags)
+ int flags,
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion,
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion)
{
/* modify force flag if not doing nonbonded */
if (!fr->bNonbonded)
flags &= ~GMX_FORCE_NONBONDED;
}
+ GMX_ASSERT(coordinates->size() >= static_cast<unsigned int>(fr->natoms_force + 1) ||
+ fr->natoms_force == 0, "We might need 1 element extra for SIMD");
+ GMX_ASSERT(force->size() >= static_cast<unsigned int>(fr->natoms_force + 1) ||
+ fr->natoms_force == 0, "We might need 1 element extra for SIMD");
+
+ rvec *x = as_rvec_array(coordinates->data());
+
switch (inputrec->cutoff_scheme)
{
case ecutsVERLET:
top,
groups,
box, x, hist,
- f, vir_force,
+ force, vir_force,
mdatoms,
enerd, fcd,
- lambda, graph,
+ lambda.data(), graph,
fr, fr->ic,
vsite, mu_tot,
- t, field, ed,
+ t, ed,
bBornRadii,
- flags);
+ flags,
+ ddOpenBalanceRegion,
+ ddCloseBalanceRegion);
break;
case ecutsGROUP:
do_force_cutsGROUP(fplog, cr, inputrec,
top,
groups,
box, x, hist,
- f, vir_force,
+ force, vir_force,
mdatoms,
enerd, fcd,
- lambda, graph,
+ lambda.data(), graph,
fr, vsite, mu_tot,
- t, field, ed,
+ t, ed,
bBornRadii,
- flags);
+ flags,
+ ddOpenBalanceRegion,
+ ddCloseBalanceRegion);
break;
default:
gmx_incons("Invalid cut-off scheme passed!");
}
+
+ /* In case we don't have constraints and are using GPUs, the next balancing
+ * region starts here.
+ * Some "special" work at the end of do_force_cuts?, such as vsite spread,
+ * virial calculation and COM pulling, is not thus not included in
+ * the balance timing, which is ok as most tasks do communication.
+ */
+ if (ddOpenBalanceRegion == DdOpenBalanceRegionBeforeForceComputation::yes)
+ {
+ ddOpenBalanceRegionCpu(cr->dd, DdAllowBalanceRegionReopen::no);
+ }
}
dvdl_dum = 0;
/* constrain the current position */
- constrain(NULL, TRUE, FALSE, constr, &(top->idef),
+ constrain(nullptr, TRUE, FALSE, constr, &(top->idef),
ir, cr, step, 0, 1.0, md,
- state->x, state->x, NULL,
+ as_rvec_array(state->x.data()), as_rvec_array(state->x.data()), nullptr,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- NULL, NULL, nrnb, econqCoord);
+ nullptr, nullptr, nrnb, econqCoord);
if (EI_VV(ir->eI))
{
/* constrain the inital velocity, and save it */
/* also may be useful if we need the ekin from the halfstep for velocity verlet */
- constrain(NULL, TRUE, FALSE, constr, &(top->idef),
+ constrain(nullptr, TRUE, FALSE, constr, &(top->idef),
ir, cr, step, 0, 1.0, md,
- state->x, state->v, state->v,
+ as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), as_rvec_array(state->v.data()),
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- NULL, NULL, nrnb, econqVeloc);
+ nullptr, nullptr, nrnb, econqVeloc);
}
/* constrain the inital velocities at t-dt/2 */
if (EI_STATE_VELOCITY(ir->eI) && ir->eI != eiVV)
gmx_step_str(step, buf));
}
dvdl_dum = 0;
- constrain(NULL, TRUE, FALSE, constr, &(top->idef),
+ constrain(nullptr, TRUE, FALSE, constr, &(top->idef),
ir, cr, step, -1, 1.0, md,
- state->x, savex, NULL,
+ as_rvec_array(state->x.data()), savex, nullptr,
fr->bMolPBC, state->box,
state->lambda[efptBONDED], &dvdl_dum,
- state->v, NULL, nrnb, econqCoord);
+ as_rvec_array(state->v.data()), nullptr, nrnb, econqCoord);
for (i = start; i < end; i++)
{
}
}
-void do_pbc_first(FILE *fplog, matrix box, t_forcerec *fr,
- t_graph *graph, rvec x[])
-{
- if (fplog)
- {
- fprintf(fplog, "Removing pbc first time\n");
- }
- calc_shifts(box, fr->shift_vec);
- if (graph)
- {
- mk_mshift(fplog, graph, fr->ePBC, box, x);
- if (gmx_debug_at)
- {
- p_graph(debug, "do_pbc_first 1", graph);
- }
- shift_self(graph, box, x);
- /* By doing an extra mk_mshift the molecules that are broken
- * because they were e.g. imported from another software
- * will be made whole again. Such are the healing powers
- * of GROMACS.
- */
- mk_mshift(fplog, graph, fr->ePBC, box, x);
- if (gmx_debug_at)
- {
- p_graph(debug, "do_pbc_first 2", graph);
- }
- }
- if (fplog)
- {
- fprintf(fplog, "Done rmpbc\n");
- }
-}
-
static void low_do_pbc_mtop(FILE *fplog, int ePBC, matrix box,
const gmx_mtop_t *mtop, rvec x[],
gmx_bool bFirst)
else
{
/* Pass NULL iso fplog to avoid graph prints for each molecule type */
- mk_graph_ilist(NULL, mtop->moltype[molb->type].ilist,
+ mk_graph_ilist(nullptr, mtop->moltype[molb->type].ilist,
0, molb->natoms_mol, FALSE, FALSE, graph);
for (mol = 0; mol < molb->nmol; mol++)
}
// TODO This can be cleaned up a lot, and move back to runner.cpp
-void finish_run(FILE *fplog, t_commrec *cr,
- t_inputrec *inputrec,
+void finish_run(FILE *fplog, const gmx::MDLogger &mdlog, t_commrec *cr,
+ const t_inputrec *inputrec,
t_nrnb nrnb[], gmx_wallcycle_t wcycle,
gmx_walltime_accounting_t walltime_accounting,
nonbonded_verlet_t *nbv,
gmx_bool bWriteStat)
{
- t_nrnb *nrnb_tot = NULL;
+ t_nrnb *nrnb_tot = nullptr;
double delta_t = 0;
double nbfs = 0, mflop = 0;
double elapsed_time,
if (!walltime_accounting_get_valid_finish(walltime_accounting))
{
- md_print_warn(cr, fplog,
- "Simulation ended prematurely, no performance report will be written.");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("Simulation ended prematurely, no performance report will be written.");
printReport = false;
}
if (printReport)
{
- struct gmx_wallclock_gpu_t* gputimes = use_GPU(nbv) ? nbnxn_gpu_get_timings(nbv->gpu_nbv) : NULL;
+ struct gmx_wallclock_gpu_t* gputimes = use_GPU(nbv) ? nbnxn_gpu_get_timings(nbv->gpu_nbv) : nullptr;
- wallcycle_print(fplog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
+ wallcycle_print(fplog, mdlog, cr->nnodes, cr->npmenodes, nthreads_pp, nthreads_pme,
elapsed_time_over_all_ranks,
wcycle, cycle_sum, gputimes);
}
}
-extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0)
+extern void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0)
{
/* this function works, but could probably use a logic rewrite to keep all the different
types of efep straight. */
- int i;
+ if ((ir->efep == efepNO) && (ir->bSimTemp == FALSE))
+ {
+ return;
+ }
+
t_lambda *fep = ir->fepvals;
+ *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
+ if checkpoint is set -- a kludge is in for now
+ to prevent this.*/
- if ((ir->efep == efepNO) && (ir->bSimTemp == FALSE))
+ for (int i = 0; i < efptNR; i++)
{
- for (i = 0; i < efptNR; i++)
+ /* overwrite lambda state with init_lambda for now for backwards compatibility */
+ if (fep->init_lambda >= 0) /* if it's -1, it was never initializd */
{
- lambda[i] = 0.0;
+ lambda[i] = fep->init_lambda;
if (lam0)
{
- lam0[i] = 0.0;
+ lam0[i] = lambda[i];
}
}
- return;
- }
- else
- {
- *fep_state = fep->init_fep_state; /* this might overwrite the checkpoint
- if checkpoint is set -- a kludge is in for now
- to prevent this.*/
- for (i = 0; i < efptNR; i++)
+ else
{
- /* overwrite lambda state with init_lambda for now for backwards compatibility */
- if (fep->init_lambda >= 0) /* if it's -1, it was never initializd */
- {
- lambda[i] = fep->init_lambda;
- if (lam0)
- {
- lam0[i] = lambda[i];
- }
- }
- else
+ lambda[i] = fep->all_lambda[i][*fep_state];
+ if (lam0)
{
- lambda[i] = fep->all_lambda[i][*fep_state];
- if (lam0)
- {
- lam0[i] = lambda[i];
- }
+ lam0[i] = lambda[i];
}
}
- if (ir->bSimTemp)
+ }
+ if (ir->bSimTemp)
+ {
+ /* need to rescale control temperatures to match current state */
+ for (int i = 0; i < ir->opts.ngtc; i++)
{
- /* need to rescale control temperatures to match current state */
- for (i = 0; i < ir->opts.ngtc; i++)
+ if (ir->opts.ref_t[i] > 0)
{
- if (ir->opts.ref_t[i] > 0)
- {
- ir->opts.ref_t[i] = ir->simtempvals->temperatures[*fep_state];
- }
+ ir->opts.ref_t[i] = ir->simtempvals->temperatures[*fep_state];
}
}
}
/* Send to the log the information on the current lambdas */
- if (fplog != NULL)
+ if (fplog != nullptr)
{
fprintf(fplog, "Initial vector of lambda components:[ ");
- for (i = 0; i < efptNR; i++)
+ for (const auto &l : lambda)
{
- fprintf(fplog, "%10.4f ", lambda[i]);
+ fprintf(fplog, "%10.4f ", l);
}
fprintf(fplog, "]\n");
}
void init_md(FILE *fplog,
- t_commrec *cr, t_inputrec *ir, const gmx_output_env_t *oenv,
+ t_commrec *cr, gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *ir, const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
double *t, double *t0,
- real *lambda, int *fep_state, double *lam0,
+ gmx::ArrayRef<real> lambda, int *fep_state, double *lam0,
t_nrnb *nrnb, gmx_mtop_t *mtop,
gmx_update_t **upd,
int nfile, const t_filenm fnm[],
gmx_mdoutf_t *outf, t_mdebin **mdebin,
tensor force_vir, tensor shake_vir, rvec mu_tot,
- gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
+ gmx_bool *bSimAnn, t_vcm **vcm,
gmx_wallcycle_t wcycle)
{
int i;
}
if (*bSimAnn)
{
- update_annealing_target_temp(ir, ir->init_t, upd ? *upd : NULL);
+ update_annealing_target_temp(ir, ir->init_t, upd ? *upd : nullptr);
}
- if (vcm != NULL)
+ if (vcm != nullptr)
{
*vcm = init_vcm(fplog, &mtop->groups, ir);
}
- if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES))
+ if (EI_DYNAMICS(ir->eI) && !mdrunOptions.continuationOptions.appendFiles)
{
if (ir->etc == etcBERENDSEN)
{
please_cite(fplog, "Goga2012");
}
}
- if ((ir->et[XX].n > 0) || (ir->et[YY].n > 0) || (ir->et[ZZ].n > 0))
- {
- please_cite(fplog, "Caleman2008a");
- }
init_nrnb(nrnb);
if (nfile != -1)
{
- *outf = init_mdoutf(fplog, nfile, fnm, Flags, cr, ir, mtop, oenv, wcycle);
+ *outf = init_mdoutf(fplog, nfile, fnm, mdrunOptions, cr, outputProvider, ir, mtop, oenv, wcycle);
- *mdebin = init_mdebin((Flags & MD_APPENDFILES) ? NULL : mdoutf_get_fp_ene(*outf),
+ *mdebin = init_mdebin(mdrunOptions.continuationOptions.appendFiles ? nullptr : mdoutf_get_fp_ene(*outf),
mtop, ir, mdoutf_get_fp_dhdl(*outf));
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/vcm.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/arrayref.h"
struct gmx_constr;
struct gmx_localtop_t;
struct gmx_output_env_t;
struct gmx_update_t;
+struct MdrunOptions;
struct nonbonded_verlet_t;
-struct t_graph;
struct t_mdatoms;
struct t_nrnb;
-typedef struct gmx_global_stat *gmx_global_stat_t;
+namespace gmx
+{
+class IMDOutputProvider;
+class MDLogger;
+}
-void do_pbc_first(FILE *log, matrix box, t_forcerec *fr,
- t_graph *graph, rvec x[]);
+typedef struct gmx_global_stat *gmx_global_stat_t;
void do_pbc_first_mtop(FILE *fplog, int ePBC, matrix box,
const gmx_mtop_t *mtop, rvec x[]);
gmx_walltime_accounting_t walltime_accounting,
const char *name);
-void finish_run(FILE *log, t_commrec *cr,
- t_inputrec *inputrec,
+void finish_run(FILE *log, const gmx::MDLogger &mdlog, t_commrec *cr,
+ const t_inputrec *inputrec,
t_nrnb nrnb[], gmx_wallcycle_t wcycle,
gmx_walltime_accounting_t walltime_accounting,
nonbonded_verlet_t *nbv,
matrix box, real lambda, tensor pres, tensor virial,
real *prescorr, real *enercorr, real *dvdlcorr);
-void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, real *lambda, double *lam0);
+void initialize_lambdas(FILE *fplog, t_inputrec *ir, int *fep_state, gmx::ArrayRef<real> lambda, double *lam0);
void do_constrain_first(FILE *log, gmx_constr *constr,
t_inputrec *inputrec, t_mdatoms *md,
t_forcerec *fr, gmx_localtop_t *top);
void init_md(FILE *fplog,
- t_commrec *cr, t_inputrec *ir, const gmx_output_env_t *oenv,
+ t_commrec *cr, gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *ir, const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
double *t, double *t0,
- real *lambda, int *fep_state, double *lam0,
+ gmx::ArrayRef<real> lambda, int *fep_state, double *lam0,
t_nrnb *nrnb, gmx_mtop_t *mtop,
gmx_update_t **upd,
int nfile, const t_filenm fnm[],
gmx_mdoutf_t *outf, t_mdebin **mdebin,
tensor force_vir, tensor shake_vir,
rvec mu_tot,
- gmx_bool *bSimAnn, t_vcm **vcm, unsigned long Flags,
+ gmx_bool *bSimAnn, t_vcm **vcm,
gmx_wallcycle_t wcycle);
/* Routine in sim_util.c */
* signals can be sent together with other data). This means that the
* only meaningful values are positive, negative or zero.
*
- * Note that xlc on BG/Q requires sig to be of size char (see unit tests
- * of ArrayRef for details).
- *
* isLocal permits (for example) replica-exchange to require that any
* checkpointing is synchronized across all simulations, by setting
* isLocal to false, so that the trigger for action is set only when
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static int mk_sblocks(FILE *fp, t_graph *g, int maxsid, t_sid sid[])
{
int ng, nnodes;
- int nW, nG, nB; /* Number of Grey, Black, White */
- int fW, fG; /* First of each category */
- egCol *egc = NULL; /* The colour of each node */
+ int nW, nG, nB; /* Number of Grey, Black, White */
+ int fW, fG; /* First of each category */
+ egCol *egc = nullptr; /* The colour of each node */
int g0, nblock;
if (!g->nbound)
t_sid *sid;
int nsid;
- g = mk_graph(NULL, idef, at_start, at_end, TRUE, bSettle);
+ g = mk_graph(nullptr, idef, at_start, at_end, TRUE, bSettle);
if (debug)
{
p_graph(debug, "Graaf Dracula", g);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int inn[egNR];
real copyenerd[F_NRE];
int nener, j;
- real *rmsd_data = NULL;
+ real *rmsd_data = nullptr;
double nb;
gmx_bool bVV, bTemp, bEner, bPres, bConstrVir, bEkinAveVel, bReadEkin;
bool checkNumberOfBondedInteractions = flags & CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2016, by the GROMACS development team, led by
+# Copyright (c) 2014,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# the research papers on the package. Check out http://www.gromacs.org.
gmx_add_unit_test(MdlibUnitTest mdlib-test
+ calc_verletbuf.cpp
settle.cpp
shake.cpp
simulationsignal.cpp)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Tests for the Verlet buffer calculation algorithm.
+ *
+ * \author Berk Hess <hess@kth.se>
+ */
+#include "gmxpre.h"
+
+#include "gromacs/mdlib/calc_verletbuf.h"
+
+#include <algorithm>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/functions.h"
+
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+class VerletBufferConstraintTest : public ::testing::Test
+{
+};
+
+/* This test covers the displacement correction for constrained atoms.
+ * This test does not check exact values, but rather checks that the MSD
+ * estimate for a constrained atom is smaller than that of a free atom
+ * and checks that the MSD is not smaller and also not much larger
+ * than the maximum of the exact value for rotational MSD beyond
+ * the location of the maximum. Furthermore, we check that the MSD estimate
+ * never decreases, as this is a requirement for the Verlet buffer size
+ * estimation. Together these criteria provide tight margins on
+ * the shape and values of the estimate.
+ *
+ * Additionally we check the 3D MSD for the COM of the two atoms.
+ */
+TEST_F(VerletBufferConstraintTest, EqualMasses)
+{
+ // The location and value of the MSD maximum for the exact displacement
+ // is described in the source file. We need to divide the maximum given
+ // there by 2, since sigma2 is per DOF for the 2 DOF constraint rotation.
+ const real sigma2RelMaxLocation = 4.5119;
+ const real sigma2RelMaxValue = 2.5695/2;
+
+ // Our max of our current estimate is 3% above the exact value.
+ const real sigma2RelMaxMargin = 1.04;
+
+ // The exact parameter values here don't actually matter.
+ real mass = 10;
+ real arm = 0.1;
+
+ atom_nonbonded_kinetic_prop_t prop;
+ prop.mass = mass;
+ prop.type = -1;
+ prop.q = 0;
+ prop.bConstr = TRUE;
+ prop.con_mass = mass;
+ prop.con_len = 2*arm;
+
+ // We scan a range of rotation distributions by scanning over T.
+ int numPointsBeforeMax = 0;
+ int numPointsAfterMax = 0;
+ real sigma2_2d_prev = 0;
+ for (int i = 0; i <= 200; i++)
+ {
+ real ktFac = i*0.01;
+ // The rotational displacement is Gaussian with a sigma^2 of:
+ real sigma2_rot = ktFac/(2*mass);
+
+ // Get the estimate for the Cartesian displacement.
+ real sigma2_2d, sigma2_3d;
+ constrained_atom_sigma2(ktFac, &prop, &sigma2_2d, &sigma2_3d);
+
+ // Check we are not decreasing sigma2_2d
+ EXPECT_EQ(std::max(sigma2_2d_prev, sigma2_2d), sigma2_2d);
+ // Check that sigma2_2d is not larger than sigma2 for free motion.
+ EXPECT_EQ(std::min(sigma2_rot, sigma2_2d), sigma2_2d);
+
+ // Check that we don't underestimate sigma2_rot beyond the real maximum
+ // and that our overestimate is tight.
+ real sigma2Rel = sigma2_rot/gmx::square(arm);
+ if (sigma2Rel >= sigma2RelMaxLocation)
+ {
+ EXPECT_EQ(std::max(sigma2_2d, sigma2RelMaxValue*gmx::square(arm)), sigma2_2d);
+ EXPECT_EQ(std::min(sigma2_2d, sigma2RelMaxMargin*sigma2RelMaxValue*gmx::square(arm)), sigma2_2d);
+
+ numPointsAfterMax++;
+ }
+ else
+ {
+ numPointsBeforeMax++;
+ }
+
+ // Also check sigma2 for the COM of the two atoms
+ EXPECT_REAL_EQ_TOL(sigma2_rot, sigma2_3d, test::defaultRealTolerance());
+ }
+
+ GMX_RELEASE_ASSERT(numPointsBeforeMax >= 20 && numPointsAfterMax >= 20, "This test only provides full coverage when we test a sufficient number of points before and after the location of the maximum value for the exact formula.");
+}
+
+} // namespace anonymous
+
+} // namespace gmx
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/idef.h"
#include "gromacs/topology/topology.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/unique_cptr.h"
#include "testutils/testasserts.h"
// Set up the topology. We still have to make some raw pointers,
// but they are put into scope guards for automatic cleanup.
- gmx_mtop_t *mtop;
+ gmx_mtop_t *mtop;
snew(mtop, 1);
- scoped_cptr<gmx_mtop_t> mtopGuard(mtop);
+ const unique_cptr<gmx_mtop_t> mtopGuard(mtop);
mtop->mols.nr = 1;
mtop->nmoltype = 1;
snew(mtop->moltype, mtop->nmoltype);
- scoped_cptr<gmx_moltype_t> moltypeGuard(mtop->moltype);
+ const unique_cptr<gmx_moltype_t> moltypeGuard(mtop->moltype);
mtop->nmolblock = 1;
snew(mtop->molblock, mtop->nmolblock);
- scoped_cptr<gmx_molblock_t> molblockGuard(mtop->molblock);
+ const unique_cptr<gmx_molblock_t> molblockGuard(mtop->molblock);
mtop->molblock[0].type = 0;
- std::vector<int> iatoms;
+ std::vector<int> iatoms;
for (int i = 0; i < numSettles; ++i)
{
iatoms.push_back(settleType);
// Set up the SETTLE parameters.
mtop->ffparams.ntypes = 1;
snew(mtop->ffparams.iparams, mtop->ffparams.ntypes);
- scoped_cptr<t_iparams> iparamsGuard(mtop->ffparams.iparams);
- const real dOH = 0.09572;
- const real dHH = 0.15139;
+ const unique_cptr<t_iparams> iparamsGuard(mtop->ffparams.iparams);
+ const real dOH = 0.09572;
+ const real dHH = 0.15139;
mtop->ffparams.iparams[settleType].settle.doh = dOH;
mtop->ffparams.iparams[settleType].settle.dhh = dHH;
startingPositions.data(), updatedPositions_.data(), reciprocalTimeStep,
useVelocities ? velocities_.data() : nullptr,
calcVirial, virial, &errorOccured);
+ settle_free(settled);
EXPECT_FALSE(errorOccured) << testDescription;
// The necessary tolerances for the test to pass were determined
}
}
-using ::testing::Bool;
// Scan the full Cartesian product of numbers of SETTLE interactions
// (4 and 17 are chosen to test cases that do and do not match
// hardware SIMD widths), and whether or not we use PBC, velocities or
-// calculate the virial contribution. It would be nicer to generate
-// these combinations with ::testing::Combine, but gcc 4.6 can't cope
-// with the template meta-programming required to generate the tuples.
+// calculate the virial contribution.
INSTANTIATE_TEST_CASE_P(WithParameters, SettleTest,
- ::testing::Values(SettleTestParameters(1, true, true, true),
- SettleTestParameters(4, true, true, true),
- SettleTestParameters(17, true, true, true),
- SettleTestParameters(1, false, true, true),
- SettleTestParameters(4, false, true, true),
- SettleTestParameters(17, false, true, true),
- SettleTestParameters(1, true, false, true),
- SettleTestParameters(4, true, false, true),
- SettleTestParameters(17, true, false, true),
- SettleTestParameters(1, false, false, true),
- SettleTestParameters(4, false, false, true),
- SettleTestParameters(17, false, false, true),
- SettleTestParameters(1, true, true, false),
- SettleTestParameters(4, true, true, false),
- SettleTestParameters(17, true, true, false),
- SettleTestParameters(1, false, true, false),
- SettleTestParameters(4, false, true, false),
- SettleTestParameters(17, false, true, false),
- SettleTestParameters(1, true, false, false),
- SettleTestParameters(4, true, false, false),
- SettleTestParameters(17, true, false, false),
- SettleTestParameters(1, false, false, false),
- SettleTestParameters(4, false, false, false),
- SettleTestParameters(17, false, false, false)));
-
+ ::testing::Combine(::testing::Values(1, 4, 7),
+ ::testing::Bool(),
+ ::testing::Bool(),
+ ::testing::Bool()));
} // namespace
} // namespace
gmx_groups_t *groups;
gmx_mtop_atomloop_all_t aloop;
int i, grp;
- t_atom *atom;
+ const t_atom *atom;
if (ngacc > 0)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformrealdistribution.h"
{
/*! \brief Do test particle insertion.
- \copydoc integrator_t (FILE *fplog, t_commrec *cr,
+ \copydoc integrator_t (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
gmx_edsam_t ed,
t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
+ const ReplicaExchangeParameters &replExParams,
+ gmx_membed_t gmx_unused *membed,
gmx_walltime_accounting_t walltime_accounting)
*/
-double do_tpi(FILE *fplog, t_commrec *cr,
+double do_tpi(FILE *fplog, t_commrec *cr, const gmx::MDLogger gmx_unused &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int gmx_unused nstglobalcomm,
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t gmx_unused *vsite, gmx_constr_t gmx_unused constr,
- int gmx_unused stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
+ ObservablesHistory gmx_unused *observablesHistory,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t gmx_unused ed,
t_forcerec *fr,
- int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
+ const ReplicaExchangeParameters gmx_unused &replExParams,
gmx_membed_t gmx_unused *membed,
- real gmx_unused cpt_period, real gmx_unused max_hours,
- int gmx_unused imdport,
- unsigned long gmx_unused Flags,
gmx_walltime_accounting_t walltime_accounting)
{
- gmx_localtop_t *top;
- gmx_groups_t *groups;
- gmx_enerdata_t *enerd;
- rvec *f;
- real lambda, t, temp, beta, drmax, epot;
- double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
- t_trxstatus *status;
- t_trxframe rerun_fr;
- gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS;
- tensor force_vir, shake_vir, vir, pres;
- int cg_tp, a_tp0, a_tp1, ngid, gid_tp, nener, e;
- rvec *x_mol;
- rvec mu_tot, x_init, dx, x_tp;
- int nnodes, frame;
- gmx_int64_t frame_step_prev, frame_step;
- gmx_int64_t nsteps, stepblocksize = 0, step;
- gmx_int64_t seed;
- int i;
- FILE *fp_tpi = NULL;
- char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
- double dbl, dump_ener;
- gmx_bool bCavity;
- int nat_cavity = 0, d;
- real *mass_cavity = NULL, mass_tot;
- int nbin;
- double invbinw, *bin, refvolshift, logV, bUlogV;
- real prescorr, enercorr, dvdlcorr;
- gmx_bool bEnergyOutOfBounds;
- const char *tpid_leg[2] = {"direct", "reweighted"};
+ gmx_localtop_t *top;
+ gmx_groups_t *groups;
+ gmx_enerdata_t *enerd;
+ PaddedRVecVector f {};
+ real lambda, t, temp, beta, drmax, epot;
+ double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
+ t_trxstatus *status;
+ t_trxframe rerun_fr;
+ gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS;
+ tensor force_vir, shake_vir, vir, pres;
+ int cg_tp, a_tp0, a_tp1, ngid, gid_tp, nener, e;
+ rvec *x_mol;
+ rvec mu_tot, x_init, dx, x_tp;
+ int nnodes, frame;
+ gmx_int64_t frame_step_prev, frame_step;
+ gmx_int64_t nsteps, stepblocksize = 0, step;
+ gmx_int64_t seed;
+ int i;
+ FILE *fp_tpi = nullptr;
+ char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
+ double dbl, dump_ener;
+ gmx_bool bCavity;
+ int nat_cavity = 0, d;
+ real *mass_cavity = nullptr, mass_tot;
+ int nbin;
+ double invbinw, *bin, refvolshift, logV, bUlogV;
+ real prescorr, enercorr, dvdlcorr;
+ gmx_bool bEnergyOutOfBounds;
+ const char *tpid_leg[2] = {"direct", "reweighted"};
+
+ GMX_UNUSED_VALUE(outputProvider);
/* Since there is no upper limit to the insertion energies,
* we need to set an upper limit for the distribution output.
if (bCavity)
{
ptr = getenv("GMX_TPIC_MASSES");
- if (ptr == NULL)
+ if (ptr == nullptr)
{
nat_cavity = 1;
}
sscanf(dump_pdb, "%20lf", &dump_ener);
}
- atoms2md(top_global, inputrec, 0, NULL, top_global->natoms, mdatoms);
+ atoms2md(top_global, inputrec, -1, nullptr, top_global->natoms, mdatoms);
update_mdatoms(mdatoms, inputrec->fepvals->init_lambda);
snew(enerd, 1);
init_enerdata(groups->grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
- snew(f, top_global->natoms);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ f.resize(top_global->natoms + 1);
/* Print to log file */
walltime_accounting_start(walltime_accounting);
}
bRFExcl = (bCharge && EEL_RF(fr->eeltype));
- calc_cgcm(fplog, cg_tp, cg_tp+1, &(top->cgs), state_global->x, fr->cg_cm);
+ calc_cgcm(fplog, cg_tp, cg_tp+1, &(top->cgs), as_rvec_array(state_global->x.data()), fr->cg_cm);
if (bCavity)
{
if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog)
copy_rvec(x_mol[i-a_tp0], state_global->x[i]);
}
/* Rotate the molecule randomly */
- rotate_conf(a_tp1-a_tp0, state_global->x+a_tp0, NULL,
+ rotate_conf(a_tp1-a_tp0, as_rvec_array(state_global->x.data())+a_tp0, nullptr,
2*M_PI*dist(rng),
2*M_PI*dist(rng),
2*M_PI*dist(rng));
cr->nnodes = 1;
do_force(fplog, cr, inputrec,
step, nrnb, wcycle, top, &top_global->groups,
- state_global->box, state_global->x, &state_global->hist,
- f, force_vir, mdatoms, enerd, fcd,
+ state_global->box, &state_global->x, &state_global->hist,
+ &f, force_vir, mdatoms, enerd, fcd,
state_global->lambda,
- NULL, fr, NULL, mu_tot, t, NULL, NULL, FALSE,
+ nullptr, fr, nullptr, mu_tot, t, nullptr, FALSE,
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
(bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS : 0) |
- (bStateChanged ? GMX_FORCE_STATECHANGED : 0));
+ (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
+ DdOpenBalanceRegionBeforeForceComputation::no,
+ DdCloseBalanceRegionAfterForceComputation::no);
cr->nnodes = nnodes;
bStateChanged = FALSE;
bNS = FALSE;
{
sprintf(str, "t%g_step%d.pdb", t, (int)step);
sprintf(str2, "t: %f step %d ener: %f", t, (int)step, epot);
- write_sto_conf_mtop(str, str2, top_global, state_global->x, state_global->v,
+ write_sto_conf_mtop(str, str2, top_global, as_rvec_array(state_global->x.data()), as_rvec_array(state_global->v.data()),
inputrec->ePBC, state_global->box);
}
if (fp_tpi)
{
- if (bVerbose || frame%10 == 0 || frame < 10)
+ if (mdrunOptions.verbose || frame%10 == 0 || frame < 10)
{
fprintf(stderr, "mu %10.3e <mu> %10.3e\n",
-log(sum_embU/nsteps)/beta, -log(VembU_all/V_all)/beta);
} /* End of the loop */
walltime_accounting_end(walltime_accounting);
- close_trj(status);
+ close_trx(status);
- if (fp_tpi != NULL)
+ if (fp_tpi != nullptr)
{
xvgrclose(fp_tpi);
}
- if (fplog != NULL)
+ if (fplog != nullptr)
{
fprintf(fplog, "\n");
fprintf(fplog, " <V> = %12.5e nm^3\n", V_all/frame);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/update.h"
#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/observableshistory.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/smalloc.h"
void
-do_md_trajectory_writing(FILE *fplog,
- t_commrec *cr,
- int nfile,
- const t_filenm fnm[],
- gmx_int64_t step,
- gmx_int64_t step_rel,
- double t,
- t_inputrec *ir,
- t_state *state,
- t_state *state_global,
- gmx_mtop_t *top_global,
- t_forcerec *fr,
- gmx_mdoutf_t outf,
- t_mdebin *mdebin,
- gmx_ekindata_t *ekind,
- rvec *f,
- int *nchkpt,
- gmx_bool bCPT,
- gmx_bool bRerunMD,
- gmx_bool bLastStep,
- gmx_bool bDoConfOut,
- gmx_bool bSumEkinhOld
+do_md_trajectory_writing(FILE *fplog,
+ t_commrec *cr,
+ int nfile,
+ const t_filenm fnm[],
+ gmx_int64_t step,
+ gmx_int64_t step_rel,
+ double t,
+ t_inputrec *ir,
+ t_state *state,
+ t_state *state_global,
+ ObservablesHistory *observablesHistory,
+ gmx_mtop_t *top_global,
+ t_forcerec *fr,
+ gmx_mdoutf_t outf,
+ t_mdebin *mdebin,
+ gmx_ekindata_t *ekind,
+ PaddedRVecVector *f,
+ int *nchkpt,
+ gmx_bool bCPT,
+ gmx_bool bRerunMD,
+ gmx_bool bLastStep,
+ gmx_bool bDoConfOut,
+ gmx_bool bSumEkinhOld
)
{
int mdof_flags;
- rvec *x_for_confout = NULL;
+ rvec *x_for_confout = nullptr;
mdof_flags = 0;
if (do_per_step(step, ir->nstxout))
update_ekinstate(&state_global->ekinstate, ekind);
state_global->ekinstate.bUpToDate = TRUE;
}
- update_energyhistory(state_global->enerhist, mdebin);
+
+ update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
}
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
- step, t, state, state_global, f);
+ step, t, state, state_global, observablesHistory, f);
if (bCPT)
{
(*nchkpt)++;
bDoConfOut && MASTER(cr) &&
!bRerunMD)
{
- if (fr->bMolPBC && state->x == state_global->x)
+ if (fr->bMolPBC && state == state_global)
{
/* This (single-rank) run needs to allocate a
temporary array of size natoms so that any
identical, and makes .edr restarts binary
identical. */
snew(x_for_confout, state_global->natoms);
- copy_rvecn(state_global->x, x_for_confout, 0, state_global->natoms);
+ copy_rvecn(as_rvec_array(state_global->x.data()), x_for_confout, 0, state_global->natoms);
}
else
{
/* With DD, or no bMolPBC, it doesn't matter if
- we change state_global->x */
- x_for_confout = state_global->x;
+ we change as_rvec_array(state_global->x.data()) */
+ x_for_confout = as_rvec_array(state_global->x.data());
}
/* x and v have been collected in mdoutf_write_to_trajectory_files,
}
write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
*top_global->name, top_global,
- x_for_confout, state_global->v,
+ x_for_confout, as_rvec_array(state_global->v.data()),
ir->ePBC, state->box);
- if (fr->bMolPBC && state->x == state_global->x)
+ if (fr->bMolPBC && state == state_global)
{
sfree(x_for_confout);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_ekindata_t;
struct gmx_mtop_t;
+struct ObservablesHistory;
struct t_commrec;
struct t_filenm;
t_inputrec *ir,
t_state *state,
t_state *state_global,
+ ObservablesHistory *observablesHistory,
struct gmx_mtop_t *top_global,
t_forcerec *fr,
gmx_mdoutf_t outf,
t_mdebin *mdebin,
struct gmx_ekindata_t *ekind,
- rvec *f,
+ PaddedRVecVector *f,
int *nchkpt,
gmx_bool bCPT,
gmx_bool bRerunMD,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/group.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/boxutilities.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
struct gmx_update_t
{
- gmx_stochd_t *sd;
+ gmx_stochd_t *sd;
/* xprime for constraint algorithms */
- rvec *xp;
- int xp_nalloc;
+ PaddedRVecVector xp;
/* Variables for the deform algorithm */
- gmx_int64_t deformref_step;
- matrix deformref_box;
+ gmx_int64_t deformref_step;
+ matrix deformref_box;
};
+static bool isTemperatureCouplingStep(gmx_int64_t step, const t_inputrec *ir)
+{
+ /* We should only couple after a step where energies were determined (for leapfrog versions)
+ or the step energies are determined, for velocity verlet versions */
+ int offset;
+ if (EI_VV(ir->eI))
+ {
+ offset = 0;
+ }
+ else
+ {
+ offset = 1;
+ }
+ return ir->etc != etcNO &&
+ (ir->nsttcouple == 1 ||
+ do_per_step(step + ir->nsttcouple - offset, ir->nsttcouple));
+}
-static void do_update_md(int start, int nrend,
- double dt, int nstpcouple,
- t_grp_tcstat *tcstat,
- double nh_vxi[],
- gmx_bool bNEMD, t_grp_acc *gstat, rvec accel[],
- ivec nFreeze[],
- real invmass[],
- unsigned short ptype[], unsigned short cFREEZE[],
- unsigned short cACC[], unsigned short cTC[],
- rvec x[], rvec xprime[], rvec v[],
- rvec f[], matrix M,
- gmx_bool bNH, gmx_bool bPR)
+static bool isPressureCouplingStep(gmx_int64_t step, const t_inputrec *ir)
{
- double imass, w_dt;
- int gf = 0, ga = 0, gt = 0;
- rvec vrel;
- real vn, vv, va, vb, vnrel;
- real lg, vxi = 0, u;
- int n, d;
+ GMX_ASSERT(ir->epc != epcMTTK, "MTTK pressure coupling is not handled here");
- if (bNH || bPR)
+ int offset;
+ if (ir->epc == epcBERENDSEN)
{
- /* Update with coupling to extended ensembles, used for
- * Nose-Hoover and Parrinello-Rahman coupling
- * Nose-Hoover uses the reversible leap-frog integrator from
- * Holian et al. Phys Rev E 52(3) : 2338, 1995
- */
- for (n = start; n < nrend; n++)
+ offset = 0;
+ }
+ else
+ {
+ offset = 1;
+ }
+ /* We should only couple after a step where pressures were determined */
+ return ir->epc != etcNO &&
+ (ir->nstpcouple == 1 ||
+ do_per_step(step + ir->nstpcouple - offset, ir->nstpcouple));
+}
+
+/*! \brief Sets the number of different temperature coupling values */
+enum class NumTempScaleValues
+{
+ single, //!< Single T-scaling value (either one group or all values =1)
+ multiple //!< Multiple T-scaling values, need to use T-group indices
+};
+
+/*! \brief Sets if to apply no or diagonal Parrinello-Rahman pressure scaling
+ *
+ * Note that this enum is only used in updateMdLeapfrogSimple(), which does
+ * not handle fully anistropic Parrinello-Rahman scaling, so we only have
+ * options \p no and \p diagonal here and no anistropic option.
+ */
+enum class ApplyParrinelloRahmanVScaling
+{
+ no, //!< Do not apply velocity scaling (not a PR-coupling run or step)
+ diagonal //!< Apply velocity scaling using a diagonal matrix
+};
+
+/*! \brief Integrate using leap-frog with T-scaling and optionally diagonal Parrinello-Rahman p-coupling
+ *
+ * \tparam numTempScaleValues The number of different T-couple values
+ * \tparam applyPRVScaling Apply Parrinello-Rahman velocity scaling
+ * \param[in] start Index of first atom to update
+ * \param[in] nrend Last atom to update: \p nrend - 1
+ * \param[in] dt The time step
+ * \param[in] dtPressureCouple Time step for pressure coupling
+ * \param[in] invMassPerDim 1/mass per atom and dimension
+ * \param[in] tcstat Temperature coupling information
+ * \param[in] cTC T-coupling group index per atom
+ * \param[in] pRVScaleMatrixDiagonal Parrinello-Rahman v-scale matrix diagonal
+ * \param[in] x Input coordinates
+ * \param[out] xprime Updated coordinates
+ * \param[inout] v Velocities
+ * \param[in] f Forces
+ *
+ * We expect this template to get good SIMD acceleration by most compilers,
+ * unlike the more complex general template.
+ * Note that we might get even better SIMD acceleration when we introduce
+ * aligned (and padded) memory, possibly with some hints for the compilers.
+ */
+template<NumTempScaleValues numTempScaleValues,
+ ApplyParrinelloRahmanVScaling applyPRVScaling>
+static void
+updateMdLeapfrogSimple(int start,
+ int nrend,
+ real dt,
+ real dtPressureCouple,
+ const rvec * gmx_restrict invMassPerDim,
+ const t_grp_tcstat * tcstat,
+ const unsigned short * cTC,
+ const rvec pRVScaleMatrixDiagonal,
+ const rvec * gmx_restrict x,
+ rvec * gmx_restrict xprime,
+ rvec * gmx_restrict v,
+ const rvec * gmx_restrict f)
+{
+ real lambdaGroup;
+
+ if (numTempScaleValues == NumTempScaleValues::single)
+ {
+ lambdaGroup = tcstat[0].lambda;
+ }
+
+ for (int a = start; a < nrend; a++)
+ {
+ if (numTempScaleValues == NumTempScaleValues::multiple)
{
- imass = invmass[n];
- if (cFREEZE)
- {
- gf = cFREEZE[n];
- }
- if (cACC)
- {
- ga = cACC[n];
- }
- if (cTC)
- {
- gt = cTC[n];
- }
- lg = tcstat[gt].lambda;
- if (bNH)
+ lambdaGroup = tcstat[cTC[a]].lambda;
+ }
+
+ for (int d = 0; d < DIM; d++)
+ {
+ /* Note that using rvec invMassPerDim results in more efficient
+ * SIMD code, but this increases the cache pressure.
+ * For large systems with PME on the CPU this slows down the
+ * (then already slow) update by 20%. If all data remains in cache,
+ * using rvec is much faster.
+ */
+ real vNew = lambdaGroup*v[a][d] + f[a][d]*invMassPerDim[a][d]*dt;
+
+ if (applyPRVScaling == ApplyParrinelloRahmanVScaling::diagonal)
{
- vxi = nh_vxi[gt];
+ vNew -= dtPressureCouple*pRVScaleMatrixDiagonal[d]*v[a][d];
}
- rvec_sub(v[n], gstat[ga].u, vrel);
+ v[a][d] = vNew;
+ xprime[a][d] = x[a][d] + vNew*dt;
+ }
+ }
+}
- for (d = 0; d < DIM; d++)
- {
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
- {
- vnrel = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d]
- - nstpcouple*iprod(M[d], vrel)))/(1 + 0.5*vxi*dt);
- /* do not scale the mean velocities u */
- vn = gstat[ga].u[d] + accel[ga][d]*dt + vnrel;
- v[n][d] = vn;
- xprime[n][d] = x[n][d]+vn*dt;
- }
- else
+/*! \brief Sets the NEMD acceleration type */
+enum class AccelerationType
+{
+ none, group, cosine
+};
+
+/*! \brief Integrate using leap-frog with support for everything
+ *
+ * \tparam accelerationType Type of NEMD acceleration
+ * \param[in] start Index of first atom to update
+ * \param[in] nrend Last atom to update: \p nrend - 1
+ * \param[in] doNoseHoover If to apply Nose-Hoover T-coupling
+ * \param[in] dt The time step
+ * \param[in] dtPressureCouple Time step for pressure coupling, is 0 when no pressure coupling should be applied at this step
+ * \param[in] ir The input parameter record
+ * \param[in] md Atom properties
+ * \param[in] ekind Kinetic energy data
+ * \param[in] box The box dimensions
+ * \param[in] x Input coordinates
+ * \param[out] xprime Updated coordinates
+ * \param[inout] v Velocities
+ * \param[in] f Forces
+ * \param[in] nh_vxi Nose-Hoover velocity scaling factors
+ * \param[in] M Parrinello-Rahman scaling matrix
+ */
+template<AccelerationType accelerationType>
+static void
+updateMdLeapfrogGeneral(int start,
+ int nrend,
+ bool doNoseHoover,
+ real dt,
+ real dtPressureCouple,
+ const t_inputrec * ir,
+ const t_mdatoms * md,
+ const gmx_ekindata_t * ekind,
+ const matrix box,
+ const rvec * gmx_restrict x,
+ rvec * gmx_restrict xprime,
+ rvec * gmx_restrict v,
+ const rvec * gmx_restrict f,
+ const double * gmx_restrict nh_vxi,
+ const matrix M)
+{
+ /* This is a version of the leap-frog integrator that supports
+ * all combinations of T-coupling, P-coupling and NEMD.
+ * Nose-Hoover uses the reversible leap-frog integrator from
+ * Holian et al. Phys Rev E 52(3) : 2338, 1995
+ */
+
+ const unsigned short * cTC = md->cTC;
+ const t_grp_tcstat * tcstat = ekind->tcstat;
+
+ const unsigned short * cACC = md->cACC;
+ const rvec * accel = ir->opts.acc;
+ const t_grp_acc * grpstat = ekind->grpstat;
+
+ const rvec * gmx_restrict invMassPerDim = md->invMassPerDim;
+
+ /* Initialize group values, changed later when multiple groups are used */
+ int ga = 0;
+ int gt = 0;
+ real factorNH = 0;
+
+ for (int n = start; n < nrend; n++)
+ {
+ if (cTC)
+ {
+ gt = cTC[n];
+ }
+ real lg = tcstat[gt].lambda;
+
+ rvec vRel;
+ real cosineZ, vCosine;
+#ifdef __INTEL_COMPILER
+#pragma warning( disable : 280 )
+#endif
+ switch (accelerationType)
+ {
+ case AccelerationType::none:
+ copy_rvec(v[n], vRel);
+ break;
+ case AccelerationType::group:
+ if (cACC)
{
- v[n][d] = 0.0;
- xprime[n][d] = x[n][d];
+ ga = cACC[n];
}
+ /* Avoid scaling the group velocity */
+ rvec_sub(v[n], grpstat[ga].u, vRel);
+ break;
+ case AccelerationType::cosine:
+ cosineZ = std::cos(x[n][ZZ]*static_cast<real>(M_PI)/box[ZZ][ZZ]);
+ vCosine = cosineZ*ekind->cosacc.vcos;
+ /* Avoid scaling the cosine profile velocity */
+ copy_rvec(v[n], vRel);
+ vRel[XX] -= vCosine;
+ break;
+ }
+
+ if (doNoseHoover)
+ {
+ /* Here we account for multiple time stepping, by increasing
+ * the Nose-Hoover correction by nsttcouple
+ */
+ factorNH = 0.5*ir->nsttcouple*dt*nh_vxi[gt];
+ }
+
+ for (int d = 0; d < DIM; d++)
+ {
+ real vNew =
+ (lg*vRel[d] + (f[n][d]*invMassPerDim[n][d]*dt - factorNH*vRel[d]
+ - dtPressureCouple*iprod(M[d], vRel)))/(1 + factorNH);
+ switch (accelerationType)
+ {
+ case AccelerationType::none:
+ break;
+ case AccelerationType::group:
+ /* Add back the mean velocity and apply acceleration */
+ vNew += grpstat[ga].u[d] + accel[ga][d]*dt;
+ break;
+ case AccelerationType::cosine:
+ if (d == XX)
+ {
+ /* Add back the mean velocity and apply acceleration */
+ vNew += vCosine + cosineZ*ekind->cosacc.cos_accel*dt;
+ }
+ break;
}
+ v[n][d] = vNew;
+ xprime[n][d] = x[n][d] + vNew*dt;
+ }
+ }
+}
+
+/*! \brief Handles the Leap-frog MD x and v integration */
+static void do_update_md(int start,
+ int nrend,
+ gmx_int64_t step,
+ real dt,
+ const t_inputrec * ir,
+ const t_mdatoms * md,
+ const gmx_ekindata_t * ekind,
+ const matrix box,
+ const rvec * gmx_restrict x,
+ rvec * gmx_restrict xprime,
+ rvec * gmx_restrict v,
+ const rvec * gmx_restrict f,
+ const double * gmx_restrict nh_vxi,
+ const matrix M)
+{
+ GMX_ASSERT(nrend == start || xprime != x, "For SIMD optimization certain compilers need to have xprime != x");
+
+ /* Note: Berendsen pressure scaling is handled after do_update_md() */
+ bool doTempCouple = isTemperatureCouplingStep(step, ir);
+ bool doNoseHoover = (ir->etc == etcNOSEHOOVER && doTempCouple);
+ bool doParrinelloRahman = (ir->epc == epcPARRINELLORAHMAN && isPressureCouplingStep(step, ir));
+ bool doPROffDiagonal = (doParrinelloRahman && (M[YY][XX] != 0 || M[ZZ][XX] != 0 || M[ZZ][YY] != 0));
+
+ real dtPressureCouple = (doParrinelloRahman ? ir->nstpcouple*dt : 0);
+
+ /* NEMD (also cosine) acceleration is applied in updateMdLeapFrogGeneral */
+ bool doAcceleration = (ekind->bNEMD || ekind->cosacc.cos_accel != 0);
+
+ if (doNoseHoover || doPROffDiagonal || doAcceleration)
+ {
+ if (!doAcceleration)
+ {
+ updateMdLeapfrogGeneral<AccelerationType::none>
+ (start, nrend, doNoseHoover, dt, dtPressureCouple,
+ ir, md, ekind, box, x, xprime, v, f, nh_vxi, M);
+ }
+ else if (ekind->bNEMD)
+ {
+ updateMdLeapfrogGeneral<AccelerationType::group>
+ (start, nrend, doNoseHoover, dt, dtPressureCouple,
+ ir, md, ekind, box, x, xprime, v, f, nh_vxi, M);
+ }
+ else
+ {
+ updateMdLeapfrogGeneral<AccelerationType::cosine>
+ (start, nrend, doNoseHoover, dt, dtPressureCouple,
+ ir, md, ekind, box, x, xprime, v, f, nh_vxi, M);
}
}
- else if (cFREEZE != NULL ||
- nFreeze[0][XX] || nFreeze[0][YY] || nFreeze[0][ZZ] ||
- bNEMD)
+ else
{
- /* Update with Berendsen/v-rescale coupling and freeze or NEMD */
- for (n = start; n < nrend; n++)
+ /* We determine if we have a single T-coupling lambda value for all
+ * atoms. That allows for better SIMD acceleration in the template.
+ * If we do not do temperature coupling (in the run or this step),
+ * all scaling values are 1, so we effectively have a single value.
+ */
+ bool haveSingleTempScaleValue = (!doTempCouple || ekind->ngtc == 1);
+
+ /* Extract some pointers needed by all cases */
+ const unsigned short *cTC = md->cTC;
+ const t_grp_tcstat *tcstat = ekind->tcstat;
+ const rvec *invMassPerDim = md->invMassPerDim;
+
+ if (doParrinelloRahman)
{
- w_dt = invmass[n]*dt;
- if (cFREEZE)
- {
- gf = cFREEZE[n];
- }
- if (cACC)
+ GMX_ASSERT(!doPROffDiagonal, "updateMdLeapfrogSimple only support diagonal Parrinello-Rahman scaling matrices");
+
+ rvec diagM;
+ for (int d = 0; d < DIM; d++)
{
- ga = cACC[n];
+ diagM[d] = M[d][d];
}
- if (cTC)
+
+ if (haveSingleTempScaleValue)
{
- gt = cTC[n];
+ updateMdLeapfrogSimple
+ <NumTempScaleValues::single,
+ ApplyParrinelloRahmanVScaling::diagonal>
+ (start, nrend, dt, dtPressureCouple,
+ invMassPerDim, tcstat, cTC, diagM, x, xprime, v, f);
}
- lg = tcstat[gt].lambda;
-
- for (d = 0; d < DIM; d++)
+ else
{
- vn = v[n][d];
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell) && !nFreeze[gf][d])
- {
- vv = lg*vn + f[n][d]*w_dt;
-
- /* do not scale the mean velocities u */
- u = gstat[ga].u[d];
- va = vv + accel[ga][d]*dt;
- vb = va + (1.0-lg)*u;
- v[n][d] = vb;
- xprime[n][d] = x[n][d]+vb*dt;
- }
- else
- {
- v[n][d] = 0.0;
- xprime[n][d] = x[n][d];
- }
+ updateMdLeapfrogSimple
+ <NumTempScaleValues::multiple,
+ ApplyParrinelloRahmanVScaling::diagonal>
+ (start, nrend, dt, dtPressureCouple,
+ invMassPerDim, tcstat, cTC, diagM, x, xprime, v, f);
}
}
- }
- else
- {
- /* Plain update with Berendsen/v-rescale coupling */
- for (n = start; n < nrend; n++)
+ else
{
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
+ if (haveSingleTempScaleValue)
{
- w_dt = invmass[n]*dt;
- if (cTC)
- {
- gt = cTC[n];
- }
- lg = tcstat[gt].lambda;
-
- for (d = 0; d < DIM; d++)
- {
- vn = lg*v[n][d] + f[n][d]*w_dt;
- v[n][d] = vn;
- xprime[n][d] = x[n][d] + vn*dt;
- }
+ updateMdLeapfrogSimple
+ <NumTempScaleValues::single,
+ ApplyParrinelloRahmanVScaling::no>
+ (start, nrend, dt, dtPressureCouple,
+ invMassPerDim, tcstat, cTC, nullptr, x, xprime, v, f);
}
else
{
- for (d = 0; d < DIM; d++)
- {
- v[n][d] = 0.0;
- xprime[n][d] = x[n][d];
- }
+ updateMdLeapfrogSimple
+ <NumTempScaleValues::multiple,
+ ApplyParrinelloRahmanVScaling::no>
+ (start, nrend, dt, dtPressureCouple,
+ invMassPerDim, tcstat, cTC, nullptr, x, xprime, v, f);
}
}
}
}
-static void do_update_vv_vel(int start, int nrend, double dt,
+static void do_update_vv_vel(int start, int nrend, real dt,
rvec accel[], ivec nFreeze[], real invmass[],
unsigned short ptype[], unsigned short cFREEZE[],
- unsigned short cACC[], rvec v[], rvec f[],
+ unsigned short cACC[], rvec v[], const rvec f[],
gmx_bool bExtended, real veta, real alpha)
{
- double w_dt;
int gf = 0, ga = 0;
int n, d;
- double g, mv1, mv2;
+ real g, mv1, mv2;
if (bExtended)
{
g = 0.25*dt*veta*alpha;
- mv1 = exp(-g);
+ mv1 = std::exp(-g);
mv2 = gmx::series_sinhx(g);
}
else
}
for (n = start; n < nrend; n++)
{
- w_dt = invmass[n]*dt;
+ real w_dt = invmass[n]*dt;
if (cFREEZE)
{
gf = cFREEZE[n];
}
} /* do_update_vv_vel */
-static void do_update_vv_pos(int start, int nrend, double dt,
+static void do_update_vv_pos(int start, int nrend, real dt,
ivec nFreeze[],
unsigned short ptype[], unsigned short cFREEZE[],
- rvec x[], rvec xprime[], rvec v[],
+ const rvec x[], rvec xprime[], rvec v[],
gmx_bool bExtended, real veta)
{
int gf = 0;
int n, d;
- double g, mr1, mr2;
+ real g, mr1, mr2;
/* Would it make more sense if Parrinello-Rahman was put here? */
if (bExtended)
{
g = 0.5*dt*veta;
- mr1 = exp(g);
+ mr1 = std::exp(g);
mr2 = gmx::series_sinhx(g);
}
else
}
} /* do_update_vv_pos */
-static void do_update_visc(int start, int nrend,
- double dt, int nstpcouple,
- t_grp_tcstat *tcstat,
- double nh_vxi[],
- real invmass[],
- unsigned short ptype[], unsigned short cTC[],
- rvec x[], rvec xprime[], rvec v[],
- rvec f[], matrix M, matrix box, real
- cos_accel, real vcos,
- gmx_bool bNH, gmx_bool bPR)
-{
- double imass, w_dt;
- int gt = 0;
- real vn, vc;
- real lg, vxi = 0, vv;
- real fac, cosz;
- rvec vrel;
- int n, d;
-
- fac = 2*M_PI/(box[ZZ][ZZ]);
-
- if (bNH || bPR)
- {
- /* Update with coupling to extended ensembles, used for
- * Nose-Hoover and Parrinello-Rahman coupling
- */
- for (n = start; n < nrend; n++)
- {
- imass = invmass[n];
- if (cTC)
- {
- gt = cTC[n];
- }
- lg = tcstat[gt].lambda;
- cosz = cos(fac*x[n][ZZ]);
-
- copy_rvec(v[n], vrel);
-
- vc = cosz*vcos;
- vrel[XX] -= vc;
- if (bNH)
- {
- vxi = nh_vxi[gt];
- }
- for (d = 0; d < DIM; d++)
- {
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
- {
- vn = (lg*vrel[d] + dt*(imass*f[n][d] - 0.5*vxi*vrel[d]
- - nstpcouple*iprod(M[d], vrel)))/(1 + 0.5*vxi*dt);
- if (d == XX)
- {
- vn += vc + dt*cosz*cos_accel;
- }
- v[n][d] = vn;
- xprime[n][d] = x[n][d]+vn*dt;
- }
- else
- {
- xprime[n][d] = x[n][d];
- }
- }
- }
- }
- else
- {
- /* Classic version of update, used with berendsen coupling */
- for (n = start; n < nrend; n++)
- {
- w_dt = invmass[n]*dt;
- if (cTC)
- {
- gt = cTC[n];
- }
- lg = tcstat[gt].lambda;
- cosz = cos(fac*x[n][ZZ]);
-
- for (d = 0; d < DIM; d++)
- {
- vn = v[n][d];
-
- if ((ptype[n] != eptVSite) && (ptype[n] != eptShell))
- {
- if (d == XX)
- {
- vc = cosz*vcos;
- /* Do not scale the cosine velocity profile */
- vv = vc + lg*(vn - vc + f[n][d]*w_dt);
- /* Add the cosine accelaration profile */
- vv += dt*cosz*cos_accel;
- }
- else
- {
- vv = lg*(vn + f[n][d]*w_dt);
- }
- v[n][d] = vv;
- xprime[n][d] = x[n][d]+vv*dt;
- }
- else
- {
- v[n][d] = 0.0;
- xprime[n][d] = x[n][d];
- }
- }
- }
- }
-}
-
static gmx_stochd_t *init_stochd(const t_inputrec *ir)
{
gmx_stochd_t *sd;
{
if (opts->tau_t[gt] > 0)
{
- sdc[gt].em = exp(-ir->delta_t/opts->tau_t[gt]);
+ sdc[gt].em = std::exp(-ir->delta_t/opts->tau_t[gt]);
}
else
{
gmx_update_t *init_update(const t_inputrec *ir)
{
- gmx_update_t *upd;
-
- snew(upd, 1);
+ gmx_update_t *upd = new(gmx_update_t);
if (ir->eI == eiBD || EI_SD(ir->eI) || ir->etc == etcVRESCALE || ETC_ANDERSEN(ir->etc))
{
update_temperature_constants(upd, ir);
- upd->xp = NULL;
- upd->xp_nalloc = 0;
+ upd->xp.resize(0);
return upd;
}
-void update_realloc(gmx_update_t *upd, int state_nalloc)
+void update_realloc(gmx_update_t *upd, int natoms)
{
GMX_ASSERT(upd, "upd must be allocated before its fields can be reallocated");
- if (state_nalloc > upd->xp_nalloc)
- {
- upd->xp_nalloc = state_nalloc;
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries. */
- srenew(upd->xp, upd->xp_nalloc + 1);
- }
+
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries. */
+ upd->xp.resize(natoms + 1);
}
static void do_update_sd1(gmx_stochd_t *sd,
- int start, int nrend, double dt,
+ int start, int nrend, real dt,
rvec accel[], ivec nFreeze[],
real invmass[], unsigned short ptype[],
unsigned short cFREEZE[], unsigned short cACC[],
unsigned short cTC[],
- rvec x[], rvec xprime[], rvec v[], rvec f[],
+ const rvec x[], rvec xprime[], rvec v[], const rvec f[],
gmx_bool bDoConstr,
gmx_bool bFirstHalfConstr,
gmx_int64_t step, int seed, int* gatindex)
}
}
-static void do_update_bd(int start, int nrend, double dt,
+static void do_update_bd(int start, int nrend, real dt,
ivec nFreeze[],
real invmass[], unsigned short ptype[],
unsigned short cFREEZE[], unsigned short cTC[],
- rvec x[], rvec xprime[], rvec v[],
- rvec f[], real friction_coefficient,
+ const rvec x[], rvec xprime[], rvec v[],
+ const rvec f[], real friction_coefficient,
real *rf, gmx_int64_t step, int seed,
int* gatindex)
{
}
static void dump_it_all(FILE gmx_unused *fp, const char gmx_unused *title,
- int gmx_unused natoms, rvec gmx_unused x[], rvec gmx_unused xp[],
- rvec gmx_unused v[], rvec gmx_unused f[])
+ int gmx_unused natoms,
+ const gmx_unused PaddedRVecVector *x,
+ const gmx_unused PaddedRVecVector *xp,
+ const gmx_unused PaddedRVecVector *v,
+ const gmx_unused PaddedRVecVector *f)
{
#ifdef DEBUG
if (fp)
{
fprintf(fp, "%s\n", title);
- pr_rvecs(fp, 0, "x", x, natoms);
- pr_rvecs(fp, 0, "xp", xp, natoms);
- pr_rvecs(fp, 0, "v", v, natoms);
- pr_rvecs(fp, 0, "f", f, natoms);
+ pr_rvecs(fp, 0, "x", as_rvec_array(x->data()), natoms);
+ pr_rvecs(fp, 0, "xp", as_rvec_array(xp->data()), natoms);
+ pr_rvecs(fp, 0, "v", as_rvec_array(v->data()), natoms);
+ if (f != NULL)
+ {
+ pr_rvecs(fp, 0, "f", as_rvec_array(f->data()), natoms);
+ }
}
#endif
}
{
if (ekind->cosacc.cos_accel == 0)
{
- calc_ke_part_normal(state->v, opts, md, ekind, nrnb, bEkinAveVel);
+ calc_ke_part_normal(as_rvec_array(state->v.data()), opts, md, ekind, nrnb, bEkinAveVel);
}
else
{
- calc_ke_part_visc(state->box, state->x, state->v, opts, md, ekind, nrnb, bEkinAveVel);
+ calc_ke_part_visc(state->box, as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), opts, md, ekind, nrnb, bEkinAveVel);
}
}
snew(ekinstate->ekinh, ekinstate->ekin_n);
snew(ekinstate->ekinf, ekinstate->ekin_n);
snew(ekinstate->ekinh_old, ekinstate->ekin_n);
- snew(ekinstate->ekinscalef_nhc, ekinstate->ekin_n);
- snew(ekinstate->ekinscaleh_nhc, ekinstate->ekin_n);
- snew(ekinstate->vscale_nhc, ekinstate->ekin_n);
+ ekinstate->ekinscalef_nhc.resize(ekinstate->ekin_n);
+ ekinstate->ekinscaleh_nhc.resize(ekinstate->ekin_n);
+ ekinstate->vscale_nhc.resize(ekinstate->ekin_n);
ekinstate->dekindl = 0;
ekinstate->mvcos = 0;
}
t_mdatoms *md)
{
- gmx_bool bTCouple = FALSE;
- real dttc;
- int i, offset;
+ bool doTemperatureCoupling = false;
/* if using vv with trotter decomposition methods, we do this elsewhere in the code */
- if (inputrec->etc != etcNO &&
- !(inputrecNvtTrotter(inputrec) || inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec)))
+ if (!(EI_VV(inputrec->eI) &&
+ (inputrecNvtTrotter(inputrec) || inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec))))
{
- /* We should only couple after a step where energies were determined (for leapfrog versions)
- or the step energies are determined, for velocity verlet versions */
-
- if (EI_VV(inputrec->eI))
- {
- offset = 0;
- }
- else
- {
- offset = 1;
- }
- bTCouple = (inputrec->nsttcouple == 1 ||
- do_per_step(step+inputrec->nsttcouple-offset,
- inputrec->nsttcouple));
+ doTemperatureCoupling = isTemperatureCouplingStep(step, inputrec);
}
- if (bTCouple)
+ if (doTemperatureCoupling)
{
- dttc = inputrec->nsttcouple*inputrec->delta_t;
+ real dttc = inputrec->nsttcouple*inputrec->delta_t;
switch (inputrec->etc)
{
case etcNO:
break;
case etcBERENDSEN:
- berendsen_tcoupl(inputrec, ekind, dttc);
+ berendsen_tcoupl(inputrec, ekind, dttc, state->therm_integral);
break;
case etcNOSEHOOVER:
nosehoover_tcoupl(&(inputrec->opts), ekind, dttc,
- state->nosehoover_xi, state->nosehoover_vxi, MassQ);
+ state->nosehoover_xi.data(), state->nosehoover_vxi.data(), MassQ);
break;
case etcVRESCALE:
vrescale_tcoupl(inputrec, step, ekind, dttc,
- state->therm_integral);
+ state->therm_integral.data());
break;
}
/* rescale in place here */
if (EI_VV(inputrec->eI))
{
- rescale_velocities(ekind, md, 0, md->homenr, state->v);
+ rescale_velocities(ekind, md, 0, md->homenr, as_rvec_array(state->v.data()));
}
}
else
{
/* Set the T scaling lambda to 1 to have no scaling */
- for (i = 0; (i < inputrec->opts.ngtc); i++)
+ for (int i = 0; (i < inputrec->opts.ngtc); i++)
{
ekind->tcstat[i].lambda = 1.0;
}
}
}
-void update_pcouple(FILE *fplog,
- gmx_int64_t step,
- t_inputrec *inputrec,
- t_state *state,
- matrix pcoupl_mu,
- matrix M,
- gmx_bool bInitStep)
+void update_pcouple_before_coordinates(FILE *fplog,
+ gmx_int64_t step,
+ const t_inputrec *inputrec,
+ t_state *state,
+ matrix parrinellorahmanMu,
+ matrix M,
+ gmx_bool bInitStep)
{
- gmx_bool bPCouple = FALSE;
- real dtpc = 0;
- int i;
-
- /* if using Trotter pressure, we do this in coupling.c, so we leave it false. */
- if (inputrec->epc != epcNO && (!(inputrecNptTrotter(inputrec) || inputrecNphTrotter(inputrec))))
- {
- /* We should only couple after a step where energies were determined */
- bPCouple = (inputrec->nstpcouple == 1 ||
- do_per_step(step+inputrec->nstpcouple-1,
- inputrec->nstpcouple));
- }
-
- clear_mat(pcoupl_mu);
- for (i = 0; i < DIM; i++)
- {
- pcoupl_mu[i][i] = 1.0;
- }
-
- clear_mat(M);
-
- if (bPCouple)
+ /* Berendsen P-coupling is completely handled after the coordinate update.
+ * Trotter P-coupling is handled by separate calls to trotter_update().
+ */
+ if (inputrec->epc == epcPARRINELLORAHMAN &&
+ isPressureCouplingStep(step, inputrec))
{
- dtpc = inputrec->nstpcouple*inputrec->delta_t;
+ real dtpc = inputrec->nstpcouple*inputrec->delta_t;
- switch (inputrec->epc)
- {
- /* We can always pcoupl, even if we did not sum the energies
- * the previous step, since state->pres_prev is only updated
- * when the energies have been summed.
- */
- case (epcNO):
- break;
- case (epcBERENDSEN):
- if (!bInitStep)
- {
- berendsen_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev, state->box,
- pcoupl_mu);
- }
- break;
- case (epcPARRINELLORAHMAN):
- parrinellorahman_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev,
- state->box, state->box_rel, state->boxv,
- M, pcoupl_mu, bInitStep);
- break;
- default:
- break;
- }
+ parrinellorahman_pcoupl(fplog, step, inputrec, dtpc, state->pres_prev,
+ state->box, state->box_rel, state->boxv,
+ M, parrinellorahmanMu, bInitStep);
}
}
t_state *state,
gmx_bool bMolPBC,
t_graph *graph,
- rvec force[], /* forces on home particles */
+ PaddedRVecVector *force, /* forces on home particles */
t_idef *idef,
tensor vir_part,
t_commrec *cr,
gmx_bool bCalcVir)
{
gmx_bool bLastStep, bLog = FALSE, bEner = FALSE, bDoConstr = FALSE;
- double dt;
- int start, homenr, nrend, i;
tensor vir_con;
int nth, th;
/* for now, SD update is here -- though it really seems like it
should be reformulated as a velocity verlet method, since it has two parts */
- start = 0;
- homenr = md->homenr;
- nrend = start+homenr;
+ int start = 0;
+ int homenr = md->homenr;
+ int nrend = start+homenr;
- dt = inputrec->delta_t;
+ /* Cast delta_t from double to real to make the integrators faster.
+ * The only reason for having delta_t double is to get accurate values
+ * for t=delta_t*step when step is larger than float precision.
+ * For integration dt the accuracy of real suffices, since with
+ * integral += dt*integrand the increment is nearly always (much) smaller
+ * than the integral (and the integrand has real precision).
+ */
+ real dt = inputrec->delta_t;
/*
* Steps (7C, 8C)
wallcycle_start(wcycle, ewcCONSTR);
if (EI_VV(inputrec->eI) && bFirstHalf)
{
- constrain(NULL, bLog, bEner, constr, idef,
+ constrain(nullptr, bLog, bEner, constr, idef,
inputrec, cr, step, 1, 1.0, md,
- state->x, state->v, state->v,
+ as_rvec_array(state->x.data()), as_rvec_array(state->v.data()), as_rvec_array(state->v.data()),
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
- NULL, bCalcVir ? &vir_con : NULL, nrnb, econqVeloc);
+ nullptr, bCalcVir ? &vir_con : nullptr, nrnb, econqVeloc);
}
else
{
- constrain(NULL, bLog, bEner, constr, idef,
+ constrain(nullptr, bLog, bEner, constr, idef,
inputrec, cr, step, 1, 1.0, md,
- state->x, upd->xp, NULL,
+ as_rvec_array(state->x.data()), as_rvec_array(upd->xp.data()), nullptr,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
- state->v, bCalcVir ? &vir_con : NULL, nrnb, econqCoord);
+ as_rvec_array(state->v.data()), bCalcVir ? &vir_con : nullptr, nrnb, econqCoord);
}
wallcycle_stop(wcycle, ewcCONSTR);
where();
dump_it_all(fplog, "After Shake",
- state->natoms, state->x, upd->xp, state->v, force);
+ state->natoms, &state->x, &upd->xp, &state->v, force);
if (bCalcVir)
{
inputrec->opts.acc, inputrec->opts.nFreeze,
md->invmass, md->ptype,
md->cFREEZE, md->cACC, md->cTC,
- state->x, upd->xp, state->v, force,
+ as_rvec_array(state->x.data()), as_rvec_array(upd->xp.data()), as_rvec_array(state->v.data()), as_rvec_array(force->data()),
bDoConstr, FALSE,
step, inputrec->ld_seed,
- DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ DOMAINDECOMP(cr) ? cr->dd->gatindex : nullptr);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
/* Constrain the coordinates upd->xp for half a time step */
wallcycle_start(wcycle, ewcCONSTR);
- constrain(NULL, bLog, bEner, constr, idef,
+ constrain(nullptr, bLog, bEner, constr, idef,
inputrec, cr, step, 1, 0.5, md,
- state->x, upd->xp, NULL,
+ as_rvec_array(state->x.data()), as_rvec_array(upd->xp.data()), nullptr,
bMolPBC, state->box,
state->lambda[efptBONDED], dvdlambda,
- state->v, NULL, nrnb, econqCoord);
+ as_rvec_array(state->v.data()), nullptr, nrnb, econqCoord);
wallcycle_stop(wcycle, ewcCONSTR);
}
*/
wallcycle_start_nocount(wcycle, ewcUPDATE);
- if (md->cFREEZE != NULL && constr != NULL)
+ if (md->cFREEZE != nullptr && constr != nullptr)
{
/* If we have atoms that are frozen along some, but not all
* dimensions, the constraints will have moved them also along
if (graph && (graph->nnodes > 0))
{
- unshift_x(graph, state->box, state->x, upd->xp);
+ unshift_x(graph, state->box, as_rvec_array(state->x.data()), as_rvec_array(upd->xp.data()));
if (TRICLINIC(state->box))
{
inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
}
else
{
+ /* The copy is performance sensitive, so use a bare pointer */
+ rvec *xp = as_rvec_array(upd->xp.data());
#ifndef __clang_analyzer__
// cppcheck-suppress unreadVariable
nth = gmx_omp_nthreads_get(emntUpdate);
#endif
#pragma omp parallel for num_threads(nth) schedule(static)
- for (i = start; i < nrend; i++)
+ for (int i = start; i < nrend; i++)
{
// Trivial statement, does not throw
- copy_rvec(upd->xp[i], state->x[i]);
+ copy_rvec(xp[i], state->x[i]);
}
}
wallcycle_stop(wcycle, ewcUPDATE);
dump_it_all(fplog, "After unshift",
- state->natoms, state->x, upd->xp, state->v, force);
+ state->natoms, &state->x, &upd->xp, &state->v, force);
}
/* ############# END the update of velocities and positions ######### */
}
-void update_box(FILE *fplog,
- gmx_int64_t step,
- t_inputrec *inputrec, /* input record and box stuff */
- t_mdatoms *md,
- t_state *state,
- rvec force[], /* forces on home particles */
- matrix pcoupl_mu,
- t_nrnb *nrnb,
- gmx_update_t *upd)
+void update_pcouple_after_coordinates(FILE *fplog,
+ gmx_int64_t step,
+ const t_inputrec *inputrec,
+ const t_mdatoms *md,
+ const matrix pressure,
+ const matrix forceVirial,
+ const matrix constraintVirial,
+ const matrix parrinellorahmanMu,
+ t_state *state,
+ t_nrnb *nrnb,
+ gmx_update_t *upd)
{
- double dt;
- int start, homenr, i, n, m;
+ int start = 0;
+ int homenr = md->homenr;
- start = 0;
- homenr = md->homenr;
-
- dt = inputrec->delta_t;
+ /* Cast to real for faster code, no loss in precision (see comment above) */
+ real dt = inputrec->delta_t;
where();
case (epcNO):
break;
case (epcBERENDSEN):
- /* We should only scale after a step where the pressure (kinetic
- * energy and virial) was calculated. This happens after the
- * coordinate update, whereas the current routine is called before
- * that, so we scale when step % nstpcouple = 1 instead of 0.
- */
- if (inputrec->nstpcouple == 1 || (step % inputrec->nstpcouple == 1))
+ if (isPressureCouplingStep(step, inputrec))
{
- berendsen_pscale(inputrec, pcoupl_mu, state->box, state->box_rel,
- start, homenr, state->x, md->cFREEZE, nrnb);
+ real dtpc = inputrec->nstpcouple*dt;
+ matrix mu;
+ berendsen_pcoupl(fplog, step, inputrec, dtpc,
+ pressure, state->box,
+ forceVirial, constraintVirial,
+ mu, &state->baros_integral);
+ berendsen_pscale(inputrec, mu, state->box, state->box_rel,
+ start, homenr, as_rvec_array(state->x.data()),
+ md->cFREEZE, nrnb);
}
break;
case (epcPARRINELLORAHMAN):
- /* The box velocities were updated in do_pr_pcoupl in the update
- * iteration, but we dont change the box vectors until we get here
- * since we need to be able to shift/unshift above.
- */
- for (i = 0; i < DIM; i++)
+ if (isPressureCouplingStep(step, inputrec))
{
- for (m = 0; m <= i; m++)
+ /* The box velocities were updated in do_pr_pcoupl,
+ * but we dont change the box vectors until we get here
+ * since we need to be able to shift/unshift above.
+ */
+ real dtpc = inputrec->nstpcouple*dt;
+ for (int i = 0; i < DIM; i++)
{
- state->box[i][m] += dt*state->boxv[i][m];
+ for (int m = 0; m <= i; m++)
+ {
+ state->box[i][m] += dtpc*state->boxv[i][m];
+ }
}
- }
- preserve_box_shape(inputrec, state->box_rel, state->box);
+ preserve_box_shape(inputrec, state->box_rel, state->box);
- /* Scale the coordinates */
- for (n = start; (n < start+homenr); n++)
- {
- tmvmul_ur0(pcoupl_mu, state->x[n], state->x[n]);
+ /* Scale the coordinates */
+ for (int n = start; n < start + homenr; n++)
+ {
+ tmvmul_ur0(parrinellorahmanMu, state->x[n], state->x[n]);
+ }
}
break;
case (epcMTTK):
ln V_new = ln V_old + 3*dt*veta => V_new = V_old*exp(3*dt*veta) =>
Side length scales as exp(veta*dt) */
- msmul(state->box, exp(state->veta*dt), state->box);
+ msmul(state->box, std::exp(state->veta*dt), state->box);
/* Relate veta to boxv. veta = d(eta)/dT = (1/DIM)*1/V dV/dT.
o If we assume isotropic scaling, and box length scaling
if (inputrecDeform(inputrec))
{
- deform(upd, start, homenr, state->x, state->box, inputrec, step);
+ deform(upd, start, homenr, as_rvec_array(state->x.data()), state->box, inputrec, step);
}
where();
dump_it_all(fplog, "After update",
- state->natoms, state->x, upd->xp, state->v, force);
+ state->natoms, &state->x, &upd->xp, &state->v, nullptr);
}
void update_coords(FILE *fplog,
t_inputrec *inputrec, /* input record and box stuff */
t_mdatoms *md,
t_state *state,
- rvec *f, /* forces on home particles */
+ PaddedRVecVector *f, /* forces on home particles */
t_fcdata *fcd,
gmx_ekindata_t *ekind,
matrix M,
t_commrec *cr, /* these shouldn't be here -- need to think about it */
gmx_constr_t constr)
{
- gmx_bool bNH, bPR, bDoConstr = FALSE;
- double dt, alpha;
- int start, homenr, nrend;
- int nth, th;
-
- bDoConstr = (NULL != constr);
+ gmx_bool bDoConstr = (nullptr != constr);
/* Running the velocity half does nothing except for velocity verlet */
if ((UpdatePart == etrtVELOCITY1 || UpdatePart == etrtVELOCITY2) &&
gmx_incons("update_coords called for velocity without VV integrator");
}
- start = 0;
- homenr = md->homenr;
- nrend = start+homenr;
+ int start = 0;
+ int homenr = md->homenr;
+ int nrend = start+homenr;
- dt = inputrec->delta_t;
+ /* Cast to real for faster code, no loss in precision (see comment above) */
+ real dt = inputrec->delta_t;
/* We need to update the NMR restraint history when time averaging is used */
if (state->flags & (1<<estDISRE_RM3TAV))
update_orires_history(fcd, &state->hist);
}
-
- bNH = inputrec->etc == etcNOSEHOOVER;
- bPR = ((inputrec->epc == epcPARRINELLORAHMAN) || (inputrec->epc == epcMTTK));
-
/* ############# START The update of velocities and positions ######### */
where();
dump_it_all(fplog, "Before update",
- state->natoms, state->x, upd->xp, state->v, f);
+ state->natoms, &state->x, &upd->xp, &state->v, f);
- nth = gmx_omp_nthreads_get(emntUpdate);
+ int nth = gmx_omp_nthreads_get(emntUpdate);
-#pragma omp parallel for num_threads(nth) schedule(static) private(alpha)
- for (th = 0; th < nth; th++)
+#pragma omp parallel for num_threads(nth) schedule(static)
+ for (int th = 0; th < nth; th++)
{
try
{
start_th = start + ((nrend-start)* th )/nth;
end_th = start + ((nrend-start)*(th+1))/nth;
+ const rvec *x_rvec = as_rvec_array(state->x.data());
+ rvec *xp_rvec = as_rvec_array(upd->xp.data());
+ rvec *v_rvec = as_rvec_array(state->v.data());
+ const rvec *f_rvec = as_rvec_array(f->data());
+
switch (inputrec->eI)
{
case (eiMD):
- if (ekind->cosacc.cos_accel == 0)
- {
- do_update_md(start_th, end_th,
- dt, inputrec->nstpcouple,
- ekind->tcstat, state->nosehoover_vxi,
- ekind->bNEMD, ekind->grpstat, inputrec->opts.acc,
- inputrec->opts.nFreeze,
- md->invmass, md->ptype,
- md->cFREEZE, md->cACC, md->cTC,
- state->x, upd->xp, state->v, f, M,
- bNH, bPR);
- }
- else
- {
- do_update_visc(start_th, end_th,
- dt, inputrec->nstpcouple,
- ekind->tcstat, state->nosehoover_vxi,
- md->invmass, md->ptype,
- md->cTC, state->x, upd->xp, state->v, f, M,
- state->box,
- ekind->cosacc.cos_accel,
- ekind->cosacc.vcos,
- bNH, bPR);
- }
+ do_update_md(start_th, end_th, step, dt,
+ inputrec, md, ekind, state->box,
+ x_rvec, xp_rvec, v_rvec, f_rvec,
+ state->nosehoover_vxi.data(), M);
break;
case (eiSD1):
/* With constraints, the SD1 update is done in 2 parts */
inputrec->opts.acc, inputrec->opts.nFreeze,
md->invmass, md->ptype,
md->cFREEZE, md->cACC, md->cTC,
- state->x, upd->xp, state->v, f,
+ x_rvec, xp_rvec, v_rvec, f_rvec,
bDoConstr, TRUE,
- step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : nullptr);
break;
case (eiBD):
do_update_bd(start_th, end_th, dt,
inputrec->opts.nFreeze, md->invmass, md->ptype,
md->cFREEZE, md->cTC,
- state->x, upd->xp, state->v, f,
+ x_rvec, xp_rvec, v_rvec, f_rvec,
inputrec->bd_fric,
upd->sd->bd_rf,
- step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
+ step, inputrec->ld_seed, DOMAINDECOMP(cr) ? cr->dd->gatindex : nullptr);
break;
case (eiVV):
case (eiVVAK):
- alpha = 1.0 + DIM/((double)inputrec->opts.nrdf[0]); /* assuming barostat coupled to group 0. */
+ {
+ gmx_bool bExtended = (inputrec->etc == etcNOSEHOOVER ||
+ inputrec->epc == epcPARRINELLORAHMAN ||
+ inputrec->epc == epcMTTK);
+
+ /* assuming barostat coupled to group 0 */
+ real alpha = 1.0 + DIM/static_cast<real>(inputrec->opts.nrdf[0]);
switch (UpdatePart)
{
case etrtVELOCITY1:
inputrec->opts.acc, inputrec->opts.nFreeze,
md->invmass, md->ptype,
md->cFREEZE, md->cACC,
- state->v, f,
- (bNH || bPR), state->veta, alpha);
+ v_rvec, f_rvec,
+ bExtended, state->veta, alpha);
break;
case etrtPOSITION:
do_update_vv_pos(start_th, end_th, dt,
inputrec->opts.nFreeze,
md->ptype, md->cFREEZE,
- state->x, upd->xp, state->v,
- (bNH || bPR), state->veta);
+ x_rvec, xp_rvec, v_rvec,
+ bExtended, state->veta);
break;
}
break;
+ }
default:
gmx_fatal(FARGS, "Don't know how to update coordinates");
break;
real rate = (ir->delta_t)/ir->opts.tau_t[0];
- if (ir->etc == etcANDERSEN && constr != NULL)
+ if (ir->etc == etcANDERSEN && constr != nullptr)
{
/* Currently, Andersen thermostat does not support constrained
systems. Functionality exists in the andersen_tcoupl
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDLIB_UPDATE_H
#define GMX_MDLIB_UPDATE_H
+#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-struct ekinstate_t;
+class ekinstate_t;
struct gmx_constr;
struct gmx_ekindata_t;
struct gmx_enerdata_t;
struct t_inputrec;
struct t_mdatoms;
struct t_nrnb;
-struct t_state;
+class t_state;
/* Abstract type for update */
struct gmx_update_t;
/* Update the size of per-atom arrays (e.g. after DD re-partitioning,
which might increase the number of home atoms). */
-void update_realloc(gmx_update_t *upd, int state_nalloc);
+void update_realloc(gmx_update_t *upd, int natoms);
/* Store the box at step step
* as a reference state for simulations with box deformation.
t_mdatoms *md
);
-void update_pcouple(FILE *fplog,
- gmx_int64_t step,
- t_inputrec *inputrec,
- t_state *state,
- matrix pcoupl_mu,
- matrix M,
- gmx_bool bInitStep);
+/* Update Parrinello-Rahman, to be called before the coordinate update */
+void update_pcouple_before_coordinates(FILE *fplog,
+ gmx_int64_t step,
+ const t_inputrec *inputrec,
+ t_state *state,
+ matrix parrinellorahmanMu,
+ matrix M,
+ gmx_bool bInitStep);
+
+/* Update the box, to be called after the coordinate update.
+ * For Berendsen P-coupling, also calculates the scaling factor
+ * and scales the coordinates.
+ * When the deform option is used, scales coordinates and box here.
+ */
+void update_pcouple_after_coordinates(FILE *fplog,
+ gmx_int64_t step,
+ const t_inputrec *inputrec,
+ const t_mdatoms *md,
+ const matrix pressure,
+ const matrix forceVirial,
+ const matrix constraintVirial,
+ const matrix parrinellorahmanMu,
+ t_state *state,
+ t_nrnb *nrnb,
+ gmx_update_t *upd);
void update_coords(FILE *fplog,
gmx_int64_t step,
t_inputrec *inputrec, /* input record and box stuff */
t_mdatoms *md,
t_state *state,
- rvec *f, /* forces on home particles */
+ PaddedRVecVector *f, /* forces on home particles */
t_fcdata *fcd,
gmx_ekindata_t *ekind,
matrix M,
t_state *state,
gmx_bool bMolPBC,
t_graph *graph,
- rvec force[], /* forces on home particles */
+ PaddedRVecVector *force, /* forces on home particles */
t_idef *idef,
tensor vir_part,
t_commrec *cr,
/* Return TRUE if OK, FALSE in case of Shake Error */
-void update_box(FILE *fplog,
- gmx_int64_t step,
- t_inputrec *inputrec, /* input record and box stuff */
- t_mdatoms *md,
- t_state *state,
- rvec force[], /* forces on home particles */
- matrix pcoupl_mu,
- t_nrnb *nrnb,
- gmx_update_t *upd);
-/* Return TRUE if OK, FALSE in case of Shake Error */
-
void calc_ke_part(t_state *state, t_grpopts *opts, t_mdatoms *md,
gmx_ekindata_t *ekind, t_nrnb *nrnb, gmx_bool bEkinAveVel);
/*
restore_ekinstate_from_state(t_commrec *cr,
gmx_ekindata_t *ekind, const ekinstate_t *ekinstate);
-void berendsen_tcoupl(t_inputrec *ir, gmx_ekindata_t *ekind, real dt);
+void berendsen_tcoupl(const t_inputrec *ir, const gmx_ekindata_t *ekind, real dt,
+ std::vector<double> &therm_integral);
void andersen_tcoupl(t_inputrec *ir, gmx_int64_t step,
const t_commrec *cr, const t_mdatoms *md, t_state *state, real rate, const gmx_bool *randomize, const real *boltzfac);
void nosehoover_tcoupl(t_grpopts *opts, gmx_ekindata_t *ekind, real dt,
double xi[], double vxi[], t_extmass *MassQ);
-t_state *init_bufstate(const t_state *template_state);
-
-void destroy_bufstate(t_state *state);
-
void trotter_update(t_inputrec *ir, gmx_int64_t step, gmx_ekindata_t *ekind,
gmx_enerdata_t *enerd, t_state *state, tensor vir, t_mdatoms *md,
t_extmass *MassQ, int **trotter_seqlist, int trotter_seqno);
int **init_npt_vars(t_inputrec *ir, t_state *state, t_extmass *Mass, gmx_bool bTrotter);
-real NPT_energy(t_inputrec *ir, t_state *state, t_extmass *MassQ);
+real NPT_energy(const t_inputrec *ir, const t_state *state, const t_extmass *MassQ);
/* computes all the pressure/tempertature control energy terms to get a conserved energy */
void NBaroT_trotter(t_grpopts *opts, real dt,
double therm_integral[]);
/* Compute temperature scaling. For V-rescale it is done in update. */
-real vrescale_energy(t_grpopts *opts, double therm_integral[]);
-/* Returns the V-rescale contribution to the conserved energy */
-
void rescale_velocities(gmx_ekindata_t *ekind, t_mdatoms *mdatoms,
int start, int end, rvec v[]);
/* Rescale the velocities with the scaling factor in ekind */
*/
void parrinellorahman_pcoupl(FILE *fplog, gmx_int64_t step,
- t_inputrec *ir, real dt, tensor pres,
+ const t_inputrec *ir, real dt, const tensor pres,
tensor box, tensor box_rel, tensor boxv,
tensor M, matrix mu,
gmx_bool bFirstStep);
void berendsen_pcoupl(FILE *fplog, gmx_int64_t step,
- t_inputrec *ir, real dt, tensor pres, matrix box,
- matrix mu);
-
+ const t_inputrec *ir, real dt,
+ const tensor pres, const matrix box,
+ const matrix force_vir, const matrix constraint_vir,
+ matrix mu, double *baros_integral);
-void berendsen_pscale(t_inputrec *ir, matrix mu,
+void berendsen_pscale(const t_inputrec *ir, const matrix mu,
matrix box, matrix box_rel,
int start, int nr_atoms,
- rvec x[], unsigned short cFREEZE[],
+ rvec x[], const unsigned short cFREEZE[],
t_nrnb *nrnb);
void correct_ekin(FILE *log, int start, int end, rvec v[],
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
{
ilist[i].nr = 0;
ilist[i].nalloc = 0;
- ilist[i].iatoms = NULL;
+ ilist[i].iatoms = nullptr;
}
}
/* Returns the sum of the vsite ilist sizes over all vsite types */
-static int vsiteIlistNrCount(const t_ilist *ilist)
+gmx_unused static int vsiteIlistNrCount(const t_ilist *ilist)
{
int nr = 0;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
const t_pbc *pbc_null2;
int *vsite_pbc;
- if (v != NULL)
+ if (v != nullptr)
{
inv_dt = 1.0/dt;
}
inv_dt = 1.0;
}
- bPBCAll = (pbc_null != NULL && !vsite->bHaveChargeGroups);
+ bPBCAll = (pbc_null != nullptr && !vsite->bHaveChargeGroups);
- pbc_null2 = NULL;
- vsite_pbc = NULL;
+ pbc_null2 = nullptr;
+ vsite_pbc = nullptr;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
if (ilist[ftype].nr == 0)
{
pbc_null2 = pbc_null;
}
- else if (pbc_null != NULL)
+ else if (pbc_null != nullptr)
{
vsite_pbc = vsite->vsite_pbc_loc[ftype - c_ftypeVsiteStart];
}
pbc_atom = avsite;
copy_rvec(x[avsite], xpbc);
}
- else if (vsite_pbc != NULL)
+ else if (vsite_pbc != nullptr)
{
pbc_atom = vsite_pbc[i/(1 + nra)];
if (pbc_atom > -2)
}
else
{
- pbc_null2 = NULL;
+ pbc_null2 = nullptr;
}
}
else
rvec_add(xpbc, dx, x[avsite]);
}
}
- if (v != NULL)
+ if (v != nullptr)
{
/* Calculate velocity of vsite... */
rvec vv;
}
else
{
- pbc_null = NULL;
+ pbc_null = nullptr;
}
if (bDomDec)
const gmx_moltype_t *molt = &mtop->moltype[molb->type];
for (int mol = 0; mol < molb->nmol; mol++)
{
- construct_vsites(vsite, x+as, 0.0, NULL,
+ construct_vsites(vsite, x+as, 0.0, nullptr,
mtop->ffparams.iparams, molt->ilist,
- epbcNONE, TRUE, NULL, NULL);
+ epbcNONE, TRUE, nullptr, nullptr);
as += molt->atoms.nr;
}
}
const t_pbc *pbc_null2;
const int *vsite_pbc;
- bPBCAll = (pbc_null != NULL && !vsite->bHaveChargeGroups);
+ bPBCAll = (pbc_null != nullptr && !vsite->bHaveChargeGroups);
/* this loop goes backwards to be able to build *
* higher type vsites from lower types */
- pbc_null2 = NULL;
- vsite_pbc = NULL;
+ pbc_null2 = nullptr;
+ vsite_pbc = nullptr;
for (int ftype = c_ftypeVsiteEnd - 1; ftype >= c_ftypeVsiteStart; ftype--)
{
if (ilist[ftype].nr == 0)
{
pbc_null2 = pbc_null;
}
- else if (pbc_null != NULL)
+ else if (pbc_null != nullptr)
{
vsite_pbc = vsite->vsite_pbc_loc[ftype - c_ftypeVsiteStart];
}
for (int i = 0; i < nr; )
{
- if (vsite_pbc != NULL)
+ if (vsite_pbc != nullptr)
{
if (vsite_pbc[i/(1 + nra)] > -2)
{
}
else
{
- pbc_null2 = NULL;
+ pbc_null2 = nullptr;
}
}
/* This is wasting some CPU time as we now do this multiple times
* per MD step.
*/
- pbc_null = set_pbc_dd(&pbc, ePBC, cr->dd ? cr->dd->nc : NULL, FALSE, box);
+ pbc_null = set_pbc_dd(&pbc, ePBC, cr->dd ? cr->dd->nc : nullptr, FALSE, box);
}
else
{
- pbc_null = NULL;
+ pbc_null = nullptr;
}
if (DOMAINDECOMP(cr))
VsiteThread *tData = vsite->tData[thread];
rvec *fshift_t;
- if (thread == 0 || fshift == NULL)
+ if (thread == 0 || fshift == nullptr)
{
fshift_t = fshift;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
- if (fshift != NULL)
+ if (fshift != nullptr)
{
for (int th = 1; th < vsite->nthreads; th++)
{
if (nvsite == 0)
{
- return NULL;
+ return nullptr;
}
snew(vsite, 1);
int *a2cg = atom2cg(&molt->cgs);
vsite->vsite_pbc_molt[mt] = get_vsite_pbc(mtop->ffparams.iparams,
molt->ilist,
- molt->atoms.atom, NULL,
+ molt->atoms.atom, nullptr,
&molt->cgs, a2cg);
sfree(a2cg);
}
}
}
- vsite->taskIndex = NULL;
+ vsite->taskIndex = nullptr;
vsite->taskIndexNalloc = 0;
return vsite;
/* Make an atom to charge group index */
int *a2cg = atom2cg(&top->cgs);
vsite->vsite_pbc_loc = get_vsite_pbc(top->idef.iparams,
- top->idef.il, NULL, md,
+ top->idef.il, nullptr, md,
&top->cgs, a2cg);
sfree(a2cg);
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015, by the GROMACS development team, led by
+# Copyright (c) 2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-file(GLOB MDRUNUTILITY_SOURCES *.cpp)
-set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${MDRUNUTILITY_SOURCES} PARENT_SCOPE)
+gmx_add_libgromacs_sources(
+ handlerestart.cpp
+ mdmodules.cpp
+ threadaffinity.cpp
+ )
if (BUILD_TESTING)
-# add_subdirectory(tests)
+ add_subdirectory(tests)
endif()
int nfile, const t_filenm fnm[],
const char *part_suffix,
gmx_bool *bAddPart,
- gmx_bool *bDoAppendFiles)
+ bool *bDoAppendFiles)
{
t_fileio *fp;
int nfiles;
*/
strcpy(suf_up, part_suffix);
upstring(suf_up);
- *bAddPart = (strstr(fn, part_suffix) != NULL ||
- strstr(fn, suf_up) != NULL);
+ *bAddPart = (strstr(fn, part_suffix) != nullptr ||
+ strstr(fn, suf_up) != nullptr);
}
sfree(outputfiles);
gmx_bool bTryToAppendFiles,
const int NFILE,
t_filenm fnm[],
- gmx_bool *bDoAppendFiles,
- gmx_bool *bStartFromCpt)
+ bool *bDoAppendFiles,
+ bool *bStartFromCpt)
{
gmx_bool bAddPart;
int sim_part, sim_part_fn;
}
else
{
- fpmulti = NULL;
+ fpmulti = nullptr;
}
check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_bool bTryToAppendFiles,
const int NFILE,
t_filenm fnm[],
- gmx_bool *bDoAppendFiles,
- gmx_bool *bStartFromCpt);
+ bool *bDoAppendFiles,
+ bool *bStartFromCpt);
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "mdmodules.h"
+
+#include <memory>
+
+#include "gromacs/applied-forces/electricfield.h"
+#include "gromacs/mdtypes/iforceprovider.h"
+#include "gromacs/mdtypes/imdmodule.h"
+#include "gromacs/mdtypes/imdoutputprovider.h"
+#include "gromacs/mdtypes/imdpoptionprovider.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/options/options.h"
+#include "gromacs/options/optionsection.h"
+#include "gromacs/options/treesupport.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/keyvaluetreetransform.h"
+#include "gromacs/utility/smalloc.h"
+
+namespace gmx
+{
+
+class MDModules::Impl : public IMDOutputProvider
+{
+ public:
+
+ Impl()
+ : field_(createElectricFieldModule())
+ {
+ }
+
+ void makeModuleOptions(Options *options)
+ {
+ // Create a section for applied-forces modules
+ auto appliedForcesOptions = options->addSection(OptionSection("applied-forces"));
+ field_->mdpOptionProvider()->initMdpOptions(&appliedForcesOptions);
+ // In future, other sections would also go here.
+ }
+
+ // From IMDOutputProvider
+ virtual void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
+ bool bAppendFiles, const gmx_output_env_t *oenv)
+ {
+ field_->outputProvider()->initOutput(fplog, nfile, fnm, bAppendFiles, oenv);
+ }
+ virtual void finishOutput()
+ {
+ field_->outputProvider()->finishOutput();
+ }
+
+ std::unique_ptr<IMDModule> field_;
+ std::unique_ptr<ForceProviders> forceProviders_;
+};
+
+MDModules::MDModules() : impl_(new Impl)
+{
+}
+
+MDModules::~MDModules()
+{
+}
+
+void MDModules::initMdpTransform(IKeyValueTreeTransformRules *rules)
+{
+ auto appliedForcesScope = rules->scopedTransform("/applied-forces");
+ impl_->field_->mdpOptionProvider()->initMdpTransform(appliedForcesScope.rules());
+}
+
+void MDModules::buildMdpOutput(KeyValueTreeObjectBuilder *builder)
+{
+ impl_->field_->mdpOptionProvider()->buildMdpOutput(builder);
+}
+
+void MDModules::assignOptionsToModules(const KeyValueTreeObject ¶ms,
+ IKeyValueTreeErrorHandler *errorHandler)
+{
+ Options moduleOptions;
+ impl_->makeModuleOptions(&moduleOptions);
+ // The actual output is in the data fields of the modules that
+ // were set up in the module options.
+ assignOptionsFromKeyValueTree(&moduleOptions, params, errorHandler);
+}
+
+void MDModules::adjustInputrecBasedOnModules(t_inputrec *ir)
+{
+ Options moduleOptions;
+ impl_->makeModuleOptions(&moduleOptions);
+
+ checkForUnknownOptionsInKeyValueTree(*ir->params, moduleOptions);
+
+ std::unique_ptr<KeyValueTreeObject> params(
+ new KeyValueTreeObject(
+ adjustKeyValueTreeFromOptions(*ir->params, moduleOptions)));
+ delete ir->params;
+ ir->params = params.release();
+}
+
+IMDOutputProvider *MDModules::outputProvider()
+{
+ return impl_.get();
+}
+
+ForceProviders *MDModules::initForceProviders()
+{
+ GMX_RELEASE_ASSERT(impl_->forceProviders_ == nullptr,
+ "Force providers initialized multiple times");
+ impl_->forceProviders_.reset(new ForceProviders);
+ impl_->field_->initForceProviders(impl_->forceProviders_.get());
+ return impl_->forceProviders_.get();
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::MDModules.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_mdrunutility
+ */
+#ifndef GMX_MDRUNUTILITY_MDMODULES_H
+#define GMX_MDRUNUTILITY_MDMODULES_H
+
+#include "gromacs/utility/classhelpers.h"
+
+struct ForceProviders;
+
+struct t_inputrec;
+
+namespace gmx
+{
+
+class KeyValueTreeObjectBuilder;
+class KeyValueTreeObject;
+class IKeyValueTreeErrorHandler;
+class IKeyValueTreeTransformRules;
+class IMDOutputProvider;
+class KeyValueTreeObject;
+
+/*! \libinternal \brief
+ * Manages the collection of all modules used for mdrun.
+ *
+ * This class acts as a central place for constructing modules for mdrun
+ * and wiring up dependencies between them. This class should be the only
+ * place that contains the full list of modules, although in the future, some
+ * code (e.g., in tools) may benefit from the ability to only create one or a
+ * few modules and use them.
+ *
+ * The general idea is that each module takes care of its own data rather than
+ * mdrun having to know about all the details of each type of force calculation.
+ * Initially this is applied for simple things like electric field calculations
+ * but later more complex forces will be supported too.
+ *
+ * Currently, where the set of modules needs to be accessed, either a pointer
+ * to MDModules is passed around, or an instance of IMDOutputProvider or
+ * ForceProviders returned from MDModules. These objects returned from
+ * MDModules call the corresponding methods in the relevant modules.
+ * In the future, some additional logic may need to be introduced at
+ * the call sites that can also influence the signature of the methods,
+ * similar to what ForceProviders already does for force computation.
+ *
+ * The assignOptionsToModules() and adjustInputrecBasedOnModules() methods of
+ * this class also take responsibility for wiring up the options (and their
+ * defaults) for each module.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdrunutility
+ */
+class MDModules
+{
+ public:
+ MDModules();
+ ~MDModules();
+
+ /*! \brief
+ * Initializes a transform from mdp values to sectioned options.
+ *
+ * \see IMdpOptionProvider::initMdpTransform()
+ *
+ * Initializes the combined transform from all modules.
+ */
+ void initMdpTransform(IKeyValueTreeTransformRules *rules);
+
+ /*! \brief Initializes a builder of flat mdp-style key-value pairs
+ * suitable for output.
+ *
+ * If used as input to initMdpTransform(), the key-value pairs
+ * resulting from this function would leave the module
+ * settings unchanged.
+ *
+ * Once the transition from mdp to key-value input is
+ * complete, this method will probably not exist.
+ */
+ void buildMdpOutput(KeyValueTreeObjectBuilder *builder);
+
+ /*! \brief
+ * Sets input parameters from `params` for each module.
+ *
+ * \param[in] params Contains keys and values from user
+ * input (and defaults) to configure modules that have
+ * registered options with those keys.
+ * \param[out] errorHandler Called to report errors.
+ */
+ void assignOptionsToModules(const KeyValueTreeObject ¶ms,
+ IKeyValueTreeErrorHandler *errorHandler);
+
+ /*! \brief
+ * Normalizes inputrec parameters to match current code version.
+ *
+ * This orders the parameters in `ir->param` to match the current code
+ * and adds any missing defaults. It also throws an error if the
+ * inputrec contains parameters that are not recognized by any module.
+ */
+ void adjustInputrecBasedOnModules(t_inputrec *ir);
+
+ /*! \brief
+ * Returns an interface for initializing and finalizing output for modules.
+ */
+ IMDOutputProvider *outputProvider();
+ /*! \brief
+ * Returns an object for computing forces from the modules.
+ */
+ ForceProviders *initForceProviders();
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2016,2017, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test_object_library(mdrunutility-test-shared
+ threadaffinitytest.cpp)
+
+gmx_add_unit_test(MdrunUtilityUnitTests mdrunutility-test
+ threadaffinity.cpp
+ $<TARGET_OBJECTS:mdrunutility-test-shared>)
+
+gmx_add_mpi_unit_test(MdrunUtilityMpiUnitTests mdrunutility-mpi-test 4
+ threadaffinity-mpi.cpp
+ $<TARGET_OBJECTS:mdrunutility-test-shared>)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include <array>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/basenetwork.h"
+
+#include "testutils/mpitest.h"
+
+#include "threadaffinitytest.h"
+
+namespace
+{
+
+using gmx::test::ThreadAffinityTestHelper;
+
+TEST(ThreadAffinityMultiRankTest, PinsWholeNode)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setLogicalProcessorCount(4);
+ helper.expectPinningMessage(false, 1);
+ helper.expectAffinitySet(gmx_node_rank());
+ helper.setAffinity(1);
+}
+
+TEST(ThreadAffinityMultiRankTest, PinsWithOffsetAndStride)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffON);
+ helper.setOffsetAndStride(1, 2);
+ helper.setLogicalProcessorCount(8);
+ helper.expectWarningMatchingRegex("Applying core pinning offset 1");
+ helper.expectPinningMessage(true, 2);
+ helper.expectAffinitySet(1 + 2*gmx_node_rank());
+ helper.setAffinity(1);
+}
+
+TEST(ThreadAffinityMultiRankTest, PinsTwoNodes)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setPhysicalNodeId(gmx_node_rank()/2);
+ helper.setLogicalProcessorCount(2);
+ helper.expectPinningMessage(false, 1);
+ helper.expectAffinitySet(gmx_node_rank()%2);
+ helper.setAffinity(1);
+}
+
+TEST(ThreadAffinityMultiRankTest, DoesNothingWhenDisabled)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffOFF);
+ helper.setLogicalProcessorCount(4);
+ helper.setAffinity(1);
+}
+
+TEST(ThreadAffinityMultiRankTest, HandlesTooManyThreadsWithAuto)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setLogicalProcessorCount(6);
+ helper.expectWarningMatchingRegex("Oversubscribing the CPU");
+ helper.expectGenericFailureMessage();
+ helper.setAffinity(2);
+}
+
+TEST(ThreadAffinityMultiRankTest, HandlesTooManyThreadsWithForce)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffON);
+ helper.setLogicalProcessorCount(6);
+ helper.expectWarningMatchingRegex("Oversubscribing the CPU");
+ helper.expectGenericFailureMessage();
+ helper.setAffinity(2);
+}
+
+class ThreadAffinityHeterogeneousNodesTest : public ::testing::Test
+{
+ public:
+ int currentNode() const { return gmx_node_rank() / 2; }
+ int indexInNode() const { return gmx_node_rank() % 2; }
+ bool isMaster() const { return gmx_node_rank() == 0; }
+
+ void setupNodes(ThreadAffinityTestHelper *helper, std::array<int, 2> cores)
+ {
+ const int node = currentNode();
+ helper->setPhysicalNodeId(node);
+ helper->setLogicalProcessorCount(cores[node]);
+ }
+ void expectNodeAffinitySet(ThreadAffinityTestHelper *helper, int node, int core)
+ {
+ if (currentNode() == node)
+ {
+ helper->expectAffinitySet(core);
+ }
+ }
+};
+
+TEST_F(ThreadAffinityHeterogeneousNodesTest, PinsOnMasterOnly)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffON);
+ setupNodes(&helper, {{2, 1}});
+ helper.expectWarningMatchingRegexIf("Oversubscribing the CPU", isMaster() || currentNode() == 1);
+ helper.expectGenericFailureMessageIf(isMaster() || currentNode() == 1);
+ if (currentNode() == 0)
+ {
+ helper.expectPinningMessage(false, 1);
+ }
+ expectNodeAffinitySet(&helper, 0, indexInNode());
+ helper.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityHeterogeneousNodesTest, PinsOnNonMasterOnly)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffON);
+ setupNodes(&helper, {{1, 2}});
+ helper.expectWarningMatchingRegexIf("Oversubscribing the CPU", currentNode() == 0);
+ helper.expectGenericFailureMessageIf(currentNode() == 0);
+ if (currentNode() == 1)
+ {
+ helper.expectPinningMessage(false, 1);
+ }
+ expectNodeAffinitySet(&helper, 1, indexInNode());
+ helper.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityHeterogeneousNodesTest, HandlesUnknownHardwareOnNonMaster)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffON);
+ setupNodes(&helper, {{2, 0}});
+ helper.expectWarningMatchingRegexIf("No information on available cores", isMaster() || currentNode() == 1);
+ helper.expectGenericFailureMessageIf(isMaster() || currentNode() == 1);
+ if (currentNode() == 0)
+ {
+ helper.expectPinningMessage(false, 1);
+ }
+ expectNodeAffinitySet(&helper, 0, indexInNode());
+ helper.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityHeterogeneousNodesTest, PinsAutomaticallyOnMasterOnly)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ setupNodes(&helper, {{2, 1}});
+ helper.expectWarningMatchingRegexIf("Oversubscribing the CPU", isMaster() || currentNode() == 1);
+ helper.expectGenericFailureMessageIf(isMaster() || currentNode() == 1);
+ if (currentNode() == 0)
+ {
+ helper.expectPinningMessage(false, 1);
+ }
+ expectNodeAffinitySet(&helper, 0, indexInNode());
+ helper.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityHeterogeneousNodesTest, PinsAutomaticallyOnNonMasterOnly)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ setupNodes(&helper, {{1, 2}});
+ helper.expectWarningMatchingRegexIf("Oversubscribing the CPU", currentNode() == 0);
+ helper.expectGenericFailureMessageIf(currentNode() == 0);
+ if (currentNode() == 1)
+ {
+ helper.expectPinningMessage(false, 1);
+ }
+ expectNodeAffinitySet(&helper, 1, indexInNode());
+ helper.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityHeterogeneousNodesTest, HandlesInvalidOffsetOnNonMasterOnly)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffON);
+ helper.setOffsetAndStride(2, 0);
+ setupNodes(&helper, {{4, 2}});
+ helper.expectWarningMatchingRegex("Applying core pinning offset 2");
+ helper.expectWarningMatchingRegexIf("Requested offset too large", isMaster() || currentNode() == 1);
+ helper.expectGenericFailureMessageIf(isMaster() || currentNode() == 1);
+ if (currentNode() == 0)
+ {
+ helper.expectPinningMessage(false, 1);
+ }
+ expectNodeAffinitySet(&helper, 0, indexInNode()+2);
+ helper.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityHeterogeneousNodesTest, HandlesInvalidStrideOnNonMasterOnly)
+{
+ GMX_MPI_TEST(4);
+ ThreadAffinityTestHelper helper;
+ helper.setAffinityOption(threadaffON);
+ helper.setOffsetAndStride(0, 2);
+ setupNodes(&helper, {{4, 2}});
+ helper.expectWarningMatchingRegexIf("Requested stride too large", isMaster() || currentNode() == 1);
+ helper.expectGenericFailureMessageIf(isMaster() || currentNode() == 1);
+ if (currentNode() == 0)
+ {
+ helper.expectPinningMessage(true, 2);
+ }
+ expectNodeAffinitySet(&helper, 0, 2*indexInNode());
+ helper.setAffinity(1);
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "gromacs/mdrunutility/threadaffinity.h"
+
+#include "config.h"
+
+#include <gtest/gtest.h>
+
+#include "threadaffinitytest.h"
+
+namespace
+{
+
+class ThreadAffinityTest : public ::testing::Test
+{
+ public:
+
+ gmx::test::ThreadAffinityTestHelper helper_;
+};
+
+TEST_F(ThreadAffinityTest, DoesNothingWhenDisabled)
+{
+ helper_.setAffinityOption(threadaffOFF);
+ helper_.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityTest, DoesNothingWhenNotSupported)
+{
+ helper_.setAffinitySupported(false);
+ helper_.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityTest, DoesNothingWithAutoAndTooFewThreads)
+{
+ helper_.setLogicalProcessorCount(4);
+ helper_.expectWarningMatchingRegex("The number of threads is not equal to the number of");
+ helper_.expectGenericFailureMessage();
+ helper_.setAffinity(2);
+}
+
+TEST_F(ThreadAffinityTest, DoesNothingWithAutoAndTooManyThreads)
+{
+ helper_.setLogicalProcessorCount(4);
+ helper_.expectWarningMatchingRegex("Oversubscribing the CPU");
+ helper_.expectGenericFailureMessage();
+ helper_.setAffinity(8);
+}
+
+TEST_F(ThreadAffinityTest, DoesNothingWithUnknownHardware)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setLogicalProcessorCount(0);
+ helper_.expectWarningMatchingRegex("No information on available cores");
+ helper_.expectGenericFailureMessage();
+ helper_.setAffinity(2);
+}
+
+TEST_F(ThreadAffinityTest, DoesNothingWithTooManyThreads)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setLogicalProcessorCount(4);
+ helper_.expectWarningMatchingRegex("Oversubscribing the CPU");
+ helper_.expectGenericFailureMessage();
+ helper_.setAffinity(8);
+}
+
+TEST_F(ThreadAffinityTest, DoesNothingWithTooLargeOffset)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setOffsetAndStride(2, 0);
+ helper_.setLogicalProcessorCount(4);
+ helper_.expectWarningMatchingRegex("Applying core pinning offset 2");
+ helper_.expectWarningMatchingRegex("Requested offset too large");
+ helper_.expectGenericFailureMessage();
+ helper_.setAffinity(3);
+}
+
+TEST_F(ThreadAffinityTest, DoesNothingWithTooLargeStride)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setOffsetAndStride(0, 2);
+ helper_.setLogicalProcessorCount(4);
+ helper_.expectWarningMatchingRegex("Requested stride too large");
+ helper_.expectGenericFailureMessage();
+ helper_.setAffinity(3);
+}
+
+TEST_F(ThreadAffinityTest, PinsSingleThreadWithAuto)
+{
+ helper_.setLogicalProcessorCount(1);
+ helper_.expectAffinitySet(0);
+ helper_.expectPinningMessage(false, 1);
+ helper_.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityTest, PinsSingleThreadWhenForced)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setLogicalProcessorCount(2);
+ helper_.expectPinningMessage(false, 2);
+ helper_.expectAffinitySet(0);
+ helper_.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityTest, PinsSingleThreadWithOffsetWhenForced)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setOffsetAndStride(2, 0);
+ helper_.setLogicalProcessorCount(4);
+ helper_.expectWarningMatchingRegex("Applying core pinning offset 2");
+ helper_.expectPinningMessage(false, 2);
+ helper_.expectAffinitySet(2);
+ helper_.setAffinity(1);
+}
+
+TEST_F(ThreadAffinityTest, HandlesPinningFailureWithSingleThread)
+{
+ helper_.setLogicalProcessorCount(1);
+ helper_.expectPinningMessage(false, 1);
+ helper_.expectGenericFailureMessage();
+ helper_.expectAffinitySetThatFails(0);
+ helper_.setAffinity(1);
+}
+
+// TODO: If it wouldn't result in a multitude of #if's, it would be nice
+// to somehow indicate in a no-OpenMP build that some tests are missing.
+#if GMX_OPENMP
+TEST_F(ThreadAffinityTest, PinsMultipleThreadsWithAuto)
+{
+ helper_.setLogicalProcessorCount(2);
+ helper_.expectPinningMessage(false, 1);
+ helper_.expectAffinitySet({0, 1});
+ helper_.setAffinity(2);
+}
+
+TEST_F(ThreadAffinityTest, PinsMultipleThreadsWithStrideWhenForced)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setOffsetAndStride(0, 2);
+ helper_.setLogicalProcessorCount(4);
+ helper_.expectPinningMessage(true, 2);
+ helper_.expectAffinitySet({0, 2});
+ helper_.setAffinity(2);
+}
+
+TEST_F(ThreadAffinityTest, HandlesPinningFailureWithOneThreadFailing)
+{
+ helper_.setAffinityOption(threadaffON);
+ helper_.setLogicalProcessorCount(2);
+ helper_.expectPinningMessage(false, 1);
+ helper_.expectGenericFailureMessage();
+ helper_.expectAffinitySet(0);
+ helper_.expectAffinitySetThatFails(1);
+ helper_.setAffinity(2);
+}
+#endif
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "threadaffinitytest.h"
+
+#include "config.h"
+
+#include <gmock/gmock.h>
+
+#include "gromacs/hardware/hardwaretopology.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+namespace gmx
+{
+namespace test
+{
+
+MockThreadAffinityAccess::MockThreadAffinityAccess()
+ : supported_(true), physicalNodeId_(0)
+{
+ using ::testing::_;
+ using ::testing::Return;
+ ON_CALL(*this, setCurrentThreadAffinityToCore(_))
+ .WillByDefault(Return(true));
+}
+
+MockThreadAffinityAccess::~MockThreadAffinityAccess()
+{
+}
+
+
+ThreadAffinityTestHelper::ThreadAffinityTestHelper()
+{
+ snew(cr_, 1);
+ cr_->nnodes = gmx_node_num();
+ cr_->nodeid = gmx_node_rank();
+ cr_->rank_intranode = cr_->nodeid;
+ cr_->duty = DUTY_PP;
+#if GMX_MPI
+ cr_->mpi_comm_mysim = MPI_COMM_WORLD;
+#endif
+ hwOpt_.thread_affinity = threadaffAUTO;
+}
+
+ThreadAffinityTestHelper::~ThreadAffinityTestHelper()
+{
+ sfree(cr_);
+}
+
+void ThreadAffinityTestHelper::setLogicalProcessorCount(int logicalProcessorCount)
+{
+ hwTop_.reset(new HardwareTopology(logicalProcessorCount));
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_MDRUNUTILITY_TESTS_THREADAFFINITYTEST_H
+#define GMX_MDRUNUTILITY_TESTS_THREADAFFINITYTEST_H
+
+#include <initializer_list>
+#include <memory>
+
+#include <gmock/gmock.h>
+
+#include "gromacs/hardware/hw_info.h"
+#include "gromacs/mdrunutility/threadaffinity.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/loggertest.h"
+
+struct t_commrec;
+
+namespace gmx
+{
+
+class HardwareTopology;
+
+namespace test
+{
+
+class MockThreadAffinityAccess : public IThreadAffinityAccess
+{
+ public:
+ MockThreadAffinityAccess();
+ ~MockThreadAffinityAccess();
+
+ void setSupported(bool supported) { supported_ = supported; }
+ void setPhysicalNodeId(int nodeId) { physicalNodeId_ = nodeId; }
+
+ virtual bool isThreadAffinitySupported() const { return supported_; }
+ virtual int physicalNodeId() const { return physicalNodeId_; }
+ MOCK_METHOD1(setCurrentThreadAffinityToCore, bool(int core));
+
+ private:
+ bool supported_;
+ int physicalNodeId_;
+};
+
+class ThreadAffinityTestHelper
+{
+ public:
+ ThreadAffinityTestHelper();
+ ~ThreadAffinityTestHelper();
+
+ void setAffinitySupported(bool supported)
+ {
+ affinityAccess_.setSupported(supported);
+ }
+ void setAffinityOption(int affinityOption)
+ {
+ hwOpt_.thread_affinity = affinityOption;
+ }
+ void setOffsetAndStride(int offset, int stride)
+ {
+ hwOpt_.core_pinning_offset = offset;
+ hwOpt_.core_pinning_stride = stride;
+ }
+
+ void setPhysicalNodeId(int nodeId)
+ {
+ affinityAccess_.setPhysicalNodeId(nodeId);
+ }
+
+ void setLogicalProcessorCount(int logicalProcessorCount);
+
+ void expectAffinitySet(int core)
+ {
+ EXPECT_CALL(affinityAccess_, setCurrentThreadAffinityToCore(core));
+ }
+ void expectAffinitySet(std::initializer_list<int> cores)
+ {
+ for (int core : cores)
+ {
+ expectAffinitySet(core);
+ }
+ }
+ void expectAffinitySetThatFails(int core)
+ {
+ using ::testing::Return;
+ EXPECT_CALL(affinityAccess_, setCurrentThreadAffinityToCore(core))
+ .WillOnce(Return(false));
+ }
+
+ void expectWarningMatchingRegex(const char *re)
+ {
+ expectWarningMatchingRegexIf(re, true);
+ }
+ void expectWarningMatchingRegexIf(const char *re, bool condition)
+ {
+ expectLogMessageMatchingRegexIf(MDLogger::LogLevel::Warning, re, condition);
+ }
+ void expectInfoMatchingRegex(const char *re)
+ {
+ expectInfoMatchingRegexIf(re, true);
+ }
+ void expectInfoMatchingRegexIf(const char *re, bool condition)
+ {
+ expectLogMessageMatchingRegexIf(MDLogger::LogLevel::Info, re, condition);
+ }
+ void expectGenericFailureMessage()
+ {
+ expectGenericFailureMessageIf(true);
+ }
+ void expectGenericFailureMessageIf(bool condition)
+ {
+ expectWarningMatchingRegexIf("NOTE: Thread affinity setting failed.", condition);
+ }
+ void expectPinningMessage(bool userSpecifiedStride, int stride)
+ {
+ std::string pattern = formatString("Pinning threads .* %s.* stride of %d",
+ userSpecifiedStride ? "user" : "auto",
+ stride);
+ expectInfoMatchingRegex(pattern.c_str());
+ }
+ void expectLogMessageMatchingRegexIf(MDLogger::LogLevel level,
+ const char *re, bool condition)
+ {
+ if (condition)
+ {
+ logHelper_.expectEntryMatchingRegex(level, re);
+ }
+ }
+
+ void setAffinity(int nthread_local)
+ {
+ if (hwTop_ == nullptr)
+ {
+ setLogicalProcessorCount(1);
+ }
+ gmx_set_thread_affinity(logHelper_.logger(), cr_, &hwOpt_, *hwTop_,
+ nthread_local, &affinityAccess_);
+ }
+
+ private:
+ t_commrec *cr_;
+ gmx_hw_opt_t hwOpt_;
+ std::unique_ptr<HardwareTopology> hwTop_;
+ MockThreadAffinityAccess affinityAccess_;
+ LoggerTestHelper logHelper_;
+};
+
+} // namespace test
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "thread_mpi/threads.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/hardware/hardwaretopology.h"
#include "gromacs/hardware/hw_info.h"
-#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/utility/basenetwork.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/programcontext.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/unique_cptr.h"
+namespace
+{
+
+class DefaultThreadAffinityAccess : public gmx::IThreadAffinityAccess
+{
+ public:
+ virtual bool isThreadAffinitySupported() const
+ {
+ return tMPI_Thread_setaffinity_support() == TMPI_SETAFFINITY_SUPPORT_YES;
+ }
+ virtual int physicalNodeId() const
+ {
+ return gmx_physicalnode_id_hash();
+ }
+ virtual bool setCurrentThreadAffinityToCore(int core)
+ {
+ const int ret = tMPI_Thread_setaffinity_single(tMPI_Thread_self(), core);
+ return ret == 0;
+ }
+};
+
+//! Global instance of DefaultThreadAffinityAccess
+DefaultThreadAffinityAccess g_defaultAffinityAccess;
+
+} // namespace
+
+gmx::IThreadAffinityAccess::~IThreadAffinityAccess()
+{
+}
static bool invalidWithinSimulation(const t_commrec *cr, bool invalidLocally)
{
}
static bool
-get_thread_affinity_layout(FILE *fplog,
+get_thread_affinity_layout(const gmx::MDLogger &mdlog,
const t_commrec *cr,
- const gmx_hw_info_t * hwinfo,
+ const gmx::HardwareTopology &hwTop,
int threads,
bool automatic,
int pin_offset, int * pin_stride,
bool haveTopology;
bool invalidValue;
- const gmx::HardwareTopology &hwTop = *hwinfo->hardwareTopology;
-
haveTopology = (hwTop.supportLevel() >= gmx::HardwareTopology::SupportLevel::Basic);
if (pin_offset < 0)
else
{
/* topology information not available or invalid, ignore it */
- hwThreads = hwinfo->nthreads_hw_avail;
- *localityOrder = NULL;
+ hwThreads = hwTop.machine().logicalProcessorCount;
+ *localityOrder = nullptr;
}
// Only warn about the first problem per node. Otherwise, the first test
// failing would essentially always cause also the other problems get
if (invalidWithinSimulation(cr, invalidValue))
{
/* We don't know anything about the hardware, don't pin */
- md_print_warn(cr, fplog,
- "NOTE: No information on available cores, thread pinning disabled.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: No information on available cores, thread pinning disabled.");
alreadyWarned = true;
}
bool validLayout = !invalidValue;
bool warn = (invalidValue && threads > 1 && threads < hwThreads);
if (invalidWithinSimulation(cr, warn) && !alreadyWarned)
{
- md_print_warn(cr, fplog,
- "NOTE: The number of threads is not equal to the number of (logical) cores\n"
- " and the -pin option is set to auto: will not pin thread to cores.\n"
- " This can lead to significant performance degradation.\n"
- " Consider using -pin on (and -pinoffset in case you run multiple jobs).\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: The number of threads is not equal to the number of (logical) cores\n"
+ " and the -pin option is set to auto: will not pin thread to cores.\n"
+ " This can lead to significant performance degradation.\n"
+ " Consider using -pin on (and -pinoffset in case you run multiple jobs).");
alreadyWarned = true;
}
validLayout = validLayout && !invalidValue;
invalidValue = (threads > hwThreads);
if (invalidWithinSimulation(cr, invalidValue) && !alreadyWarned)
{
- md_print_warn(cr, fplog,
- "NOTE: Oversubscribing a CPU, will not pin threads.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: Oversubscribing the CPU, will not pin threads");
alreadyWarned = true;
}
validLayout = validLayout && !invalidValue;
invalidValue = (pin_offset + threads > hwThreads);
if (invalidWithinSimulation(cr, invalidValue) && !alreadyWarned)
{
- md_print_warn(cr, fplog,
- "WARNING: Requested offset too large for available cores, thread pinning disabled.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "WARNING: Requested offset too large for available cores, thread pinning disabled.");
alreadyWarned = true;
}
if (invalidWithinSimulation(cr, invalidValue) && !alreadyWarned)
{
/* We are oversubscribing, don't pin */
- md_print_warn(cr, fplog,
- "WARNING: Requested stride too large for available cores, thread pinning disabled.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "WARNING: Requested stride too large for available cores, thread pinning disabled.");
}
validLayout = validLayout && !invalidValue;
- if (validLayout && fplog != NULL)
+ if (validLayout)
{
- fprintf(fplog, "Pinning threads with a%s logical core stride of %d\n",
+ GMX_LOG(mdlog.info).appendTextFormatted(
+ "Pinning threads with a%s logical core stride of %d",
bPickPinStride ? "n auto-selected" : " user-specified",
*pin_stride);
}
}
static bool set_affinity(const t_commrec *cr, int nthread_local, int thread0_id_node,
- int offset, int core_pinning_stride, int *localityOrder)
+ int offset, int core_pinning_stride, int *localityOrder,
+ gmx::IThreadAffinityAccess *affinityAccess)
{
// Set the per-thread affinity. In order to be able to check the success
// of affinity settings, we will set nth_affinity_set to 1 on threads
{
int thread_id, thread_id_node;
int index, core;
- gmx_bool setaffinity_ret;
thread_id = gmx_omp_get_thread_num();
thread_id_node = thread0_id_node + thread_id;
core = index;
}
- setaffinity_ret = tMPI_Thread_setaffinity_single(tMPI_Thread_self(), core);
+ const bool ret = affinityAccess->setCurrentThreadAffinityToCore(core);
/* store the per-thread success-values of the setaffinity */
- nth_affinity_set += (setaffinity_ret == 0);
+ nth_affinity_set += (ret ? 1 : 0);
if (debug)
{
fprintf(debug, "On rank %2d, thread %2d, index %2d, core %2d the affinity setting returned %d\n",
- cr->nodeid, gmx_omp_get_thread_num(), index, core, setaffinity_ret);
+ cr->nodeid, gmx_omp_get_thread_num(), index, core, ret ? 1 : 0);
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
nthread_local > 1 ? "s" : "");
}
+ // TODO: This output should also go through mdlog.
fprintf(stderr, "NOTE: %sAffinity setting %sfailed.\n", sbuf1, sbuf2);
}
return allAffinitiesSet;
if only PME is using threads.
*/
void
-gmx_set_thread_affinity(FILE *fplog,
- const t_commrec *cr,
- const gmx_hw_opt_t *hw_opt,
- const gmx_hw_info_t *hwinfo)
+gmx_set_thread_affinity(const gmx::MDLogger &mdlog,
+ const t_commrec *cr,
+ const gmx_hw_opt_t *hw_opt,
+ const gmx::HardwareTopology &hwTop,
+ int nthread_local,
+ gmx::IThreadAffinityAccess *affinityAccess)
{
- int thread0_id_node,
- nthread_local, nthread_node;
+ int thread0_id_node, nthread_node;
int * localityOrder = nullptr;
if (hw_opt->thread_affinity == threadaffOFF)
return;
}
+ if (affinityAccess == nullptr)
+ {
+ affinityAccess = &g_defaultAffinityAccess;
+ }
+
/* If the tMPI thread affinity setting is not supported encourage the user
* to report it as it's either a bug or an exotic platform which we might
* want to support. */
- if (tMPI_Thread_setaffinity_support() != TMPI_SETAFFINITY_SUPPORT_YES)
+ if (!affinityAccess->isThreadAffinitySupported())
{
/* we know Mac OS & BlueGene do not support setting thread affinity, so there's
no point in warning the user in that case. In any other case
the user might be able to do something about it. */
#if !defined(__APPLE__) && !defined(__bg__)
- md_print_warn(cr, fplog,
- "NOTE: Cannot set thread affinities on the current platform.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: Cannot set thread affinities on the current platform.");
#endif /* __APPLE__ */
return;
}
- /* threads on this MPI process or TMPI thread */
- if (cr->duty & DUTY_PP)
- {
- nthread_local = gmx_omp_nthreads_get(emntNonbonded);
- }
- else
- {
- nthread_local = gmx_omp_nthreads_get(emntPME);
- }
-
/* map the current process to cores */
thread0_id_node = 0;
nthread_node = nthread_local;
MPI_Comm comm_intra;
MPI_Comm_split(MPI_COMM_WORLD,
- gmx_physicalnode_id_hash(), cr->rank_intranode,
+ affinityAccess->physicalNodeId(), cr->rank_intranode,
&comm_intra);
MPI_Scan(&nthread_local, &thread0_id_node, 1, MPI_INT, MPI_SUM, comm_intra);
/* MPI_Scan is inclusive, but here we need exclusive */
int core_pinning_stride = hw_opt->core_pinning_stride;
if (offset != 0)
{
- md_print_info(cr, fplog, "Applying core pinning offset %d\n", offset);
+ GMX_LOG(mdlog.warning).appendTextFormatted("Applying core pinning offset %d", offset);
}
bool automatic = (hw_opt->thread_affinity == threadaffAUTO);
bool validLayout
- = get_thread_affinity_layout(fplog, cr, hwinfo, nthread_node, automatic,
+ = get_thread_affinity_layout(mdlog, cr, hwTop, nthread_node, automatic,
offset, &core_pinning_stride, &localityOrder);
- gmx::scoped_guard_sfree localityOrderGuard(localityOrder);
+ const gmx::sfree_guard localityOrderGuard(localityOrder);
bool allAffinitiesSet;
if (validLayout)
{
allAffinitiesSet = set_affinity(cr, nthread_local, thread0_id_node,
- offset, core_pinning_stride, localityOrder);
+ offset, core_pinning_stride, localityOrder,
+ affinityAccess);
}
else
{
}
if (invalidWithinSimulation(cr, !allAffinitiesSet))
{
- md_print_warn(cr, fplog,
- "NOTE: Thread affinity setting failed. This can cause performance degradation.\n"
- " If you think your settings are correct, ask on the gmx-users list.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: Thread affinity setting failed. This can cause performance degradation.\n"
+ " If you think your settings are correct, ask on the gmx-users list.");
}
}
* Note that this will only work on Linux as we use a GNU feature.
*/
void
-gmx_check_thread_affinity_set(FILE *fplog,
- const t_commrec *cr,
- gmx_hw_opt_t *hw_opt,
- int gmx_unused nthreads_hw_avail,
- gmx_bool bAfterOpenmpInit)
+gmx_check_thread_affinity_set(const gmx::MDLogger &mdlog,
+ const t_commrec *cr,
+ gmx_hw_opt_t *hw_opt,
+ int gmx_unused nthreads_hw_avail,
+ gmx_bool bAfterOpenmpInit)
{
GMX_RELEASE_ASSERT(hw_opt, "hw_opt must be a non-NULL pointer");
if (!gmx_omp_check_thread_affinity(&message))
{
/* TODO: with -pin auto we should only warn when using all cores */
- md_print_warn(cr, fplog, "%s", message);
+ GMX_LOG(mdlog.warning).asParagraph().appendText(message);
sfree(message);
hw_opt->thread_affinity = threadaffOFF;
}
{
if (!bAfterOpenmpInit)
{
- md_print_warn(cr, fplog,
- "Non-default thread affinity set, disabling internal thread affinity");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "Non-default thread affinity set, disabling internal thread affinity");
}
else
{
- md_print_warn(cr, fplog,
- "Non-default thread affinity set probably by the OpenMP library,\n"
- "disabling internal thread affinity");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "Non-default thread affinity set probably by the OpenMP library,\n"
+ "disabling internal thread affinity");
}
hw_opt->thread_affinity = threadaffOFF;
}
/* Only warn once, at the last check (bAfterOpenmpInit==TRUE) */
if (bAfterOpenmpInit)
{
- md_print_warn(cr, fplog,
- "Overriding thread affinity set outside %s\n",
- gmx::getProgramContext().displayName());
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "Overriding thread affinity set outside %s",
+ gmx::getProgramContext().displayName());
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
-#include "gromacs/hardware/hw_info.h"
#include "gromacs/utility/basedefinitions.h"
+struct gmx_hw_opt_t;
struct t_commrec;
+namespace gmx
+{
+
+class HardwareTopology;
+class MDLogger;
+
+class IThreadAffinityAccess
+{
+ public:
+ virtual bool isThreadAffinitySupported() const = 0;
+ virtual int physicalNodeId() const = 0;
+ virtual bool setCurrentThreadAffinityToCore(int core) = 0;
+
+ protected:
+ virtual ~IThreadAffinityAccess();
+};
+
+} // namespace gmx
+
/*! \brief
* Sets the thread affinity using the requested setting stored in hw_opt.
- *
- * The hardware topology is requested from hwinfo, when present.
*/
void
-gmx_set_thread_affinity(FILE *fplog,
- const t_commrec *cr,
- const gmx_hw_opt_t *hw_opt,
- const gmx_hw_info_t *hwinfo);
+gmx_set_thread_affinity(const gmx::MDLogger &mdlog,
+ const t_commrec *cr,
+ const gmx_hw_opt_t *hw_opt,
+ const gmx::HardwareTopology &hwTop,
+ int nthread_local,
+ gmx::IThreadAffinityAccess *affinityAccess);
/*! \brief
* Checks the process affinity mask and if it is found to be non-zero,
* variables for setting the affinity are set.
*/
void
-gmx_check_thread_affinity_set(FILE *fplog, const t_commrec *cr,
+gmx_check_thread_affinity_set(const gmx::MDLogger &mdlog, const t_commrec *cr,
gmx_hw_opt_t *hw_opt, int ncpus,
gmx_bool bAfterOpenmpInit);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
MPI_Comm mpi_comm_mysim;
MPI_Comm mpi_comm_mygroup;
- /* MPI ranks within a physical node for hardware access */
- int nrank_intranode; /* nr of ranks on this physical node */
- int rank_intranode; /* our rank on this physical node */
- int nrank_pp_intranode; /* as nrank_intranode, for particle-particle only */
- int rank_pp_intranode; /* as rank_intranode, for particle-particle only */
+ /* MPI ranks and a communicator within a physical node for hardware access */
+ MPI_Comm mpi_comm_physicalnode; /* communicator for all ranks of the physical node
+ * NOTE: this communicator should only be used during initialization and finalization, as it can contain ranks from PP, PME and multiple simulations with multisim
+ */
+ int nrank_intranode; /* nr of ranks on this physical node */
+ int rank_intranode; /* our rank on this physical node */
+ int nrank_pp_intranode; /* as nrank_intranode, for particle-particle only */
+ int rank_pp_intranode; /* as rank_intranode, for particle-particle only */
gmx_nodecomm_t nc;
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*
+ * This file contains data types containing essential dynamics and
+ * flooding data to be stored in the checkpoint file.
+ */
+
+#ifndef GMX_MDLIB_EDSAMHISTORY_H
+#define GMX_MDLIB_EDSAMHISTORY_H
+
+/* Helper structure to be able to make essential dynamics / flooding group(s) whole
+ *
+ * If one uses essential dynamics or flooding on a group of atoms from
+ * more than one molecule, we cannot make this group whole with
+ * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
+ * representation at the beginning of the simulation and keep track
+ * of the shifts to always get it into that representation.
+ * For proper restarts from a checkpoint we store the positions of the
+ * reference group at the time of checkpoint writing.
+ */
+typedef struct edsamhistory_t
+{
+ gmx_bool bFromCpt; // Did we start from a checkpoint file?
+ int nED; // No. of ED/Flooding data sets, if <1 no ED
+ int *nref; // No. of atoms in i'th reference structure
+ int *nav; // Same for average structure
+ rvec **old_sref; // Positions of the reference atoms at the last time step (with correct PBC representation)
+ rvec **old_sref_p; // Pointer to these positions
+ rvec **old_sav; // Same for the average positions
+ rvec **old_sav_p; // Pointer to these positions
+}
+edsamhistory_t;
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+
+/*! \libinternal \file
+ *
+ *
+ * \brief
+ * This file contains datatypes for energy statistics history.
+ *
+ * \author Berk Hess
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+
#ifndef GMX_MDLIB_ENERGYHISTORY_H
#define GMX_MDLIB_ENERGYHISTORY_H
+#include <memory>
+#include <vector>
+
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-/* energy history for delta_h histograms */
-typedef struct delta_h_history_t
-{
- int nndh; /* the number of energy difference lists */
- int *ndh; /* the number in each energy difference list */
- real **dh; /* the energy difference lists */
+//! \cond INTERNAL
- double start_time; /* the start time of these energy diff blocks */
- double start_lambda; /* lambda at start time */
+//! \brief Energy history for delta_h histograms in between energy file frames
+class delta_h_history_t
+{
+ public:
+ //! Vector (size number of intermediate data points) of vector of Hamiltonian differences for each foreign lambda
+ std::vector<std::vector<real> > dh;
+ //! The start time of these energy diff blocks
+ double start_time;
+ //! Lambda at start time
+ double start_lambda;
+ //! Whether the lambda value is set. Here for backward-compatibility.
+ gmx_bool start_lambda_set;
- gmx_bool start_lambda_set; /* whether the lambda value is set. Here
- For backward-compatibility. */
-} delta_h_history_t;
+ //! Constructor
+ delta_h_history_t() : dh(),
+ start_time(0),
+ start_lambda(0),
+ start_lambda_set(false)
+ {
+ }
+};
-typedef struct energyhistory_t
+//! \brief Energy statistics history, only used for output and reporting
+class energyhistory_t
{
- gmx_int64_t nsteps; /* The number of steps in the history */
- gmx_int64_t nsum; /* The nr. of steps in the ener_ave and ener_sum */
- double * ener_ave; /* Energy term history sum to get fluctuations */
- double * ener_sum; /* Energy term history sum to get fluctuations */
- int nener; /* Number of energy terms in two previous arrays */
- gmx_int64_t nsteps_sim; /* The number of steps in ener_sum_sim */
- gmx_int64_t nsum_sim; /* The number of frames in ener_sum_sim */
- double * ener_sum_sim; /* Energy term history sum of the whole sim */
+ public:
+ gmx_int64_t nsteps; //! The number of steps in the history
+ gmx_int64_t nsum; //! Nr. of steps in the ener_ave and ener_sum
+ std::vector<double> ener_ave; //! Energy terms difference^2 sum to get fluctuations
+ std::vector<double> ener_sum; //! Energy terms sum
+ gmx_int64_t nsteps_sim; //! The number of steps in ener_sum_sim
+ gmx_int64_t nsum_sim; //! The number of frames in ener_sum_sim
+ std::vector<double> ener_sum_sim; //! Energy term history sum of the whole sim
- delta_h_history_t *dht; /* The BAR energy differences */
-}
-energyhistory_t;
+ //! History for energy difference for foreign lambdas (useful for BAR)
+ std::unique_ptr<delta_h_history_t> deltaHForeignLambdas;
-/* \brief Initialize an energy history structure
- */
-void init_energyhistory(energyhistory_t * enerhist);
+ //! Constructor
+ energyhistory_t() : nsteps(0),
+ nsum(0),
+ ener_ave(),
+ ener_sum(),
+ nsteps_sim(0),
+ nsum_sim(0),
+ ener_sum_sim(0)
+ {
+ }
+};
-/* \brief Destroy an energy history structure
- */
-void done_energyhistory(energyhistory_t * enerhist);
+//! \endcond
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const t_iatom *forceatomsStart; /* Pointer to the start of the disre forceatoms */
} t_disresdata;
+/* All coefficients for the matrix equation for the orientation tensor */
+struct OriresMatEq
+{
+ real rhs[5]; /* The right hand side of the matrix equation */
+ real mat[5][5]; /* The matrix */
+};
/* Orientation restraining stuff */
typedef struct t_oriresdata {
- real fc; /* Force constant for the restraints */
- real edt; /* Multiplication factor for time averaging */
- real edt_1; /* 1 - edt */
- real exp_min_t_tau; /* Factor for slowly switching on the force */
- int nr; /* The number of orientation restraints */
- int nex; /* The number of experiments */
- int nref; /* The number of atoms for the fit */
- real *mref; /* The masses of the reference atoms */
- rvec *xref; /* The reference coordinates for the fit (nref) */
- rvec *xtmp; /* Temporary array for fitting (nref) */
- matrix R; /* Rotation matrix to rotate to the reference coor. */
- tensor *S; /* Array of order tensors for each experiment (nexp) */
- rvec5 *Dinsl; /* The order matrix D for all restraints (nr x 5) */
- rvec5 *Dins; /* The ensemble averaged D (nr x 5) */
- rvec5 *Dtav; /* The time and ensemble averaged D (nr x 5) */
- real *oinsl; /* The calculated instantaneous orientations */
- real *oins; /* The calculated emsemble averaged orientations */
- real *otav; /* The calculated time and ensemble averaged orient. */
- real rmsdev; /* The weighted (using kfac) RMS deviation */
- rvec5 *tmp; /* An array of temporary 5-vectors (nex); */
- real ***TMP; /* An array of temporary 5x5 matrices (nex); */
- real *eig; /* Eigenvalues/vectors, for output only (nex x 12) */
+ real fc; /* Force constant for the restraints */
+ real edt; /* Multiplication factor for time averaging */
+ real edt_1; /* 1 - edt */
+ real exp_min_t_tau; /* Factor for slowly switching on the force */
+ int nr; /* The number of orientation restraints */
+ int nex; /* The number of experiments */
+ int typeMin; /* The minimum iparam type index for restraints */
+ int nref; /* The number of atoms for the fit */
+ real *mref; /* The masses of the reference atoms */
+ rvec *xref; /* The reference coordinates for the fit (nref) */
+ rvec *xtmp; /* Temporary array for fitting (nref) */
+ matrix R; /* Rotation matrix to rotate to the reference coor. */
+ tensor *S; /* Array of order tensors for each experiment (nexp) */
+ rvec5 *Dinsl; /* The order matrix D for all restraints (nr x 5) */
+ rvec5 *Dins; /* The ensemble averaged D (nr x 5) */
+ rvec5 *Dtav; /* The time and ensemble averaged D (nr x 5) */
+ real *oinsl; /* The calculated instantaneous orientations */
+ real *oins; /* The calculated emsemble averaged orientations */
+ real *otav; /* The calculated time and ensemble averaged orient. */
+ real rmsdev; /* The weighted (using kfac) RMS deviation */
+ OriresMatEq *tmpEq; /* An temporary array of matrix + rhs */
+ real *eig; /* Eigenvalues/vectors, for output only (nex x 12) */
/* variables for diagonalization with diagonalize_orires_tensors()*/
double **M;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_MDTYPES_TYPES_FORCEREC_H
#include "gromacs/math/vectypes.h"
+#ifdef __cplusplus
+#include "gromacs/math/paddedvector.h"
+#endif
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/idef.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-} /* fixes auto-indentation problems */
-#endif
+struct ForceProviders;
/* Abstract type for PME that is defined only in the routine that use them. */
struct gmx_genborn_t;
struct t_nblist;
struct t_nblists;
struct t_QMMMrec;
-struct gmx_hw_info_t;
-struct gmx_gpu_opt_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
/* macros for the cginfo data in forcerec
*
};
extern const char *egrp_nm[egNR+1];
-typedef struct gmx_grppairener_t {
+struct gmx_grppairener_t
+{
int nener; /* The number of energy group pairs */
real *ener[egNR]; /* Energy terms for each pair of groups */
-} gmx_grppairener_t;
-
-typedef struct gmx_enerdata_t {
- real term[F_NRE]; /* The energies for all different interaction types */
- gmx_grppairener_t grpp;
- double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
- double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
- int n_lambda;
- int fep_state; /*current fep state -- just for printing */
- double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
- real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
- gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */
-} gmx_enerdata_t;
+};
+
+struct gmx_enerdata_t
+{
+ real term[F_NRE]; /* The energies for all different interaction types */
+ struct gmx_grppairener_t grpp;
+ double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
+ double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
+ int n_lambda;
+ int fep_state; /*current fep state -- just for printing */
+ double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
+ real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
+ struct gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */
+};
/* The idea is that dvdl terms with linear lambda dependence will be added
* automatically to enerpart_lambda. Terms with non-linear lambda dependence
* should explicitly determine the energies at foreign lambda points
* when n_lambda > 0.
*/
-typedef struct {
+struct cginfo_mb_t
+{
int cg_start;
int cg_end;
int cg_mod;
int *cginfo;
-} cginfo_mb_t;
+};
/* Forward declaration of type for managing Ewald tables */
struct gmx_ewald_tab_t;
-typedef struct ewald_corr_thread_t ewald_corr_thread_t;
+struct ewald_corr_thread_t;
-typedef struct t_forcerec {
- interaction_const_t *ic;
+struct t_forcerec {
+ struct interaction_const_t *ic;
/* Domain Decomposition */
gmx_bool bDomDec;
rvec posres_com;
rvec posres_comB;
- const struct gmx_hw_info_t *hwinfo;
- const struct gmx_gpu_opt_t *gpu_opt;
gmx_bool use_simd_kernels;
/* Interaction for calculated in kernels. In many cases this is similar to
/* solvent_opt contains the enum for the most common solvent
* in the system, which will be optimized.
* It can be set to esolNO to disable all water optimization */
- int solvent_opt;
- int nWatMol;
- gmx_bool bGrid;
- gmx_bool bExcl_IntraCGAll_InterCGNone;
- cginfo_mb_t *cginfo_mb;
- int *cginfo;
- rvec *cg_cm;
- int cg_nalloc;
- rvec *shift_vec;
+ int solvent_opt;
+ int nWatMol;
+ gmx_bool bGrid;
+ gmx_bool bExcl_IntraCGAll_InterCGNone;
+ struct cginfo_mb_t *cginfo_mb;
+ int *cginfo;
+ rvec *cg_cm;
+ int cg_nalloc;
+ rvec *shift_vec;
/* The neighborlists including tables */
int nnblists;
/* Forces that should not enter into the virial summation:
* PPPM/PME/Ewald/posres
+ * If such forces are present in the system, bF_NoVirSum=TRUE.
*/
- gmx_bool bF_NoVirSum;
- int f_novirsum_n;
- int f_novirsum_nalloc;
- rvec *f_novirsum_alloc;
- /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
- * points to the normal force vectors wen pressure is not requested.
+ gmx_bool bF_NoVirSum;
+#ifdef __cplusplus
+ /* TODO: Replace the pointer by an object once we got rid of C */
+ PaddedRVecVector *forceBufferNoVirialSummation;
+#else
+ void *forceBufferNoVirialSummation_dummy;
+#endif
+ /* Pointer that points to forceNoVirialSummation when virial is calcaluted,
+ * points to the normal force vector when the virial is not requested
+ * or when bF_NoVirSum == FALSE.
*/
- rvec *f_novirsum;
+#ifdef __cplusplus
+ PaddedRVecVector *f_novirsum;
+#else
+ void *f_novirsum_xdummy;
+#endif
/* Long-range forces and virial for PPPM/PME/Ewald */
struct gmx_pme_t *pmedata;
struct bonded_threading_t *bonded_threading;
/* Ewald correction thread local virial and energy data */
- int nthread_ewc;
- ewald_corr_thread_t *ewc_t;
-} t_forcerec;
+ int nthread_ewc;
+ struct ewald_corr_thread_t *ewc_t;
+
+ struct ForceProviders *forceProviders;
+};
/* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
* been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
#ifdef __cplusplus
}
#endif
+
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements classes from iforceprovider.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_mdtypes
+ */
+#include "gmxpre.h"
+
+#include "iforceprovider.h"
+
+#include <vector>
+
+#include "gromacs/utility/arrayref.h"
+
+using namespace gmx;
+
+class ForceProviders::Impl
+{
+ public:
+ std::vector<IForceProvider *> withVirialContribution_;
+ std::vector<IForceProvider *> withoutVirialContribution_;
+};
+
+ForceProviders::ForceProviders()
+ : impl_(new Impl)
+{
+}
+
+ForceProviders::~ForceProviders()
+{
+}
+
+void ForceProviders::addForceProvider(gmx::IForceProvider *provider)
+{
+ impl_->withVirialContribution_.push_back(provider);
+}
+
+void ForceProviders::addForceProviderWithoutVirialContribution(gmx::IForceProvider *provider)
+{
+ impl_->withoutVirialContribution_.push_back(provider);
+}
+
+bool ForceProviders::hasForcesWithoutVirialContribution() const
+{
+ return !impl_->withoutVirialContribution_.empty();
+}
+
+void ForceProviders::calculateForces(const t_commrec *cr,
+ const t_mdatoms *mdatoms,
+ const matrix box,
+ double t,
+ const rvec *x,
+ gmx::ArrayRef<gmx::RVec> force,
+ gmx::ArrayRef<gmx::RVec> f_novirsum) const
+{
+ for (auto provider : impl_->withVirialContribution_)
+ {
+ provider->calculateForces(cr, mdatoms, box, t, x, force);
+ }
+ for (auto provider : impl_->withoutVirialContribution_)
+ {
+ provider->calculateForces(cr, mdatoms, box, t, x, f_novirsum);
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::IForceProvider and ForceProviders.
+ *
+ * See \ref page_mdmodules for an overview of this and associated interfaces.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+#ifndef GMX_MDTYPES_IFORCEPROVIDER_H
+#define GMX_MDTYPES_IFORCEPROVIDER_H
+
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/classhelpers.h"
+
+struct t_commrec;
+struct t_forcerec;
+struct t_mdatoms;
+
+namespace gmx
+{
+
+template <typename T>
+class ArrayRef;
+
+/*! \libinternal \brief
+ * Interface for a component that provides forces during MD.
+ *
+ * Modules implementing IMDModule generally implement this internally, and use
+ * IMDModule::initForceProviders() to register their implementation in
+ * ForceProviders.
+ *
+ * The interface most likely requires additional generalization for use in
+ * other modules than the current electric field implementation.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+class IForceProvider
+{
+ public:
+ /*! \brief
+ * Computes forces.
+ *
+ * \param[in] cr Communication record for parallel operations
+ * \param[in] mdatoms Atom information
+ * \param[in] box The box
+ * \param[in] t The actual time in the simulation (ps)
+ * \param[in] x The coordinates
+ * \param[inout] force The forces
+ */
+ virtual void calculateForces(const t_commrec *cr,
+ const t_mdatoms *mdatoms,
+ const matrix box,
+ double t,
+ const rvec *x,
+ gmx::ArrayRef<gmx::RVec> force) = 0;
+
+ protected:
+ ~IForceProvider() {}
+};
+
+} // namespace gmx
+
+/*! \libinternal \brief
+ * Evaluates forces from a collection of gmx::IForceProvider.
+ *
+ * This class is a `struct` outside the `gmx` namespace to make it possible to
+ * forward-declare it in forcerec.h, which still needs to compile when included
+ * from the C group kernels.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+struct ForceProviders
+{
+ public:
+ ForceProviders();
+ ~ForceProviders();
+
+ /*! \brief
+ * Adds a provider.
+ */
+ void addForceProvider(gmx::IForceProvider *provider);
+ /*! \brief
+ * Adds a provider whose forces should not contribute to the virial.
+ */
+ void addForceProviderWithoutVirialContribution(gmx::IForceProvider *provider);
+
+ //! Whether there are modules that do not contribute to the virial.
+ bool hasForcesWithoutVirialContribution() const;
+
+ //! Computes forces.
+ void calculateForces(const t_commrec *cr,
+ const t_mdatoms *mdatoms,
+ const matrix box,
+ double t,
+ const rvec *x,
+ gmx::ArrayRef<gmx::RVec> force,
+ gmx::ArrayRef<gmx::RVec> f_novirsum) const;
+
+ private:
+ class Impl;
+
+ gmx::PrivateImplPointer<Impl> impl_;
+};
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::IMDModule.
+ *
+ * See \ref page_mdmodules for an overview of this and associated interfaces.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+#ifndef GMX_MDTYPES_IMDMODULE_H
+#define GMX_MDTYPES_IMDMODULE_H
+
+struct ForceProviders;
+
+namespace gmx
+{
+
+class IMDOutputProvider;
+class IMdpOptionProvider;
+
+/*! \libinternal \brief
+ * Extension module for \Gromacs simulations.
+ *
+ * The methods that return other interfaces can in the future return null for
+ * those interfaces that the module does not need to implement, but currently
+ * the callers are not prepared to generically handle various cases.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+class IMDModule
+{
+ public:
+ virtual ~IMDModule() {}
+
+ //! Returns an interface for handling mdp input (and tpr I/O).
+ virtual IMdpOptionProvider *mdpOptionProvider() = 0;
+ //! Returns an interface for handling output files during simulation.
+ virtual IMDOutputProvider *outputProvider() = 0;
+ //! Initializes force providers from this module.
+ virtual void initForceProviders(ForceProviders *forceProviders) = 0;
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::IMDOutputProvider.
+ *
+ * See \ref page_mdmodules for an overview of this and associated interfaces.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+#ifndef GMX_MDTYPES_IMDOUTPUTPROVIDER_H
+#define GMX_MDTYPES_IMDOUTPUTPROVIDER_H
+
+#include <cstdio>
+
+struct gmx_output_env_t;
+struct t_filenm;
+
+namespace gmx
+{
+
+/*! \libinternal \brief
+ * Interface for handling additional output files during a simulation.
+ *
+ * This interface provides a mechanism for additional modules to initialize
+ * and finalize output files during the simulation. Writing values to the
+ * output files is currently handled elsewhere (e.g., when the module has
+ * computed its forces).
+ *
+ * The interface is not very generic, as it has been written purely based on
+ * extraction of existing functions related to electric field handling.
+ * Also, the command-line parameters to specify the output files cannot be
+ * specified by the module, but are hard-coded in mdrun.
+ * This needs to be generalized when more modules are moved to use the
+ * interface.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+class IMDOutputProvider
+{
+ public:
+ /*! \brief
+ * Initializes file output from a simulation run.
+ *
+ * \param[in] fplog File pointer for log messages
+ * \param[in] nfile Number of files
+ * \param[in] fnm Array of filenames and properties
+ * \param[in] bAppendFiles Whether or not we should append to files
+ * \param[in] oenv The output environment for xvg files
+ */
+ virtual void initOutput(FILE *fplog, int nfile, const t_filenm fnm[],
+ bool bAppendFiles, const gmx_output_env_t *oenv) = 0;
+
+ //! Finalizes output from a simulation run.
+ virtual void finishOutput() = 0;
+
+ protected:
+ ~IMDOutputProvider() {}
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::IMdpOptionProvider.
+ *
+ * See \ref page_mdmodules for an overview of this and associated interfaces.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+#ifndef GMX_MDTYPES_IMDPOPTIONPROVIDER_H
+#define GMX_MDTYPES_IMDPOPTIONPROVIDER_H
+
+namespace gmx
+{
+
+class IKeyValueTreeTransformRules;
+class IOptionsContainerWithSections;
+class KeyValueTreeObjectBuilder;
+
+/*! \libinternal \brief
+ * Interface for handling mdp/tpr input to a mdrun module.
+ *
+ * This interface provides a mechanism for modules to contribute data that
+ * traditionally has been kept in t_inputrec. This is essentially parameters
+ * read from an mdp file and subsequently stored in a tpr file.
+ *
+ * The main method to implement is initMdpOptions(). This declares a set of
+ * options in nested sections. When declaring options, the module defines its
+ * own internal variables where the values will be stored (see \ref
+ * module_options for an overview). The section structure for the options also
+ * defines an internal data representation in the form of a generic key-value
+ * tree. This is used to store the values in the tpr file, and also for
+ * broadcasting, gmx dump, and gmx check.
+ *
+ * Implementation of initMdpTransform() is required for populating the options
+ * from the current flat mdp format. It specifies how the mdp parameters map
+ * into the options structure/internal key-value tree specified in
+ * initMdpOptions().
+ *
+ * See \ref page_mdmodules for more details on how mdp parsing and related
+ * functionality works with this interface.
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+class IMdpOptionProvider
+{
+ public:
+ /*! \brief
+ * Initializes a transform from mdp values to sectioned options.
+ *
+ * The transform is specified from a flat KeyValueTreeObject that
+ * contains each mdp value as a property, to a structured
+ * key-value tree that should match the options defined in
+ * initMdpOptions().
+ *
+ * This method may be removed once the flat mdp file is replaced with a
+ * more structure input file (that can be directly read into the
+ * internal key-value tree), and there is no longer any need for
+ * backward compatibility with old files.
+ */
+ virtual void initMdpTransform(IKeyValueTreeTransformRules *transform) = 0;
+ /*! \brief
+ * Initializes options that declare input (mdp) parameters for this
+ * module.
+ */
+ virtual void initMdpOptions(IOptionsContainerWithSections *options) = 0;
+ //! Prepares to write a flat key-value tree like an mdp file.
+ virtual void buildMdpOutput(KeyValueTreeObjectBuilder *builder) const = 0;
+
+ protected:
+ ~IMdpOptionProvider() {}
+};
+
+} // namespace gmx
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2010, The GROMACS development team.
- * Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "inputrec.h"
#include <cstdio>
+#include <cstdlib>
#include <cstring>
#include <algorithm>
+#include "gromacs/math/veccompare.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/pull-params.h"
#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/compare.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/keyvaluetree.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/textwriter.h"
#include "gromacs/utility/txtdump.h"
//! Macro to select a bool name
const int nstmin_berendsen_pcouple = 10;
const int nstmin_harmonic = 20;
+t_inputrec::t_inputrec()
+{
+ std::memset(this, 0, sizeof(*this));
+ snew(fepvals, 1);
+ snew(expandedvals, 1);
+ snew(simtempvals, 1);
+}
+
+t_inputrec::~t_inputrec()
+{
+ done_inputrec(this);
+}
+
static int nst_wanted(const t_inputrec *ir)
{
if (ir->nstlist > 0)
return (ir_vdw_is_zero_at_cutoff(ir) || ir->vdwtype == evdwUSER);
}
-void init_inputrec(t_inputrec *ir)
-{
- std::memset(ir, 0, sizeof(*ir));
- snew(ir->fepvals, 1);
- snew(ir->expandedvals, 1);
- snew(ir->simtempvals, 1);
-}
-
static void done_pull_group(t_pull_group *pgrp)
{
if (pgrp->nat > 0)
sfree(pull->coord);
}
-void done_inputrec(t_inputrec *ir)
+static void done_lambdas(t_lambda *fep)
{
- int m;
-
- for (m = 0; (m < DIM); m++)
+ if (fep->n_lambda > 0)
{
- if (ir->ex[m].a)
- {
- sfree(ir->ex[m].a);
- }
- if (ir->ex[m].phi)
- {
- sfree(ir->ex[m].phi);
- }
- if (ir->et[m].a)
- {
- sfree(ir->et[m].a);
- }
- if (ir->et[m].phi)
+ for (int i = 0; i < efptNR; i++)
{
- sfree(ir->et[m].phi);
+ sfree(fep->all_lambda[i]);
}
}
+ sfree(fep->all_lambda);
+}
+void done_inputrec(t_inputrec *ir)
+{
sfree(ir->opts.nrdf);
sfree(ir->opts.ref_t);
sfree(ir->opts.annealing);
sfree(ir->opts.SAsteps);
sfree(ir->opts.bOPT);
sfree(ir->opts.bTS);
+ sfree(ir->opts.egp_flags);
+ done_lambdas(ir->fepvals);
+ sfree(ir->fepvals);
+ sfree(ir->expandedvals);
+ sfree(ir->simtempvals);
if (ir->pull)
{
done_pull_params(ir->pull);
sfree(ir->pull);
}
+ delete ir->params;
}
static void pr_qm_opts(FILE *fp, int indent, const char *title, const t_grpopts *opts)
}
}
-static void pr_cosine(FILE *fp, int indent, const char *title, const t_cosines *cos,
- gmx_bool bMDPformat)
-{
- int j;
-
- if (bMDPformat)
- {
- fprintf(fp, "%s = %d\n", title, cos->n);
- }
- else
- {
- indent = pr_title(fp, indent, title);
- pr_indent(fp, indent);
- fprintf(fp, "n = %d\n", cos->n);
- if (cos->n > 0)
- {
- pr_indent(fp, indent+2);
- fprintf(fp, "a =");
- for (j = 0; (j < cos->n); j++)
- {
- fprintf(fp, " %e", cos->a[j]);
- }
- fprintf(fp, "\n");
- pr_indent(fp, indent+2);
- fprintf(fp, "phi =");
- for (j = 0; (j < cos->n); j++)
- {
- fprintf(fp, " %e", cos->phi[j]);
- }
- fprintf(fp, "\n");
- }
- }
-}
-
#define PS(t, s) pr_str(fp, indent, t, s)
#define PI(t, s) pr_int(fp, indent, t, s)
#define PSTEP(t, s) pr_int64(fp, indent, t, s)
pr_simtempvals(fp, indent, ir->simtempvals, ir->fepvals->n_lambda);
}
- /* ELECTRIC FIELDS */
- pr_cosine(fp, indent, "E-x", &(ir->ex[XX]), bMDPformat);
- pr_cosine(fp, indent, "E-xt", &(ir->et[XX]), bMDPformat);
- pr_cosine(fp, indent, "E-y", &(ir->ex[YY]), bMDPformat);
- pr_cosine(fp, indent, "E-yt", &(ir->et[YY]), bMDPformat);
- pr_cosine(fp, indent, "E-z", &(ir->ex[ZZ]), bMDPformat);
- pr_cosine(fp, indent, "E-zt", &(ir->et[ZZ]), bMDPformat);
-
/* ION/WATER SWAPPING FOR COMPUTATIONAL ELECTROPHYSIOLOGY */
PS("swapcoords", ESWAPTYPE(ir->eSwapCoords));
if (ir->eSwapCoords != eswapNO)
PR("userreal3", ir->userreal3);
PR("userreal4", ir->userreal4);
+ if (!bMDPformat)
+ {
+ gmx::TextWriter writer(fp);
+ writer.wrapperSettings().setIndent(indent);
+ gmx::dumpKeyValueTree(&writer, *ir->params);
+ }
+
pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat);
}
}
#undef PR
#undef PI
+static void cmp_grpopts(FILE *fp, const t_grpopts *opt1, const t_grpopts *opt2, real ftol, real abstol)
+{
+ int i, j;
+ char buf1[256], buf2[256];
+
+ cmp_int(fp, "inputrec->grpopts.ngtc", -1, opt1->ngtc, opt2->ngtc);
+ cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc);
+ cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz);
+ cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener);
+ for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++)
+ {
+ cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol);
+ cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol);
+ cmp_real(fp, "inputrec->grpopts.tau_t", i, opt1->tau_t[i], opt2->tau_t[i], ftol, abstol);
+ cmp_int(fp, "inputrec->grpopts.annealing", i, opt1->annealing[i], opt2->annealing[i]);
+ cmp_int(fp, "inputrec->grpopts.anneal_npoints", i,
+ opt1->anneal_npoints[i], opt2->anneal_npoints[i]);
+ if (opt1->anneal_npoints[i] == opt2->anneal_npoints[i])
+ {
+ sprintf(buf1, "inputrec->grpopts.anneal_time[%d]", i);
+ sprintf(buf2, "inputrec->grpopts.anneal_temp[%d]", i);
+ for (j = 0; j < opt1->anneal_npoints[i]; j++)
+ {
+ cmp_real(fp, buf1, j, opt1->anneal_time[i][j], opt2->anneal_time[i][j], ftol, abstol);
+ cmp_real(fp, buf2, j, opt1->anneal_temp[i][j], opt2->anneal_temp[i][j], ftol, abstol);
+ }
+ }
+ }
+ if (opt1->ngener == opt2->ngener)
+ {
+ for (i = 0; i < opt1->ngener; i++)
+ {
+ for (j = i; j < opt1->ngener; j++)
+ {
+ sprintf(buf1, "inputrec->grpopts.egp_flags[%d]", i);
+ cmp_int(fp, buf1, j,
+ opt1->egp_flags[opt1->ngener*i+j],
+ opt2->egp_flags[opt1->ngener*i+j]);
+ }
+ }
+ }
+ for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++)
+ {
+ cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol);
+ }
+ for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++)
+ {
+ cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]);
+ }
+}
+
+static void cmp_pull(FILE *fp)
+{
+ fprintf(fp, "WARNING: Both files use COM pulling, but comparing of the pull struct is not implemented (yet). The pull parameters could be the same or different.\n");
+}
+
+static void cmp_simtempvals(FILE *fp, const t_simtemp *simtemp1, const t_simtemp *simtemp2, int n_lambda, real ftol, real abstol)
+{
+ int i;
+ cmp_int(fp, "inputrec->simtempvals->eSimTempScale", -1, simtemp1->eSimTempScale, simtemp2->eSimTempScale);
+ cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high, simtemp2->simtemp_high, ftol, abstol);
+ cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low, simtemp2->simtemp_low, ftol, abstol);
+ for (i = 0; i < n_lambda; i++)
+ {
+ cmp_real(fp, "inputrec->simtempvals->temperatures", -1, simtemp1->temperatures[i], simtemp2->temperatures[i], ftol, abstol);
+ }
+}
+
+static void cmp_expandedvals(FILE *fp, const t_expanded *expand1, const t_expanded *expand2, int n_lambda, real ftol, real abstol)
+{
+ int i;
+
+ cmp_bool(fp, "inputrec->fepvals->bInit_weights", -1, expand1->bInit_weights, expand2->bInit_weights);
+ cmp_bool(fp, "inputrec->fepvals->bWLoneovert", -1, expand1->bWLoneovert, expand2->bWLoneovert);
+
+ for (i = 0; i < n_lambda; i++)
+ {
+ cmp_real(fp, "inputrec->expandedvals->init_lambda_weights", -1,
+ expand1->init_lambda_weights[i], expand2->init_lambda_weights[i], ftol, abstol);
+ }
+
+ cmp_int(fp, "inputrec->expandedvals->lambda-stats", -1, expand1->elamstats, expand2->elamstats);
+ cmp_int(fp, "inputrec->expandedvals->lambda-mc-move", -1, expand1->elmcmove, expand2->elmcmove);
+ cmp_int(fp, "inputrec->expandedvals->lmc-repeats", -1, expand1->lmc_repeats, expand2->lmc_repeats);
+ cmp_int(fp, "inputrec->expandedvals->lmc-gibbsdelta", -1, expand1->gibbsdeltalam, expand2->gibbsdeltalam);
+ cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart, expand2->lmc_forced_nstart);
+ cmp_int(fp, "inputrec->expandedvals->lambda-weights-equil", -1, expand1->elmceq, expand2->elmceq);
+ cmp_int(fp, "inputrec->expandedvals->,weight-equil-number-all-lambda", -1, expand1->equil_n_at_lam, expand2->equil_n_at_lam);
+ cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples, expand2->equil_samples);
+ cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps, expand2->equil_steps);
+ cmp_real(fp, "inputrec->expandedvals->weight-equil-wl-delta", -1, expand1->equil_wl_delta, expand2->equil_wl_delta, ftol, abstol);
+ cmp_real(fp, "inputrec->expandedvals->weight-equil-count-ratio", -1, expand1->equil_ratio, expand2->equil_ratio, ftol, abstol);
+ cmp_bool(fp, "inputrec->expandedvals->symmetrized-transition-matrix", -1, expand1->bSymmetrizedTMatrix, expand2->bSymmetrizedTMatrix);
+ cmp_int(fp, "inputrec->expandedvals->nstTij", -1, expand1->nstTij, expand2->nstTij);
+ cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin, expand2->minvarmin); /*default is reasonable */
+ cmp_int(fp, "inputrec->expandedvals->weight-c-range", -1, expand1->c_range, expand2->c_range); /* default is just C=0 */
+ cmp_real(fp, "inputrec->expandedvals->wl-scale", -1, expand1->wl_scale, expand2->wl_scale, ftol, abstol);
+ cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta, expand2->init_wl_delta, ftol, abstol);
+ cmp_real(fp, "inputrec->expandedvals->wl-ratio", -1, expand1->wl_ratio, expand2->wl_ratio, ftol, abstol);
+ cmp_int(fp, "inputrec->expandedvals->nstexpanded", -1, expand1->nstexpanded, expand2->nstexpanded);
+ cmp_int(fp, "inputrec->expandedvals->lmc-seed", -1, expand1->lmc_seed, expand2->lmc_seed);
+ cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp, ftol, abstol);
+}
+
+static void cmp_fepvals(FILE *fp, const t_lambda *fep1, const t_lambda *fep2, real ftol, real abstol)
+{
+ int i, j;
+ cmp_int(fp, "inputrec->nstdhdl", -1, fep1->nstdhdl, fep2->nstdhdl);
+ cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state, fep2->init_fep_state, ftol, abstol);
+ cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda, ftol, abstol);
+ cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda);
+ for (i = 0; i < efptNR; i++)
+ {
+ for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++)
+ {
+ cmp_double(fp, "inputrec->fepvals->all_lambda", -1, fep1->all_lambda[i][j], fep2->all_lambda[i][j], ftol, abstol);
+ }
+ }
+ cmp_int(fp, "inputrec->fepvals->lambda_neighbors", 1, fep1->lambda_neighbors,
+ fep2->lambda_neighbors);
+ cmp_real(fp, "inputrec->fepvals->sc_alpha", -1, fep1->sc_alpha, fep2->sc_alpha, ftol, abstol);
+ cmp_int(fp, "inputrec->fepvals->sc_power", -1, fep1->sc_power, fep2->sc_power);
+ cmp_real(fp, "inputrec->fepvals->sc_r_power", -1, fep1->sc_r_power, fep2->sc_r_power, ftol, abstol);
+ cmp_real(fp, "inputrec->fepvals->sc_sigma", -1, fep1->sc_sigma, fep2->sc_sigma, ftol, abstol);
+ cmp_int(fp, "inputrec->fepvals->edHdLPrintEnergy", -1, fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy);
+ cmp_bool(fp, "inputrec->fepvals->bScCoul", -1, fep1->bScCoul, fep1->bScCoul);
+ cmp_int(fp, "inputrec->separate_dhdl_file", -1, fep1->separate_dhdl_file, fep2->separate_dhdl_file);
+ cmp_int(fp, "inputrec->dhdl_derivatives", -1, fep1->dhdl_derivatives, fep2->dhdl_derivatives);
+ cmp_int(fp, "inputrec->dh_hist_size", -1, fep1->dh_hist_size, fep2->dh_hist_size);
+ cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing, ftol, abstol);
+}
+
+void cmp_inputrec(FILE *fp, const t_inputrec *ir1, const t_inputrec *ir2, real ftol, real abstol)
+{
+ fprintf(fp, "comparing inputrec\n");
+
+ /* gcc 2.96 doesnt like these defines at all, but issues a huge list
+ * of warnings. Maybe it will change in future versions, but for the
+ * moment I've spelled them out instead. /EL 000820
+ * #define CIB(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
+ * #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
+ * #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol)
+ */
+ cmp_int(fp, "inputrec->eI", -1, ir1->eI, ir2->eI);
+ cmp_int64(fp, "inputrec->nsteps", ir1->nsteps, ir2->nsteps);
+ cmp_int64(fp, "inputrec->init_step", ir1->init_step, ir2->init_step);
+ cmp_int(fp, "inputrec->simulation_part", -1, ir1->simulation_part, ir2->simulation_part);
+ cmp_int(fp, "inputrec->ePBC", -1, ir1->ePBC, ir2->ePBC);
+ cmp_int(fp, "inputrec->bPeriodicMols", -1, ir1->bPeriodicMols, ir2->bPeriodicMols);
+ cmp_int(fp, "inputrec->cutoff_scheme", -1, ir1->cutoff_scheme, ir2->cutoff_scheme);
+ cmp_int(fp, "inputrec->ns_type", -1, ir1->ns_type, ir2->ns_type);
+ cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist);
+ cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm);
+ cmp_int(fp, "inputrec->comm_mode", -1, ir1->comm_mode, ir2->comm_mode);
+ cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog);
+ cmp_int(fp, "inputrec->nstxout", -1, ir1->nstxout, ir2->nstxout);
+ cmp_int(fp, "inputrec->nstvout", -1, ir1->nstvout, ir2->nstvout);
+ cmp_int(fp, "inputrec->nstfout", -1, ir1->nstfout, ir2->nstfout);
+ cmp_int(fp, "inputrec->nstcalcenergy", -1, ir1->nstcalcenergy, ir2->nstcalcenergy);
+ cmp_int(fp, "inputrec->nstenergy", -1, ir1->nstenergy, ir2->nstenergy);
+ cmp_int(fp, "inputrec->nstxout_compressed", -1, ir1->nstxout_compressed, ir2->nstxout_compressed);
+ cmp_double(fp, "inputrec->init_t", -1, ir1->init_t, ir2->init_t, ftol, abstol);
+ cmp_double(fp, "inputrec->delta_t", -1, ir1->delta_t, ir2->delta_t, ftol, abstol);
+ cmp_real(fp, "inputrec->x_compression_precision", -1, ir1->x_compression_precision, ir2->x_compression_precision, ftol, abstol);
+ cmp_real(fp, "inputrec->fourierspacing", -1, ir1->fourier_spacing, ir2->fourier_spacing, ftol, abstol);
+ cmp_int(fp, "inputrec->nkx", -1, ir1->nkx, ir2->nkx);
+ cmp_int(fp, "inputrec->nky", -1, ir1->nky, ir2->nky);
+ cmp_int(fp, "inputrec->nkz", -1, ir1->nkz, ir2->nkz);
+ cmp_int(fp, "inputrec->pme_order", -1, ir1->pme_order, ir2->pme_order);
+ cmp_real(fp, "inputrec->ewald_rtol", -1, ir1->ewald_rtol, ir2->ewald_rtol, ftol, abstol);
+ cmp_int(fp, "inputrec->ewald_geometry", -1, ir1->ewald_geometry, ir2->ewald_geometry);
+ cmp_real(fp, "inputrec->epsilon_surface", -1, ir1->epsilon_surface, ir2->epsilon_surface, ftol, abstol);
+ cmp_int(fp, "inputrec->bContinuation", -1, ir1->bContinuation, ir2->bContinuation);
+ cmp_int(fp, "inputrec->bShakeSOR", -1, ir1->bShakeSOR, ir2->bShakeSOR);
+ cmp_int(fp, "inputrec->etc", -1, ir1->etc, ir2->etc);
+ cmp_int(fp, "inputrec->bPrintNHChains", -1, ir1->bPrintNHChains, ir2->bPrintNHChains);
+ cmp_int(fp, "inputrec->epc", -1, ir1->epc, ir2->epc);
+ cmp_int(fp, "inputrec->epct", -1, ir1->epct, ir2->epct);
+ cmp_real(fp, "inputrec->tau_p", -1, ir1->tau_p, ir2->tau_p, ftol, abstol);
+ cmp_rvec(fp, "inputrec->ref_p(x)", -1, ir1->ref_p[XX], ir2->ref_p[XX], ftol, abstol);
+ cmp_rvec(fp, "inputrec->ref_p(y)", -1, ir1->ref_p[YY], ir2->ref_p[YY], ftol, abstol);
+ cmp_rvec(fp, "inputrec->ref_p(z)", -1, ir1->ref_p[ZZ], ir2->ref_p[ZZ], ftol, abstol);
+ cmp_rvec(fp, "inputrec->compress(x)", -1, ir1->compress[XX], ir2->compress[XX], ftol, abstol);
+ cmp_rvec(fp, "inputrec->compress(y)", -1, ir1->compress[YY], ir2->compress[YY], ftol, abstol);
+ cmp_rvec(fp, "inputrec->compress(z)", -1, ir1->compress[ZZ], ir2->compress[ZZ], ftol, abstol);
+ cmp_int(fp, "refcoord_scaling", -1, ir1->refcoord_scaling, ir2->refcoord_scaling);
+ cmp_rvec(fp, "inputrec->posres_com", -1, ir1->posres_com, ir2->posres_com, ftol, abstol);
+ cmp_rvec(fp, "inputrec->posres_comB", -1, ir1->posres_comB, ir2->posres_comB, ftol, abstol);
+ cmp_real(fp, "inputrec->verletbuf_tol", -1, ir1->verletbuf_tol, ir2->verletbuf_tol, ftol, abstol);
+ cmp_real(fp, "inputrec->rlist", -1, ir1->rlist, ir2->rlist, ftol, abstol);
+ cmp_real(fp, "inputrec->rtpi", -1, ir1->rtpi, ir2->rtpi, ftol, abstol);
+ cmp_int(fp, "inputrec->coulombtype", -1, ir1->coulombtype, ir2->coulombtype);
+ cmp_int(fp, "inputrec->coulomb_modifier", -1, ir1->coulomb_modifier, ir2->coulomb_modifier);
+ cmp_real(fp, "inputrec->rcoulomb_switch", -1, ir1->rcoulomb_switch, ir2->rcoulomb_switch, ftol, abstol);
+ cmp_real(fp, "inputrec->rcoulomb", -1, ir1->rcoulomb, ir2->rcoulomb, ftol, abstol);
+ cmp_int(fp, "inputrec->vdwtype", -1, ir1->vdwtype, ir2->vdwtype);
+ cmp_int(fp, "inputrec->vdw_modifier", -1, ir1->vdw_modifier, ir2->vdw_modifier); cmp_real(fp, "inputrec->rvdw_switch", -1, ir1->rvdw_switch, ir2->rvdw_switch, ftol, abstol);
+ cmp_real(fp, "inputrec->rvdw", -1, ir1->rvdw, ir2->rvdw, ftol, abstol);
+ cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol);
+ cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol);
+ cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol);
+ cmp_int(fp, "inputrec->implicit_solvent", -1, ir1->implicit_solvent, ir2->implicit_solvent);
+ cmp_int(fp, "inputrec->gb_algorithm", -1, ir1->gb_algorithm, ir2->gb_algorithm);
+ cmp_int(fp, "inputrec->nstgbradii", -1, ir1->nstgbradii, ir2->nstgbradii);
+ cmp_real(fp, "inputrec->rgbradii", -1, ir1->rgbradii, ir2->rgbradii, ftol, abstol);
+ cmp_real(fp, "inputrec->gb_saltconc", -1, ir1->gb_saltconc, ir2->gb_saltconc, ftol, abstol);
+ cmp_real(fp, "inputrec->gb_epsilon_solvent", -1, ir1->gb_epsilon_solvent, ir2->gb_epsilon_solvent, ftol, abstol);
+ cmp_real(fp, "inputrec->gb_obc_alpha", -1, ir1->gb_obc_alpha, ir2->gb_obc_alpha, ftol, abstol);
+ cmp_real(fp, "inputrec->gb_obc_beta", -1, ir1->gb_obc_beta, ir2->gb_obc_beta, ftol, abstol);
+ cmp_real(fp, "inputrec->gb_obc_gamma", -1, ir1->gb_obc_gamma, ir2->gb_obc_gamma, ftol, abstol);
+ cmp_real(fp, "inputrec->gb_dielectric_offset", -1, ir1->gb_dielectric_offset, ir2->gb_dielectric_offset, ftol, abstol);
+ cmp_int(fp, "inputrec->sa_algorithm", -1, ir1->sa_algorithm, ir2->sa_algorithm);
+ cmp_real(fp, "inputrec->sa_surface_tension", -1, ir1->sa_surface_tension, ir2->sa_surface_tension, ftol, abstol);
+
+ cmp_int(fp, "inputrec->eDispCorr", -1, ir1->eDispCorr, ir2->eDispCorr);
+ cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol);
+ cmp_int(fp, "inputrec->efep", -1, ir1->efep, ir2->efep);
+ cmp_fepvals(fp, ir1->fepvals, ir2->fepvals, ftol, abstol);
+ cmp_int(fp, "inputrec->bSimTemp", -1, ir1->bSimTemp, ir2->bSimTemp);
+ if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp))
+ {
+ cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
+ }
+ cmp_int(fp, "inputrec->bExpanded", -1, ir1->bExpanded, ir2->bExpanded);
+ if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded))
+ {
+ cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
+ }
+ cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall);
+ cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type);
+ cmp_int(fp, "inputrec->wall_atomtype[0]", -1, ir1->wall_atomtype[0], ir2->wall_atomtype[0]);
+ cmp_int(fp, "inputrec->wall_atomtype[1]", -1, ir1->wall_atomtype[1], ir2->wall_atomtype[1]);
+ cmp_real(fp, "inputrec->wall_density[0]", -1, ir1->wall_density[0], ir2->wall_density[0], ftol, abstol);
+ cmp_real(fp, "inputrec->wall_density[1]", -1, ir1->wall_density[1], ir2->wall_density[1], ftol, abstol);
+ cmp_real(fp, "inputrec->wall_ewald_zfac", -1, ir1->wall_ewald_zfac, ir2->wall_ewald_zfac, ftol, abstol);
+
+ cmp_bool(fp, "inputrec->bPull", -1, ir1->bPull, ir2->bPull);
+ if (ir1->bPull && ir2->bPull)
+ {
+ cmp_pull(fp);
+ }
+
+ cmp_int(fp, "inputrec->eDisre", -1, ir1->eDisre, ir2->eDisre);
+ cmp_real(fp, "inputrec->dr_fc", -1, ir1->dr_fc, ir2->dr_fc, ftol, abstol);
+ cmp_int(fp, "inputrec->eDisreWeighting", -1, ir1->eDisreWeighting, ir2->eDisreWeighting);
+ cmp_int(fp, "inputrec->bDisreMixed", -1, ir1->bDisreMixed, ir2->bDisreMixed);
+ cmp_int(fp, "inputrec->nstdisreout", -1, ir1->nstdisreout, ir2->nstdisreout);
+ cmp_real(fp, "inputrec->dr_tau", -1, ir1->dr_tau, ir2->dr_tau, ftol, abstol);
+ cmp_real(fp, "inputrec->orires_fc", -1, ir1->orires_fc, ir2->orires_fc, ftol, abstol);
+ cmp_real(fp, "inputrec->orires_tau", -1, ir1->orires_tau, ir2->orires_tau, ftol, abstol);
+ cmp_int(fp, "inputrec->nstorireout", -1, ir1->nstorireout, ir2->nstorireout);
+ cmp_real(fp, "inputrec->em_stepsize", -1, ir1->em_stepsize, ir2->em_stepsize, ftol, abstol);
+ cmp_real(fp, "inputrec->em_tol", -1, ir1->em_tol, ir2->em_tol, ftol, abstol);
+ cmp_int(fp, "inputrec->niter", -1, ir1->niter, ir2->niter);
+ cmp_real(fp, "inputrec->fc_stepsize", -1, ir1->fc_stepsize, ir2->fc_stepsize, ftol, abstol);
+ cmp_int(fp, "inputrec->nstcgsteep", -1, ir1->nstcgsteep, ir2->nstcgsteep);
+ cmp_int(fp, "inputrec->nbfgscorr", 0, ir1->nbfgscorr, ir2->nbfgscorr);
+ cmp_int(fp, "inputrec->eConstrAlg", -1, ir1->eConstrAlg, ir2->eConstrAlg);
+ cmp_int(fp, "inputrec->nProjOrder", -1, ir1->nProjOrder, ir2->nProjOrder);
+ cmp_real(fp, "inputrec->LincsWarnAngle", -1, ir1->LincsWarnAngle, ir2->LincsWarnAngle, ftol, abstol);
+ cmp_int(fp, "inputrec->nLincsIter", -1, ir1->nLincsIter, ir2->nLincsIter);
+ cmp_real(fp, "inputrec->bd_fric", -1, ir1->bd_fric, ir2->bd_fric, ftol, abstol);
+ cmp_int64(fp, "inputrec->ld_seed", ir1->ld_seed, ir2->ld_seed);
+ cmp_real(fp, "inputrec->cos_accel", -1, ir1->cos_accel, ir2->cos_accel, ftol, abstol);
+ cmp_rvec(fp, "inputrec->deform(a)", -1, ir1->deform[XX], ir2->deform[XX], ftol, abstol);
+ cmp_rvec(fp, "inputrec->deform(b)", -1, ir1->deform[YY], ir2->deform[YY], ftol, abstol);
+ cmp_rvec(fp, "inputrec->deform(c)", -1, ir1->deform[ZZ], ir2->deform[ZZ], ftol, abstol);
+
+
+ cmp_int(fp, "inputrec->userint1", -1, ir1->userint1, ir2->userint1);
+ cmp_int(fp, "inputrec->userint2", -1, ir1->userint2, ir2->userint2);
+ cmp_int(fp, "inputrec->userint3", -1, ir1->userint3, ir2->userint3);
+ cmp_int(fp, "inputrec->userint4", -1, ir1->userint4, ir2->userint4);
+ cmp_real(fp, "inputrec->userreal1", -1, ir1->userreal1, ir2->userreal1, ftol, abstol);
+ cmp_real(fp, "inputrec->userreal2", -1, ir1->userreal2, ir2->userreal2, ftol, abstol);
+ cmp_real(fp, "inputrec->userreal3", -1, ir1->userreal3, ir2->userreal3, ftol, abstol);
+ cmp_real(fp, "inputrec->userreal4", -1, ir1->userreal4, ir2->userreal4, ftol, abstol);
+ cmp_grpopts(fp, &(ir1->opts), &(ir2->opts), ftol, abstol);
+ gmx::TextWriter writer(fp);
+ gmx::compareKeyValueTrees(&writer, *ir1->params, *ir2->params, ftol, abstol);
+}
+
+void comp_pull_AB(FILE *fp, pull_params_t *pull, real ftol, real abstol)
+{
+ int i;
+
+ for (i = 0; i < pull->ncoord; i++)
+ {
+ fprintf(fp, "comparing pull coord %d\n", i);
+ cmp_real(fp, "pull-coord->k", -1, pull->coord[i].k, pull->coord[i].kB, ftol, abstol);
+ }
+}
+
gmx_bool inputrecDeform(const t_inputrec *ir)
{
return (ir->deform[XX][XX] != 0 || ir->deform[YY][YY] != 0 || ir->deform[ZZ][ZZ] != 0 ||
(ir->ewald_geometry == eewg3DC || ir->epsilon_surface != 0));
}
-gmx_bool inputrecElecField(const t_inputrec *ir)
-{
- return (ir->ex[XX].n > 0 || ir->ex[YY].n > 0 || ir->ex[ZZ].n > 0);
-}
-
gmx_bool inputrecExclForces(const t_inputrec *ir)
{
return (EEL_FULL(ir->coulombtype) || (EEL_RF(ir->coulombtype)) ||
return ( ( (ir->eI == eiVV) || (ir->eI == eiVVAK) ) &&
(ir->epc == epcMTTK) && (ir->etc != etcNOSEHOOVER) );
}
+
+bool integratorHasConservedEnergyQuantity(const t_inputrec *ir)
+{
+ if (!EI_MD(ir->eI))
+ {
+ // Energy minimization or stochastic integrator: no conservation
+ return false;
+ }
+ else if (ir->etc == etcNO && ir->epc == epcNO)
+ {
+ // The total energy is conserved, no additional conserved quanitity
+ return false;
+ }
+ else
+ {
+ // Shear stress with Parrinello-Rahman is not supported (tedious)
+ bool shearWithPR =
+ ((ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK) &&
+ (ir->ref_p[YY][XX] != 0 || ir->ref_p[ZZ][XX] != 0 || ir->ref_p[ZZ][YY] != 0));
+
+ return !ETC_ANDERSEN(ir->etc) && !shearWithPR;
+ }
+}
+
+int inputrec2nboundeddim(const t_inputrec *ir)
+{
+ if (ir->nwall == 2 && ir->ePBC == epbcXY)
+ {
+ return 3;
+ }
+ else
+ {
+ return ePBC2npbcdim(ir->ePBC);
+ }
+}
+
+int ndof_com(const t_inputrec *ir)
+{
+ int n = 0;
+
+ switch (ir->ePBC)
+ {
+ case epbcXYZ:
+ case epbcNONE:
+ n = 3;
+ break;
+ case epbcXY:
+ n = (ir->nwall == 0 ? 3 : 2);
+ break;
+ case epbcSCREW:
+ n = 1;
+ break;
+ default:
+ gmx_incons("Unknown pbc in calc_nrdf");
+ }
+
+ return n;
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \brief
- * Declares inputrec data structure and utilities.
- *
- * \inpublicapi
- * \ingroup module_mdtypes
- */
#ifndef GMX_MDTYPES_INPUTREC_H
#define GMX_MDTYPES_INPUTREC_H
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-typedef struct {
- //! Number of terms
- int n;
- //! Coeffients (V / nm)
- real *a;
- //! Phase angles
- real *phi;
-} t_cosines;
-
-typedef struct {
- real E0; /* Field strength (V/nm) */
- real omega; /* Frequency (1/ps) */
- real t0; /* Centre of the Gaussian pulse (ps) */
- real sigma; /* Width of the Gaussian pulse (FWHM) (ps) */
-} t_efield;
-
#define EGP_EXCL (1<<0)
#define EGP_TABLE (1<<1)
+struct pull_params_t;
+
+namespace gmx
+{
+class KeyValueTreeObject;
+}
+
typedef struct t_grpopts {
int ngtc; /* # T-Coupl groups */
int nhchainlength; /* # of nose-hoover chains per group */
* swapcoords.cpp */
} t_swapcoords;
-typedef struct t_inputrec {
+struct t_inputrec
+{
+ t_inputrec();
+ explicit t_inputrec(const t_inputrec &) = delete;
+ t_inputrec &operator=(const t_inputrec &) = delete;
+ ~t_inputrec();
+
int eI; /* Integration method */
gmx_int64_t nsteps; /* number of steps to be taken */
int simulation_part; /* Used in checkpointing to separate chunks */
struct pull_t *pull_work; /* The COM pull force calculation data structure; TODO this pointer should live somewhere else */
/* Enforced rotation data */
- gmx_bool bRot; /* Calculate enforced rotation potential(s)? */
- t_rot *rot; /* The data for enforced rotation potentials */
-
- int eSwapCoords; /* Do ion/water position exchanges (CompEL)? */
- t_swapcoords *swap;
-
- gmx_bool bIMD; /* Allow interactive MD sessions for this .tpr? */
- t_IMD *imd; /* Interactive molecular dynamics */
-
- real cos_accel; /* Acceleration for viscosity calculation */
- tensor deform; /* Triclinic deformation velocities (nm/ps) */
- int userint1; /* User determined parameters */
- int userint2;
- int userint3;
- int userint4;
- real userreal1;
- real userreal2;
- real userreal3;
- real userreal4;
- t_grpopts opts; /* Group options */
- t_cosines ex[DIM]; /* Electric field stuff (spatial part) */
- t_cosines et[DIM]; /* Electric field stuff (time part) */
- gmx_bool bQMMM; /* QM/MM calculation */
- int QMconstraints; /* constraints on QM bonds */
- int QMMMscheme; /* Scheme: ONIOM or normal */
- real scalefactor; /* factor for scaling the MM charges in QM calc.*/
+ gmx_bool bRot; /* Calculate enforced rotation potential(s)? */
+ t_rot *rot; /* The data for enforced rotation potentials */
+
+ int eSwapCoords; /* Do ion/water position exchanges (CompEL)? */
+ t_swapcoords *swap;
+
+ gmx_bool bIMD; /* Allow interactive MD sessions for this .tpr? */
+ t_IMD *imd; /* Interactive molecular dynamics */
+
+ real cos_accel; /* Acceleration for viscosity calculation */
+ tensor deform; /* Triclinic deformation velocities (nm/ps) */
+ int userint1; /* User determined parameters */
+ int userint2;
+ int userint3;
+ int userint4;
+ real userreal1;
+ real userreal2;
+ real userreal3;
+ real userreal4;
+ t_grpopts opts; /* Group options */
+ gmx_bool bQMMM; /* QM/MM calculation */
+ int QMconstraints; /* constraints on QM bonds */
+ int QMMMscheme; /* Scheme: ONIOM or normal */
+ real scalefactor; /* factor for scaling the MM charges in QM calc.*/
/* Fields for removed features go here (better caching) */
- gmx_bool bAdress; // Whether AdResS is enabled - always false if a valid .tpr was read
- gmx_bool useTwinRange; // Whether twin-range scheme is active - always false if a valid .tpr was read
-} t_inputrec;
+ gmx_bool bAdress; // Whether AdResS is enabled - always false if a valid .tpr was read
+ gmx_bool useTwinRange; // Whether twin-range scheme is active - always false if a valid .tpr was read
+
+ gmx::KeyValueTreeObject *params;
+};
int ir_optimal_nstcalcenergy(const t_inputrec *ir);
*/
gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec *ir);
-/*! \brief Initiate input record structure
- *
- * Initialiazes all the arrays and pointers to NULL.
- *
- * \param[in] ir Inputrec must be pre-allocated
- */
-void init_inputrec(t_inputrec *ir);
-
/*! \brief Free memory from input record.
*
* All arrays and pointers will be freed.
void pr_inputrec(FILE *fp, int indent, const char *title, const t_inputrec *ir,
gmx_bool bMDPformat);
+void cmp_inputrec(FILE *fp, const t_inputrec *ir1, const t_inputrec *ir2, real ftol, real abstol);
+
+void comp_pull_AB(FILE *fp, pull_params_t *pull, real ftol, real abstol);
+
+
gmx_bool inputrecDeform(const t_inputrec *ir);
gmx_bool inputrecDynamicBox(const t_inputrec *ir);
gmx_bool inputrecTwinRange(const t_inputrec *ir);
-gmx_bool inputrecElecField(const t_inputrec *ir);
-
gmx_bool inputrecExclForces(const t_inputrec *ir);
gmx_bool inputrecNptTrotter(const t_inputrec *ir);
gmx_bool inputrecNphTrotter(const t_inputrec *ir);
+/* Returns true for MD integator with T and/or P-coupling that supports
+ * calculating the conserved energy quantity.
+ */
+bool integratorHasConservedEnergyQuantity(const t_inputrec *ir);
+
+/*! \brief Return the number of bounded dimensions
+ *
+ * \param[in] ir The input record with MD parameters
+ * \return the number of dimensions in which
+ * the coordinates of the particles are bounded, starting at X.
+ */
+int inputrec2nboundeddim(const t_inputrec *ir);
+
+/*! \brief Returns the number of degrees of freedom in center of mass motion
+ *
+ * \param[in] ir the inputrec structure
+ * \return the number of degrees of freedom of the center of mass
+ */
+int ndof_com(const t_inputrec *ir);
+
#endif /* GMX_MDTYPES_INPUTREC_H */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* potential = r^-p + c2/3*rsw^3 + c3/4*rsw^4 + cpot
* With a constant potential shift c2 and c3 are both 0.
*/
-typedef struct {
+struct shift_consts_t
+{
real c2;
real c3;
real cpot;
-} shift_consts_t;
+};
/* Used with potential switching:
* rsw = max(r - r_switch, 0)
* force = force*dsw - potential*sw
* potential *= sw
*/
-typedef struct {
+struct switch_consts_t
+{
real c3;
real c4;
real c5;
-} switch_consts_t;
+};
-typedef struct {
+struct interaction_const_t
+{
int cutoff_scheme;
/* VdW */
- int vdwtype;
- int vdw_modifier;
- real rvdw;
- real rvdw_switch;
- shift_consts_t dispersion_shift;
- shift_consts_t repulsion_shift;
- switch_consts_t vdw_switch;
+ int vdwtype;
+ int vdw_modifier;
+ real rvdw;
+ real rvdw_switch;
+ struct shift_consts_t dispersion_shift;
+ struct shift_consts_t repulsion_shift;
+ struct switch_consts_t vdw_switch;
/* TODO: remove this variable, used for not modyfing the group kernels,
* it is equal to -dispersion_shift->cpot
*/
/* Coulomb */
real rcoulomb;
- /* Cut-off */
- real rlist;
-
/* PME/Ewald */
real ewaldcoeff_q;
real ewaldcoeff_lj;
quadruplets are: F[i], F[i+1]-F[i], V[i], 0, this is used with
single precision x86 SIMD for aligned loads */
real *tabq_vdw_FDV0;
-
-} interaction_const_t;
+};
#ifdef __cplusplus
}
"normal", "ONIOM", nullptr
};
-const char *eMultentOpt_names[eMultentOptNR+1] = {
- "multiple_entries", "no", "use_last", nullptr
-};
-
const char *gmx_nblist_geometry_names[GMX_NBLIST_GEOMETRY_NR+1] = {
"Particle-Particle", "Water3-Particle", "Water3-Water3", "Water4-Particle", "Water4-Water4", "CG-CG", nullptr
};
//! Macro to pick QMMMM scheme name
#define EQMMMSCHEME(e) enum_name(e, eQMMMschemeNR, eQMMMscheme_names)
-//! Internal stuff for multiple value options in mdp files
-enum {
- eMultentOptName, eMultentOptNo, eMultentOptLast, eMultentOptNR
-};
-//! Multiple value option names
-extern const char *eMultentOpt_names[eMultentOptNR+1];
-
/*! \brief Neighborlist geometry type.
*
* Kernels will compute interactions between two particles,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_MDTYPES_MDATOM_H
#define GMX_MDTYPES_MDATOM_H
+#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
real *massB;
//! Atomic mass in present state
real *massT;
- //! Inverse atomic mass
+ //! Inverse atomic mass per atom, 0 for vsites and shells
real *invmass;
+ //! Inverse atomic mass per atom and dimension, 0 for vsites, shells and frozen dimensions
+ rvec *invMassPerDim;
//! Atomic charge in A state
real *chargeA;
//! Atomic charge in B state
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ *
+ * \brief
+ * This file contains the definition of a container for history data
+ * for simulation observables.
+ *
+ * The container is used for storing the simulation state data that needs
+ * to be written to / read from checkpoint file. This struct should only
+ * contain pure observable data. Microstate data should be in t_state.
+ * The state of the mdrun machinery is also stored elsewhere.
+ *
+ * \author Berk Hess
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+
+#ifndef GMX_MDLIB_OBSERVABLESHISTORY_H
+#define GMX_MDLIB_OBSERVABLESHISTORY_H
+
+#include <memory>
+
+class energyhistory_t;
+struct edsamhistory_t;
+struct swaphistory_t;
+
+/*! \libinternal \brief Observables history, for writing/reading to/from checkpoint file
+ */
+struct ObservablesHistory
+{
+ //! History for energy observables, used for output only
+ std::unique_ptr<energyhistory_t> energyHistory;
+
+ //! Essential dynamics and flooding history
+ std::unique_ptr<edsamhistory_t> edsamHistory;
+
+ //! Ion/water position swapping history
+ std::unique_ptr<swaphistory_t> swapHistory;
+};
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include "gromacs/math/vec.h"
+#include "gromacs/math/veccompare.h"
#include "gromacs/mdtypes/df_history.h"
-#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/swaphistory.h"
+#include "gromacs/pbcutil/boxutilities.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/compare.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
/* The source code in this file should be thread-safe.
Please keep it that way. */
-static void zero_history(history_t *hist)
+history_t::history_t() : disre_initf(0),
+ ndisrepairs(0),
+ disre_rm3tav(nullptr),
+ orire_initf(0),
+ norire_Dtav(0),
+ orire_Dtav(nullptr)
{
- hist->disre_initf = 0;
- hist->ndisrepairs = 0;
- hist->disre_rm3tav = NULL;
- hist->orire_initf = 0;
- hist->norire_Dtav = 0;
- hist->orire_Dtav = NULL;
-}
-
-static void zero_ekinstate(ekinstate_t *eks)
-{
- eks->ekin_n = 0;
- eks->ekinh = NULL;
- eks->ekinf = NULL;
- eks->ekinh_old = NULL;
- eks->ekinscalef_nhc = NULL;
- eks->ekinscaleh_nhc = NULL;
- eks->vscale_nhc = NULL;
- eks->dekindl = 0;
- eks->mvcos = 0;
-}
+};
-static void init_swapstate(swapstate_t *swapstate)
+ekinstate_t::ekinstate_t() : bUpToDate(FALSE),
+ ekin_n(0),
+ ekinh(nullptr),
+ ekinf(nullptr),
+ ekinh_old(nullptr),
+ ekin_total(),
+ ekinscalef_nhc(),
+ ekinscaleh_nhc(),
+ vscale_nhc(),
+ dekindl(0),
+ mvcos(0)
{
- /* Ion/water position swapping */
- swapstate->eSwapCoords = 0;
- swapstate->nIonTypes = 0;
- swapstate->nAverage = 0;
- swapstate->fluxleak = 0;
- swapstate->fluxleak_p = NULL;
- swapstate->bFromCpt = 0;
- swapstate->nat[eChan0] = 0;
- swapstate->nat[eChan1] = 0;
- swapstate->xc_old_whole[eChan0] = NULL;
- swapstate->xc_old_whole[eChan1] = NULL;
- swapstate->xc_old_whole_p[eChan0] = NULL;
- swapstate->xc_old_whole_p[eChan1] = NULL;
- swapstate->ionType = NULL;
-}
+ clear_mat(ekin_total);
+};
void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength)
{
- int i, j;
-
state->ngtc = ngtc;
state->nnhpres = nnhpres;
state->nhchainlength = nhchainlength;
- if (state->ngtc > 0)
+ state->nosehoover_xi.resize(state->nhchainlength*state->ngtc, 0);
+ state->nosehoover_vxi.resize(state->nhchainlength*state->ngtc, 0);
+ state->therm_integral.resize(state->ngtc, 0);
+ state->baros_integral = 0.0;
+ state->nhpres_xi.resize(state->nhchainlength*nnhpres, 0);
+ state->nhpres_vxi.resize(state->nhchainlength*nnhpres, 0);
+}
+
+
+/* Checkpoint code relies on this function having no effect if
+ state->natoms is > 0 and passed as natoms. */
+void state_change_natoms(t_state *state, int natoms)
+{
+ state->natoms = natoms;
+ if (state->natoms > 0)
{
- snew(state->nosehoover_xi, state->nhchainlength*state->ngtc);
- snew(state->nosehoover_vxi, state->nhchainlength*state->ngtc);
- snew(state->therm_integral, state->ngtc);
- for (i = 0; i < state->ngtc; i++)
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ if (state->flags & (1 << estX))
{
- for (j = 0; j < state->nhchainlength; j++)
- {
- state->nosehoover_xi[i*state->nhchainlength + j] = 0.0;
- state->nosehoover_vxi[i*state->nhchainlength + j] = 0.0;
- }
+ state->x.resize(state->natoms + 1);
}
- for (i = 0; i < state->ngtc; i++)
+ if (state->flags & (1 << estV))
{
- state->therm_integral[i] = 0.0;
+ state->v.resize(state->natoms + 1);
}
- }
- else
- {
- state->nosehoover_xi = NULL;
- state->nosehoover_vxi = NULL;
- state->therm_integral = NULL;
- }
-
- if (state->nnhpres > 0)
- {
- snew(state->nhpres_xi, state->nhchainlength*nnhpres);
- snew(state->nhpres_vxi, state->nhchainlength*nnhpres);
- for (i = 0; i < nnhpres; i++)
+ if (state->flags & (1 << estCGP))
{
- for (j = 0; j < state->nhchainlength; j++)
- {
- state->nhpres_xi[i*nhchainlength + j] = 0.0;
- state->nhpres_vxi[i*nhchainlength + j] = 0.0;
- }
+ state->cg_p.resize(state->natoms + 1);
}
}
else
{
- state->nhpres_xi = NULL;
- state->nhpres_vxi = NULL;
+ state->x.resize(0);
+ state->v.resize(0);
+ state->cg_p.resize(0);
}
}
-
-void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda)
+void init_dfhist_state(t_state *state, int dfhistNumLambda)
{
- int i;
-
- state->natoms = natoms;
- state->flags = 0;
- state->fep_state = 0;
- state->lambda = 0;
- snew(state->lambda, efptNR);
- for (i = 0; i < efptNR; i++)
+ if (dfhistNumLambda > 0)
{
- state->lambda[i] = 0;
- }
- state->veta = 0;
- clear_mat(state->box);
- clear_mat(state->box_rel);
- clear_mat(state->boxv);
- clear_mat(state->pres_prev);
- clear_mat(state->svir_prev);
- clear_mat(state->fvir_prev);
- init_gtc_state(state, ngtc, nnhpres, nhchainlength);
- state->nalloc = state->natoms;
- if (state->nalloc > 0)
- {
- /* We need to allocate one element extra, since we might use
- * (unaligned) 4-wide SIMD loads to access rvec entries.
- */
- snew(state->x, state->nalloc + 1);
- snew(state->v, state->nalloc + 1);
+ snew(state->dfhist, 1);
+ init_df_history(state->dfhist, dfhistNumLambda);
}
else
{
- state->x = NULL;
- state->v = NULL;
+ state->dfhist = nullptr;
}
- state->cg_p = NULL;
- zero_history(&state->hist);
- zero_ekinstate(&state->ekinstate);
- snew(state->enerhist, 1);
- init_energyhistory(state->enerhist);
- init_df_history(&state->dfhist, nlambda);
- init_swapstate(&state->swapstate);
- state->ddp_count = 0;
- state->ddp_count_cg_gl = 0;
- state->cg_gl = NULL;
- state->cg_gl_nalloc = 0;
}
-void done_state(t_state *state)
+void comp_state(const t_state *st1, const t_state *st2,
+ gmx_bool bRMSD, real ftol, real abstol)
{
- if (state->x)
+ int i, j, nc;
+
+ fprintf(stdout, "comparing flags\n");
+ cmp_int(stdout, "flags", -1, st1->flags, st2->flags);
+ fprintf(stdout, "comparing box\n");
+ cmp_rvecs(stdout, "box", DIM, st1->box, st2->box, FALSE, ftol, abstol);
+ fprintf(stdout, "comparing box_rel\n");
+ cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
+ fprintf(stdout, "comparing boxv\n");
+ cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
+ if (st1->flags & (1<<estSVIR_PREV))
{
- sfree(state->x);
+ fprintf(stdout, "comparing shake vir_prev\n");
+ cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
}
- if (state->v)
+ if (st1->flags & (1<<estFVIR_PREV))
{
- sfree(state->v);
+ fprintf(stdout, "comparing force vir_prev\n");
+ cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
}
- if (state->cg_p)
+ if (st1->flags & (1<<estPRES_PREV))
{
- sfree(state->cg_p);
+ fprintf(stdout, "comparing prev_pres\n");
+ cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
}
- state->nalloc = 0;
- if (state->cg_gl)
+ cmp_int(stdout, "ngtc", -1, st1->ngtc, st2->ngtc);
+ cmp_int(stdout, "nhchainlength", -1, st1->nhchainlength, st2->nhchainlength);
+ if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength)
{
- sfree(state->cg_gl);
+ for (i = 0; i < st1->ngtc; i++)
+ {
+ nc = i*st1->nhchainlength;
+ for (j = 0; j < nc; j++)
+ {
+ cmp_real(stdout, "nosehoover_xi",
+ i, st1->nosehoover_xi[nc+j], st2->nosehoover_xi[nc+j], ftol, abstol);
+ }
+ }
}
- state->cg_gl_nalloc = 0;
- if (state->lambda)
+ cmp_int(stdout, "nnhpres", -1, st1->nnhpres, st2->nnhpres);
+ if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength)
{
- sfree(state->lambda);
+ for (i = 0; i < st1->nnhpres; i++)
+ {
+ nc = i*st1->nhchainlength;
+ for (j = 0; j < nc; j++)
+ {
+ cmp_real(stdout, "nosehoover_xi",
+ i, st1->nhpres_xi[nc+j], st2->nhpres_xi[nc+j], ftol, abstol);
+ }
+ }
+ }
+
+ cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
+ if (st1->natoms == st2->natoms)
+ {
+ if ((st1->flags & (1<<estX)) && (st2->flags & (1<<estX)))
+ {
+ fprintf(stdout, "comparing x\n");
+ cmp_rvecs(stdout, "x", st1->natoms, as_rvec_array(st1->x.data()), as_rvec_array(st2->x.data()), bRMSD, ftol, abstol);
+ }
+ if ((st1->flags & (1<<estV)) && (st2->flags & (1<<estV)))
+ {
+ fprintf(stdout, "comparing v\n");
+ cmp_rvecs(stdout, "v", st1->natoms, as_rvec_array(st1->v.data()), as_rvec_array(st2->v.data()), bRMSD, ftol, abstol);
+ }
}
- if (state->ngtc > 0)
+}
+
+rvec *getRvecArrayFromPaddedRVecVector(const PaddedRVecVector *v,
+ unsigned int n)
+{
+ GMX_ASSERT(v->size() >= n, "We can't copy more elements than the vector size");
+
+ rvec *dest;
+
+ snew(dest, n);
+
+ const rvec *vPtr = as_rvec_array(v->data());
+ for (unsigned int i = 0; i < n; i++)
{
- sfree(state->nosehoover_xi);
- sfree(state->nosehoover_vxi);
- sfree(state->therm_integral);
+ copy_rvec(vPtr[i], dest[i]);
}
+
+ return dest;
}
-t_state *serial_init_local_state(t_state *state_global)
+t_state::t_state() : natoms(0),
+ ngtc(0),
+ nnhpres(0),
+ nhchainlength(0),
+ flags(0),
+ fep_state(0),
+ lambda(),
+ nosehoover_xi(),
+ nosehoover_vxi(),
+ nhpres_xi(),
+ nhpres_vxi(),
+ therm_integral(),
+ baros_integral(0),
+ veta(0),
+ vol0(0),
+ x(),
+ v(),
+ cg_p(),
+ ekinstate(),
+ hist(),
+ dfhist(nullptr),
+ ddp_count(0),
+ ddp_count_cg_gl(0),
+ cg_gl()
{
- int i;
- t_state *state_local;
+ // It would be nicer to initialize these with {} or {{0}} in the
+ // above initialization list, but uncrustify doesn't understand
+ // that.
+ // TODO Fix this if we switch to clang-format some time.
+ // cppcheck-suppress useInitializationList
+ lambda = {{ 0 }};
+ clear_mat(box);
+ clear_mat(box_rel);
+ clear_mat(boxv);
+ clear_mat(pres_prev);
+ clear_mat(svir_prev);
+ clear_mat(fvir_prev);
+}
- snew(state_local, 1);
+void set_box_rel(const t_inputrec *ir, t_state *state)
+{
+ /* Make sure the box obeys the restrictions before we fix the ratios */
+ correct_box(nullptr, 0, state->box, nullptr);
+
+ clear_mat(state->box_rel);
- /* Copy all the contents */
- *state_local = *state_global;
- snew(state_local->lambda, efptNR);
- /* local storage for lambda */
- for (i = 0; i < efptNR; i++)
+ if (inputrecPreserveShape(ir))
{
- state_local->lambda[i] = state_global->lambda[i];
+ const int ndim = ir->epct == epctSEMIISOTROPIC ? 2 : 3;
+ do_box_rel(ndim, ir->deform, state->box_rel, state->box, true);
}
+}
- return state_local;
+void preserve_box_shape(const t_inputrec *ir, matrix box_rel, matrix box)
+{
+ if (inputrecPreserveShape(ir))
+ {
+ const int ndim = ir->epct == epctSEMIISOTROPIC ? 2 : 3;
+ do_box_rel(ndim, ir->deform, box_rel, box, false);
+ }
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+
+/*! \file
+ *
+ * \brief
+ * This file contains the definition of the microstate of the simulated system
+ *
+ * History of observables that needs to be checkpointed should be stored
+ * in ObservablesHistory.
+ * The state of the mdrun machinery that needs to be checkpointed is also
+ * stored elsewhere.
+ *
+ * \author Berk Hess
+ *
+ * \inlibraryapi
+ * \ingroup module_mdtypes
+ */
+
#ifndef GMX_MDTYPES_STATE_H
#define GMX_MDTYPES_STATE_H
+#include <array>
+#include <vector>
+
+#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-struct energyhistory_t;
+struct t_inputrec;
/*
* The t_state struct should contain all the (possibly) non-static
* Currently the random seeds for SD and BD are missing.
*/
-/* These enums are used in flags as (1<<est...).
+/* \brief Enum for all entries in \p t_state
+ *
+ * These enums are used in flags as (1<<est...).
* The order of these enums should not be changed,
* since that affects the checkpoint (.cpt) file format.
*/
enum {
estLAMBDA,
- estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI, estTC_INT,
- estX, estV, est_SDX_NOTSUPPORTED, estCGP,
- estLD_RNG, estLD_RNGI,
+ estBOX, estBOX_REL, estBOXV, estPRES_PREV, estNH_XI, estTHERM_INT,
+ estX, estV, estSDX_NOTSUPPORTED, estCGP,
+ estLD_RNG_NOTSUPPORTED, estLD_RNGI_NOTSUPPORTED,
estDISRE_INITF, estDISRE_RM3TAV,
estORIRE_INITF, estORIRE_DTAV,
estSVIR_PREV, estNH_VXI, estVETA, estVOL0, estNHPRES_XI, estNHPRES_VXI, estFVIR_PREV,
- estFEPSTATE, estMC_RNG, estMC_RNGI,
+ estFEPSTATE, estMC_RNG_NOTSUPPORTED, estMC_RNGI_NOTSUPPORTED,
+ estBAROS_INT,
estNR
};
-#define EST_DISTR(e) (!(((e) >= estLAMBDA && (e) <= estTC_INT) || ((e) >= estSVIR_PREV && (e) <= estMC_RNGI)))
-
-/* The names of the state entries, defined in src/gmxlib/checkpoint.c */
+//! \brief The names of the state entries, defined in src/gmxlib/checkpoint.c
extern const char *est_names[estNR];
-typedef struct history_t
+/*! \libinternal \brief History information for NMR distance and orientation restraints
+ *
+ * Often this is only used for reporting observables, and thus should not
+ * actually be part of the microstate. But with time-dependent restraining
+ * they are actually part of the (non-Markovian) microstate.
+ * \todo Rename this with a more descriptive name.
+ */
+class history_t
{
- real disre_initf; /* The scaling factor for initializing the time av. */
- int ndisrepairs; /* The number of distance restraints */
- real *disre_rm3tav; /* The r^-3 time averaged pair distances */
- real orire_initf; /* The scaling factor for initializing the time av. */
- int norire_Dtav; /* The number of matrix element in dtav (npair*5) */
- real *orire_Dtav; /* The time averaged orientation tensors */
-} history_t;
-
-/* Struct used for checkpointing only.
+ public:
+ //! Constructor
+ history_t();
+
+ real disre_initf; //!< The scaling factor for initializing the time av.
+ int ndisrepairs; //!< The number of distance restraints
+ real *disre_rm3tav; //!< The r^-3 time averaged pair distances
+ real orire_initf; //!< The scaling factor for initializing the time av.
+ int norire_Dtav; //!< The number of matrix element in dtav (npair*5)
+ real *orire_Dtav; //!< The time averaged orientation tensors
+};
+
+/*! \libinternal \brief Struct used for checkpointing only
+ *
* This struct would not be required with unlimited precision.
* But because of limited precision, the COM motion removal implementation
* can cause the kinetic energy in the MD loop to differ by a few bits from
* the kinetic energy one would determine from state.v.
*/
-typedef struct ekinstate_t
+class ekinstate_t
{
- gmx_bool bUpToDate;
- int ekin_n;
- tensor *ekinh;
- tensor *ekinf;
- tensor *ekinh_old;
- tensor ekin_total;
- double *ekinscalef_nhc;
- double *ekinscaleh_nhc;
- double *vscale_nhc;
- real dekindl;
- real mvcos;
-} ekinstate_t;
+ public:
+ ekinstate_t();
+ gmx_bool bUpToDate; //!< Test if all data is up to date
+ int ekin_n; //!< The number of tensors
+ tensor *ekinh; //!< Half step Ekin, size \p ekin_n
+ tensor *ekinf; //!< Full step Ekin, size \p ekin_n
+ tensor *ekinh_old; //!< Half step Ekin of the previous step, size \p ekin_n
+ tensor ekin_total; //!< Total kinetic energy
+ std::vector<double> ekinscalef_nhc; //!< Nose-Hoover Ekin scaling factors for full step Ekin
+ std::vector<double> ekinscaleh_nhc; //!< Nose-Hoover Ekin scaling factors for half step Ekin
+ std::vector<double> vscale_nhc; //!< Nose-Hoover velocity scaling factors
+ real dekindl; //!< dEkin/dlambda, with free-energy
+ real mvcos; //!< Cosine(z) component of the momentum, for viscosity calculations
+};
+
+/*! \brief Free-energy sampling history struct
+ *
+ * \todo Split out into microstate and observables history.
+ */
typedef struct df_history_t
{
- int nlambda; /* total number of lambda states - for history*/
+ int nlambda; //!< total number of lambda states - for history
- gmx_bool bEquil; /* Have we reached equilibration */
- int *n_at_lam; /* number of points observed at each lambda */
- real *wl_histo; /* histogram for WL flatness determination */
- real wl_delta; /* current wang-landau delta */
+ gmx_bool bEquil; //!< Have we reached equilibration
+ int *n_at_lam; //!< number of points observed at each lambda
+ real *wl_histo; //!< histogram for WL flatness determination
+ real wl_delta; //!< current wang-landau delta
- real *sum_weights; /* weights of the states */
- real *sum_dg; /* free energies of the states -- not actually used for weighting, but informational */
- real *sum_minvar; /* corrections to weights for minimum variance */
- real *sum_variance; /* variances of the states */
+ real *sum_weights; //!< weights of the states
+ real *sum_dg; //!< free energies of the states -- not actually used for weighting, but informational
+ real *sum_minvar; //!< corrections to weights for minimum variance
+ real *sum_variance; //!< variances of the states
- real **accum_p; /* accumulated bennett weights for n+1 */
- real **accum_m; /* accumulated bennett weights for n-1 */
- real **accum_p2; /* accumulated squared bennett weights for n+1 */
- real **accum_m2; /* accumulated squared bennett weights for n-1 */
+ real **accum_p; //!< accumulated bennett weights for n+1
+ real **accum_m; //!< accumulated bennett weights for n-1
+ real **accum_p2; //!< accumulated squared bennett weights for n+1
+ real **accum_m2; //!< accumulated squared bennett weights for n-1
- real **Tij; /* transition matrix */
- real **Tij_empirical; /* Empirical transition matrix */
+ real **Tij; //!< transition matrix
+ real **Tij_empirical; //!< Empirical transition matrix
} df_history_t;
-typedef struct edsamstate_t
-{
- /* If one uses essential dynamics or flooding on a group of atoms from
- * more than one molecule, we cannot make this group whole with
- * do_pbc_first_mtop(). We assume that the ED group has the correct PBC
- * representation at the beginning of the simulation and keep track
- * of the shifts to always get it into that representation.
- * For proper restarts from a checkpoint we store the positions of the
- * reference group at the time of checkpoint writing */
- gmx_bool bFromCpt; /* Did we start from a checkpoint file? */
- int nED; /* No. of ED/Flooding data sets, if <1 no ED */
- int *nref; /* No. of atoms in i'th reference structure */
- int *nav; /* Same for average structure */
- rvec **old_sref; /* Positions of the reference atoms
- at the last time step (with correct PBC
- representation) */
- rvec **old_sref_p; /* Pointer to these positions */
- rvec **old_sav; /* Same for the average positions */
- rvec **old_sav_p;
-}
-edsamstate_t;
-
-typedef struct swapstateIons_t
-{
- int nMolReq[eCompNR]; /* Requested # of molecules per compartment */
- int *nMolReq_p[eCompNR]; /* Pointer to this data (for .cpt writing) */
- int inflow_net[eCompNR]; /* Flux determined from the # of swaps */
- int *inflow_net_p[eCompNR]; /* Pointer to this data */
- int *nMolPast[eCompNR]; /* Array with nAverage entries for history */
- int *nMolPast_p[eCompNR]; /* Pointer points to the first entry only */
- /* */
- /* Channel flux detection, this is counting only and has no influence on whether swaps */
- /* are performed or not: */
- int fluxfromAtoB[eCompNR]; /* Flux determined from the split cylinders */
- int *fluxfromAtoB_p[eCompNR]; /* Pointer to this data */
- int nMol; /* # of molecules, size of the following arrays */
- unsigned char *comp_from; /* Ion came from which compartment? */
- unsigned char *channel_label; /* Through which channel did this ion pass? */
-} swapstateIons_t;
-
-typedef struct swapstate_t
-{
- int eSwapCoords; /* Swapping along x, y, or z-direction? */
- int nIonTypes; /* Number of ion types, this is the size of */
- /* the following arrays */
- int nAverage; /* Use average over this many swap attempt */
- /* steps when determining the ion counts */
- int fluxleak; /* Ions not going through any channel (bad!) */
- int *fluxleak_p; /* Pointer to this data */
- /* */
- /* To also make multimeric channel proteins whole, we save the last whole configuration */
- /* of the channels in the checkpoint file. If we have no checkpoint file, we assume */
- /* that the starting configuration has the correct PBC representation after making the */
- /* individual molecules whole */
- gmx_bool bFromCpt; /* Did we start from a checkpoint file? */
- int nat[eChanNR]; /* Size of xc_old_whole, i.e. the number of */
- /* atoms in each channel */
- rvec *xc_old_whole[eChanNR]; /* Last known whole positions of the two */
- /* channels (important for multimeric ch.!) */
- rvec **xc_old_whole_p[eChanNR]; /* Pointer to these positions */
- swapstateIons_t *ionType;
-}
-swapstate_t;
-
-
-typedef struct t_state
+
+/*! \brief The microstate of the system
+ *
+ * The global state will contain complete data for all used entries.
+ * The local state with domain decomposition will have partial entries
+ * for which \p stateEntryIsAtomProperty() is true. Some entries that
+ * are used in the global state might not be present in the local state.
+ * \todo Move pure observables history to ObservablesHistory.
+ */
+class t_state
{
- int natoms;
- int ngtc;
- int nnhpres;
- int nhchainlength; /* number of nose-hoover chains */
- int flags; /* Flags telling which entries are present */
- int fep_state; /* indicates which of the alchemical states we are in */
- real *lambda; /* lambda vector */
- matrix box; /* box vector coordinates */
- matrix box_rel; /* Relitaive box vectors to preserve shape */
- matrix boxv; /* box velocitites for Parrinello-Rahman pcoupl */
- matrix pres_prev; /* Pressure of the previous step for pcoupl */
- matrix svir_prev; /* Shake virial for previous step for pcoupl */
- matrix fvir_prev; /* Force virial of the previous step for pcoupl */
- double *nosehoover_xi; /* for Nose-Hoover tcoupl (ngtc) */
- double *nosehoover_vxi; /* for N-H tcoupl (ngtc) */
- double *nhpres_xi; /* for Nose-Hoover pcoupl for barostat */
- double *nhpres_vxi; /* for Nose-Hoover pcoupl for barostat */
- double *therm_integral; /* for N-H/V-rescale tcoupl (ngtc) */
- real veta; /* trotter based isotropic P-coupling */
- real vol0; /* initial volume,required for computing NPT conserverd quantity */
- int nalloc; /* Allocation size for x and v when !=NULL*/
- rvec *x; /* the coordinates (natoms) */
- rvec *v; /* the velocities (natoms) */
- rvec *cg_p; /* p vector for conjugate gradient minimization */
-
- history_t hist; /* Time history for restraints */
-
- ekinstate_t ekinstate; /* The state of the kinetic energy data */
-
- struct energyhistory_t *enerhist; /* Energy history for statistics */
- swapstate_t swapstate; /* Position swapping */
- df_history_t dfhist; /*Free energy history for free energy analysis */
- edsamstate_t edsamstate; /* Essential dynamics / flooding history */
-
- int ddp_count; /* The DD partitioning count for this state */
- int ddp_count_cg_gl; /* The DD part. count for index_gl */
- int ncg_gl; /* The number of local charge groups */
- int *cg_gl; /* The global cg number of the local cgs */
- int cg_gl_nalloc; /* Allocation size of cg_gl; */
-} t_state;
+ public:
+ //! Constructor
+ t_state();
+
+ // All things public
+ int natoms; //!< Number of atoms, local + non-local; this is the size of \p x, \p v and \p cg_p, when used
+ int ngtc; //!< The number of temperature coupling groups
+ int nnhpres; //!< The NH-chain length for the MTTK barostat
+ int nhchainlength; //!< The NH-chain length for temperature coupling
+ int flags; //!< Set of bit-flags telling which entries are present, see enum at the top of the file
+ int fep_state; //!< indicates which of the alchemical states we are in
+ std::array<real, efptNR> lambda; //!< Free-energy lambda vector
+ matrix box; //!< Matrix of box vectors
+ matrix box_rel; //!< Relative box vectors to preserve box shape
+ matrix boxv; //!< Box velocities for Parrinello-Rahman P-coupling
+ matrix pres_prev; //!< Pressure of the previous step for pcoupl
+ matrix svir_prev; //!< Shake virial for previous step for pcoupl
+ matrix fvir_prev; //!< Force virial of the previous step for pcoupl
+ std::vector<double> nosehoover_xi; //!< Nose-Hoover coordinates (ngtc)
+ std::vector<double> nosehoover_vxi; //!< Nose-Hoover velocities (ngtc)
+ std::vector<double> nhpres_xi; //!< Pressure Nose-Hoover coordinates
+ std::vector<double> nhpres_vxi; //!< Pressure Nose-Hoover velocities
+ std::vector<double> therm_integral; //!< Work exterted N-H/V-rescale T-coupling (ngtc)
+ double baros_integral; //!< For Berendsen P-coupling conserved quantity
+ real veta; //!< Trotter based isotropic P-coupling
+ real vol0; //!< Initial volume,required for computing MTTK conserved quantity
+ PaddedRVecVector x; //!< The coordinates (natoms)
+ PaddedRVecVector v; //!< The velocities (natoms)
+ PaddedRVecVector cg_p; //!< p vector for conjugate gradient minimization
+
+ ekinstate_t ekinstate; //!< The state of the kinetic energy
+
+ /* History for special algorithms, should be moved to a history struct */
+ history_t hist; //!< Time history for restraints
+ df_history_t *dfhist; //!< Free-energy history for free energy analysis
+
+ int ddp_count; //!< The DD partitioning count for this state
+ int ddp_count_cg_gl; //!< The DD partitioning count for index_gl
+ std::vector<int> cg_gl; //!< The global cg number of the local cgs
+};
+
+#ifndef DOXYGEN
+/* We don't document the structs below, as they don't belong here.
+ * TODO: Move the next two structs out of state.h.
+ */
typedef struct t_extmass
{
double *vscale_nhc;
} t_vetavars;
+#endif // DOXYGEN
+
+//! Resizes the T- and P-coupling state variables
void init_gtc_state(t_state *state, int ngtc, int nnhpres, int nhchainlength);
-void init_state(t_state *state, int natoms, int ngtc, int nnhpres, int nhchainlength, int nlambda);
+//! Change the number of atoms represented by this state, allocating memory as needed.
+void state_change_natoms(t_state *state, int natoms);
+
+//! Allocates memory for free-energy history
+void init_dfhist_state(t_state *state, int dfhistNumLambda);
+
+/*! \brief Compares two states, write the differences to stdout */
+void comp_state(const t_state *st1, const t_state *st2, gmx_bool bRMSD, real ftol, real abstol);
+
+/*! \brief Allocates an rvec pointer and copy the contents of v to it */
+rvec *getRvecArrayFromPaddedRVecVector(const PaddedRVecVector *v,
+ unsigned int n);
-t_state *serial_init_local_state(t_state *state_global);
+/*! \brief Determine the relative box components
+ *
+ * Set box_rel e.g. used in mdrun state, used to preserve the box shape
+ * \param[in] ir Input record
+ * \param[inout] state State
+ */
+void set_box_rel(const t_inputrec *ir, t_state *state);
-void done_state(t_state *state);
+/*! \brief Make sure the relative box shape remains the same
+ *
+ * This function ensures that the relative box dimensions are
+ * preserved, which otherwise might diffuse away due to rounding
+ * errors in pressure coupling or the deform option.
+ *
+ * \param[in] ir Input record
+ * \param[in] box_rel Relative box dimensions
+ * \param[inout] box The corrected actual box dimensions
+ */
+void preserve_box_shape(const t_inputrec *ir, matrix box_rel, matrix box);
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*
+ * This file contains data types containing ioin/water position exchange
+ * data to be stored in the checkpoint file.
+ */
+
+#ifndef GMX_MDLIB_SWAPHISTORY_H
+#define GMX_MDLIB_SWAPHISTORY_H
+
+/* History of an ion type used in position swapping
+ */
+typedef struct swapstateIons_t
+{
+ int nMolReq[eCompNR]; // Requested # of molecules per compartment
+ int *nMolReq_p[eCompNR]; // Pointer to this data (for checkpoint writing)
+ int inflow_net[eCompNR]; // Flux determined from the # of swaps
+ int *inflow_net_p[eCompNR]; // Pointer to this data
+ int *nMolPast[eCompNR]; // Array with nAverage entries for history
+ int *nMolPast_p[eCompNR]; // Pointer points to the first entry only
+
+ // Channel flux detection, this is counting only and has no influence on whether swaps are performed or not: */
+ int fluxfromAtoB[eCompNR]; // Flux determined from the split cylinders
+ int *fluxfromAtoB_p[eCompNR]; // Pointer to this data
+ int nMol; // Number of molecules, size of the following arrays
+ unsigned char *comp_from; // Ion came from which compartment?
+ unsigned char *channel_label; // Through which channel did this ion pass?
+} swapstateIons_t;
+
+/* Position swapping state
+ *
+ * To also make multimeric channel proteins whole, we save the last whole configuration
+ * of the channels in the checkpoint file. If we have no checkpoint file, we assume
+ * that the starting configuration has the correct PBC representation after making the
+ * individual molecules whole
+ *
+ * \todo move out of this file to ObservablesHistory
+ *
+ */
+typedef struct swaphistory_t
+{
+ int eSwapCoords; // Swapping along x, y, or z-direction?
+ int nIonTypes; // Number of ion types, this is the size of the following arrays
+ int nAverage; // Use average over this many swap attempt steps when determining the ion counts
+ int fluxleak; // Ions not going through any channel (bad!)
+ int *fluxleak_p; // Pointer to this data
+ gmx_bool bFromCpt; // Did we start from a checkpoint file?
+ int nat[eChanNR]; // Size of xc_old_whole, i.e. the number of atoms in each channel
+ rvec *xc_old_whole[eChanNR]; // Last known whole positions of the two channels (important for multimeric ch.!)
+ rvec **xc_old_whole_p[eChanNR]; // Pointer to these positions
+ swapstateIons_t *ionType; // History information for one ion type
+}
+swaphistory_t;
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
//! Initializes a text table column with given values.
ColumnData(const char *title, int width, bool bWrap)
- : title_(title != NULL ? title : ""),
+ : title_(title != nullptr ? title : ""),
width_(width), bWrap_(bWrap), firstLine_(0),
nextLineIndex_(0), nextLineOffset_(0)
{
void TextTableFormatter::addColumn(const char *title, int width, bool bWrap)
{
- if (title != NULL && title[0] != '\0')
+ if (title != nullptr && title[0] != '\0')
{
impl_->bPrintHeader_ = true;
}
- impl_->columns_.push_back(Impl::ColumnData(title, width, bWrap));
+ impl_->columns_.emplace_back(title, width, bWrap);
}
void TextTableFormatter::setFirstColumnIndent(int indent)
{
if (overflow > columnWidth && column->bWrap_)
{
- columnLines.push_back(std::string());
+ columnLines.emplace_back();
continue;
}
columnWidth -= overflow;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
impl_->currentTopicAsString().c_str())));
}
const IHelpTopic *newTopic = topic.findSubTopic(name);
- if (newTopic == NULL)
+ if (newTopic == nullptr)
{
if (impl_->isAtRootTopic())
{
const IHelpTopic &topic = impl_->currentTopic();
const char *title = topic.title();
HelpWriterContext context(impl_->rootContext_);
- context.enterSubSection(title != NULL ? title : "");
+ context.enterSubSection(title != nullptr ? title : "");
topic.writeHelp(context);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const IHelpTopic *
AbstractSimpleHelpTopic::findSubTopic(const char * /* name */) const
{
- return NULL;
+ return nullptr;
}
void AbstractSimpleHelpTopic::writeHelp(const HelpWriterContext &context) const
Impl::SubTopicMap::const_iterator topic = impl_->subTopicMap_.find(name);
if (topic == impl_->subTopicMap_.end())
{
- return NULL;
+ return nullptr;
}
return topic->second;
}
}
TextWriter &file = context.outputFile();
TextTableFormatter formatter;
- formatter.addColumn(NULL, maxNameLength + 1, false);
- formatter.addColumn(NULL, 72 - maxNameLength, true);
+ formatter.addColumn(nullptr, maxNameLength + 1, false);
+ formatter.addColumn(nullptr, 72 - maxNameLength, true);
formatter.setFirstColumnIndent(4);
file.writeLine(title);
for (topic = impl_->subTopicMap_.begin(); topic != impl_->subTopicMap_.end(); ++topic)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
default:
GMX_RELEASE_ASSERT(false, "Output format not implemented for links");
}
- impl_->links_.push_back(Impl::LinkItem(linkName, replacement));
+ impl_->links_.emplace_back(linkName, replacement);
}
/********************************************************************
{
consoleOptionsFormatter_.reset(new TextTableFormatter());
consoleOptionsFormatter_->setFirstColumnIndent(1);
- consoleOptionsFormatter_->addColumn(NULL, 7, false);
- consoleOptionsFormatter_->addColumn(NULL, 18, false);
- consoleOptionsFormatter_->addColumn(NULL, 16, false);
- consoleOptionsFormatter_->addColumn(NULL, 28, false);
+ consoleOptionsFormatter_->addColumn(nullptr, 7, false);
+ consoleOptionsFormatter_->addColumn(nullptr, 18, false);
+ consoleOptionsFormatter_->addColumn(nullptr, 16, false);
+ consoleOptionsFormatter_->addColumn(nullptr, 28, false);
}
return *consoleOptionsFormatter_;
}
void addReplacement(const std::string &search,
const std::string &replace)
{
- replacements_.push_back(ReplaceItem(search, replace));
+ replacements_.emplace_back(search, replace);
}
//! Replaces links in a given string.
std::string HelpWriterContext::Impl::replaceLinks(const std::string &input) const
{
std::string result(input);
- if (state_->links_ != NULL)
+ if (state_->links_ != nullptr)
{
HelpLinks::Impl::LinkList::const_iterator link;
for (link = state_->links_->impl_->links_.begin();
*/
HelpWriterContext::HelpWriterContext(TextWriter *writer, HelpOutputFormat format)
- : impl_(new Impl(Impl::StatePointer(new Impl::SharedState(writer, format, NULL)), 0))
+ : impl_(new Impl(Impl::StatePointer(new Impl::SharedState(writer, format, nullptr)), 0))
{
}
const HelpLinks *links)
: impl_(new Impl(Impl::StatePointer(new Impl::SharedState(writer, format, links)), 0))
{
- if (links != NULL)
+ if (links != nullptr)
{
GMX_RELEASE_ASSERT(links->impl_->format_ == format,
"Links must have the same output format as the context");
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test_object_library(onlinehelp-test-shared
mock_helptopic.cpp)
-if (CMAKE_CXX_COMPILER_ID MATCHES "XL")
- # This suppression stops a very verbose cascade of messages about the
- # mocks, which is probably a compiler issue.
- # 1540-2924 (W) Cannot pass an argument of non-POD class type "const gmx::HelpWriterContext" through ellipsis.
- set_property(SOURCE mock_helptopic.cpp PROPERTY COMPILE_FLAGS "-qsuppress=1540-2924")
-endif()
-
gmx_add_unit_test(OnlineHelpUnitTests onlinehelp-test
helpformat.cpp
helpmanager.cpp
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST_F(TextTableFormatterTest, HandlesEmptyColumnTitles)
{
- formatter_.addColumn(NULL, 4, false);
+ formatter_.addColumn(nullptr, 4, false);
formatter_.addColumn("", 4, false);
- formatter_.addColumn(NULL, 14, true);
+ formatter_.addColumn(nullptr, 14, true);
formatter_.addColumn("", 14, true);
formatter_.clear();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
HelpTestBase::HelpTestBase()
- : rootTopic_("", NULL, "Root topic text"),
+ : rootTopic_("", nullptr, "Root topic text"),
writer_(&helpFile_),
context_(&writer_, gmx::eHelpOutputFormat_Console),
manager_(rootTopic_, context_)
TEST_F(HelpManagerTest, HandlesSubTopics)
{
MockHelpTopic &first =
- rootTopic_.addSubTopic("first", "First topic", NULL);
+ rootTopic_.addSubTopic("first", "First topic", nullptr);
MockHelpTopic &firstSub =
- first.addSubTopic("firstsub", "First subtopic", NULL);
- rootTopic_.addSubTopic("second", "Second topic", NULL);
+ first.addSubTopic("firstsub", "First subtopic", nullptr);
+ rootTopic_.addSubTopic("second", "Second topic", nullptr);
using ::testing::_;
EXPECT_CALL(firstSub, writeHelp(_));
TEST_F(HelpManagerTest, HandlesInvalidTopics)
{
MockHelpTopic &first =
- rootTopic_.addSubTopic("first", "First topic", NULL);
- first.addSubTopic("firstsub", "First subtopic", NULL);
- rootTopic_.addSubTopic("second", "Second topic", NULL);
+ rootTopic_.addSubTopic("first", "First topic", nullptr);
+ first.addSubTopic("firstsub", "First subtopic", nullptr);
+ rootTopic_.addSubTopic("second", "Second topic", nullptr);
ASSERT_THROW_GMX(manager_.enterTopic("unknown"), gmx::InvalidInputError);
ASSERT_NO_THROW_GMX(manager_.enterTopic("first"));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::HelpOutputFormat format,
const char *id)
{
- gmx::HelpWriterContext context(NULL, format);
+ gmx::HelpWriterContext context(nullptr, format);
std::string result
= context.substituteMarkupAndWrapToString(settings_, text);
- if (id == NULL)
+ if (id == nullptr)
{
switch (format)
{
void testFormatting(const gmx::ConstArrayRef<const char *> &text)
{
std::string testText = gmx::joinStrings(text, "\n");
- testFormatting(testText, gmx::eHelpOutputFormat_Console, NULL);
- testFormatting(testText, gmx::eHelpOutputFormat_Rst, NULL);
+ testFormatting(testText, gmx::eHelpOutputFormat_Console, nullptr);
+ testFormatting(testText, gmx::eHelpOutputFormat_Rst, nullptr);
}
gmx::TextLineWrapperSettings settings_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
MockHelpTopic::MockHelpTopic(const char *name, const char *title, const char *text)
- : name_(name), title_(title), text_(text != NULL ? text : "")
+ : name_(name), title_(title), text_(text != nullptr ? text : "")
{
if (!isNullOrEmpty(text))
{
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2010,2012,2013,2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
-file(GLOB OPTIONS_SOURCES *.cpp)
-set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${OPTIONS_SOURCES} PARENT_SCOPE)
+gmx_add_libgromacs_sources(
+ abstractoption.cpp
+ abstractsection.cpp
+ basicoptions.cpp
+ behaviorcollection.cpp
+ filenameoption.cpp
+ filenameoptionmanager.cpp
+ options.cpp
+ optionsassigner.cpp
+ optionsection.cpp
+ optionsvisitor.cpp
+ timeunitmanager.cpp
+ treesupport.cpp
+ )
gmx_install_headers(
abstractoption.h
+ abstractsection.h
basicoptions.h
filenameoption.h
filenameoptionmanager.h
ioptionsbehavior.h
ioptionscontainer.h
+ ioptionscontainerwithsections.h
+ isectionstorage.h
+ ivaluestore.h
optionfiletype.h
optionflags.h
options.h
+ optionsection.h
+ repeatingsection.h
timeunitmanager.h
+ valuestore.h
)
if (BUILD_TESTING)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/optionflags.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/variant.h"
#include "basicoptionstorage.h"
GMX_THROW(APIError("Inconsistent value counts for vector values"));
}
- if (settings.name_ != NULL)
+ if (settings.name_ != nullptr)
{
name_ = settings.name_;
}
- if (settings.descr_ != NULL)
+ if (settings.descr_ != nullptr)
{
descr_ = settings.descr_;
}
- if (storeIsSet_ != NULL)
+ if (storeIsSet_ != nullptr)
{
*storeIsSet_ = false;
}
bool AbstractOptionStorage::isBoolean() const
{
- return dynamic_cast<const BooleanOptionStorage *>(this) != NULL;
+ return dynamic_cast<const BooleanOptionStorage *>(this) != nullptr;
}
void AbstractOptionStorage::startSource()
bSetValuesHadErrors_ = false;
}
-void AbstractOptionStorage::appendValue(const std::string &value)
+void AbstractOptionStorage::appendValue(const Variant &value)
{
GMX_RELEASE_ASSERT(bInSet_, "startSet() not called");
try
{
convertValue(value);
}
- catch (...)
+ catch (const std::exception &)
{
bSetValuesHadErrors_ = true;
throw;
void AbstractOptionStorage::markAsSet()
{
setFlag(efOption_Set);
- if (storeIsSet_ != NULL)
+ if (storeIsSet_ != nullptr)
{
*storeIsSet_ = true;
}
return description;
}
-std::string OptionInfo::formatDefaultValueIfSet() const
+std::vector<Variant> OptionInfo::defaultValues() const
{
- return option().formatDefaultValueIfSet();
+ return option().defaultValues();
}
-int OptionInfo::valueCount() const
+std::vector<std::string> OptionInfo::defaultValuesAsStrings() const
{
- return option().valueCount();
+ return option().defaultValuesAsStrings();
}
-std::string OptionInfo::formatValue(int i) const
+std::vector<Variant> OptionInfo::normalizeValues(const std::vector<Variant> &values) const
{
- return option().formatValue(i);
+ return option().normalizeValues(values);
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class AbstractOptionStorage;
template <typename T> class OptionStorageTemplate;
class OptionManagerContainer;
+class Variant;
namespace internal
{
-class OptionsImpl;
+class OptionSectionImpl;
}
/*! \brief
//! Initializes the name and default values for an option.
explicit AbstractOption(const char *name)
: minValueCount_(1), maxValueCount_(1),
- name_(name), descr_(NULL), storeIsSet_(NULL)
+ name_(name), descr_(nullptr), storeIsSet_(nullptr)
{ }
/*! \brief
*/
friend class AbstractOptionStorage;
//! Needed to be able to call createStorage().
- friend class internal::OptionsImpl;
+ friend class internal::OptionSectionImpl;
};
/*! \brief
//! Initializes the name and default values for an option.
explicit OptionTemplate(const char *name)
: AbstractOption(name),
- defaultValue_(NULL), defaultValueIfSet_(NULL), store_(NULL),
- countptr_(NULL), storeVector_(NULL)
+ defaultValue_(nullptr), defaultValueIfSet_(nullptr), store_(nullptr),
+ countptr_(nullptr), storeVector_(nullptr)
{ }
/*! \brief
template <class InfoType>
bool isType() const
{
- return toType<InfoType>() != NULL;
+ return toType<InfoType>() != nullptr;
}
/*! \brief
* Convert the info object to a particular type if the type is correct.
std::string type() const;
//! Returns the description of the option.
std::string formatDescription() const;
+
/*! \brief
- * Returns the default value if set for the option as a string.
+ * Returns the default value(s) of the option.
+ *
+ * The returned values should all be of the same type, but returning
+ * each as a separate variant is currently simpler.
*
- * \see OptionTemplate::defaultValueIfSet()
+ * Currently, this can only be called before option values have been
+ * assigned.
*/
- std::string formatDefaultValueIfSet() const;
-
- //! Returns the number of values given for the option.
- int valueCount() const;
- //! Returns the i'th value of the option as a string.
- std::string formatValue(int i) const;
+ std::vector<Variant> defaultValues() const;
+ /*! \brief
+ * Returns the default value(s) of the option as strings.
+ *
+ * If there is no default value, but defaultValueIfSet() is set, that
+ * is returned instead.
+ *
+ * Currently, this can only be called before option values have been
+ * assigned.
+ */
+ std::vector<std::string> defaultValuesAsStrings() const;
+ /*! \brief
+ * Converts given values to native representation for this option.
+ *
+ * For example, strings are parsed to the type that is actually used to
+ * store the options.
+ *
+ * The return value only depends on the option type, not on the current
+ * value of the option, and the current value in the option is not
+ * changed.
+ */
+ std::vector<Variant> normalizeValues(const std::vector<Variant> &values) const;
protected:
/*! \cond libapi */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_OPTIONS_ABSTRACTOPTIONSTORAGE_H
#include <string>
+#include <vector>
#include "gromacs/options/optionflags.h"
#include "gromacs/utility/classhelpers.h"
class AbstractOption;
class OptionInfo;
class Options;
+class Variant;
/*! \libinternal \brief
* Abstract base class for converting, validating, and storing option values.
* Returns the number of option values added so far.
*/
virtual int valueCount() const = 0;
- /*! \brief
- * Returns the i'th value formatted as a string.
- *
- * If \p i is DefaultValueIfSetIndex, should format the default value
- * if set (see OptionTemplate::defaultValueIfSet()).
- */
- virtual std::string formatValue(int i) const = 0;
- //! \copydoc OptionInfo::formatDefaultValueIfSet()
- std::string formatDefaultValueIfSet() const
- { return formatValue(DefaultValueIfSetIndex); }
+ //! \copydoc OptionInfo::defaultValues()
+ virtual std::vector<Variant> defaultValues() const = 0;
+ //! \copydoc OptionInfo::defaultValuesAsStrings()
+ virtual std::vector<std::string> defaultValuesAsStrings() const = 0;
+ //! \copydoc OptionInfo::normalizeValues()
+ virtual std::vector<Variant> normalizeValues(const std::vector<Variant> &values) const = 0;
/*! \brief
* Starts adding values from a new source for the option.
*/
void startSet();
/*! \brief
- * Adds a new value for the option, converting it from a string.
+ * Adds a new value for the option.
*
- * \param[in] value String value to convert.
+ * \param[in] value Value to convert.
* \throws InvalidInputError if value cannot be converted, or
* if there are too many values.
*
* This method should only be called between startSet() and
* finishSet().
*/
- void appendValue(const std::string &value);
+ void appendValue(const Variant &value);
/*! \brief
* Performs validation and/or actions once a set of values has been
* added.
void finish();
protected:
- //! Index used with formatValue() for formatting default value if set.
- static const int DefaultValueIfSetIndex = -1;
-
/*! \brief
* Initializes the storage object from the settings object.
*
*/
virtual void clearSet() = 0;
/*! \brief
- * Adds a new value, converting it from a string.
+ * Adds a new value.
*
- * \param[in] value String value to convert.
+ * \param[in] value Value to convert.
* \throws InvalidInputError if \p value is not valid for this option
* or if there have been too many values in the set.
*
*
* \see OptionStorageTemplate::convertValue()
*/
- virtual void convertValue(const std::string &value) = 0;
+ virtual void convertValue(const Variant &value) = 0;
/*! \brief
* Performs validation and/or actions once a set of values has been
* added.
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements classes from abstractsection.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#include "gmxpre.h"
+
+#include "abstractsection.h"
+
+#include "options-impl.h"
+
+namespace gmx
+{
+
+/********************************************************************
+ * AbstractOptionSectionHandle
+ */
+
+// static
+IOptionSectionStorage *
+AbstractOptionSectionHandle::getStorage(internal::OptionSectionImpl *section)
+{
+ return section->storage_.get();
+}
+
+IOptionsContainer &AbstractOptionSectionHandle::addGroup()
+{
+ return section_->addGroup();
+}
+
+internal::OptionSectionImpl *
+AbstractOptionSectionHandle::addSectionImpl(const AbstractOptionSection §ion)
+{
+ return section_->addSectionImpl(section);
+}
+
+OptionInfo *AbstractOptionSectionHandle::addOptionImpl(const AbstractOption &settings)
+{
+ return section_->addOptionImpl(settings);
+}
+
+/********************************************************************
+ * AbstractOptionSectionInfo
+ */
+
+const std::string &AbstractOptionSectionInfo::name() const
+{
+ return section_.name_;
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares base classes for declaring option sections.
+ *
+ * This header defines base classes for option section settings that are used
+ * with IOptionsContainerWithSections::addSection(). These classes implement
+ * the "named parameter" idiom for specifying section properties.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_ABSTRACTSECTION_H
+#define GMX_OPTIONS_ABSTRACTSECTION_H
+
+#include "gromacs/options/ioptionscontainerwithsections.h"
+#include "gromacs/options/isectionstorage.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+class IOptionSectionStorage;
+
+namespace internal
+{
+class OptionSectionImpl;
+}
+
+/*! \brief
+ * Base class for specifying option section properties.
+ *
+ * \ingroup module_options
+ */
+class AbstractOptionSection
+{
+ protected:
+ //! \cond libapi
+ //! Initializes option properties with the given name.
+ explicit AbstractOptionSection(const char *name) : name_(name) {}
+
+ /*! \brief
+ * Creates a storage object corresponding to this section.
+ *
+ * Similar to AbstractOption::createStorage().
+ */
+ virtual IOptionSectionStorage *createStorage() const = 0;
+ //! \endcond
+
+ private:
+ const char *name_;
+
+ friend class internal::OptionSectionImpl;
+};
+
+/*! \brief
+ * Base class for handles to option sections.
+ *
+ * This class implements the common functionality for adding options and
+ * subsections to option sections.
+ *
+ * \ingroup module_options
+ */
+class AbstractOptionSectionHandle : public IOptionsContainerWithSections
+{
+ public:
+ // From IOptionsContainer
+ //! \copydoc IOptionsContainer::addGroup()
+ virtual IOptionsContainer &addGroup();
+
+ protected:
+ //! \cond libapi
+ /*! \brief
+ * Returns the storage for a particular type of section.
+ *
+ * This is intended for use in derived class constructors, where the
+ * handle needs access to the actual storage. The handle should know
+ * the type of storage created for the section type it deals with, so
+ * the cast should always be successful.
+ */
+ template <typename StorageType>
+ static StorageType *getStorage(internal::OptionSectionImpl *section)
+ {
+ IOptionSectionStorage *storage = getStorage(section);
+ StorageType *typedStorage
+ = dynamic_cast<StorageType *>(storage);
+ GMX_ASSERT(typedStorage != nullptr, "Mismatching section storage type");
+ return typedStorage;
+ }
+
+ //! Wraps a given section storage object.
+ explicit AbstractOptionSectionHandle(internal::OptionSectionImpl *section)
+ : section_(section)
+ {
+ }
+ //! \endcond
+
+ private:
+ // From IOptionsContainerWithSections
+ virtual internal::OptionSectionImpl *
+ addSectionImpl(const AbstractOptionSection §ion);
+ // From IOptionsContainer
+ virtual OptionInfo *addOptionImpl(const AbstractOption &settings);
+
+ /*! \brief
+ * Implementation helper for the template method.
+ *
+ * This allows encapsulating the implementation within the source file.
+ */
+ static IOptionSectionStorage *getStorage(internal::OptionSectionImpl *section);
+
+ internal::OptionSectionImpl *section_;
+};
+
+class AbstractOptionSectionInfo
+{
+ public:
+ //! Wraps a given section storage object.
+ explicit AbstractOptionSectionInfo(internal::OptionSectionImpl *section)
+ : section_(*section)
+ {
+ }
+
+ //! Returns the name of the section.
+ const std::string &name() const;
+
+ //! Returns the wrapped section storage object.
+ internal::OptionSectionImpl §ion() { return section_; }
+ //! Returns the wrapped section storage object.
+ const internal::OptionSectionImpl §ion() const { return section_; }
+
+ private:
+ internal::OptionSectionImpl §ion_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(AbstractOptionSectionInfo);
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
#include "basicoptionstorage.h"
return value ? "yes" : "no";
}
-void BooleanOptionStorage::convertValue(const std::string &value)
+void BooleanOptionStorage::initConverter(ConverterType *converter)
{
- // TODO: Case-independence
- if (value == "1" || value == "yes" || value == "true")
- {
- addValue(true);
- return;
- }
- else if (value == "0" || value == "no" || value == "false")
- {
- addValue(false);
- return;
- }
- GMX_THROW(InvalidInputError("Invalid value: '" + value + "'; supported values are: 1, 0, yes, no, true, false"));
+ converter->addConverter<std::string>(&fromStdString<bool>);
}
/********************************************************************
std::string IntegerOptionStorage::formatSingleValue(const int &value) const
{
- return formatString("%d", value);
+ return toString(value);
}
-void IntegerOptionStorage::convertValue(const std::string &value)
+void IntegerOptionStorage::initConverter(ConverterType *converter)
{
- const char *ptr = value.c_str();
- char *endptr;
- errno = 0;
- long int ival = std::strtol(ptr, &endptr, 10);
- if (errno == ERANGE
- || ival < std::numeric_limits<int>::min()
- || ival > std::numeric_limits<int>::max())
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; it causes an integer overflow"));
- }
- if (*ptr == '\0' || *endptr != '\0')
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; expected an integer"));
- }
- addValue(ival);
+ converter->addConverter<std::string>(&fromStdString<int>);
}
void IntegerOptionStorage::processSetValues(ValueList *values)
std::string Int64OptionStorage::formatSingleValue(const gmx_int64_t &value) const
{
- return formatString("%" GMX_PRId64, value);
+ return toString(value);
}
-void Int64OptionStorage::convertValue(const std::string &value)
+void Int64OptionStorage::initConverter(ConverterType *converter)
{
- const char *ptr = value.c_str();
- char *endptr;
- errno = 0;
- const gmx_int64_t ival = str_to_int64_t(ptr, &endptr);
- if (errno == ERANGE)
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; it causes an integer overflow"));
- }
- if (*ptr == '\0' || *endptr != '\0')
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; expected an integer"));
- }
- addValue(ival);
+ converter->addConverter<std::string>(&fromStdString<gmx_int64_t>);
}
/********************************************************************
std::string DoubleOptionStorage::formatSingleValue(const double &value) const
{
- return formatString("%g", value / factor_);
+ return toString(value / factor_);
}
-void DoubleOptionStorage::convertValue(const std::string &value)
+void DoubleOptionStorage::initConverter(ConverterType *converter)
{
- const char *ptr = value.c_str();
- char *endptr;
- errno = 0;
- double dval = std::strtod(ptr, &endptr);
- if (errno == ERANGE)
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; it causes an overflow/underflow"));
- }
- if (*ptr == '\0' || *endptr != '\0')
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; expected a number"));
- }
- addValue(dval * factor_);
+ converter->addConverter<std::string>(&fromStdString<double>);
+ converter->addCastConversion<float>();
+}
+
+double DoubleOptionStorage::processValue(const double &value) const
+{
+ // TODO: Consider testing for overflow when scaling with factor_.
+ return value * factor_;
}
void DoubleOptionStorage::processSetValues(ValueList *values)
GMX_RELEASE_ASSERT(factor > 0.0, "Invalid scaling factor");
if (!hasFlag(efOption_HasDefaultValue))
{
- double scale = factor / factor_;
- ValueList::iterator i;
- for (i = values().begin(); i != values().end(); ++i)
+ double scale = factor / factor_;
+ for (double &value : values())
{
- (*i) *= scale;
+ value *= scale;
}
- refreshValues();
}
factor_ = factor;
}
std::string FloatOptionStorage::formatSingleValue(const float &value) const
{
- return formatString("%g", value / factor_);
+ return toString(value / factor_);
}
-void FloatOptionStorage::convertValue(const std::string &value)
+void FloatOptionStorage::initConverter(ConverterType *converter)
{
- const char *ptr = value.c_str();
- char *endptr;
- errno = 0;
- double dval = std::strtod(ptr, &endptr);
- if (errno == ERANGE
- || dval * factor_ < -std::numeric_limits<float>::max()
- || dval * factor_ > std::numeric_limits<float>::max())
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; it causes an overflow/underflow"));
- }
- if (*ptr == '\0' || *endptr != '\0')
- {
- GMX_THROW(InvalidInputError("Invalid value: '" + value
- + "'; expected a number"));
- }
- addValue(dval * factor_);
+ converter->addConverter<std::string>(&fromStdString<float>);
+ converter->addCastConversion<double>();
+}
+
+float FloatOptionStorage::processValue(const float &value) const
+{
+ // TODO: Consider testing for overflow when scaling with factor_.
+ return value * factor_;
}
void FloatOptionStorage::processSetValues(ValueList *values)
GMX_RELEASE_ASSERT(factor > 0.0, "Invalid scaling factor");
if (!hasFlag(efOption_HasDefaultValue))
{
- double scale = factor / factor_;
- ValueList::iterator i;
- for (i = values().begin(); i != values().end(); ++i)
+ float scale = factor / factor_;
+ for (float &value : values())
{
- (*i) *= scale;
+ value *= scale;
}
- refreshValues();
}
factor_ = factor;
}
StringOptionStorage::StringOptionStorage(const StringOption &settings)
: MyBase(settings), info_(this)
{
- if (settings.defaultEnumIndex_ >= 0 && settings.enumValues_ == NULL)
+ if (settings.defaultEnumIndex_ >= 0 && settings.enumValues_ == nullptr)
{
GMX_THROW(APIError("Cannot set default enum index without enum values"));
}
- if (settings.enumValues_ != NULL)
+ if (settings.enumValues_ != nullptr)
{
int count = settings.enumValuesCount_;
if (count < 0)
{
count = 0;
- while (settings.enumValues_[count] != NULL)
+ while (settings.enumValues_[count] != nullptr)
{
++count;
}
}
for (int i = 0; i < count; ++i)
{
- if (settings.enumValues_[i] == NULL)
+ if (settings.enumValues_[i] == nullptr)
{
GMX_THROW(APIError("Enumeration value cannot be NULL"));
}
- allowed_.push_back(settings.enumValues_[i]);
+ allowed_.emplace_back(settings.enumValues_[i]);
}
if (settings.defaultEnumIndex_ >= 0)
{
GMX_THROW(APIError("Default enumeration index is out of range"));
}
const std::string *defaultValue = settings.defaultValue();
- if (defaultValue != NULL && *defaultValue != allowed_[settings.defaultEnumIndex_])
+ if (defaultValue != nullptr && *defaultValue != allowed_[settings.defaultEnumIndex_])
{
GMX_THROW(APIError("Conflicting default values"));
}
- clear();
- addValue(allowed_[settings.defaultEnumIndex_]);
- commitValues();
+ setDefaultValue(allowed_[settings.defaultEnumIndex_]);
}
}
}
return value;
}
-void StringOptionStorage::convertValue(const std::string &value)
+void StringOptionStorage::initConverter(ConverterType * /*converter*/)
{
- if (allowed_.size() == 0)
- {
- addValue(value);
- }
- else
+}
+
+std::string StringOptionStorage::processValue(const std::string &value) const
+{
+ if (allowed_.size() > 0)
{
- ValueList::const_iterator match = findEnumValue(allowed_, value);
- addValue(*match);
+ return *findEnumValue(this->allowed_, value);
}
+ return value;
}
/********************************************************************
EnumOptionStorage::EnumOptionStorage(const AbstractOption &settings,
const char *const *enumValues, int count,
int defaultValue, int defaultValueIfSet,
- EnumIndexStorePointer store)
- : MyBase(settings), info_(this), store_(move(store))
+ StorePointer store)
+ : MyBase(settings, std::move(store)), info_(this)
{
- if (enumValues == NULL)
+ if (enumValues == nullptr)
{
GMX_THROW(APIError("Allowed values must be provided to EnumOption"));
}
if (count < 0)
{
count = 0;
- while (enumValues[count] != NULL)
+ while (enumValues[count] != nullptr)
{
++count;
}
}
for (int i = 0; i < count; ++i)
{
- if (enumValues[i] == NULL)
+ if (enumValues[i] == nullptr)
{
GMX_THROW(APIError("Enumeration value cannot be NULL"));
}
- allowed_.push_back(enumValues[i]);
+ allowed_.emplace_back(enumValues[i]);
}
GMX_ASSERT(defaultValue < count, "Default enumeration value is out of range");
{
setDefaultValueIfSet(defaultValueIfSet);
}
-
- if (values().empty())
- {
- values() = store_->initialValues();
- }
- refreshEnumIndexStore();
}
std::string EnumOptionStorage::formatExtraDescription() const
return allowed_[value];
}
-void EnumOptionStorage::convertValue(const std::string &value)
-{
- std::vector<std::string>::const_iterator match = findEnumValue(allowed_, value);
- addValue(match - allowed_.begin());
-}
-
-void EnumOptionStorage::processSetValues(ValueList *values)
+Variant EnumOptionStorage::normalizeValue(const int &value) const
{
- const size_t newSize = (hasFlag(efOption_ClearOnNextSet) ? 0 : valueCount())
- + std::max<size_t>(values->size(), 1);
- store_->reserveSpace(newSize);
+ return Variant::create<std::string>(formatSingleValue(value));
}
-void EnumOptionStorage::refreshValues()
+void EnumOptionStorage::initConverter(ConverterType *converter)
{
- MyBase::refreshValues();
- refreshEnumIndexStore();
-}
-
-void EnumOptionStorage::refreshEnumIndexStore()
-{
- store_->refreshValues(values());
+ converter->addConverter<std::string>(
+ [this] (const std::string &value)
+ {
+ return findEnumValue(this->allowed_, value) - this->allowed_.begin();
+ });
}
/********************************************************************
namespace internal
{
-EnumIndexStoreInterface::~EnumIndexStoreInterface()
-{
-}
-
//! \cond internal
AbstractOptionStorage *
createEnumOptionStorage(const AbstractOption &option,
const char *const *enumValues, int count,
int defaultValue, int defaultValueIfSet,
- EnumIndexStoreInterface *store)
+ IOptionValueStore<int> *store)
{
- EnumOptionStorage::EnumIndexStorePointer storePtr(store);
+ std::unique_ptr<IOptionValueStore<int> > storePtr(store);
return new EnumOptionStorage(option, enumValues, count, defaultValue,
defaultValueIfSet, move(storePtr));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/ivaluestore.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/gmxassert.h"
//! Initializes an option with the given name.
explicit StringOption(const char *name)
- : MyBase(name), enumValues_(NULL), enumValuesCount_(0),
+ : MyBase(name), enumValues_(nullptr), enumValuesCount_(0),
defaultEnumIndex_(-1)
{
}
/*! \internal
* \brief
- * Interface for handling storage of the enum indexes.
- *
- * This interface acts as a proxy between the EnumOptionStorage class (that
- * operates on `int` values), and the actual enum variable that receives the
- * values. The implementation of this interface takes care of conversion of
- * the values and writing them out into the actual enum variables.
- *
- * \ingroup module_options
- */
-class EnumIndexStoreInterface
-{
- public:
- virtual ~EnumIndexStoreInterface();
-
- //! Returns initial values from the actual enum variables.
- virtual std::vector<int> initialValues() const = 0;
- //! Reserves space for storage in the actual enum variables.
- virtual void reserveSpace(size_t count) = 0;
- //! Updates values in the actual enum variables based on option values.
- virtual void refreshValues(const std::vector<int> &values) = 0;
-};
-
-/*! \internal
- * \brief
- * Type-specific implementation for EnumIndexStoreInterface.
+ * Type-specific implementation for IOptionValueStore for an enum option.
*
* This class is instantiated for each enum type for which EnumOption is used,
- * and takes care of managing the `int`-to-`enum` conversions as described in
- * EnumIndexStoreInterface. Having this as a template in the header allows the
- * actual storage implementation to not be in the header, which would require
- * exposing all the internals through this one header...
+ * and takes care of managing `int`-to-`enum` conversions. Having this part in
+ * the header allows the actual storage implementation to not be in the header,
+ * which would require exposing all the internals through this one header...
*
* \ingroup module_options
*/
template <typename EnumType>
-class EnumIndexStore : public EnumIndexStoreInterface
+class EnumIndexStore : public IOptionValueStore<int>
{
public:
//! Initializes the storage for the given actual enum variables.
EnumIndexStore(EnumType *store, std::vector<EnumType> *storeVector)
: store_(store), storeVector_(storeVector)
{
- }
-
- virtual std::vector<int> initialValues() const
- {
- std::vector<int> result;
- if (storeVector_ != NULL)
+ if (storeVector_ != nullptr)
{
- typename std::vector<EnumType>::const_iterator i;
- for (i = storeVector_->begin(); i != storeVector_->end(); ++i)
+ for (EnumType value : *storeVector_)
{
- result.push_back(*i);
+ intStore_.push_back(static_cast<int>(value));
}
}
- else if (store_ != NULL)
+ else if (store_ != nullptr)
{
// TODO: Copy more than one value if that would make sense.
- result.push_back(store_[0]);
+ intStore_.push_back(static_cast<int>(store_[0]));
}
- return result;
}
- virtual void reserveSpace(size_t count)
+
+ virtual int valueCount() { return static_cast<int>(intStore_.size()); }
+ virtual ArrayRef<int> values() { return intStore_; }
+ virtual void clear()
{
- if (storeVector_ != NULL)
+ intStore_.clear();
+ if (storeVector_ != nullptr)
{
- storeVector_->reserve(count);
+ storeVector_->clear();
}
}
- virtual void refreshValues(const std::vector<int> &values)
+ virtual void reserve(size_t count)
{
- if (store_ != NULL)
+ intStore_.reserve(intStore_.size() + count);
+ if (storeVector_ != nullptr)
{
- for (size_t i = 0; i < values.size(); ++i)
- {
- store_[i] = static_cast<EnumType>(values[i]);
- }
+ storeVector_->reserve(storeVector_->size() + count);
}
- if (storeVector_ != NULL)
+ }
+ virtual void append(const int &value)
+ {
+ const size_t count = intStore_.size();
+ intStore_.push_back(value);
+ if (store_ != nullptr)
{
- GMX_ASSERT(storeVector_->capacity() >= values.size(),
- "reserveSpace() should have been called earlier");
- storeVector_->resize(values.size());
- for (size_t i = 0; i < values.size(); ++i)
- {
- (*storeVector_)[i] = static_cast<EnumType>(values[i]);
- }
+ store_[count] = static_cast<EnumType>(value);
+ }
+ if (storeVector_ != nullptr)
+ {
+ storeVector_->push_back(static_cast<EnumType>(value));
}
}
private:
+ //! Stores the integer values for values().
+ std::vector<int> intStore_;
EnumType *store_;
std::vector<EnumType> *storeVector_;
};
createEnumOptionStorage(const AbstractOption &option,
const char *const *enumValues, int count,
int defaultValue, int defaultValueIfSet,
- EnumIndexStoreInterface *store);
+ IOptionValueStore<int> *store);
//! \endcond
} // namespace internal
//! Initializes an option with the given name.
explicit EnumOption(const char *name)
- : MyBase(name), enumValues_(NULL), enumValuesCount_(0)
+ : MyBase(name), enumValues_(nullptr), enumValuesCount_(0)
{
}
//! Helper function to convert default values for storate initialization.
static int convertToInt(const EnumType *defaultValue)
{
- return defaultValue != NULL ? static_cast<int>(*defaultValue) : -1;
+ return defaultValue != nullptr ? static_cast<int>(*defaultValue) : -1;
}
//! Creates a EnumOptionStorage object.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \internal \brief
* Converts, validates, and stores boolean values.
*/
-class BooleanOptionStorage : public OptionStorageTemplate<bool>
+class BooleanOptionStorage : public OptionStorageTemplateSimple<bool>
{
public:
/*! \brief
bool defaultValue() const { return valueCount() > 0 && values()[0]; }
private:
- virtual void convertValue(const std::string &value);
+ virtual void initConverter(ConverterType *converter);
BooleanOptionInfo info_;
};
/*! \internal \brief
* Converts, validates, and stores integer values.
*/
-class IntegerOptionStorage : public OptionStorageTemplate<int>
+class IntegerOptionStorage : public OptionStorageTemplateSimple<int>
{
public:
//! \copydoc BooleanOptionStorage::BooleanOptionStorage()
virtual std::string formatSingleValue(const int &value) const;
private:
- virtual void convertValue(const std::string &value);
+ virtual void initConverter(ConverterType *converter);
virtual void processSetValues(ValueList *values);
IntegerOptionInfo info_;
/*! \internal \brief
* Converts, validates, and stores integer values.
*/
-class Int64OptionStorage : public OptionStorageTemplate<gmx_int64_t>
+class Int64OptionStorage : public OptionStorageTemplateSimple<gmx_int64_t>
{
public:
//! \copydoc BooleanOptionStorage::BooleanOptionStorage()
virtual std::string formatSingleValue(const gmx_int64_t &value) const;
private:
- virtual void convertValue(const std::string &value);
+ virtual void initConverter(ConverterType *converter);
Int64OptionInfo info_;
};
/*! \internal \brief
* Converts, validates, and stores floating-point (double) values.
*/
-class DoubleOptionStorage : public OptionStorageTemplate<double>
+class DoubleOptionStorage : public OptionStorageTemplateSimple<double>
{
public:
//! \copydoc IntegerOptionStorage::IntegerOptionStorage()
void setScaleFactor(double factor);
private:
- virtual void convertValue(const std::string &value);
+ virtual void initConverter(ConverterType *converter);
+ virtual double processValue(const double &value) const;
virtual void processSetValues(ValueList *values);
DoubleOptionInfo info_;
/*! \internal \brief
* Converts, validates, and stores floating-point (float) values.
*/
-class FloatOptionStorage : public OptionStorageTemplate<float>
+class FloatOptionStorage : public OptionStorageTemplateSimple<float>
{
public:
//! \copydoc IntegerOptionStorage::IntegerOptionStorage()
void setScaleFactor(double factor);
private:
- virtual void convertValue(const std::string &value);
+ virtual void initConverter(ConverterType *converter);
+ virtual float processValue(const float &value) const;
virtual void processSetValues(ValueList *values);
FloatOptionInfo info_;
/*! \internal \brief
* Converts, validates, and stores string values.
*/
-class StringOptionStorage : public OptionStorageTemplate<std::string>
+class StringOptionStorage : public OptionStorageTemplateSimple<std::string>
{
public:
//! \copydoc DoubleOptionStorage::DoubleOptionStorage()
const ValueList &allowedValues() const { return allowed_; }
private:
- virtual void convertValue(const std::string &value);
+ virtual void initConverter(ConverterType *converter);
+ virtual std::string processValue(const std::string &value) const;
StringOptionInfo info_;
ValueList allowed_;
/*! \internal \brief
* Converts, validates, and stores enum values.
*/
-class EnumOptionStorage : public OptionStorageTemplate<int>
+class EnumOptionStorage : public OptionStorageTemplateSimple<int>
{
public:
- //! Shorthand for the enum index storage interface.
- typedef std::unique_ptr<internal::EnumIndexStoreInterface>
- EnumIndexStorePointer;
-
/*! \brief
* Initializes the storage from option settings.
*
EnumOptionStorage(const AbstractOption &settings,
const char *const *enumValues, int count,
int defaultValue, int defaultValueIfSet,
- EnumIndexStorePointer store);
+ StorePointer store);
virtual OptionInfo &optionInfo() { return info_; }
virtual std::string typeString() const { return "enum"; }
virtual std::string formatExtraDescription() const;
virtual std::string formatSingleValue(const int &value) const;
+ virtual Variant normalizeValue(const int &value) const;
//! \copydoc EnumOptionInfo::allowedValues()
const std::vector<std::string> &allowedValues() const { return allowed_; }
private:
- virtual void convertValue(const std::string &value);
- virtual void processSetValues(ValueList *values);
- virtual void refreshValues();
-
- void refreshEnumIndexStore();
+ virtual void initConverter(ConverterType *converter);
EnumOptionInfo info_;
std::vector<std::string> allowed_;
- EnumIndexStorePointer store_;
};
/*!\}*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
FileTypeHandler::FileTypeHandler(int fileType)
- : fileType_(fileType), extensionCount_(0), genericTypes_(NULL)
+ : fileType_(fileType), extensionCount_(0), genericTypes_(nullptr)
{
if (fileType_ >= 0)
{
const char *FileTypeHandler::extension(int i) const
{
GMX_ASSERT(i >= 0 && i < extensionCount_, "Invalid extension index");
- if (genericTypes_ != NULL)
+ if (genericTypes_ != nullptr)
{
return ftp2ext_with_dot(genericTypes_[i]);
}
bool
FileTypeHandler::isValidType(int fileType) const
{
- if (genericTypes_ != NULL)
+ if (genericTypes_ != nullptr)
{
for (int i = 0; i < extensionCount(); ++i)
{
{
defaultExtension_ = typeHandler.extension(0);
}
- if (settings.defaultBasename_ != NULL)
+ if (settings.defaultBasename_ != nullptr)
{
std::string defaultValue(settings.defaultBasename_);
int type = fn2ftp(settings.defaultBasename_);
return value;
}
-void FileNameOptionStorage::convertValue(const std::string &value)
+void FileNameOptionStorage::initConverter(ConverterType * /*converter*/)
{
- if (manager_ != NULL)
+}
+
+std::string FileNameOptionStorage::processValue(const std::string &value) const
+{
+ if (manager_ != nullptr)
{
std::string processedValue = manager_->completeFileName(value, info_);
if (!processedValue.empty())
"Manager returned an invalid file name");
}
}
- addValue(processedValue);
- return;
+ return processedValue;
}
}
// Currently, directory options are simple, and don't need any
// TODO: Consider splitting them into a separate DirectoryOption.
if (isDirectoryOption())
{
- addValue(value);
- return;
+ return value;
}
const int fileType = fn2ftp(value.c_str());
if (fileType == efNR)
value.c_str(), joinStrings(extensions(), ", ").c_str());
GMX_THROW(InvalidInputError(message));
}
- addValue(value);
+ return value;
}
void FileNameOptionStorage::processAll()
{
- if (manager_ != NULL && hasFlag(efOption_HasDefaultValue))
+ if (manager_ != nullptr && hasFlag(efOption_HasDefaultValue))
{
- ValueList &valueList = values();
+ ArrayRef<std::string> valueList = values();
GMX_RELEASE_ASSERT(valueList.size() == 1,
"There should be only one default value");
if (!valueList[0].empty())
GMX_ASSERT(isValidType(fn2ftp(newValue.c_str())),
"Manager returned an invalid default value");
valueList[0] = newValue;
- refreshValues();
}
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Initializes an option with the given name.
explicit FileNameOption(const char *name)
: MyBase(name), optionType_(eftUnknown), legacyType_(-1),
- defaultBasename_(NULL), defaultType_(-1),
+ defaultBasename_(nullptr), defaultType_(-1),
bLegacyOptionalBehavior_(false),
bRead_(false), bWrite_(false), bLibrary_(false),
bAllowMissing_(false)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \internal \brief
* Converts, validates, and stores file names.
*/
-class FileNameOptionStorage : public OptionStorageTemplate<std::string>
+class FileNameOptionStorage : public OptionStorageTemplateSimple<std::string>
{
public:
/*! \brief
ConstArrayRef<int> fileTypes() const;
private:
- virtual void convertValue(const std::string &value);
+ virtual void initConverter(ConverterType *converter);
+ virtual std::string processValue(const std::string &value) const;
virtual void processAll();
FileNameOptionInfo info_;
* output.
*/
virtual IOptionsContainer &addGroup() = 0;
- /*! \brief
- * Adds a recognized option.
- *
- * \param[in] settings Option description.
- * \returns OptionInfo object for the created option (never NULL).
- * \throws APIError if invalid option settings are provided.
- *
- * This method provides the internal implementation, but in most cases
- * the templated method is called from user code.
- * See the templated method for more details.
- */
- virtual OptionInfo *addOption(const AbstractOption &settings) = 0;
/*! \brief
* Adds a recognized option.
*
typename OptionType::InfoType *addOption(const OptionType &settings)
{
OptionInfo *info
- = addOption(static_cast<const AbstractOption &>(settings));
+ = addOptionImpl(static_cast<const AbstractOption &>(settings));
GMX_ASSERT(info->isType<typename OptionType::InfoType>(),
"Mismatching option info type declaration and implementation");
return info->toType<typename OptionType::InfoType>();
// (no need for the virtual, but some compilers warn otherwise)
virtual ~IOptionsContainer();
+ /*! \brief
+ * Adds a recognized option.
+ *
+ * \param[in] settings Option description.
+ * \returns OptionInfo object for the created option (never NULL).
+ * \throws APIError if invalid option settings are provided.
+ *
+ * This method provides the internal implementation, but the templated
+ * method is called from user code. See the templated method for more
+ * details.
+ */
+ virtual OptionInfo *addOptionImpl(const AbstractOption &settings) = 0;
+
GMX_DEFAULT_CONSTRUCTORS(IOptionsContainer);
};
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::IOptionsContainerWithSections.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inpublicapi
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_IOPTIONSCONTAINERWITHSECTIONS_H
+#define GMX_OPTIONS_IOPTIONSCONTAINERWITHSECTIONS_H
+
+#include "gromacs/options/ioptionscontainer.h"
+
+namespace gmx
+{
+
+class AbstractOptionSection;
+class AbstractOptionSectionHandle;
+
+namespace internal
+{
+class OptionSectionImpl;
+}
+
+/*! \brief
+ * Interface for adding input options with sections.
+ *
+ * This interface extends IOptionsContainer with an additional addSection()
+ * method that supports creating a hierarchy of sections for the options.
+ *
+ * Header optionsection.h provides OptionSection.
+ *
+ * \inpublicapi
+ * \ingroup module_options
+ */
+class IOptionsContainerWithSections : public IOptionsContainer
+{
+ public:
+ /*! \brief
+ * Adds a section to this collection.
+ *
+ * \tparam SectionType Type of the section description object.
+ * \param[in] section Section description.
+ * \returns AbstractOptionSectionHandle object for the created option.
+ * \throws APIError if invalid option settings are provided.
+ *
+ * Options can be added to the section through the returned handle.
+ *
+ * \internal
+ * \p SectionType::HandleType must specify a type that derives from
+ * AbstractinOptionSectionHandle and has a suitable constructor.
+ */
+ template <class SectionType>
+ typename SectionType::HandleType addSection(const SectionType §ion)
+ {
+ internal::OptionSectionImpl *storage
+ = addSectionImpl(static_cast<const AbstractOptionSection &>(section));
+ return typename SectionType::HandleType(storage);
+ }
+
+ protected:
+ // Disallow deletion through the interface.
+ // (no need for the virtual, but some compilers warn otherwise)
+ virtual ~IOptionsContainerWithSections();
+
+ /*! \brief
+ * Adds a section to this container.
+ *
+ * \param[in] section Section description.
+ * \returns Pointer to the internal section representation object.
+ */
+ virtual internal::OptionSectionImpl *
+ addSectionImpl(const AbstractOptionSection §ion) = 0;
+
+ GMX_DEFAULT_CONSTRUCTORS(IOptionsContainerWithSections);
+};
+
+} // namespace
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::IOptionSectionStorage.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_ISECTIONSTORAGE_H
+#define GMX_OPTIONS_ISECTIONSTORAGE_H
+
+namespace gmx
+{
+
+/*! \internal
+ * \brief
+ * Provides behavior specific to a certain option section type.
+ *
+ * \ingroup module_options
+ */
+class IOptionSectionStorage
+{
+ public:
+ virtual ~IOptionSectionStorage();
+
+ /*! \brief
+ * Called once before the first call to startSection().
+ *
+ * This is called once all options have been added to the section.
+ * The current implementation does not call this if startSection() is
+ * never called.
+ */
+ virtual void initStorage() = 0;
+ /*! \brief
+ * Called when option assignment enters this section.
+ */
+ virtual void startSection() = 0;
+ /*! \brief
+ * Called when option assignment leaves this section.
+ */
+ virtual void finishSection() = 0;
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::IOptionValueStore.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_IVALUESTORE_H
+#define GMX_OPTIONS_IVALUESTORE_H
+
+namespace gmx
+{
+
+template <typename T> class ArrayRef;
+
+/*! \internal
+ * \brief
+ * Represents the final storage location of option values.
+ *
+ * \todo
+ * Try to make this more like a write-only interface, getting rid of the need
+ * to access the stored values through this interface. That would simplify
+ * things.
+ *
+ * \ingroup module_options
+ */
+template <typename T>
+class IOptionValueStore
+{
+ public:
+ virtual ~IOptionValueStore() {}
+
+ //! Returns the number of values stored so far.
+ virtual int valueCount() = 0;
+ //! Returns a reference to the actual values.
+ virtual ArrayRef<T> values() = 0;
+ //! Removes all stored values.
+ virtual void clear() = 0;
+ //! Reserves memory for additional `count` entries.
+ virtual void reserve(size_t count) = 0;
+ //! Appends a value to the store.
+ virtual void append(const T &value) = 0;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template <class ManagerType>
ManagerType *get() const
{
- ManagerType *result = NULL;
+ ManagerType *result = nullptr;
for (ListType::const_iterator i = list_.begin(); i != list_.end(); ++i)
{
ManagerType *curr = dynamic_cast<ManagerType *>(*i);
- if (curr != NULL)
+ if (curr != nullptr)
{
- GMX_RELEASE_ASSERT(result == NULL,
+ GMX_RELEASE_ASSERT(result == nullptr,
"More than one applicable option manager is set");
result = curr;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
#include "gromacs/options/abstractoption.h"
+#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/options/ioptionscontainer.h"
+#include "gromacs/options/ioptionscontainerwithsections.h"
+#include "gromacs/options/isectionstorage.h"
#include "gromacs/options/optionmanagercontainer.h"
#include "gromacs/options/options.h"
+#include "gromacs/options/optionsection.h"
namespace gmx
{
-class AbstractOptionStorage;
-
namespace internal
{
/*! \internal
* \brief
- * Private implementation class for Options.
+ * Internal implementation class for storing an option section.
*
- * Note that in addition to Options, the OptionsAssigner and OptionsIterator
- * classes also directly access this class.
+ * All options are stored within a section: the top-level contents of an
+ * Options object are handled within an unnamed, "root" section.
+ * This class handles the common functionality for all sections, related to
+ * storing the options and subsections. Functionality specific to a section
+ * type is provided by IOptionSectionStorage.
*
* \ingroup module_options
*/
-class OptionsImpl
+class OptionSectionImpl : public IOptionsContainerWithSections
{
public:
/*! \internal \brief
typedef std::list<Group> SubgroupList;
//! Creates a group within the given Options.
- explicit Group(OptionsImpl *parent) : parent_(parent) {}
+ explicit Group(OptionSectionImpl *parent) : parent_(parent) {}
// From IOptionsContainer
virtual IOptionsContainer &addGroup();
- virtual OptionInfo *addOption(const AbstractOption &settings);
+ virtual OptionInfo *addOptionImpl(const AbstractOption &settings);
//! Containing options object.
- OptionsImpl *parent_;
+ OptionSectionImpl *parent_;
/*! \brief
* List of options, in insertion order.
*
* Pointers in this container point to the objects managed by
* Impl::optionsMap_.
*/
- OptionList options_;
+ OptionList options_;
//! List of groups, in insertion order.
- SubgroupList subgroups_;
+ SubgroupList subgroups_;
};
//! Smart pointer for managing an AbstractOptionStorage object.
typedef std::unique_ptr<AbstractOptionStorage>
AbstractOptionStoragePointer;
- //! Convenience type for list of sections.
- typedef std::vector<Options *> SubSectionList;
//! Convenience typedef for a map that contains all the options.
typedef std::map<std::string, AbstractOptionStoragePointer> OptionMap;
+ //! Smart pointer for managing subsections.
+ typedef std::unique_ptr<OptionSectionImpl> SectionPointer;
+ //! Convenience typedef for a container for subsections.
+ typedef std::vector<SectionPointer> SectionList;
+
+ //! Creates storage for a new section.
+ OptionSectionImpl(const OptionManagerContainer &managers,
+ std::unique_ptr<IOptionSectionStorage> storage,
+ const char *name)
+ : managers_(managers), storage_(std::move(storage)), info_(this),
+ name_(name), rootGroup_(this), storageInitialized_(false)
+ {
+ }
- //! Sets the name and title.
- OptionsImpl(const char *name, const char *title);
+ // From IOptionsContainerWithSections
+ virtual OptionSectionImpl *addSectionImpl(const AbstractOptionSection §ion);
+
+ // From IOptionsContainer
+ virtual IOptionsContainer &addGroup();
+ virtual OptionInfo *addOptionImpl(const AbstractOption &settings);
+
+ //! Returns section info object for this section.
+ OptionSectionInfo &info() { return info_; }
+ //! Returns section info object for this section.
+ const OptionSectionInfo &info() const { return info_; }
/*! \brief
* Finds a subsection by name.
*
* Does not throw.
*/
- Options *findSubSection(const char *name) const;
+ OptionSectionImpl *findSection(const char *name) const;
/*! \brief
* Finds an option by name.
*
AbstractOptionStorage *findOption(const char *name) const;
/*! \brief
- * Calls AbstractOptionStorage::startSource() for all options,
- * including subsections.
+ * Called when entering the section.
*
- * Does not throw.
+ * Calls AbstractOptionStorage::startSource() for all options.
*/
- void startSource();
-
- //! Name for the Options object.
- std::string name_;
+ void start();
/*! \brief
- * Option managers set for this collection.
- *
- * This is non-empty only for the top-level Options object.
+ * Calls AbstractOptionStorage::finish() for all options.
*/
- OptionManagerContainer managers_;
+ void finish();
+
+ //! Reference to the option managers in the parent Options object.
+ const OptionManagerContainer &managers_;
+ //! Type-specific storage object for this section.
+ std::unique_ptr<IOptionSectionStorage> storage_;
+ //! Info object for this section.
+ OptionSectionInfo info_;
+ //! Name of this section (empty and unused for the root section).
+ std::string name_;
/*! \brief
* Group that contains all options (and subgroups).
*
* This is used to store the insertion order of options.
*/
- Group rootGroup_;
+ Group rootGroup_;
//! Map from option names to options; owns the option storage objects.
- OptionMap optionMap_;
- /*! \brief
- * List of subsections, in insertion order.
- *
- * This container contains only references to external objects; memory
- * management is performed elsewhere.
- */
- SubSectionList subSections_;
- //! Options object that contains this object as a subsection, or NULL.
- Options *parent_;
+ OptionMap optionMap_;
+ //! List of subsections, in insertion order.
+ SectionList subsections_;
+ //! Whether initStorage() has been called for `storage_`.
+ bool storageInitialized_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(OptionSectionImpl);
+};
+
+/*! \internal
+ * \brief
+ * Private implementation class for Options.
+ *
+ * Note that in addition to Options, the OptionsAssigner class also directly
+ * accesses this class.
+ *
+ * \ingroup module_options
+ */
+class OptionsImpl
+{
+ public:
+ OptionsImpl();
+
+ //! Option managers set for this collection.
+ OptionManagerContainer managers_;
+ //! Root section for this collection.
+ OptionSectionImpl rootSection_;
};
} // namespace internal
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/abstractoption.h"
#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/options/optionsection.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
{
}
+/********************************************************************
+ * IOptionsContainerWithSections
+ */
+
+IOptionsContainerWithSections::~IOptionsContainerWithSections()
+{
+}
+
+/********************************************************************
+ * IOptionSectionStorage
+ */
+
+IOptionSectionStorage::~IOptionSectionStorage()
+{
+}
+
/********************************************************************
* OptionsImpl
*/
namespace internal
{
-OptionsImpl::OptionsImpl(const char *name, const char * /*title*/)
- : name_(name != NULL ? name : ""), rootGroup_(this),
- parent_(NULL)
+OptionsImpl::OptionsImpl()
+ : rootSection_(managers_, nullptr, "")
+{
+}
+
+/********************************************************************
+ * OptionSectionImpl
+ */
+
+OptionSectionImpl *
+OptionSectionImpl::addSectionImpl(const AbstractOptionSection §ion)
+{
+ const char *name = section.name_;
+ // Make sure that there are no duplicate sections.
+ GMX_RELEASE_ASSERT(findSection(name) == nullptr, "Duplicate subsection name");
+ std::unique_ptr<IOptionSectionStorage> storage(section.createStorage());
+ subsections_.push_back(SectionPointer(new OptionSectionImpl(managers_, std::move(storage), name)));
+ return subsections_.back().get();
+}
+
+IOptionsContainer &OptionSectionImpl::addGroup()
{
+ return rootGroup_.addGroup();
}
-Options *OptionsImpl::findSubSection(const char *name) const
+OptionInfo *OptionSectionImpl::addOptionImpl(const AbstractOption &settings)
{
- SubSectionList::const_iterator i;
- for (i = subSections_.begin(); i != subSections_.end(); ++i)
+ return rootGroup_.addOptionImpl(settings);
+}
+
+OptionSectionImpl *OptionSectionImpl::findSection(const char *name) const
+{
+ for (const auto §ion : subsections_)
{
- if ((*i)->name() == name)
+ if (section->name_ == name)
{
- return *i;
+ return section.get();
}
}
- return NULL;
+ return nullptr;
}
-AbstractOptionStorage *OptionsImpl::findOption(const char *name) const
+AbstractOptionStorage *OptionSectionImpl::findOption(const char *name) const
{
OptionMap::const_iterator i = optionMap_.find(name);
if (i == optionMap_.end())
{
- return NULL;
+ return nullptr;
}
return i->second.get();
}
-void OptionsImpl::startSource()
+void OptionSectionImpl::start()
{
- OptionMap::const_iterator i;
- for (i = optionMap_.begin(); i != optionMap_.end(); ++i)
+ for (const auto &entry : optionMap_)
+ {
+ entry.second->startSource();
+ }
+ if (storage_ != nullptr)
+ {
+ if (!storageInitialized_)
+ {
+ storage_->initStorage();
+ storageInitialized_ = true;
+ }
+ storage_->startSection();
+ }
+}
+
+void OptionSectionImpl::finish()
+{
+ // TODO: Consider how to customize these error messages based on context.
+ ExceptionInitializer errors("Invalid input values");
+ for (const auto &entry : optionMap_)
+ {
+ AbstractOptionStorage &option = *entry.second;
+ try
+ {
+ option.finish();
+ }
+ catch (UserInputError &ex)
+ {
+ ex.prependContext("In option " + option.name());
+ errors.addCurrentExceptionAsNested();
+ }
+ }
+ if (errors.hasNestedExceptions())
{
- AbstractOptionStorage &option = *i->second;
- option.startSource();
+ // TODO: This exception type may not always be appropriate.
+ GMX_THROW(InvalidInputError(errors));
}
- SubSectionList::const_iterator j;
- for (j = subSections_.begin(); j != subSections_.end(); ++j)
+ if (storage_ != nullptr)
{
- Options §ion = **j;
- section.impl_->startSource();
+ storage_->finishSection();
}
}
/********************************************************************
- * OptionsImpl::Group
+ * OptionSectionImpl::Group
*/
-IOptionsContainer &OptionsImpl::Group::addGroup()
+IOptionsContainer &OptionSectionImpl::Group::addGroup()
{
- subgroups_.push_back(Group(parent_));
+ subgroups_.emplace_back(parent_);
return subgroups_.back();
}
-OptionInfo *OptionsImpl::Group::addOption(const AbstractOption &settings)
+OptionInfo *OptionSectionImpl::Group::addOptionImpl(const AbstractOption &settings)
{
- OptionsImpl *root = parent_;
- while (root->parent_ != NULL)
- {
- root = root->parent_->impl_.get();
- }
- AbstractOptionStoragePointer option(settings.createStorage(root->managers_));
+ OptionSectionImpl::AbstractOptionStoragePointer
+ option(settings.createStorage(parent_->managers_));
options_.reserve(options_.size() + 1);
- std::pair<OptionMap::iterator, bool> insertionResult =
+ auto insertionResult =
parent_->optionMap_.insert(std::make_pair(option->name(),
std::move(option)));
if (!insertionResult.second)
{
- GMX_THROW(APIError("Duplicate option: " + option->name()));
+ const std::string &name = insertionResult.first->second->name();
+ GMX_THROW(APIError("Duplicate option: " + name));
}
AbstractOptionStorage &insertedOption = *insertionResult.first->second;
options_.push_back(&insertedOption);
* Options
*/
-Options::Options(const char *name, const char *title)
- : impl_(new OptionsImpl(name, title))
+Options::Options()
+ : impl_(new OptionsImpl)
{
}
{
}
-const std::string &Options::name() const
-{
- return impl_->name_;
-}
-
void Options::addManager(IOptionManager *manager)
{
- GMX_RELEASE_ASSERT(impl_->parent_ == NULL,
- "Can only add a manager in a top-level Options object");
// This ensures that all options see the same set of managers.
- GMX_RELEASE_ASSERT(impl_->optionMap_.empty(),
+ GMX_RELEASE_ASSERT(impl_->rootSection_.optionMap_.empty(),
"Can only add a manager before options");
// This check could be relaxed if we instead checked that the subsections
// do not have options.
- GMX_RELEASE_ASSERT(impl_->subSections_.empty(),
+ GMX_RELEASE_ASSERT(impl_->rootSection_.subsections_.empty(),
"Can only add a manager before subsections");
impl_->managers_.add(manager);
}
-void Options::addSubSection(Options *section)
+internal::OptionSectionImpl *Options::addSectionImpl(const AbstractOptionSection §ion)
{
- // This is required, because managers are used from the root Options
- // object, so they are only seen after the subsection has been added.
- GMX_RELEASE_ASSERT(section->impl_->optionMap_.empty(),
- "Can only add a subsection before it has any options");
- GMX_RELEASE_ASSERT(section->impl_->managers_.empty(),
- "Can only have managers in a top-level Options object");
- // Make sure that section is not already inserted somewhere.
- GMX_RELEASE_ASSERT(section->impl_->parent_ == NULL,
- "Cannot add as subsection twice");
- // Make sure that there are no duplicate sections.
- GMX_RELEASE_ASSERT(impl_->findSubSection(section->name().c_str()) == NULL,
- "Duplicate subsection name");
- impl_->subSections_.push_back(section);
- section->impl_->parent_ = this;
+ return impl_->rootSection_.addSectionImpl(section);
}
IOptionsContainer &Options::addGroup()
{
- return impl_->rootGroup_.addGroup();
+ return impl_->rootSection_.addGroup();
+}
+
+OptionInfo *Options::addOptionImpl(const AbstractOption &settings)
+{
+ return impl_->rootSection_.addOptionImpl(settings);
}
-OptionInfo *Options::addOption(const AbstractOption &settings)
+OptionSectionInfo &Options::rootSection()
{
- return impl_->rootGroup_.addOption(settings);
+ return impl_->rootSection_.info();
+}
+
+const OptionSectionInfo &Options::rootSection() const
+{
+ return impl_->rootSection_.info();
}
void Options::finish()
{
- // TODO: Consider how to customize these error messages based on context.
- ExceptionInitializer errors("Invalid input values");
- OptionsImpl::OptionMap::const_iterator i;
- for (i = impl_->optionMap_.begin(); i != impl_->optionMap_.end(); ++i)
- {
- AbstractOptionStorage &option = *i->second;
- try
- {
- option.finish();
- }
- catch (UserInputError &ex)
- {
- ex.prependContext("In option " + option.name());
- errors.addCurrentExceptionAsNested();
- }
- }
- OptionsImpl::SubSectionList::const_iterator j;
- for (j = impl_->subSections_.begin(); j != impl_->subSections_.end(); ++j)
- {
- Options §ion = **j;
- try
- {
- section.finish();
- }
- catch (const UserInputError &)
- {
- errors.addCurrentExceptionAsNested();
- }
- }
- if (errors.hasNestedExceptions())
- {
- // TODO: This exception type may not always be appropriate.
- GMX_THROW(InvalidInputError(errors));
- }
+ impl_->rootSection_.finish();
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <string>
-#include "gromacs/options/ioptionscontainer.h"
+#include "gromacs/options/ioptionscontainerwithsections.h"
#include "gromacs/utility/classhelpers.h"
namespace gmx
{
class AbstractOption;
+class OptionSection;
+class OptionSectionInfo;
class OptionsAssigner;
-class OptionsIterator;
namespace internal
{
* Collection of options.
*
* See \ref module_options for an overview of how the options work.
- * The IOptionsContainer interface documents how to add options.
+ * The IOptionsContainerWithSections interface documents how to add options.
*
* In order to keep the public interface of this class simple, functionality
* to assign values to options is provided by a separate OptionsAssigner class.
* \inpublicapi
* \ingroup module_options
*/
-class Options : public IOptionsContainer
+class Options : public IOptionsContainerWithSections
{
public:
- /*! \brief
- * Initializes the name and title of an option collection.
- *
- * \param[in] name Single-word name.
- * \param[in] title Descriptive title.
- *
- * Copies the input strings.
- */
- Options(const char *name, const char *title);
+ //! Initializes an empty options root container.
+ Options();
~Options();
- //! Returns the short name of the option collection.
- const std::string &name() const;
-
/*! \brief
* Adds an option manager.
*
* The Options object (and its contained options) only stores a
* reference to the object.
*
- * This method cannot be called after adding options or subsections.
+ * This method cannot be called after adding options or sections.
*/
void addManager(IOptionManager *manager);
- /*! \brief
- * Adds an option collection as a subsection of this collection.
- *
- * \param[in] section Subsection to add.
- *
- * The name() field of \p section is used as the name of the
- * subsection. If an attempt is made to add two different subsections
- * with the same name, this function asserts.
- *
- * \p section should not have any options added at the point this
- * method is called.
- *
- * Only a pointer to the provided object is stored. The caller is
- * responsible that the object exists for the lifetime of the
- * collection.
- * It is not possible to add the same Options object as a subsection to
- * several different Options.
- * If an attempt is made, the function asserts.
- */
- void addSubSection(Options *section);
-
// From IOptionsContainer
virtual IOptionsContainer &addGroup();
- virtual OptionInfo *addOption(const AbstractOption &settings);
- using IOptionsContainer::addOption;
+
+ //! Returns a handle to the root section.
+ OptionSectionInfo &rootSection();
+ //! Returns a handle to the root section.
+ const OptionSectionInfo &rootSection() const;
/*! \brief
* Notifies the collection that all option values are assigned.
void finish();
private:
+ // From IOptionsContainerWithSections
+ virtual internal::OptionSectionImpl *
+ addSectionImpl(const AbstractOptionSection §ion);
+ // From IOptionsContainer
+ virtual OptionInfo *addOptionImpl(const AbstractOption &settings);
+
PrivateImplPointer<internal::OptionsImpl> impl_;
- //! Needed for the implementation to access subsections.
- friend class internal::OptionsImpl;
//! Needed to be able to extend the interface of this object.
friend class OptionsAssigner;
- //! Needed to be able to extend the interface of this object.
- friend class OptionsIterator;
- //! Needed to be able to extend the interface of this object.
- friend class OptionsModifyingIterator;
};
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/options.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/variant.h"
#include "options-impl.h"
class OptionsAssigner::Impl
{
public:
+ //! Shorthand for the internal type used to represent a section.
+ typedef internal::OptionSectionImpl Section;
+
//! Sets the option object to assign to.
explicit Impl(Options *options);
//! Returns true if a subsection has been set.
- bool inSubSection() const { return sectionStack_.size() > 1; }
+ bool inSection() const { return sectionStack_.size() > 1; }
//! Returns the Options object for the current section.
- Options ¤tSection() const { return *sectionStack_.back(); }
+ Section ¤tSection() const { return *sectionStack_.back(); }
/*! \brief
* Finds an option by the given name.
*
*
* The first element always points to \a options_.
*/
- std::vector<Options *> sectionStack_;
+ std::vector<Section *> sectionStack_;
//! Current option being assigned to, or NULL if none.
AbstractOptionStorage *currentOption_;
/*! \brief
OptionsAssigner::Impl::Impl(Options *options)
: options_(*options), bAcceptBooleanNoPrefix_(false),
- currentOption_(NULL), currentValueCount_(0), reverseBoolean_(false)
+ currentOption_(nullptr), currentValueCount_(0), reverseBoolean_(false)
{
- sectionStack_.push_back(&options_);
+ sectionStack_.push_back(&options_.impl_->rootSection_);
}
AbstractOptionStorage *
OptionsAssigner::Impl::findOption(const char *name)
{
- GMX_RELEASE_ASSERT(currentOption_ == NULL,
+ GMX_RELEASE_ASSERT(currentOption_ == nullptr,
"Cannot search for another option while processing one");
- const Options §ion = currentSection();
- AbstractOptionStorage *option = section.impl_->findOption(name);
- if (option == NULL && bAcceptBooleanNoPrefix_)
+ const Section §ion = currentSection();
+ AbstractOptionStorage *option = section.findOption(name);
+ if (option == nullptr && bAcceptBooleanNoPrefix_)
{
if (name[0] == 'n' && name[1] == 'o')
{
- option = section.impl_->findOption(name + 2);
- if (option != NULL && option->isBoolean())
+ option = section.findOption(name + 2);
+ if (option != nullptr && option->isBoolean())
{
reverseBoolean_ = true;
}
else
{
- option = NULL;
+ option = nullptr;
}
}
}
void OptionsAssigner::start()
{
- impl_->options_.impl_->startSource();
+ impl_->options_.impl_->rootSection_.start();
}
-void OptionsAssigner::startSubSection(const char *name)
+void OptionsAssigner::startSection(const char *name)
{
- Options *section = impl_->currentSection().impl_->findSubSection(name);
- if (section == NULL)
+ Impl::Section *section = impl_->currentSection().findSection(name);
+ if (section == nullptr)
{
GMX_THROW(InvalidInputError("Unknown subsection"));
}
impl_->sectionStack_.push_back(section);
+ section->start();
}
void OptionsAssigner::startOption(const char *name)
bool OptionsAssigner::tryStartOption(const char *name)
{
- GMX_RELEASE_ASSERT(impl_->currentOption_ == NULL, "finishOption() not called");
+ GMX_RELEASE_ASSERT(impl_->currentOption_ == nullptr, "finishOption() not called");
AbstractOptionStorage *option = impl_->findOption(name);
- if (option == NULL)
+ if (option == nullptr)
{
return false;
}
}
void OptionsAssigner::appendValue(const std::string &value)
+{
+ appendValue(Variant(value));
+}
+
+void OptionsAssigner::appendValue(const Variant &value)
{
AbstractOptionStorage *option = impl_->currentOption_;
- GMX_RELEASE_ASSERT(option != NULL, "startOption() not called");
+ GMX_RELEASE_ASSERT(option != nullptr, "startOption() not called");
++impl_->currentValueCount_;
option->appendValue(value);
}
void OptionsAssigner::finishOption()
{
AbstractOptionStorage *option = impl_->currentOption_;
- GMX_RELEASE_ASSERT(option != NULL, "startOption() not called");
+ GMX_RELEASE_ASSERT(option != nullptr, "startOption() not called");
bool bBoolReverseValue = false;
if (option->isBoolean())
{
if (impl_->currentValueCount_ == 0)
{
// Should not throw, otherwise something is wrong.
- // TODO: Get rid of the hard-coded values.
- option->appendValue(impl_->reverseBoolean_ ? "0" : "1");
+ option->appendValue(Variant::create<bool>(!impl_->reverseBoolean_));
}
else if (impl_->reverseBoolean_)
{
bBoolReverseValue = true;
}
}
- impl_->currentOption_ = NULL;
+ impl_->currentOption_ = nullptr;
impl_->reverseBoolean_ = false;
option->finishSet();
if (bBoolReverseValue)
}
}
-void OptionsAssigner::finishSubSection()
+void OptionsAssigner::finishSection()
{
// Should only be called if we are in a subsection.
- GMX_RELEASE_ASSERT(impl_->inSubSection(), "startSubSection() not called");
+ GMX_RELEASE_ASSERT(impl_->inSection(), "startSection() not called");
+ Impl::Section *section = impl_->sectionStack_.back();
+ section->finish();
impl_->sectionStack_.pop_back();
}
void OptionsAssigner::finish()
{
- GMX_RELEASE_ASSERT(impl_->currentOption_ == NULL, "finishOption() not called");
- GMX_RELEASE_ASSERT(!impl_->inSubSection(), "finishSubSection() not called");
+ GMX_RELEASE_ASSERT(impl_->currentOption_ == nullptr, "finishOption() not called");
+ GMX_RELEASE_ASSERT(!impl_->inSection(), "finishSection() not called");
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
class Options;
+class Variant;
/*! \libinternal \brief
* Decorator class for assigning values to Options.
assigner.startOption("opt1");
assigner.appendValue("3");
assigner.finishOption();
- assigner.startSubSection("section");
+ assigner.startSection("section");
assigner.startOption("opt2"); // Now in the subsection
assigner.appendValue("yes");
assigner.finishOption();
- assigner.finishSubSection()
+ assigner.finishSection()
assigner.startOption("opt3"); // Again in the main options
assigner.appendValue("2");
assigner.finishOption();
*
* Strong exception safety guarantee.
*/
- void startSubSection(const char *name);
+ void startSection(const char *name);
/*! \brief
* Starts assigning values for an option.
*
/*! \brief
* Appends a value to the value list of the current option.
*
- * \param[in] value String representation of the value to assign.
+ * \param[in] value Value to assign.
* \throws InvalidInputError if the value cannot be converted or if
* there are too many values for an option.
*
* OptionStorageTemplate::convertValue() method of the storage class
* implementing the option where the value is assigned to.
*/
+ void appendValue(const Variant &value);
+ /*! \brief
+ * Appends a value to the value list of the current option.
+ *
+ * \param[in] value Value to assign.
+ *
+ * See appendValue(const Variant &) for more details.
+ */
void appendValue(const std::string &value);
/*! \brief
* Finish assigning values for the current option.
*
* Does not throw.
*/
- void finishSubSection();
+ void finishSection();
/*! \brief
* Finish assigning options through the object.
*
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "optionsection.h"
+
+#include "gromacs/options/isectionstorage.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+class OptionSectionStorage : public IOptionSectionStorage
+{
+ public:
+ virtual void initStorage() {}
+ virtual void startSection() {}
+ virtual void finishSection() {}
+};
+
+} // namespace
+
+IOptionSectionStorage *OptionSection::createStorage() const
+{
+ return new OptionSectionStorage();
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::OptionSection and gmx::OptionSectionInfo.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inpublicapi
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_OPTIONSECTION_H
+#define GMX_OPTIONS_OPTIONSECTION_H
+
+#include "gromacs/options/abstractsection.h"
+#include "gromacs/utility/classhelpers.h"
+
+namespace gmx
+{
+
+class OptionSectionHandle;
+
+/*! \brief
+ * Declares a simple option section.
+ *
+ * This class declares a simple section that only provides structure for
+ * grouping the options, but does not otherwise influence the behavior of the
+ * contained options.
+ *
+ * \inpublicapi
+ * \ingroup module_options
+ */
+class OptionSection : public AbstractOptionSection
+{
+ public:
+ //! AbstractOptionSectionHandle corresponding to this option type.
+ typedef OptionSectionHandle HandleType;
+
+ //! Creates a section with the given name.
+ explicit OptionSection(const char *name) : AbstractOptionSection(name) {}
+
+ private:
+ virtual IOptionSectionStorage *createStorage() const;
+};
+
+/*! \brief
+ * Allows adding options to an OptionSection.
+ *
+ * An instance of this class is returned from
+ * IOptionsContainerWithSections::addSection(), and supports adding options and
+ * subsections to a section created with OptionSection.
+ *
+ * \inpublicapi
+ * \ingroup module_options
+ */
+class OptionSectionHandle : public AbstractOptionSectionHandle
+{
+ public:
+ //! Wraps a given section storage object.
+ explicit OptionSectionHandle(internal::OptionSectionImpl *section)
+ : AbstractOptionSectionHandle(section)
+ {
+ }
+};
+
+class OptionSectionInfo : public AbstractOptionSectionInfo
+{
+ public:
+ //! Wraps a given section storage object.
+ explicit OptionSectionInfo(internal::OptionSectionImpl *section)
+ : AbstractOptionSectionInfo(section)
+ {
+ }
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/abstractoption.h"
#include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/options/valuestore.h"
+#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/variant.h"
+
+#include "valueconverter.h"
namespace gmx
{
*
* \tparam T Assignable type that stores a single option value.
*
- * Provides an implementation of the clearSet(), valueCount(), and processSet()
- * methods of AbstractOptionStorage, as well as a basic no-action
- * implementation of processAll(). Two new virtual methods are added:
- * processSetValues() and refreshValues(). The default implementation of
- * processSetValues() does nothing, and refreshValues() is used to update
- * secondary storage after values have been added/changed.
- * This leaves typeString(), formatValue(), and convertValue() to be
- * implemented in derived classes. processSetValues() and processAll() can
- * also be implemented if necessary.
+ * Provides an implementation of the clearSet(), valueCount(), processSet(),
+ * and defaultValuesAsStrings() methods of AbstractOptionStorage, as well as a
+ * basic no-action implementation of processAll(). Two new virtual methods are
+ * added: processSetValues() and formatSingleValue().
+ * This leaves typeString(), convertValue() and formatStringValue() to be
+ * implemented in derived classes.
+ * processSetValues() and processAll() can also be implemented if necessary.
*
* Implements transaction support for adding values within a set: all calls to
* addValue() add the value to a temporary storage, processSetValues() operates
//! Type of the container that contains the current values.
typedef std::vector<T> ValueList;
- virtual ~OptionStorageTemplate();
-
// No implementation in this class for the pure virtual methods, but
// the declarations are still included for clarity.
// The various copydoc calls are needed with Doxygen 1.8.10, although
// things work without with 1.8.5...
virtual std::string typeString() const = 0;
//! \copydoc gmx::AbstractOptionStorage::valueCount()
- virtual int valueCount() const { return static_cast<int>(values_->size()); }
- /*! \copydoc gmx::AbstractOptionStorage::formatValue()
+ virtual int valueCount() const { return store_->valueCount(); }
+ //! \copydoc gmx::AbstractOptionStorage::defaultValues()
+ virtual std::vector<Variant> defaultValues() const;
+ /*! \copydoc gmx::AbstractOptionStorage::defaultValuesAsStrings()
*
- * OptionStorageTemplate implements handling of DefaultValueIfSetIndex
- * in this method, as well as checking that \p i is a valid index.
+ * OptionStorageTemplate implements handling of defaultValueIfSet()
+ * cases and composing the vector.
* Derived classes must implement formatSingleValue() to provide the
* actual formatting for a value of type \p T.
*/
- virtual std::string formatValue(int i) const;
+ virtual std::vector<std::string> defaultValuesAsStrings() const;
protected:
+ //! Smart pointer for managing the final storage interface.
+ typedef std::unique_ptr<IOptionValueStore<T> > StorePointer;
+
/*! \brief
* Initializes the storage from option settings.
*
* Initializes the storage from base option settings.
*
* \param[in] settings Option settings.
+ * \param[in] store Final storage location.
* \throws APIError if invalid settings have been provided.
*
* This constructor works for cases where there is no matching
* OptionTemplate (e.g., EnumOption).
*/
- explicit OptionStorageTemplate(const AbstractOption &settings);
+ OptionStorageTemplate(const AbstractOption &settings,
+ StorePointer store);
//! \copydoc gmx::AbstractOptionStorage::clearSet()
virtual void clearSet();
* should be considered whether the implementation can be made strongly
* exception safe.
*/
- virtual void convertValue(const std::string &value) = 0;
+ virtual void convertValue(const Variant &value) = 0;
/*! \brief
* Processes values for a set after all have been converted.
*
* \returns \p value formatted as a string.
*
* The derived class must provide this method to format values a
- * strings. Called by formatValue() to do the actual formatting.
+ * strings. Called by defaultValuesAsStrings() to do the actual
+ * formatting.
*/
virtual std::string formatSingleValue(const T &value) const = 0;
- /*! \brief
- * Removes all values from the storage.
- *
- * Does not throw.
- */
- void clear() { values_->clear(); }
/*! \brief
* Adds a value to a temporary storage.
*
* See addValue() for cases where this method should be used in derived
* classes.
*
- * Calls refreshValues() and clearSet() if it is successful.
+ * Calls clearSet() if it is successful.
*/
void commitValues();
- /*! \brief
- * Updates alternative store locations.
- *
- * Derived classes should override this method if they implement
- * alternative store locations, and copy/translate values from the
- * values() vector to these alternative storages. They should also
- * call the base class implementation as part of their implementation.
- *
- * Should be called in derived classes if values are modified directly
- * through the values() method, e.g., in processAll(). Does not need
- * to be called if commitValues() is used.
- *
- * Does not throw, and derived classes should not change that.
- */
- virtual void refreshValues();
/*! \brief
* Sets the default value for the option.
* Provides derived classes access to the current list of values.
*
* The non-const variant should only be used from processAll() in
- * derived classes if necessary, and refreshValues() should be called
- * if any changes are made.
+ * derived classes if necessary.
*/
- ValueList &values() { return *values_; }
+ ArrayRef<T> values() { return store_->values(); }
//! Provides derived classes access to the current list of values.
- const ValueList &values() const { return *values_; }
+ ConstArrayRef<T> values() const { return store_->values(); }
private:
+ //! Creates the internal storage object for final values..
+ StorePointer createStore(ValueList *storeVector,
+ T *store, int *storeCount,
+ int initialCount);
+
/*! \brief
* Vector for temporary storage of values before commitSet() is called.
*/
ValueList setValues_;
+ //! Final storage for option values.
+ const StorePointer store_;
+ // This never releases ownership.
+ std::unique_ptr<T> defaultValueIfSet_;
+
+ // Copy and assign disallowed by base.
+};
+
+
+/*! \libinternal \brief
+ * Simplified option storage template for options that have one-to-one value
+ * conversion.
+ *
+ * \tparam T Assignable type that stores a single option value.
+ *
+ * To implement an option that always map a single input value to a single
+ * output value, derive from this class instead of OptionStorageTemplate.
+ * This class implements convertValue() in terms of two new virtual methods:
+ * initConverter() and processValue().
+ *
+ * To specify how different types of values need to be converted, implement
+ * initConverter().
+ * To do common post-processing of the values after conversion, but before they
+ * are added to the underlying storage, override processValue().
+ *
+ * \inlibraryapi
+ * \ingroup module_options
+ */
+template <typename T>
+class OptionStorageTemplateSimple : public OptionStorageTemplate<T>
+{
+ public:
+ //! Alias for the template class for use in base classes.
+ typedef OptionStorageTemplateSimple<T> MyBase;
+
+ protected:
+ //! Alias for the converter parameter type for initConverter().
+ typedef OptionValueConverterSimple<T> ConverterType;
+
+ //! Initializes the storage.
+ template <class U>
+ explicit OptionStorageTemplateSimple(const OptionTemplate<T, U> &settings,
+ OptionFlags staticFlags = OptionFlags())
+ : OptionStorageTemplate<T>(settings, staticFlags), initialized_(false)
+ {
+ }
+ //! Initializes the storage.
+ OptionStorageTemplateSimple(const AbstractOption &settings,
+ typename OptionStorageTemplate<T>::StorePointer store)
+ : OptionStorageTemplate<T>(settings, std::move(store)), initialized_(false)
+ {
+ }
+
+ virtual std::vector<Variant>
+ normalizeValues(const std::vector<Variant> &values) const
+ {
+ const_cast<MyBase *>(this)->ensureConverterInitialized();
+ std::vector<Variant> result;
+ for (const auto &value : values)
+ {
+ result.push_back(normalizeValue(converter_.convert(value)));
+ }
+ return result;
+ }
+
+ /*! \brief
+ * Specifies how different types are converted.
+ *
+ * See OptionValueConverterSimple for more details.
+ */
+ virtual void initConverter(ConverterType *converter) = 0;
+ /*! \brief
+ * Post-processes a value after conversion to the output type.
+ *
+ * \param[in] value Value after conversion.
+ * \returns Value to store for the option.
+ *
+ * The default implementation only provides an identity mapping.
+ */
+ virtual T processValue(const T &value) const
+ {
+ return value;
+ }
/*! \brief
- * Vector for primary storage of option values.
+ * Converts a single value to normalized type.
*
- * Is never NULL; points either to externally provided vector, or an
- * internally allocated one. The allocation is performed by the
- * constructor.
+ * \param[in] value Value after conversion.
+ * \returns Value to store for the option.
*
- * Primarily, modifications to values are done only to this storage,
- * and other storage locations are updated only when refreshValues() is
- * called.
+ * This can be overridden to serialize a different type than `T`
+ * when using the option with KeyValueTreeObject.
*/
- ValueList *values_;
- T *store_;
- int *countptr_;
- // These never release ownership.
- std::unique_ptr<ValueList> ownedValues_;
- std::unique_ptr<T> defaultValueIfSet_;
+ virtual Variant normalizeValue(const T &value) const
+ {
+ return Variant::create<T>(processValue(value));
+ }
- // Copy and assign disallowed by base.
+ private:
+ virtual void convertValue(const Variant &variant)
+ {
+ ensureConverterInitialized();
+ this->addValue(processValue(converter_.convert(variant)));
+ }
+ void ensureConverterInitialized()
+ {
+ if (!initialized_)
+ {
+ initConverter(&converter_);
+ initialized_ = true;
+ }
+ }
+
+ ConverterType converter_;
+ bool initialized_;
};
+/********************************************************************
+ * OptionStorageTemplate implementation
+ */
+
template <typename T>
template <class U>
OptionStorageTemplate<T>::OptionStorageTemplate(const OptionTemplate<T, U> &settings,
OptionFlags staticFlags)
: AbstractOptionStorage(settings, staticFlags),
- values_(settings.storeVector_),
- store_(settings.store_),
- countptr_(settings.countptr_)
+ store_(createStore(settings.storeVector_,
+ settings.store_, settings.countptr_,
+ (settings.isVector() ?
+ settings.maxValueCount_ : settings.minValueCount_)))
{
- // If the maximum number of values is not known, storage to
- // caller-allocated memory is unsafe.
- if (store_ != NULL && (maxValueCount() < 0 || hasFlag(efOption_MultipleTimes)))
- {
- GMX_THROW(APIError("Cannot set user-allocated storage for arbitrary number of values"));
- }
- if (values_ == NULL)
- {
- ownedValues_.reset(new std::vector<T>);
- values_ = ownedValues_.get();
- }
if (hasFlag(efOption_NoDefaultValue)
- && (settings.defaultValue_ != NULL
- || settings.defaultValueIfSet_ != NULL))
+ && (settings.defaultValue_ != nullptr
+ || settings.defaultValueIfSet_ != nullptr))
{
GMX_THROW(APIError("Option does not support default value, but one is set"));
}
- if (store_ != NULL && countptr_ == NULL && !isVector()
- && minValueCount() != maxValueCount())
- {
- GMX_THROW(APIError("Count storage is not set, although the number of produced values is not known"));
- }
if (!hasFlag(efOption_NoDefaultValue))
{
setFlag(efOption_HasDefaultValue);
- if (settings.defaultValue_ != NULL)
+ if (settings.defaultValue_ != nullptr)
{
setDefaultValue(*settings.defaultValue_);
}
- else if (ownedValues_.get() != NULL && store_ != NULL)
- {
- values_->clear();
- int count = (settings.isVector() ?
- settings.maxValueCount_ : settings.minValueCount_);
- for (int i = 0; i < count; ++i)
- {
- values_->push_back(store_[i]);
- }
- }
- if (settings.defaultValueIfSet_ != NULL)
+ if (settings.defaultValueIfSet_ != nullptr)
{
setDefaultValueIfSet(*settings.defaultValueIfSet_);
}
template <typename T>
-// cppcheck-suppress uninitMemberVar
-OptionStorageTemplate<T>::OptionStorageTemplate(const AbstractOption &settings)
- : AbstractOptionStorage(settings, OptionFlags()),
- store_(NULL), countptr_(NULL),
- ownedValues_(new std::vector<T>())
+OptionStorageTemplate<T>::OptionStorageTemplate(const AbstractOption &settings,
+ StorePointer store)
+ : AbstractOptionStorage(settings, OptionFlags()), store_(std::move(store))
+{
+}
+
+
+template <typename T>
+std::unique_ptr<IOptionValueStore<T> > OptionStorageTemplate<T>::createStore(
+ ValueList *storeVector, T *store, int *storeCount, int initialCount)
{
- values_ = ownedValues_.get();
+ if (storeVector != nullptr)
+ {
+ GMX_RELEASE_ASSERT(store == nullptr && storeCount == nullptr,
+ "Cannot specify more than one storage location");
+ return StorePointer(new OptionValueStoreVector<T>(storeVector));
+ }
+ else if (store != nullptr)
+ {
+ // If the maximum number of values is not known, storage to
+ // caller-allocated memory is unsafe.
+ if (maxValueCount() < 0 || hasFlag(efOption_MultipleTimes))
+ {
+ GMX_THROW(APIError("Cannot set user-allocated storage for arbitrary number of values"));
+ }
+ if (storeCount == nullptr && !isVector() && minValueCount() != maxValueCount())
+ {
+ GMX_THROW(APIError("Count storage is not set, although the number of produced values is not known"));
+ }
+ if (hasFlag(efOption_NoDefaultValue))
+ {
+ initialCount = 0;
+ }
+ return StorePointer(new OptionValueStorePlain<T>(store, storeCount, initialCount));
+ }
+ GMX_RELEASE_ASSERT(storeCount == nullptr,
+ "Cannot specify count storage without value storage");
+ return StorePointer(new OptionValueStoreNull<T>());
}
template <typename T>
-OptionStorageTemplate<T>::~OptionStorageTemplate()
+std::vector<Variant> OptionStorageTemplate<T>::defaultValues() const
{
+ std::vector<Variant> result;
+ if (hasFlag(efOption_NoDefaultValue))
+ {
+ return result;
+ }
+ GMX_RELEASE_ASSERT(hasFlag(efOption_HasDefaultValue),
+ "Current option implementation can only provide default values before assignment");
+ for (const auto &value : values())
+ {
+ result.push_back(Variant::create<T>(value));
+ }
+ return normalizeValues(result);
}
template <typename T>
-std::string OptionStorageTemplate<T>::formatValue(int i) const
+std::vector<std::string> OptionStorageTemplate<T>::defaultValuesAsStrings() const
{
- GMX_RELEASE_ASSERT(i == DefaultValueIfSetIndex || (i >= 0 && i < valueCount()),
- "Invalid value index");
- if (i == DefaultValueIfSetIndex)
+ std::vector<std::string> result;
+ if (hasFlag(efOption_NoDefaultValue))
+ {
+ return result;
+ }
+ GMX_RELEASE_ASSERT(hasFlag(efOption_HasDefaultValue),
+ "Current option implementation can only provide default values before assignment");
+ for (const auto &value : values())
{
- if (defaultValueIfSet_.get() != NULL)
+ result.push_back(formatSingleValue(value));
+ }
+ if (result.empty() || (result.size() == 1 && result[0].empty()))
+ {
+ result.clear();
+ if (defaultValueIfSet_.get() != nullptr)
{
- return formatSingleValue(*defaultValueIfSet_);
+ result.push_back(formatSingleValue(*defaultValueIfSet_));
}
- return std::string();
}
- return formatSingleValue(values()[i]);
+ return result;
}
void OptionStorageTemplate<T>::processSet()
{
processSetValues(&setValues_);
- if (setValues_.empty() && defaultValueIfSet_.get() != NULL)
+ if (setValues_.empty() && defaultValueIfSet_.get() != nullptr)
{
addValue(*defaultValueIfSet_);
setFlag(efOption_HasDefaultValue);
{
if (hasFlag(efOption_ClearOnNextSet))
{
- values_->swap(setValues_);
+ store_->clear();
}
- else
+ store_->reserve(setValues_.size());
+ for (T value : setValues_)
{
- values_->reserve(values_->size() + setValues_.size());
- values_->insert(values_->end(), setValues_.begin(), setValues_.end());
+ store_->append(value);
}
clearSet();
- refreshValues();
-}
-
-
-template <typename T>
-void OptionStorageTemplate<T>::refreshValues()
-{
- if (countptr_ != NULL)
- {
- *countptr_ = static_cast<int>(values_->size());
- }
- if (store_ != NULL)
- {
- for (size_t i = 0; i < values_->size(); ++i)
- {
- store_[i] = (*values_)[i];
- }
- }
}
if (hasFlag(efOption_HasDefaultValue))
{
setFlag(efOption_ExplicitDefaultValue);
- clear();
- clearSet();
- addValue(value);
- // TODO: As this is called from the constructor, it should not call
- // virtual functions.
- commitValues();
+ store_->clear();
+ store_->append(value);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/abstractoptionstorage.h"
#include "gromacs/options/options.h"
+#include "gromacs/options/optionsection.h"
#include "options-impl.h"
//! Helper function to recursively visit all options in a group.
template <class VisitorType>
-void acceptOptionsGroup(const OptionsImpl::Group &group, VisitorType *visitor)
+void acceptOptionsGroup(const internal::OptionSectionImpl::Group &group, VisitorType *visitor)
{
- OptionsImpl::Group::OptionList::const_iterator option;
- for (option = group.options_.begin(); option != group.options_.end(); ++option)
+ for (const auto &option : group.options_)
{
- visitOption(visitor, (*option)->optionInfo());
+ visitOption(visitor, option->optionInfo());
}
- OptionsImpl::Group::SubgroupList::const_iterator subgroup;
- for (subgroup = group.subgroups_.begin(); subgroup != group.subgroups_.end(); ++subgroup)
+ for (const auto &subgroup : group.subgroups_)
{
- acceptOptionsGroup(*subgroup, visitor);
+ acceptOptionsGroup(subgroup, visitor);
}
}
*/
OptionsIterator::OptionsIterator(const Options &options)
- : options_(options)
+ : section_(options.rootSection().section())
{
}
-void OptionsIterator::acceptSubSections(OptionsVisitor *visitor) const
+OptionsIterator::OptionsIterator(const OptionSectionInfo §ion)
+ : section_(section.section())
{
- const OptionsImpl::SubSectionList &subSectionList =
- options_.impl_->subSections_;
- OptionsImpl::SubSectionList::const_iterator i;
- for (i = subSectionList.begin(); i != subSectionList.end(); ++i)
+}
+
+void OptionsIterator::acceptSections(OptionsVisitor *visitor) const
+{
+ for (const auto §ion : section_.subsections_)
{
- visitor->visitSubSection(*(*i));
+ visitor->visitSection(section->info());
}
}
void OptionsIterator::acceptOptions(OptionsVisitor *visitor) const
{
- acceptOptionsGroup(options_.impl_->rootGroup_, visitor);
+ acceptOptionsGroup(section_.rootGroup_, visitor);
}
/********************************************************************
*/
OptionsModifyingIterator::OptionsModifyingIterator(Options *options)
- : options_(*options)
+ : section_(options->rootSection().section())
+{
+}
+
+OptionsModifyingIterator::OptionsModifyingIterator(OptionSectionInfo *section)
+ : section_(section->section())
{
}
-void OptionsModifyingIterator::acceptSubSections(OptionsModifyingVisitor *visitor) const
+void OptionsModifyingIterator::acceptSections(OptionsModifyingVisitor *visitor) const
{
- const OptionsImpl::SubSectionList &subSectionList =
- options_.impl_->subSections_;
- OptionsImpl::SubSectionList::const_iterator i;
- for (i = subSectionList.begin(); i != subSectionList.end(); ++i)
+ for (auto §ion : section_.subsections_)
{
- visitor->visitSubSection(*i);
+ visitor->visitSection(§ion->info());
}
}
void OptionsModifyingIterator::acceptOptions(OptionsModifyingVisitor *visitor) const
{
- acceptOptionsGroup(options_.impl_->rootGroup_, visitor);
+ acceptOptionsGroup(section_.rootGroup_, visitor);
}
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
class Options;
+class OptionSectionInfo;
+
+namespace internal
+{
+class OptionSectionImpl;
+}
/*! \libinternal \brief
* Pure interface for visiting options in a Options object.
public:
virtual ~OptionsVisitor() {}
- /*! \brief
- * Called for each subsection in Options.
- */
- virtual void visitSubSection(const Options §ion) = 0;
- /*! \brief
- * Called for each option in Options.
- */
+ //! Called for each section.
+ virtual void visitSection(const OptionSectionInfo §ion) = 0;
+ //! Called for each option.
virtual void visitOption(const OptionInfo &option) = 0;
};
public:
virtual ~OptionsTypeVisitor() {}
- virtual void visitSubSection(const Options §ion) = 0;
+ virtual void visitSection(const OptionSectionInfo §ion) = 0;
/*! \brief
* Called for each option of type \p InfoType.
*/
/*! \libinternal \brief
* Decorator class for visiting options in a Options object.
*
- * This class provides an interface for looping through subsections and
+ * This class provides an interface for looping through sections and
* options in a Options object.
*
* Typical use (loop over all options, iteratively descending into
class Visitor : public gmx::OptionsVisitor
{
public:
- void visitSubSection(const Options §ion)
+ virtual void visitSection(const OptionSectionInfo §ion)
{
OptionsIterator iterator(section);
- iterator.acceptSubSections(this);
+ iterator.acceptSections(this);
iterator.acceptOptions(this);
}
- void visitOption(const OptionInfo &option)
+ virtual void visitOption(const OptionInfo &option)
{
// Do something.
}
}
- Visitor().visitSubSection(options);
+ Visitor().visitSection(options.rootSection());
* \endcode
*
* \inlibraryapi
public:
/*! \brief
* Creates an object for visiting options in a Options object.
+ *
+ * The created iterator iterates over the "root" section in the Options
+ * object.
*/
explicit OptionsIterator(const Options &options);
+ //! Creates an object for visiting options in an options section.
+ explicit OptionsIterator(const OptionSectionInfo §ion);
- /*! \brief
- * Visits each subsection in the wrapped Options object.
- */
- void acceptSubSections(OptionsVisitor *visitor) const;
- /*! \brief
- * Visits each option in the wrapped Options object.
- */
+ //! Visits each section in the wrapped section.
+ void acceptSections(OptionsVisitor *visitor) const;
+ //! Visits each option in the wrapped section.
void acceptOptions(OptionsVisitor *visitor) const;
private:
- //! The wrapped Options object.
- const Options &options_;
+ //! The wrapped section object.
+ const internal::OptionSectionImpl §ion_;
GMX_DISALLOW_COPY_AND_ASSIGN(OptionsIterator);
};
public:
virtual ~OptionsModifyingVisitor() {}
- /*! \brief
- * Called for each subsection in Options.
- */
- virtual void visitSubSection(Options *section) = 0;
- /*! \brief
- * Called for each option in Options.
- */
+ //! Called for each section.
+ virtual void visitSection(OptionSectionInfo *section) = 0;
+ //! Called for each option.
virtual void visitOption(OptionInfo *option) = 0;
};
public:
virtual ~OptionsModifyingTypeVisitor() {}
- virtual void visitSubSection(Options *section) = 0;
+ virtual void visitSection(OptionSectionInfo *section) = 0;
/*! \brief
* Called for each option of type \p InfoType.
*/
virtual void visitOption(OptionInfo *option)
{
InfoType *subtype = option->toType<InfoType>();
- if (subtype != NULL)
+ if (subtype != nullptr)
{
visitOptionType(subtype);
}
public:
/*! \brief
* Creates an object for visiting options in a Options object.
+ *
+ * The created iterator iterates over the "root" section in the Options
+ * object.
*/
explicit OptionsModifyingIterator(Options *options);
+ //! Creates an object for visiting options in an options section.
+ explicit OptionsModifyingIterator(OptionSectionInfo *section);
- /*! \brief
- * Visits each subsection in the wrapped Options object.
- */
- void acceptSubSections(OptionsModifyingVisitor *visitor) const;
- /*! \brief
- * Visits each option in the wrapped Options object.
- */
+ //! Visits each section in the wrapped section.
+ void acceptSections(OptionsModifyingVisitor *visitor) const;
+ //! Visits each option in the wrapped section.
void acceptOptions(OptionsModifyingVisitor *visitor) const;
private:
- //! The wrapped Options object.
- Options &options_;
+ //! The wrapped section object.
+ internal::OptionSectionImpl §ion_;
GMX_DISALLOW_COPY_AND_ASSIGN(OptionsModifyingIterator);
};
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares gmx::RepeatingOptionSection and related classes.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inpublicapi
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_REPEATINGSECTION_H
+#define GMX_OPTIONS_REPEATINGSECTION_H
+
+#include <memory>
+#include <vector>
+
+#include "gromacs/options/abstractsection.h"
+#include "gromacs/options/ioptionscontainerwithsections.h"
+#include "gromacs/options/isectionstorage.h"
+#include "gromacs/options/valuestore.h"
+
+namespace gmx
+{
+
+template <class T> class RepeatingOptionSectionHandle;
+template <class T> class RepeatingOptionSectionStorage;
+
+/*! \brief
+ * Declares an option section that creates a structure for each instance.
+ *
+ * \tparam T Structure that stores the values for an instance of the section.
+ *
+ * This class declares a section that can be specified multiple times, and
+ * creates an instance of `T` for each instance. Options within the section
+ * can store their values in the created structure.
+ *
+ * \inpublicapi
+ * \ingroup module_options
+ */
+template <class T>
+class RepeatingOptionSection : public AbstractOptionSection
+{
+ public:
+ //! AbstractOptionSectionHandle corresponding to this option type.
+ typedef RepeatingOptionSectionHandle<T> HandleType;
+
+ //! Creates a section with the given name.
+ explicit RepeatingOptionSection(const char *name)
+ : AbstractOptionSection(name), values_(nullptr)
+ {
+ }
+
+ //! Specifies a vector to receive the section structures.
+ RepeatingOptionSection &storeVector(std::vector<T> *values)
+ {
+ values_ = values;
+ return *this;
+ }
+
+ private:
+ virtual IOptionSectionStorage *createStorage() const;
+
+ std::vector<T> *values_;
+
+ //! Allows accessing the properties when initializing the storage.
+ friend class RepeatingOptionSectionStorage<T>;
+};
+
+/*! \internal
+ * \brief
+ * Implements handling of the structures that stores per-section values.
+ *
+ * \ingroup module_options
+ */
+template <class T>
+class RepeatingOptionSectionStorage : public IOptionSectionStorage
+{
+ public:
+ //! Initializes the storage for given section properties.
+ explicit RepeatingOptionSectionStorage(const RepeatingOptionSection<T> §ion)
+ : store_(new OptionValueStoreVector<T>(section.values_)), currentData_()
+ {
+ }
+
+ virtual void initStorage()
+ {
+ defaultValues_ = currentData_;
+ }
+ virtual void startSection()
+ {
+ resetSection();
+ }
+ virtual void finishSection()
+ {
+ store_->append(currentData_);
+ resetSection();
+ }
+
+ private:
+ void resetSection()
+ {
+ currentData_ = defaultValues_;
+ }
+
+ //! Final storage location for the section structures.
+ const std::unique_ptr<IOptionValueStore<T> > store_;
+ T defaultValues_;
+ /*! \brief
+ * Stores the values for the current in-process section.
+ *
+ * Options within the section store their values to this structure, and
+ * they are then copied to the final storage when the section finishes.
+ */
+ T currentData_;
+
+ //! Allows binding option storage to the current section data structure.
+ friend class RepeatingOptionSectionHandle<T>;
+};
+
+template <class T>
+IOptionSectionStorage *RepeatingOptionSection<T>::createStorage() const
+{
+ return new RepeatingOptionSectionStorage<T>(*this);
+}
+
+/*! \brief
+ * Allows adding options to an RepeatingOptionSection.
+ *
+ * An instance of this class is returned from
+ * IOptionsContainerWithSections::addSection(), and supports adding options and
+ * subsections to a section created with OptionSection.
+ *
+ * Example:
+ * \code
+ struct SectionData { int value; }
+ // as class attribute
+ std::vector<SectionData> values;
+
+ void MyClass::initOptions(gmx::IOptionsContainerWithSections *options)
+ {
+ auto sec = options->addSection(gmx::RepeatingOptionSection<SectionData>("sec").storeVector(&values));
+ sec->addOption(gmx::IntegerOption("arg").store(&sec.bind().value));
+ }
+ \endcode
+ *
+ * \inpublicapi
+ * \ingroup module_options
+ */
+template <class T>
+class RepeatingOptionSectionHandle : public AbstractOptionSectionHandle
+{
+ public:
+ //! Wraps a given section storage object.
+ explicit RepeatingOptionSectionHandle(internal::OptionSectionImpl *section)
+ : AbstractOptionSectionHandle(section),
+ storage_(getStorage<RepeatingOptionSectionStorage<T> >(section))
+ {
+ }
+
+ /*! \brief
+ * Supports storing option values within the per-section data structure.
+ *
+ * See class documentation for an example.
+ */
+ T &bind()
+ {
+ return storage_->currentData_;
+ }
+
+ private:
+ RepeatingOptionSectionStorage<T> *storage_;
+};
+
+} // namespace gmx
+
+#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2014,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
filenameoptionmanager.cpp
option.cpp
optionsassigner.cpp
- timeunitmanager.cpp)
+ repeatingsection.cpp
+ timeunitmanager.cpp
+ treesupport.cpp
+ )
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \param[in] settings Storage settings.
*/
- MockOptionStorage(const MockOption &settings);
+ explicit MockOptionStorage(const MockOption &settings);
/*! \brief
* Calls addValue("dummy") in the base class.
{
addValue("dummy");
}
- // using MyBase::markAsSet;
- // using MyBase::addValue;
- // using MyBase::commitValues;
- // "using" is correct but MSVC gives error C2248. Workaround:
- //! \copydoc gmx::OptionStorageTemplate::markAsSet()
- void markAsSet()
- {
- MyBase::markAsSet();
- }
- //! \copydoc gmx::OptionStorageTemplate::addValue()
- void addValue(const std::string &value)
- {
- MyBase::addValue(value);
- }
- //! \copydoc gmx::OptionStorageTemplate::commitValues()
- void commitValues()
- {
- MyBase::commitValues();
- }
+ using MyBase::markAsSet;
+ using MyBase::addValue;
+ using MyBase::commitValues;
virtual gmx::OptionInfo &optionInfo() { return info_; }
// These are not used.
{
return "";
}
+ virtual std::vector<gmx::Variant>
+ normalizeValues(const std::vector<gmx::Variant> &values) const
+ {
+ return values;
+ }
+
+ virtual void convertValue(const gmx::Variant &value)
+ {
+ convertValue(value.cast<std::string>());
+ }
MOCK_METHOD1(convertValue, void(const std::string &value));
MOCK_METHOD1(processSetValues, void(ValueList *values));
*/
TEST(AbstractOptionStorageTest, HandlesSetInFinish)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<std::string> values;
MockOptionInfo *info = options.addOption(
MockOption("name").required().storeVector(&values));
*/
TEST(AbstractOptionStorageTest, HandlesValueRemoval)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<std::string> values;
MockOptionInfo *info = options.addOption(
MockOption("name").storeVector(&values).multiValue());
*/
TEST(AbstractOptionStorageTest, HandlesValueAddition)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<std::string> values;
MockOptionInfo *info = options.addOption(
MockOption("name").storeVector(&values).multiValue());
*/
TEST(AbstractOptionStorageTest, HandlesTooManyValueAddition)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<std::string> values;
MockOptionInfo *info = options.addOption(
MockOption("name").storeVector(&values).valueCount(2));
*/
TEST(AbstractOptionStorageTest, AllowsEmptyValues)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<std::string> values;
MockOptionInfo *info = options.addOption(
MockOption("name").storeVector(&values).valueCount(0));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST(FileNameOptionTest, HandlesRequiredDefaultValueWithoutExtension)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value).required()
TEST(FileNameOptionTest, HandlesRequiredOptionWithoutValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value).required()
TEST(FileNameOptionTest, HandlesOptionalUnsetOption)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value)
TEST(FileNameOptionTest, HandlesOptionalDefaultValueWithoutExtension)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value)
TEST(FileNameOptionTest, HandlesRequiredCustomDefaultExtension)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value).required()
TEST(FileNameOptionTest, HandlesOptionalCustomDefaultExtension)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value)
TEST(FileNameOptionTest, GivesErrorOnUnknownFileSuffix)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value)
TEST(FileNameOptionTest, GivesErrorOnInvalidFileSuffix)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
ASSERT_NO_THROW_GMX(options.addOption(
FileNameOption("f").store(&value)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
public:
FileNameOptionManagerTest()
- : options_(NULL, NULL)
{
manager_.setInputRedirector(&redirector_);
options_.addManager(&manager_);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
TEST(OptionsTest, FailsOnNonsafeStorage)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = -1;
using gmx::IntegerOption;
ASSERT_THROW_GMX(options.addOption(IntegerOption("name").store(&value)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/options.h"
+#include "gromacs/options/optionsection.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/variant.h"
#include "testutils/testasserts.h"
TEST(OptionsAssignerTest, HandlesMissingRequiredParameter)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = 0;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerTest, HandlesRequiredParameterWithDefaultValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = 0;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerTest, HandlesInvalidMultipleParameter)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<int> values;
bool bIsSet = false;
using gmx::IntegerOption;
TEST(OptionsAssignerTest, HandlesMultipleParameter)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<int> values;
bool bIsSet = false;
using gmx::IntegerOption;
TEST(OptionsAssignerTest, HandlesMissingValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value1 = 0, value2 = 0;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value1)));
TEST(OptionsAssignerTest, HandlesExtraValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value1 = 0;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value1)));
TEST(OptionsAssignerTest, HandlesGroups)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
gmx::IOptionsContainer &group1 = options.addGroup();
gmx::IOptionsContainer &group2 = options.addGroup();
int value = 3;
EXPECT_EQ(6, value2);
}
-TEST(OptionsAssignerTest, HandlesSubSections)
+TEST(OptionsAssignerTest, HandlesSections)
{
- gmx::Options options(NULL, NULL);
- gmx::Options sub1("section1", NULL);
- gmx::Options sub2("section2", NULL);
+ using gmx::OptionSection;
+ gmx::Options options;
+ auto sub1 = options.addSection(OptionSection("section1"));
+ auto sub2 = options.addSection(OptionSection("section2"));
int value = 3;
int value1 = 1;
int value2 = 2;
using gmx::IntegerOption;
- ASSERT_NO_THROW(options.addSubSection(&sub1));
- ASSERT_NO_THROW(options.addSubSection(&sub2));
- ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value)));
- ASSERT_NO_THROW(sub1.addOption(IntegerOption("p").store(&value1)));
- ASSERT_NO_THROW(sub2.addOption(IntegerOption("p").store(&value2)));
+ ASSERT_NO_THROW_GMX(options.addOption(IntegerOption("p").store(&value)));
+ ASSERT_NO_THROW_GMX(sub1.addOption(IntegerOption("p").store(&value1)));
+ ASSERT_NO_THROW_GMX(sub2.addOption(IntegerOption("p").store(&value2)));
gmx::OptionsAssigner assigner(&options);
EXPECT_NO_THROW(assigner.start());
- ASSERT_NO_THROW(assigner.startSubSection("section1"));
+ ASSERT_NO_THROW(assigner.startSection("section1"));
ASSERT_NO_THROW(assigner.startOption("p"));
EXPECT_NO_THROW(assigner.appendValue("5"));
EXPECT_NO_THROW(assigner.finishOption());
- EXPECT_NO_THROW(assigner.finishSubSection());
+ EXPECT_NO_THROW(assigner.finishSection());
ASSERT_NO_THROW(assigner.startOption("p"));
EXPECT_NO_THROW(assigner.appendValue("4"));
EXPECT_NO_THROW(assigner.finishOption());
- ASSERT_NO_THROW(assigner.startSubSection("section2"));
+ ASSERT_NO_THROW(assigner.startSection("section2"));
ASSERT_NO_THROW(assigner.startOption("p"));
EXPECT_NO_THROW(assigner.appendValue("6"));
EXPECT_NO_THROW(assigner.finishOption());
- EXPECT_NO_THROW(assigner.finishSubSection());
+ EXPECT_NO_THROW(assigner.finishSection());
EXPECT_NO_THROW(assigner.finish());
EXPECT_NO_THROW(options.finish());
TEST(OptionsAssignerTest, HandlesMultipleSources)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = -1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value)));
TEST(OptionsAssignerBooleanTest, StoresYesValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
bool value = false;
using gmx::BooleanOption;
ASSERT_NO_THROW(options.addOption(BooleanOption("p").store(&value)));
TEST(OptionsAssignerBooleanTest, SetsBooleanWithoutExplicitValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
bool value = false;
using gmx::BooleanOption;
ASSERT_NO_THROW(options.addOption(BooleanOption("p").store(&value)));
TEST(OptionsAssignerBooleanTest, ClearsBooleanWithPrefixNo)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
bool value = true;
using gmx::BooleanOption;
ASSERT_NO_THROW(options.addOption(BooleanOption("p").store(&value)));
TEST(OptionsAssignerBooleanTest, HandlesBooleanWithPrefixAndValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
bool value = false;
using gmx::BooleanOption;
ASSERT_NO_THROW(options.addOption(BooleanOption("p").store(&value)));
TEST(OptionsAssignerIntegerTest, StoresSingleValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = 1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value)));
TEST(OptionsAssignerIntegerTest, HandlesEmptyValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = 1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value)));
TEST(OptionsAssignerIntegerTest, HandlesInvalidValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = 1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value)));
TEST(OptionsAssignerIntegerTest, HandlesOverflow)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = 1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(&value)));
TEST(OptionsAssignerIntegerTest, StoresDefaultValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = -1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerIntegerTest, StoresDefaultValueIfSet)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = -1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerIntegerTest, HandlesDefaultValueIfSetWhenNotSet)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = -1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerIntegerTest, HandlesBothDefaultValues)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int value = -1;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerIntegerTest, StoresToVector)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<int> values;
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerIntegerTest, HandlesVectors)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int vec[3] = {0, 0, 0};
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(vec).vector()));
TEST(OptionsAssignerIntegerTest, HandlesVectorFromSingleValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int vec[3] = {0, 0, 0};
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(vec).vector()));
TEST(OptionsAssignerIntegerTest, HandlesVectorsWithDefaultValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int vec[3] = {3, 2, 1};
using gmx::IntegerOption;
ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(vec).vector()));
TEST(OptionsAssignerIntegerTest, HandlesVectorsWithDefaultValueWithInvalidAssignment)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
int vec[3] = {3, 2, 1};
- std::vector<int> vec2(vec, vec+3);
using gmx::IntegerOption;
- ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(vec)
- .storeVector(&vec2).vector()));
+ ASSERT_NO_THROW(options.addOption(IntegerOption("p").store(vec).vector()));
gmx::OptionsAssigner assigner(&options);
EXPECT_NO_THROW(assigner.start());
EXPECT_EQ(3, vec[0]);
EXPECT_EQ(2, vec[1]);
EXPECT_EQ(1, vec[2]);
- ASSERT_EQ(3U, vec2.size());
- EXPECT_EQ(3, vec2[0]);
- EXPECT_EQ(2, vec2[1]);
- EXPECT_EQ(1, vec2[2]);
}
TEST(OptionsAssignerDoubleTest, StoresSingleValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
double value = 0.0;
using gmx::DoubleOption;
ASSERT_NO_THROW(options.addOption(DoubleOption("p").store(&value)));
EXPECT_DOUBLE_EQ(2.7, value);
}
+TEST(OptionsAssignerDoubleTest, StoresValueFromFloat)
+{
+ gmx::Options options;
+ double value = 0.0;
+ using gmx::DoubleOption;
+ ASSERT_NO_THROW(options.addOption(DoubleOption("p").store(&value)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW(assigner.start());
+ ASSERT_NO_THROW(assigner.startOption("p"));
+ ASSERT_NO_THROW(assigner.appendValue(gmx::Variant::create<float>(2.7)));
+ EXPECT_NO_THROW(assigner.finishOption());
+ EXPECT_NO_THROW(assigner.finish());
+ EXPECT_NO_THROW(options.finish());
+
+ EXPECT_FLOAT_EQ(2.7, value);
+}
+
TEST(OptionsAssignerDoubleTest, HandlesEmptyValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
double value = 1.0;
using gmx::DoubleOption;
ASSERT_NO_THROW(options.addOption(DoubleOption("p").store(&value)));
EXPECT_DOUBLE_EQ(1.0, value);
}
+TEST(OptionsAssignerDoubleTest, HandlesPreSetScaleValue)
+{
+ gmx::Options options;
+ double value = 1.0;
+ using gmx::DoubleOption;
+ gmx::DoubleOptionInfo *info = options.addOption(DoubleOption("p").store(&value));
+ EXPECT_NO_THROW(info->setScaleFactor(10));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW(assigner.start());
+ ASSERT_NO_THROW(assigner.startOption("p"));
+ ASSERT_NO_THROW(assigner.appendValue("2.7"));
+ EXPECT_NO_THROW(assigner.finishOption());
+ EXPECT_NO_THROW(assigner.finish());
+ EXPECT_NO_THROW(options.finish());
+
+ EXPECT_DOUBLE_EQ(27, value);
+}
+
+TEST(OptionsAssignerDoubleTest, HandlesPostSetScaleValue)
+{
+ gmx::Options options;
+ double value = 1.0;
+ using gmx::DoubleOption;
+ gmx::DoubleOptionInfo *info = options.addOption(DoubleOption("p").store(&value));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW(assigner.start());
+ ASSERT_NO_THROW(assigner.startOption("p"));
+ ASSERT_NO_THROW(assigner.appendValue("2.7"));
+ EXPECT_NO_THROW(assigner.finishOption());
+ EXPECT_NO_THROW(assigner.finish());
+ EXPECT_NO_THROW(info->setScaleFactor(10));
+ EXPECT_NO_THROW(options.finish());
+
+ EXPECT_DOUBLE_EQ(27, value);
+}
+
/********************************************************************
* Tests for string assignment
TEST(OptionsAssignerStringTest, StoresSingleValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(StringOption("p").store(&value)));
TEST(OptionsAssignerStringTest, HandlesEnumValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerStringTest, HandlesEnumValueFromNullTerminatedArray)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
- const char * const allowed[] = { "none", "test", "value", NULL };
+ const char * const allowed[] = { "none", "test", "value", nullptr };
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
StringOption("p").store(&value)
TEST(OptionsAssignerStringTest, HandlesIncorrectEnumValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerStringTest, CompletesEnumValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerStringTest, HandlesEnumWithNoValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerStringTest, HandlesEnumDefaultValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value;
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerStringTest, HandlesEnumDefaultValueFromVariable)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::string value("test");
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerStringTest, HandlesEnumDefaultValueFromVector)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<std::string> value;
- value.push_back("test");
- value.push_back("value");
+ value.emplace_back("test");
+ value.emplace_back("value");
using gmx::StringOption;
ASSERT_NO_THROW(options.addOption(
StringOption("p").storeVector(&value).valueCount(2)
TEST(OptionsAssignerEnumTest, StoresSingleValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
TestEnum value = etestNone;
using gmx::EnumOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerEnumTest, StoresVectorValues)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<TestEnum> values;
using gmx::EnumOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerEnumTest, HandlesInitialValueOutOfRange)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
TestEnum value = etestNR;
using gmx::EnumOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerEnumTest, HandlesEnumDefaultValue)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
TestEnum value = etestNone;
using gmx::EnumOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerEnumTest, HandlesEnumDefaultValueFromVariable)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
TestEnum value = etestTest;
using gmx::EnumOption;
ASSERT_NO_THROW(options.addOption(
TEST(OptionsAssignerEnumTest, HandlesEnumDefaultValueFromVector)
{
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
std::vector<TestEnum> value;
value.push_back(etestNone);
value.push_back(etestTest);
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Output">
+ <Int Name="a">3</Int>
+ <Object Name="s">
+ <Int Name="a">1</Int>
+ </Object>
+ <Object Name="r">
+ <Int Name="a">2</Int>
+ </Object>
+ </Object>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Output">
+ <Int Name="a">2</Int>
+ </Object>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Output">
+ <Sequence Name="a">
+ <Int Name="Length">3</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ <Int>3</Int>
+ </Sequence>
+ </Object>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <Int Name="b">1</Int>
+ </Object>
+ <Object Name="Output">
+ <Int Name="a">2</Int>
+ <Int Name="b">1</Int>
+ </Object>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <String Name="a">2</String>
+ </Object>
+ <Object Name="Output">
+ <Int Name="a">2</Int>
+ </Object>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <Int Name="a">1</Int>
+ <Int Name="c">1</Int>
+ <Int Name="b">1</Int>
+ </Object>
+ <Object Name="Output">
+ <Int Name="b">1</Int>
+ <Int Name="a">1</Int>
+ <Int Name="c">1</Int>
+ </Object>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <Bool Name="a">true</Bool>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = true
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (true - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <Real Name="a">1.5</Real>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = 1.5
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (1.5 - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <String Name="a">foo</String>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = foo
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (foo - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <String Name="a">foo</String>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = foo
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (foo - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <Real Name="a">1.5</Real>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = 1.5
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (1.5 - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <Int64 Name="a">2</Int64>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = 2
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (2 - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <Int Name="a">2</Int>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = 2
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (2 - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <Object Name="Adjusted">
+ <String Name="a">s</String>
+ </Object>
+ <String Name="Dumped"><![CDATA[
+a = s
+]]></String>
+ <String Name="Compared"><![CDATA[
+]]></String>
+ <String Name="ComparedAgainstEmpty"><![CDATA[
+/a (s - missing)
+]]></String>
+</ReferenceData>
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests functionality related to repeating sections.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#include "gmxpre.h"
+
+#include "gromacs/options/repeatingsection.h"
+
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
+#include "gromacs/options/optionsassigner.h"
+
+#include "testutils/testasserts.h"
+
+namespace
+{
+
+using gmx::RepeatingOptionSection;
+
+struct SectionData
+{
+ int value;
+};
+
+TEST(RepeatingOptionSectionTest, HandlesNoInstance)
+{
+ std::vector<SectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<SectionData>("section")
+ .storeVector(&values));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ EXPECT_EQ(0U, values.size());
+}
+
+TEST(RepeatingOptionSectionTest, HandlesNoInstanceWithRequiredOption)
+{
+ std::vector<SectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<SectionData>("section")
+ .storeVector(&values));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)
+ .required()));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ EXPECT_EQ(0U, values.size());
+}
+
+TEST(RepeatingOptionSectionTest, HandlesSingleInstance)
+{
+ std::vector<SectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<SectionData>("section")
+ .storeVector(&values));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ ASSERT_NO_THROW_GMX(assigner.startOption("p"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("4"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ ASSERT_EQ(1U, values.size());
+ EXPECT_EQ(4, values[0].value);
+}
+
+TEST(RepeatingOptionSectionTest, HandlesDefaultValue)
+{
+ std::vector<SectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<SectionData>("section")
+ .storeVector(&values));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)
+ .defaultValue(3)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ ASSERT_EQ(1U, values.size());
+ EXPECT_EQ(3, values[0].value);
+}
+
+TEST(RepeatingOptionSectionTest, HandlesTwoInstances)
+{
+ std::vector<SectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<SectionData>("section")
+ .storeVector(&values));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ ASSERT_NO_THROW_GMX(assigner.startOption("p"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("4"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ ASSERT_NO_THROW_GMX(assigner.startOption("p"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("5"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ ASSERT_EQ(2U, values.size());
+ EXPECT_EQ(4, values[0].value);
+ EXPECT_EQ(5, values[1].value);
+}
+
+TEST(RepeatingOptionSectionTest, HandlesUnsetOptionWithImplicitDefault)
+{
+ std::vector<SectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<SectionData>("section")
+ .storeVector(&values));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ ASSERT_NO_THROW_GMX(assigner.startOption("p"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("4"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ ASSERT_EQ(2U, values.size());
+ EXPECT_EQ(4, values[0].value);
+ EXPECT_EQ(0, values[1].value);
+}
+
+TEST(RepeatingOptionSectionTest, HandlesUnsetOptionWithExplicitDefault)
+{
+ std::vector<SectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<SectionData>("section")
+ .storeVector(&values));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)
+ .defaultValue(1)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ ASSERT_NO_THROW_GMX(assigner.startOption("p"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("4"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ ASSERT_EQ(2U, values.size());
+ EXPECT_EQ(4, values[0].value);
+ EXPECT_EQ(1, values[1].value);
+}
+
+struct NestedSectionData
+{
+ int value;
+ std::vector<SectionData> subsec;
+};
+
+TEST(RepeatingOptionSectionTest, HandlesNestedSections)
+{
+ std::vector<NestedSectionData> values;
+ gmx::Options options;
+ auto sec = options.addSection(
+ RepeatingOptionSection<NestedSectionData>("section")
+ .storeVector(&values));
+ auto subsec = sec.addSection(
+ RepeatingOptionSection<SectionData>("subsec")
+ .storeVector(&sec.bind().subsec));
+ using gmx::IntegerOption;
+ ASSERT_NO_THROW_GMX(sec.addOption(IntegerOption("p").store(&sec.bind().value)));
+ ASSERT_NO_THROW_GMX(subsec.addOption(IntegerOption("p").store(&subsec.bind().value)));
+
+ gmx::OptionsAssigner assigner(&options);
+ EXPECT_NO_THROW_GMX(assigner.start());
+ ASSERT_NO_THROW_GMX(assigner.startSection("section"));
+ ASSERT_NO_THROW_GMX(assigner.startOption("p"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("4"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ ASSERT_NO_THROW_GMX(assigner.startSection("subsec"));
+ ASSERT_NO_THROW_GMX(assigner.startOption("p"));
+ EXPECT_NO_THROW_GMX(assigner.appendValue("5"));
+ EXPECT_NO_THROW_GMX(assigner.finishOption());
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ EXPECT_NO_THROW_GMX(assigner.finishSection());
+ EXPECT_NO_THROW_GMX(assigner.finish());
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ ASSERT_EQ(1U, values.size());
+ EXPECT_EQ(4, values[0].value);
+ ASSERT_EQ(1U, values[0].subsec.size());
+ EXPECT_EQ(5, values[0].subsec[0].value);
+}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
gmx::TimeUnitBehavior behavior;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
double value = 0.0;
using gmx::DoubleOption;
ASSERT_NO_THROW_GMX(options.addOption(DoubleOption("p").store(&value).timeValue()));
{
gmx::TimeUnitBehavior behavior;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
double value = 1.5, value2 = 0.0;
using gmx::DoubleOption;
ASSERT_NO_THROW_GMX(options.addOption(DoubleOption("p").store(&value).timeValue()));
{
gmx::TimeUnitBehavior behavior;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
double value = 0.0;
using gmx::DoubleOption;
ASSERT_NO_THROW_GMX(options.addOption(DoubleOption("p").store(&value).timeValue()));
{
gmx::TimeUnitBehavior behavior;
- gmx::Options options(NULL, NULL);
+ gmx::Options options;
double value = 0.0;
using gmx::DoubleOption;
ASSERT_NO_THROW_GMX(options.addOption(DoubleOption("p").store(&value).timeValue()));
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests option support for operations on KeyValueTree.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#include "gmxpre.h"
+
+#include "gromacs/options/treesupport.h"
+
+#include <string>
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/options.h"
+#include "gromacs/options/optionsection.h"
+#include "gromacs/options/repeatingsection.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/inmemoryserializer.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/keyvaluetreeserializer.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace
+{
+
+/********************************************************************
+ * Tests for assignOptionsFromKeyValueTree()
+ */
+
+TEST(TreeValueSupportAssignTest, AssignsFromTree)
+{
+ int a0 = 0, a1 = 0;
+ std::string b1;
+
+ gmx::Options options;
+ options.addOption(gmx::IntegerOption("a").store(&a0));
+ auto sec = options.addSection(gmx::OptionSection("s"));
+ sec.addOption(gmx::IntegerOption("a").store(&a1));
+ sec.addOption(gmx::StringOption("b").store(&b1));
+
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<int>("a", 2);
+ auto obj = builder.rootObject().addObject("s");
+ obj.addValue<int>("a", 1);
+ obj.addValue<std::string>("b", "foo");
+ gmx::KeyValueTreeObject tree = builder.build();
+
+ ASSERT_NO_THROW_GMX(gmx::assignOptionsFromKeyValueTree(&options, tree, nullptr));
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ EXPECT_EQ(2, a0);
+ EXPECT_EQ(1, a1);
+ EXPECT_EQ("foo", b1);
+}
+
+struct SectionData
+{
+ int a;
+};
+
+TEST(TreeValueSupportAssignTest, AssignsFromTreeWithArrays)
+{
+ std::vector<int> a0;
+ std::vector<SectionData> s;
+
+ gmx::Options options;
+ options.addOption(gmx::IntegerOption("a").storeVector(&a0).multiValue());
+ auto sec = options.addSection(gmx::RepeatingOptionSection<SectionData>("s").storeVector(&s));
+ sec.addOption(gmx::IntegerOption("a").store(&sec.bind().a));
+
+ gmx::KeyValueTreeBuilder builder;
+ auto array = builder.rootObject().addUniformArray<int>("a");
+ array.addValue(1);
+ array.addValue(2);
+ auto objArray = builder.rootObject().addObjectArray("s");
+ auto obj1 = objArray.addObject();
+ obj1.addValue<int>("a", 3);
+ auto obj2 = objArray.addObject();
+ obj2.addValue<int>("a", 4);
+ gmx::KeyValueTreeObject tree = builder.build();
+
+ ASSERT_NO_THROW_GMX(gmx::assignOptionsFromKeyValueTree(&options, tree, nullptr));
+ EXPECT_NO_THROW_GMX(options.finish());
+
+ ASSERT_EQ(2U, a0.size());
+ EXPECT_EQ(1, a0[0]);
+ EXPECT_EQ(2, a0[1]);
+ ASSERT_EQ(2U, s.size());
+ EXPECT_EQ(3, s[0].a);
+ EXPECT_EQ(4, s[1].a);
+}
+
+TEST(TreeValueSupportAssignErrorTest, HandlesInvalidValue)
+{
+ int a1 = 0;
+
+ gmx::Options options;
+ auto sec = options.addSection(gmx::OptionSection("s"));
+ sec.addOption(gmx::IntegerOption("a").store(&a1));
+
+ gmx::KeyValueTreeBuilder builder;
+ auto obj = builder.rootObject().addObject("s");
+ obj.addValue<std::string>("a", "foo");
+ gmx::KeyValueTreeObject tree = builder.build();
+
+ EXPECT_THROW_GMX(gmx::assignOptionsFromKeyValueTree(&options, tree, nullptr),
+ gmx::InvalidInputError);
+}
+
+/********************************************************************
+ * Tests for checkForUnknownOptionsInKeyValueTree()
+ */
+
+class TreeValueSupportCheckTest : public ::testing::Test
+{
+ public:
+ TreeValueSupportCheckTest()
+ {
+ auto sec1 = options_.addSection(gmx::OptionSection("s"));
+ auto sec2 = options_.addSection(gmx::OptionSection("r"));
+ options_.addOption(gmx::IntegerOption("a"));
+ sec1.addOption(gmx::IntegerOption("a"));
+ sec1.addOption(gmx::IntegerOption("b"));
+ sec2.addOption(gmx::IntegerOption("b"));
+ }
+
+ gmx::Options options_;
+ gmx::KeyValueTreeBuilder builder_;
+};
+
+TEST_F(TreeValueSupportCheckTest, HandlesEmpty)
+{
+ EXPECT_NO_THROW_GMX(gmx::checkForUnknownOptionsInKeyValueTree(builder_.build(), options_));
+}
+
+TEST_F(TreeValueSupportCheckTest, HandlesMatchingTree)
+{
+ auto root = builder_.rootObject();
+ root.addValue<int>("a", 1);
+ auto obj1 = root.addObject("s");
+ obj1.addValue<int>("a", 1);
+ obj1.addValue<int>("b", 2);
+ auto obj2 = root.addObject("r");
+ obj2.addValue<int>("b", 3);
+
+ EXPECT_NO_THROW_GMX(gmx::checkForUnknownOptionsInKeyValueTree(builder_.build(), options_));
+}
+
+TEST_F(TreeValueSupportCheckTest, HandlesSmallerTree1)
+{
+ auto root = builder_.rootObject();
+ root.addValue<int>("a", 1);
+ auto obj1 = root.addObject("s");
+ obj1.addValue<int>("b", 2);
+
+ EXPECT_NO_THROW_GMX(gmx::checkForUnknownOptionsInKeyValueTree(builder_.build(), options_));
+}
+
+TEST_F(TreeValueSupportCheckTest, HandlesSmallerTree2)
+{
+ auto root = builder_.rootObject();
+ auto obj1 = root.addObject("s");
+ obj1.addValue<int>("a", 1);
+ obj1.addValue<int>("b", 2);
+
+ EXPECT_NO_THROW_GMX(gmx::checkForUnknownOptionsInKeyValueTree(builder_.build(), options_));
+}
+
+TEST_F(TreeValueSupportCheckTest, DetectsExtraValue)
+{
+ auto root = builder_.rootObject();
+ auto obj2 = root.addObject("r");
+ obj2.addValue<int>("a", 1);
+ obj2.addValue<int>("b", 3);
+
+ EXPECT_THROW_GMX(gmx::checkForUnknownOptionsInKeyValueTree(builder_.build(), options_),
+ gmx::InvalidInputError);
+}
+
+/********************************************************************
+ * Tests for adjustKeyValueTreeFromOptions()
+ */
+
+class TreeValueSupportAdjustTest : public ::testing::Test
+{
+ public:
+ void runTest()
+ {
+ gmx::test::TestReferenceData refdata;
+ gmx::test::TestReferenceChecker checker(refdata.rootChecker());
+ gmx::KeyValueTreeObject tree(builder_.build());
+ checker.checkKeyValueTreeObject(tree, "Input");
+ ASSERT_NO_THROW_GMX(tree = gmx::adjustKeyValueTreeFromOptions(tree, options_));
+ checker.checkKeyValueTreeObject(tree, "Output");
+ }
+
+ gmx::Options options_;
+ gmx::KeyValueTreeBuilder builder_;
+};
+
+TEST_F(TreeValueSupportAdjustTest, FillsDefaultValues)
+{
+ options_.addOption(gmx::IntegerOption("a").defaultValue(2));
+ runTest();
+}
+
+TEST_F(TreeValueSupportAdjustTest, FillsDefaultVectorValues)
+{
+ int v[3] = {1, 2, 3};
+ options_.addOption(gmx::IntegerOption("a").store(v).vector());
+ runTest();
+}
+
+TEST_F(TreeValueSupportAdjustTest, FillsDefaultObjectValues)
+{
+ auto sec1 = options_.addSection(gmx::OptionSection("s"));
+ sec1.addOption(gmx::IntegerOption("a").defaultValue(1));
+ auto sec2 = options_.addSection(gmx::OptionSection("r"));
+ sec2.addOption(gmx::IntegerOption("a").defaultValue(2));
+ options_.addOption(gmx::IntegerOption("a").defaultValue(3));
+ runTest();
+}
+
+TEST_F(TreeValueSupportAdjustTest, NormalizesValues)
+{
+ options_.addOption(gmx::IntegerOption("a"));
+ builder_.rootObject().addValue<std::string>("a", "2");
+ runTest();
+}
+
+TEST_F(TreeValueSupportAdjustTest, MergesDefaultValues)
+{
+ builder_.rootObject().addValue<int>("b", 1);
+ options_.addOption(gmx::IntegerOption("a").defaultValue(2));
+ options_.addOption(gmx::IntegerOption("b").defaultValue(3));
+ runTest();
+}
+
+TEST_F(TreeValueSupportAdjustTest, OrdersValues)
+{
+ builder_.rootObject().addValue<int>("a", 1);
+ builder_.rootObject().addValue<int>("c", 1);
+ builder_.rootObject().addValue<int>("b", 1);
+ options_.addOption(gmx::IntegerOption("b").defaultValue(2));
+ options_.addOption(gmx::IntegerOption("a").defaultValue(1));
+ options_.addOption(gmx::IntegerOption("c").defaultValue(3));
+ // TODO: This does not actually test the correct ordering, since the
+ // reference data is not currently order-sensitive, but the order can be
+ // checked manually from the reference data.
+ runTest();
+}
+
+/********************************************************************
+ * Support for different option types
+ */
+
+class TreeValueSupportTest : public ::testing::Test
+{
+ public:
+ void runTest()
+ {
+ gmx::test::TestReferenceData refdata;
+ gmx::test::TestReferenceChecker checker(refdata.rootChecker());
+ gmx::KeyValueTreeObject tree(builder_.build());
+ checker.checkKeyValueTreeObject(tree, "Input");
+ // Check that adjustment works.
+ ASSERT_NO_THROW_GMX(tree = gmx::adjustKeyValueTreeFromOptions(tree, options_));
+ checker.checkKeyValueTreeObject(tree, "Adjusted");
+ // Check that assignment works.
+ ASSERT_NO_THROW_GMX(gmx::assignOptionsFromKeyValueTree(&options_, tree, nullptr));
+ // Check that serialization works.
+ {
+ std::vector<char> buffer = serializeTree(tree);
+ gmx::InMemoryDeserializer deserializer(buffer);
+ gmx::KeyValueTreeObject output
+ = gmx::deserializeKeyValueTree(&deserializer);
+ SCOPED_TRACE("After serialization/deserialization\n Buffer: "
+ + formatBuffer(buffer));
+ checker.checkKeyValueTreeObject(output, "Adjusted");
+ }
+ // Check that dumping works.
+ {
+ gmx::StringOutputStream stream;
+ gmx::TextWriter writer(&stream);
+ ASSERT_NO_THROW_GMX(gmx::dumpKeyValueTree(&writer, tree));
+ checker.checkTextBlock(stream.toString(), "Dumped");
+ }
+ // Check that comparison works.
+ {
+ gmx::StringOutputStream stream;
+ gmx::TextWriter writer(&stream);
+ ASSERT_NO_THROW_GMX(gmx::compareKeyValueTrees(&writer, tree, tree, 0.0, 0.0));
+ checker.checkTextBlock(stream.toString(), "Compared");
+ }
+ // Check that comparison works against an empty tree.
+ {
+ gmx::StringOutputStream stream;
+ gmx::TextWriter writer(&stream);
+ gmx::KeyValueTreeObject empty;
+ ASSERT_NO_THROW_GMX(gmx::compareKeyValueTrees(&writer, tree, empty, 0.0, 0.0));
+ checker.checkTextBlock(stream.toString(), "ComparedAgainstEmpty");
+ }
+ }
+
+ gmx::Options options_;
+ gmx::KeyValueTreeBuilder builder_;
+
+ private:
+ std::vector<char> serializeTree(const gmx::KeyValueTreeObject &tree)
+ {
+ gmx::InMemorySerializer serializer;
+ gmx::serializeKeyValueTree(tree, &serializer);
+ return serializer.finishAndGetBuffer();
+ }
+
+ std::string formatBuffer(const std::vector<char> &buffer)
+ {
+ return gmx::formatAndJoin(buffer, " ", [](char c) { return gmx::formatString("%02x", (unsigned char)c); });
+ }
+};
+
+TEST_F(TreeValueSupportTest, SupportsBooleanOption)
+{
+ options_.addOption(gmx::BooleanOption("a").defaultValue(true));
+ runTest();
+}
+
+TEST_F(TreeValueSupportTest, SupportsIntegerOption)
+{
+ options_.addOption(gmx::IntegerOption("a").defaultValue(2));
+ runTest();
+}
+
+TEST_F(TreeValueSupportTest, SupportsInt64Option)
+{
+ options_.addOption(gmx::Int64Option("a").defaultValue(2));
+ runTest();
+}
+
+TEST_F(TreeValueSupportTest, SupportsStringOption)
+{
+ options_.addOption(gmx::StringOption("a").defaultValue("s"));
+ runTest();
+}
+
+TEST_F(TreeValueSupportTest, SupportsFloatOption)
+{
+ options_.addOption(gmx::FloatOption("a").defaultValue(1.5));
+ runTest();
+}
+
+TEST_F(TreeValueSupportTest, SupportsDoubleOption)
+{
+ options_.addOption(gmx::DoubleOption("a").defaultValue(1.5));
+ runTest();
+}
+
+TEST_F(TreeValueSupportTest, SupportsEnumIntOption)
+{
+ const char *const values[] = {"foo", "bar"};
+ options_.addOption(gmx::EnumIntOption("a").enumValue(values).defaultValue(0));
+ runTest();
+}
+
+//! Enum for testing EnumOption.
+enum class TestEnum
+{
+ Foo, Bar
+};
+
+TEST_F(TreeValueSupportTest, SupportsEnumOption)
+{
+ const char *const values[] = {"foo", "bar"};
+ options_.addOption(gmx::EnumOption<TestEnum>("a").enumValue(values)
+ .defaultValue(TestEnum::Foo));
+ runTest();
+}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
TimeUnitBehavior::TimeUnitBehavior()
- : timeUnit_(TimeUnit_Default), timeUnitStore_(NULL)
+ : timeUnit_(TimeUnit_Default), timeUnitStore_(nullptr)
{
}
GMX_RELEASE_ASSERT(timeUnit >= 0 && timeUnit <= TimeUnit_s,
"Invalid time unit");
timeUnit_ = timeUnit;
- if (timeUnitStore_ != NULL)
+ if (timeUnitStore_ != nullptr)
{
*timeUnitStore_ = timeUnit;
}
void TimeUnitBehavior::setTimeUnitFromEnvironment()
{
const char *const value = std::getenv("GMXTIMEUNIT");
- if (value != NULL)
+ if (value != nullptr)
{
ConstArrayRef<const char *> timeUnits(g_timeUnits);
ConstArrayRef<const char *>::const_iterator i =
//! Initializes a scaler with the given factor.
explicit TimeOptionScaler(double factor) : factor_(factor) {}
- void visitSubSection(Options *section)
+ void visitSection(OptionSectionInfo *section)
{
OptionsModifyingIterator iterator(section);
- iterator.acceptSubSections(this);
+ iterator.acceptSections(this);
iterator.acceptOptions(this);
}
void TimeUnitBehavior::optionsFinishing(Options *options)
{
double factor = TimeUnitManager(timeUnit()).timeScaleFactor();
- TimeOptionScaler<DoubleOptionInfo>(factor).visitSubSection(options);
- TimeOptionScaler<FloatOptionInfo>(factor).visitSubSection(options);
- if (timeUnitStore_ != NULL)
+ TimeOptionScaler<DoubleOptionInfo>(factor).visitSection(&options->rootSection());
+ TimeOptionScaler<FloatOptionInfo>(factor).visitSection(&options->rootSection());
+ if (timeUnitStore_ != nullptr)
{
*timeUnitStore_ = static_cast<TimeUnit>(timeUnit_);
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions from treesupport.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#include "gmxpre.h"
+
+#include "treesupport.h"
+
+#include <set>
+#include <string>
+#include <vector>
+
+#include "gromacs/options/options.h"
+#include "gromacs/options/optionsassigner.h"
+#include "gromacs/options/optionsection.h"
+#include "gromacs/options/optionsvisitor.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/ikeyvaluetreeerror.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+class TreeAssignHelper
+{
+ public:
+ TreeAssignHelper(Options *options, IKeyValueTreeErrorHandler *errorHandler)
+ : assigner_(options), errorHandler_(errorHandler)
+ {
+ if (errorHandler_ == nullptr)
+ {
+ errorHandler_ = defaultKeyValueTreeErrorHandler();
+ }
+ }
+
+ void assignAll(const KeyValueTreeObject &root)
+ {
+ assigner_.start();
+ assignSubTree(root);
+ assigner_.finish();
+ }
+
+ private:
+ void assignSubTree(const KeyValueTreeObject &tree)
+ {
+ // TODO: Use the error handler also in other case.
+ for (const KeyValueTreeProperty &prop : tree.properties())
+ {
+ context_.append(prop.key());
+ if (prop.value().isArray())
+ {
+ assignArray(prop.key(), prop.value().asArray());
+ }
+ else if (prop.value().isObject())
+ {
+ assigner_.startSection(prop.key().c_str());
+ assignSubTree(prop.value().asObject());
+ assigner_.finishSection();
+ }
+ else
+ {
+ assigner_.startOption(prop.key().c_str());
+ try
+ {
+ assigner_.appendValue(prop.value().asVariant());
+ }
+ catch (UserInputError &ex)
+ {
+ if (!errorHandler_->onError(&ex, context_))
+ {
+ throw;
+ }
+ }
+ assigner_.finishOption();
+ }
+ context_.pop_back();
+ }
+ }
+
+ void assignArray(const std::string &key,
+ const KeyValueTreeArray &array)
+ {
+ if (array.isObjectArray())
+ {
+ for (const KeyValueTreeValue &value : array.values())
+ {
+ assigner_.startSection(key.c_str());
+ assignSubTree(value.asObject());
+ assigner_.finishSection();
+ }
+ }
+ else
+ {
+ assigner_.startOption(key.c_str());
+ for (const KeyValueTreeValue &value : array.values())
+ {
+ assigner_.appendValue(value.asVariant());
+ }
+ assigner_.finishOption();
+ }
+ }
+
+ OptionsAssigner assigner_;
+ IKeyValueTreeErrorHandler *errorHandler_;
+ KeyValueTreePath context_;
+};
+
+class TreeCheckHelper : private OptionsVisitor
+{
+ public:
+ TreeCheckHelper(const KeyValueTreeObject &root)
+ : currentObject_(&root), currentKnownNames_(nullptr)
+ {
+ }
+
+ bool hasUnknownPaths() const { return !unknownPaths_.empty(); }
+ const std::vector<KeyValueTreePath> &unknownPaths() const
+ {
+ return unknownPaths_;
+ }
+
+ void processOptionSection(const OptionSectionInfo §ion)
+ {
+ OptionsIterator iterator(section);
+ std::set<std::string> knownNames;
+ currentKnownNames_ = &knownNames;
+ iterator.acceptOptions(this);
+ iterator.acceptSections(this);
+ currentKnownNames_ = nullptr;
+ for (const auto &prop : currentObject_->properties())
+ {
+ if (knownNames.count(prop.key()) == 0)
+ {
+ unknownPaths_.push_back(currentPath_ + prop.key());
+ }
+ }
+ }
+
+ private:
+ virtual void visitSection(const OptionSectionInfo §ion)
+ {
+ const std::string &name = section.name();
+ if (currentObject_->keyExists(name))
+ {
+ currentKnownNames_->insert(name);
+ auto parentObject = currentObject_;
+ auto parentKnownNames = currentKnownNames_;
+ // TODO: Consider what to do with mismatching types.
+ currentObject_ = &(*currentObject_)[name].asObject();
+ currentPath_.append(name);
+ processOptionSection(section);
+ currentPath_.pop_back();
+ currentObject_ = parentObject;
+ currentKnownNames_ = parentKnownNames;
+ }
+ }
+ virtual void visitOption(const OptionInfo &option)
+ {
+ const std::string &name = option.name();
+ if (currentObject_->keyExists(name))
+ {
+ currentKnownNames_->insert(name);
+ // TODO: Consider what to do with mismatching types.
+ }
+ }
+
+ KeyValueTreePath currentPath_;
+ const KeyValueTreeObject *currentObject_;
+ std::set<std::string> *currentKnownNames_;
+ std::vector<KeyValueTreePath> unknownPaths_;
+
+};
+
+class TreeAdjustHelper : private OptionsVisitor
+{
+ public:
+ TreeAdjustHelper(const KeyValueTreeObject &root,
+ KeyValueTreeBuilder *builder)
+ : currentSourceObject_(&root),
+ currentObjectBuilder_(builder->rootObject())
+ {
+ }
+
+ void processOptionSection(const OptionSectionInfo §ion)
+ {
+ OptionsIterator iterator(section);
+ iterator.acceptOptions(this);
+ iterator.acceptSections(this);
+ }
+
+ private:
+ virtual void visitSection(const OptionSectionInfo §ion)
+ {
+ const std::string &name = section.name();
+ auto parentBuilder = currentObjectBuilder_;
+ auto parentObject = currentSourceObject_;
+ currentObjectBuilder_ = currentObjectBuilder_.addObject(name);
+ currentSourceObject_ =
+ (currentSourceObject_ != nullptr && currentSourceObject_->keyExists(name)
+ ? &(*currentSourceObject_)[name].asObject()
+ : nullptr);
+ processOptionSection(section);
+ currentSourceObject_ = parentObject;
+ currentObjectBuilder_ = parentBuilder;
+ }
+ virtual void visitOption(const OptionInfo &option)
+ {
+ const std::string &name = option.name();
+ if (currentSourceObject_ == nullptr || !currentSourceObject_->keyExists(name))
+ {
+ std::vector<Variant> values = option.defaultValues();
+ if (values.size() == 1)
+ {
+ currentObjectBuilder_.addRawValue(name, std::move(values[0]));
+ }
+ else if (values.size() > 1)
+ {
+ auto arrayBuilder = currentObjectBuilder_.addArray(name);
+ for (Variant &value : values)
+ {
+ arrayBuilder.addRawValue(std::move(value));
+ }
+ }
+ }
+ else
+ {
+ const KeyValueTreeValue &value = (*currentSourceObject_)[name];
+ GMX_RELEASE_ASSERT(!value.isObject(), "Value objects not supported in this context");
+ std::vector<Variant> values;
+ if (value.isArray())
+ {
+ for (const auto &arrayValue : value.asArray().values())
+ {
+ GMX_RELEASE_ASSERT(!value.isObject() && !value.isArray(),
+ "Complex values not supported in this context");
+ values.push_back(arrayValue.asVariant());
+ }
+ }
+ else
+ {
+ values.push_back(value.asVariant());
+ }
+ values = option.normalizeValues(values);
+ if (values.empty())
+ {
+ }
+ else if (values.size() == 1)
+ {
+ currentObjectBuilder_.addRawValue(name, std::move(values[0]));
+ }
+ else
+ {
+ auto array = currentObjectBuilder_.addArray(name);
+ for (auto &arrayValue : values)
+ {
+ array.addRawValue(std::move(arrayValue));
+ }
+ }
+ }
+ }
+
+ const KeyValueTreeObject *currentSourceObject_;
+ KeyValueTreeObjectBuilder currentObjectBuilder_;
+};
+
+} // namespace
+
+//! \cond libapi
+
+void assignOptionsFromKeyValueTree(Options *options,
+ const KeyValueTreeObject &tree,
+ IKeyValueTreeErrorHandler *errorHandler)
+{
+ TreeAssignHelper helper(options, errorHandler);
+ helper.assignAll(tree);
+}
+
+void checkForUnknownOptionsInKeyValueTree(const KeyValueTreeObject &tree,
+ const Options &options)
+{
+ TreeCheckHelper helper(tree);
+ helper.processOptionSection(options.rootSection());
+ if (helper.hasUnknownPaths())
+ {
+ std::string paths(formatAndJoin(helper.unknownPaths(), "\n ",
+ [](const KeyValueTreePath &path) { return path.toString(); }));
+ std::string message("Unknown input values:\n " + paths);
+ GMX_THROW(InvalidInputError(message));
+ }
+}
+
+KeyValueTreeObject
+adjustKeyValueTreeFromOptions(const KeyValueTreeObject &tree,
+ const Options &options)
+{
+ KeyValueTreeBuilder builder;
+ TreeAdjustHelper helper(tree, &builder);
+ helper.processOptionSection(options.rootSection());
+ return builder.build();
+}
+
+//! \endcond
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares functions for using keyvaluetree.h with Options.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_TREESUPPORT_H
+#define GMX_OPTIONS_TREESUPPORT_H
+
+namespace gmx
+{
+
+class IKeyValueTreeErrorHandler;
+class KeyValueTreeObject;
+class Options;
+
+//! \cond libapi
+
+/*! \libinternal \brief
+ * Assigns option values from a given KeyValueTreeObject.
+ *
+ * Each property with a simple value (or an array of simple values) is assigned
+ * to an option with the same name. Objects and arrays of objects are assigned
+ * to sections with the same name.
+ *
+ * \ingroup module_options
+ */
+void assignOptionsFromKeyValueTree(Options *options,
+ const KeyValueTreeObject &tree,
+ IKeyValueTreeErrorHandler *errorHandler);
+/*! \libinternal \brief
+ * Checks that a given KeyValueTreeObject can be assigned to given Options.
+ *
+ * Throws an exception if `tree` contains any values that are not recognized by
+ * `options`. Does not verify the type of the values, only that an option with
+ * the correct names exists.
+ *
+ * \ingroup module_options
+ */
+void checkForUnknownOptionsInKeyValueTree(const KeyValueTreeObject &tree,
+ const Options &options);
+/*! \libinternal \brief
+ * Adjusts a KeyValueTreeObject to the structure of given Options.
+ *
+ * Assumes that all values in the input KeyValueTreeObject are valid values for
+ * the options. The output has all the values in the input, but in the order
+ * they are in the options. Values are also converted to the native type for
+ * the underlying option (e.g., strings are parsed to integers if the option
+ * accepts those). For any option that does not have a corresponding value in
+ * the input, the output has it with a default value (if one exists for the
+ * option).
+ *
+ * Any values in `tree` that do not have matching options are not present in
+ * the output. If this is not desirable, call
+ * checkForUnknownOptionsInKeyValueTree() before calling this function to
+ * ensure that no such values are present.
+ *
+ * Does not currently work for option sections in an array.
+ *
+ * \ingroup module_options
+ */
+KeyValueTreeObject
+adjustKeyValueTreeFromOptions(const KeyValueTreeObject &tree,
+ const Options &options);
+
+//! \endcond
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Provides gmx::OptionValueConverterSimple.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_VALUECONVERTER_H
+#define GMX_OPTIONS_VALUECONVERTER_H
+
+#include <functional>
+#include <map>
+#include <typeindex>
+
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/variant.h"
+
+namespace gmx
+{
+
+/*! \libinternal \brief
+ * Helper for converting from Variant to a given type.
+ *
+ * \tparam OutType Type this converter converts to.
+ *
+ * Default-constructed converter only supports identity mapping from the a
+ * Variant holding `OutType`. To add support for additional input types,
+ * provide conversion functions with addConverter(). To use a non-identity
+ * mapping for an `OutType` -> `OutType` conversion, provide an alternative
+ * conversion from `OutType` with addConverter().
+ *
+ * \inlibraryapi
+ * \ingroup module_options
+ */
+template <typename OutType>
+class OptionValueConverterSimple
+{
+ public:
+ /*! \brief
+ * Converts a Variant value to the output type.
+ *
+ * \returns Converted value.
+ * \throws InvalidInputError If the input Variant has a type that is
+ * not recognized by any conversion.
+ */
+ OutType convert(const Variant &value) const
+ {
+ std::type_index type(value.type());
+ auto iter = converters_.find(type);
+ if (iter == converters_.end())
+ {
+ if (value.isType<OutType>())
+ {
+ return value.cast<OutType>();
+ }
+ GMX_THROW(InvalidInputError("Invalid type of value"));
+ }
+ return iter->second(value);
+ }
+
+ /*! \brief
+ * Adds a supported conversion.
+ *
+ * \tparam InType Type to convert from.
+ * \param func Function to convert from `InType` to `OutType`.
+ */
+ template <typename InType>
+ void addConverter(std::function<OutType(const InType &)> func)
+ {
+ converters_[std::type_index(typeid(InType))] =
+ [func] (const Variant &value)
+ {
+ return func(value.cast<InType>());
+ };
+ }
+ /*! \brief
+ * Adds a supported conversion from a type that can be directly cast.
+ *
+ * \tparam InType Type to convert from with a simple cast.
+ */
+ template <typename InType>
+ void addCastConversion()
+ {
+ converters_[std::type_index(typeid(InType))] =
+ [] (const Variant &value)
+ {
+ return static_cast<OutType>(value.cast<InType>());
+ };
+ }
+
+ private:
+ typedef std::function<OutType(const Variant &value)> ConversionFunction;
+
+ std::map<std::type_index, ConversionFunction> converters_;
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \file
+ * \brief
+ * Declares implementations for IOptionValueStore.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_options
+ */
+#ifndef GMX_OPTIONS_VALUESTORE_H
+#define GMX_OPTIONS_VALUESTORE_H
+
+#include <vector>
+
+#include "gromacs/options/ivaluestore.h"
+#include "gromacs/utility/arrayref.h"
+
+namespace gmx
+{
+
+template <typename T>
+class OptionValueStorePlain : public IOptionValueStore<T>
+{
+ public:
+ OptionValueStorePlain(T *store, int *storeCount, int initialCount)
+ : count_(initialCount), store_(store), storeCount_(storeCount)
+ {
+ }
+
+ virtual int valueCount() { return count_; }
+ virtual ArrayRef<T> values() { return ArrayRef<T>::fromArray(store_, count_); }
+ virtual void clear()
+ {
+ count_ = 0;
+ if (storeCount_ != nullptr)
+ {
+ *storeCount_ = count_;
+ }
+ }
+ virtual void reserve(size_t /*count*/)
+ {
+ }
+ virtual void append(const T &value)
+ {
+ store_[count_] = value;
+ ++count_;
+ if (storeCount_ != nullptr)
+ {
+ *storeCount_ = count_;
+ }
+ }
+
+ private:
+ int count_;
+ T *store_;
+ int *storeCount_;
+};
+
+template <typename T>
+class OptionValueStoreVector : public IOptionValueStore<T>
+{
+ public:
+ // cppcheck-suppress uninitMemberVar
+ explicit OptionValueStoreVector(std::vector<T> *store) : store_(store) {}
+
+ virtual int valueCount() { return static_cast<int>(store_->size()); }
+ virtual ArrayRef<T> values() { return *store_; }
+ virtual void clear() { store_->clear(); }
+ virtual void reserve(size_t count)
+ {
+ store_->reserve(store_->size() + count);
+ }
+ virtual void append(const T &value)
+ {
+ store_->push_back(value);
+ }
+
+ private:
+ std::vector<T> *store_;
+};
+
+// Specialization that works around std::vector<bool> specialities.
+template <>
+// cppcheck-suppress noConstructor
+class OptionValueStoreVector<bool> : public IOptionValueStore<bool>
+{
+ public:
+ explicit OptionValueStoreVector(std::vector<bool> *store) : store_(store)
+ {
+ }
+
+ virtual int valueCount() { return static_cast<int>(store_->size()); }
+ virtual ArrayRef<bool> values()
+ {
+ return ArrayRef<bool>::fromArray(reinterpret_cast<bool *>(boolStore_.data()),
+ boolStore_.size());
+ }
+ virtual void clear()
+ {
+ boolStore_.clear();
+ store_->clear();
+ }
+ virtual void reserve(size_t count)
+ {
+ boolStore_.reserve(boolStore_.size() + count);
+ store_->reserve(store_->size() + count);
+ }
+ virtual void append(const bool &value)
+ {
+ boolStore_.push_back({value});
+ store_->push_back(value);
+ }
+
+ private:
+ struct Bool
+ {
+ bool value;
+ };
+
+ std::vector<Bool> boolStore_;
+ std::vector<bool> *store_;
+};
+
+/*! \internal
+ * \brief
+ * Value storage that does not store anywhere.
+ *
+ * This is needed because even though the values are not stored anywhere, the
+ * code still expects to access them later through valueCount() and values().
+ *
+ * \ingroup module_options
+ */
+template <typename T>
+class OptionValueStoreNull : public IOptionValueStore<T>
+{
+ public:
+ OptionValueStoreNull() : store_(&vector_) {}
+
+ virtual int valueCount() { return store_.valueCount(); }
+ virtual ArrayRef<T> values() { return store_.values(); }
+ virtual void clear() { store_.clear(); }
+ virtual void reserve(size_t count) { store_.reserve(count); }
+ virtual void append(const T &value) { store_.append(value); }
+
+ private:
+ std::vector<T> vector_;
+ OptionValueStoreVector<T> store_;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "boxutilities.h"
-#include <cmath>
-
#include <algorithm>
+#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/mdtypes/inputrec.h"
-#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/state.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/real.h"
-/*! \brief Change box components to preserve the relative box shape
- *
- * Change box components to box[XX][XX]*box_rel to preserve the relative box shape
- */
-static void do_box_rel(t_inputrec *ir, matrix box_rel, matrix b, gmx_bool bInit)
+void do_box_rel(int ndim, const matrix deform, matrix box_rel,
+ matrix b, bool bInit)
{
- int d, d2;
-
- for (d = YY; d <= ZZ; d++)
+ for (int d = YY; d <= ZZ; ++d)
{
- for (d2 = XX; d2 <= (ir->epct == epctSEMIISOTROPIC ? YY : ZZ); d2++)
+ for (int d2 = XX; d2 < ndim; ++d2)
{
/* We need to check if this box component is deformed
* or if deformation of another component might cause
* changes in this component due to box corrections.
*/
- if (ir->deform[d][d2] == 0 &&
- !(d == ZZ && d2 == XX && ir->deform[d][YY] != 0 &&
- (b[YY][d2] != 0 || ir->deform[YY][d2] != 0)))
+ if (deform[d][d2] == 0 &&
+ !(d == ZZ && d2 == XX && deform[d][YY] != 0 &&
+ (b[YY][d2] != 0 || deform[YY][d2] != 0)))
{
if (bInit)
{
}
}
-void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b)
+namespace gmx
{
- if (inputrecPreserveShape(ir))
- {
- do_box_rel(ir, box_rel, b, FALSE);
- }
-}
-void set_box_rel(t_inputrec *ir, t_state *state)
+namespace
{
- /* Make sure the box obeys the restrictions before we fix the ratios */
- correct_box(NULL, 0, state->box, NULL);
- clear_mat(state->box_rel);
+//! Whether two box elements are equal (with a tolerance).
+bool boxElementEqual(real element1, real element2)
+{
+ // Compare with a relative tolerance (for big boxes) and with
+ // an absolute tolerance (small boxes are generally not specified with very
+ // high number of decimals).
+ return gmx_within_tol(element1, element2, 10*GMX_REAL_EPS)
+ || std::fabs(element1 - element2) < 1e-3;
+}
- if (inputrecPreserveShape(ir))
- {
- do_box_rel(ir, state->box_rel, state->box, TRUE);
- }
+} // namespace
+
+bool boxesAreEqual(const matrix box1, const matrix box2)
+{
+ return boxElementEqual(box1[XX][XX], box2[XX][XX])
+ && boxElementEqual(box1[YY][XX], box2[YY][XX])
+ && boxElementEqual(box1[YY][YY], box2[YY][YY])
+ && boxElementEqual(box1[ZZ][XX], box2[ZZ][XX])
+ && boxElementEqual(box1[ZZ][YY], box2[ZZ][YY])
+ && boxElementEqual(box1[ZZ][ZZ], box2[ZZ][ZZ]);
}
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdio.h>
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/basedefinitions.h"
-#include "gromacs/utility/real.h"
-struct t_inputrec;
-struct t_state;
-
-/*! \brief Make sure the relative box shape remains the same
- *
- * This function ensures that the relative box dimensions are
- * preserved, which otherwise might diffuse away due to rounding
- * errors in pressure coupling or the deform option.
+/*! \brief Change box components to preserve the relative box shape
*
- * \param[in] ir Input record
- * \param[in] box_rel Relative box
- * \param[out] b The corrected box
+ * Change box components to box[XX][XX]*box_rel to preserve the relative box shape
*/
-void preserve_box_shape(t_inputrec *ir, matrix box_rel, matrix b);
+void do_box_rel(int ndim, const matrix deform, matrix box_rel,
+ matrix b, bool bInit);
-/*! \brief Determine the relative box components
- *
- * Set state->box_rel used in mdrun to preserve the box shape
- * \param[in] ir Input record
- * \param[inout] state Structure containing the box
+namespace gmx
+{
+
+/*! \brief
+ * Returns whether two boxes are of equal size and shape (within reasonable
+ * tolerance).
*/
-void set_box_rel(struct t_inputrec *ir, t_state *state);
+bool boxesAreEqual(const matrix box1, const matrix box2);
+
+} // namespace gmx
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
add_gbond(g, ia[1], ia[2]);
add_gbond(g, ia[1], ia[3]);
}
- else if (part == NULL)
+ else if (part == nullptr)
{
/* Simply add this bond */
for (j = 1; j < np; j++)
{
if (interaction_function[i].flags & IF_CHEMBOND)
{
- mk_igraph(g, i, &(ilist[i]), at_start, at_end, NULL);
+ mk_igraph(g, i, &(ilist[i]), at_start, at_end, nullptr);
}
}
else
{
/* This is a special thing used in splitter.c to generate shake-blocks */
- mk_igraph(g, F_CONSTR, &(ilist[F_CONSTR]), at_start, at_end, NULL);
+ mk_igraph(g, F_CONSTR, &(ilist[F_CONSTR]), at_start, at_end, nullptr);
if (bSettle)
{
- mk_igraph(g, F_SETTLE, &(ilist[F_SETTLE]), at_start, at_end, NULL);
+ mk_igraph(g, F_SETTLE, &(ilist[F_SETTLE]), at_start, at_end, nullptr);
}
}
g->nbound = 0;
}
g->negc = 0;
- g->egc = NULL;
+ g->egc = nullptr;
sfree(nbond);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
real gmx_unused *pbc_simd)
{
#if GMX_SIMD_HAVE_REAL
- if (pbc != NULL && pbc->ePBC != epbcNONE)
+ if (pbc != nullptr && pbc->ePBC != epbcNONE)
{
rvec inv_box_diag = {0, 0, 0};
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
-#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/utility/exceptions.h"
const char *epbc_names[epbcNR+1] =
{
- "xyz", "no", "xy", "screw", NULL
+ "xyz", "no", "xy", "screw", nullptr
};
/* Skip 0 so we have more chance of detecting if we forgot to call set_pbc. */
return npbcdim;
}
-int inputrec2nboundeddim(const t_inputrec *ir)
-{
- if (ir->nwall == 2 && ir->ePBC == epbcXY)
- {
- return 3;
- }
- else
- {
- return ePBC2npbcdim(ir->ePBC);
- }
-}
-
void dump_pbc(FILE *fp, t_pbc *pbc)
{
rvec sum_box;
if (ePBC == epbcNONE)
{
- return NULL;
+ return nullptr;
}
if ((box[XX][YY] != 0) || (box[XX][ZZ] != 0) || (box[YY][ZZ] != 0))
}
else
{
- ptr = NULL;
+ ptr = nullptr;
}
return ptr;
return bCorrected;
}
-int ndof_com(t_inputrec *ir)
-{
- int n = 0;
-
- switch (ir->ePBC)
- {
- case epbcXYZ:
- case epbcNONE:
- n = 3;
- break;
- case epbcXY:
- n = (ir->nwall == 0 ? 3 : 2);
- break;
- case epbcSCREW:
- n = 1;
- break;
- default:
- gmx_incons("Unknown pbc in calc_nrdf");
- }
-
- return n;
-}
-
//! Do the real arithmetic for filling the pbc struct
static void low_set_pbc(t_pbc *pbc, int ePBC,
const ivec dd_pbc, const matrix box)
}
else
{
- if (ePBC == epbcSCREW && NULL != dd_pbc)
+ if (ePBC == epbcSCREW && nullptr != dd_pbc)
{
/* This combinated should never appear here */
gmx_incons("low_set_pbc called with screw pbc and dd_nc != NULL");
ePBC = guess_ePBC(box);
}
- low_set_pbc(pbc, ePBC, NULL, box);
+ low_set_pbc(pbc, ePBC, nullptr, box);
}
t_pbc *set_pbc_dd(t_pbc *pbc, int ePBC,
{
pbc->ePBC = ePBC;
- return NULL;
+ return nullptr;
}
if (nullptr == domdecCells)
{
- low_set_pbc(pbc, ePBC, NULL, box);
+ low_set_pbc(pbc, ePBC, nullptr, box);
}
else
{
}
}
- return (pbc->ePBC != epbcNONE ? pbc : NULL);
+ return (pbc->ePBC != epbcNONE ? pbc : nullptr);
}
void pbc_dx(const t_pbc *pbc, const rvec x1, const rvec x2, rvec dx)
}
}
-//! Compute the box image corresponding to input vectors
-gmx_bool image_rect(ivec xi, ivec xj, ivec box_size, real rlong2, int *shift, real *r2)
-{
- int m, t;
- int dx, b, b_2;
- real dxr, rij2;
-
- rij2 = 0.0;
- t = 0;
- for (m = 0; (m < DIM); m++)
- {
- dx = xi[m]-xj[m];
- t *= DIM;
- b = box_size[m];
- b_2 = b/2;
- if (dx < -b_2)
- {
- t += 2;
- dx += b;
- }
- else if (dx > b_2)
- {
- dx -= b;
- }
- else
- {
- t += 1;
- }
- dxr = dx;
- rij2 += dxr*dxr;
- if (rij2 >= rlong2)
- {
- return FALSE;
- }
- }
-
- *shift = t;
- *r2 = rij2;
- return TRUE;
-}
-
-gmx_bool image_cylindric(ivec xi, ivec xj, ivec box_size, real rlong2,
- int *shift, real *r2)
-{
- int m, t;
- int dx, b, b_2;
- real dxr, rij2;
-
- rij2 = 0.0;
- t = 0;
- for (m = 0; (m < DIM); m++)
- {
- dx = xi[m]-xj[m];
- t *= DIM;
- b = box_size[m];
- b_2 = b/2;
- if (dx < -b_2)
- {
- t += 2;
- dx += b;
- }
- else if (dx > b_2)
- {
- dx -= b;
- }
- else
- {
- t += 1;
- }
-
- dxr = dx;
- rij2 += dxr*dxr;
- if (m < ZZ)
- {
- if (rij2 >= rlong2)
- {
- return FALSE;
- }
- }
- }
-
- *shift = t;
- *r2 = rij2;
- return TRUE;
-}
-
void calc_shifts(const matrix box, rvec shift_vec[])
{
int k, l, m, d, n, test;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/real.h"
struct gmx_domdec_t;
-struct t_inputrec;
#ifdef __cplusplus
extern "C" {
*/
int ePBC2npbcdim(int ePBC);
-/*! \brief Return the number of bounded directories
- *
- * \param[in] ir The input record with MD parameters
- * \return the number of dimensions in which
- * the coordinates of the particles are bounded, starting at X.
- */
-int inputrec2nboundeddim(const t_inputrec *ir);
-
/*! \brief Dump the contents of the pbc structure to the file
*
* \param[in] fp The file pointer to write to
*/
gmx_bool correct_box(FILE *fplog, int step, tensor box, struct t_graph *graph);
-/*! \brief Returns the number of degrees of freedom in center of mass motion
- *
- * \param[in] ir the inputrec structure
- * \return the number of degrees of freedom of the center of mass
- */
-int ndof_com(t_inputrec *ir);
-
/*! \brief Initiate the periodic boundary condition algorithms.
*
* pbc_dx will not use pbc and return the normal difference vector
*/
void pbc_dx_d(const t_pbc *pbc, const dvec x1, const dvec x2, dvec dx);
-/*! \brief Calculate the distance between xi and xj for a rectangular box.
- *
- * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
- * \param[in] xi Box index
- * \param[in] xj Box index
- * \param[in] box The box of grid cells
- * \param[in] rlong2 Cutoff squared
- * \param[out] shift The shift code
- * \param[out] r2 The distance (squared???)
- * \return TRUE when the distance is SMALLER than rlong2
- */
-gmx_bool image_rect(ivec xi, ivec xj, imatrix box,
- real rlong2, int *shift, real *r2);
-
-/*! \brief Calculate the distance between xi and xj for a triclinic box.
- *
- * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
- * \param[in] xi Box index
- * \param[in] xj Box index
- * \param[in] box Matrix of box grid cells
- * \param[in] rlong2 Cutoff squared
- * \param[out] shift The shift code
- * \param[out] r2 The distance (squared???)
- * \return TRUE when the distance is SMALLER than rlong2
- */
-gmx_bool image_tri(const ivec xi, const ivec xj, const imatrix box,
- real rlong2, int *shift, real *r2);
-
-/*! \brief Compute distance vector when using cylindrical cutoff
- *
- * Calculate the distance between xi and xj for a rectangular box
- * using a cylindric cutoff for long-range only.
- * It is assumed that rlong2 is scaled the same way as the ivecs xi and xj.
- * \param[in] xi Box index
- * \param[in] xj Box index
- * \param[in] box_size Number of box grid cells
- * \param[in] rlong2 Cutoff squared
- * \param[out] shift The shift code
- * \param[out] r2 The distance (squared???)
- * \return TRUE when the distance is SMALLER than rlong2 (in X and Y dir)
- */
-gmx_bool image_cylindric(const ivec xi, const ivec xj, const ivec box_size,
- real rlong2, int *shift, real *r2);
-
/*! \brief Computes shift vectors
*
* This routine calculates ths shift vectors necessary to use the
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
rmpbc_graph_t *gr;
if (ePBC == epbcNONE
- || NULL == gpbc
- || NULL == gpbc->idef
+ || nullptr == gpbc
+ || nullptr == gpbc->idef
|| gpbc->idef->ntypes <= 0)
{
- return NULL;
+ return nullptr;
}
- gr = NULL;
+ gr = nullptr;
for (i = 0; i < gpbc->ngraph; i++)
{
if (natoms == gpbc->graph[i].natoms)
gr = &gpbc->graph[i];
}
}
- if (gr == NULL)
+ if (gr == nullptr)
{
/* We'd like to check with the number of atoms in the topology,
* but we don't have that available.
srenew(gpbc->graph, gpbc->ngraph);
gr = &gpbc->graph[gpbc->ngraph-1];
gr->natoms = natoms;
- gr->gr = mk_graph(NULL, gpbc->idef, 0, natoms, FALSE, FALSE);
+ gr->gr = mk_graph(nullptr, gpbc->idef, 0, natoms, FALSE, FALSE);
}
return gr->gr;
{
int i;
- if (NULL != gpbc)
+ if (nullptr != gpbc)
{
for (i = 0; i < gpbc->ngraph; i++)
{
done_graph(gpbc->graph[i].gr);
sfree(gpbc->graph[i].gr);
}
- if (gpbc->graph != NULL)
+ if (gpbc->graph != nullptr)
{
sfree(gpbc->graph);
}
static int gmx_rmpbc_ePBC(gmx_rmpbc_t gpbc, const matrix box)
{
- if (NULL != gpbc && gpbc->ePBC >= 0)
+ if (nullptr != gpbc && gpbc->ePBC >= 0)
{
return gpbc->ePBC;
}
ePBC = gmx_rmpbc_ePBC(gpbc, box);
gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
- if (gr != NULL)
+ if (gr != nullptr)
{
mk_mshift(stdout, gr, ePBC, box, x);
shift_self(gr, box, x);
ePBC = gmx_rmpbc_ePBC(gpbc, box);
gr = gmx_rmpbc_get_graph(gpbc, ePBC, natoms);
- if (gr != NULL)
+ if (gr != nullptr)
{
mk_mshift(stdout, gr, ePBC, box, x);
shift_x(gr, box, x, x_s);
{
ePBC = gmx_rmpbc_ePBC(gpbc, fr->box);
gr = gmx_rmpbc_get_graph(gpbc, ePBC, fr->natoms);
- if (gr != NULL)
+ if (gr != nullptr)
{
mk_mshift(stdout, gr, ePBC, fr->box, fr->x);
shift_self(gr, fr->box, fr->x);
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull_internal.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/mutex.h"
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
static FILE *open_pull_out(const char *fn, struct pull_t *pull,
const gmx_output_env_t *oenv,
- gmx_bool bCoord, unsigned long Flags)
+ gmx_bool bCoord,
+ const ContinuationOptions &continuationOptions)
{
FILE *fp;
int nsets, c, m;
char **setname, buf[50];
- if (Flags & MD_APPENDFILES)
+ if (continuationOptions.appendFiles)
{
fp = gmx_fio_fopen(fn, "a+");
}
/* Accumulate the forces, in case we have multiple constraint steps */
pcrd->f_scal += dr_tot[c]/((pull->group[pcrd->params.group[0]].invtm + pull->group[pcrd->params.group[1]].invtm)*dt*dt);
- if (vir != NULL && pcrd->params.eGeom != epullgDIRPBC && bMaster)
+ if (vir != nullptr && pcrd->params.eGeom != epullgDIRPBC && bMaster)
{
double f_invr;
/* Adds the pull contribution to the virial */
static void add_virial_coord(tensor vir, const pull_coord_work_t *pcrd)
{
- if (vir != NULL && pcrd->params.eGeom != epullgDIRPBC)
+ if (vir != nullptr && pcrd->params.eGeom != epullgDIRPBC)
{
/* Add the pull contribution for each distance vector to the virial. */
add_virial_coord_dr(vir, pcrd->dr01, pcrd->f01);
}
+/* We use a global mutex for locking access to the pull data structure
+ * during registration of external pull potential providers.
+ * We could use a different, local mutex for each pull object, but the overhead
+ * is extremely small here and registration is only done during initialization.
+ */
+static gmx::Mutex registrationMutex;
+
+using Lock = gmx::lock_guard<gmx::Mutex>;
+
void register_external_pull_potential(struct pull_t *pull,
int coord_index,
const char *provider)
{
- GMX_RELEASE_ASSERT(pull != NULL, "register_external_pull_potential called before init_pull");
- GMX_RELEASE_ASSERT(provider != NULL, "register_external_pull_potential called with NULL as provider name");
+ GMX_RELEASE_ASSERT(pull != nullptr, "register_external_pull_potential called before init_pull");
+ GMX_RELEASE_ASSERT(provider != nullptr, "register_external_pull_potential called with NULL as provider name");
if (coord_index < 0 || coord_index > pull->ncoord - 1)
{
provider, coord_index + 1, epull_names[pcrd->params.eType], epull_names[epullEXTERNAL]);
}
- GMX_RELEASE_ASSERT(pcrd->params.externalPotentialProvider != NULL, "The external potential provider string for a pull coordinate is NULL");
+ GMX_RELEASE_ASSERT(pcrd->params.externalPotentialProvider != nullptr, "The external potential provider string for a pull coordinate is NULL");
if (gmx_strcasecmp(provider, pcrd->params.externalPotentialProvider) != 0)
{
provider, coord_index + 1, pcrd->params.externalPotentialProvider);
}
+ /* Lock to avoid (extremely unlikely) simultaneous reading and writing of
+ * pcrd->bExternalPotentialProviderHasBeenRegistered and
+ * pull->numUnregisteredExternalPotentials.
+ */
+ Lock registrationLock(registrationMutex);
+
if (pcrd->bExternalPotentialProviderHasBeenRegistered)
{
- gmx_fatal(FARGS, "Module '%s' attempted to register an external potential for pull coordinate %d multiple times",
+ gmx_fatal(FARGS, "Module '%s' attempted to register an external potential for pull coordinate %d more than once",
provider, coord_index + 1);
}
pcrd->bExternalPotentialProviderHasBeenRegistered = true;
pull->numUnregisteredExternalPotentials--;
- GMX_RELEASE_ASSERT(pull->numUnregisteredExternalPotentials >= 0, "Negative unregisterd potentials, the pull code in inconsistent");
+ GMX_RELEASE_ASSERT(pull->numUnregisteredExternalPotentials >= 0, "Negative unregistered potentials, the pull code is inconsistent");
}
{
real dVdl = 0;
- pull_calc_coms(cr, pull, md, pbc, t, x, NULL);
+ pull_calc_coms(cr, pull, md, pbc, t, x, nullptr);
for (int c = 0; c < pull->ncoord; c++)
{
}
do_pull_pot_coord(pull, c, pbc, t, lambda,
- &V, MASTER(cr) ? vir : NULL, &dVdl);
+ &V, MASTER(cr) ? vir : nullptr, &dVdl);
/* Distribute the force over the atoms in the pulled groups */
apply_forces_coord(pull, c, md, f);
{
pg->nalloc_loc = over_alloc_dd(pg->nat_loc+1);
srenew(pg->ind_loc, pg->nalloc_loc);
- if (pg->epgrppbc == epgrppbcCOS || pg->params.weight != NULL)
+ if (pg->epgrppbc == epgrppbcCOS || pg->params.weight != nullptr)
{
srenew(pg->weight_loc, pg->nalloc_loc);
}
}
pg->ind_loc[pg->nat_loc] = ii;
- if (pg->params.weight != NULL)
+ if (pg->params.weight != nullptr)
{
pg->weight_loc[pg->nat_loc] = pg->params.weight[i];
}
}
else
{
- ga2la = NULL;
+ ga2la = nullptr;
}
/* We always make the master node participate, such that it can do i/o
* and to simplify MC type extensions people might have.
*/
- bMustParticipate = (comm->bParticipateAll || dd == NULL || DDMASTER(dd));
+ bMustParticipate = (comm->bParticipateAll || dd == nullptr || DDMASTER(dd));
for (g = 0; g < pull->ngroup; g++)
{
(comm->bParticipate &&
comm->must_count >= comm->setup_count - history_count);
- if (debug && dd != NULL)
+ if (debug && dd != nullptr)
{
fprintf(debug, "Our DD rank (%3d) pull #atoms>0 or master: %d, will be part %d\n",
dd->rank, bMustParticipate, bWillParticipate);
const gmx_mtop_t *mtop,
const t_inputrec *ir, real lambda)
{
- int i, ii, d, nfrozen, ndim;
- real m, w, mbd;
- double tmass, wmass, wwmass;
- const gmx_groups_t *groups;
- gmx_mtop_atomlookup_t alook;
- t_atom *atom;
-
if (EI_ENERGY_MINIMIZATION(ir->eI) || ir->eI == eiBD)
{
/* There are no masses in the integrator.
{
pg->nat_loc = 0;
pg->nalloc_loc = 0;
- pg->ind_loc = NULL;
- pg->weight_loc = NULL;
+ pg->ind_loc = nullptr;
+ pg->weight_loc = nullptr;
}
else
{
}
}
- groups = &mtop->groups;
+ const gmx_groups_t *groups = &mtop->groups;
- alook = gmx_mtop_atomlookup_init(mtop);
-
- nfrozen = 0;
- tmass = 0;
- wmass = 0;
- wwmass = 0;
- for (i = 0; i < pg->params.nat; i++)
+ /* Count frozen dimensions and (weighted) mass */
+ int nfrozen = 0;
+ double tmass = 0;
+ double wmass = 0;
+ double wwmass = 0;
+ int molb = 0;
+ for (int i = 0; i < pg->params.nat; i++)
{
- ii = pg->params.ind[i];
- gmx_mtop_atomnr_to_atom(alook, ii, &atom);
+ int ii = pg->params.ind[i];
if (bConstraint && ir->opts.nFreeze)
{
- for (d = 0; d < DIM; d++)
+ for (int d = 0; d < DIM; d++)
{
if (pulldim_con[d] == 1 &&
ir->opts.nFreeze[ggrpnr(groups, egcFREEZE, ii)][d])
}
}
}
+ const t_atom &atom = mtopGetAtomParameters(mtop, ii, &molb);
+ real m;
if (ir->efep == efepNO)
{
- m = atom->m;
+ m = atom.m;
}
else
{
- m = (1 - lambda)*atom->m + lambda*atom->mB;
+ m = (1 - lambda)*atom.m + lambda*atom.mB;
}
+ real w;
if (pg->params.nweight > 0)
{
w = pg->params.weight[i];
}
else if (ir->eI == eiBD)
{
+ real mbd;
if (ir->bd_fric)
{
mbd = ir->bd_fric*ir->delta_t;
}
else
{
- if (groups->grpnr[egcTC] == NULL)
+ if (groups->grpnr[egcTC] == nullptr)
{
mbd = ir->delta_t/ir->opts.tau_t[0];
}
wwmass += m*w*w;
}
- gmx_mtop_atomlookup_destroy(alook);
-
if (wmass == 0)
{
/* We can have single atom groups with zero mass with potential pulling
}
else
{
- ndim = 0;
- for (d = 0; d < DIM; d++)
+ int ndim = 0;
+ for (int d = 0; d < DIM; d++)
{
ndim += pulldim_con[d]*pg->params.nat;
}
int nfile, const t_filenm fnm[],
const gmx_mtop_t *mtop, t_commrec *cr,
const gmx_output_env_t *oenv, real lambda,
- gmx_bool bOutFile, unsigned long Flags)
+ gmx_bool bOutFile,
+ const ContinuationOptions &continuationOptions)
{
struct pull_t *pull;
pull_comm_t *comm;
/* Copy the pull parameters */
pull->params = *pull_params;
/* Avoid pointer copies */
- pull->params.group = NULL;
- pull->params.coord = NULL;
+ pull->params.group = nullptr;
+ pull->params.coord = nullptr;
pull->ncoord = pull_params->ncoord;
pull->ngroup = pull_params->ngroup;
}
else
{
- if (pgrp->params.weight != NULL)
+ if (pgrp->params.weight != nullptr)
{
gmx_fatal(FARGS, "Pull groups can not have relative weights and cosine weighting at same time");
}
#if GMX_MPI
/* Use a sub-communicator when we have more than 32 ranks */
- comm->bParticipateAll = (cr == NULL || !DOMAINDECOMP(cr) ||
+ comm->bParticipateAll = (cr == nullptr || !DOMAINDECOMP(cr) ||
cr->dd->nnodes <= 32 ||
- getenv("GMX_PULL_PARTICIPATE_ALL") != NULL);
+ getenv("GMX_PULL_PARTICIPATE_ALL") != nullptr);
/* This sub-commicator is not used with comm->bParticipateAll,
* so we can always initialize it to NULL.
*/
comm->setup_count = 0;
comm->must_count = 0;
- if (!comm->bParticipateAll && fplog != NULL)
+ if (!comm->bParticipateAll && fplog != nullptr)
{
fprintf(fplog, "Will use a sub-communicator for pull communication\n");
}
- comm->rbuf = NULL;
- comm->dbuf = NULL;
- comm->dbuf_cyl = NULL;
+ comm->rbuf = nullptr;
+ comm->dbuf = nullptr;
+ comm->dbuf_cyl = nullptr;
/* We still need to initialize the PBC reference coordinates */
pull->bSetPBCatoms = TRUE;
/* Only do I/O when we are doing dynamics and if we are the MASTER */
- pull->out_x = NULL;
- pull->out_f = NULL;
+ pull->out_x = nullptr;
+ pull->out_f = nullptr;
if (bOutFile)
{
/* Check for px and pf filename collision, if we are writing
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
pull->out_x = open_pull_out(px_appended.c_str(), pull, oenv,
- TRUE, Flags);
+ TRUE, continuationOptions);
pull->out_f = open_pull_out(pf_appended.c_str(), pull, oenv,
- FALSE, Flags);
+ FALSE, continuationOptions);
return pull;
}
else
if (pull->params.nstxout != 0)
{
pull->out_x = open_pull_out(opt2fn("-px", nfile, fnm), pull, oenv,
- TRUE, Flags);
+ TRUE, continuationOptions);
}
if (pull->params.nstfout != 0)
{
pull->out_f = open_pull_out(opt2fn("-pf", nfile, fnm), pull, oenv,
- FALSE, Flags);
+ FALSE, continuationOptions);
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
extern "C" {
#endif
+struct ContinuationOptions;
struct gmx_mtop_t;
struct gmx_output_env_t;
struct pull_params_t;
* will exit with a (release) assertion failure when used incorrely or
* with a fatal error when the user (mdp) input in inconsistent.
*
+ * Thread-safe for simultaneous registration from multiple threads.
+ *
* \param[in,out] pull The pull struct.
* \param[in] coord_index The pull coordinate index to register the external potential for.
* \param[in] provider Provider string, should match the potential-provider pull coordinate mdp option.
* \param oenv Output options.
* \param lambda FEP lambda.
* \param bOutFile Open output files?
- * \param Flags Flags passed over from main, used to determine
- * whether or not we are appending.
+ * \param continuationOptions Options for continuing from checkpoint file
*/
-struct pull_t *init_pull(FILE *fplog,
- const pull_params_t *pull_params,
- const t_inputrec *ir,
- int nfile,
- const t_filenm fnm[],
- const gmx_mtop_t *mtop,
- t_commrec * cr,
- const gmx_output_env_t *oenv,
- real lambda,
- gmx_bool bOutFile,
- unsigned long Flags);
+struct pull_t *init_pull(FILE *fplog,
+ const pull_params_t *pull_params,
+ const t_inputrec *ir,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx_mtop_t *mtop,
+ t_commrec * cr,
+ const gmx_output_env_t *oenv,
+ real lambda,
+ gmx_bool bOutFile,
+ const ContinuationOptions &continuationOptions);
/*! \brief Close the pull output files.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include "gromacs/commandline/filenm.h"
-#include "gromacs/domdec/domdec.h"
+#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/pleasecite.h"
real *mpi_inbuf; /* MPI buffer */
real *mpi_outbuf; /* MPI buffer */
int mpi_bufsize; /* Allocation size of in & outbuf */
- unsigned long Flags; /* mdrun flags */
+ gmx_bool appendFiles; /* If true, append output files */
gmx_bool bOut; /* Used to skip first output when appending to
* avoid duplicate entries in rotation outfiles */
} t_gmx_enfrot;
static double** allocate_square_matrix(int dim)
{
int i;
- double** mat = NULL;
+ double** mat = nullptr;
snew(mat, dim);
} /* END of loop over slabs */
/* Output on the master */
- if ( (NULL != out_slabs) && bOutStep)
+ if ( (nullptr != out_slabs) && bOutStep)
{
fprintf(out_slabs, "%12.3e%6d", time, g);
for (j = erg->slab_first; j <= erg->slab_last; j++)
t_rotgrp *rotg;
- if (rot->enfrot->Flags & MD_APPENDFILES)
+ if (rot->enfrot->appendFiles)
{
fp = gmx_fio_fopen(fn, "a");
}
char buf[50], buf2[75];
gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
gmx_bool bFlex;
- char *LegendStr = NULL;
+ char *LegendStr = nullptr;
- if (rot->enfrot->Flags & MD_APPENDFILES)
+ if (rot->enfrot->appendFiles)
{
fp = gmx_fio_fopen(fn, "a");
}
char buf[100];
- if (rot->enfrot->Flags & MD_APPENDFILES)
+ if (rot->enfrot->appendFiles)
{
fp = gmx_fio_fopen(fn, "a");
}
t_rotgrp *rotg;
- if (rot->enfrot->Flags & MD_APPENDFILES)
+ if (rot->enfrot->appendFiles)
{
fp = gmx_fio_fopen(fn, "a");
}
int i, j, k;
rvec zet = {0.0, 0.0, 1.0};
rvec rot_axis = {0.0, 0.0, 0.0};
- rvec *rotated_str = NULL;
+ rvec *rotated_str = nullptr;
real ooanorm;
real angle;
matrix rotmat;
rvec axis)
{
int i, j, k;
- rvec *ref_s_1 = NULL;
- rvec *act_s_1 = NULL;
+ rvec *ref_s_1 = nullptr;
+ rvec *act_s_1 = nullptr;
rvec shift;
double **Rmat, **RtR, **eigvec;
double eigval[3];
}
/* Weight positions with sqrt(weight) */
- if (NULL != weight)
+ if (nullptr != weight)
{
weigh_coords(ref_s_1, weight, natoms);
weigh_coords(act_s_1, weight, natoms);
static real flex_fit_angle(t_rotgrp *rotg)
{
int i;
- rvec *fitcoords = NULL;
+ rvec *fitcoords = nullptr;
rvec center; /* Center of positions passed to the fit routine */
real fitangle; /* Angle of the rotation group derived by fitting */
rvec coord;
/* Remember how many we allocated */
erg->nslabs_alloc = nslabs;
- if ( (NULL != fplog) && bVerbose)
+ if ( (nullptr != fplog) && bVerbose)
{
fprintf(fplog, "%s allocating memory to store data for %d slabs (rotation group %d).\n",
RotStr, nslabs, g);
int i, ii;
rvec coord, xref, *xdum;
gmx_bool bFlex, bColl;
- t_atom *atom;
gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
int ref_firstindex, ref_lastindex;
- gmx_mtop_atomlookup_t alook = NULL;
real mass, totalmass;
real start = 0.0;
double t_start;
}
else
{
- erg->PotAngleFit = NULL;
+ erg->PotAngleFit = nullptr;
}
/* xc_ref_ind needs to be set to identity in the serial case */
/* Copy the masses so that the center can be determined. For all types of
* enforced rotation, we store the masses in the erg->mc array. */
- if (rotg->bMassW)
- {
- alook = gmx_mtop_atomlookup_init(mtop);
- }
snew(erg->mc, rotg->nat);
if (bFlex)
{
snew(erg->m_loc, rotg->nat);
}
totalmass = 0.0;
+ int molb = 0;
for (i = 0; i < rotg->nat; i++)
{
if (rotg->bMassW)
{
- gmx_mtop_atomnr_to_atom(alook, rotg->ind[i], &atom);
- mass = atom->m;
+ mass = mtopGetAtomMass(mtop, rotg->ind[i], &molb);
}
else
{
}
erg->invmass = 1.0/totalmass;
- if (rotg->bMassW)
- {
- gmx_mtop_atomlookup_destroy(alook);
- }
-
/* Set xc_ref_center for any rotation potential */
if ((rotg->eType == erotgISO) || (rotg->eType == erotgPM) || (rotg->eType == erotgRM) || (rotg->eType == erotgRM2))
{
extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const gmx_output_env_t *oenv,
- gmx_bool bVerbose, unsigned long Flags)
+ const MdrunOptions &mdrunOptions)
{
t_rot *rot;
t_rotgrp *rotg;
int g;
- int nat_max = 0; /* Size of biggest rotation group */
- gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
- gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
- rvec *x_pbc = NULL; /* Space for the pbc-correct atom positions */
+ int nat_max = 0; /* Size of biggest rotation group */
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ rvec *x_pbc = nullptr; /* Space for the pbc-correct atom positions */
- if (MASTER(cr) && bVerbose)
+ if (MASTER(cr) && mdrunOptions.verbose)
{
fprintf(stdout, "%s Initializing ...\n", RotStr);
}
rot = ir->rot;
snew(rot->enfrot, 1);
- er = rot->enfrot;
- er->Flags = Flags;
+ er = rot->enfrot;
+ er->appendFiles = mdrunOptions.continuationOptions.appendFiles;
/* When appending, skip first output to avoid duplicate entries in the data files */
- if (er->Flags & MD_APPENDFILES)
+ if (er->appendFiles)
{
er->bOut = FALSE;
}
}
/* Output every step for reruns */
- if (er->Flags & MD_RERUN)
+ if (mdrunOptions.rerun)
{
- if (NULL != fplog)
+ if (nullptr != fplog)
{
fprintf(fplog, "%s rerun - will write rotation output every available step.\n", RotStr);
}
rot->nstsout = 1;
}
- er->out_slabs = NULL;
+ er->out_slabs = nullptr;
if (MASTER(cr) && HaveFlexibleGroups(rot) )
{
er->out_slabs = open_slab_out(opt2fn("-rs", nfile, fnm), rot);
* When ir->bContinuation=TRUE this has already been done, but ok. */
snew(x_pbc, mtop->natoms);
copy_rvecn(x, x_pbc, 0, mtop->natoms);
- do_pbc_first_mtop(NULL, ir->ePBC, box, mtop, x_pbc);
+ do_pbc_first_mtop(nullptr, ir->ePBC, box, mtop, x_pbc);
/* All molecules will be whole now, but not necessarily in the home box.
* Additionally, if a rotation group consists of more than one molecule
* (e.g. two strands of DNA), each one of them can end up in a different
{
rotg = &rot->grp[g];
- if (NULL != fplog)
+ if (nullptr != fplog)
{
fprintf(fplog, "%s group %d type '%s'\n", RotStr, g, erotg_names[rotg->eType]);
}
{
erg->nat_loc = 0;
erg->nalloc_loc = 0;
- erg->ind_loc = NULL;
+ erg->ind_loc = nullptr;
}
else
{
erg->nat_loc = rotg->nat;
erg->ind_loc = rotg->ind;
}
- init_rot_group(fplog, cr, g, rotg, x_pbc, mtop, bVerbose, er->out_slabs, box, ir,
- !(er->Flags & MD_APPENDFILES) ); /* Do not output the reference centers
- * again if we are appending */
+ init_rot_group(fplog, cr, g, rotg, x_pbc, mtop, mdrunOptions.verbose, er->out_slabs, box, ir,
+ !er->appendFiles); /* Do not output the reference centers
+ * again if we are appending */
}
}
else
{
er->mpi_bufsize = 0;
- er->mpi_inbuf = NULL;
- er->mpi_outbuf = NULL;
+ er->mpi_inbuf = nullptr;
+ er->mpi_outbuf = nullptr;
}
/* Only do I/O on the MASTER */
- er->out_angles = NULL;
- er->out_rot = NULL;
- er->out_torque = NULL;
+ er->out_angles = nullptr;
+ er->out_rot = nullptr;
+ er->out_torque = nullptr;
if (MASTER(cr))
{
er->out_rot = open_rot_out(opt2fn("-ro", nfile, fnm), rot, oenv);
rvec x[],
real t,
gmx_int64_t step,
- gmx_wallcycle_t wcycle,
gmx_bool bNS)
{
int g, i, ii;
t_rotgrp *rotg;
gmx_bool outstep_slab, outstep_rot;
gmx_bool bColl;
- gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
- gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
+ gmx_enfrot_t er; /* Pointer to the enforced rotation buffer variables */
+ gmx_enfrotgrp_t erg; /* Pointer to enforced rotation group data */
rvec transvec;
- t_gmx_potfit *fit = NULL; /* For fit type 'potential' determine the fit
- angle via the potential minimum */
-
- /* Enforced rotation cycle counting: */
- gmx_cycles_t cycles_comp; /* Cycles for the enf. rotation computation
- only, does not count communication. This
- counter is used for load-balancing */
+ t_gmx_potfit *fit = nullptr; /* For fit type 'potential' determine the fit
+ angle via the potential minimum */
#ifdef TAKETIME
double t0;
/**************************************************************************/
/* Done communicating, we can start to count cycles for the load balancing now ... */
- cycles_comp = gmx_cycles_read();
-
+ if (DOMAINDECOMP(cr))
+ {
+ ddReopenBalanceRegionCpu(cr->dd);
+ }
#ifdef TAKETIME
t0 = MPI_Wtime();
fprintf(stderr, "%s calculation (step %d) took %g seconds.\n", RotStr, step, MPI_Wtime()-t0);
}
#endif
-
- /* Stop the enforced rotation cycle counter and add the computation-only
- * cycles to the force cycles for load balancing */
- cycles_comp = gmx_cycles_read() - cycles_comp;
-
- if (DOMAINDECOMP(cr) && wcycle)
- {
- dd_cycles_add(cr->dd, cycles_comp, ddCyclF);
- }
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_PULLING_PULL_ROTATION_H
#define GMX_PULLING_PULL_ROTATION_H
+#include <stdio.h>
+
#include "gromacs/math/vectypes.h"
-#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/basedefinitions.h"
struct gmx_domdec_t;
struct gmx_mtop_t;
struct gmx_output_env_t;
+struct MdrunOptions;
struct t_commrec;
struct t_filenm;
struct t_inputrec;
* \param box The simulation box.
* \param mtop Molecular topology.
* \param oenv Needed to open the rotation output xvgr file.
- * \param bVerbose Whether to print extra status information.
- * \param Flags Flags passed over from main, used to determine
- * whether or not we are doing a rerun.
+ * \param mdrunOptions Options for mdrun.
*/
extern void init_rot(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
struct t_commrec *cr, rvec *x, matrix box, gmx_mtop_t *mtop, const gmx_output_env_t *oenv,
- gmx_bool bVerbose, unsigned long Flags);
+ const MdrunOptions &mdrunOptions);
/*! \brief Make a selection of the home atoms for all enforced rotation groups.
* \param x The positions of all the local particles.
* \param t Time.
* \param step The time step.
- * \param wcycle During the potential calculation the wallcycles are
- * counted. Later they enter the dynamic load balancing.
* \param bNS After domain decomposition / neighbor searching several
* local arrays have to be updated (masses, shifts)
*/
extern void do_rotation(struct t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t,
- gmx_int64_t step, gmx_wallcycle_t wcycle, gmx_bool bNS);
+ gmx_int64_t step, gmx_bool bNS);
/*! \brief Add the enforced rotation forces to the official force array.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int n,
real *data)
{
- if (cr != NULL && PAR(cr))
+ if (cr != nullptr && PAR(cr))
{
if (comm->bParticipateAll)
{
int n,
double *data)
{
- if (cr != NULL && PAR(cr))
+ if (cr != nullptr && PAR(cr))
{
if (comm->bParticipateAll)
{
{
int a;
- if (cr != NULL && DOMAINDECOMP(cr))
+ if (cr != nullptr && DOMAINDECOMP(cr))
{
if (ga2la_get_home(cr->dd->ga2la, pgrp->params.pbcatom, &a))
{
rvec g_x, dx, dir;
double inv_cyl_r2;
pull_comm_t *comm;
- gmx_ga2la_t *ga2la = NULL;
+ gmx_ga2la_t *ga2la = nullptr;
comm = &pull->comm;
- if (comm->dbuf_cyl == NULL)
+ if (comm->dbuf_cyl == nullptr)
{
snew(comm->dbuf_cyl, pull->ncoord*stride);
}
comm->dbuf_cyl[c*stride+8] = radf_fac1[ZZ];
}
- if (cr != NULL && PAR(cr))
+ if (cr != nullptr && PAR(cr))
{
/* Sum the contributions over the ranks */
pull_reduce_double(cr, comm, pull->ncoord*stride, comm->dbuf_cyl);
{
int ii = pgrp->ind_loc[i];
real wm;
- if (pgrp->weight_loc == NULL)
+ if (pgrp->weight_loc == nullptr)
{
wm = mass[ii];
sum_wm += wm;
sum_csm += static_cast<double>(cw*sw*m);
sum_ssm += static_cast<double>(sw*sw*m);
- if (xp != NULL)
+ if (xp != nullptr)
{
real cw = std::cos(xp[ii][cosdim]*twopi_box);
real sw = std::sin(xp[ii][cosdim]*twopi_box);
comm = &pull->comm;
- if (comm->rbuf == NULL)
+ if (comm->rbuf == nullptr)
{
snew(comm->rbuf, pull->ngroup);
}
- if (comm->dbuf == NULL)
+ if (comm->dbuf == nullptr)
{
snew(comm->dbuf, 3*pull->ngroup);
}
{
pull_set_pbcatoms(cr, pull, x, comm->rbuf);
- if (cr != NULL && DOMAINDECOMP(cr))
+ if (cr != nullptr && DOMAINDECOMP(cr))
{
/* We can keep these PBC reference coordinates fixed for nstlist
* steps, since atoms won't jump over PBC.
}
}
- if (pgrp->weight_loc == NULL)
+ if (pgrp->weight_loc == nullptr)
{
sum_com->sum_wwm = sum_com->sum_wm;
}
* produce errors. Even for newer compilers, libstdc++ and libc++ appear to
* use different algorithms to generate it, which means their values differ
* in contrast to the uniform and normal distributions where they are
- * identical. To avoid both the gcc-4.6 bug and make it easier to use GROMACS
- * unit tests that depend on random numbers we have our own implementation.
+ * identical. To avoid both compiler bugs and make it easier to use
+ * GROMACS unit tests that depend on random numbers, we have our
+ * own implementation.
*
* Be warned that the gamma distribution works like the standard
* normal distribution and keeps drawing values from the random engine
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
public:
//! \brief Smallest value that can be returned from random engine.
- static gmx_constexpr
+#if !defined(_MSC_VER)
+ static constexpr
+#else
+ // Avoid constexpr bug in MSVC 2015, note that max() below does work
+ static
+#endif
result_type min() { return std::numeric_limits<result_type>::min(); }
//! \brief Largest value that can be returned from random engine.
- static gmx_constexpr
+ static constexpr
result_type max() { return std::numeric_limits<result_type>::max(); }
/*! \brief Construct random engine with 2x64 key values
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/gmxassert.h"
void
-gmx_calc_cog(const t_topology * /* top */, rvec x[], int nrefat, const int index[], rvec xout)
+gmx_calc_cog(const gmx_mtop_t * /* top */, rvec x[], int nrefat, const int index[], rvec xout)
{
int m, ai;
* mass are calculated, and hence a topology with masses is required.
*/
void
-gmx_calc_com(const t_topology *top, rvec x[], int nrefat, const int index[], rvec xout)
+gmx_calc_com(const gmx_mtop_t *top, rvec x[], int nrefat, const int index[], rvec xout)
{
- int m, j, ai;
- real mass, mtot;
-
- GMX_RELEASE_ASSERT(top != nullptr,
+ GMX_RELEASE_ASSERT(gmx_mtop_has_masses(top),
"No masses available while mass weighting was requested");
clear_rvec(xout);
- mtot = 0;
- for (m = 0; m < nrefat; ++m)
+ real mtot = 0;
+ int molb = 0;
+ for (int m = 0; m < nrefat; ++m)
{
- ai = index[m];
- mass = top->atoms.atom[ai].m;
- for (j = 0; j < DIM; ++j)
+ const int ai = index[m];
+ const real mass = mtopGetAtomMass(top, ai, &molb);
+ for (int j = 0; j < DIM; ++j)
{
xout[j] += mass * x[ai][j];
}
* \param[out] fout Force on the COG position for the indexed atoms.
*/
void
-gmx_calc_cog_f(const t_topology *top, rvec f[], int nrefat, const int index[], rvec fout)
+gmx_calc_cog_f(const gmx_mtop_t *top, rvec f[], int nrefat, const int index[], rvec fout)
{
- int m, j, ai;
- real mass, mtot;
-
- GMX_RELEASE_ASSERT(top != nullptr,
+ GMX_RELEASE_ASSERT(gmx_mtop_has_masses(top),
"No masses available while mass weighting was requested");
clear_rvec(fout);
- mtot = 0;
- for (m = 0; m < nrefat; ++m)
+ real mtot = 0;
+ int molb = 0;
+ for (int m = 0; m < nrefat; ++m)
{
- ai = index[m];
- mass = top->atoms.atom[ai].m;
- for (j = 0; j < DIM; ++j)
+ const int ai = index[m];
+ const real mass = mtopGetAtomMass(top, ai, &molb);
+ for (int j = 0; j < DIM; ++j)
{
fout[j] += f[ai][j] / mass;
}
}
void
-gmx_calc_com_f(const t_topology * /* top */, rvec f[], int nrefat, const int index[], rvec fout)
+gmx_calc_com_f(const gmx_mtop_t * /* top */, rvec f[], int nrefat, const int index[], rvec fout)
{
clear_rvec(fout);
for (int m = 0; m < nrefat; ++m)
* Other parameters are passed unmodified to these functions.
*/
void
-gmx_calc_comg(const t_topology *top, rvec x[], int nrefat, const int index[],
+gmx_calc_comg(const gmx_mtop_t *top, rvec x[], int nrefat, const int index[],
bool bMass, rvec xout)
{
if (bMass)
* Other parameters are passed unmodified to these functions.
*/
void
-gmx_calc_comg_f(const t_topology *top, rvec f[], int nrefat, const int index[],
+gmx_calc_comg_f(const gmx_mtop_t *top, rvec f[], int nrefat, const int index[],
bool bMass, rvec fout)
{
if (bMass)
* Works exactly as gmx_calc_com_pbc(), but calculates the center of geometry.
*/
void
-gmx_calc_cog_pbc(const t_topology *top, rvec x[], t_pbc *pbc,
+gmx_calc_cog_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], rvec xout)
{
const real tol = 1e-4;
* Modified from src/tools/gmx_sorient.c in Gromacs distribution.
*/
void
-gmx_calc_com_pbc(const t_topology *top, rvec x[], t_pbc *pbc,
+gmx_calc_com_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], rvec xout)
{
- const real tol = 1e-4;
- bool bChanged;
- int m, j, ai, iter;
- real mass, mtot;
- rvec dx, xtest;
-
- GMX_RELEASE_ASSERT(top != nullptr,
+ GMX_RELEASE_ASSERT(gmx_mtop_has_masses(top),
"No masses available while mass weighting was requested");
/* First simple calculation */
clear_rvec(xout);
- mtot = 0;
- for (m = 0; m < nrefat; ++m)
+ real mtot = 0;
+ int molb = 0;
+ for (int m = 0; m < nrefat; ++m)
{
- ai = index[m];
- mass = top->atoms.atom[ai].m;
- for (j = 0; j < DIM; ++j)
+ const int ai = index[m];
+ const real mass = mtopGetAtomMass(top, ai, &molb);
+ for (int j = 0; j < DIM; ++j)
{
xout[j] += mass * x[ai][j];
}
/* Now check if any atom is more than half the box from the COM */
if (pbc)
{
- iter = 0;
+ const real tol = 1e-4;
+ bool bChanged;
do
{
bChanged = false;
- for (m = 0; m < nrefat; ++m)
+ molb = 0;
+ for (int m = 0; m < nrefat; ++m)
{
- ai = index[m];
- mass = top->atoms.atom[ai].m / mtot;
+ rvec dx, xtest;
+ const int ai = index[m];
+ const real mass = mtopGetAtomMass(top, ai, &molb) / mtot;
pbc_dx(pbc, x[ai], xout, dx);
rvec_add(xout, dx, xtest);
- for (j = 0; j < DIM; ++j)
+ for (int j = 0; j < DIM; ++j)
{
if (fabs(xtest[j] - x[ai][j]) > tol)
{
}
}
}
- iter++;
}
while (bChanged);
}
* Other parameters are passed unmodified to these functions.
*/
void
-gmx_calc_comg_pbc(const t_topology *top, rvec x[], t_pbc *pbc,
+gmx_calc_comg_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], bool bMass, rvec xout)
{
if (bMass)
void
-gmx_calc_cog_block(const t_topology * /* top */, rvec x[], const t_block *block, const int index[],
+gmx_calc_cog_block(const gmx_mtop_t * /* top */, rvec x[], const t_block *block, const int index[],
rvec xout[])
{
int b, i, ai;
* mass are calculated, and hence a topology with masses is required.
*/
void
-gmx_calc_com_block(const t_topology *top, rvec x[], const t_block *block, const int index[],
+gmx_calc_com_block(const gmx_mtop_t *top, rvec x[], const t_block *block, const int index[],
rvec xout[])
{
- int b, i, ai, d;
- rvec xb;
- real mass, mtot;
-
- GMX_RELEASE_ASSERT(top != nullptr,
+ GMX_RELEASE_ASSERT(gmx_mtop_has_masses(top),
"No masses available while mass weighting was requested");
- for (b = 0; b < block->nr; ++b)
+ int molb = 0;
+ for (int b = 0; b < block->nr; ++b)
{
+ rvec xb;
clear_rvec(xb);
- mtot = 0;
- for (i = block->index[b]; i < block->index[b+1]; ++i)
+ real mtot = 0;
+ for (int i = block->index[b]; i < block->index[b+1]; ++i)
{
- ai = index[i];
- mass = top->atoms.atom[ai].m;
- for (d = 0; d < DIM; ++d)
+ const int ai = index[i];
+ const real mass = mtopGetAtomMass(top, ai, &molb);
+ for (int d = 0; d < DIM; ++d)
{
xb[d] += mass * x[ai][d];
}
* \param[out] fout \p block->nr Forces on COG positions.
*/
void
-gmx_calc_cog_f_block(const t_topology *top, rvec f[], const t_block *block, const int index[],
+gmx_calc_cog_f_block(const gmx_mtop_t *top, rvec f[], const t_block *block, const int index[],
rvec fout[])
{
- int b, i, ai, d;
- rvec fb;
- real mass, mtot;
-
- GMX_RELEASE_ASSERT(top != nullptr,
+ GMX_RELEASE_ASSERT(gmx_mtop_has_masses(top),
"No masses available while mass weighting was requested");
- for (b = 0; b < block->nr; ++b)
+ int molb = 0;
+ for (int b = 0; b < block->nr; ++b)
{
+ rvec fb;
clear_rvec(fb);
- mtot = 0;
- for (i = block->index[b]; i < block->index[b+1]; ++i)
+ real mtot = 0;
+ for (int i = block->index[b]; i < block->index[b+1]; ++i)
{
- ai = index[i];
- mass = top->atoms.atom[ai].m;
- for (d = 0; d < DIM; ++d)
+ const int ai = index[i];
+ const real mass = mtopGetAtomMass(top, ai, &molb);
+ for (int d = 0; d < DIM; ++d)
{
fb[d] += f[ai][d] / mass;
}
}
void
-gmx_calc_com_f_block(const t_topology * /* top */, rvec f[], const t_block *block, const int index[],
+gmx_calc_com_f_block(const gmx_mtop_t * /* top */, rvec f[], const t_block *block, const int index[],
rvec fout[])
{
for (int b = 0; b < block->nr; ++b)
* Other parameters are passed unmodified to these functions.
*/
void
-gmx_calc_comg_block(const t_topology *top, rvec x[], const t_block *block, const int index[],
+gmx_calc_comg_block(const gmx_mtop_t *top, rvec x[], const t_block *block, const int index[],
bool bMass, rvec xout[])
{
if (bMass)
* Other parameters are passed unmodified to these functions.
*/
void
-gmx_calc_comg_f_block(const t_topology *top, rvec f[], const t_block *block, const int index[],
+gmx_calc_comg_f_block(const gmx_mtop_t *top, rvec f[], const t_block *block, const int index[],
bool bMass, rvec fout[])
{
if (bMass)
* crashes.
*/
void
-gmx_calc_comg_blocka(const t_topology *top, rvec x[], const t_blocka *block,
+gmx_calc_comg_blocka(const gmx_mtop_t *top, rvec x[], const t_blocka *block,
bool bMass, rvec xout[])
{
/* TODO: It would probably be better to do this without the type cast */
- gmx_calc_comg_block(top, x, (t_block *)block, block->a, bMass, xout);
+ gmx_calc_comg_block(top, x, reinterpret_cast<const t_block *>(block), block->a, bMass, xout);
}
/*!
* crashes.
*/
void
-gmx_calc_comg_f_blocka(const t_topology *top, rvec f[], const t_blocka *block,
+gmx_calc_comg_f_blocka(const gmx_mtop_t *top, rvec f[], const t_blocka *block,
bool bMass, rvec fout[])
{
/* TODO: It would probably be better to do this without the type cast */
- gmx_calc_comg_f_block(top, f, (t_block *)block, block->a, bMass, fout);
+ gmx_calc_comg_f_block(top, f, reinterpret_cast<const t_block *>(block), block->a, bMass, fout);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/math/vectypes.h"
+struct gmx_mtop_t;
struct t_block;
struct t_blocka;
struct t_pbc;
-struct t_topology;
/*! \brief
* Calculate a single center of geometry.
* \param[out] xout COG position for the indexed atoms.
*/
void
-gmx_calc_cog(const t_topology *top, rvec x[], int nrefat, const int index[], rvec xout);
+gmx_calc_cog(const gmx_mtop_t *top, rvec x[], int nrefat, const int index[], rvec xout);
/** Calculate a single center of mass. */
void
-gmx_calc_com(const t_topology *top, rvec x[], int nrefat, const int index[], rvec xout);
+gmx_calc_com(const gmx_mtop_t *top, rvec x[], int nrefat, const int index[], rvec xout);
/** Calculate force on a single center of geometry. */
void
-gmx_calc_cog_f(const t_topology *top, rvec f[], int nrefat, const int index[], rvec fout);
+gmx_calc_cog_f(const gmx_mtop_t *top, rvec f[], int nrefat, const int index[], rvec fout);
/*! \brief
* Calculate force on a single center of mass.
*
* \param[out] fout Force on the COM position for the indexed atoms.
*/
void
-gmx_calc_com_f(const t_topology *top, rvec f[], int nrefat, const int index[], rvec fout);
+gmx_calc_com_f(const gmx_mtop_t *top, rvec f[], int nrefat, const int index[], rvec fout);
/** Calculate a single center of mass/geometry. */
void
-gmx_calc_comg(const t_topology *top, rvec x[], int nrefat, const int index[],
+gmx_calc_comg(const gmx_mtop_t *top, rvec x[], int nrefat, const int index[],
bool bMass, rvec xout);
/** Calculate force on a single center of mass/geometry. */
void
-gmx_calc_comg_f(const t_topology *top, rvec f[], int nrefat, const int index[],
+gmx_calc_comg_f(const gmx_mtop_t *top, rvec f[], int nrefat, const int index[],
bool bMass, rvec fout);
/** Calculate a single center of geometry iteratively, taking PBC into account. */
void
-gmx_calc_cog_pbc(const t_topology *top, rvec x[], t_pbc *pbc,
+gmx_calc_cog_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], rvec xout);
/** Calculate a single center of mass iteratively, taking PBC into account. */
void
-gmx_calc_com_pbc(const t_topology *top, rvec x[], t_pbc *pbc,
+gmx_calc_com_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], rvec xout);
/** Calculate a single center of mass/geometry iteratively with PBC. */
void
-gmx_calc_comg_pbc(const t_topology *top, rvec x[], t_pbc *pbc,
+gmx_calc_comg_pbc(const gmx_mtop_t *top, rvec x[], const t_pbc *pbc,
int nrefat, const int index[], bool bMass, rvec xout);
/*! \brief
* \param[out] xout \p block->nr COG positions.
*/
void
-gmx_calc_cog_block(const t_topology *top, rvec x[], const t_block *block,
+gmx_calc_cog_block(const gmx_mtop_t *top, rvec x[], const t_block *block,
const int index[], rvec xout[]);
/** Calculate centers of mass for a blocked index. */
void
-gmx_calc_com_block(const t_topology *top, rvec x[], const t_block *block,
+gmx_calc_com_block(const gmx_mtop_t *top, rvec x[], const t_block *block,
const int index[], rvec xout[]);
/** Calculate forces on centers of geometry for a blocked index. */
void
-gmx_calc_cog_f_block(const t_topology *top, rvec f[], const t_block *block,
+gmx_calc_cog_f_block(const gmx_mtop_t *top, rvec f[], const t_block *block,
const int index[], rvec fout[]);
/*! \brief
* Calculate forces on centers of mass for a blocked index.
* \param[out] fout \p block->nr Forces on COM positions.
*/
void
-gmx_calc_com_f_block(const t_topology *top, rvec f[], const t_block *block,
+gmx_calc_com_f_block(const gmx_mtop_t *top, rvec f[], const t_block *block,
const int index[], rvec fout[]);
/** Calculate centers of mass/geometry for a blocked index. */
void
-gmx_calc_comg_block(const t_topology *top, rvec x[], const t_block *block,
+gmx_calc_comg_block(const gmx_mtop_t *top, rvec x[], const t_block *block,
const int index[], bool bMass, rvec xout[]);
/** Calculate forces on centers of mass/geometry for a blocked index. */
void
-gmx_calc_comg_f_block(const t_topology *top, rvec f[], const t_block *block,
+gmx_calc_comg_f_block(const gmx_mtop_t *top, rvec f[], const t_block *block,
const int index[], bool bMass, rvec fout[]);
/** Calculate centers of mass/geometry for a set of blocks; */
void
-gmx_calc_comg_blocka(const t_topology *top, rvec x[], const t_blocka *block,
+gmx_calc_comg_blocka(const gmx_mtop_t *top, rvec x[], const t_blocka *block,
bool bMass, rvec xout[]);
/** Calculate forces on centers of mass/geometry for a set of blocks; */
void
-gmx_calc_comg_f_blocka(const t_topology *top, rvec x[], const t_blocka *block,
+gmx_calc_comg_f_blocka(const gmx_mtop_t *top, rvec x[], const t_blocka *block,
bool bMass, rvec xout[]);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
sfree(cdata);
}
- cdata = NULL;
+ cdata = nullptr;
}
} // namespace gmx
* reference positions use the whole residue/molecule. */
if (root->type == SEL_EXPRESSION)
{
- bool bSelection = (sel != NULL);
+ bool bSelection = (sel != nullptr);
int flags = bSelection ? POS_COMPLMAX : POS_COMPLWHOLE;
if (bSelection)
{
if (root->type != SEL_ROOT && root->type != SEL_MODIFIER
&& root->type != SEL_SUBEXPRREF && root->type != SEL_SUBEXPR)
{
- sel = NULL;
+ sel = nullptr;
}
/* Recurse into children */
SelectionTreeElementPointer child = root->child;
{
sel->evaluate = &_gmx_sel_evaluate_subexpr_staticeval;
sel->cdata->evaluate = sel->evaluate;
- sel->child->mempool = NULL;
+ sel->child->mempool = nullptr;
sel->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
if (sel->v.type == GROUP_VALUE || sel->v.type == POS_VALUE)
{
if (root->child->type != SEL_SUBEXPR
|| (root->child->v.type != GROUP_VALUE && !(root->flags & SEL_ATOMVAL)))
{
- gmx_ana_index_set(&root->u.cgrp, -1, 0, 0);
+ gmx_ana_index_set(&root->u.cgrp, -1, nullptr, 0);
}
else if (root->child->cdata->flags & SEL_CDATA_FULLEVAL)
{
sel->freeExpressionData();
/* Make the item static */
sel->type = SEL_CONST;
- sel->evaluate = NULL;
- sel->cdata->evaluate = NULL;
+ sel->evaluate = nullptr;
+ sel->cdata->evaluate = nullptr;
/* Set the group value.
* freeExpressionData() frees the cgrp group, so we can just override it.
* */
* is prevented by using \ref SEL_METHODINIT and \ref SEL_OUTINIT flags.
*/
static void
-init_method(const SelectionTreeElementPointer &sel, t_topology *top, int isize)
+init_method(const SelectionTreeElementPointer &sel, const gmx_mtop_t *top, int isize)
{
/* Find out whether there are any atom-valued parameters */
bool bAtomVal = false;
sel->flags |= SEL_ALLOCDATA;
for (i = 0; i < isize; ++i)
{
- if (sel->v.u.s[i] == NULL)
+ if (sel->v.u.s[i] == nullptr)
{
snew(sel->v.u.s[i], 2);
}
child.reset(new SelectionTreeElement(SEL_CONST, SelectionLocation::createEmpty()));
child->flags = SEL_FLAGSSET | SEL_SINGLEVAL | SEL_ALLOCVAL | SEL_ALLOCDATA;
_gmx_selelem_set_vtype(child, GROUP_VALUE);
- child->evaluate = NULL;
+ child->evaluate = nullptr;
_gmx_selvalue_reserve(&child->v, 1);
gmx_ana_index_copy(child->v.u.g, sel->v.u.g, true);
init_item_compilerdata(child);
* If we reach here with a NOT expression, the NOT expression
* is also static, and will be made a constant later, so don't waste
* time copying the group. */
- child->evaluate = NULL;
+ child->evaluate = nullptr;
if (sel->u.boolt == BOOL_NOT
|| ((sel->cdata->flags & SEL_CDATA_STATICEVAL)
&& sel->u.boolt == BOOL_OR))
{
- child->cdata->evaluate = NULL;
+ child->cdata->evaluate = nullptr;
}
else
{
|| ((root->child->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
&& !(root->child->cdata->flags & SEL_CDATA_FULLEVAL))))
{
- root->evaluate = NULL;
+ root->evaluate = nullptr;
if (root->cdata)
{
- root->cdata->evaluate = NULL;
+ root->cdata->evaluate = nullptr;
}
}
if ((expr->flags & SEL_VARNUMVAL)
|| ((expr->flags & SEL_SINGLEVAL) && expr->v.type != GROUP_VALUE))
{
- gmx_ana_index_set(&root->u.cgrp, -1, NULL, 0);
+ gmx_ana_index_set(&root->u.cgrp, -1, nullptr, 0);
}
else if (expr->cdata->gmax->isize == gall->isize)
{
/* For selections, store the maximum group for
* gmx_ana_selcollection_evaluate_fin() as the value of the root
* element (unused otherwise). */
- if (expr->type != SEL_SUBEXPR && expr->v.u.p->m.mapb.a != NULL)
+ if (expr->type != SEL_SUBEXPR && expr->v.u.p->m.mapb.a != nullptr)
{
SelectionTreeElementPointer child = expr;
sel->cdata->evaluate = sel->evaluate;
sel->child->freeValues();
- sel->child->mempool = NULL;
+ sel->child->mempool = nullptr;
_gmx_selvalue_setstore(&sel->child->v, sel->v.u.ptr);
sel->child->flags &= ~(SEL_ALLOCVAL | SEL_ALLOCDATA);
}
&& (sel->cdata->flags & SEL_CDATA_SIMPLESUBEXPR)
&& (sel->cdata->flags & SEL_CDATA_STATICMULTIEVALSUBEXPR))
{
- sel->evaluate = NULL;
- sel->cdata->evaluate = NULL;
+ sel->evaluate = nullptr;
+ sel->cdata->evaluate = nullptr;
}
}
sc->mempool = _gmx_sel_mempool_create();
_gmx_sel_evaluate_init(&evaldata, sc->mempool, &sc->gall,
- sc->top, NULL, NULL);
+ sc->top, nullptr, nullptr);
/* Clear the symbol table because it is not possible to parse anything
* after compilation, and variable references in the symbol table can
mark_subexpr_dynamic(item->child, true);
}
set_evaluation_function(item, &analyze_static);
- item->evaluate(&evaldata, item, NULL);
+ item->evaluate(&evaldata, item, nullptr);
item = item->next;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param mp Memory pool from which to reserve memory.
*/
explicit MempoolGroupReserver(gmx_sel_mempool_t *mp)
- : mp_(mp), g_(NULL)
+ : mp_(mp), g_(nullptr)
{
}
//! Frees any memory allocated using this reserver.
~MempoolGroupReserver()
{
- if (g_ != NULL)
+ if (g_ != nullptr)
{
_gmx_sel_mempool_free_group(mp_, g_);
}
*/
void reserve(gmx_ana_index_t *g, int count)
{
- GMX_RELEASE_ASSERT(g_ == NULL, "Can only reserve one element with one instance");
+ GMX_RELEASE_ASSERT(g_ == nullptr, "Can only reserve one element with one instance");
_gmx_sel_mempool_alloc_group(mp_, g, count);
g_ = g;
}
public:
//! Constructs an assigner without an initial assignment.
SelelemTemporaryValueAssigner()
- : old_ptr_(NULL), old_nalloc_(0)
+ : old_ptr_(nullptr), old_nalloc_(0)
{
}
/*! \brief
void
_gmx_sel_evaluate_init(gmx_sel_evaluate_t *data,
gmx_sel_mempool_t *mp, gmx_ana_index_t *gall,
- t_topology *top, t_trxframe *fr, t_pbc *pbc)
+ const gmx_mtop_t *top, t_trxframe *fr, t_pbc *pbc)
{
data->mp = mp;
data->gall = gall;
{
/* Clear the evaluation group of subexpressions */
if (sel->child && sel->child->type == SEL_SUBEXPR
- && sel->child->evaluate != NULL)
+ && sel->child->evaluate != nullptr)
{
sel->child->u.cgrp.isize = 0;
/* Not strictly necessary, because the value will be overwritten
}
if (sel->evaluate)
{
- sel->evaluate(&data, sel, NULL);
+ sel->evaluate(&data, sel, nullptr);
}
sel = sel->next;
}
}
sel->child->evaluate(data, sel->child,
- sel->u.cgrp.isize < 0 ? NULL : &sel->u.cgrp);
+ sel->u.cgrp.isize < 0 ? nullptr : &sel->u.cgrp);
}
void
{
int i, j;
- if (g != NULL && sel->child->evaluate != NULL)
+ if (g != nullptr && sel->child->evaluate != nullptr)
{
sel->child->evaluate(data, sel->child, g);
}
else
{
child->flags |= SEL_EVALFRAME;
- child->evaluate(data, child, NULL);
+ child->evaluate(data, child, nullptr);
}
}
child = child->next;
gmx_ana_index_t *g)
{
_gmx_sel_evaluate_method_params(data, sel, g);
+ gmx::SelMethodEvalContext context(data->top, data->fr, data->pbc);
if (sel->flags & SEL_INITFRAME)
{
sel->flags &= ~SEL_INITFRAME;
- sel->u.expr.method->init_frame(data->top, data->fr, data->pbc,
- sel->u.expr.mdata);
+ sel->u.expr.method->init_frame(context, sel->u.expr.mdata);
}
if (sel->u.expr.pc)
{
gmx_ana_poscalc_update(sel->u.expr.pc, sel->u.expr.pos, g,
data->fr, data->pbc);
- sel->u.expr.method->pupdate(data->top, data->fr, data->pbc,
- sel->u.expr.pos, &sel->v,
+ sel->u.expr.method->pupdate(context, sel->u.expr.pos, &sel->v,
sel->u.expr.mdata);
if ((sel->flags & SEL_ATOMVAL) && sel->v.nr < g->isize)
{
}
else
{
- sel->u.expr.method->update(data->top, data->fr, data->pbc, g,
- &sel->v, sel->u.expr.mdata);
+ sel->u.expr.method->update(context, g, &sel->v, sel->u.expr.mdata);
}
}
gmx_ana_index_t *g)
{
_gmx_sel_evaluate_method_params(data, sel, g);
+ gmx::SelMethodEvalContext context(data->top, data->fr, data->pbc);
if (sel->flags & SEL_INITFRAME)
{
sel->flags &= ~SEL_INITFRAME;
- sel->u.expr.method->init_frame(data->top, data->fr, data->pbc,
- sel->u.expr.mdata);
+ sel->u.expr.method->init_frame(context, sel->u.expr.mdata);
}
if (sel->child && sel->child->v.type != POS_VALUE)
{
GMX_THROW(gmx::NotImplementedError("Non-position valued modifiers not implemented"));
}
- sel->u.expr.method->pupdate(data->top, data->fr, data->pbc,
- NULL, &sel->v, sel->u.expr.mdata);
+ sel->u.expr.method->pupdate(context, nullptr, &sel->v, sel->u.expr.mdata);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "selelem.h"
struct gmx_ana_index_t;
+struct gmx_mtop_t;
struct gmx_sel_mempool_t;
struct t_pbc;
-struct t_topology;
struct t_trxframe;
/*! \internal \brief
/** Index group that contains all the atoms. */
gmx_ana_index_t *gall;
/** Topology information. */
- t_topology *top;
+ const gmx_mtop_t *top;
/** Current frame. */
t_trxframe *fr;
/** PBC data. */
void
_gmx_sel_evaluate_init(gmx_sel_evaluate_t *data,
gmx_sel_mempool_t *mp, gmx_ana_index_t *gall,
- t_topology *top, t_trxframe *fr, t_pbc *pbc);
+ const gmx_mtop_t *top, t_trxframe *fr, t_pbc *pbc);
/** Evaluates the children of a general selection element. */
void
_gmx_sel_evaluate_children(gmx_sel_evaluate_t *data,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/topology/block.h"
#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_lookup.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
struct gmx_ana_indexgrps_t
{
//! Initializes an empty set of groups.
- explicit gmx_ana_indexgrps_t(int nr) : nr(nr), g(NULL)
+ explicit gmx_ana_indexgrps_t(int nr) : nr(nr), g(nullptr)
{
names.reserve(nr);
snew(g, nr);
* If both are null, the index group structure is initialized empty.
*/
void
-gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
+gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, gmx_mtop_t *top,
const char *fnm)
{
- t_blocka *block = NULL;
- char **names = NULL;
+ t_blocka *block = nullptr;
+ char **names = nullptr;
if (fnm)
{
else if (top)
{
block = new_blocka();
- analyse(&top->atoms, block, &names, FALSE, FALSE);
+ // TODO: Propagate mtop further.
+ t_atoms atoms = gmx_mtop_global_atoms(top);
+ analyse(&atoms, block, &names, FALSE, FALSE);
+ done_atom(&atoms);
}
else
{
grp->index[j] = block->a[block->index[i]+j];
}
grp->nalloc_index = grp->isize;
- (*g)->names.push_back(names[i]);
+ (*g)->names.emplace_back(names[i]);
}
}
catch (...)
{
if (n < 0 || n >= g->nr)
{
- return NULL;
+ return nullptr;
}
return &g->g[n];
}
return false;
}
- if (destName != NULL)
+ if (destName != nullptr)
{
*destName = src->names[n];
}
gmx_ana_index_clear(gmx_ana_index_t *g)
{
g->isize = 0;
- g->index = NULL;
+ g->index = nullptr;
g->nalloc_index = 0;
}
* \ingroup module_selection
*/
static bool
-next_group_index(int atomIndex, t_topology *top, e_index_t type, int *id)
+next_group_index(int atomIndex, const gmx_mtop_t *top, e_index_t type, int *id)
{
int prev = *id;
switch (type)
*id = atomIndex;
break;
case INDEX_RES:
- *id = top->atoms.atom[atomIndex].resind;
+ {
+ int resind, molb = 0;
+ mtopGetAtomAndResidueName(top, atomIndex, &molb, nullptr, nullptr, nullptr, &resind);
+ *id = resind;
break;
+ }
case INDEX_MOL:
if (*id >= 0 && top->mols.index[*id] > atomIndex)
{
* \p g should be sorted.
*/
void
-gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
+gmx_ana_index_make_block(t_blocka *t, const gmx_mtop_t *top, gmx_ana_index_t *g,
e_index_t type, bool bComplete)
{
if (type == INDEX_UNKNOWN)
t->index[0] = 0;
t->index[1] = 0;
t->nra = 0;
- t->a = NULL;
+ t->a = nullptr;
t->nalloc_a = 0;
return;
}
// TODO: Check callers and either check these there as well, or turn these
// into exceptions.
- GMX_RELEASE_ASSERT(top != NULL || (type != INDEX_RES && type != INDEX_MOL),
+ GMX_RELEASE_ASSERT(top != nullptr || (type != INDEX_RES && type != INDEX_MOL),
"Topology must be provided for residue or molecule blocks");
GMX_RELEASE_ASSERT(!(type == INDEX_MOL && top->mols.nr == 0),
"Molecule information must be present for molecule blocks");
t->nra = 0;
/* We may allocate some extra memory here because we don't know in
* advance how much will be needed. */
- if (t->nalloc_a < top->atoms.nr)
+ if (t->nalloc_a < top->natoms)
{
- srenew(t->a, top->atoms.nr);
- t->nalloc_a = top->atoms.nr;
+ srenew(t->a, top->natoms);
+ t->nalloc_a = top->natoms;
}
}
else
}
/* Clear counters */
t->nr = 0;
- int j = 0; /* j is used by residue completion for the first atom not stored */
- int id = -1;
+ int id = -1;
+ int molb = 0;
for (int i = 0; i < g->isize; ++i)
{
+ const int ai = g->index[i];
/* Find the ID number of the atom/residue/molecule corresponding to
* the atom. */
- if (next_group_index(g->index[i], top, type, &id))
+ if (next_group_index(ai, top, type, &id))
{
/* If this is the first atom in a new block, initialize the block. */
if (bComplete)
switch (type)
{
case INDEX_RES:
- while (top->atoms.atom[j].resind != id)
+ {
+ int molnr, atnr_mol;
+ mtopGetMolblockIndex(top, ai, &molb, &molnr, &atnr_mol);
+ const t_atoms &mol_atoms = top->moltype[top->molblock[molb].type].atoms;
+ int last_atom = atnr_mol + 1;
+ while (last_atom < mol_atoms.nr
+ && mol_atoms.atom[last_atom].resind == id)
+ {
+ ++last_atom;
+ }
+ int first_atom = atnr_mol - 1;
+ while (first_atom >= 0
+ && mol_atoms.atom[first_atom].resind == id)
{
- ++j;
+ --first_atom;
}
- while (j < top->atoms.nr && top->atoms.atom[j].resind == id)
+ int first_mol_atom = top->molblock[molb].globalAtomStart;
+ first_mol_atom += molnr*top->molblock[molb].natoms_mol;
+ first_atom = first_mol_atom + first_atom + 1;
+ last_atom = first_mol_atom + last_atom - 1;
+ for (int j = first_atom; j <= last_atom; ++j)
{
t->a[t->nra++] = j;
- ++j;
}
break;
-
+ }
case INDEX_MOL:
- for (j = top->mols.index[id]; j < top->mols.index[id+1]; ++j)
+ for (int j = top->mols.index[id]; j < top->mols.index[id+1]; ++j)
{
t->a[t->nra++] = j;
}
* The atoms in \p g are assumed to be sorted.
*/
bool
-gmx_ana_index_has_full_blocks(gmx_ana_index_t *g, t_block *b)
+gmx_ana_index_has_full_blocks(const gmx_ana_index_t *g, const t_block *b)
{
int i, j, bi;
return true;
}
+/*!
+ * \brief Returns if an atom is at a residue boundary.
+ *
+ * \param[in] top Topology data.
+ * \param[in] a Atom index to check, should be -1 <= \p a < top->natoms.
+ * \param[in,out] molb The molecule block of atom a
+ * \returns true if atoms \p a and \p a + 1 are in different residues, false otherwise.
+ */
+static bool is_at_residue_boundary(const gmx_mtop_t *top, int a, int *molb)
+{
+ if (a == -1 || a + 1 == top->natoms)
+ {
+ return true;
+ }
+ int resindA;
+ mtopGetAtomAndResidueName(top, a, molb,
+ nullptr, nullptr, nullptr, &resindA);
+ int resindAPlusOne;
+ mtopGetAtomAndResidueName(top, a + 1, molb,
+ nullptr, nullptr, nullptr, &resindAPlusOne);
+ return resindAPlusOne != resindA;
+}
+
/*!
* \param[in] g Index group to check.
* \param[in] type Block data to check against.
*/
bool
gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type,
- t_topology *top)
+ const gmx_mtop_t *top)
{
+ if (g->isize == 0)
+ {
+ return true;
+ }
+
// TODO: Consider whether unsorted groups need to be supported better.
switch (type)
{
case INDEX_RES:
{
- int i, ai;
- int id, prev;
-
- prev = -1;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ int aPrev = -1;
+ for (int i = 0; i < g->isize; ++i)
{
- ai = g->index[i];
- id = top->atoms.atom[ai].resind;
- if (id != prev)
+ const int a = g->index[i];
+ // Check if a is consecutive or on a residue boundary
+ if (a != aPrev + 1)
{
- if (ai > 0 && top->atoms.atom[ai-1].resind == id)
+ if (!is_at_residue_boundary(top, aPrev, &molb))
{
return false;
}
- if (i > 0 && g->index[i-1] < top->atoms.nr - 1
- && top->atoms.atom[g->index[i-1]+1].resind == prev)
+ if (!is_at_residue_boundary(top, a - 1, &molb))
{
return false;
}
}
- prev = id;
+ aPrev = a;
}
- if (g->index[i-1] < top->atoms.nr - 1
- && top->atoms.atom[g->index[i-1]+1].resind == prev)
+ GMX_ASSERT(g->isize > 0, "We return above when isize=0");
+ const int a = g->index[g->isize - 1];
+ if (!is_at_residue_boundary(top, a, &molb))
{
return false;
}
gmx_ana_indexmap_clear(gmx_ana_indexmap_t *m)
{
m->type = INDEX_UNKNOWN;
- m->refid = NULL;
- m->mapid = NULL;
+ m->refid = nullptr;
+ m->mapid = nullptr;
m->mapb.nr = 0;
- m->mapb.index = NULL;
+ m->mapb.index = nullptr;
m->mapb.nalloc_index = 0;
m->mapb.nra = 0;
- m->mapb.a = NULL;
+ m->mapb.a = nullptr;
m->mapb.nalloc_a = 0;
- m->orgid = NULL;
+ m->orgid = nullptr;
m->b.nr = 0;
- m->b.index = NULL;
+ m->b.index = nullptr;
m->b.nra = 0;
- m->b.a = NULL;
+ m->b.a = nullptr;
m->b.nalloc_index = 0;
m->b.nalloc_a = 0;
m->bStatic = true;
*/
void
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
- t_topology *top, e_index_t type)
+ const gmx_mtop_t *top, e_index_t type)
{
m->type = type;
gmx_ana_index_make_block(&m->b, top, g, type, false);
}
int
-gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, t_topology *top,
+gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, const gmx_mtop_t *top,
e_index_t type)
{
GMX_RELEASE_ASSERT(m->bStatic,
"Changing original IDs is not supported after starting "
"to use the mapping");
- GMX_RELEASE_ASSERT(top != NULL || (type != INDEX_RES && type != INDEX_MOL),
+ GMX_RELEASE_ASSERT(top != nullptr || (type != INDEX_RES && type != INDEX_MOL),
"Topology must be provided for residue or molecule blocks");
GMX_RELEASE_ASSERT(!(type == INDEX_MOL && top->mols.nr == 0),
"Molecule information must be present for molecule blocks");
class TextWriter;
}
-struct t_topology;
+struct gmx_mtop_t;
/** Stores a set of index groups. */
struct gmx_ana_indexgrps_t;
/*@{*/
/** Reads index groups from a file or constructs them from topology. */
void
-gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, t_topology *top,
+gmx_ana_indexgrps_init(gmx_ana_indexgrps_t **g, gmx_mtop_t *top,
const char *fnm);
/** Frees memory allocated for index groups. */
void
/*@{*/
/** Partition a group based on topology information. */
void
-gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
+gmx_ana_index_make_block(t_blocka *t, const gmx_mtop_t *top, gmx_ana_index_t *g,
e_index_t type, bool bComplete);
/** Checks whether a group consists of full blocks. */
bool
-gmx_ana_index_has_full_blocks(gmx_ana_index_t *g, t_block *b);
+gmx_ana_index_has_full_blocks(const gmx_ana_index_t *g, const t_block *b);
/** Checks whether a group consists of full blocks. */
bool
gmx_ana_index_has_full_ablocks(gmx_ana_index_t *g, t_blocka *b);
/** Checks whether a group consists of full residues/molecules. */
bool
-gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type, t_topology *top);
+gmx_ana_index_has_complete_elems(gmx_ana_index_t *g, e_index_t type,
+ const gmx_mtop_t *top);
/** Initializes an empty index group mapping. */
void
/** Initializes an index group mapping. */
void
gmx_ana_indexmap_init(gmx_ana_indexmap_t *m, gmx_ana_index_t *g,
- t_topology *top, e_index_t type);
+ const gmx_mtop_t *top, e_index_t type);
/*! \brief
* Initializes `orgid` entries based on topology grouping.
*
* Strong exception safety guarantee.
*/
int
-gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, t_topology *top,
+gmx_ana_indexmap_init_orgid_group(gmx_ana_indexmap_t *m, const gmx_mtop_t *top,
e_index_t type);
/** Sets an index group mapping to be static. */
void
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(mp, 1);
mp->currsize = 0;
mp->freesize = 0;
- mp->buffer = NULL;
- mp->freeptr = NULL;
+ mp->buffer = nullptr;
+ mp->freeptr = nullptr;
mp->nblocks = 0;
- mp->blockstack = NULL;
+ mp->blockstack = nullptr;
mp->blockstack_nalloc = 0;
mp->maxsize = 0;
return mp;
void *
_gmx_sel_mempool_alloc(gmx_sel_mempool_t *mp, size_t size)
{
- void *ptr = NULL;
+ void *ptr = nullptr;
size_t size_walign;
size_walign = ((size + ALIGN_STEP - 1) / ALIGN_STEP) * ALIGN_STEP;
{
int size;
- if (ptr == NULL)
+ if (ptr == nullptr)
{
return;
}
_gmx_sel_mempool_free_group(gmx_sel_mempool_t *mp, gmx_ana_index_t *g)
{
_gmx_sel_mempool_free(mp, g->index);
- g->index = NULL;
+ g->index = nullptr;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* \todo
* The grid implementation could still be optimized in several different ways:
- * - Pruning grid cells from the search list if they are completely outside
- * the sphere that is being considered.
- * - A better heuristic could be added for falling back to simple loops for a
- * small number of reference particles.
- * - A better heuristic for selecting the grid size.
+ * - A better heuristic for selecting the grid size or falling back to a
+ * simple all-pairs search.
* - A multi-level grid implementation could be used to be able to use small
* grids for short cutoffs with very inhomogeneous particle distributions
* without a memory cost.
bool usesGridSearch() const { return bGrid_; }
private:
- /*! \brief
- * Checks the efficiency and possibility of doing grid-based searching.
- *
- * \param[in] bForce If `true`, grid search will be forced if possible.
- * \returns `false` if grid search is not suitable.
- */
- bool checkGridSearchEfficiency(bool bForce);
/*! \brief
* Determines a suitable grid size and sets up the cells.
*
* \returns Linear index of \p cell.
*/
int getGridCellIndex(const ivec cell) const;
+ /*! \brief
+ * Calculates linear index of a grid cell from fractional coordinates.
+ *
+ * \param[in] cell Cell indices (must be within the grid).
+ * \returns Linear index of \p cell.
+ */
+ int getGridCellIndex(const rvec cell) const;
/*! \brief
* Adds an index into a grid cell.
*
*/
void initCellRange(const rvec centerCell, ivec cell,
ivec upperBound, int dim) const;
+ /*! \brief
+ * Computes the extent of the cutoff sphere on a particular cell edge.
+ *
+ * \param[in] centerCell Fractional cell coordiates of the particle
+ * for which pairs are being searched.
+ * \param[in] cell Current cell (for dimensions `>dim`).
+ * \param[in] dim Dimension to compute in this call.
+ * \returns Fractional extent of the cutoff sphere when looping
+ * over cells in dimension `dim`, for `cell[d]` (`d > dim`).
+ *
+ * Input parameters are as for initCellRange(), except that if `cell`
+ * is over a periodic boundary from `centerCell`, triclinic shifts
+ * should have been applied to `centerCell` X/Y components.
+ */
+ real computeCutoffExtent(const RVec centerCell, const ivec cell, int dim) const;
/*! \brief
* Advances cell pair loop to the next cell.
*
explicit AnalysisNeighborhoodPairSearchImpl(const AnalysisNeighborhoodSearchImpl &search)
: search_(search)
{
+ selfSearchMode_ = false;
testPosCount_ = 0;
- testPositions_ = NULL;
- testExclusionIds_ = NULL;
- testIndices_ = NULL;
+ testPositions_ = nullptr;
+ testExclusionIds_ = nullptr;
+ testIndices_ = nullptr;
nexcl_ = 0;
- excl_ = NULL;
+ excl_ = nullptr;
clear_rvec(xtest_);
clear_rvec(testcell_);
clear_ivec(currCell_);
//! Initializes a search to find reference positions neighboring \p x.
void startSearch(const AnalysisNeighborhoodPositions &positions);
+ //! Initializes a search to find reference position pairs.
+ void startSelfSearch();
//! Searches for the next neighbor.
template <class Action>
bool searchNext(Action action);
//! Parent search object.
const AnalysisNeighborhoodSearchImpl &search_;
+ //! Whether we are searching for ref-ref pairs.
+ bool selfSearchMode_;
//! Number of test positions.
int testPosCount_;
//! Reference to the test positions.
rvec xtest_;
//! Stores the previous returned position during a pair loop.
int previ_;
- //! Stores the pair distance corresponding to previ_;
+ //! Stores the pair distance corresponding to previ_.
real prevr2_;
- //! Stores the shortest distance vector corresponding to previ_;
+ //! Stores the shortest distance vector corresponding to previ_.
rvec prevdx_;
//! Stores the current exclusion index during loops.
int exclind_;
//! Stores the fractional test particle cell location during loops.
rvec testcell_;
+ //! Stores the cell index corresponding to testcell_.
+ int testCellIndex_;
//! Stores the current cell during pair loops.
ivec currCell_;
//! Stores the current loop upper bounds for each dimension during pair loops.
}
bXY_ = false;
nref_ = 0;
- xref_ = NULL;
- refExclusionIds_ = NULL;
- refIndices_ = NULL;
+ xref_ = nullptr;
+ refExclusionIds_ = nullptr;
+ refIndices_ = nullptr;
std::memset(&pbc_, 0, sizeof(pbc_));
bGrid_ = false;
return pairSearch;
}
-bool AnalysisNeighborhoodSearchImpl::checkGridSearchEfficiency(bool bForce)
-{
- // Find the extent of the sphere in cells.
- ivec range;
- for (int dd = 0; dd < DIM; ++dd)
- {
- range[dd] = static_cast<int>(ceil(cutoff_ * invCellSize_[dd]));
- }
-
- // Calculate the fraction of cell pairs that need to be searched,
- // and check that the cutoff is not too large for periodic dimensions.
- real coveredCells = 1.0;
- for (int dd = 0; dd < DIM; ++dd)
- {
- const int cellCount = ncelldim_[dd];
- const int coveredCount = 2 * range[dd] + 1;
- if (bGridPBC_[dd])
- {
- if (coveredCount > cellCount)
- {
- // Cutoff is too close to half the box size for grid searching
- // (it is not possible to find a single shift for every pair of
- // grid cells).
- return false;
- }
- coveredCells *= coveredCount;
- }
- else
- {
- if (range[dd] >= cellCount - 1)
- {
- range[dd] = cellCount - 1;
- coveredCells *= cellCount;
- }
- else if (coveredCount > cellCount)
- {
- // The sum of range+1, range+2, ..., range+N/2, ... range+1.
- coveredCells *= range[dd] +
- static_cast<real>((cellCount + 1)/2 * (cellCount/2 + 1)) / cellCount;
- }
- else
- {
- // The sum of range+1, ..., 2*range+1, ..., 2*range+1, ... range+1.
- coveredCells *= coveredCount -
- static_cast<real>(range[dd] * (range[dd] + 1)) / cellCount;
- }
- }
- }
- // Magic constant that would need tuning for optimal performance:
- // Don't do grid searching if nearly all cell pairs would anyways need to
- // be looped through.
- const int totalCellCount = ncelldim_[XX] * ncelldim_[YY] * ncelldim_[ZZ];
- if (!bForce && coveredCells >= 0.5 * totalCellCount)
- {
- return false;
- }
- return true;
-}
-
bool AnalysisNeighborhoodSearchImpl::initGridCells(
const matrix box, bool bSingleCell[DIM], int posCount)
{
bSingleCell[dd] = true;
if (bGridPBC_[dd])
{
+ // TODO: Consider if a fallback would be possible/better.
return false;
}
}
else
{
cellCount = std::max(1, static_cast<int>(box[dd][dd] / targetsize));
- // TODO: If the cell count is one or two, it would be better to
- // just fall back to bSingleCell[dd] = true, and leave the rest to
- // the efficiency check later.
+ // TODO: If the cell count is one or two, it could be better to
+ // just fall back to bSingleCell[dd] = true.
if (bGridPBC_[dd] && cellCount < 3)
{
return false;
return false;
}
+ // TODO: Use this again (can be useful when tuning initGridCells()),
+ // or remove throughout.
+ GMX_UNUSED_VALUE(bForce);
+
switch (pbc.ePBC)
{
case epbcNONE:
else
{
invCellSize_[dd] = 1.0 / cellSize_[dd];
+ // TODO: It could be better to avoid this when determining the cell
+ // size, but this can still remain here as a fallback to avoid
+ // incorrect results.
+ if (std::ceil(2*cutoff_*invCellSize_[dd]) >= ncelldim_[dd])
+ {
+ // Cutoff is too close to half the box size for grid searching
+ // (it is not possible to find a single shift for every pair of
+ // grid cells).
+ return false;
+ }
}
}
if (bTric_)
cellShiftZX_ = box[ZZ][XX] * invCellSize_[XX];
cellShiftYX_ = box[YY][XX] * invCellSize_[XX];
}
- return checkGridSearchEfficiency(bForce);
+ return true;
}
void AnalysisNeighborhoodSearchImpl::mapPointToGridCell(const rvec x,
+ cell[ZZ] * ncelldim_[XX] * ncelldim_[YY];
}
-void AnalysisNeighborhoodSearchImpl::addToGridCell(const rvec cell, int i)
+int AnalysisNeighborhoodSearchImpl::getGridCellIndex(const rvec cell) const
{
ivec icell;
for (int dd = 0; dd < DIM; ++dd)
}
icell[dd] = cellIndex;
}
- const int ci = getGridCellIndex(icell);
+ return getGridCellIndex(icell);
+}
+
+void AnalysisNeighborhoodSearchImpl::addToGridCell(const rvec cell, int i)
+{
+ const int ci = getGridCellIndex(cell);
cells_[ci].push_back(i);
}
void AnalysisNeighborhoodSearchImpl::initCellRange(
const rvec centerCell, ivec currCell, ivec upperBound, int dim) const
{
- // TODO: Prune off cells that are completely outside the cutoff.
- const real range = cutoff_ * invCellSize_[dim];
- real startOffset = centerCell[dim] - range;
- real endOffset = centerCell[dim] + range;
+ RVec shiftedCenter(centerCell);
+ // Shift the center to the cell coordinates of currCell, so that
+ // computeCutoffExtent() can assume simple rectangular grid.
if (bTric_)
{
- switch (dim)
+ if (dim == XX)
{
- case ZZ:
- break;
- case YY:
- if (currCell[ZZ] < 0)
- {
- startOffset += cellShiftZY_;
- endOffset += cellShiftZY_;
- }
- else if (currCell[ZZ] >= ncelldim_[ZZ])
- {
- startOffset -= cellShiftZY_;
- endOffset -= cellShiftZY_;
- }
- break;
- case XX:
- if (currCell[ZZ] < 0)
- {
- startOffset += cellShiftZX_;
- endOffset += cellShiftZX_;
- }
- else if (currCell[ZZ] >= ncelldim_[ZZ])
- {
- startOffset -= cellShiftZX_;
- endOffset -= cellShiftZX_;
- }
- if (currCell[YY] < 0)
- {
- startOffset += cellShiftYX_;
- endOffset += cellShiftYX_;
- }
- else if (currCell[YY] >= ncelldim_[YY])
- {
- startOffset -= cellShiftYX_;
- endOffset -= cellShiftYX_;
- }
- break;
+ if (currCell[ZZ] < 0)
+ {
+ shiftedCenter[XX] += cellShiftZX_;
+ }
+ else if (currCell[ZZ] >= ncelldim_[ZZ])
+ {
+ shiftedCenter[XX] -= cellShiftZX_;
+ }
+ if (currCell[YY] < 0)
+ {
+ shiftedCenter[XX] += cellShiftYX_;
+ }
+ else if (currCell[YY] >= ncelldim_[YY])
+ {
+ shiftedCenter[XX] -= cellShiftYX_;
+ }
+ }
+ if (dim == XX || dim == YY)
+ {
+ if (currCell[ZZ] < 0)
+ {
+ shiftedCenter[YY] += cellShiftZY_;
+ }
+ else if (currCell[ZZ] >= ncelldim_[ZZ])
+ {
+ shiftedCenter[YY] -= cellShiftZY_;
+ }
}
}
+ const real range = computeCutoffExtent(shiftedCenter, currCell, dim) * invCellSize_[dim];
+ real startOffset = shiftedCenter[dim] - range;
+ real endOffset = shiftedCenter[dim] + range;
// For non-periodic dimensions, clamp to the actual grid edges.
if (!bGridPBC_[dim])
{
upperBound[dim] = static_cast<int>(floor(endOffset));
}
+real AnalysisNeighborhoodSearchImpl::computeCutoffExtent(
+ const RVec centerCell, const ivec cell, int dim) const
+{
+ if (dim == ZZ)
+ {
+ return cutoff_;
+ }
+
+ real dist2 = 0;
+ for (int d = dim + 1; d < DIM; ++d)
+ {
+ real dimDist = cell[d] - centerCell[d];
+ if (dimDist < -1)
+ {
+ dimDist += 1;
+ }
+ else if (dimDist <= 0)
+ {
+ continue;
+ }
+ dist2 += dimDist*dimDist*cellSize_[d]*cellSize_[d];
+ }
+ if (dist2 >= cutoff2_)
+ {
+ return 0;
+ }
+ return std::sqrt(cutoff2_ - dist2);
+}
+
bool AnalysisNeighborhoodSearchImpl::nextCell(
const rvec centerCell, ivec cell, ivec upperBound) const
{
GMX_RELEASE_ASSERT(positions.index_ == -1,
"Individual indexed positions not supported as reference");
bXY_ = bXY;
- if (bXY_ && pbc != NULL && pbc->ePBC != epbcNONE)
+ if (bXY_ && pbc != nullptr && pbc->ePBC != epbcNONE)
{
if (pbc->ePBC != epbcXY && pbc->ePBC != epbcXYZ)
{
clear_rvec(box[ZZ]);
set_pbc(&pbc_, epbcXY, box);
}
- else if (pbc != NULL)
+ else if (pbc != nullptr)
{
pbc_ = *pbc;
}
for (int i = 0; i < nref_; ++i)
{
- const int ii = (refIndices_ != NULL) ? refIndices_[i] : i;
+ const int ii = (refIndices_ != nullptr) ? refIndices_[i] : i;
rvec refcell;
mapPointToGridCell(positions.x_[ii], refcell, xrefAlloc_[i]);
addToGridCell(refcell, i);
}
}
- else if (refIndices_ != NULL)
+ else if (refIndices_ != nullptr)
{
xrefAlloc_.resize(nref_);
xref_ = as_rvec_array(xrefAlloc_.data());
xref_ = positions.x_;
}
excls_ = excls;
- refExclusionIds_ = NULL;
- if (excls != NULL)
+ refExclusionIds_ = nullptr;
+ if (excls != nullptr)
{
// TODO: Check that the IDs are ascending, or remove the limitation.
refExclusionIds_ = positions.exclusionIds_;
- GMX_RELEASE_ASSERT(refExclusionIds_ != NULL,
+ GMX_RELEASE_ASSERT(refExclusionIds_ != nullptr,
"Exclusion IDs must be set for reference positions "
"when exclusions are enabled");
}
void AnalysisNeighborhoodPairSearchImpl::reset(int testIndex)
{
- testIndex_ = testIndex;
+ testIndex_ = testIndex;
+ testCellIndex_ = -1;
+ previ_ = -1;
+ prevr2_ = 0.0;
+ clear_rvec(prevdx_);
+ exclind_ = 0;
+ prevcai_ = -1;
if (testIndex_ >= 0 && testIndex_ < testPosCount_)
{
const int index =
- (testIndices_ != NULL ? testIndices_[testIndex] : testIndex);
+ (testIndices_ != nullptr ? testIndices_[testIndex] : testIndex);
if (search_.bGrid_)
{
search_.mapPointToGridCell(testPositions_[index], testcell_, xtest_);
search_.initCellRange(testcell_, currCell_, cellBound_, ZZ);
search_.initCellRange(testcell_, currCell_, cellBound_, YY);
search_.initCellRange(testcell_, currCell_, cellBound_, XX);
+ if (selfSearchMode_)
+ {
+ testCellIndex_ = search_.getGridCellIndex(testcell_);
+ }
}
else
{
copy_rvec(testPositions_[index], xtest_);
+ if (selfSearchMode_)
+ {
+ previ_ = testIndex_;
+ }
}
- if (search_.excls_ != NULL)
+ if (search_.excls_ != nullptr)
{
const int exclIndex = testExclusionIds_[index];
if (exclIndex < search_.excls_->nr)
else
{
nexcl_ = 0;
- excl_ = NULL;
+ excl_ = nullptr;
}
}
}
- previ_ = -1;
- prevr2_ = 0.0;
- clear_rvec(prevdx_);
- exclind_ = 0;
- prevcai_ = -1;
}
void AnalysisNeighborhoodPairSearchImpl::nextTestPosition()
if (exclind_ < nexcl_)
{
const int index =
- (search_.refIndices_ != NULL ? search_.refIndices_[j] : j);
+ (search_.refIndices_ != nullptr ? search_.refIndices_[j] : j);
const int refId = search_.refExclusionIds_[index];
while (exclind_ < nexcl_ && excl_[exclind_] < refId)
{
void AnalysisNeighborhoodPairSearchImpl::startSearch(
const AnalysisNeighborhoodPositions &positions)
{
+ selfSearchMode_ = false;
testPosCount_ = positions.count_;
testPositions_ = positions.x_;
testExclusionIds_ = positions.exclusionIds_;
testIndices_ = positions.indices_;
- GMX_RELEASE_ASSERT(search_.excls_ == NULL || testExclusionIds_ != NULL,
+ GMX_RELEASE_ASSERT(search_.excls_ == nullptr || testExclusionIds_ != nullptr,
"Exclusion IDs must be set when exclusions are enabled");
if (positions.index_ < 0)
{
}
}
+void AnalysisNeighborhoodPairSearchImpl::startSelfSearch()
+{
+ selfSearchMode_ = true;
+ testPosCount_ = search_.nref_;
+ testPositions_ = search_.xref_;
+ testExclusionIds_ = search_.refExclusionIds_;
+ testIndices_ = search_.refIndices_;
+ GMX_RELEASE_ASSERT(search_.excls_ == nullptr || testIndices_ == nullptr,
+ "Exclusion IDs not implemented with indexed ref positions");
+ reset(0);
+}
+
template <class Action>
bool AnalysisNeighborhoodPairSearchImpl::searchNext(Action action)
{
{
rvec shift;
const int ci = search_.shiftCell(currCell_, shift);
+ if (selfSearchMode_ && ci > testCellIndex_)
+ {
+ continue;
+ }
const int cellSize = static_cast<int>(search_.cells_[ci].size());
for (; cai < cellSize; ++cai)
{
const int i = search_.cells_[ci][cai];
+ if (selfSearchMode_ && ci == testCellIndex_ && i >= testIndex_)
+ {
+ continue;
+ }
if (isExcluded(i))
{
continue;
typedef std::vector<SearchImplPointer> SearchList;
Impl()
- : cutoff_(0), excls_(NULL), mode_(eSearchMode_Automatic), bXY_(false)
+ : cutoff_(0), excls_(nullptr), mode_(eSearchMode_Automatic), bXY_(false)
{
}
~Impl()
return AnalysisNeighborhoodPair(closestPoint, 0, minDist2, dx);
}
+AnalysisNeighborhoodPairSearch
+AnalysisNeighborhoodSearch::startSelfPairSearch() const
+{
+ GMX_RELEASE_ASSERT(impl_, "Accessing an invalid search object");
+ Impl::PairSearchImplPointer pairSearch(impl_->getPairSearch());
+ pairSearch->startSelfSearch();
+ return AnalysisNeighborhoodPairSearch(pairSearch);
+}
+
AnalysisNeighborhoodPairSearch
AnalysisNeighborhoodSearch::startPairSearch(
const AnalysisNeighborhoodPositions &positions) const
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* to methods that accept positions.
*/
AnalysisNeighborhoodPositions(const rvec &x)
- : count_(1), index_(-1), x_(&x), exclusionIds_(NULL), indices_(NULL)
+ : count_(1), index_(-1), x_(&x), exclusionIds_(nullptr), indices_(nullptr)
{
}
/*! \brief
* Initializes positions from an array of position vectors.
*/
AnalysisNeighborhoodPositions(const rvec x[], int count)
- : count_(count), index_(-1), x_(x), exclusionIds_(NULL), indices_(NULL)
+ : count_(count), index_(-1), x_(x), exclusionIds_(nullptr), indices_(nullptr)
{
}
/*! \brief
*/
AnalysisNeighborhoodPositions(const std::vector<RVec> &x)
: count_(x.size()), index_(-1), x_(as_rvec_array(x.data())),
- exclusionIds_(NULL), indices_(NULL)
+ exclusionIds_(nullptr), indices_(nullptr)
{
}
* variable (see sm_distance.cpp).
*
* \todo
- * Consider merging nearestPoint() and minimumDistance() by adding the distance
- * to AnalysisNeighborhoodPair.
+ * Consider removing minimumDistance(), as nearestPoint() already returns the
+ * distance.
*
* \inpublicapi
* \ingroup module_selection
AnalysisNeighborhood::SearchMode mode() const;
/*! \brief
- * Check whether a point is within a neighborhood.
+ * Checks whether a point is within a neighborhood.
*
* \param[in] positions Set of test positions to use.
* \returns true if any of the test positions is within the cutoff of
nearestPoint(const AnalysisNeighborhoodPositions &positions) const;
/*! \brief
- * Start a search to find reference positions within a cutoff.
+ * Starts a search to find all reference position pairs within a cutoff.
+ *
+ * \returns Initialized search object to loop through all reference
+ * position pairs within the configured cutoff.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * This works as if the reference positions were passed to
+ * startPairSearch(), except that it only returns each pair once,
+ * instead of returning both i-j and j-i pairs, as startPairSearch()
+ * does. i-i pairs are not returned. Note that the order of ref/test
+ * indices in the returned pairs is not predictable. That is, one of
+ * i-j or j-i is always returned, but there is no control which one.
+ */
+ AnalysisNeighborhoodPairSearch
+ startSelfPairSearch() const;
+
+ /*! \brief
+ * Starts a search to find reference positions within a cutoff.
*
* \param[in] positions Set of test positions to use.
* \returns Initialized search object to loop through all reference
* positions within the configured cutoff.
* \throws std::bad_alloc if out of memory.
+ *
+ * If you want to pass the same positions here as you used for the
+ * reference positions, consider using startSelfPairSearch().
+ * It can be up to 50% faster.
*/
AnalysisNeighborhoodPairSearch
startPairSearch(const AnalysisNeighborhoodPositions &positions) const;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/unique_cptr.h"
#include "parsetree.h"
#include "scanner.h"
if (nparam == 0)
{
- return NULL;
+ return nullptr;
}
/* Find the first non-null parameter */
i = 0;
- while (i < nparam && param[i].name == NULL)
+ while (i < nparam && param[i].name == nullptr)
{
++i;
}
/* Process the special case of a NULL parameter */
- if (name == NULL)
+ if (name == nullptr)
{
- return (i == 0) ? NULL : ¶m[i-1];
+ return (i == 0) ? nullptr : ¶m[i-1];
}
for (; i < nparam; ++i)
{
return ¶m[i];
}
}
- return NULL;
+ return nullptr;
}
/*! \brief
try
{
SelectionTreeElementPointer expr =
- _gmx_sel_init_position(value->expr, NULL, scanner);
+ _gmx_sel_init_position(value->expr, nullptr, scanner);
*value = SelectionParserValue::createExpr(expr);
}
catch (UserInputError &ex)
param->flags &= ~SPAR_DYNAMIC;
GMX_RELEASE_ASSERT(param->val.type == INT_VALUE || param->val.type == REAL_VALUE,
"Invalid range parameter type");
- int *idata = NULL;
- real *rdata = NULL;
- scoped_guard_sfree dataGuard;
+ int *idata = nullptr;
+ real *rdata = nullptr;
+ sfree_guard dataGuard;
if (param->val.type == INT_VALUE)
{
snew(idata, values.size()*2);
{
*param->nvalptr = param->val.nr;
}
- param->nvalptr = NULL;
+ param->nvalptr = nullptr;
}
/*! \brief
if (param->val.type == POS_VALUE)
{
gmx_ana_pos_reserve(param->val.u.p, valueCount, 0);
- gmx_ana_indexmap_init(¶m->val.u.p->m, NULL, NULL, INDEX_UNKNOWN);
+ gmx_ana_indexmap_init(¶m->val.u.p->m, nullptr, nullptr, INDEX_UNKNOWN);
gmx_ana_pos_set_nr(param->val.u.p, valueCount);
}
else
{
*param->nvalptr = param->val.nr;
}
- param->nvalptr = NULL;
+ param->nvalptr = nullptr;
}
/*! \brief
{
*param->nvalptr = param->val.nr;
}
- param->nvalptr = NULL;
+ param->nvalptr = nullptr;
return;
}
{
*param->nvalptr = 1;
}
- param->nvalptr = NULL;
+ param->nvalptr = nullptr;
if (param->val.type == INT_VALUE || param->val.type == REAL_VALUE
|| param->val.type == STR_VALUE)
{
{
*param->nvalptr = param->val.nr;
}
- param->nvalptr = NULL;
+ param->nvalptr = nullptr;
}
/*! \brief
const std::string &svalue = value.stringValue();
int i = 1;
int match = 0;
- while (param->val.u.s[i] != NULL)
+ while (param->val.u.s[i] != nullptr)
{
if (startsWith(param->val.u.s[i], svalue))
{
if (params[i].val.type != POS_VALUE
&& (params[i].flags & (SPAR_VARNUM | SPAR_ATOMVAL)))
{
- GMX_RELEASE_ASSERT(params[i].val.u.ptr == NULL,
+ GMX_RELEASE_ASSERT(params[i].val.u.ptr == nullptr,
"value pointer is not NULL "
"although it should be for SPAR_VARNUM "
"and SPAR_ATOMVAL parameters");
GMX_RELEASE_ASSERT(!((params[i].flags & SPAR_VARNUM)
&& (params[i].flags & SPAR_DYNAMIC))
- || params[i].nvalptr != NULL,
+ || params[i].nvalptr != nullptr,
"nvalptr is NULL but both "
"SPAR_VARNUM and SPAR_DYNAMIC are specified");
}
else
{
- GMX_RELEASE_ASSERT(params[i].val.u.ptr != NULL,
+ GMX_RELEASE_ASSERT(params[i].val.u.ptr != nullptr,
"value pointer is NULL");
}
}
try
{
// Always assigned afterwards, but cppcheck does not see that.
- gmx_ana_selparam_t *oparam = NULL;
+ gmx_ana_selparam_t *oparam = nullptr;
/* Find the parameter and make some checks */
if (!pparam->name().empty())
{
nullParamIndex = -1;
oparam
= gmx_ana_selparam_find(pparam->name().c_str(), nparam, params);
- GMX_RELEASE_ASSERT(oparam != NULL, "Inconsistent selection parameter");
+ GMX_RELEASE_ASSERT(oparam != nullptr, "Inconsistent selection parameter");
}
else if (nullParamIndex >= 0)
{
oparam = ¶ms[nullParamIndex];
- if (oparam->name != NULL)
+ if (oparam->name != nullptr)
{
std::string text(_gmx_sel_lexer_get_text(scanner, pparam->location()));
std::string message
if (!(params[i].flags & SPAR_OPTIONAL) && !(params[i].flags & SPAR_SET))
{
std::string message;
- if (params[i].name == NULL)
+ if (params[i].name == nullptr)
{
message = formatString("'%s' should be followed by a value/expression",
root->name().c_str());
-/* A Bison parser, made by GNU Bison 2.7.12-4996. */
+/* A Bison parser, made by GNU Bison 3.0.4. */
/* Bison implementation for Yacc-like parsers in C
-
- Copyright (C) 1984, 1989-1990, 2000-2013 Free Software Foundation, Inc.
-
+
+ Copyright (C) 1984, 1989-1990, 2000-2015 Free Software Foundation, Inc.
+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
-
+
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>. */
special exception, which will cause the skeleton and the resulting
Bison output files to be licensed under the GNU General Public
License without this special exception.
-
+
This special exception was added by the Free Software Foundation in
version 2.2 of Bison. */
#define YYBISON 1
/* Bison version. */
-#define YYBISON_VERSION "2.7.12-4996"
+#define YYBISON_VERSION "3.0.4"
/* Skeleton name. */
#define YYSKELETON_NAME "yacc.c"
#define YYPULL 0
/* "%code top" blocks. */
-/* Line 349 of yacc.c */
-#line 43 "parser.y"
+#line 43 "parser.y" /* yacc.c:316 */
/*! \internal \file parser.cpp
* \brief Generated (from parser.y by Bison) parser for the selection language.
*/
#include "gmxpre.h"
-
-/* Line 349 of yacc.c */
-#line 80 "parser.cpp"
+#line 77 "parser.cpp" /* yacc.c:316 */
/* Substitute the variable and function names. */
#define yypush_parse _gmx_sel_yypush_parse
#define yypstate _gmx_sel_yypstate
#define yylex _gmx_sel_yylex
#define yyerror _gmx_sel_yyerror
-#define yylval _gmx_sel_yylval
-#define yychar _gmx_sel_yychar
#define yydebug _gmx_sel_yydebug
#define yynerrs _gmx_sel_yynerrs
-#define yylloc _gmx_sel_yylloc
+
/* Copy the first part of user declarations. */
-/* Line 371 of yacc.c */
-#line 56 "parser.y"
+#line 56 "parser.y" /* yacc.c:339 */
-#include "gromacs/utility/scoped_cptr.h"
+#include "gromacs/utility/unique_cptr.h"
#include "parser_internal.h"
-using gmx::scoped_guard_sfree;
+using gmx::sfree_guard;
using gmx::SelectionParserValue;
using gmx::SelectionParserValueList;
using gmx::SelectionParserValueListPointer;
#pragma warning(disable: 4065)
#endif
-/* Line 371 of yacc.c */
-#line 118 "parser.cpp"
+#line 111 "parser.cpp" /* yacc.c:339 */
-# ifndef YY_NULL
+# ifndef YY_NULLPTR
# if defined __cplusplus && 201103L <= __cplusplus
-# define YY_NULL nullptr
+# define YY_NULLPTR nullptr
# else
-# define YY_NULL 0
+# define YY_NULLPTR 0
# endif
# endif
by #include "parser.h". */
#ifndef YY__GMX_SEL_YY_PARSER_H_INCLUDED
# define YY__GMX_SEL_YY_PARSER_H_INCLUDED
-/* Enabling traces. */
+/* Debug traces. */
#ifndef YYDEBUG
# define YYDEBUG 1
#endif
extern int _gmx_sel_yydebug;
#endif
/* "%code requires" blocks. */
-/* Line 387 of yacc.c */
-#line 1 "parser.y"
+#line 1 "parser.y" /* yacc.c:355 */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-/* Line 387 of yacc.c */
-#line 76 "parser.y"
+#line 76 "parser.y" /* yacc.c:355 */
#include "parsetree.h"
#include "selelem.h"
#define YYLTYPE ::gmx::SelectionLocation
+#line 184 "parser.cpp" /* yacc.c:355 */
-/* Line 387 of yacc.c */
-#line 196 "parser.cpp"
-
-/* Tokens. */
+/* Token type. */
#ifndef YYTOKENTYPE
# define YYTOKENTYPE
- /* Put the tokens into the symbol table, so that GDB and other debuggers
- know about them. */
- enum yytokentype {
- INVALID = 258,
- TOK_INT = 259,
- TOK_REAL = 260,
- STR = 261,
- IDENTIFIER = 262,
- CMD_SEP = 263,
- GROUP = 264,
- TO = 265,
- VARIABLE_NUMERIC = 266,
- VARIABLE_GROUP = 267,
- VARIABLE_POS = 268,
- KEYWORD_NUMERIC = 269,
- KEYWORD_STR = 270,
- KEYWORD_POS = 271,
- KEYWORD_GROUP = 272,
- METHOD_NUMERIC = 273,
- METHOD_GROUP = 274,
- METHOD_POS = 275,
- MODIFIER = 276,
- EMPTY_POSMOD = 277,
- PARAM = 278,
- END_OF_METHOD = 279,
- OF = 280,
- CMP_OP = 281,
- PARAM_REDUCT = 282,
- XOR = 283,
- OR = 284,
- AND = 285,
- NOT = 286,
- UNARY_NEG = 287,
- NUM_REDUCT = 288
- };
+ enum yytokentype
+ {
+ INVALID = 258,
+ TOK_INT = 259,
+ TOK_REAL = 260,
+ STR = 261,
+ IDENTIFIER = 262,
+ CMD_SEP = 263,
+ GROUP = 264,
+ TO = 265,
+ VARIABLE_NUMERIC = 266,
+ VARIABLE_GROUP = 267,
+ VARIABLE_POS = 268,
+ KEYWORD_NUMERIC = 269,
+ KEYWORD_STR = 270,
+ KEYWORD_POS = 271,
+ KEYWORD_GROUP = 272,
+ METHOD_NUMERIC = 273,
+ METHOD_GROUP = 274,
+ METHOD_POS = 275,
+ MODIFIER = 276,
+ EMPTY_POSMOD = 277,
+ PARAM = 278,
+ END_OF_METHOD = 279,
+ OF = 280,
+ CMP_OP = 281,
+ PARAM_REDUCT = 282,
+ OR = 283,
+ XOR = 284,
+ AND = 285,
+ NOT = 286,
+ UNARY_NEG = 287,
+ NUM_REDUCT = 288
+ };
#endif
-
+/* Value type. */
#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
-typedef union YYSTYPE
+
+union YYSTYPE
{
-/* Line 387 of yacc.c */
-#line 83 "parser.y"
+#line 83 "parser.y" /* yacc.c:355 */
int i;
real r;
gmx::SelectionParserParameter *param;
gmx::SelectionParserParameterListPointer *plist;
+#line 245 "parser.cpp" /* yacc.c:355 */
+};
-/* Line 387 of yacc.c */
-#line 260 "parser.cpp"
-} YYSTYPE;
+typedef union YYSTYPE YYSTYPE;
# define YYSTYPE_IS_TRIVIAL 1
-# define yystype YYSTYPE /* obsolescent; will be withdrawn */
# define YYSTYPE_IS_DECLARED 1
#endif
+/* Location type. */
#if ! defined YYLTYPE && ! defined YYLTYPE_IS_DECLARED
-typedef struct YYLTYPE
+typedef struct YYLTYPE YYLTYPE;
+struct YYLTYPE
{
int first_line;
int first_column;
int last_line;
int last_column;
-} YYLTYPE;
-# define yyltype YYLTYPE /* obsolescent; will be withdrawn */
+};
# define YYLTYPE_IS_DECLARED 1
# define YYLTYPE_IS_TRIVIAL 1
#endif
+
#ifndef YYPUSH_MORE_DEFINED
# define YYPUSH_MORE_DEFINED
enum { YYPUSH_MORE = 4 };
typedef struct _gmx_sel_yypstate _gmx_sel_yypstate;
-#if defined __STDC__ || defined __cplusplus
int _gmx_sel_yypush_parse (_gmx_sel_yypstate *ps, int pushed_char, YYSTYPE const *pushed_val, YYLTYPE *pushed_loc, void *scanner);
-#else
-int _gmx_sel_yypush_parse ();
-#endif
-#if defined __STDC__ || defined __cplusplus
_gmx_sel_yypstate * _gmx_sel_yypstate_new (void);
-#else
-_gmx_sel_yypstate * _gmx_sel_yypstate_new ();
-#endif
-#if defined __STDC__ || defined __cplusplus
void _gmx_sel_yypstate_delete (_gmx_sel_yypstate *ps);
-#else
-void _gmx_sel_yypstate_delete ();
-#endif
#endif /* !YY__GMX_SEL_YY_PARSER_H_INCLUDED */
/* Copy the second part of user declarations. */
-/* Line 390 of yacc.c */
-#line 310 "parser.cpp"
+#line 285 "parser.cpp" /* yacc.c:358 */
#ifdef short
# undef short
#ifdef YYTYPE_INT8
typedef YYTYPE_INT8 yytype_int8;
-#elif (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
-typedef signed char yytype_int8;
#else
-typedef short int yytype_int8;
+typedef signed char yytype_int8;
#endif
#ifdef YYTYPE_UINT16
# define YYSIZE_T __SIZE_TYPE__
# elif defined size_t
# define YYSIZE_T size_t
-# elif ! defined YYSIZE_T && (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
+# elif ! defined YYSIZE_T
# include <stddef.h> /* INFRINGES ON USER NAME SPACE */
# define YYSIZE_T size_t
# else
# endif
#endif
-#ifndef __attribute__
-/* This feature is available in gcc versions 2.5 and later. */
-# if (! defined __GNUC__ || __GNUC__ < 2 \
- || (__GNUC__ == 2 && __GNUC_MINOR__ < 5))
-# define __attribute__(Spec) /* empty */
+#ifndef YY_ATTRIBUTE
+# if (defined __GNUC__ \
+ && (2 < __GNUC__ || (__GNUC__ == 2 && 96 <= __GNUC_MINOR__))) \
+ || defined __SUNPRO_C && 0x5110 <= __SUNPRO_C
+# define YY_ATTRIBUTE(Spec) __attribute__(Spec)
+# else
+# define YY_ATTRIBUTE(Spec) /* empty */
+# endif
+#endif
+
+#ifndef YY_ATTRIBUTE_PURE
+# define YY_ATTRIBUTE_PURE YY_ATTRIBUTE ((__pure__))
+#endif
+
+#ifndef YY_ATTRIBUTE_UNUSED
+# define YY_ATTRIBUTE_UNUSED YY_ATTRIBUTE ((__unused__))
+#endif
+
+#if !defined _Noreturn \
+ && (!defined __STDC_VERSION__ || __STDC_VERSION__ < 201112)
+# if defined _MSC_VER && 1200 <= _MSC_VER
+# define _Noreturn __declspec (noreturn)
+# else
+# define _Noreturn YY_ATTRIBUTE ((__noreturn__))
# endif
#endif
# define YYUSE(E) /* empty */
#endif
-
-/* Identity function, used to suppress warnings about constant conditions. */
-#ifndef lint
-# define YYID(N) (N)
-#else
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
-static int
-YYID (int yyi)
+#if defined __GNUC__ && 407 <= __GNUC__ * 100 + __GNUC_MINOR__
+/* Suppress an incorrect diagnostic about yylval being uninitialized. */
+# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN \
+ _Pragma ("GCC diagnostic push") \
+ _Pragma ("GCC diagnostic ignored \"-Wuninitialized\"")\
+ _Pragma ("GCC diagnostic ignored \"-Wmaybe-uninitialized\"")
+# define YY_IGNORE_MAYBE_UNINITIALIZED_END \
+ _Pragma ("GCC diagnostic pop")
#else
-static int
-YYID (yyi)
- int yyi;
+# define YY_INITIAL_VALUE(Value) Value
#endif
-{
- return yyi;
-}
+#ifndef YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
+# define YY_IGNORE_MAYBE_UNINITIALIZED_END
#endif
+#ifndef YY_INITIAL_VALUE
+# define YY_INITIAL_VALUE(Value) /* Nothing. */
+#endif
+
#if ! defined yyoverflow || YYERROR_VERBOSE
/* The parser invokes alloca or malloc; define the necessary symbols. */
# ifdef YYSTACK_ALLOC
- /* Pacify GCC's `empty if-body' warning. */
-# define YYSTACK_FREE(Ptr) do { /* empty */; } while (YYID (0))
+ /* Pacify GCC's 'empty if-body' warning. */
+# define YYSTACK_FREE(Ptr) do { /* empty */; } while (0)
# ifndef YYSTACK_ALLOC_MAXIMUM
/* The OS might guarantee only one guard page at the bottom of the stack,
and a page size can be as small as 4096 bytes. So we cannot safely
# endif
# if (defined __cplusplus && ! defined EXIT_SUCCESS \
&& ! ((defined YYMALLOC || defined malloc) \
- && (defined YYFREE || defined free)))
+ && (defined YYFREE || defined free)))
# include <stdlib.h> /* INFRINGES ON USER NAME SPACE */
# ifndef EXIT_SUCCESS
# define EXIT_SUCCESS 0
# endif
# ifndef YYMALLOC
# define YYMALLOC malloc
-# if ! defined malloc && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
+# if ! defined malloc && ! defined EXIT_SUCCESS
void *malloc (YYSIZE_T); /* INFRINGES ON USER NAME SPACE */
# endif
# endif
# ifndef YYFREE
# define YYFREE free
-# if ! defined free && ! defined EXIT_SUCCESS && (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
+# if ! defined free && ! defined EXIT_SUCCESS
void free (void *); /* INFRINGES ON USER NAME SPACE */
# endif
# endif
#if (! defined yyoverflow \
&& (! defined __cplusplus || defined GMX_YYFORCE_C_STACK_EXTENSION \
- || (defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL \
- && defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
+ || (defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL \
+ && defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
/* A type that is properly aligned for any stack member. */
union yyalloc
elements in the stack, and YYPTR gives the new location of the
stack. Advance YYPTR to a properly aligned location for the next
stack. */
-# define YYSTACK_RELOCATE(Stack_alloc, Stack) \
- do \
- { \
- YYSIZE_T yynewbytes; \
- YYCOPY (&yyptr->Stack_alloc, Stack, yysize); \
- Stack = &yyptr->Stack_alloc; \
- yynewbytes = yystacksize * sizeof (*Stack) + YYSTACK_GAP_MAXIMUM; \
- yyptr += yynewbytes / sizeof (*yyptr); \
- } \
- while (YYID (0))
+# define YYSTACK_RELOCATE(Stack_alloc, Stack) \
+ do \
+ { \
+ YYSIZE_T yynewbytes; \
+ YYCOPY (&yyptr->Stack_alloc, Stack, yysize); \
+ Stack = &yyptr->Stack_alloc; \
+ yynewbytes = yystacksize * sizeof (*Stack) + YYSTACK_GAP_MAXIMUM; \
+ yyptr += yynewbytes / sizeof (*yyptr); \
+ } \
+ while (0)
#endif
for (yyi = 0; yyi < (Count); yyi++) \
(Dst)[yyi] = (Src)[yyi]; \
} \
- while (YYID (0))
+ while (0)
# endif
# endif
#endif /* !YYCOPY_NEEDED */
#define YYNNTS 25
/* YYNRULES -- Number of rules. */
#define YYNRULES 90
-/* YYNRULES -- Number of states. */
+/* YYNSTATES -- Number of states. */
#define YYNSTATES 154
-/* YYTRANSLATE(YYLEX) -- Bison symbol number corresponding to YYLEX. */
+/* YYTRANSLATE[YYX] -- Symbol number corresponding to YYX as returned
+ by yylex, with out-of-bounds checking. */
#define YYUNDEFTOK 2
#define YYMAXUTOK 288
-#define YYTRANSLATE(YYX) \
+#define YYTRANSLATE(YYX) \
((unsigned int) (YYX) <= YYMAXUTOK ? yytranslate[YYX] : YYUNDEFTOK)
-/* YYTRANSLATE[YYLEX] -- Bison symbol number corresponding to YYLEX. */
+/* YYTRANSLATE[TOKEN-NUM] -- Symbol number corresponding to TOKEN-NUM
+ as returned by yylex, without out-of-bounds checking. */
static const yytype_uint8 yytranslate[] =
{
0, 2, 2, 2, 2, 2, 2, 2, 2, 2,
};
#if YYDEBUG
-/* YYPRHS[YYN] -- Index of the first RHS symbol of rule number YYN in
- YYRHS. */
-static const yytype_uint16 yyprhs[] =
-{
- 0, 0, 3, 4, 7, 10, 13, 14, 16, 18,
- 20, 23, 27, 31, 35, 37, 39, 43, 47, 49,
- 52, 54, 57, 59, 61, 63, 65, 68, 72, 76,
- 80, 84, 87, 90, 92, 94, 96, 98, 100, 103,
- 107, 112, 116, 120, 122, 124, 127, 132, 136, 140,
- 144, 148, 152, 155, 159, 163, 165, 168, 176, 180,
- 183, 187, 189, 191, 193, 195, 198, 199, 202, 205,
- 207, 211, 212, 215, 219, 221, 225, 227, 230, 234,
- 236, 238, 240, 242, 244, 246, 248, 250, 252, 256,
- 260
-};
-
-/* YYRHS -- A `-1'-separated list of the rules' RHS. */
-static const yytype_int8 yyrhs[] =
-{
- 50, 0, -1, -1, 50, 51, -1, 52, 8, -1,
- 1, 8, -1, -1, 4, -1, 57, -1, 53, -1,
- 6, 53, -1, 7, 39, 58, -1, 7, 39, 61,
- -1, 7, 39, 63, -1, 63, -1, 58, -1, 40,
- 53, 41, -1, 53, 21, 64, -1, 4, -1, 33,
- 4, -1, 5, -1, 33, 5, -1, 54, -1, 55,
- -1, 6, -1, 7, -1, 31, 58, -1, 58, 30,
- 58, -1, 58, 29, 58, -1, 40, 58, 41, -1,
- 61, 26, 61, -1, 9, 57, -1, 9, 4, -1,
- 22, -1, 16, -1, 42, -1, 43, -1, 39, -1,
- 59, 17, -1, 59, 15, 69, -1, 59, 15, 60,
- 69, -1, 59, 14, 69, -1, 59, 19, 64, -1,
- 4, -1, 5, -1, 59, 14, -1, 59, 14, 25,
- 63, -1, 59, 18, 64, -1, 61, 32, 61, -1,
- 61, 33, 61, -1, 61, 34, 61, -1, 61, 35,
- 61, -1, 33, 61, -1, 61, 37, 61, -1, 40,
- 61, 41, -1, 57, -1, 59, 15, -1, 44, 56,
- 45, 56, 45, 56, 46, -1, 40, 63, 41, -1,
- 20, 64, -1, 16, 25, 58, -1, 12, -1, 11,
- -1, 13, -1, 65, -1, 65, 24, -1, -1, 65,
- 66, -1, 23, 67, -1, 68, -1, 47, 68, 48,
- -1, -1, 68, 71, -1, 68, 45, 71, -1, 70,
- -1, 47, 70, 48, -1, 72, -1, 70, 72, -1,
- 70, 45, 72, -1, 58, -1, 63, -1, 61, -1,
- 62, -1, 73, -1, 54, -1, 55, -1, 57, -1,
- 73, -1, 54, 10, 54, -1, 54, 10, 55, -1,
- 55, 10, 56, -1
-};
-
-/* YYRLINE[YYN] -- source line where rule number YYN was defined. */
+ /* YYRLINE[YYN] -- Source line where rule number YYN was defined. */
static const yytype_uint16 yyrline[] =
{
- 0, 199, 199, 204, 215, 216, 236, 241, 252, 264,
- 270, 277, 284, 291, 301, 302, 309, 310, 324, 325,
- 329, 330, 333, 334, 337, 338, 346, 357, 368, 379,
- 383, 394, 401, 410, 411, 416, 417, 418, 422, 430,
- 438, 446, 457, 472, 483, 497, 505, 513, 524, 530,
- 536, 542, 548, 554, 560, 567, 578, 593, 602, 606,
- 616, 630, 638, 646, 659, 661, 667, 672, 683, 692,
- 693, 698, 703, 711, 722, 723, 727, 733, 741, 751,
- 757, 763, 769, 775, 779, 785, 791, 798, 802, 808,
- 814
+ 0, 199, 199, 204, 217, 218, 238, 243, 254, 266,
+ 272, 279, 286, 293, 303, 304, 311, 312, 326, 327,
+ 331, 332, 335, 336, 339, 340, 348, 359, 370, 381,
+ 385, 396, 403, 412, 413, 418, 419, 420, 424, 432,
+ 440, 448, 459, 474, 485, 499, 507, 515, 526, 532,
+ 538, 544, 550, 556, 562, 569, 580, 595, 604, 608,
+ 618, 632, 640, 648, 661, 663, 669, 674, 685, 694,
+ 695, 700, 705, 713, 724, 725, 729, 735, 743, 753,
+ 759, 765, 771, 777, 781, 787, 793, 800, 804, 810,
+ 816
};
#endif
"VARIABLE_GROUP", "VARIABLE_POS", "KEYWORD_NUMERIC", "KEYWORD_STR",
"KEYWORD_POS", "KEYWORD_GROUP", "METHOD_NUMERIC", "METHOD_GROUP",
"METHOD_POS", "MODIFIER", "EMPTY_POSMOD", "PARAM", "END_OF_METHOD", "OF",
- "CMP_OP", "PARAM_REDUCT", "XOR", "OR", "AND", "NOT", "'+'", "'-'", "'*'",
+ "CMP_OP", "PARAM_REDUCT", "OR", "XOR", "AND", "NOT", "'+'", "'-'", "'*'",
"'/'", "UNARY_NEG", "'^'", "NUM_REDUCT", "'='", "'('", "')'", "'~'",
"'?'", "'['", "','", "']'", "'{'", "'}'", "$accept", "commands",
"command", "cmd_plain", "selection", "integer_number", "real_number",
"str_expr", "pos_expr", "method_params", "method_param_list",
"method_param", "value_list", "value_list_contents", "basic_value_list",
"basic_value_list_contents", "value_item", "basic_value_item",
- "value_item_range", YY_NULL
+ "value_item_range", YY_NULLPTR
};
#endif
# ifdef YYPRINT
-/* YYTOKNUM[YYLEX-NUM] -- Internal token number corresponding to
- token YYLEX-NUM. */
+/* YYTOKNUM[NUM] -- (External) token number corresponding to the
+ (internal) symbol number NUM (which must be that of a token). */
static const yytype_uint16 yytoknum[] =
{
0, 256, 257, 258, 259, 260, 261, 262, 263, 264,
};
# endif
-/* YYR1[YYN] -- Symbol number of symbol that rule YYN derives. */
-static const yytype_uint8 yyr1[] =
-{
- 0, 49, 50, 50, 51, 51, 52, 52, 52, 52,
- 52, 52, 52, 52, 53, 53, 53, 53, 54, 54,
- 55, 55, 56, 56, 57, 57, 58, 58, 58, 58,
- 58, 58, 58, 59, 59, 60, 60, 60, 58, 58,
- 58, 58, 58, 61, 61, 61, 61, 61, 61, 61,
- 61, 61, 61, 61, 61, 62, 62, 63, 63, 63,
- 63, 58, 61, 63, 64, 64, 65, 65, 66, 67,
- 67, 68, 68, 68, 69, 69, 70, 70, 70, 71,
- 71, 71, 71, 71, 72, 72, 72, 72, 73, 73,
- 73
-};
+#define YYPACT_NINF -85
-/* YYR2[YYN] -- Number of symbols composing right hand side of rule YYN. */
-static const yytype_uint8 yyr2[] =
+#define yypact_value_is_default(Yystate) \
+ (!!((Yystate) == (-85)))
+
+#define YYTABLE_NINF -22
+
+#define yytable_value_is_error(Yytable_value) \
+ 0
+
+ /* YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
+ STATE-NUM. */
+static const yytype_int16 yypact[] =
{
- 0, 2, 0, 2, 2, 2, 0, 1, 1, 1,
- 2, 3, 3, 3, 1, 1, 3, 3, 1, 2,
- 1, 2, 1, 1, 1, 1, 2, 3, 3, 3,
- 3, 2, 2, 1, 1, 1, 1, 1, 2, 3,
- 4, 3, 3, 1, 1, 2, 4, 3, 3, 3,
- 3, 3, 2, 3, 3, 1, 2, 7, 3, 2,
- 3, 1, 1, 1, 1, 2, 0, 2, 2, 1,
- 3, 0, 2, 3, 1, 3, 1, 2, 3, 1,
- 1, 1, 1, 1, 1, 1, 1, 1, 3, 3,
- 3
+ -85, 10, -85, -2, 26, -85, 273, 0, 55, -85,
+ -85, -85, 40, -85, -85, 310, 204, 273, 69, -85,
+ 62, 82, -85, -3, 139, 312, -85, -85, -85, 82,
+ 296, -85, -85, -85, -85, 310, -85, 96, -85, 310,
+ -85, 204, -6, 73, 15, 71, 220, 67, -85, -85,
+ 135, -85, -85, 83, -85, -85, 310, 310, 41, 185,
+ -85, -85, -85, 204, 204, 204, 204, 204, 204, 296,
+ -3, 312, -85, -3, 97, -85, -85, 71, 319, 91,
+ -85, -85, -85, -85, -85, -85, 69, -85, 113, -85,
+ 24, 206, 137, 140, -85, -85, 90, -85, -85, -85,
+ -85, -85, 85, -85, -85, -85, 330, 167, 167, 73,
+ 73, 73, 67, -85, -85, 229, 107, 40, 24, -85,
+ 174, 69, 69, 206, -85, -85, 155, 153, 159, 326,
+ 259, 137, 140, -85, -3, 179, 330, -85, -85, -85,
+ -85, 69, -85, -85, -85, -85, -85, -85, 160, 164,
+ -85, 185, 119, -85
};
-/* YYDEFACT[STATE-NAME] -- Default reduction number in state STATE-NUM.
- Performed when YYTABLE doesn't specify something else to do. Zero
- means the default is an error. */
+ /* YYDEFACT[STATE-NUM] -- Default reduction number in state STATE-NUM.
+ Performed when YYTABLE does not specify something else to do. Zero
+ means the default is an error. */
static const yytype_uint8 yydefact[] =
{
2, 0, 1, 0, 43, 44, 24, 25, 0, 62,
73, 56, 0, 57
};
-/* YYDEFGOTO[NTERM-NUM]. */
+ /* YYPGOTO[NTERM-NUM]. */
+static const yytype_int8 yypgoto[] =
+{
+ -85, -85, -85, -85, 7, -17, -15, -84, -1, 116,
+ 19, -85, 12, -85, 3, 75, -85, -85, -85, 63,
+ -53, 92, 52, -65, -63
+};
+
+ /* YYDEFGOTO[NTERM-NUM]. */
static const yytype_int16 yydefgoto[] =
{
-1, 1, 19, 20, 21, 92, 93, 53, 94, 134,
103, 96, 139, 97, 98
};
-/* YYPACT[STATE-NUM] -- Index in YYTABLE of the portion describing
- STATE-NUM. */
-#define YYPACT_NINF -85
-static const yytype_int16 yypact[] =
-{
- -85, 10, -85, -2, 17, -85, 273, -12, 55, -85,
- -85, -85, 9, -85, -85, 310, 204, 273, 69, -85,
- 31, 44, -85, 110, 179, 312, -85, -85, -85, 44,
- 296, -85, -85, -85, -85, 310, -85, 96, -85, 310,
- -85, 204, -6, 33, 15, 124, 220, 58, -85, -85,
- 139, -85, -85, 56, -85, -85, 310, 310, 41, 185,
- -85, -85, -85, 204, 204, 204, 204, 204, 204, 296,
- 110, 312, -85, 110, 61, -85, -85, 124, 319, 78,
- -85, -85, -85, -85, -85, -85, 69, -85, 80, -85,
- 24, 206, 102, 106, -85, -85, 90, -85, -85, -85,
- -85, -85, 85, -85, -85, -85, 330, 213, 213, 33,
- 33, 33, 58, -85, -85, 229, 83, 9, 24, -85,
- 174, 69, 69, 206, -85, -85, 155, 137, 140, 326,
- 259, 102, 106, -85, 110, 187, 330, -85, -85, -85,
- -85, 69, -85, -85, -85, -85, -85, -85, 142, 146,
- -85, 185, 111, -85
-};
-
-/* YYPGOTO[NTERM-NUM]. */
-static const yytype_int8 yypgoto[] =
-{
- -85, -85, -85, -85, 7, -17, -15, -84, -1, 116,
- 19, -85, 12, -85, 3, 75, -85, -85, -85, 45,
- -53, 72, 39, -65, -63
-};
-
-/* YYTABLE[YYPACT[STATE-NUM]]. What to do in state STATE-NUM. If
- positive, shift that token. If negative, reduce the rule which
- number is the opposite. If YYTABLE_NINF, syntax error. */
-#define YYTABLE_NINF -22
+ /* YYTABLE[YYPACT[STATE-NUM]] -- What to do in state STATE-NUM. If
+ positive, shift that token. If negative, reduce the rule whose
+ number is the opposite. If YYTABLE_NINF, syntax error. */
static const yytype_int16 yytable[] =
{
22, 51, 116, 52, 26, 95, 27, 34, 79, 26,
2, 3, 61, 29, 4, 5, 6, 7, -6, 8,
- 47, 9, 10, 11, 44, -7, 12, 30, 43, 46,
- 13, 124, 14, 72, 35, 42, 55, 11, 145, 54,
+ 47, 9, 10, 11, 44, 56, 12, 57, 43, 46,
+ 13, 124, 14, 72, -7, 42, 55, 11, 145, 30,
117, 15, 71, 16, 13, 48, 49, 32, 33, 125,
17, 46, 140, 78, 18, 124, 80, 152, 146, 31,
- 42, 32, 33, 140, 118, 55, 90, 140, 18, 51,
- 68, 52, 112, 48, 49, 106, 107, 108, 109, 110,
+ 42, 32, 33, 140, 118, 35, 90, 140, 18, 51,
+ 54, 52, 112, 48, 49, 106, 107, 108, 109, 110,
111, 46, 42, 42, 42, 42, 42, 42, 91, 48,
- 49, 32, 33, 119, 48, 49, 32, 33, 131, 83,
- 132, 86, 50, 90, 143, 51, 144, 52, 113, 131,
- 57, 132, 121, 131, 133, 132, 122, 23, 50, 74,
- 75, 112, 23, 50, 51, 133, 52, 136, 141, 133,
- 87, 40, 91, 45, 135, 123, 104, 105, 136, 56,
- 57, 43, 136, 84, 85, 135, 70, -18, 42, 135,
- -20, 73, -19, 56, 57, 77, -21, 153, 126, 127,
- 128, 32, 33, 120, 8, 81, 9, 10, 11, 150,
- 0, 12, 88, 89, 0, 13, 0, 14, 48, 49,
- 32, 33, 0, 0, 0, 77, 15, 0, 129, 48,
- 49, 32, 33, 58, 59, 69, 60, 61, 62, 18,
- 130, 58, 151, 147, 60, 61, 62, 50, 28, 5,
+ 49, 32, 33, 119, 48, 49, 32, 33, 131, 56,
+ 132, 57, 50, 55, 143, 51, 144, 52, 83, 131,
+ 68, 132, 81, 131, 133, 132, 90, 23, 50, 74,
+ 75, 112, 23, 50, 51, 133, 52, 136, 86, 133,
+ 87, 40, 91, 45, 135, 123, 104, 105, 136, 84,
+ 85, 43, 136, 57, 113, 135, 70, 121, 42, 135,
+ 122, 73, 141, 58, 59, 77, 60, 61, 62, 127,
+ 128, 32, 33, -18, 8, 153, 9, 10, 11, -20,
+ -19, 12, 88, 89, -21, 13, 126, 14, 48, 49,
+ 32, 33, 150, 120, 0, 77, 15, 0, 129, 48,
+ 49, 32, 33, 58, 151, 69, 60, 61, 62, 18,
+ 130, 66, 67, 147, 68, 0, 0, 50, 28, 5,
48, 49, 32, 33, 0, 9, 0, 0, 50, 123,
38, 0, 142, 0, 99, 0, 14, 100, 101, 0,
0, 0, 91, 127, 128, 32, 33, 16, 8, 50,
- 9, 10, 11, 0, 41, 12, 63, 66, 67, 13,
- 68, 14, 64, 65, 66, 67, 0, 68, 0, 0,
+ 9, 10, 11, 0, 41, 12, 63, 0, 0, 13,
+ 0, 14, 64, 65, 66, 67, 0, 68, 0, 0,
15, 82, 129, 127, 128, 32, 33, 0, 8, 69,
9, 10, 11, 18, 130, 12, 0, 28, 5, 13,
0, 14, 8, 0, 9, 10, 11, 0, 0, 12,
82, 0, 64, 65, 66, 67, 41, 68
};
-#define yypact_value_is_default(Yystate) \
- (!!((Yystate) == (-85)))
-
-#define yytable_value_is_error(Yytable_value) \
- YYID (0)
-
static const yytype_int16 yycheck[] =
{
1, 18, 86, 18, 1, 58, 8, 8, 14, 6,
0, 1, 18, 6, 4, 5, 6, 7, 8, 9,
- 17, 11, 12, 13, 17, 8, 16, 39, 16, 17,
- 20, 96, 22, 30, 25, 16, 21, 13, 122, 8,
+ 17, 11, 12, 13, 17, 28, 16, 30, 16, 17,
+ 20, 96, 22, 30, 8, 16, 21, 13, 122, 39,
16, 31, 30, 33, 20, 4, 5, 6, 7, 102,
40, 39, 115, 41, 44, 120, 41, 141, 123, 4,
- 41, 6, 7, 126, 40, 21, 25, 130, 44, 86,
- 37, 86, 69, 4, 5, 63, 64, 65, 66, 67,
+ 41, 6, 7, 126, 40, 25, 25, 130, 44, 86,
+ 8, 86, 69, 4, 5, 63, 64, 65, 66, 67,
68, 69, 63, 64, 65, 66, 67, 68, 47, 4,
- 5, 6, 7, 90, 4, 5, 6, 7, 115, 41,
- 115, 45, 33, 25, 121, 122, 121, 122, 47, 126,
- 30, 126, 10, 130, 115, 130, 10, 1, 33, 23,
+ 5, 6, 7, 90, 4, 5, 6, 7, 115, 28,
+ 115, 30, 33, 21, 121, 122, 121, 122, 41, 126,
+ 37, 126, 41, 130, 115, 130, 25, 1, 33, 23,
24, 118, 6, 33, 141, 126, 141, 115, 45, 130,
- 55, 15, 47, 17, 115, 45, 61, 62, 126, 29,
- 30, 129, 130, 4, 5, 126, 30, 10, 129, 130,
- 10, 35, 10, 29, 30, 39, 10, 46, 113, 4,
- 5, 6, 7, 91, 9, 41, 11, 12, 13, 130,
- -1, 16, 56, 57, -1, 20, -1, 22, 4, 5,
- 6, 7, -1, -1, -1, 69, 31, -1, 33, 4,
+ 55, 15, 47, 17, 115, 45, 61, 62, 126, 4,
+ 5, 129, 130, 30, 47, 126, 30, 10, 129, 130,
+ 10, 35, 45, 14, 15, 39, 17, 18, 19, 4,
+ 5, 6, 7, 10, 9, 46, 11, 12, 13, 10,
+ 10, 16, 56, 57, 10, 20, 113, 22, 4, 5,
+ 6, 7, 130, 91, -1, 69, 31, -1, 33, 4,
5, 6, 7, 14, 15, 40, 17, 18, 19, 44,
- 45, 14, 15, 48, 17, 18, 19, 33, 4, 5,
+ 45, 34, 35, 48, 37, -1, -1, 33, 4, 5,
4, 5, 6, 7, -1, 11, -1, -1, 33, 45,
16, -1, 48, -1, 39, -1, 22, 42, 43, -1,
-1, -1, 47, 4, 5, 6, 7, 33, 9, 33,
- 11, 12, 13, -1, 40, 16, 26, 34, 35, 20,
- 37, 22, 32, 33, 34, 35, -1, 37, -1, -1,
+ 11, 12, 13, -1, 40, 16, 26, -1, -1, 20,
+ -1, 22, 32, 33, 34, 35, -1, 37, -1, -1,
31, 41, 33, 4, 5, 6, 7, -1, 9, 40,
11, 12, 13, 44, 45, 16, -1, 4, 5, 20,
-1, 22, 9, -1, 11, 12, 13, -1, -1, 16,
41, -1, 32, 33, 34, 35, 40, 37
};
-/* YYSTOS[STATE-NUM] -- The (internal number of the) accessing
- symbol of state STATE-NUM. */
+ /* YYSTOS[STATE-NUM] -- The (internal number of the) accessing
+ symbol of state STATE-NUM. */
static const yytype_uint8 yystos[] =
{
0, 50, 0, 1, 4, 5, 6, 7, 9, 11,
52, 53, 57, 58, 59, 61, 63, 8, 4, 53,
39, 4, 6, 7, 57, 25, 64, 65, 16, 40,
58, 40, 59, 61, 53, 58, 61, 63, 4, 5,
- 33, 54, 55, 56, 8, 21, 29, 30, 14, 15,
+ 33, 54, 55, 56, 8, 21, 28, 30, 14, 15,
17, 18, 19, 26, 32, 33, 34, 35, 37, 40,
58, 61, 63, 58, 23, 24, 66, 58, 61, 14,
41, 41, 41, 41, 4, 5, 45, 64, 58, 58,
71, 15, 56, 46
};
-#define yyerrok (yyerrstatus = 0)
-#define yyclearin (yychar = YYEMPTY)
-#define YYEMPTY (-2)
-#define YYEOF 0
-
-#define YYACCEPT goto yyacceptlab
-#define YYABORT goto yyabortlab
-#define YYERROR goto yyerrorlab
-
-
-/* Like YYERROR except do call yyerror. This remains here temporarily
- to ease the transition to the new meaning of YYERROR, for GCC.
- Once GCC version 2 has supplanted version 1, this can go. However,
- YYFAIL appears to be in use. Nevertheless, it is formally deprecated
- in Bison 2.4.2's NEWS entry, where a plan to phase it out is
- discussed. */
-
-#define YYFAIL goto yyerrlab
-#if defined YYFAIL
- /* This is here to suppress warnings from the GCC cpp's
- -Wunused-macros. Normally we don't worry about that warning, but
- some users do, and we want to make it easy for users to remove
- YYFAIL uses, which will produce warnings from Bison 2.5. */
-#endif
+ /* YYR1[YYN] -- Symbol number of symbol that rule YYN derives. */
+static const yytype_uint8 yyr1[] =
+{
+ 0, 49, 50, 50, 51, 51, 52, 52, 52, 52,
+ 52, 52, 52, 52, 53, 53, 53, 53, 54, 54,
+ 55, 55, 56, 56, 57, 57, 58, 58, 58, 58,
+ 58, 58, 58, 59, 59, 60, 60, 60, 58, 58,
+ 58, 58, 58, 61, 61, 61, 61, 61, 61, 61,
+ 61, 61, 61, 61, 61, 62, 62, 63, 63, 63,
+ 63, 58, 61, 63, 64, 64, 65, 65, 66, 67,
+ 67, 68, 68, 68, 69, 69, 70, 70, 70, 71,
+ 71, 71, 71, 71, 72, 72, 72, 72, 73, 73,
+ 73
+};
+
+ /* YYR2[YYN] -- Number of symbols on the right hand side of rule YYN. */
+static const yytype_uint8 yyr2[] =
+{
+ 0, 2, 0, 2, 2, 2, 0, 1, 1, 1,
+ 2, 3, 3, 3, 1, 1, 3, 3, 1, 2,
+ 1, 2, 1, 1, 1, 1, 2, 3, 3, 3,
+ 3, 2, 2, 1, 1, 1, 1, 1, 2, 3,
+ 4, 3, 3, 1, 1, 2, 4, 3, 3, 3,
+ 3, 3, 2, 3, 3, 1, 2, 7, 3, 2,
+ 3, 1, 1, 1, 1, 2, 0, 2, 2, 1,
+ 3, 0, 2, 3, 1, 3, 1, 2, 3, 1,
+ 1, 1, 1, 1, 1, 1, 1, 1, 3, 3,
+ 3
+};
+
+
+#define yyerrok (yyerrstatus = 0)
+#define yyclearin (yychar = YYEMPTY)
+#define YYEMPTY (-2)
+#define YYEOF 0
+
+#define YYACCEPT goto yyacceptlab
+#define YYABORT goto yyabortlab
+#define YYERROR goto yyerrorlab
+
#define YYRECOVERING() (!!yyerrstatus)
else \
{ \
yyerror (&yylloc, scanner, YY_("syntax error: cannot back up")); \
- YYERROR; \
- } \
-while (YYID (0))
+ YYERROR; \
+ } \
+while (0)
/* Error token number */
-#define YYTERROR 1
-#define YYERRCODE 256
+#define YYTERROR 1
+#define YYERRCODE 256
/* YYLLOC_DEFAULT -- Set CURRENT to span from RHS[1] to RHS[N].
#ifndef YYLLOC_DEFAULT
# define YYLLOC_DEFAULT(Current, Rhs, N) \
do \
- if (YYID (N)) \
+ if (N) \
{ \
(Current).first_line = YYRHSLOC (Rhs, 1).first_line; \
(Current).first_column = YYRHSLOC (Rhs, 1).first_column; \
(Current).first_column = (Current).last_column = \
YYRHSLOC (Rhs, 0).last_column; \
} \
- while (YYID (0))
+ while (0)
#endif
#define YYRHSLOC(Rhs, K) ((Rhs)[K])
+/* Enable debugging if requested. */
+#if YYDEBUG
+
+# ifndef YYFPRINTF
+# include <stdio.h> /* INFRINGES ON USER NAME SPACE */
+# define YYFPRINTF fprintf
+# endif
+
+# define YYDPRINTF(Args) \
+do { \
+ if (yydebug) \
+ YYFPRINTF Args; \
+} while (0)
+
+
/* YY_LOCATION_PRINT -- Print the location on the stream.
This macro was not mandated originally: define only if we know
we won't break user code: when these are the locations we know. */
/* Print *YYLOCP on YYO. Private, do not rely on its existence. */
-__attribute__((__unused__))
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
+YY_ATTRIBUTE_UNUSED
static unsigned
yy_location_print_ (FILE *yyo, YYLTYPE const * const yylocp)
-#else
-static unsigned
-yy_location_print_ (yyo, yylocp)
- FILE *yyo;
- YYLTYPE const * const yylocp;
-#endif
{
unsigned res = 0;
int end_col = 0 != yylocp->last_column ? yylocp->last_column - 1 : 0;
if (0 <= yylocp->first_line)
{
- res += fprintf (yyo, "%d", yylocp->first_line);
+ res += YYFPRINTF (yyo, "%d", yylocp->first_line);
if (0 <= yylocp->first_column)
- res += fprintf (yyo, ".%d", yylocp->first_column);
+ res += YYFPRINTF (yyo, ".%d", yylocp->first_column);
}
if (0 <= yylocp->last_line)
{
if (yylocp->first_line < yylocp->last_line)
{
- res += fprintf (yyo, "-%d", yylocp->last_line);
+ res += YYFPRINTF (yyo, "-%d", yylocp->last_line);
if (0 <= end_col)
- res += fprintf (yyo, ".%d", end_col);
+ res += YYFPRINTF (yyo, ".%d", end_col);
}
else if (0 <= end_col && yylocp->first_column < end_col)
- res += fprintf (yyo, "-%d", end_col);
+ res += YYFPRINTF (yyo, "-%d", end_col);
}
return res;
}
#endif
-/* YYLEX -- calling `yylex' with the right arguments. */
-#ifdef YYLEX_PARAM
-# define YYLEX yylex (&yylval, &yylloc, YYLEX_PARAM)
-#else
-# define YYLEX yylex (&yylval, &yylloc)
-#endif
-
-/* Enable debugging if requested. */
-#if YYDEBUG
-
-# ifndef YYFPRINTF
-# include <stdio.h> /* INFRINGES ON USER NAME SPACE */
-# define YYFPRINTF fprintf
-# endif
-
-# define YYDPRINTF(Args) \
-do { \
- if (yydebug) \
- YYFPRINTF Args; \
-} while (YYID (0))
+# define YY_SYMBOL_PRINT(Title, Type, Value, Location) \
+do { \
+ if (yydebug) \
+ { \
+ YYFPRINTF (stderr, "%s ", Title); \
+ yy_symbol_print (stderr, \
+ Type, Value, Location, scanner); \
+ YYFPRINTF (stderr, "\n"); \
+ } \
+} while (0)
-# define YY_SYMBOL_PRINT(Title, Type, Value, Location) \
-do { \
- if (yydebug) \
- { \
- YYFPRINTF (stderr, "%s ", Title); \
- yy_symbol_print (stderr, \
- Type, Value, Location, scanner); \
- YYFPRINTF (stderr, "\n"); \
- } \
-} while (YYID (0))
+/*----------------------------------------.
+| Print this symbol's value on YYOUTPUT. |
+`----------------------------------------*/
-/*--------------------------------.
-| Print this symbol on YYOUTPUT. |
-`--------------------------------*/
-
-/*ARGSUSED*/
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
static void
yy_symbol_value_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, YYLTYPE const * const yylocationp, void *scanner)
-#else
-static void
-yy_symbol_value_print (yyoutput, yytype, yyvaluep, yylocationp, scanner)
- FILE *yyoutput;
- int yytype;
- YYSTYPE const * const yyvaluep;
- YYLTYPE const * const yylocationp;
- void *scanner;
-#endif
{
FILE *yyo gmx_unused = yyoutput;
YYUSE (yyo);
- if (!yyvaluep)
- return;
YYUSE (yylocationp);
YYUSE (scanner);
+ if (!yyvaluep)
+ return;
# ifdef YYPRINT
if (yytype < YYNTOKENS)
YYPRINT (yyoutput, yytoknum[yytype], *yyvaluep);
-# else
- YYUSE (yyoutput);
# endif
YYUSE (yytype);
}
| Print this symbol on YYOUTPUT. |
`--------------------------------*/
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
static void
yy_symbol_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, YYLTYPE const * const yylocationp, void *scanner)
-#else
-static void
-yy_symbol_print (yyoutput, yytype, yyvaluep, yylocationp, scanner)
- FILE *yyoutput;
- int yytype;
- YYSTYPE const * const yyvaluep;
- YYLTYPE const * const yylocationp;
- void *scanner;
-#endif
{
- if (yytype < YYNTOKENS)
- YYFPRINTF (yyoutput, "token %s (", yytname[yytype]);
- else
- YYFPRINTF (yyoutput, "nterm %s (", yytname[yytype]);
+ YYFPRINTF (yyoutput, "%s %s (",
+ yytype < YYNTOKENS ? "token" : "nterm", yytname[yytype]);
YY_LOCATION_PRINT (yyoutput, *yylocationp);
YYFPRINTF (yyoutput, ": ");
| TOP (included). |
`------------------------------------------------------------------*/
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
static void
yy_stack_print (yytype_int16 *yybottom, yytype_int16 *yytop)
-#else
-static void
-yy_stack_print (yybottom, yytop)
- yytype_int16 *yybottom;
- yytype_int16 *yytop;
-#endif
{
YYFPRINTF (stderr, "Stack now");
for (; yybottom <= yytop; yybottom++)
YYFPRINTF (stderr, "\n");
}
-# define YY_STACK_PRINT(Bottom, Top) \
-do { \
- if (yydebug) \
- yy_stack_print ((Bottom), (Top)); \
-} while (YYID (0))
+# define YY_STACK_PRINT(Bottom, Top) \
+do { \
+ if (yydebug) \
+ yy_stack_print ((Bottom), (Top)); \
+} while (0)
/*------------------------------------------------.
| Report that the YYRULE is going to be reduced. |
`------------------------------------------------*/
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
-static void
-yy_reduce_print (YYSTYPE *yyvsp, YYLTYPE *yylsp, int yyrule, void *scanner)
-#else
static void
-yy_reduce_print (yyvsp, yylsp, yyrule, scanner)
- YYSTYPE *yyvsp;
- YYLTYPE *yylsp;
- int yyrule;
- void *scanner;
-#endif
+yy_reduce_print (yytype_int16 *yyssp, YYSTYPE *yyvsp, YYLTYPE *yylsp, int yyrule, void *scanner)
{
+ unsigned long int yylno = yyrline[yyrule];
int yynrhs = yyr2[yyrule];
int yyi;
- unsigned long int yylno = yyrline[yyrule];
YYFPRINTF (stderr, "Reducing stack by rule %d (line %lu):\n",
- yyrule - 1, yylno);
+ yyrule - 1, yylno);
/* The symbols being reduced. */
for (yyi = 0; yyi < yynrhs; yyi++)
{
YYFPRINTF (stderr, " $%d = ", yyi + 1);
- yy_symbol_print (stderr, yyrhs[yyprhs[yyrule] + yyi],
- &(yyvsp[(yyi + 1) - (yynrhs)])
- , &(yylsp[(yyi + 1) - (yynrhs)]) , scanner);
+ yy_symbol_print (stderr,
+ yystos[yyssp[yyi + 1 - yynrhs]],
+ &(yyvsp[(yyi + 1) - (yynrhs)])
+ , &(yylsp[(yyi + 1) - (yynrhs)]) , scanner);
YYFPRINTF (stderr, "\n");
}
}
-# define YY_REDUCE_PRINT(Rule) \
-do { \
- if (yydebug) \
- yy_reduce_print (yyvsp, yylsp, Rule, scanner); \
-} while (YYID (0))
+# define YY_REDUCE_PRINT(Rule) \
+do { \
+ if (yydebug) \
+ yy_reduce_print (yyssp, yyvsp, yylsp, Rule, scanner); \
+} while (0)
/* Nonzero means print parse trace. It is left uninitialized so that
multiple parsers can coexist. */
/* YYINITDEPTH -- initial size of the parser's stacks. */
-#ifndef YYINITDEPTH
+#ifndef YYINITDEPTH
# define YYINITDEPTH 200
#endif
# define yystrlen strlen
# else
/* Return the length of YYSTR. */
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
static YYSIZE_T
yystrlen (const char *yystr)
-#else
-static YYSIZE_T
-yystrlen (yystr)
- const char *yystr;
-#endif
{
YYSIZE_T yylen;
for (yylen = 0; yystr[yylen]; yylen++)
# else
/* Copy YYSRC to YYDEST, returning the address of the terminating '\0' in
YYDEST. */
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
static char *
yystpcpy (char *yydest, const char *yysrc)
-#else
-static char *
-yystpcpy (yydest, yysrc)
- char *yydest;
- const char *yysrc;
-#endif
{
char *yyd = yydest;
const char *yys = yysrc;
char const *yyp = yystr;
for (;;)
- switch (*++yyp)
- {
- case '\'':
- case ',':
- goto do_not_strip_quotes;
-
- case '\\':
- if (*++yyp != '\\')
- goto do_not_strip_quotes;
- /* Fall through. */
- default:
- if (yyres)
- yyres[yyn] = *yyp;
- yyn++;
- break;
-
- case '"':
- if (yyres)
- yyres[yyn] = '\0';
- return yyn;
- }
+ switch (*++yyp)
+ {
+ case '\'':
+ case ',':
+ goto do_not_strip_quotes;
+
+ case '\\':
+ if (*++yyp != '\\')
+ goto do_not_strip_quotes;
+ /* Fall through. */
+ default:
+ if (yyres)
+ yyres[yyn] = *yyp;
+ yyn++;
+ break;
+
+ case '"':
+ if (yyres)
+ yyres[yyn] = '\0';
+ return yyn;
+ }
do_not_strip_quotes: ;
}
yysyntax_error (YYSIZE_T *yymsg_alloc, char **yymsg,
yytype_int16 *yyssp, int yytoken)
{
- YYSIZE_T yysize0 = yytnamerr (YY_NULL, yytname[yytoken]);
+ YYSIZE_T yysize0 = yytnamerr (YY_NULLPTR, yytname[yytoken]);
YYSIZE_T yysize = yysize0;
enum { YYERROR_VERBOSE_ARGS_MAXIMUM = 5 };
/* Internationalized format string. */
- const char *yyformat = YY_NULL;
+ const char *yyformat = YY_NULLPTR;
/* Arguments of yyformat. */
char const *yyarg[YYERROR_VERBOSE_ARGS_MAXIMUM];
/* Number of reported tokens (one for the "unexpected", one per
int yycount = 0;
/* There are many possibilities here to consider:
- - Assume YYFAIL is not used. It's too flawed to consider. See
- <http://lists.gnu.org/archive/html/bison-patches/2009-12/msg00024.html>
- for details. YYERROR is fine as it does not invoke this
- function.
- If this state is a consistent state with a default action, then
the only way this function was invoked is if the default action
is an error action. In that case, don't check for expected
}
yyarg[yycount++] = yytname[yyx];
{
- YYSIZE_T yysize1 = yysize + yytnamerr (YY_NULL, yytname[yyx]);
+ YYSIZE_T yysize1 = yysize + yytnamerr (YY_NULLPTR, yytname[yyx]);
if (! (yysize <= yysize1
&& yysize1 <= YYSTACK_ALLOC_MAXIMUM))
return 2;
| Release the memory associated to this symbol. |
`-----------------------------------------------*/
-/*ARGSUSED*/
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
static void
yydestruct (const char *yymsg, int yytype, YYSTYPE *yyvaluep, YYLTYPE *yylocationp, void *scanner)
-#else
-static void
-yydestruct (yymsg, yytype, yyvaluep, yylocationp, scanner)
- const char *yymsg;
- int yytype;
- YYSTYPE *yyvaluep;
- YYLTYPE *yylocationp;
- void *scanner;
-#endif
{
YYUSE (yyvaluep);
YYUSE (yylocationp);
YYUSE (scanner);
-
if (!yymsg)
yymsg = "Deleting";
YY_SYMBOL_PRINT (yymsg, yytype, yyvaluep, yylocationp);
+ YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
switch (yytype)
{
- case 6: /* STR */
-/* Line 1393 of yacc.c */
-#line 178 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1393 of yacc.c */
-#line 1473 "parser.cpp"
+ case 6: /* STR */
+#line 178 "parser.y" /* yacc.c:1257 */
+ { free(((*yyvaluep).str)); }
+#line 1313 "parser.cpp" /* yacc.c:1257 */
break;
- case 7: /* IDENTIFIER */
-/* Line 1393 of yacc.c */
-#line 178 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1393 of yacc.c */
-#line 1480 "parser.cpp"
+
+ case 7: /* IDENTIFIER */
+#line 178 "parser.y" /* yacc.c:1257 */
+ { free(((*yyvaluep).str)); }
+#line 1319 "parser.cpp" /* yacc.c:1257 */
break;
- case 16: /* KEYWORD_POS */
-/* Line 1393 of yacc.c */
-#line 178 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1393 of yacc.c */
-#line 1487 "parser.cpp"
+
+ case 16: /* KEYWORD_POS */
+#line 178 "parser.y" /* yacc.c:1257 */
+ { free(((*yyvaluep).str)); }
+#line 1325 "parser.cpp" /* yacc.c:1257 */
break;
- case 23: /* PARAM */
-/* Line 1393 of yacc.c */
-#line 179 "parser.y"
- { if(((*yyvaluep).str)) free(((*yyvaluep).str)); };
-/* Line 1393 of yacc.c */
-#line 1494 "parser.cpp"
+
+ case 23: /* PARAM */
+#line 179 "parser.y" /* yacc.c:1257 */
+ { if(((*yyvaluep).str)) free(((*yyvaluep).str)); }
+#line 1331 "parser.cpp" /* yacc.c:1257 */
break;
- case 26: /* CMP_OP */
-/* Line 1393 of yacc.c */
-#line 178 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1393 of yacc.c */
-#line 1501 "parser.cpp"
+
+ case 26: /* CMP_OP */
+#line 178 "parser.y" /* yacc.c:1257 */
+ { free(((*yyvaluep).str)); }
+#line 1337 "parser.cpp" /* yacc.c:1257 */
break;
- case 50: /* commands */
-/* Line 1393 of yacc.c */
-#line 180 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1508 "parser.cpp"
+
+ case 50: /* commands */
+#line 180 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1343 "parser.cpp" /* yacc.c:1257 */
break;
- case 51: /* command */
-/* Line 1393 of yacc.c */
-#line 180 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1515 "parser.cpp"
+
+ case 51: /* command */
+#line 180 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1349 "parser.cpp" /* yacc.c:1257 */
break;
- case 52: /* cmd_plain */
-/* Line 1393 of yacc.c */
-#line 180 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1522 "parser.cpp"
+
+ case 52: /* cmd_plain */
+#line 180 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1355 "parser.cpp" /* yacc.c:1257 */
break;
- case 53: /* selection */
-/* Line 1393 of yacc.c */
-#line 180 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1529 "parser.cpp"
+
+ case 53: /* selection */
+#line 180 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1361 "parser.cpp" /* yacc.c:1257 */
break;
- case 57: /* string */
-/* Line 1393 of yacc.c */
-#line 178 "parser.y"
- { free(((*yyvaluep).str)); };
-/* Line 1393 of yacc.c */
-#line 1536 "parser.cpp"
+
+ case 57: /* string */
+#line 178 "parser.y" /* yacc.c:1257 */
+ { free(((*yyvaluep).str)); }
+#line 1367 "parser.cpp" /* yacc.c:1257 */
break;
- case 58: /* sel_expr */
-/* Line 1393 of yacc.c */
-#line 181 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1543 "parser.cpp"
+
+ case 58: /* sel_expr */
+#line 181 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1373 "parser.cpp" /* yacc.c:1257 */
break;
- case 59: /* pos_mod */
-/* Line 1393 of yacc.c */
-#line 179 "parser.y"
- { if(((*yyvaluep).str)) free(((*yyvaluep).str)); };
-/* Line 1393 of yacc.c */
-#line 1550 "parser.cpp"
+
+ case 59: /* pos_mod */
+#line 179 "parser.y" /* yacc.c:1257 */
+ { if(((*yyvaluep).str)) free(((*yyvaluep).str)); }
+#line 1379 "parser.cpp" /* yacc.c:1257 */
break;
- case 61: /* num_expr */
-/* Line 1393 of yacc.c */
-#line 181 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1557 "parser.cpp"
+
+ case 61: /* num_expr */
+#line 181 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1385 "parser.cpp" /* yacc.c:1257 */
break;
- case 62: /* str_expr */
-/* Line 1393 of yacc.c */
-#line 181 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1564 "parser.cpp"
+
+ case 62: /* str_expr */
+#line 181 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1391 "parser.cpp" /* yacc.c:1257 */
break;
- case 63: /* pos_expr */
-/* Line 1393 of yacc.c */
-#line 181 "parser.y"
- { delete ((*yyvaluep).sel); };
-/* Line 1393 of yacc.c */
-#line 1571 "parser.cpp"
+
+ case 63: /* pos_expr */
+#line 181 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).sel); }
+#line 1397 "parser.cpp" /* yacc.c:1257 */
break;
- case 64: /* method_params */
-/* Line 1393 of yacc.c */
-#line 182 "parser.y"
- { delete ((*yyvaluep).plist); };
-/* Line 1393 of yacc.c */
-#line 1578 "parser.cpp"
+
+ case 64: /* method_params */
+#line 182 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).plist); }
+#line 1403 "parser.cpp" /* yacc.c:1257 */
break;
- case 65: /* method_param_list */
-/* Line 1393 of yacc.c */
-#line 182 "parser.y"
- { delete ((*yyvaluep).plist); };
-/* Line 1393 of yacc.c */
-#line 1585 "parser.cpp"
+
+ case 65: /* method_param_list */
+#line 182 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).plist); }
+#line 1409 "parser.cpp" /* yacc.c:1257 */
break;
- case 66: /* method_param */
-/* Line 1393 of yacc.c */
-#line 182 "parser.y"
- { delete ((*yyvaluep).param); };
-/* Line 1393 of yacc.c */
-#line 1592 "parser.cpp"
+
+ case 66: /* method_param */
+#line 182 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).param); }
+#line 1415 "parser.cpp" /* yacc.c:1257 */
break;
- case 67: /* value_list */
-/* Line 1393 of yacc.c */
-#line 183 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1393 of yacc.c */
-#line 1599 "parser.cpp"
+
+ case 67: /* value_list */
+#line 183 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).vlist); }
+#line 1421 "parser.cpp" /* yacc.c:1257 */
break;
- case 68: /* value_list_contents */
-/* Line 1393 of yacc.c */
-#line 183 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1393 of yacc.c */
-#line 1606 "parser.cpp"
+
+ case 68: /* value_list_contents */
+#line 183 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).vlist); }
+#line 1427 "parser.cpp" /* yacc.c:1257 */
break;
- case 69: /* basic_value_list */
-/* Line 1393 of yacc.c */
-#line 183 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1393 of yacc.c */
-#line 1613 "parser.cpp"
+
+ case 69: /* basic_value_list */
+#line 183 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).vlist); }
+#line 1433 "parser.cpp" /* yacc.c:1257 */
break;
- case 70: /* basic_value_list_contents */
-/* Line 1393 of yacc.c */
-#line 183 "parser.y"
- { delete ((*yyvaluep).vlist); };
-/* Line 1393 of yacc.c */
-#line 1620 "parser.cpp"
+
+ case 70: /* basic_value_list_contents */
+#line 183 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).vlist); }
+#line 1439 "parser.cpp" /* yacc.c:1257 */
break;
- case 71: /* value_item */
-/* Line 1393 of yacc.c */
-#line 184 "parser.y"
- { delete ((*yyvaluep).val); };
-/* Line 1393 of yacc.c */
-#line 1627 "parser.cpp"
+
+ case 71: /* value_item */
+#line 184 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).val); }
+#line 1445 "parser.cpp" /* yacc.c:1257 */
break;
- case 72: /* basic_value_item */
-/* Line 1393 of yacc.c */
-#line 184 "parser.y"
- { delete ((*yyvaluep).val); };
-/* Line 1393 of yacc.c */
-#line 1634 "parser.cpp"
+
+ case 72: /* basic_value_item */
+#line 184 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).val); }
+#line 1451 "parser.cpp" /* yacc.c:1257 */
break;
- case 73: /* value_item_range */
-/* Line 1393 of yacc.c */
-#line 184 "parser.y"
- { delete ((*yyvaluep).val); };
-/* Line 1393 of yacc.c */
-#line 1641 "parser.cpp"
+
+ case 73: /* value_item_range */
+#line 184 "parser.y" /* yacc.c:1257 */
+ { delete ((*yyvaluep).val); }
+#line 1457 "parser.cpp" /* yacc.c:1257 */
break;
+
default:
break;
}
+ YY_IGNORE_MAYBE_UNINITIALIZED_END
}
int yyerrstatus;
/* The stacks and their tools:
- `yyss': related to states.
- `yyvs': related to semantic values.
- `yyls': related to locations.
+ 'yyss': related to states.
+ 'yyvs': related to semantic values.
+ 'yyls': related to locations.
Refer to the stacks through separate pointers, to allow yyoverflow
to reallocate them elsewhere. */
};
/* Initialize the parser data structure. */
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
yypstate *
yypstate_new (void)
-#else
-yypstate *
-yypstate_new ()
-
-#endif
{
yypstate *yyps;
yyps = (yypstate *) malloc (sizeof *yyps);
if (!yyps)
- return YY_NULL;
+ return YY_NULLPTR;
yyps->yynew = 1;
return yyps;
}
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
void
yypstate_delete (yypstate *yyps)
-#else
-void
-yypstate_delete (yyps)
- yypstate *yyps;
-#endif
{
#ifndef yyoverflow
/* If the stack was reallocated but the parse did not complete, then the
| yypush_parse. |
`---------------*/
-#if (defined __STDC__ || defined __C99__FUNC__ \
- || defined __cplusplus || defined _MSC_VER)
int
yypush_parse (yypstate *yyps, int yypushed_char, YYSTYPE const *yypushed_val, YYLTYPE *yypushed_loc, void *scanner)
-#else
-int
-yypush_parse (yyps, yypushed_char, yypushed_val, yypushed_loc, scanner)
- yypstate *yyps;
- int yypushed_char;
- YYSTYPE const *yypushed_val;
- YYLTYPE *yypushed_loc;
- void *scanner;
-#endif
{
/* The lookahead symbol. */
int yychar;
-#if defined __GNUC__ && 407 <= __GNUC__ * 100 + __GNUC_MINOR__
-/* Suppress an incorrect diagnostic about yylval being uninitialized. */
-# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN \
- _Pragma ("GCC diagnostic push") \
- _Pragma ("GCC diagnostic ignored \"-Wuninitialized\"")\
- _Pragma ("GCC diagnostic ignored \"-Wmaybe-uninitialized\"")
-# define YY_IGNORE_MAYBE_UNINITIALIZED_END \
- _Pragma ("GCC diagnostic pop")
-#else
+/* The semantic value of the lookahead symbol. */
/* Default value used for initialization, for pacifying older GCCs
or non-GCC compilers. */
-static YYSTYPE yyval_default;
-# define YY_INITIAL_VALUE(Value) = Value
-#endif
+YY_INITIAL_VALUE (static YYSTYPE yyval_default;)
+YYSTYPE yylval YY_INITIAL_VALUE (= yyval_default);
+
+/* Location data for the lookahead symbol. */
static YYLTYPE yyloc_default
# if defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL
= { 1, 1, 1, 1 }
# endif
;
-#ifndef YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
-# define YY_IGNORE_MAYBE_UNINITIALIZED_BEGIN
-# define YY_IGNORE_MAYBE_UNINITIALIZED_END
-#endif
-#ifndef YY_INITIAL_VALUE
-# define YY_INITIAL_VALUE(Value) /* Nothing. */
-#endif
-
-/* The semantic value of the lookahead symbol. */
-YYSTYPE yylval YY_INITIAL_VALUE(yyval_default);
-
-/* Location data for the lookahead symbol. */
YYLTYPE yylloc = yyloc_default;
-
int yyn;
int yyresult;
/* Lookahead token as an internal (translated) token number. */
#ifdef yyoverflow
{
- /* Give user a chance to reallocate the stack. Use copies of
- these so that the &'s don't force the real ones into
- memory. */
- YYSTYPE *yyvs1 = yyvs;
- yytype_int16 *yyss1 = yyss;
- YYLTYPE *yyls1 = yyls;
-
- /* Each stack pointer address is followed by the size of the
- data in use in that stack, in bytes. This used to be a
- conditional around just the two extra args, but that might
- be undefined if yyoverflow is a macro. */
- yyoverflow (YY_("memory exhausted"),
- &yyss1, yysize * sizeof (*yyssp),
- &yyvs1, yysize * sizeof (*yyvsp),
- &yyls1, yysize * sizeof (*yylsp),
- &yystacksize);
-
- yyls = yyls1;
- yyss = yyss1;
- yyvs = yyvs1;
+ /* Give user a chance to reallocate the stack. Use copies of
+ these so that the &'s don't force the real ones into
+ memory. */
+ YYSTYPE *yyvs1 = yyvs;
+ yytype_int16 *yyss1 = yyss;
+ YYLTYPE *yyls1 = yyls;
+
+ /* Each stack pointer address is followed by the size of the
+ data in use in that stack, in bytes. This used to be a
+ conditional around just the two extra args, but that might
+ be undefined if yyoverflow is a macro. */
+ yyoverflow (YY_("memory exhausted"),
+ &yyss1, yysize * sizeof (*yyssp),
+ &yyvs1, yysize * sizeof (*yyvsp),
+ &yyls1, yysize * sizeof (*yylsp),
+ &yystacksize);
+
+ yyls = yyls1;
+ yyss = yyss1;
+ yyvs = yyvs1;
}
#else /* no yyoverflow */
# ifndef YYSTACK_RELOCATE
# else
/* Extend the stack our own way. */
if (YYMAXDEPTH <= yystacksize)
- goto yyexhaustedlab;
+ goto yyexhaustedlab;
yystacksize *= 2;
if (YYMAXDEPTH < yystacksize)
- yystacksize = YYMAXDEPTH;
+ yystacksize = YYMAXDEPTH;
{
- yytype_int16 *yyss1 = yyss;
- union yyalloc *yyptr =
- (union yyalloc *) YYSTACK_ALLOC (YYSTACK_BYTES (yystacksize));
- if (! yyptr)
- goto yyexhaustedlab;
- YYSTACK_RELOCATE (yyss_alloc, yyss);
- YYSTACK_RELOCATE (yyvs_alloc, yyvs);
- YYSTACK_RELOCATE (yyls_alloc, yyls);
+ yytype_int16 *yyss1 = yyss;
+ union yyalloc *yyptr =
+ (union yyalloc *) YYSTACK_ALLOC (YYSTACK_BYTES (yystacksize));
+ if (! yyptr)
+ goto yyexhaustedlab;
+ YYSTACK_RELOCATE (yyss_alloc, yyss);
+ YYSTACK_RELOCATE (yyvs_alloc, yyvs);
+ YYSTACK_RELOCATE (yyls_alloc, yyls);
# undef YYSTACK_RELOCATE
- if (yyss1 != yyssa)
- YYSTACK_FREE (yyss1);
+ if (yyss1 != yyssa)
+ YYSTACK_FREE (yyss1);
}
# endif
#endif /* no yyoverflow */
yylsp = yyls + yysize - 1;
YYDPRINTF ((stderr, "Stack size increased to %lu\n",
- (unsigned long int) yystacksize));
+ (unsigned long int) yystacksize));
if (yyss + yystacksize - 1 <= yyssp)
- YYABORT;
+ YYABORT;
}
YYDPRINTF ((stderr, "Entering state %d\n", yystate));
yylen = yyr2[yyn];
/* If YYLEN is nonzero, implement the default value of the action:
- `$$ = $1'.
+ '$$ = $1'.
Otherwise, the following line sets YYVAL to garbage.
This behavior is undocumented and Bison
switch (yyn)
{
case 2:
-/* Line 1787 of yacc.c */
-#line 199 "parser.y"
+#line 199 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
set_empty((yyval.sel));
END_ACTION_TOPLEVEL;
}
+#line 1818 "parser.cpp" /* yacc.c:1646 */
break;
case 3:
-/* Line 1787 of yacc.c */
-#line 205 "parser.y"
+#line 205 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_append_selection(get((yyvsp[(2) - (2)].sel)), get((yyvsp[(1) - (2)].sel)), scanner));
- if (_gmx_sel_parser_should_finish(scanner))
+ set((yyval.sel), _gmx_sel_append_selection(get((yyvsp[0].sel)), get((yyvsp[-1].sel)), scanner));
+ if (_gmx_sel_parser_should_finish(scanner)) {
+ delete (yyval.sel);
YYACCEPT;
+ }
END_ACTION_TOPLEVEL;
}
+#line 1832 "parser.cpp" /* yacc.c:1646 */
break;
case 4:
-/* Line 1787 of yacc.c */
-#line 215 "parser.y"
- { (yyval.sel) = (yyvsp[(1) - (2)].sel); }
+#line 217 "parser.y" /* yacc.c:1646 */
+ { (yyval.sel) = (yyvsp[-1].sel); }
+#line 1838 "parser.cpp" /* yacc.c:1646 */
break;
case 5:
-/* Line 1787 of yacc.c */
-#line 217 "parser.y"
+#line 219 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
_gmx_sel_lexer_clear_method_stack(scanner);
set_empty((yyval.sel));
END_ACTION_TOPLEVEL;
}
+#line 1858 "parser.cpp" /* yacc.c:1646 */
break;
case 6:
-/* Line 1787 of yacc.c */
-#line 236 "parser.y"
+#line 238 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
set_empty((yyval.sel));
END_ACTION;
}
+#line 1868 "parser.cpp" /* yacc.c:1646 */
break;
case 7:
-/* Line 1787 of yacc.c */
-#line 242 "parser.y"
+#line 244 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
SelectionTreeElementPointer s
- = _gmx_sel_init_group_by_id((yyvsp[(1) - (1)].i), scanner);
+ = _gmx_sel_init_group_by_id((yyvsp[0].i), scanner);
SelectionTreeElementPointer p
= _gmx_sel_init_position(s, NULL, scanner);
if (!p) YYERROR;
set((yyval.sel), _gmx_sel_init_selection(NULL, p, scanner));
END_ACTION;
}
+#line 1883 "parser.cpp" /* yacc.c:1646 */
break;
case 8:
-/* Line 1787 of yacc.c */
-#line 253 "parser.y"
+#line 255 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard((yyvsp[(1) - (1)].str));
+ const sfree_guard nameGuard((yyvsp[0].str));
SelectionTreeElementPointer s
- = _gmx_sel_init_group_by_name((yyvsp[(1) - (1)].str), scanner);
+ = _gmx_sel_init_group_by_name((yyvsp[0].str), scanner);
SelectionTreeElementPointer p
= _gmx_sel_init_position(s, NULL, scanner);
if (!p) YYERROR;
set((yyval.sel), _gmx_sel_init_selection(NULL, p, scanner));
END_ACTION;
}
+#line 1899 "parser.cpp" /* yacc.c:1646 */
break;
case 9:
-/* Line 1787 of yacc.c */
-#line 265 "parser.y"
+#line 267 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_selection(NULL, get((yyvsp[(1) - (1)].sel)), scanner));
+ set((yyval.sel), _gmx_sel_init_selection(NULL, get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 1909 "parser.cpp" /* yacc.c:1646 */
break;
case 10:
-/* Line 1787 of yacc.c */
-#line 271 "parser.y"
+#line 273 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard((yyvsp[(1) - (2)].str));
- set((yyval.sel), _gmx_sel_init_selection((yyvsp[(1) - (2)].str), get((yyvsp[(2) - (2)].sel)), scanner));
+ const sfree_guard nameGuard((yyvsp[-1].str));
+ set((yyval.sel), _gmx_sel_init_selection((yyvsp[-1].str), get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 1920 "parser.cpp" /* yacc.c:1646 */
break;
case 11:
-/* Line 1787 of yacc.c */
-#line 278 "parser.y"
+#line 280 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), get((yyvsp[(3) - (3)].sel)), scanner));
+ const sfree_guard nameGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_assign_variable((yyvsp[-2].str), get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 1931 "parser.cpp" /* yacc.c:1646 */
break;
case 12:
-/* Line 1787 of yacc.c */
-#line 285 "parser.y"
+#line 287 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), get((yyvsp[(3) - (3)].sel)), scanner));
+ const sfree_guard nameGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_assign_variable((yyvsp[-2].str), get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 1942 "parser.cpp" /* yacc.c:1646 */
break;
case 13:
-/* Line 1787 of yacc.c */
-#line 292 "parser.y"
+#line 294 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_assign_variable((yyvsp[(1) - (3)].str), get((yyvsp[(3) - (3)].sel)), scanner));
+ const sfree_guard nameGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_assign_variable((yyvsp[-2].str), get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 1953 "parser.cpp" /* yacc.c:1646 */
break;
case 14:
-/* Line 1787 of yacc.c */
-#line 301 "parser.y"
- { (yyval.sel) = (yyvsp[(1) - (1)].sel); }
+#line 303 "parser.y" /* yacc.c:1646 */
+ { (yyval.sel) = (yyvsp[0].sel); }
+#line 1959 "parser.cpp" /* yacc.c:1646 */
break;
case 15:
-/* Line 1787 of yacc.c */
-#line 303 "parser.y"
+#line 305 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_position(get((yyvsp[(1) - (1)].sel)), NULL, scanner));
+ set((yyval.sel), _gmx_sel_init_position(get((yyvsp[0].sel)), NULL, scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 1970 "parser.cpp" /* yacc.c:1646 */
break;
case 16:
-/* Line 1787 of yacc.c */
-#line 309 "parser.y"
- { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
+#line 311 "parser.y" /* yacc.c:1646 */
+ { (yyval.sel) = (yyvsp[-1].sel); }
+#line 1976 "parser.cpp" /* yacc.c:1646 */
break;
case 17:
-/* Line 1787 of yacc.c */
-#line 311 "parser.y"
+#line 313 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_modifier((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), get((yyvsp[(1) - (3)].sel)), scanner));
+ set((yyval.sel), _gmx_sel_init_modifier((yyvsp[-1].meth), get((yyvsp[0].plist)), get((yyvsp[-2].sel)), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 1987 "parser.cpp" /* yacc.c:1646 */
break;
case 18:
-/* Line 1787 of yacc.c */
-#line 324 "parser.y"
- { (yyval.i) = (yyvsp[(1) - (1)].i); }
+#line 326 "parser.y" /* yacc.c:1646 */
+ { (yyval.i) = (yyvsp[0].i); }
+#line 1993 "parser.cpp" /* yacc.c:1646 */
break;
case 19:
-/* Line 1787 of yacc.c */
-#line 325 "parser.y"
- { (yyval.i) = -(yyvsp[(2) - (2)].i); }
+#line 327 "parser.y" /* yacc.c:1646 */
+ { (yyval.i) = -(yyvsp[0].i); }
+#line 1999 "parser.cpp" /* yacc.c:1646 */
break;
case 20:
-/* Line 1787 of yacc.c */
-#line 329 "parser.y"
- { (yyval.r) = (yyvsp[(1) - (1)].r); }
+#line 331 "parser.y" /* yacc.c:1646 */
+ { (yyval.r) = (yyvsp[0].r); }
+#line 2005 "parser.cpp" /* yacc.c:1646 */
break;
case 21:
-/* Line 1787 of yacc.c */
-#line 330 "parser.y"
- { (yyval.r) = -(yyvsp[(2) - (2)].r); }
+#line 332 "parser.y" /* yacc.c:1646 */
+ { (yyval.r) = -(yyvsp[0].r); }
+#line 2011 "parser.cpp" /* yacc.c:1646 */
break;
case 22:
-/* Line 1787 of yacc.c */
-#line 333 "parser.y"
- { (yyval.r) = (yyvsp[(1) - (1)].i); }
+#line 335 "parser.y" /* yacc.c:1646 */
+ { (yyval.r) = (yyvsp[0].i); }
+#line 2017 "parser.cpp" /* yacc.c:1646 */
break;
case 23:
-/* Line 1787 of yacc.c */
-#line 334 "parser.y"
- { (yyval.r) = (yyvsp[(1) - (1)].r); }
+#line 336 "parser.y" /* yacc.c:1646 */
+ { (yyval.r) = (yyvsp[0].r); }
+#line 2023 "parser.cpp" /* yacc.c:1646 */
break;
case 24:
-/* Line 1787 of yacc.c */
-#line 337 "parser.y"
- { (yyval.str) = (yyvsp[(1) - (1)].str); }
+#line 339 "parser.y" /* yacc.c:1646 */
+ { (yyval.str) = (yyvsp[0].str); }
+#line 2029 "parser.cpp" /* yacc.c:1646 */
break;
case 25:
-/* Line 1787 of yacc.c */
-#line 338 "parser.y"
- { (yyval.str) = (yyvsp[(1) - (1)].str); }
+#line 340 "parser.y" /* yacc.c:1646 */
+ { (yyval.str) = (yyvsp[0].str); }
+#line 2035 "parser.cpp" /* yacc.c:1646 */
break;
case 26:
-/* Line 1787 of yacc.c */
-#line 347 "parser.y"
+#line 349 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionTreeElementPointer arg(get((yyvsp[(2) - (2)].sel)));
+ SelectionTreeElementPointer arg(get((yyvsp[0].sel)));
SelectionTreeElementPointer sel(
new SelectionTreeElement(SEL_BOOLEAN, (yyloc)));
sel->u.boolt = BOOL_NOT;
set((yyval.sel), sel);
END_ACTION;
}
+#line 2050 "parser.cpp" /* yacc.c:1646 */
break;
case 27:
-/* Line 1787 of yacc.c */
-#line 358 "parser.y"
+#line 360 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionTreeElementPointer arg1(get((yyvsp[(1) - (3)].sel))), arg2(get((yyvsp[(3) - (3)].sel)));
+ SelectionTreeElementPointer arg1(get((yyvsp[-2].sel))), arg2(get((yyvsp[0].sel)));
SelectionTreeElementPointer sel(
new SelectionTreeElement(SEL_BOOLEAN, (yyloc)));
sel->u.boolt = BOOL_AND;
set((yyval.sel), sel);
END_ACTION;
}
+#line 2065 "parser.cpp" /* yacc.c:1646 */
break;
case 28:
-/* Line 1787 of yacc.c */
-#line 369 "parser.y"
+#line 371 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionTreeElementPointer arg1(get((yyvsp[(1) - (3)].sel))), arg2(get((yyvsp[(3) - (3)].sel)));
+ SelectionTreeElementPointer arg1(get((yyvsp[-2].sel))), arg2(get((yyvsp[0].sel)));
SelectionTreeElementPointer sel(
new SelectionTreeElement(SEL_BOOLEAN, (yyloc)));
sel->u.boolt = BOOL_OR;
set((yyval.sel), sel);
END_ACTION;
}
+#line 2080 "parser.cpp" /* yacc.c:1646 */
break;
case 29:
-/* Line 1787 of yacc.c */
-#line 379 "parser.y"
- { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
+#line 381 "parser.y" /* yacc.c:1646 */
+ { (yyval.sel) = (yyvsp[-1].sel); }
+#line 2086 "parser.cpp" /* yacc.c:1646 */
break;
case 30:
-/* Line 1787 of yacc.c */
-#line 384 "parser.y"
+#line 386 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree opGuard((yyvsp[(2) - (3)].str));
- set((yyval.sel), _gmx_sel_init_comparison(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), (yyvsp[(2) - (3)].str), scanner));
+ const sfree_guard opGuard((yyvsp[-1].str));
+ set((yyval.sel), _gmx_sel_init_comparison(get((yyvsp[-2].sel)), get((yyvsp[0].sel)), (yyvsp[-1].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2098 "parser.cpp" /* yacc.c:1646 */
break;
case 31:
-/* Line 1787 of yacc.c */
-#line 395 "parser.y"
+#line 397 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard((yyvsp[(2) - (2)].str));
- set((yyval.sel), _gmx_sel_init_group_by_name((yyvsp[(2) - (2)].str), scanner));
+ const sfree_guard nameGuard((yyvsp[0].str));
+ set((yyval.sel), _gmx_sel_init_group_by_name((yyvsp[0].str), scanner));
END_ACTION;
}
+#line 2109 "parser.cpp" /* yacc.c:1646 */
break;
case 32:
-/* Line 1787 of yacc.c */
-#line 402 "parser.y"
+#line 404 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_group_by_id((yyvsp[(2) - (2)].i), scanner));
+ set((yyval.sel), _gmx_sel_init_group_by_id((yyvsp[0].i), scanner));
END_ACTION;
}
+#line 2119 "parser.cpp" /* yacc.c:1646 */
break;
case 33:
-/* Line 1787 of yacc.c */
-#line 410 "parser.y"
+#line 412 "parser.y" /* yacc.c:1646 */
{ (yyval.str) = NULL; }
+#line 2125 "parser.cpp" /* yacc.c:1646 */
break;
case 34:
-/* Line 1787 of yacc.c */
-#line 411 "parser.y"
- { (yyval.str) = (yyvsp[(1) - (1)].str); }
+#line 413 "parser.y" /* yacc.c:1646 */
+ { (yyval.str) = (yyvsp[0].str); }
+#line 2131 "parser.cpp" /* yacc.c:1646 */
break;
case 35:
-/* Line 1787 of yacc.c */
-#line 416 "parser.y"
+#line 418 "parser.y" /* yacc.c:1646 */
{ (yyval.smt) = gmx::eStringMatchType_RegularExpression; }
+#line 2137 "parser.cpp" /* yacc.c:1646 */
break;
case 36:
-/* Line 1787 of yacc.c */
-#line 417 "parser.y"
+#line 419 "parser.y" /* yacc.c:1646 */
{ (yyval.smt) = gmx::eStringMatchType_Wildcard; }
+#line 2143 "parser.cpp" /* yacc.c:1646 */
break;
case 37:
-/* Line 1787 of yacc.c */
-#line 418 "parser.y"
+#line 420 "parser.y" /* yacc.c:1646 */
{ (yyval.smt) = gmx::eStringMatchType_Exact; }
+#line 2149 "parser.cpp" /* yacc.c:1646 */
break;
case 38:
-/* Line 1787 of yacc.c */
-#line 423 "parser.y"
+#line 425 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (2)].str));
- set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), SelectionParserValueListPointer(), (yyvsp[(1) - (2)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-1].str));
+ set((yyval.sel), _gmx_sel_init_keyword((yyvsp[0].meth), SelectionParserValueListPointer(), (yyvsp[-1].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2161 "parser.cpp" /* yacc.c:1646 */
break;
case 39:
-/* Line 1787 of yacc.c */
-#line 431 "parser.y"
+#line 433 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_init_keyword_strmatch((yyvsp[(2) - (3)].meth), gmx::eStringMatchType_Auto, get((yyvsp[(3) - (3)].vlist)), (yyvsp[(1) - (3)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_init_keyword_strmatch((yyvsp[-1].meth), gmx::eStringMatchType_Auto, get((yyvsp[0].vlist)), (yyvsp[-2].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2173 "parser.cpp" /* yacc.c:1646 */
break;
case 40:
-/* Line 1787 of yacc.c */
-#line 439 "parser.y"
+#line 441 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (4)].str));
- set((yyval.sel), _gmx_sel_init_keyword_strmatch((yyvsp[(2) - (4)].meth), (yyvsp[(3) - (4)].smt), get((yyvsp[(4) - (4)].vlist)), (yyvsp[(1) - (4)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-3].str));
+ set((yyval.sel), _gmx_sel_init_keyword_strmatch((yyvsp[-2].meth), (yyvsp[-1].smt), get((yyvsp[0].vlist)), (yyvsp[-3].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2185 "parser.cpp" /* yacc.c:1646 */
break;
case 41:
-/* Line 1787 of yacc.c */
-#line 447 "parser.y"
+#line 449 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].vlist)), (yyvsp[(1) - (3)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_init_keyword((yyvsp[-1].meth), get((yyvsp[0].vlist)), (yyvsp[-2].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2197 "parser.cpp" /* yacc.c:1646 */
break;
case 42:
-/* Line 1787 of yacc.c */
-#line 458 "parser.y"
+#line 460 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_init_method((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), (yyvsp[(1) - (3)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_init_method((yyvsp[-1].meth), get((yyvsp[0].plist)), (yyvsp[-2].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2209 "parser.cpp" /* yacc.c:1646 */
break;
case 43:
-/* Line 1787 of yacc.c */
-#line 473 "parser.y"
+#line 475 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
new SelectionTreeElement(SEL_CONST, (yyloc)));
_gmx_selelem_set_vtype(sel, INT_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
- sel->v.u.i[0] = (yyvsp[(1) - (1)].i);
+ sel->v.u.i[0] = (yyvsp[0].i);
set((yyval.sel), sel);
END_ACTION;
}
+#line 2224 "parser.cpp" /* yacc.c:1646 */
break;
case 44:
-/* Line 1787 of yacc.c */
-#line 484 "parser.y"
+#line 486 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
new SelectionTreeElement(SEL_CONST, (yyloc)));
_gmx_selelem_set_vtype(sel, REAL_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
- sel->v.u.r[0] = (yyvsp[(1) - (1)].r);
+ sel->v.u.r[0] = (yyvsp[0].r);
set((yyval.sel), sel);
END_ACTION;
}
+#line 2239 "parser.cpp" /* yacc.c:1646 */
break;
case 45:
-/* Line 1787 of yacc.c */
-#line 498 "parser.y"
+#line 500 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (2)].str));
- set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), SelectionParserValueListPointer(), (yyvsp[(1) - (2)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-1].str));
+ set((yyval.sel), _gmx_sel_init_keyword((yyvsp[0].meth), SelectionParserValueListPointer(), (yyvsp[-1].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2251 "parser.cpp" /* yacc.c:1646 */
break;
case 46:
-/* Line 1787 of yacc.c */
-#line 506 "parser.y"
+#line 508 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (4)].str));
- set((yyval.sel), _gmx_sel_init_keyword_of((yyvsp[(2) - (4)].meth), get((yyvsp[(4) - (4)].sel)), (yyvsp[(1) - (4)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-3].str));
+ set((yyval.sel), _gmx_sel_init_keyword_of((yyvsp[-2].meth), get((yyvsp[0].sel)), (yyvsp[-3].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2263 "parser.cpp" /* yacc.c:1646 */
break;
case 47:
-/* Line 1787 of yacc.c */
-#line 514 "parser.y"
+#line 516 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_init_method((yyvsp[(2) - (3)].meth), get((yyvsp[(3) - (3)].plist)), (yyvsp[(1) - (3)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_init_method((yyvsp[-1].meth), get((yyvsp[0].plist)), (yyvsp[-2].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2275 "parser.cpp" /* yacc.c:1646 */
break;
case 48:
-/* Line 1787 of yacc.c */
-#line 525 "parser.y"
+#line 527 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '+', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[-2].sel)), get((yyvsp[0].sel)), '+', scanner));
END_ACTION;
}
+#line 2285 "parser.cpp" /* yacc.c:1646 */
break;
case 49:
-/* Line 1787 of yacc.c */
-#line 531 "parser.y"
+#line 533 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '-', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[-2].sel)), get((yyvsp[0].sel)), '-', scanner));
END_ACTION;
}
+#line 2295 "parser.cpp" /* yacc.c:1646 */
break;
case 50:
-/* Line 1787 of yacc.c */
-#line 537 "parser.y"
+#line 539 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '*', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[-2].sel)), get((yyvsp[0].sel)), '*', scanner));
END_ACTION;
}
+#line 2305 "parser.cpp" /* yacc.c:1646 */
break;
case 51:
-/* Line 1787 of yacc.c */
-#line 543 "parser.y"
+#line 545 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '/', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[-2].sel)), get((yyvsp[0].sel)), '/', scanner));
END_ACTION;
}
+#line 2315 "parser.cpp" /* yacc.c:1646 */
break;
case 52:
-/* Line 1787 of yacc.c */
-#line 549 "parser.y"
+#line 551 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(2) - (2)].sel)), SelectionTreeElementPointer(), '-', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[0].sel)), SelectionTreeElementPointer(), '-', scanner));
END_ACTION;
}
+#line 2325 "parser.cpp" /* yacc.c:1646 */
break;
case 53:
-/* Line 1787 of yacc.c */
-#line 555 "parser.y"
+#line 557 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[(1) - (3)].sel)), get((yyvsp[(3) - (3)].sel)), '^', scanner));
+ set((yyval.sel), _gmx_sel_init_arithmetic(get((yyvsp[-2].sel)), get((yyvsp[0].sel)), '^', scanner));
END_ACTION;
}
+#line 2335 "parser.cpp" /* yacc.c:1646 */
break;
case 54:
-/* Line 1787 of yacc.c */
-#line 560 "parser.y"
- { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
+#line 562 "parser.y" /* yacc.c:1646 */
+ { (yyval.sel) = (yyvsp[-1].sel); }
+#line 2341 "parser.cpp" /* yacc.c:1646 */
break;
case 55:
-/* Line 1787 of yacc.c */
-#line 568 "parser.y"
+#line 570 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
SelectionTreeElementPointer sel(
new SelectionTreeElement(SEL_CONST, (yyloc)));
_gmx_selelem_set_vtype(sel, STR_VALUE);
_gmx_selvalue_reserve(&sel->v, 1);
- sel->v.u.s[0] = (yyvsp[(1) - (1)].str);
+ sel->v.u.s[0] = (yyvsp[0].str);
set((yyval.sel), sel);
END_ACTION;
}
+#line 2356 "parser.cpp" /* yacc.c:1646 */
break;
case 56:
-/* Line 1787 of yacc.c */
-#line 579 "parser.y"
+#line 581 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard((yyvsp[(1) - (2)].str));
- set((yyval.sel), _gmx_sel_init_keyword((yyvsp[(2) - (2)].meth), SelectionParserValueListPointer(), (yyvsp[(1) - (2)].str), scanner));
+ const sfree_guard posmodGuard((yyvsp[-1].str));
+ set((yyval.sel), _gmx_sel_init_keyword((yyvsp[0].meth), SelectionParserValueListPointer(), (yyvsp[-1].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2368 "parser.cpp" /* yacc.c:1646 */
break;
case 57:
-/* Line 1787 of yacc.c */
-#line 594 "parser.y"
+#line 596 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_const_position((yyvsp[(2) - (7)].r), (yyvsp[(4) - (7)].r), (yyvsp[(6) - (7)].r), scanner));
+ set((yyval.sel), _gmx_sel_init_const_position((yyvsp[-5].r), (yyvsp[-3].r), (yyvsp[-1].r), scanner));
END_ACTION;
}
+#line 2378 "parser.cpp" /* yacc.c:1646 */
break;
case 58:
-/* Line 1787 of yacc.c */
-#line 602 "parser.y"
- { (yyval.sel) = (yyvsp[(2) - (3)].sel); }
+#line 604 "parser.y" /* yacc.c:1646 */
+ { (yyval.sel) = (yyvsp[-1].sel); }
+#line 2384 "parser.cpp" /* yacc.c:1646 */
break;
case 59:
-/* Line 1787 of yacc.c */
-#line 607 "parser.y"
+#line 609 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_method((yyvsp[(1) - (2)].meth), get((yyvsp[(2) - (2)].plist)), NULL, scanner));
+ set((yyval.sel), _gmx_sel_init_method((yyvsp[-1].meth), get((yyvsp[0].plist)), NULL, scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2395 "parser.cpp" /* yacc.c:1646 */
break;
case 60:
-/* Line 1787 of yacc.c */
-#line 617 "parser.y"
+#line 619 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree keywordGuard((yyvsp[(1) - (3)].str));
- set((yyval.sel), _gmx_sel_init_position(get((yyvsp[(3) - (3)].sel)), (yyvsp[(1) - (3)].str), scanner));
+ const sfree_guard keywordGuard((yyvsp[-2].str));
+ set((yyval.sel), _gmx_sel_init_position(get((yyvsp[0].sel)), (yyvsp[-2].str), scanner));
CHECK_SEL((yyval.sel));
END_ACTION;
}
+#line 2407 "parser.cpp" /* yacc.c:1646 */
break;
case 61:
-/* Line 1787 of yacc.c */
-#line 631 "parser.y"
+#line 633 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel)), scanner));
+ set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 2417 "parser.cpp" /* yacc.c:1646 */
break;
case 62:
-/* Line 1787 of yacc.c */
-#line 639 "parser.y"
+#line 641 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel)), scanner));
+ set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 2427 "parser.cpp" /* yacc.c:1646 */
break;
case 63:
-/* Line 1787 of yacc.c */
-#line 647 "parser.y"
+#line 649 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[(1) - (1)].sel)), scanner));
+ set((yyval.sel), _gmx_sel_init_variable_ref(get((yyvsp[0].sel)), scanner));
END_ACTION;
}
+#line 2437 "parser.cpp" /* yacc.c:1646 */
break;
case 64:
-/* Line 1787 of yacc.c */
-#line 660 "parser.y"
- { (yyval.plist) = (yyvsp[(1) - (1)].plist); }
+#line 662 "parser.y" /* yacc.c:1646 */
+ { (yyval.plist) = (yyvsp[0].plist); }
+#line 2443 "parser.cpp" /* yacc.c:1646 */
break;
case 65:
-/* Line 1787 of yacc.c */
-#line 662 "parser.y"
- { (yyval.plist) = (yyvsp[(1) - (2)].plist); }
+#line 664 "parser.y" /* yacc.c:1646 */
+ { (yyval.plist) = (yyvsp[-1].plist); }
+#line 2449 "parser.cpp" /* yacc.c:1646 */
break;
case 66:
-/* Line 1787 of yacc.c */
-#line 667 "parser.y"
+#line 669 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
set((yyval.plist), SelectionParserParameter::createList());
END_ACTION;
}
+#line 2459 "parser.cpp" /* yacc.c:1646 */
break;
case 67:
-/* Line 1787 of yacc.c */
-#line 673 "parser.y"
+#line 675 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionParserParameterListPointer list(get((yyvsp[(1) - (2)].plist)));
- list->push_back(get((yyvsp[(2) - (2)].param)));
+ SelectionParserParameterListPointer list(get((yyvsp[-1].plist)));
+ list->push_back(get((yyvsp[0].param)));
set((yyval.plist), std::move(list));
END_ACTION;
}
+#line 2471 "parser.cpp" /* yacc.c:1646 */
break;
case 68:
-/* Line 1787 of yacc.c */
-#line 684 "parser.y"
+#line 686 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard((yyvsp[(1) - (2)].str));
- set((yyval.param), SelectionParserParameter::create((yyvsp[(1) - (2)].str), get((yyvsp[(2) - (2)].vlist)), (yyloc)));
+ const sfree_guard nameGuard((yyvsp[-1].str));
+ set((yyval.param), SelectionParserParameter::create((yyvsp[-1].str), get((yyvsp[0].vlist)), (yyloc)));
END_ACTION;
}
+#line 2482 "parser.cpp" /* yacc.c:1646 */
break;
case 69:
-/* Line 1787 of yacc.c */
-#line 692 "parser.y"
- { (yyval.vlist) = (yyvsp[(1) - (1)].vlist); }
+#line 694 "parser.y" /* yacc.c:1646 */
+ { (yyval.vlist) = (yyvsp[0].vlist); }
+#line 2488 "parser.cpp" /* yacc.c:1646 */
break;
case 70:
-/* Line 1787 of yacc.c */
-#line 693 "parser.y"
- { (yyval.vlist) = (yyvsp[(2) - (3)].vlist); }
+#line 695 "parser.y" /* yacc.c:1646 */
+ { (yyval.vlist) = (yyvsp[-1].vlist); }
+#line 2494 "parser.cpp" /* yacc.c:1646 */
break;
case 71:
-/* Line 1787 of yacc.c */
-#line 698 "parser.y"
+#line 700 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
set((yyval.vlist), SelectionParserValue::createList());
END_ACTION;
}
+#line 2504 "parser.cpp" /* yacc.c:1646 */
break;
case 72:
-/* Line 1787 of yacc.c */
-#line 704 "parser.y"
+#line 706 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionParserValueListPointer list(get((yyvsp[(1) - (2)].vlist)));
- list->push_back(get((yyvsp[(2) - (2)].val)));
+ SelectionParserValueListPointer list(get((yyvsp[-1].vlist)));
+ list->push_back(get((yyvsp[0].val)));
set((yyval.vlist), std::move(list));
END_ACTION;
}
+#line 2516 "parser.cpp" /* yacc.c:1646 */
break;
case 73:
-/* Line 1787 of yacc.c */
-#line 712 "parser.y"
+#line 714 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionParserValueListPointer list(get((yyvsp[(1) - (3)].vlist)));
- list->push_back(get((yyvsp[(3) - (3)].val)));
+ SelectionParserValueListPointer list(get((yyvsp[-2].vlist)));
+ list->push_back(get((yyvsp[0].val)));
set((yyval.vlist), std::move(list));
END_ACTION;
}
+#line 2528 "parser.cpp" /* yacc.c:1646 */
break;
case 74:
-/* Line 1787 of yacc.c */
-#line 722 "parser.y"
- { (yyval.vlist) = (yyvsp[(1) - (1)].vlist); }
+#line 724 "parser.y" /* yacc.c:1646 */
+ { (yyval.vlist) = (yyvsp[0].vlist); }
+#line 2534 "parser.cpp" /* yacc.c:1646 */
break;
case 75:
-/* Line 1787 of yacc.c */
-#line 723 "parser.y"
- { (yyval.vlist) = (yyvsp[(2) - (3)].vlist); }
+#line 725 "parser.y" /* yacc.c:1646 */
+ { (yyval.vlist) = (yyvsp[-1].vlist); }
+#line 2540 "parser.cpp" /* yacc.c:1646 */
break;
case 76:
-/* Line 1787 of yacc.c */
-#line 728 "parser.y"
+#line 730 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.vlist), SelectionParserValue::createList(get((yyvsp[(1) - (1)].val))));
+ set((yyval.vlist), SelectionParserValue::createList(get((yyvsp[0].val))));
END_ACTION;
}
+#line 2550 "parser.cpp" /* yacc.c:1646 */
break;
case 77:
-/* Line 1787 of yacc.c */
-#line 734 "parser.y"
+#line 736 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionParserValueListPointer list(get((yyvsp[(1) - (2)].vlist)));
- list->push_back(get((yyvsp[(2) - (2)].val)));
+ SelectionParserValueListPointer list(get((yyvsp[-1].vlist)));
+ list->push_back(get((yyvsp[0].val)));
set((yyval.vlist), std::move(list));
END_ACTION;
}
+#line 2562 "parser.cpp" /* yacc.c:1646 */
break;
case 78:
-/* Line 1787 of yacc.c */
-#line 742 "parser.y"
+#line 744 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- SelectionParserValueListPointer list(get((yyvsp[(1) - (3)].vlist)));
- list->push_back(get((yyvsp[(3) - (3)].val)));
+ SelectionParserValueListPointer list(get((yyvsp[-2].vlist)));
+ list->push_back(get((yyvsp[0].val)));
set((yyval.vlist), std::move(list));
END_ACTION;
}
+#line 2574 "parser.cpp" /* yacc.c:1646 */
break;
case 79:
-/* Line 1787 of yacc.c */
-#line 752 "parser.y"
+#line 754 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
+ set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[0].sel))));
END_ACTION;
}
+#line 2584 "parser.cpp" /* yacc.c:1646 */
break;
case 80:
-/* Line 1787 of yacc.c */
-#line 758 "parser.y"
+#line 760 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
+ set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[0].sel))));
END_ACTION;
}
+#line 2594 "parser.cpp" /* yacc.c:1646 */
break;
case 81:
-/* Line 1787 of yacc.c */
-#line 764 "parser.y"
+#line 766 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
+ set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[0].sel))));
END_ACTION;
}
+#line 2604 "parser.cpp" /* yacc.c:1646 */
break;
case 82:
-/* Line 1787 of yacc.c */
-#line 770 "parser.y"
+#line 772 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[(1) - (1)].sel))));
+ set((yyval.val), SelectionParserValue::createExpr(get((yyvsp[0].sel))));
END_ACTION;
}
+#line 2614 "parser.cpp" /* yacc.c:1646 */
break;
case 83:
-/* Line 1787 of yacc.c */
-#line 775 "parser.y"
- { (yyval.val) = (yyvsp[(1) - (1)].val); }
+#line 777 "parser.y" /* yacc.c:1646 */
+ { (yyval.val) = (yyvsp[0].val); }
+#line 2620 "parser.cpp" /* yacc.c:1646 */
break;
case 84:
-/* Line 1787 of yacc.c */
-#line 780 "parser.y"
+#line 782 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createInteger((yyvsp[(1) - (1)].i), (yyloc)));
+ set((yyval.val), SelectionParserValue::createInteger((yyvsp[0].i), (yyloc)));
END_ACTION;
}
+#line 2630 "parser.cpp" /* yacc.c:1646 */
break;
case 85:
-/* Line 1787 of yacc.c */
-#line 786 "parser.y"
+#line 788 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createReal((yyvsp[(1) - (1)].r), (yyloc)));
+ set((yyval.val), SelectionParserValue::createReal((yyvsp[0].r), (yyloc)));
END_ACTION;
}
+#line 2640 "parser.cpp" /* yacc.c:1646 */
break;
case 86:
-/* Line 1787 of yacc.c */
-#line 792 "parser.y"
+#line 794 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- scoped_guard_sfree stringGuard((yyvsp[(1) - (1)].str));
- set((yyval.val), SelectionParserValue::createString((yyvsp[(1) - (1)].str), (yyloc)));
+ const sfree_guard stringGuard((yyvsp[0].str));
+ set((yyval.val), SelectionParserValue::createString((yyvsp[0].str), (yyloc)));
END_ACTION;
}
+#line 2651 "parser.cpp" /* yacc.c:1646 */
break;
case 87:
-/* Line 1787 of yacc.c */
-#line 798 "parser.y"
- { (yyval.val) = (yyvsp[(1) - (1)].val); }
+#line 800 "parser.y" /* yacc.c:1646 */
+ { (yyval.val) = (yyvsp[0].val); }
+#line 2657 "parser.cpp" /* yacc.c:1646 */
break;
case 88:
-/* Line 1787 of yacc.c */
-#line 803 "parser.y"
+#line 805 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createIntegerRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].i), (yyloc)));
+ set((yyval.val), SelectionParserValue::createIntegerRange((yyvsp[-2].i), (yyvsp[0].i), (yyloc)));
END_ACTION;
}
+#line 2667 "parser.cpp" /* yacc.c:1646 */
break;
case 89:
-/* Line 1787 of yacc.c */
-#line 809 "parser.y"
+#line 811 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].i), (yyvsp[(3) - (3)].r), (yyloc)));
+ set((yyval.val), SelectionParserValue::createRealRange((yyvsp[-2].i), (yyvsp[0].r), (yyloc)));
END_ACTION;
}
+#line 2677 "parser.cpp" /* yacc.c:1646 */
break;
case 90:
-/* Line 1787 of yacc.c */
-#line 815 "parser.y"
+#line 817 "parser.y" /* yacc.c:1646 */
{
BEGIN_ACTION;
- set((yyval.val), SelectionParserValue::createRealRange((yyvsp[(1) - (3)].r), (yyvsp[(3) - (3)].r), (yyloc)));
+ set((yyval.val), SelectionParserValue::createRealRange((yyvsp[-2].r), (yyvsp[0].r), (yyloc)));
END_ACTION;
}
+#line 2687 "parser.cpp" /* yacc.c:1646 */
break;
-/* Line 1787 of yacc.c */
-#line 2917 "parser.cpp"
+#line 2691 "parser.cpp" /* yacc.c:1646 */
default: break;
}
/* User semantic actions sometimes alter yychar, and that requires
*++yyvsp = yyval;
*++yylsp = yyloc;
- /* Now `shift' the result of the reduction. Determine what state
+ /* Now 'shift' the result of the reduction. Determine what state
that goes to, based on the state we popped back to and the rule
number reduced by. */
goto yynewstate;
-/*------------------------------------.
-| yyerrlab -- here on detecting error |
-`------------------------------------*/
+/*--------------------------------------.
+| yyerrlab -- here on detecting error. |
+`--------------------------------------*/
yyerrlab:
/* Make sure we have latest lookahead translation. See comments at
user semantic actions for why this is necessary. */
if (yyerrstatus == 3)
{
/* If just tried and failed to reuse lookahead token after an
- error, discard it. */
+ error, discard it. */
if (yychar <= YYEOF)
- {
- /* Return failure if at end of input. */
- if (yychar == YYEOF)
- YYABORT;
- }
+ {
+ /* Return failure if at end of input. */
+ if (yychar == YYEOF)
+ YYABORT;
+ }
else
- {
- yydestruct ("Error: discarding",
- yytoken, &yylval, &yylloc, scanner);
- yychar = YYEMPTY;
- }
+ {
+ yydestruct ("Error: discarding",
+ yytoken, &yylval, &yylloc, scanner);
+ yychar = YYEMPTY;
+ }
}
/* Else will try to reuse lookahead token after shifting the error
goto yyerrorlab;
yyerror_range[1] = yylsp[1-yylen];
- /* Do not reclaim the symbols of the rule which action triggered
+ /* Do not reclaim the symbols of the rule whose action triggered
this YYERROR. */
YYPOPSTACK (yylen);
yylen = 0;
| yyerrlab1 -- common code for both syntax error and YYERROR. |
`-------------------------------------------------------------*/
yyerrlab1:
- yyerrstatus = 3; /* Each real token shifted decrements this. */
+ yyerrstatus = 3; /* Each real token shifted decrements this. */
for (;;)
{
yyn = yypact[yystate];
if (!yypact_value_is_default (yyn))
- {
- yyn += YYTERROR;
- if (0 <= yyn && yyn <= YYLAST && yycheck[yyn] == YYTERROR)
- {
- yyn = yytable[yyn];
- if (0 < yyn)
- break;
- }
- }
+ {
+ yyn += YYTERROR;
+ if (0 <= yyn && yyn <= YYLAST && yycheck[yyn] == YYTERROR)
+ {
+ yyn = yytable[yyn];
+ if (0 < yyn)
+ break;
+ }
+ }
/* Pop the current state because it cannot handle the error token. */
if (yyssp == yyss)
- YYABORT;
+ YYABORT;
yyerror_range[1] = *yylsp;
yydestruct ("Error: popping",
- yystos[yystate], yyvsp, yylsp, scanner);
+ yystos[yystate], yyvsp, yylsp, scanner);
YYPOPSTACK (1);
yystate = *yyssp;
YY_STACK_PRINT (yyss, yyssp);
yydestruct ("Cleanup: discarding lookahead",
yytoken, &yylval, &yylloc, scanner);
}
- /* Do not reclaim the symbols of the rule which action triggered
+ /* Do not reclaim the symbols of the rule whose action triggered
this YYABORT or YYACCEPT. */
YYPOPSTACK (yylen);
YY_STACK_PRINT (yyss, yyssp);
while (yyssp != yyss)
{
yydestruct ("Cleanup: popping",
- yystos[*yyssp], yyvsp, yylsp, scanner);
+ yystos[*yyssp], yyvsp, yylsp, scanner);
YYPOPSTACK (1);
}
#ifndef yyoverflow
if (yymsg != yymsgbuf)
YYSTACK_FREE (yymsg);
#endif
- /* Make sure YYID is used. */
- return YYID (yyresult);
+ return yyresult;
}
-
-
-/* A Bison parser, made by GNU Bison 2.7.12-4996. */
+/* A Bison parser, made by GNU Bison 3.0.4. */
/* Bison interface for Yacc-like parsers in C
-
- Copyright (C) 1984, 1989-1990, 2000-2013 Free Software Foundation, Inc.
-
+
+ Copyright (C) 1984, 1989-1990, 2000-2015 Free Software Foundation, Inc.
+
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
-
+
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
-
+
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>. */
special exception, which will cause the skeleton and the resulting
Bison output files to be licensed under the GNU General Public
License without this special exception.
-
+
This special exception was added by the Free Software Foundation in
version 2.2 of Bison. */
#ifndef YY__GMX_SEL_YY_PARSER_H_INCLUDED
# define YY__GMX_SEL_YY_PARSER_H_INCLUDED
-/* Enabling traces. */
+/* Debug traces. */
#ifndef YYDEBUG
# define YYDEBUG 1
#endif
extern int _gmx_sel_yydebug;
#endif
/* "%code requires" blocks. */
-/* Line 2053 of yacc.c */
-#line 1 "parser.y"
+#line 1 "parser.y" /* yacc.c:1909 */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-
-/* Line 2053 of yacc.c */
-#line 76 "parser.y"
+#line 76 "parser.y" /* yacc.c:1909 */
#include "parsetree.h"
#include "selelem.h"
#define YYLTYPE ::gmx::SelectionLocation
+#line 87 "parser.h" /* yacc.c:1909 */
-/* Line 2053 of yacc.c */
-#line 92 "parser.h"
-
-/* Tokens. */
+/* Token type. */
#ifndef YYTOKENTYPE
# define YYTOKENTYPE
- /* Put the tokens into the symbol table, so that GDB and other debuggers
- know about them. */
- enum yytokentype {
- INVALID = 258,
- TOK_INT = 259,
- TOK_REAL = 260,
- STR = 261,
- IDENTIFIER = 262,
- CMD_SEP = 263,
- GROUP = 264,
- TO = 265,
- VARIABLE_NUMERIC = 266,
- VARIABLE_GROUP = 267,
- VARIABLE_POS = 268,
- KEYWORD_NUMERIC = 269,
- KEYWORD_STR = 270,
- KEYWORD_POS = 271,
- KEYWORD_GROUP = 272,
- METHOD_NUMERIC = 273,
- METHOD_GROUP = 274,
- METHOD_POS = 275,
- MODIFIER = 276,
- EMPTY_POSMOD = 277,
- PARAM = 278,
- END_OF_METHOD = 279,
- OF = 280,
- CMP_OP = 281,
- PARAM_REDUCT = 282,
- XOR = 283,
- OR = 284,
- AND = 285,
- NOT = 286,
- UNARY_NEG = 287,
- NUM_REDUCT = 288
- };
+ enum yytokentype
+ {
+ INVALID = 258,
+ TOK_INT = 259,
+ TOK_REAL = 260,
+ STR = 261,
+ IDENTIFIER = 262,
+ CMD_SEP = 263,
+ GROUP = 264,
+ TO = 265,
+ VARIABLE_NUMERIC = 266,
+ VARIABLE_GROUP = 267,
+ VARIABLE_POS = 268,
+ KEYWORD_NUMERIC = 269,
+ KEYWORD_STR = 270,
+ KEYWORD_POS = 271,
+ KEYWORD_GROUP = 272,
+ METHOD_NUMERIC = 273,
+ METHOD_GROUP = 274,
+ METHOD_POS = 275,
+ MODIFIER = 276,
+ EMPTY_POSMOD = 277,
+ PARAM = 278,
+ END_OF_METHOD = 279,
+ OF = 280,
+ CMP_OP = 281,
+ PARAM_REDUCT = 282,
+ OR = 283,
+ XOR = 284,
+ AND = 285,
+ NOT = 286,
+ UNARY_NEG = 287,
+ NUM_REDUCT = 288
+ };
#endif
-
+/* Value type. */
#if ! defined YYSTYPE && ! defined YYSTYPE_IS_DECLARED
-typedef union YYSTYPE
+
+union YYSTYPE
{
-/* Line 2053 of yacc.c */
-#line 83 "parser.y"
+#line 83 "parser.y" /* yacc.c:1909 */
int i;
real r;
gmx::SelectionParserParameter *param;
gmx::SelectionParserParameterListPointer *plist;
+#line 148 "parser.h" /* yacc.c:1909 */
+};
-/* Line 2053 of yacc.c */
-#line 156 "parser.h"
-} YYSTYPE;
+typedef union YYSTYPE YYSTYPE;
# define YYSTYPE_IS_TRIVIAL 1
-# define yystype YYSTYPE /* obsolescent; will be withdrawn */
# define YYSTYPE_IS_DECLARED 1
#endif
+/* Location type. */
#if ! defined YYLTYPE && ! defined YYLTYPE_IS_DECLARED
-typedef struct YYLTYPE
+typedef struct YYLTYPE YYLTYPE;
+struct YYLTYPE
{
int first_line;
int first_column;
int last_line;
int last_column;
-} YYLTYPE;
-# define yyltype YYLTYPE /* obsolescent; will be withdrawn */
+};
# define YYLTYPE_IS_DECLARED 1
# define YYLTYPE_IS_TRIVIAL 1
#endif
+
#ifndef YYPUSH_MORE_DEFINED
# define YYPUSH_MORE_DEFINED
enum { YYPUSH_MORE = 4 };
typedef struct _gmx_sel_yypstate _gmx_sel_yypstate;
-#if defined __STDC__ || defined __cplusplus
int _gmx_sel_yypush_parse (_gmx_sel_yypstate *ps, int pushed_char, YYSTYPE const *pushed_val, YYLTYPE *pushed_loc, void *scanner);
-#else
-int _gmx_sel_yypush_parse ();
-#endif
-#if defined __STDC__ || defined __cplusplus
_gmx_sel_yypstate * _gmx_sel_yypstate_new (void);
-#else
-_gmx_sel_yypstate * _gmx_sel_yypstate_new ();
-#endif
-#if defined __STDC__ || defined __cplusplus
void _gmx_sel_yypstate_delete (_gmx_sel_yypstate *ps);
-#else
-void _gmx_sel_yypstate_delete ();
-#endif
#endif /* !YY__GMX_SEL_YY_PARSER_H_INCLUDED */
--- parser.cpp 2014-11-03 06:56:28.000000000 +0200
+++ parser.cpp 2014-11-03 06:57:35.000000000 +0200
-@@ -470,7 +470,7 @@
+@@ -437,7 +437,7 @@
#if (! defined yyoverflow \
- && (! defined __cplusplus \
+ && (! defined __cplusplus || defined GMX_YYFORCE_C_STACK_EXTENSION \
- || (defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL \
- && defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
+ || (defined YYLTYPE_IS_TRIVIAL && YYLTYPE_IS_TRIVIAL \
+ && defined YYSTYPE_IS_TRIVIAL && YYSTYPE_IS_TRIVIAL)))
-@@ -1076,7 +1076,7 @@
- void *scanner;
- #endif
+@@ -955,7 +955,7 @@
+ static void
+ yy_symbol_value_print (FILE *yyoutput, int yytype, YYSTYPE const * const yyvaluep, YYLTYPE const * const yylocationp, void *scanner)
{
- FILE *yyo = yyoutput;
+ FILE *yyo gmx_unused = yyoutput;
YYUSE (yyo);
- if (!yyvaluep)
- return;
+ YYUSE (yylocationp);
+ YYUSE (scanner);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gmxpre.h"
}
%{
-#include "gromacs/utility/scoped_cptr.h"
+#include "gromacs/utility/unique_cptr.h"
#include "parser_internal.h"
-using gmx::scoped_guard_sfree;
+using gmx::sfree_guard;
using gmx::SelectionParserValue;
using gmx::SelectionParserValueList;
using gmx::SelectionParserValueListPointer;
%define api.push-pull push
%locations
-%name-prefix="_gmx_sel_yy"
+%name-prefix "_gmx_sel_yy"
%parse-param { void *scanner }
%%
{
BEGIN_ACTION;
set($$, _gmx_sel_append_selection(get($2), get($1), scanner));
- if (_gmx_sel_parser_should_finish(scanner))
+ if (_gmx_sel_parser_should_finish(scanner)) {
+ delete $$;
YYACCEPT;
+ }
END_ACTION_TOPLEVEL;
}
;
| string
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard($1);
+ const sfree_guard nameGuard($1);
SelectionTreeElementPointer s
= _gmx_sel_init_group_by_name($1, scanner);
SelectionTreeElementPointer p
| STR selection
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard($1);
+ const sfree_guard nameGuard($1);
set($$, _gmx_sel_init_selection($1, get($2), scanner));
END_ACTION;
}
| IDENTIFIER '=' sel_expr
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard($1);
+ const sfree_guard nameGuard($1);
set($$, _gmx_sel_assign_variable($1, get($3), scanner));
END_ACTION;
}
| IDENTIFIER '=' num_expr
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard($1);
+ const sfree_guard nameGuard($1);
set($$, _gmx_sel_assign_variable($1, get($3), scanner));
END_ACTION;
}
| IDENTIFIER '=' pos_expr
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard($1);
+ const sfree_guard nameGuard($1);
set($$, _gmx_sel_assign_variable($1, get($3), scanner));
END_ACTION;
}
sel_expr: num_expr CMP_OP num_expr
{
BEGIN_ACTION;
- scoped_guard_sfree opGuard($2);
+ const sfree_guard opGuard($2);
set($$, _gmx_sel_init_comparison(get($1), get($3), $2, scanner));
CHECK_SEL($$);
END_ACTION;
sel_expr: GROUP string
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard($2);
+ const sfree_guard nameGuard($2);
set($$, _gmx_sel_init_group_by_name($2, scanner));
END_ACTION;
}
sel_expr: pos_mod KEYWORD_GROUP
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, SelectionParserValueListPointer(), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_STR basic_value_list
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_keyword_strmatch($2, gmx::eStringMatchType_Auto, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_STR str_match_type basic_value_list
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_keyword_strmatch($2, $3, get($4), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_NUMERIC basic_value_list
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
sel_expr: pos_mod METHOD_GROUP method_params
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_method($2, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
num_expr: pos_mod KEYWORD_NUMERIC %prec NUM_REDUCT
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, SelectionParserValueListPointer(), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_NUMERIC OF pos_expr
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_keyword_of($2, get($4), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod METHOD_NUMERIC method_params
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_method($2, get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
| pos_mod KEYWORD_STR
{
BEGIN_ACTION;
- scoped_guard_sfree posmodGuard($1);
+ const sfree_guard posmodGuard($1);
set($$, _gmx_sel_init_keyword($2, SelectionParserValueListPointer(), $1, scanner));
CHECK_SEL($$);
END_ACTION;
pos_expr: KEYWORD_POS OF sel_expr %prec PARAM_REDUCT
{
BEGIN_ACTION;
- scoped_guard_sfree keywordGuard($1);
+ const sfree_guard keywordGuard($1);
set($$, _gmx_sel_init_position(get($3), $1, scanner));
CHECK_SEL($$);
END_ACTION;
PARAM value_list
{
BEGIN_ACTION;
- scoped_guard_sfree nameGuard($1);
+ const sfree_guard nameGuard($1);
set($$, SelectionParserParameter::create($1, get($2), @$));
END_ACTION;
}
| string %prec PARAM_REDUCT
{
BEGIN_ACTION;
- scoped_guard_sfree stringGuard($1);
+ const sfree_guard stringGuard($1);
set($$, SelectionParserValue::createString($1, @$));
END_ACTION;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
template <typename ValueType> static
ValueType get(ValueType *src)
{
- GMX_RELEASE_ASSERT(src != NULL, "Semantic value pointers should be non-NULL");
+ GMX_RELEASE_ASSERT(src != nullptr, "Semantic value pointers should be non-NULL");
const std::unique_ptr<ValueType> srcGuard(src);
return ValueType(std::move(*src));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bool canContinue = false;
gmx::GromacsException *gromacsException
= dynamic_cast<gmx::GromacsException *>(ex);
- if (gromacsException != NULL)
+ if (gromacsException != nullptr)
{
gromacsException->prependContext(formatCurrentErrorContext(scanner));
- canContinue = (dynamic_cast<gmx::UserInputError *>(ex) != NULL);
+ canContinue = (dynamic_cast<gmx::UserInputError *>(ex) != nullptr);
}
_gmx_sel_lexer_set_exception(scanner, std::current_exception());
return canContinue;
ex.prependContext(context);
gmx::TextWriter *statusWriter
= _gmx_sel_lexer_get_status_writer(scanner);
- if (statusWriter != NULL)
+ if (statusWriter != nullptr)
{
gmx::formatExceptionMessageToWriter(statusWriter, ex);
return true;
const char *name,
SelectionParserValueListPointer values,
const SelectionLocation &location)
- : name_(name != NULL ? name : ""), location_(location),
+ : name_(name != nullptr ? name : ""), location_(location),
values_(values ? std::move(values)
: SelectionParserValueListPointer(new SelectionParserValueList))
{
for (i = 0; i < nparams; ++i)
{
param[i].flags &= ~SPAR_SET;
- _gmx_selvalue_setstore(¶m[i].val, NULL);
+ _gmx_selvalue_setstore(¶m[i].val, nullptr);
if (param[i].flags & SPAR_VARNUM)
{
param[i].val.nr = -1;
}
/* Duplicate the enum value array if it is given statically */
- if ((param[i].flags & SPAR_ENUMVAL) && orgparam[i].val.u.ptr != NULL)
+ if ((param[i].flags & SPAR_ENUMVAL) && orgparam[i].val.u.ptr != nullptr)
{
int n;
/* Count the values */
n = 1;
- while (orgparam[i].val.u.s[n] != NULL)
+ while (orgparam[i].val.u.s[n] != nullptr)
{
++n;
}
(n+1)*sizeof(param[i].val.u.s[0]));
}
}
- mdata = NULL;
+ mdata = nullptr;
if (sel->u.expr.method->init_data)
{
mdata = sel->u.expr.method->init_data(nparams, param);
}
SelectionParserParameterList params;
params.push_back(
- SelectionParserParameter::createFromExpression(NULL, child));
+ SelectionParserParameter::createFromExpression(nullptr, child));
params.push_back(
- SelectionParserParameter::create(NULL, std::move(args), location));
+ SelectionParserParameter::create(nullptr, std::move(args), location));
_gmx_sel_parse_params(params, root->u.expr.method->nparams,
root->u.expr.method->param, root, scanner);
}
else
{
params->push_front(
- SelectionParserParameter::createFromExpression(NULL, sel));
+ SelectionParserParameter::createFromExpression(nullptr, sel));
root = modifier;
}
/* Process the parameters */
_gmx_selelem_set_kwpos_type(root.get(), type);
/* Create the parameters for the parameter parser. */
SelectionParserParameterList params;
- params.push_back(SelectionParserParameter::createFromExpression(NULL, expr));
+ params.push_back(SelectionParserParameter::createFromExpression(nullptr, expr));
/* Parse the parameters. */
_gmx_sel_parse_params(params, root->u.expr.method->nparams,
root->u.expr.method->param, root, scanner);
SEL_GROUPREF, _gmx_sel_lexer_get_current_location(scanner)));
_gmx_selelem_set_vtype(sel, GROUP_VALUE);
sel->setName(gmx::formatString("group %d", id));
- sel->u.gref.name = NULL;
+ sel->u.gref.name = nullptr;
sel->u.gref.id = id;
if (_gmx_sel_lexer_has_groups_set(scanner))
/* Print out some information if the parser is interactive */
gmx::TextWriter *statusWriter = _gmx_sel_lexer_get_status_writer(scanner);
- if (statusWriter != NULL)
+ if (statusWriter != nullptr)
{
const std::string message
= gmx::formatString("Selection '%s' parsed",
sc->varstrs[sc->nvars] = gmx_strdup(pselstr);
++sc->nvars;
gmx::TextWriter *statusWriter = _gmx_sel_lexer_get_status_writer(scanner);
- if (statusWriter != NULL)
+ if (statusWriter != nullptr)
{
const std::string message
= gmx::formatString("Variable '%s' parsed", pselstr);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Can be NULL if none of the calculations require topology data or if
* setTopology() has not been called.
*/
- t_topology *top_;
+ const gmx_mtop_t *top_;
//! Pointer to the first data structure.
gmx_ana_poscalc_t *first_;
//! Pointer to the last data structure.
"part_mol_com", "part_mol_cog",
"dyn_res_com", "dyn_res_cog",
"dyn_mol_com", "dyn_mol_cog",
- NULL,
+ nullptr,
};
/*! \brief
namespace gmx
{
+namespace
+{
+
+//! Helper function for determining required topology information.
+PositionCalculationCollection::RequiredTopologyInfo
+requiredTopologyInfo(e_poscalc_t type, int flags)
+{
+ if (type != POS_ATOM)
+ {
+ if ((flags & POS_MASS) || (flags & POS_FORCES))
+ {
+ return PositionCalculationCollection::RequiredTopologyInfo::TopologyAndMasses;
+ }
+ if (type == POS_RES || type == POS_MOL)
+ {
+ return PositionCalculationCollection::RequiredTopologyInfo::Topology;
+ }
+ }
+ return PositionCalculationCollection::RequiredTopologyInfo::None;
+}
+
+} // namespace
+
// static
void
PositionCalculationCollection::typeFromEnum(const char *post,
}
}
+// static
+PositionCalculationCollection::RequiredTopologyInfo
+PositionCalculationCollection::requiredTopologyInfoForType(const char *post,
+ bool forces)
+{
+ e_poscalc_t type;
+ int flags = (forces ? POS_FORCES : 0);
+ PositionCalculationCollection::typeFromEnum(post, &type, &flags);
+ return requiredTopologyInfo(type, flags);
+}
+
/********************************************************************
* PositionCalculationCollection::Impl
*/
PositionCalculationCollection::Impl::Impl()
- : top_(NULL), first_(NULL), last_(NULL), bInit_(false)
+ : top_(nullptr), first_(nullptr), last_(nullptr), bInit_(false)
{
}
{
// Loop backwards, because there can be internal references in that are
// correctly handled by this direction.
- while (last_ != NULL)
+ while (last_ != nullptr)
{
GMX_ASSERT(last_->refcount == 1,
"Dangling references to position calculations");
gmx_ana_poscalc_t *before)
{
GMX_RELEASE_ASSERT(pc->coll == this, "Inconsistent collections");
- if (before == NULL)
+ if (before == nullptr)
{
- pc->next = NULL;
+ pc->next = nullptr;
pc->prev = last_;
- if (last_ != NULL)
+ if (last_ != nullptr)
{
last_->next = pc;
}
}
before->prev = pc;
}
- if (pc->prev == NULL)
+ if (pc->prev == nullptr)
{
first_ = pc;
}
PositionCalculationCollection::Impl::removeCalculation(gmx_ana_poscalc_t *pc)
{
GMX_RELEASE_ASSERT(pc->coll == this, "Inconsistent collections");
- if (pc->prev != NULL)
+ if (pc->prev != nullptr)
{
pc->prev->next = pc->next;
}
{
first_ = pc->next;
}
- if (pc->next != NULL)
+ if (pc->next != nullptr)
{
pc->next->prev = pc->prev;
}
{
last_ = pc->prev;
}
- pc->prev = pc->next = NULL;
+ pc->prev = pc->next = nullptr;
}
gmx_ana_poscalc_t *
gmx_ana_poscalc_set_flags(pc, flags);
pc->refcount = 1;
pc->coll = this;
- insertCalculation(pc, NULL);
+ insertCalculation(pc, nullptr);
return pc;
}
}
void
-PositionCalculationCollection::setTopology(t_topology *top)
+PositionCalculationCollection::setTopology(const gmx_mtop_t *top)
{
impl_->top_ = top;
}
static void
set_poscalc_maxindex(gmx_ana_poscalc_t *pc, gmx_ana_index_t *g, bool bBase)
{
- t_topology *top = pc->coll->top_;
+ const gmx_mtop_t *top = pc->coll->top_;
gmx_ana_index_make_block(&pc->b, top, g, pc->itype, pc->flags & POS_COMPLWHOLE);
/* Set the type to POS_ATOM if the calculation in fact is such. */
if (pc->b.nr == pc->b.nra)
sfree(pc);
}
-/*!
- * \param[in] pc Position calculation data to query.
- * \returns true if \p pc requires topology for initialization and/or
- * evaluation, false otherwise.
- */
-bool
-gmx_ana_poscalc_requires_top(gmx_ana_poscalc_t *pc)
+gmx::PositionCalculationCollection::RequiredTopologyInfo
+gmx_ana_poscalc_required_topology_info(gmx_ana_poscalc_t *pc)
{
- if ((pc->flags & POS_MASS) || pc->type == POS_RES || pc->type == POS_MOL
- || ((pc->flags & POS_FORCES) && pc->type != POS_ATOM))
- {
- return true;
- }
- return false;
+ return gmx::requiredTopologyInfo(pc->type, pc->flags);
}
/*!
*/
void
gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc, gmx_ana_pos_t *p,
- gmx_ana_index_t *g, t_trxframe *fr, t_pbc *pbc)
+ gmx_ana_index_t *g, t_trxframe *fr, const t_pbc *pbc)
{
int i, bi, bj;
}
if (pc->sbase)
{
- gmx_ana_poscalc_update(pc->sbase, NULL, NULL, fr, pbc);
+ gmx_ana_poscalc_update(pc->sbase, nullptr, nullptr, fr, pbc);
}
if (!p)
{
}
}
gmx::ConstArrayRef<int> index = pc->coll->getFrameIndices(pc->b.nra, pc->b.a);
- const t_topology *top = pc->coll->top_;
+ const gmx_mtop_t *top = pc->coll->top_;
const bool bMass = pc->flags & POS_MASS;
switch (pc->type)
{
struct gmx_ana_index_t;
struct gmx_ana_pos_t;
+struct gmx_mtop_t;
struct t_pbc;
-struct t_topology;
struct t_trxframe;
namespace gmx
class PositionCalculationCollection
{
public:
+ //! Describes what topology information is needed for position calculation.
+ enum class RequiredTopologyInfo
+ {
+ None, //!< No topology is needed.
+ Topology, //!< Topology is needed (residue/molecule info).
+ TopologyAndMasses //!< Masses are needed.
+ };
+
/*! \brief
* Array of strings acceptable for position calculation type enum.
*
* \see typeEnumValues
*/
static void typeFromEnum(const char *post, e_poscalc_t *type, int *flags);
+ /*! \brief
+ * Returns what information is needed for position evaluation.
+ *
+ * \param[in] post Position type (see typeFromEnum()).
+ * \param[in] forces Whether forces are needed.
+ * \returns What topology information is required for initializing
+ * and/or evaluating the positions.
+ */
+ static RequiredTopologyInfo requiredTopologyInfoForType(const char *post, bool forces);
/*! \brief
* Creates a new position calculation collection object.
*
* Does not throw.
*/
- void setTopology(t_topology *top);
+ void setTopology(const gmx_mtop_t *top);
/*! \brief
* Prints information about calculations.
*
/** Frees the memory allocated for position calculation. */
void
gmx_ana_poscalc_free(gmx_ana_poscalc_t *pc);
-/** Returns true if the position calculation requires topology information. */
-bool
-gmx_ana_poscalc_requires_top(gmx_ana_poscalc_t *pc);
+/*! \brief
+ * Returns true if the position calculation requires topology information.
+ *
+ * \param[in] pc Position calculation data to query.
+ * \returns Which topology information \p pc requires for initialization
+ * and/or evaluation.
+ */
+gmx::PositionCalculationCollection::RequiredTopologyInfo
+gmx_ana_poscalc_required_topology_info(gmx_ana_poscalc_t *pc);
/** Updates a single COM/COG structure for a frame. */
void
gmx_ana_poscalc_update(gmx_ana_poscalc_t *pc,
gmx_ana_pos_t *p, gmx_ana_index_t *g,
- t_trxframe *fr, t_pbc *pbc);
+ t_trxframe *fr, const t_pbc *pbc);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx_ana_pos_t::gmx_ana_pos_t()
{
- x = NULL;
- v = NULL;
- f = NULL;
+ x = nullptr;
+ v = nullptr;
+ f = nullptr;
gmx_ana_indexmap_clear(&m);
nalloc_x = 0;
}
copy_rvec(x, pos->x[0]);
clear_rvec(pos->v[0]);
clear_rvec(pos->f[0]);
- gmx_ana_indexmap_init(&pos->m, NULL, NULL, INDEX_UNKNOWN);
+ gmx_ana_indexmap_init(&pos->m, nullptr, nullptr, INDEX_UNKNOWN);
}
/*!
// when we have return statements followed by break. Instead, we add breaks
// manually.
#define YY_BREAK
+
+#ifdef __INTEL_COMPILER
+// Ignore unused variables in generated code.
+#pragma warning(disable:593)
+#endif
#define YY_NO_UNISTD_H 1
-#line 577 "scanner.cpp"
+#line 582 "scanner.cpp"
#define INITIAL 0
#define matchof 1
}
{
-#line 99 "scanner.l"
+#line 104 "scanner.l"
}
-#line 875 "scanner.cpp"
+#line 880 "scanner.cpp"
while ( /*CONSTCOND*/1 ) /* loops until end-of-file is reached */
{
case 1:
YY_RULE_SETUP
-#line 132 "scanner.l"
+#line 137 "scanner.l"
break;
YY_BREAK
case 2:
YY_RULE_SETUP
-#line 133 "scanner.l"
+#line 138 "scanner.l"
{ yylval->i = strtol(yytext, NULL, 10); ADD_TOKEN; return TOK_INT; }
YY_BREAK
case 3:
YY_RULE_SETUP
-#line 134 "scanner.l"
+#line 139 "scanner.l"
{ yylval->r = strtod(yytext, NULL); ADD_TOKEN; return TOK_REAL; }
YY_BREAK
case 4:
YY_RULE_SETUP
-#line 135 "scanner.l"
+#line 140 "scanner.l"
{ yylval->str = gmx_strndup(yytext+1, yyleng-2); ADD_TOKEN; return STR; }
YY_BREAK
case 5:
/* rule 5 can match eol */
YY_RULE_SETUP
-#line 137 "scanner.l"
+#line 142 "scanner.l"
{ _gmx_sel_lexer_add_token(yylloc, " ", 1, state); break; }
YY_BREAK
case 6:
/* rule 6 can match eol */
YY_RULE_SETUP
-#line 138 "scanner.l"
+#line 143 "scanner.l"
{
if (yytext[0] == ';' || state->statusWriter != NULL)
{
}
YY_BREAK
case YY_STATE_EOF(cmdstart):
-#line 152 "scanner.l"
+#line 157 "scanner.l"
{ state->bCmdStart = true; yyterminate(); }
YY_BREAK
case YY_STATE_EOF(INITIAL):
case YY_STATE_EOF(matchof):
case YY_STATE_EOF(matchbool):
-#line 153 "scanner.l"
+#line 158 "scanner.l"
{ state->bCmdStart = true; return CMD_SEP; }
YY_BREAK
case 7:
YY_RULE_SETUP
-#line 156 "scanner.l"
+#line 161 "scanner.l"
{ ADD_TOKEN; yylval->i = 1; return TOK_INT; }
YY_BREAK
case 8:
YY_RULE_SETUP
-#line 157 "scanner.l"
+#line 162 "scanner.l"
{ ADD_TOKEN; yylval->i = 0; return TOK_INT; }
YY_BREAK
case 9:
YY_RULE_SETUP
-#line 159 "scanner.l"
+#line 164 "scanner.l"
{ ADD_TOKEN; return GROUP; }
YY_BREAK
case 10:
YY_RULE_SETUP
-#line 160 "scanner.l"
+#line 165 "scanner.l"
{ ADD_TOKEN; return TO; }
YY_BREAK
case 11:
YY_RULE_SETUP
-#line 161 "scanner.l"
+#line 166 "scanner.l"
{ ADD_TOKEN; BEGIN(0); return OF; }
YY_BREAK
case 12:
YY_RULE_SETUP
-#line 162 "scanner.l"
+#line 167 "scanner.l"
{ ADD_TOKEN; return AND; }
YY_BREAK
case 13:
YY_RULE_SETUP
-#line 163 "scanner.l"
+#line 168 "scanner.l"
{ ADD_TOKEN; return OR; }
YY_BREAK
case 14:
YY_RULE_SETUP
-#line 164 "scanner.l"
+#line 169 "scanner.l"
{ ADD_TOKEN; return XOR; }
YY_BREAK
case 15:
YY_RULE_SETUP
-#line 165 "scanner.l"
+#line 170 "scanner.l"
{ ADD_TOKEN; return NOT; }
YY_BREAK
case 16:
YY_RULE_SETUP
-#line 166 "scanner.l"
+#line 171 "scanner.l"
{ yylval->str = gmx_strndup(yytext, yyleng); ADD_TOKEN; return CMP_OP; }
YY_BREAK
case 17:
YY_RULE_SETUP
-#line 168 "scanner.l"
+#line 173 "scanner.l"
{ return _gmx_sel_lexer_process_identifier(yylval, yylloc, yytext, yyleng, state); }
YY_BREAK
case 18:
/* rule 18 can match eol */
YY_RULE_SETUP
-#line 170 "scanner.l"
+#line 175 "scanner.l"
{ _gmx_sel_lexer_add_token(yylloc, " ", 1, state); break; }
YY_BREAK
case 19:
YY_RULE_SETUP
-#line 171 "scanner.l"
+#line 176 "scanner.l"
{ yylval->str = gmx_strndup(yytext, yyleng); ADD_TOKEN; return STR; }
YY_BREAK
case 20:
YY_RULE_SETUP
-#line 172 "scanner.l"
+#line 177 "scanner.l"
{ ADD_TOKEN; return yytext[0]; }
YY_BREAK
case 21:
YY_RULE_SETUP
-#line 173 "scanner.l"
+#line 178 "scanner.l"
YY_FATAL_ERROR( "flex scanner jammed" );
YY_BREAK
-#line 1060 "scanner.cpp"
+#line 1065 "scanner.cpp"
case YY_END_OF_BUFFER:
{
#define YYTABLES_NAME "yytables"
-#line 173 "scanner.l"
+#line 178 "scanner.l"
// when we have return statements followed by break. Instead, we add breaks
// manually.
#define YY_BREAK
+
+#ifdef __INTEL_COMPILER
+// Ignore unused variables in generated code.
+#pragma warning(disable:593)
+#endif
%}
INTEGER [[:digit:]]+
#undef YY_DECL
#endif
-#line 173 "scanner.l"
+#line 178 "scanner.l"
#line 363 "scanner_flex.h"
#undef _gmx_sel_yyIN_HEADER
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (bBoolNo)
{
- GMX_RELEASE_ASSERT(param->name != NULL,
+ GMX_RELEASE_ASSERT(param->name != nullptr,
"bBoolNo should only be set for a parameters with a name");
snew(yylval->str, strlen(param->name) + 3);
yylval->str[0] = 'n';
}
else
{
- yylval->str = param->name ? gmx_strdup(param->name) : NULL;
+ yylval->str = param->name ? gmx_strdup(param->name) : nullptr;
}
return PARAM;
}
if (!bPosMod && method->type != POS_VALUE)
{
state->nextMethodSymbol = symbol;
- _gmx_sel_lexer_add_token(yylloc, NULL, 0, state);
+ _gmx_sel_lexer_add_token(yylloc, nullptr, 0, state);
return EMPTY_POSMOD;
}
_gmx_sel_lexer_add_token(yylloc, symbol->name().c_str(), -1, state);
{
/* Remove all methods from the stack */
state->msp = -1;
- if (method->param[1].name == NULL)
+ if (method->param[1].name == nullptr)
{
state->nextparam = &method->param[1];
}
}
else
{
- if (method->param[0].name == NULL)
+ if (method->param[0].name == nullptr)
{
state->nextparam = &method->param[0];
}
if (state->neom > 0)
{
--state->neom;
- _gmx_sel_lexer_add_token(yylloc, NULL, 0, state);
+ _gmx_sel_lexer_add_token(yylloc, nullptr, 0, state);
return END_OF_METHOD;
}
- state->nextparam = NULL;
+ state->nextparam = nullptr;
state->bBoolNo = false;
_gmx_sel_lexer_add_token(yylloc, param->name, -1, state);
return init_param_token(yylval, param, bBoolNo);
if (state->nextMethodSymbol)
{
const gmx::SelectionParserSymbol *symbol = state->nextMethodSymbol;
- state->nextMethodSymbol = NULL;
+ state->nextMethodSymbol = nullptr;
return init_method_token(yylval, yylloc, symbol, true, state);
}
return 0;
/* Check if the identifier matches with a parameter name */
if (state->msp >= 0)
{
- gmx_ana_selparam_t *param = NULL;
+ gmx_ana_selparam_t *param = nullptr;
bool bBoolNo = false;
int sp = state->msp;
while (!param && sp >= 0)
for (i = 0; i < state->mstack[sp]->nparams; ++i)
{
/* Skip NULL parameters and too long parameters */
- if (state->mstack[sp]->param[i].name == NULL
+ if (state->mstack[sp]->param[i].name == nullptr
|| strlen(state->mstack[sp]->param[i].name) > yyleng)
{
continue;
state->mstack_alloc = 20;
state->msp = -1;
state->neom = 0;
- state->nextparam = NULL;
- state->nextMethodSymbol = NULL;
+ state->nextparam = nullptr;
+ state->nextMethodSymbol = nullptr;
state->prev_pos_kw = 0;
state->bBoolNo = false;
state->bMatchOf = false;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/selection/nbsearch.h"
#include "gromacs/selection/position.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
*
* Does not throw if enough space has been reserved for the output vectors.
*/
-void computeMassesAndCharges(const t_topology *top, const gmx_ana_pos_t &pos,
+void computeMassesAndCharges(const gmx_mtop_t *top, const gmx_ana_pos_t &pos,
std::vector<real> *masses,
std::vector<real> *charges)
{
GMX_ASSERT(top != NULL, "Should not have been called with NULL topology");
masses->clear();
charges->clear();
+ int molb = 0;
for (int b = 0; b < pos.count(); ++b)
{
real mass = 0.0;
real charge = 0.0;
for (int i = pos.m.mapb.index[b]; i < pos.m.mapb.index[b+1]; ++i)
{
- const int index = pos.m.mapb.a[i];
- mass += top->atoms.atom[index].m;
- charge += top->atoms.atom[index].q;
+ const int index = pos.m.mapb.a[i];
+ const t_atom &atom = mtopGetAtomParameters(top, index, &molb);
+ mass += atom.m;
+ charge += atom.q;
}
masses->push_back(mass);
charges->push_back(charge);
}
void
-SelectionData::initializeMassesAndCharges(const t_topology *top)
+SelectionData::initializeMassesAndCharges(const gmx_mtop_t *top)
{
GMX_ASSERT(posMass_.empty() && posCharge_.empty(),
"Should not be called more than once");
posMass_.reserve(posCount());
posCharge_.reserve(posCount());
- if (top == NULL)
+ if (top == nullptr)
{
posMass_.resize(posCount(), 1.0);
posCharge_.resize(posCount(), 0.0);
void
-SelectionData::refreshMassesAndCharges(const t_topology *top)
+SelectionData::refreshMassesAndCharges(const gmx_mtop_t *top)
{
- if (top != NULL && isDynamic() && !hasFlag(efSelection_DynamicMask))
+ if (top != nullptr && isDynamic() && !hasFlag(efSelection_DynamicMask))
{
computeMassesAndCharges(top, rawPositions_, &posMass_, &posCharge_);
}
void
-SelectionData::restoreOriginalPositions(const t_topology *top)
+SelectionData::restoreOriginalPositions(const gmx_mtop_t *top)
{
if (isDynamic())
{
int
-Selection::initOriginalIdsToGroup(t_topology *top, e_index_t type)
+Selection::initOriginalIdsToGroup(const gmx_mtop_t *top, e_index_t type)
{
try
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/gmxassert.h"
-struct t_topology;
+struct gmx_mtop_t;
namespace gmx
{
*
* Strong exception safety guarantee.
*/
- void initializeMassesAndCharges(const t_topology *top);
+ void initializeMassesAndCharges(const gmx_mtop_t *top);
/*! \brief
* Updates masses and charges after dynamic selection has been
* evaluated.
*
* Called by SelectionEvaluator.
*/
- void refreshMassesAndCharges(const t_topology *top);
+ void refreshMassesAndCharges(const gmx_mtop_t *top);
/*! \brief
* Updates the covered fraction after a selection has been evaluated.
*
* \a rootElement_ object.
* Called by SelectionEvaluator::evaluateFinal().
*/
- void restoreOriginalPositions(const t_topology *top);
+ void restoreOriginalPositions(const gmx_mtop_t *top);
private:
//! Name of the selection.
* assigned results in undefined behavior.
* isValid() returns `false` for the selection until it is initialized.
*/
- Selection() : sel_(NULL) {}
+ Selection() : sel_(nullptr) {}
/*! \brief
* Creates a new selection object.
*
explicit Selection(internal::SelectionData *sel) : sel_(sel) {}
//! Returns whether the selection object is initialized.
- bool isValid() const { return sel_ != NULL; }
+ bool isValid() const { return sel_ != nullptr; }
//! Returns whether two selection objects wrap the same selection.
bool operator==(const Selection &other) const
return constArrayRefFromArray(data().rawPositions_.x, posCount());
}
//! Returns whether velocities are available for this selection.
- bool hasVelocities() const { return data().rawPositions_.v != NULL; }
+ bool hasVelocities() const { return data().rawPositions_.v != nullptr; }
/*! \brief
* Returns velocities for this selection as a continuous array.
*
return constArrayRefFromArray(data().rawPositions_.v, posCount());
}
//! Returns whether forces are available for this selection.
- bool hasForces() const { return sel_->rawPositions_.f != NULL; }
+ bool hasForces() const { return sel_->rawPositions_.f != nullptr; }
/*! \brief
* Returns forces for this selection as a continuous array.
*
* \see setOriginalId()
* \see SelectionPosition::mappedId()
*/
- int initOriginalIdsToGroup(t_topology *top, e_index_t type);
+ int initOriginalIdsToGroup(const gmx_mtop_t *top, e_index_t type);
/*! \brief
* Prints out one-line description of the selection.
ConstArrayRef<int> atomIndices() const
{
const int *atoms = sel_->rawPositions_.m.mapb.a;
- if (atoms == NULL)
+ if (atoms == nullptr)
{
return ConstArrayRef<int>();
}
#include "poscalc.h"
#include "selelem.h"
+struct gmx_mtop_t;
struct gmx_sel_mempool_t;
struct t_pbc;
-struct t_topology;
struct t_trxframe;
namespace gmx
typedef std::vector<SelectionDataPointer> SelectionDataList;
class SelectionParserSymbolTable;
+struct SelectionTopologyProperties;
} // namespace gmx
char **varstrs;
/** Topology for the collection. */
- t_topology *top;
+ const gmx_mtop_t *top;
/** Index group that contains all the atoms. */
gmx_ana_index_t gall;
/** Memory pool used for selection evaluation. */
void resolveExternalGroups(const gmx::SelectionTreeElementPointer &root,
ExceptionInitializer *errors);
+ //! Whether forces have been requested for some selection.
+ bool areForcesRequested() const;
+ /*! \brief
+ * Returns topology properties needed for a certain position type.
+ */
+ SelectionTopologyProperties
+ requiredTopologyPropertiesForPositionType(const std::string &post,
+ bool forces) const;
+
//! Internal data, used for interfacing with old C code.
gmx_ana_selcollection_t sc_;
//! Default reference position type for selections.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selhelp.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/exceptions.h"
*/
SelectionCollection::Impl::Impl()
- : debugLevel_(0), bExternalGroupsSet_(false), grps_(NULL)
+ : debugLevel_(0), bExternalGroupsSet_(false), grps_(nullptr)
{
sc_.nvars = 0;
- sc_.varstrs = NULL;
- sc_.top = NULL;
+ sc_.varstrs = nullptr;
+ sc_.top = nullptr;
gmx_ana_index_clear(&sc_.gall);
- sc_.mempool = NULL;
+ sc_.mempool = nullptr;
sc_.symtab.reset(new SelectionParserSymbolTable);
gmx_ana_index_clear(&requiredAtoms_);
gmx_ana_selmethod_register_defaults(sc_.symtab.get());
bool promptLine(TextInputStream *inputStream, TextWriter *statusWriter,
std::string *line)
{
- if (statusWriter != NULL)
+ if (statusWriter != nullptr)
{
statusWriter->writeString("> ");
}
while (endsWith(*line, "\\\n"))
{
line->resize(line->length() - 2);
- if (statusWriter != NULL)
+ if (statusWriter != nullptr)
{
statusWriter->writeString("... ");
}
{
line->resize(line->length() - 1);
}
- else if (statusWriter != NULL)
+ else if (statusWriter != nullptr)
{
statusWriter->writeLine();
}
gmx_ana_indexgrps_t *grps, size_t firstSelection,
int maxCount, const std::string &context, bool bFirst)
{
- if (grps != NULL)
+ if (grps != nullptr)
{
writer->writeLine("Available static index groups:");
gmx_ana_indexgrps_print(writer, grps, 0);
void printHelp(TextWriter *writer, gmx_ana_selcollection_t *sc,
const std::string &line)
{
- if (sc->rootHelp.get() == NULL)
+ if (sc->rootHelp.get() == nullptr)
{
sc->rootHelp = createSelectionHelpTopic();
}
if (bInteractive)
{
TextWriter *statusWriter = _gmx_sel_lexer_get_status_writer(scanner);
- if (statusWriter != NULL)
+ if (statusWriter != nullptr)
{
printCurrentStatus(statusWriter, sc, grps, oldCount, maxnr, context, true);
}
int status;
while (promptLine(inputStream, statusWriter, &line))
{
- if (statusWriter != NULL)
+ if (statusWriter != nullptr)
{
line = stripString(line);
if (line.empty())
}
{
YYLTYPE location;
- status = _gmx_sel_yypush_parse(parserState.get(), 0, NULL,
+ status = _gmx_sel_yypush_parse(parserState.get(), 0, nullptr,
&location, scanner);
}
// TODO: Remove added selections from the collection if parsing failed?
result.reserve(nr);
for (i = sc->sel.begin() + oldCount; i != sc->sel.end(); ++i)
{
- result.push_back(Selection(i->get()));
+ result.emplace_back(i->get());
}
return result;
}
}
}
+//! Checks whether the given topology properties are available.
+void checkTopologyProperties(const gmx_mtop_t *top,
+ const SelectionTopologyProperties &props)
+{
+ if (top == nullptr)
+ {
+ if (props.hasAny())
+ {
+ GMX_THROW(InconsistentInputError("Selection requires topology information, but none provided"));
+ }
+ return;
+ }
+ if (props.needsMasses && !gmx_mtop_has_masses(top))
+ {
+ GMX_THROW(InconsistentInputError("Selection requires mass information, but it is not available in the topology"));
+ }
+}
+
} // namespace
}
+bool SelectionCollection::Impl::areForcesRequested() const
+{
+ for (const auto &sel : sc_.sel)
+ {
+ if (sel->hasFlag(gmx::efSelection_EvaluateForces))
+ {
+ return true;
+ }
+ }
+ return false;
+}
+
+
+SelectionTopologyProperties
+SelectionCollection::Impl::requiredTopologyPropertiesForPositionType(
+ const std::string &post, bool forces) const
+{
+ SelectionTopologyProperties props;
+ if (!post.empty())
+ {
+ switch (PositionCalculationCollection::requiredTopologyInfoForType(post.c_str(), forces))
+ {
+ case PositionCalculationCollection::RequiredTopologyInfo::None:
+ break;
+ case PositionCalculationCollection::RequiredTopologyInfo::Topology:
+ props.merge(SelectionTopologyProperties::topology());
+ break;
+ case PositionCalculationCollection::RequiredTopologyInfo::TopologyAndMasses:
+ props.merge(SelectionTopologyProperties::masses());
+ break;
+ }
+ }
+ return props;
+}
+
+
/********************************************************************
* SelectionCollection
*/
void
SelectionCollection::setReferencePosType(const char *type)
{
- GMX_RELEASE_ASSERT(type != NULL, "Cannot assign NULL position type");
+ GMX_RELEASE_ASSERT(type != nullptr, "Cannot assign NULL position type");
// Check that the type is valid, throw if it is not.
e_poscalc_t dummytype;
int dummyflags;
void
SelectionCollection::setOutputPosType(const char *type)
{
- GMX_RELEASE_ASSERT(type != NULL, "Cannot assign NULL position type");
+ GMX_RELEASE_ASSERT(type != nullptr, "Cannot assign NULL position type");
// Check that the type is valid, throw if it is not.
e_poscalc_t dummytype;
int dummyflags;
void
-SelectionCollection::setTopology(t_topology *top, int natoms)
+SelectionCollection::setTopology(gmx_mtop_t *top, int natoms)
{
- GMX_RELEASE_ASSERT(natoms > 0 || top != NULL,
+ GMX_RELEASE_ASSERT(natoms > 0 || top != nullptr,
"The number of atoms must be given if there is no topology");
+ checkTopologyProperties(top, requiredTopologyProperties());
// Get the number of atoms from the topology if it is not given.
if (natoms <= 0)
{
- natoms = top->atoms.nr;
+ natoms = top->natoms;
}
if (impl_->bExternalGroupsSet_)
{
gmx_ana_selcollection_t *sc = &impl_->sc_;
// Do this first, as it allocates memory, while the others don't throw.
gmx_ana_index_init_simple(&sc->gall, natoms);
- sc->pcc.setTopology(top);
sc->top = top;
+ sc->pcc.setTopology(top);
}
void
SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t *grps)
{
- GMX_RELEASE_ASSERT(grps == NULL || !impl_->bExternalGroupsSet_,
+ GMX_RELEASE_ASSERT(grps == nullptr || !impl_->bExternalGroupsSet_,
"Can only set external groups once or clear them afterwards");
impl_->grps_ = grps;
impl_->bExternalGroupsSet_ = true;
}
}
-
-bool
-SelectionCollection::requiresTopology() const
+SelectionTopologyProperties
+SelectionCollection::requiredTopologyProperties() const
{
- e_poscalc_t type;
- int flags;
+ SelectionTopologyProperties props;
- if (!impl_->rpost_.empty())
- {
- flags = 0;
- // Should not throw, because has been checked earlier.
- PositionCalculationCollection::typeFromEnum(impl_->rpost_.c_str(),
- &type, &flags);
- if (type != POS_ATOM)
- {
- return true;
- }
- }
- if (!impl_->spost_.empty())
- {
- flags = 0;
- // Should not throw, because has been checked earlier.
- PositionCalculationCollection::typeFromEnum(impl_->spost_.c_str(),
- &type, &flags);
- if (type != POS_ATOM)
- {
- return true;
- }
- }
+ // These should not throw, because has been checked earlier.
+ props.merge(impl_->requiredTopologyPropertiesForPositionType(impl_->rpost_, false));
+ const bool forcesRequested = impl_->areForcesRequested();
+ props.merge(impl_->requiredTopologyPropertiesForPositionType(impl_->spost_,
+ forcesRequested));
SelectionTreeElementPointer sel = impl_->sc_.root;
- while (sel)
+ while (sel && !props.hasAll())
{
- if (_gmx_selelem_requires_top(*sel))
- {
- return true;
- }
+ props.merge(sel->requiredTopologyProperties());
sel = sel->next;
}
- return false;
+ return props;
}
const std::string &context)
{
return parseInteractive(count, &StandardInputStream::instance(),
- bInteractive ? &TextOutputFile::standardError() : NULL,
+ bInteractive ? &TextOutputFile::standardError() : nullptr,
context);
}
std::unique_ptr<TextWriter> initStatusWriter(TextOutputStream *statusStream)
{
std::unique_ptr<TextWriter> statusWriter;
- if (statusStream != NULL)
+ if (statusStream != nullptr)
{
statusWriter.reset(new TextWriter(statusStream));
statusWriter->wrapperSettings().setLineLength(78);
yyscan_t scanner;
TextInputFile file(filename);
// TODO: Exception-safe way of using the lexer.
- _gmx_sel_init_lexer(&scanner, &impl_->sc_, NULL, -1,
+ _gmx_sel_init_lexer(&scanner, &impl_->sc_, nullptr, -1,
impl_->bExternalGroupsSet_,
impl_->grps_);
_gmx_sel_set_lex_input_file(scanner, file.handle());
- return runParser(scanner, NULL, false, -1, std::string());
+ return runParser(scanner, nullptr, false, -1, std::string());
}
catch (GromacsException &ex)
{
{
yyscan_t scanner;
- _gmx_sel_init_lexer(&scanner, &impl_->sc_, NULL, -1,
+ _gmx_sel_init_lexer(&scanner, &impl_->sc_, nullptr, -1,
impl_->bExternalGroupsSet_,
impl_->grps_);
_gmx_sel_set_lex_input_str(scanner, str.c_str());
- return runParser(scanner, NULL, false, -1, std::string());
+ return runParser(scanner, nullptr, false, -1, std::string());
}
void
SelectionCollection::compile()
{
- if (impl_->sc_.top == NULL && requiresTopology())
- {
- GMX_THROW(InconsistentInputError("Selection requires topology information, but none provided"));
- }
+ checkTopologyProperties(impl_->sc_.top, requiredTopologyProperties());
if (!impl_->bExternalGroupsSet_)
{
- setIndexGroups(NULL);
+ setIndexGroups(nullptr);
}
if (impl_->debugLevel_ >= 1)
{
}
}
}
+ impl_->rpost_.clear();
+ impl_->spost_.clear();
}
void
SelectionCollection::evaluate(t_trxframe *fr, t_pbc *pbc)
{
+ checkTopologyProperties(impl_->sc_.top, requiredTopologyProperties());
if (fr->bIndex)
{
gmx_ana_index_t g;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/classhelpers.h"
struct gmx_ana_indexgrps_t;
+struct gmx_mtop_t;
struct t_pbc;
-struct t_topology;
struct t_trxframe;
namespace gmx
class SelectionEvaluator;
class TextInputStream;
class TextOutputStream;
+struct SelectionTopologyProperties;
/*! \brief
* Collection of selections.
void setDebugLevel(int debugLevel);
/*! \brief
- * Returns true if the collection requires topology information for
- * evaluation.
+ * Returns what topology information is required for evaluation.
*
- * \returns true if any selection in the collection requires topology
- * information.
+ * \returns What topology information is required for compiling and/or
+ * evaluating the selections in the collection.
*
* Before the parser functions have been called, the return value is
* based just on the position types set.
* After parser functions have been called, the return value also takes
* into account the selection keywords used.
+ * After the compiler has been called, the return value is final and
+ * also considers possible force evaluation requested for the
+ * selections.
*
* Does not throw.
*/
- bool requiresTopology() const;
+ SelectionTopologyProperties requiredTopologyProperties() const;
/*! \brief
* Returns true if the collection requires external index groups.
*
* Does not throw currently, but this is subject to change when more
* underlying code is converted to C++.
*/
- void setTopology(t_topology *top, int natoms);
+ void setTopology(gmx_mtop_t *top, int natoms);
/*! \brief
* Sets the external index groups to use for the selections.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
typedef FlagsTemplate<SelectionFlag> SelectionFlags;
//! \endcond
+/*! \brief
+ * Describes topology properties required for selection evaluation.
+ *
+ * See SelectionCollection::requiredTopologyProperties().
+ *
+ * \inpublicapi
+ * \ingroup module_selection
+ */
+struct SelectionTopologyProperties
+{
+ //! Returns a property object that requires generic topology info.
+ static SelectionTopologyProperties topology()
+ {
+ return SelectionTopologyProperties(true, false);
+ }
+ //! Returns a property object that requires atom masses.
+ static SelectionTopologyProperties masses()
+ {
+ return SelectionTopologyProperties(true, true);
+ }
+
+ //! Initializes properties that does not require anything.
+ SelectionTopologyProperties()
+ : needsTopology(false), needsMasses(false)
+ {
+ }
+ //! Initializes properties with the given flags.
+ SelectionTopologyProperties(bool needsTopology, bool needsMasses)
+ : needsTopology(needsTopology), needsMasses(needsMasses)
+ {
+ }
+
+ //! Combines flags from another properties object to this.
+ void merge(const SelectionTopologyProperties &other)
+ {
+ needsTopology = needsTopology || other.needsTopology;
+ needsMasses = needsMasses || other.needsMasses;
+ }
+ //! Whether all flags are `true` (for short-ciruiting logic).
+ bool hasAll() const { return needsTopology && needsMasses; }
+ //! Whether any flag is `true`.
+ bool hasAny() const { return needsTopology || needsMasses; }
+
+ //! Whether topology information is needed for selection evaluation.
+ bool needsTopology;
+ //! Whether atom masses are needed for selection evaluation.
+ bool needsMasses;
+};
+
}
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
virtual OptionInfo &optionInfo() { return info_; }
virtual std::string typeString() const { return "file"; }
virtual int valueCount() const { return 0; }
- virtual std::string formatValue(int /*i*/) const { return ""; }
+ virtual std::vector<Variant> defaultValues() const { return {}; }
+ virtual std::vector<std::string> defaultValuesAsStrings() const { return {}; }
+ virtual std::vector<Variant>
+ normalizeValues(const std::vector<Variant> &values) const { return values; }
private:
virtual void clearSet();
- virtual void convertValue(const std::string &value);
+ virtual void convertValue(const Variant &value);
virtual void processSet();
virtual void processAll() {}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
info_(this), manager_(*manager), defaultText_(settings.defaultText_),
selectionFlags_(settings.selectionFlags_)
{
- GMX_RELEASE_ASSERT(manager != NULL,
+ GMX_RELEASE_ASSERT(manager != nullptr,
"SelectionOptionManager must be added before SelectionOption");
GMX_RELEASE_ASSERT(!hasFlag(efOption_MultipleTimes),
"allowMultiple() is not supported for selection options");
}
+std::vector<Variant>
+SelectionOptionStorage::normalizeValues(const std::vector<Variant> & /*values*/) const
+{
+ GMX_THROW(NotImplementedError("Selection options not supported in this context"));
+}
+
+
void SelectionOptionStorage::addSelections(
const SelectionList &selections,
bool bFullValue)
}
-void SelectionOptionStorage::convertValue(const std::string &value)
+void SelectionOptionStorage::convertValue(const Variant &value)
{
- manager_.convertOptionValue(this, value, false);
+ manager_.convertOptionValue(this, value.cast<std::string>(), false);
}
void SelectionOptionStorage::processSetValues(ValueList *values)
void SelectionOptionStorage::setSelectionFlag(SelectionFlag flag, bool bSet)
{
- ValueList::iterator i;
- for (i = values().begin(); i != values().end(); ++i)
+ for (const Selection &value : values())
{
- if (flag == efSelection_OnlyStatic && bSet && i->isDynamic())
+ if (flag == efSelection_OnlyStatic && bSet && value.isDynamic())
{
MessageStringCollector errors;
errors.startContext("In option '" + name() + "'");
}
}
selectionFlags_.set(flag, bSet);
- for (i = values().begin(); i != values().end(); ++i)
+ for (Selection &value : values())
{
- i->data().setFlags(selectionFlags_);
+ value.data().setFlags(selectionFlags_);
}
}
| efOption_DontCheckMinimumCount),
info_(this), manager_(*manager), bValueParsed_(false)
{
- GMX_RELEASE_ASSERT(manager != NULL,
+ GMX_RELEASE_ASSERT(manager != nullptr,
"SelectionOptionManager must be added before SelectionFileOption");
}
bValueParsed_ = false;
}
-void SelectionFileOptionStorage::convertValue(const std::string &value)
+void SelectionFileOptionStorage::convertValue(const Variant &value)
{
if (bValueParsed_)
{
}
bValueParsed_ = true;
// TODO: Should we throw an InvalidInputError if the file does not exist?
- manager_.parseRequestedFromFile(value);
+ manager_.parseRequestedFromFile(value.cast<std::string>());
}
void SelectionFileOptionStorage::processSet()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/selection/selectioncollection.h"
#include "gromacs/selection/selectionfileoption.h"
#include "gromacs/selection/selectionoptionmanager.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/filestream.h"
namespace gmx
Impl(SelectionCollection *selections,
ITopologyProvider *topologyProvider)
: selections_(*selections), topologyProvider_(*topologyProvider),
- manager_(selections), grps_(NULL)
+ manager_(selections), grps_(nullptr)
{
}
~Impl()
{
- if (grps_ != NULL)
+ if (grps_ != nullptr)
{
gmx_ana_indexgrps_free(grps_);
}
" %s\n(with -n), but it was not used by any selection.\n",
ndxfile_.c_str());
}
- selections_.setIndexGroups(NULL);
+ selections_.setIndexGroups(nullptr);
return;
}
if (ndxfile_.empty())
{
- t_topology *top = topologyProvider_.getTopology(false);
- gmx_ana_indexgrps_init(&grps_, top, NULL);
+ gmx_mtop_t *top = topologyProvider_.getTopology(false);
+ gmx_ana_indexgrps_init(&grps_, top, nullptr);
}
else
{
- gmx_ana_indexgrps_init(&grps_, NULL, ndxfile_.c_str());
+ gmx_ana_indexgrps_init(&grps_, nullptr, ndxfile_.c_str());
}
selections_.setIndexGroups(grps_);
}
void doneIndexGroups()
{
- if (grps_ != NULL)
+ if (grps_ != nullptr)
{
- selections_.setIndexGroups(NULL);
+ selections_.setIndexGroups(nullptr);
gmx_ana_indexgrps_free(grps_);
- grps_ = NULL;
+ grps_ = nullptr;
}
}
void compileSelections()
{
- t_topology *top = topologyProvider_.getTopology(selections_.requiresTopology());
- int natoms = -1;
- if (top == NULL)
+ const bool topRequired = selections_.requiredTopologyProperties().needsTopology;
+ gmx_mtop_t *top = topologyProvider_.getTopology(topRequired);
+ int natoms = -1;
+ if (top == nullptr)
{
natoms = topologyProvider_.getAtomCount();
}
+ getMassesIfRequired(top);
selections_.setTopology(top, natoms);
selections_.compile();
+ // Situation may have changed after compilation.
+ getMassesIfRequired(top);
+ }
+
+ void getMassesIfRequired(gmx_mtop_t *top)
+ {
+ const bool massRequired = selections_.requiredTopologyProperties().needsMasses;
+ if (!massRequired)
+ {
+ return;
+ }
+ // TODO: There can be some corner cases that still hit this assert
+ // when the user has not provided the topology.
+ GMX_RELEASE_ASSERT(top != nullptr,
+ "Masses are required, but no topology is loaded");
+ for (int i = 0; i < top->nmoltype; ++i)
+ {
+ gmx_moltype_t &moltype = top->moltype[i];
+ if (!moltype.atoms.haveMass)
+ {
+ atomsSetMassesBasedOnNames(&moltype.atoms, TRUE);
+ if (!moltype.atoms.haveMass)
+ {
+ GMX_THROW(InconsistentInputError("Selections require mass information for evaluation, but it is not available in the input and could not be determined for all atoms based on atom names."));
+ }
+ }
+ }
}
SelectionCollection &selections_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/ioptionsbehavior.h"
#include "gromacs/utility/classhelpers.h"
-struct t_topology;
+struct gmx_mtop_t;
namespace gmx
{
* different values of \p required. Subsequent calls should just
* return the same topology that was loaded in the first call.
*/
- virtual t_topology *getTopology(bool required) = 0;
+ virtual gmx_mtop_t *getTopology(bool required) = 0;
/*! \brief
* Returns the number of atoms.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
SelectionOptionStorage &storage = **i;
if (storage.isRequired() && !storage.isSet())
{
- requests_.push_back(SelectionRequest(&storage));
+ requests_.emplace_back(&storage);
}
}
}
SelectionOptionManager::requestOptionDelayedParsing(
SelectionOptionStorage *storage)
{
- impl_->requests_.push_back(Impl::SelectionRequest(storage));
+ impl_->requests_.emplace_back(storage);
}
bool
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
virtual OptionInfo &optionInfo() { return info_; }
virtual std::string typeString() const { return "selection"; }
virtual std::string formatSingleValue(const Selection &value) const;
+ virtual std::vector<Variant>
+ normalizeValues(const std::vector<Variant> &values) const;
/*! \brief
* Adds selections to the storage.
void setSelectionFlag(SelectionFlag flag, bool bSet);
private:
- virtual void convertValue(const std::string &value);
+ virtual void convertValue(const Variant &value);
virtual void processSetValues(ValueList *values);
virtual void processAll();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/position.h"
+#include "gromacs/selection/selectionenums.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
const char *
_gmx_selelem_type_str(const gmx::SelectionTreeElement &sel)
{
- const char *p = NULL;
+ const char *p = nullptr;
switch (sel.type)
{
case SEL_CONST: p = "CONST"; break;
const char *
_gmx_sel_value_type_str(const gmx_ana_selvalue_t *val)
{
- const char *p = NULL;
+ const char *p = nullptr;
switch (val->type)
{
case NO_VALUE: p = "NONE"; break;
const char *
_gmx_selelem_boolean_type_str(const gmx::SelectionTreeElement &sel)
{
- const char *p = NULL;
+ const char *p = nullptr;
switch (sel.u.boolt)
{
case BOOL_NOT: p = "NOT"; break;
const SelectionLocation &location)
: location_(location)
{
+ // cppcheck-suppress useInitializationList
this->type = type;
this->flags = (type != SEL_ROOT) ? SEL_ALLOCVAL : 0;
if (type == SEL_BOOLEAN)
}
_gmx_selvalue_clear(&this->v);
std::memset(&this->u, 0, sizeof(this->u));
- this->evaluate = NULL;
- this->mempool = NULL;
- this->cdata = NULL;
+ this->evaluate = nullptr;
+ this->mempool = nullptr;
+ this->cdata = nullptr;
}
SelectionTreeElement::~SelectionTreeElement()
}
}
_gmx_selvalue_free(&v);
- if (type == SEL_SUBEXPRREF && u.param != NULL)
+ if (type == SEL_SUBEXPRREF && u.param != nullptr)
{
// TODO: This is now called from two different locations.
// It is likely that one of them is unnecessary, but that requires
if (type == SEL_EXPRESSION || type == SEL_MODIFIER)
{
_gmx_selelem_free_method(u.expr.method, u.expr.mdata);
- u.expr.mdata = NULL;
- u.expr.method = NULL;
+ u.expr.mdata = nullptr;
+ u.expr.method = nullptr;
/* Free position data */
delete u.expr.pos;
- u.expr.pos = NULL;
+ u.expr.pos = nullptr;
/* Free position calculation data */
if (u.expr.pc)
{
gmx_ana_poscalc_free(u.expr.pc);
- u.expr.pc = NULL;
+ u.expr.pc = nullptr;
}
}
if (type == SEL_ARITHMETIC)
{
sfree(u.arith.opstr);
- u.arith.opstr = NULL;
+ u.arith.opstr = nullptr;
}
if (type == SEL_SUBEXPR || type == SEL_ROOT
|| (type == SEL_CONST && v.type == GROUP_VALUE))
case INT_VALUE:
case REAL_VALUE:
_gmx_sel_mempool_free(mempool, v.u.ptr);
- _gmx_selvalue_setstore(&v, NULL);
+ _gmx_selvalue_setstore(&v, nullptr);
break;
case GROUP_VALUE:
}
}
+SelectionTopologyProperties
+SelectionTreeElement::requiredTopologyProperties() const
+{
+ SelectionTopologyProperties props;
+ if (type == SEL_EXPRESSION || type == SEL_MODIFIER)
+ {
+ bool needsTop = false;
+ bool needsMasses = false;
+ if (u.expr.method != nullptr)
+ {
+ needsTop = (u.expr.method->flags & SMETH_REQTOP);
+ needsMasses = (u.expr.method->flags & SMETH_REQMASS);
+ }
+ if (u.expr.pc != nullptr)
+ {
+ auto requiredTopologyInfo = gmx_ana_poscalc_required_topology_info(u.expr.pc);
+ needsTop = needsTop
+ || (requiredTopologyInfo != PositionCalculationCollection::RequiredTopologyInfo::None);
+ needsMasses = needsMasses
+ || (requiredTopologyInfo == PositionCalculationCollection::RequiredTopologyInfo::TopologyAndMasses);
+ }
+ if (needsTop)
+ {
+ props.merge(SelectionTopologyProperties::topology());
+ }
+ if (needsMasses)
+ {
+ props.merge(SelectionTopologyProperties::masses());
+ }
+ }
+ SelectionTreeElementPointer child = this->child;
+ while (child && !props.hasAll())
+ {
+ props.merge(child->requiredTopologyProperties());
+ child = child->next;
+ }
+ return props;
+}
+
void SelectionTreeElement::checkUnsortedAtoms(
bool bUnsortedAllowed, ExceptionInitializer *errors) const
{
{
GMX_RELEASE_ASSERT(type == SEL_GROUPREF,
"Should only be called for index group reference elements");
- if (grps == NULL)
+ if (grps == nullptr)
{
std::string message = formatString(
"Cannot match '%s', because index groups are not available.",
gmx_ana_index_t foundGroup;
std::string foundName;
- if (u.gref.name != NULL)
+ if (u.gref.name != nullptr)
{
if (!gmx_ana_indexgrps_find(&foundGroup, &foundName, grps, u.gref.name))
{
void
_gmx_selelem_free_param(gmx_ana_selparam_t *param)
{
- if (param->val.u.ptr != NULL)
+ if (param->val.u.ptr != nullptr)
{
if (param->val.type == GROUP_VALUE)
{
void
_gmx_selelem_free_method(gmx_ana_selmethod_t *method, void *mdata)
{
- sel_freefunc free_func = NULL;
+ sel_freefunc free_func = nullptr;
/* Save the pointer to the free function. */
if (method && method->free)
if ((sel.type == SEL_CONST && sel.v.type == GROUP_VALUE) || sel.type == SEL_ROOT)
{
const gmx_ana_index_t *g = sel.v.u.g;
- if (!g || g->isize == 0 || sel.evaluate != NULL)
+ if (!g || g->isize == 0 || sel.evaluate != nullptr)
{
g = &sel.u.cgrp;
}
fprintf(fp, "\n");
}
}
- else if (sel.type == SEL_SUBEXPRREF && sel.u.param != NULL)
+ else if (sel.type == SEL_SUBEXPRREF && sel.u.param != nullptr)
{
fprintf(fp, "%*c param", level*2+1, ' ');
- if (sel.u.param->name != NULL)
+ if (sel.u.param->name != nullptr)
{
fprintf(fp, " \"%s\"", sel.u.param->name);
}
child = child->next;
}
}
-
-/*!
- * \param[in] root Root of the subtree to query.
- * \returns true if \p root or any any of its elements require topology
- * information, false otherwise.
- */
-bool
-_gmx_selelem_requires_top(const gmx::SelectionTreeElement &root)
-{
- if (root.type == SEL_EXPRESSION || root.type == SEL_MODIFIER)
- {
- if (root.u.expr.method && (root.u.expr.method->flags & SMETH_REQTOP))
- {
- return true;
- }
- if (root.u.expr.pc && gmx_ana_poscalc_requires_top(root.u.expr.pc))
- {
- return true;
- }
- }
- gmx::SelectionTreeElementPointer child = root.child;
- while (child)
- {
- if (_gmx_selelem_requires_top(*child))
- {
- return true;
- }
- child = child->next;
- }
- return false;
-}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
class SelectionTreeElement;
+struct SelectionTopologyProperties;
//! Smart pointer type for selection tree element pointers.
typedef std::shared_ptr<SelectionTreeElement> SelectionTreeElementPointer;
* \param[in] name Name to set (can be NULL).
* \throws std::bad_alloc if out of memory.
*/
- void setName(const char *name) { name_ = (name != NULL ? name : ""); }
+ void setName(const char *name) { name_ = (name != nullptr ? name : ""); }
//! \copydoc setName(const char *)
void setName(const std::string &name) { name_ = name; }
/*! \brief
*/
void fillNameIfMissing(const char *selectionText);
+ /*! \brief
+ * Returns which topology properties the selection element subtree requires
+ * for evaluation.
+ *
+ * \returns List of topology properties required for evaluation.
+ */
+ SelectionTopologyProperties requiredTopologyProperties() const;
/*! \brief
* Checks that this element and its children do not contain unsupported
* elements with unsorted atoms.
_gmx_selelem_print_compiler_info(FILE *fp, const gmx::SelectionTreeElement &sel,
int level);
-/** Returns true if the selection element subtree requires topology information for evaluation. */
-bool
-_gmx_selelem_requires_top(const gmx::SelectionTreeElement &root);
-
/* In sm_insolidangle.c */
/** Returns true if the covered fraction of the selection can be calculated. */
bool
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const std::string &symname = symbol->name();
const gmx_ana_selmethod_t *method = symbol->methodValue();
methods_.push_back(std::make_pair(std::string(symname), method));
- if (method->help.nlhelp > 0 && method->help.help != NULL)
+ if (method->help.nlhelp > 0 && method->help.help != nullptr)
{
addSubTopic(HelpTopicPointer(
new KeywordDetailsHelpTopic(symname, *method)));
writeKeywordListStart(context, "Additional keywords that directly select atoms:");
printKeywordList(context, GROUP_VALUE, false);
- writeKeywordListEnd(context, NULL);
+ writeKeywordListEnd(context, nullptr);
writeKeywordListStart(context, "Keywords that directly evaluate to positions:");
printKeywordList(context, POS_VALUE, false);
writeKeywordListStart(context, "Additional keywords:");
printKeywordList(context, POS_VALUE, true);
printKeywordList(context, NO_VALUE, true);
- writeKeywordListEnd(context, NULL);
+ writeKeywordListEnd(context, nullptr);
writeKeywordSubTopics(context);
}
= (method.flags & SMETH_MODIFIER) != 0;
if (method.type == type && bModifiers == bIsModifier)
{
- const bool bHasHelp = (method.help.nlhelp > 0 && method.help.help != NULL);
+ const bool bHasHelp = (method.help.nlhelp > 0 && method.help.help != nullptr);
const bool bPrintHelpMark
= bHasHelp && context.outputFormat() == eHelpOutputFormat_Console;
file.writeString(formatString(" %c ", bPrintHelpMark ? '+' : ' '));
- if (method.help.syntax != NULL)
+ if (method.help.syntax != nullptr)
{
file.writeLine(method.help.syntax);
}
{
const gmx_ana_selmethod_t &method = *iter->second;
const bool bHasHelp
- = (method.help.nlhelp > 0 && method.help.help != NULL);
+ = (method.help.nlhelp > 0 && method.help.help != nullptr);
if (!bHasHelp || usedSymbols.count(iter->first) > 0)
{
continue;
}
std::string title;
- if (method.help.helpTitle != NULL)
+ if (method.help.helpTitle != nullptr)
{
title = method.help.helpTitle;
title.append(" - ");
}
const IHelpTopic *subTopic = findSubTopic(iter->first.c_str());
- GMX_RELEASE_ASSERT(subTopic != NULL, "Keyword subtopic no longer exists");
+ GMX_RELEASE_ASSERT(subTopic != nullptr, "Keyword subtopic no longer exists");
HelpWriterContext subContext(context);
subContext.enterSubSection(title);
subTopic->writeHelp(subContext);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/** Array of selection methods defined in the library. */
static const t_register_method smtable_def[] = {
- {NULL, &sm_cog},
- {NULL, &sm_com},
+ {nullptr, &sm_cog},
+ {nullptr, &sm_com},
- {NULL, &sm_all},
- {NULL, &sm_none},
- {NULL, &sm_atomnr},
- {NULL, &sm_resnr},
+ {nullptr, &sm_all},
+ {nullptr, &sm_none},
+ {nullptr, &sm_atomnr},
+ {nullptr, &sm_resnr},
{"resid", &sm_resnr},
- {NULL, &sm_resindex},
+ {nullptr, &sm_resindex},
{"residue", &sm_resindex},
- {NULL, &sm_molindex},
+ {nullptr, &sm_molindex},
{"mol", &sm_molindex},
{"molecule", &sm_molindex},
- {NULL, &sm_atomname},
+ {nullptr, &sm_atomname},
{"name", &sm_atomname},
- {NULL, &sm_pdbatomname},
+ {nullptr, &sm_pdbatomname},
{"pdbname", &sm_pdbatomname},
- {NULL, &sm_atomtype},
+ {nullptr, &sm_atomtype},
{"type", &sm_atomtype},
- {NULL, &sm_resname},
- {NULL, &sm_insertcode},
- {NULL, &sm_chain},
- {NULL, &sm_mass},
- {NULL, &sm_charge},
- {NULL, &sm_altloc},
- {NULL, &sm_occupancy},
- {NULL, &sm_betafactor},
+ {nullptr, &sm_resname},
+ {nullptr, &sm_insertcode},
+ {nullptr, &sm_chain},
+ {nullptr, &sm_mass},
+ {nullptr, &sm_charge},
+ {nullptr, &sm_altloc},
+ {nullptr, &sm_occupancy},
+ {nullptr, &sm_betafactor},
{"beta", &sm_betafactor},
- {NULL, &sm_x},
- {NULL, &sm_y},
- {NULL, &sm_z},
+ {nullptr, &sm_x},
+ {nullptr, &sm_y},
+ {nullptr, &sm_z},
- {NULL, &sm_distance},
+ {nullptr, &sm_distance},
{"dist", &sm_distance},
- {NULL, &sm_mindistance},
+ {nullptr, &sm_mindistance},
{"mindist", &sm_mindistance},
- {NULL, &sm_within},
- {NULL, &sm_insolidangle},
- {NULL, &sm_same},
+ {nullptr, &sm_within},
+ {nullptr, &sm_insolidangle},
+ {nullptr, &sm_same},
- {NULL, &sm_merge},
- {NULL, &sm_plus},
- {NULL, &sm_permute},
+ {nullptr, &sm_merge},
+ {nullptr, &sm_plus},
+ {nullptr, &sm_permute},
};
/*! \brief
for (i = 0; i < nparams; ++i)
{
/* Check that there is at most one NULL name, in the beginning */
- if (param[i].name == NULL && i > 0)
+ if (param[i].name == nullptr && i > 0)
{
report_error(fp, name, "error: NULL parameter should be the first one");
bOk = false;
/* Check for duplicates */
for (j = 0; j < i; ++j)
{
- if (param[j].name == NULL)
+ if (param[j].name == nullptr)
{
continue;
}
}
}
/* Check that the value pointer is NULL */
- if (param[i].nvalptr != NULL)
+ if (param[i].nvalptr != nullptr)
{
report_param_error(fp, name, param[i].name, "warning: nvalptr is set");
}
- if (param[i].val.u.ptr != NULL && !(param[i].flags & SPAR_ENUMVAL))
+ if (param[i].val.u.ptr != nullptr && !(param[i].flags & SPAR_ENUMVAL))
{
report_param_error(fp, name, param[i].name, "warning: value pointer is set");
}
/* Check that the name contains only valid characters */
- if (param[i].name == NULL)
+ if (param[i].name == nullptr)
{
continue;
}
if (method->pupdate && !(method->flags & SMETH_DYNAMIC))
{
report_error(fp, method->name, "warning: pupdate not used because the method is static");
- method->pupdate = NULL;
+ method->pupdate = nullptr;
}
}
/* Check that there is an evaluation function */
{
gmx_ana_selmethod_t *method = smtable_def[i].method;
- if (smtable_def[i].name == NULL)
+ if (smtable_def[i].name == nullptr)
{
rc = gmx_ana_selmethod_register(symtab, method->name, method);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* and the \p top pointer passed to the callbacks is guaranteed to be
* non-NULL. Should be set if the method requires topology information
* for evaluation.
+ * - \ref SMETH_REQMASS : If set, masses of atoms is always loaded
+ * and the \p top pointer passed to the callbacks is guaranteed to be
+ * non-NULL and have meaningful masses. Should be set if the method requires
+ * atom masses for evaluation. Implies \ref SMETH_REQTOP.
* - \ref SMETH_DYNAMIC : If set, the method can only be evaluated dynamically,
* i.e., it requires data from the trajectory frame.
* - \ref SMETH_MODIFIER : If set, the method is a selection modifier and
#include "selparam.h"
#include "selvalue.h"
-namespace gmx
-{
-class PositionCalculationCollection;
-class SelectionParserSymbolTable;
-} // namespace gmx
-
struct gmx_ana_index_t;
struct gmx_ana_pos_t;
struct gmx_ana_selcollection_t;
+struct gmx_mtop_t;
struct t_pbc;
-struct t_topology;
struct t_trxframe;
+namespace gmx
+{
+class PositionCalculationCollection;
+class SelectionParserSymbolTable;
+
+/*! \internal
+ * \brief
+ * Evaluation context for selection methods.
+ *
+ * This structure encapsulates common parameters passed to selection method
+ * evaluation functions. The contained values describe the evaluation context,
+ * i.e., the topology and the current trajectory frame.
+ *
+ * \ingroup module_selection
+ */
+struct SelMethodEvalContext
+{
+ //! Initializes the context with given values.
+ SelMethodEvalContext(const gmx_mtop_t *top, t_trxframe *fr, const t_pbc *pbc)
+ : top(top), fr(fr), pbc(pbc)
+ {
+ }
+
+ /*! \brief
+ * Topology.
+ *
+ * Can be NULL if \ref SMETH_REQTOP or \ref SMETH_REQMASS is not set for
+ * the method.
+ */
+ const gmx_mtop_t *top;
+ /*! \brief
+ * Trajectory frame.
+ *
+ * For static methods that are evaluated based on topology information
+ * alone, this is `NULL`.
+ */
+ t_trxframe *fr;
+ /*! \brief
+ * Periodic boundary condition information.
+ *
+ * Can be `NULL`, in which case PBC should not be used.
+ */
+ const t_pbc *pbc;
+};
+
+} // namespace gmx
+
/*! \name Selection method flags
* \anchor selmethod_flags
*/
/*@{*/
-/*! \brief
- * If set, the method requires topology information.
- */
+//! If set, the method requires topology information.
#define SMETH_REQTOP 1
-/*! \brief
- * If set, the method can only be evaluated dynamically.
- */
-#define SMETH_DYNAMIC 2
+//! If set, the method requires atom masses.
+#define SMETH_REQMASS 2
+//! If set, the method can only be evaluated dynamically.
+#define SMETH_DYNAMIC 4
/*! \brief
* If set, the method evaluates to a single value.
*
* The default is that the method evaluates to a value for each input atom.
* Cannot be combined with \ref SMETH_VARNUMVAL.
*/
-#define SMETH_SINGLEVAL 4
+#define SMETH_SINGLEVAL 8
/*! \brief
* If set, the method evaluates to an arbitrary number of values.
*
* The default is that the method evaluates to a value for each input atom.
* Cannot be combined with \ref SMETH_SINGLEVAL or with \ref GROUP_VALUE.
*/
-#define SMETH_VARNUMVAL 8
+#define SMETH_VARNUMVAL 16
/*! \brief
* If set, the method evaluates to single-character strings.
*
* Does initialization based on topology and/or parameter values.
*
* \param[in] top Topology structure
- * (can be NULL if \ref SMETH_REQTOP is not set).
+ * (can be NULL if \ref SMETH_REQTOP or \ref SMETH_REQMASS is not set).
* \param[in] npar Number of parameters in \p param.
* \param[in] param Pointer to (an initialized copy of) the method's
* \c gmx_ana_selmethod_t::param.
* This function may be called multiple times for the same method if the
* method takes parameters with \ref SPAR_ATOMVAL set.
*/
-typedef void (*sel_initfunc)(t_topology *top, int npar,
+typedef void (*sel_initfunc)(const gmx_mtop_t *top, int npar,
gmx_ana_selparam_t *param, void *data);
/*! \brief
* Initializes output data structure.
*
* \param[in] top Topology structure
- * (can be NULL if \ref SMETH_REQTOP is not set).
+ * (can be NULL if \ref SMETH_REQTOP or \ref SMETH_REQMASS is not set).
* \param[in,out] out Output data structure.
* \param[in] data Internal data structure from sel_datafunc().
* \returns 0 on success, an error code on error.
* This function may be called multiple times for the same method if the
* method takes parameters with \ref SPAR_ATOMVAL set.
*/
-typedef void (*sel_outinitfunc)(t_topology *top, gmx_ana_selvalue_t *out,
+typedef void (*sel_outinitfunc)(const gmx_mtop_t *top, gmx_ana_selvalue_t *out,
void *data);
/*! \brief
* Frees the internal data.
/*! \brief
* Initializes the evaluation for a new frame.
*
- * \param[in] top Topology structure
- * (can be NULL if \ref SMETH_REQTOP is not set).
- * \param[in] fr Current frame.
- * \param[in] pbc Initialized periodic boundary condition structure,
- * or NULL if PBC should not be used.
+ * \param[in] context Evaluation context.
* \param data Internal data structure from sel_datafunc().
* \returns 0 on success, a non-zero error code on failure.
*
* For static methods, it is called once, with \p fr and \p pbc set to
* NULL.
*/
-typedef void (*sel_framefunc)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- void *data);
+typedef void (*sel_framefunc)(const gmx::SelMethodEvalContext &context,
+ void *data);
/*! \brief
* Evaluates a selection method.
*
- * \param[in] top Topology structure
- * (can be NULL if \ref SMETH_REQTOP is not set).
- * \param[in] fr Current frame.
- * \param[in] pbc Initialized periodic boundary condition structure,
- * or NULL if PBC should not be used.
+ * \param[in] context Evaluation context.
* \param[in] g Index group for which the method should be evaluated.
* \param[out] out Output data structure.
* \param data Internal data structure from sel_datafunc().
* contains such an atom in case the \p fr has been loaded from a trajectory
* that only contains a subset of the system.
*/
-typedef void (*sel_updatefunc)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+typedef void (*sel_updatefunc)(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out,
void *data);
/*! \brief
* Evaluates a selection method using positions.
*
- * \param[in] top Topology structure
- * (can be NULL if \ref SMETH_REQTOP is not set).
- * \param[in] fr Current frame.
- * \param[in] pbc Initialized periodic boundary condition structure,
- * or NULL if PBC should not be used.
+ * \param[in] context Evaluation context.
* \param[in] pos Positions for which the method should be evaluated.
* \param[out] out Output data structure.
* \param data Internal data structure from sel_datafunc().
* contains such an atom in case the \p fr has been loaded from a trajectory
* that only contains a subset of the system.
*/
-typedef void (*sel_updatefunc_pos)(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+typedef void (*sel_updatefunc_pos)(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out,
void *data);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
_gmx_selvalue_clear(gmx_ana_selvalue_t *val)
{
val->nr = 0;
- val->u.ptr = NULL;
+ val->u.ptr = nullptr;
val->nalloc = 0;
}
}
}
// TODO: It causes a memory leak somewhere if val->nr is assigned zero here...
- val->u.ptr = NULL;
+ val->u.ptr = nullptr;
val->nalloc = 0;
}
srenew(val->u.s, n);
for (i = val->nalloc; i < n; ++i)
{
- val->u.s[i] = NULL;
+ val->u.s[i] = nullptr;
}
break;
case POS_VALUE:
- GMX_RELEASE_ASSERT(val->u.ptr == NULL,
+ GMX_RELEASE_ASSERT(val->u.ptr == nullptr,
"Reallocation of position values not supported");
val->u.p = new gmx_ana_pos_t[n];
break;
{
*ptr = val->u.ptr;
*nalloc = val->nalloc;
- val->u.ptr = NULL;
+ val->u.ptr = nullptr;
val->nalloc = 0;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/smalloc.h"
+#include "keywords.h"
#include "selmethod.h"
/** Defines the comparison operator for comparison expressions. */
* \returns 0 if the input data is valid, -1 on error.
*/
static void
-init_compare(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_compare(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Frees the memory allocated for comparison expression evaluation. */
static void
free_data_compare(void *data);
-/** Evaluates comparison expressions. */
+/*! \brief
+ * Evaluates comparison expressions.
+ *
+ * \param[in] context Not used.
+ * \param[in] g Evaluation index group.
+ * \param[out] out Output data structure (\p out->u.g is used).
+ * \param[in] data Should point to a \c t_methoddata_compare.
+ */
static void
-evaluate_compare(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_compare(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Parameters for comparison expression evaluation. */
static gmx_ana_selparam_t smparams_compare[] = {
- {"int1", {INT_VALUE, -1, {NULL}}, NULL,
+ {"int1", {INT_VALUE, -1, {nullptr}}, nullptr,
SPAR_OPTIONAL | SPAR_DYNAMIC | SPAR_ATOMVAL},
- {"real1", {REAL_VALUE, -1, {NULL}}, NULL,
+ {"real1", {REAL_VALUE, -1, {nullptr}}, nullptr,
SPAR_OPTIONAL | SPAR_DYNAMIC | SPAR_ATOMVAL},
- {"op", {STR_VALUE, 1, {NULL}}, NULL, 0},
- {"int2", {INT_VALUE, -1, {NULL}}, NULL,
+ {"op", {STR_VALUE, 1, {nullptr}}, nullptr, 0},
+ {"int2", {INT_VALUE, -1, {nullptr}}, nullptr,
SPAR_OPTIONAL | SPAR_DYNAMIC | SPAR_ATOMVAL},
- {"real2", {REAL_VALUE, -1, {NULL}}, NULL,
+ {"real2", {REAL_VALUE, -1, {nullptr}}, nullptr,
SPAR_OPTIONAL | SPAR_DYNAMIC | SPAR_ATOMVAL},
};
"cmp", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_compare), smparams_compare,
&init_data_compare,
- NULL,
+ nullptr,
&init_compare,
- NULL,
+ nullptr,
&free_data_compare,
- NULL,
+ nullptr,
&evaluate_compare,
- NULL,
- {NULL, NULL, 0, NULL},
+ nullptr,
+ {nullptr, nullptr, 0, nullptr},
};
/*! \brief
static const char *
comparison_type_str(e_comparison_t cmpt)
{
- const char *p = NULL;
+ const char *p = nullptr;
switch (cmpt)
{
case CMP_INVALID: p = "INVALID"; break;
else
{
n = 0;
- val->i = NULL;
- val->r = NULL;
+ val->i = nullptr;
+ val->r = nullptr;
}
return n;
}
}
static void
-init_compare(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_compare(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_compare *d = (t_methoddata_compare *)data;
int n1, n2;
/* Reverse the sides to place the integer on the right */
int flags;
d->left.r = d->right.r;
- d->right.r = NULL;
+ d->right.r = nullptr;
d->right.i = d->left.i;
- d->left.i = NULL;
+ d->left.i = nullptr;
flags = d->left.flags;
d->left.flags = d->right.flags;
d->right.flags = flags;
/*! \brief
* Implementation for evaluate_compare() for integer values.
*
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
* \param[in] g Evaluation index group.
* \param[out] out Output data structure (\p out->u.g is used).
* \param[in] data Should point to a \c t_methoddata_compare.
*/
static void
-evaluate_compare_int(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_compare_int(gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_compare *d = (t_methoddata_compare *)data;
int i, i1, i2, ig;
int a, b;
bool bAccept;
- GMX_UNUSED_VALUE(top);
- GMX_UNUSED_VALUE(fr);
- GMX_UNUSED_VALUE(pbc);
for (i = i1 = i2 = ig = 0; i < g->isize; ++i)
{
a = d->left.i[i1];
/*! \brief
* Implementation for evaluate_compare() if either value is non-integer.
*
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
* \param[in] g Evaluation index group.
* \param[out] out Output data structure (\p out->u.g is used).
* \param[in] data Should point to a \c t_methoddata_compare.
* This is ensured by the initialization method.
*/
static void
-evaluate_compare_real(t_topology *top, t_trxframe *fr, t_pbc *pbc,
- gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
+evaluate_compare_real(gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_compare *d = (t_methoddata_compare *)data;
int i, i1, i2, ig;
real a, b;
bool bAccept;
- GMX_UNUSED_VALUE(top);
- GMX_UNUSED_VALUE(fr);
- GMX_UNUSED_VALUE(pbc);
for (i = i1 = i2 = ig = 0; i < g->isize; ++i)
{
a = d->left.r[i1];
out->u.g->isize = ig;
}
-/*!
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
- * \param[in] g Evaluation index group.
- * \param[out] out Output data structure (\p out->u.g is used).
- * \param[in] data Should point to a \c t_methoddata_compare.
- */
static void
-evaluate_compare(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_compare(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_compare *d = (t_methoddata_compare *)data;
if (!((d->left.flags | d->right.flags) & CMP_REALVAL))
{
- evaluate_compare_int(top, fr, pbc, g, out, data);
+ evaluate_compare_int(g, out, data);
}
else
{
- evaluate_compare_real(top, fr, pbc, g, out, data);
+ evaluate_compare_real(g, out, data);
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Also checks that the cutoff is valid.
*/
static void
-init_common(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_common(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Frees the data allocated for a distance-based selection method. */
static void
free_data_common(void *data);
* Initializes the evaluation of a distance-based within selection method for a
* frame.
*
- * \param[in] top Not used.
- * \param[in] fr Current frame.
- * \param[in] pbc PBC structure.
- * \param data Should point to a \c t_methoddata_distance.
+ * \param[in] context Evaluation context.
+ * \param data Should point to a \c t_methoddata_distance.
* \returns 0 on success, a non-zero error code on error.
*
* Initializes the neighborhood search for the current frame.
*/
static void
-init_frame_common(t_topology *top, t_trxframe * fr, t_pbc *pbc, void *data);
+init_frame_common(const gmx::SelMethodEvalContext &context, void *data);
/** Evaluates the \p distance selection method. */
static void
-evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_distance(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p within selection method. */
static void
-evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_within(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
/** Parameters for the \p distance selection method. */
static gmx_ana_selparam_t smparams_distance[] = {
- {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
- {"from", {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
+ {"cutoff", {REAL_VALUE, 1, {nullptr}}, nullptr, SPAR_OPTIONAL},
+ {"from", {POS_VALUE, 1, {nullptr}}, nullptr, SPAR_DYNAMIC},
};
/** Parameters for the \p mindistance selection method. */
static gmx_ana_selparam_t smparams_mindistance[] = {
- {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
- {"from", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
+ {"cutoff", {REAL_VALUE, 1, {nullptr}}, nullptr, SPAR_OPTIONAL},
+ {"from", {POS_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
};
/** Parameters for the \p within selection method. */
static gmx_ana_selparam_t smparams_within[] = {
- {NULL, {REAL_VALUE, 1, {NULL}}, NULL, 0},
- {"of", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
+ {nullptr, {REAL_VALUE, 1, {nullptr}}, nullptr, 0},
+ {"of", {POS_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
};
//! Help title for distance selection methods.
"distance", REAL_VALUE, SMETH_DYNAMIC,
asize(smparams_distance), smparams_distance,
&init_data_common,
- NULL,
+ nullptr,
&init_common,
- NULL,
+ nullptr,
&free_data_common,
&init_frame_common,
- NULL,
+ nullptr,
&evaluate_distance,
{"distance from POS [cutoff REAL]",
helptitle_distance, asize(help_distance), help_distance},
"mindistance", REAL_VALUE, SMETH_DYNAMIC,
asize(smparams_mindistance), smparams_mindistance,
&init_data_common,
- NULL,
+ nullptr,
&init_common,
- NULL,
+ nullptr,
&free_data_common,
&init_frame_common,
- NULL,
+ nullptr,
&evaluate_distance,
{"mindistance from POS_EXPR [cutoff REAL]",
helptitle_distance, asize(help_distance), help_distance},
"within", GROUP_VALUE, SMETH_DYNAMIC,
asize(smparams_within), smparams_within,
&init_data_common,
- NULL,
+ nullptr,
&init_common,
- NULL,
+ nullptr,
&free_data_common,
&init_frame_common,
- NULL,
+ nullptr,
&evaluate_within,
{"within REAL of POS_EXPR",
helptitle_distance, asize(help_distance), help_distance},
}
static void
-init_common(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_common(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
}
static void
-init_frame_common(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc, void *data)
+init_frame_common(const gmx::SelMethodEvalContext &context, void *data)
{
t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
d->nbsearch.reset();
gmx::AnalysisNeighborhoodPositions pos(d->p.x, d->p.count());
- d->nbsearch = d->nb.initSearch(pbc, pos);
+ d->nbsearch = d->nb.initSearch(context.pbc, pos);
}
/*!
* and puts them in \p out->u.r.
*/
static void
-evaluate_distance(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_distance(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
* \c t_methoddata_distance::xref and puts them in \p out.g.
*/
static void
-evaluate_within(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_within(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_distance *d = static_cast<t_methoddata_distance *>(data);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* and allocates memory for the bins used during the evaluation.
*/
static void
-init_insolidangle(t_topology * top, int npar, gmx_ana_selparam_t * param, void *data);
+init_insolidangle(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t * param, void *data);
/** Frees the data allocated for the \p insolidangle selection method. */
static void
free_data_insolidangle(void *data);
/*! \brief
* Initializes the evaluation of the \p insolidangle selection method for a frame.
*
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc PBC structure.
- * \param data Should point to a \ref t_methoddata_insolidangle.
+ * \param[in] context Evaluation context.
+ * \param data Should point to a \ref t_methoddata_insolidangle.
*
* Creates a lookup structure that enables fast queries of whether a point
* is within the solid angle or not.
*/
static void
-init_frame_insolidangle(t_topology * top, t_trxframe * fr, t_pbc *pbc, void *data);
+init_frame_insolidangle(const gmx::SelMethodEvalContext &context, void *data);
/** Internal helper function for evaluate_insolidangle(). */
static bool
-accept_insolidangle(rvec x, t_pbc *pbc, void *data);
+accept_insolidangle(rvec x, const t_pbc *pbc, void *data);
/** Evaluates the \p insolidangle selection method. */
static void
-evaluate_insolidangle(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc,
+evaluate_insolidangle(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
/** Calculates the distance between unit vectors. */
/** Parameters for the \p insolidangle selection method. */
static gmx_ana_selparam_t smparams_insolidangle[] = {
- {"center", {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
- {"span", {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
- {"cutoff", {REAL_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
+ {"center", {POS_VALUE, 1, {nullptr}}, nullptr, SPAR_DYNAMIC},
+ {"span", {POS_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
+ {"cutoff", {REAL_VALUE, 1, {nullptr}}, nullptr, SPAR_OPTIONAL},
};
/** Help text for the \p insolidangle selection method. */
"insolidangle", GROUP_VALUE, SMETH_DYNAMIC,
asize(smparams_insolidangle), smparams_insolidangle,
&init_data_insolidangle,
- NULL,
+ nullptr,
&init_insolidangle,
- NULL,
+ nullptr,
&free_data_insolidangle,
&init_frame_insolidangle,
- NULL,
+ nullptr,
&evaluate_insolidangle,
{"insolidangle center POS span POS_EXPR [cutoff REAL]",
"Selecting atoms in a solid angle",
// cppcheck-suppress uninitdata
data->tbinsize = 0.0;
// cppcheck-suppress uninitdata
- data->tbin = NULL;
+ data->tbin = nullptr;
// cppcheck-suppress uninitdata
data->maxbins = 0;
// cppcheck-suppress uninitdata
data->nbins = 0;
// cppcheck-suppress uninitdata
- data->bin = NULL;
+ data->bin = nullptr;
param[0].val.u.p = &data->center;
param[1].val.u.p = &data->span;
}
static void
-init_insolidangle(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
+init_insolidangle(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
{
t_methoddata_insolidangle *surf = (t_methoddata_insolidangle *)data;
int i, c;
}
static void
-init_frame_insolidangle(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc, void *data)
+init_frame_insolidangle(const gmx::SelMethodEvalContext &context, void *data)
{
t_methoddata_insolidangle *d = (t_methoddata_insolidangle *)data;
rvec dx;
clear_surface_points(d);
for (i = 0; i < d->span.count(); ++i)
{
- if (pbc)
+ if (context.pbc)
{
- pbc_dx(pbc, d->span.x[i], d->center.x[0], dx);
+ pbc_dx(context.pbc, d->span.x[i], d->center.x[0], dx);
}
else
{
* \returns true if \p x is within the solid angle, false otherwise.
*/
static bool
-accept_insolidangle(rvec x, t_pbc *pbc, void *data)
+accept_insolidangle(rvec x, const t_pbc *pbc, void *data)
{
t_methoddata_insolidangle *d = (t_methoddata_insolidangle *)data;
rvec dx;
* \c t_methoddata_insolidangle::center, and stores the result in \p out->u.g.
*/
static void
-evaluate_insolidangle(t_topology * /* top */, t_trxframe * /* fr */, t_pbc *pbc,
+evaluate_insolidangle(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data)
{
out->u.g->isize = 0;
for (int b = 0; b < pos->count(); ++b)
{
- if (accept_insolidangle(pos->x[b], pbc, data))
+ if (accept_insolidangle(pos->x[b], context.pbc, data))
{
gmx_ana_pos_add_to_group(out->u.g, pos, b);
}
sfree(surf->bin[i].x);
}
surf->bin[i].n_alloc = 0;
- surf->bin[i].x = NULL;
+ surf->bin[i].x = nullptr;
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \param[in] data Should point to \ref t_methoddata_kwint.
*/
static void
-init_kwint(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_kwint(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/*! \brief
* Initializes data for real keyword evaluation.
*
* \returns 0 (the initialization always succeeds).
*/
static void
-init_kwreal(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_kwreal(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/*! \brief
* Initializes data for string keyword evaluation.
*
* \param[in] data Should point to t_methoddata_kwstr.
*/
static void
-init_kwstr(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_kwstr(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Frees the memory allocated for string keyword evaluation. */
static void
free_data_kwstr(void *data);
/** Evaluates integer selection keywords. */
static void
-evaluate_keyword_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_keyword_int(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates real selection keywords. */
static void
-evaluate_keyword_real(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_keyword_real(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates string selection keywords. */
static void
-evaluate_keyword_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_keyword_str(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/*! \internal \brief
/** Parameters for integer keyword evaluation. */
static gmx_ana_selparam_t smparams_keyword_int[] = {
- {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_ATOMVAL},
- {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_RANGES | SPAR_VARNUM},
+ {nullptr, {INT_VALUE, -1, {nullptr}}, nullptr, SPAR_ATOMVAL},
+ {nullptr, {INT_VALUE, -1, {nullptr}}, nullptr, SPAR_RANGES | SPAR_VARNUM},
};
/** Parameters for real keyword evaluation. */
static gmx_ana_selparam_t smparams_keyword_real[] = {
- {NULL, {REAL_VALUE, -1, {NULL}}, NULL, SPAR_ATOMVAL | SPAR_DYNAMIC},
- {NULL, {REAL_VALUE, -1, {NULL}}, NULL, SPAR_RANGES | SPAR_VARNUM},
+ {nullptr, {REAL_VALUE, -1, {nullptr}}, nullptr, SPAR_ATOMVAL | SPAR_DYNAMIC},
+ {nullptr, {REAL_VALUE, -1, {nullptr}}, nullptr, SPAR_RANGES | SPAR_VARNUM},
};
/** Parameters for string keyword evaluation. */
static gmx_ana_selparam_t smparams_keyword_str[] = {
- {NULL, {STR_VALUE, -1, {NULL}}, NULL, SPAR_ATOMVAL},
- {NULL, {STR_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
+ {nullptr, {STR_VALUE, -1, {nullptr}}, nullptr, SPAR_ATOMVAL},
+ {nullptr, {STR_VALUE, -1, {nullptr}}, nullptr, SPAR_VARNUM},
};
/** Selection method data for integer keyword evaluation. */
"kw_int", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_keyword_int), smparams_keyword_int,
&init_data_kwint,
- NULL,
+ nullptr,
&init_kwint,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_keyword_int,
- NULL,
- {NULL, NULL, 0, NULL},
+ nullptr,
+ {nullptr, nullptr, 0, nullptr},
};
/** Selection method data for real keyword evaluation. */
"kw_real", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_keyword_real), smparams_keyword_real,
&init_data_kwreal,
- NULL,
+ nullptr,
&init_kwreal,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_keyword_real,
- NULL,
- {NULL, NULL, 0, NULL},
+ nullptr,
+ {nullptr, nullptr, 0, nullptr},
};
/** Selection method data for string keyword evaluation. */
"kw_str", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_keyword_str), smparams_keyword_str,
&init_data_kwstr,
- NULL,
+ nullptr,
&init_kwstr,
- NULL,
+ nullptr,
&free_data_kwstr,
- NULL,
+ nullptr,
&evaluate_keyword_str,
- NULL,
- {NULL, NULL, 0, NULL},
+ nullptr,
+ {nullptr, nullptr, 0, nullptr},
};
/*! \brief
* Calls the initialization method of the wrapped keyword.
*/
static void
-init_kweval(t_topology *top, int npar, gmx_ana_selparam_t * param, void *data);
+init_kweval(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t * param, void *data);
/*! \brief
* Initializes output for keyword evaluation in an arbitrary group.
*
* \returns 0 for success.
*/
static void
-init_output_kweval(t_topology *top, gmx_ana_selvalue_t *out, void *data);
+init_output_kweval(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data);
/** Frees the data allocated for keyword evaluation in an arbitrary group. */
static void
free_data_kweval(void *data);
/** Initializes frame evaluation for keyword evaluation in an arbitrary group. */
static void
-init_frame_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
+init_frame_kweval(const gmx::SelMethodEvalContext &context, void *data);
/*! \brief
* Evaluates keywords in an arbitrary group.
*
* evaluation group.
*/
static void
-evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t *g,
+evaluate_kweval(const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g,
gmx_ana_selvalue_t *out, void *data);
/*! \brief
* Evaluates keywords in an arbitrary set of positions.
* evaluation positions.
*/
static void
-evaluate_kweval_pos(t_topology *top, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t *g,
+evaluate_kweval_pos(const gmx::SelMethodEvalContext &context, gmx_ana_index_t *g,
gmx_ana_selvalue_t *out, void *data);
/*! \internal \brief
/** Parameters for keyword evaluation in an arbitrary group. */
static gmx_ana_selparam_t smparams_kweval_group[] = {
- {NULL, {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
+ {nullptr, {GROUP_VALUE, 1, {nullptr}}, nullptr, SPAR_DYNAMIC},
};
/** Parameters for keyword evaluation from positions. */
static gmx_ana_selparam_t smparams_kweval_pos[] = {
- {NULL, {POS_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
+ {nullptr, {POS_VALUE, 1, {nullptr}}, nullptr, SPAR_DYNAMIC},
};
}
static void
-init_kwint(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_kwint(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_kwint *d = (t_methoddata_kwint *)data;
* Matching atoms are stored in \p out->u.g.
*/
static void
-evaluate_keyword_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_keyword_int(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kwint *d = (t_methoddata_kwint *)data;
}
static void
-init_kwreal(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_kwreal(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_kwreal *d = (t_methoddata_kwreal *)data;
* Matching atoms are stored in \p out->u.g.
*/
static void
-evaluate_keyword_real(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_keyword_real(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kwreal *d = (t_methoddata_kwreal *)data;
}
static void
-init_kwstr(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_kwstr(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_kwstr *d = static_cast<t_methoddata_kwstr *>(data);
for (int i = 0; i < n; ++i)
{
const char *s = param[1].val.u.s[i];
- d->matches.push_back(StringKeywordMatchItem(d->matchType, s));
+ d->matches.emplace_back(d->matchType, s);
}
}
* Matching atoms are stored in \p out->u.g.
*/
static void
-evaluate_keyword_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_keyword_str(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kwstr *d = static_cast<t_methoddata_kwstr *>(data);
********************************************************************/
static void
-init_kweval(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
+init_kweval(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
{
t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
- d->kwmethod->init(top, 0, NULL, d->kwmdata);
+ d->kwmethod->init(top, 0, nullptr, d->kwmdata);
}
static void
-init_output_kweval(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
+init_output_kweval(const gmx_mtop_t * /* top */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
}
/*!
- * \param[in] top Topology.
- * \param[in] fr Current frame.
- * \param[in] pbc PBC structure.
+ * \param[in] context Evaluation context.
* \param data Should point to a \ref t_methoddata_kweval.
- * \returns 0 on success, a non-zero error code on error.
- *
- * Creates a lookup structure that enables fast queries of whether a point
- * is within the solid angle or not.
*/
static void
-init_frame_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data)
+init_frame_kweval(const gmx::SelMethodEvalContext &context, void *data)
{
t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
- d->kwmethod->init_frame(top, fr, pbc, d->kwmdata);
+ d->kwmethod->init_frame(context, d->kwmdata);
}
static void
-evaluate_kweval(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_kweval(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
- d->kwmethod->update(top, fr, pbc, &d->g, out, d->kwmdata);
+ d->kwmethod->update(context, &d->g, out, d->kwmdata);
}
static void
-evaluate_kweval_pos(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_kweval_pos(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_kweval *d = static_cast<t_methoddata_kweval *>(data);
- d->kwmethod->pupdate(top, fr, pbc, &d->p, out, d->kwmdata);
+ d->kwmethod->pupdate(context, &d->p, out, d->kwmdata);
}
/*! \brief
sel->u.expr.method->name = data->kwmethod->name;
sel->u.expr.method->type = data->kwmethod->type;
sel->u.expr.method->flags = data->kwmethod->flags | SMETH_VARNUMVAL;
- sel->u.expr.method->init_data = NULL;
- sel->u.expr.method->set_poscoll = NULL;
- sel->u.expr.method->init = method->init ? &init_kweval : NULL;
+ sel->u.expr.method->init_data = nullptr;
+ sel->u.expr.method->set_poscoll = nullptr;
+ sel->u.expr.method->init = method->init ? &init_kweval : nullptr;
sel->u.expr.method->outinit = &init_output_kweval;
sel->u.expr.method->free = &free_data_kweval;
- sel->u.expr.method->init_frame = method->init_frame ? &init_frame_kweval : NULL;
+ sel->u.expr.method->init_frame = method->init_frame ? &init_frame_kweval : nullptr;
sel->u.expr.method->update = &evaluate_kweval;
- sel->u.expr.method->pupdate = NULL;
+ sel->u.expr.method->pupdate = nullptr;
sel->u.expr.method->nparams = asize(smparams_kweval_group);
sel->u.expr.method->param = smparams_kweval_group;
_gmx_selelem_init_method_params(sel, scanner);
void *scanner)
{
if ((method->flags & (SMETH_SINGLEVAL | SMETH_VARNUMVAL))
- || method->outinit || method->pupdate == NULL)
+ || method->outinit || method->pupdate == nullptr)
{
std::string message
= gmx::formatString("Keyword '%s' cannot be evaluated in this context",
sel->u.expr.method->name = data->kwmethod->name;
sel->u.expr.method->type = data->kwmethod->type;
sel->u.expr.method->flags = data->kwmethod->flags | SMETH_SINGLEVAL;
- sel->u.expr.method->init_data = NULL;
- sel->u.expr.method->set_poscoll = NULL;
- sel->u.expr.method->init = method->init ? &init_kweval : NULL;
- sel->u.expr.method->outinit = NULL;
+ sel->u.expr.method->init_data = nullptr;
+ sel->u.expr.method->set_poscoll = nullptr;
+ sel->u.expr.method->init = method->init ? &init_kweval : nullptr;
+ sel->u.expr.method->outinit = nullptr;
sel->u.expr.method->free = &free_data_kweval;
- sel->u.expr.method->init_frame = method->init_frame ? &init_frame_kweval : NULL;
+ sel->u.expr.method->init_frame = method->init_frame ? &init_frame_kweval : nullptr;
sel->u.expr.method->update = &evaluate_kweval_pos;
- sel->u.expr.method->pupdate = NULL;
+ sel->u.expr.method->pupdate = nullptr;
sel->u.expr.method->nparams = asize(smparams_kweval_pos);
sel->u.expr.method->param = smparams_kweval_pos;
_gmx_selelem_init_method_params(sel, scanner);
{
gmx::SelectionParserParameterList params;
params.push_back(
- gmx::SelectionParserParameter::createFromExpression(NULL, child));
+ gmx::SelectionParserParameter::createFromExpression(nullptr, child));
if (child->v.type == GROUP_VALUE)
{
return init_evaluator_group(method, params, scanner);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \returns 0 if everything is successful, -1 on error.
*/
static void
-init_merge(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_merge(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Initializes output for the \p merge selection modifier. */
static void
-init_output_merge(t_topology *top, gmx_ana_selvalue_t *out, void *data);
+init_output_merge(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data);
/** Initializes output for the \p plus selection modifier. */
static void
-init_output_plus(t_topology *top, gmx_ana_selvalue_t *out, void *data);
+init_output_plus(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data);
/** Frees the memory allocated for the merging selection modifiers. */
static void
free_data_merge(void *data);
/*! \brief
* Evaluates the \p merge selection modifier.
*
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
+ * \param[in] context Not used.
* \param[in] p Positions to merge (should point to \p data->p1).
* \param[out] out Output data structure (\p out->u.p is used).
* \param[in] data Should point to a \p t_methoddata_merge.
*/
static void
-evaluate_merge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_merge(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t * p, gmx_ana_selvalue_t *out, void *data);
/*! \brief
* Evaluates the \p plus selection modifier.
*
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
+ * \param[in] context Not used.
* \param[in] p Positions to merge (should point to \p data->p1).
* \param[out] out Output data structure (\p out->u.p is used).
* \param[in] data Should point to a \p t_methoddata_merge.
*/
static void
-evaluate_plus(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_plus(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t * p, gmx_ana_selvalue_t *out, void *data);
/** Parameters for the merging selection modifiers. */
static gmx_ana_selparam_t smparams_merge[] = {
- {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
- {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
- {"stride", {INT_VALUE, 1, {NULL}}, NULL, SPAR_OPTIONAL},
+ {nullptr, {POS_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
+ {nullptr, {POS_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
+ {"stride", {INT_VALUE, 1, {nullptr}}, nullptr, SPAR_OPTIONAL},
};
//! Help title for the merging selection modifiers.
"merge", POS_VALUE, SMETH_MODIFIER,
asize(smparams_merge), smparams_merge,
&init_data_merge,
- NULL,
+ nullptr,
&init_merge,
&init_output_merge,
&free_data_merge,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
&evaluate_merge,
{"merge POSEXPR", helptitle_merge, asize(help_merge), help_merge},
};
"plus", POS_VALUE, SMETH_MODIFIER,
asize(smparams_merge)-1, smparams_merge,
&init_data_merge,
- NULL,
+ nullptr,
&init_merge,
&init_output_plus,
&free_data_merge,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
&evaluate_plus,
{"plus POSEXPR", helptitle_merge, asize(help_merge), help_merge},
};
}
static void
-init_merge(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
+init_merge(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t * /* param */, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
* \param[in,out] data Should point to \c t_methoddata_merge.
*/
static void
-init_output_common(t_topology *top, gmx_ana_selvalue_t *out, void *data)
+init_output_common(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
}
gmx_ana_pos_reserve_for_append(out->u.p, d->p1.count() + d->p2.count(),
d->p1.m.b.nra + d->p2.m.b.nra,
- d->p1.v != NULL, d->p1.f != NULL);
+ d->p1.v != nullptr, d->p1.f != nullptr);
gmx_ana_pos_empty_init(out->u.p);
}
* \param[in,out] data Should point to \c t_methoddata_merge.
*/
static void
-init_output_merge(t_topology *top, gmx_ana_selvalue_t *out, void *data)
+init_output_merge(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
int i, j;
* \param[in,out] data Should point to \c t_methoddata_merge.
*/
static void
-init_output_plus(t_topology *top, gmx_ana_selvalue_t *out, void *data)
+init_output_plus(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
int i;
}
static void
-evaluate_merge(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_merge(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t * /* p */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
}
static void
-evaluate_plus(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_plus(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t * /* p */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_merge *d = (t_methoddata_merge *)data;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \returns 0 if the input permutation is valid, -1 on error.
*/
static void
-init_permute(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_permute(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/*! \brief
* Initializes output for the \p permute selection modifier.
*
* \param[in,out] data Should point to \c t_methoddata_permute.
*/
static void
-init_output_permute(t_topology *top, gmx_ana_selvalue_t *out, void *data);
+init_output_permute(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data);
/** Frees the memory allocated for the \p permute selection modifier. */
static void
free_data_permute(void *data);
-static void
/*! \brief
* Evaluates the \p permute selection modifier.
*
- * \param[in] top Not used.
- * \param[in] fr Not used.
- * \param[in] pbc Not used.
+ * \param[in] context Not used.
* \param[in] p Positions to permute (should point to \p data->p).
* \param[out] out Output data structure (\p out->u.p is used).
* \param[in] data Should point to a \p t_methoddata_permute.
- * \returns 0 if \p p could be permuted, -1 on error.
*
- * Returns -1 if the size of \p p is not divisible by the number of
+ * Throws if the size of \p p is not divisible by the number of
* elements in the permutation.
*/
-evaluate_permute(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+static void
+evaluate_permute(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t *p, gmx_ana_selvalue_t *out, void *data);
/** Parameters for the \p permute selection modifier. */
static gmx_ana_selparam_t smparams_permute[] = {
- {NULL, {POS_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
- {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_VARNUM},
+ {nullptr, {POS_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
+ {nullptr, {INT_VALUE, -1, {nullptr}}, nullptr, SPAR_VARNUM},
};
/** Help text for the \p permute selection modifier. */
"permute", POS_VALUE, SMETH_MODIFIER,
asize(smparams_permute), smparams_permute,
&init_data_permute,
- NULL,
+ nullptr,
&init_permute,
&init_output_permute,
&free_data_permute,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
&evaluate_permute,
{"POSEXPR permute P1 ... PN",
"Permuting selections", asize(help_permute), help_permute},
{
t_methoddata_permute *data = new t_methoddata_permute();
data->n = 0;
- data->perm = NULL;
- data->rperm = NULL;
+ data->perm = nullptr;
+ data->rperm = nullptr;
param[0].val.u.p = &data->p;
return data;
}
static void
-init_permute(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_permute(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
int i;
}
static void
-init_output_permute(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
+init_output_permute(const gmx_mtop_t * /* top */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
int i, j, b;
out->u.p->m.type = d->p.m.type;
gmx_ana_pos_reserve_for_append(out->u.p, d->p.count(), d->p.m.b.nra,
- d->p.v != NULL, d->p.f != NULL);
+ d->p.v != nullptr, d->p.f != nullptr);
gmx_ana_pos_empty_init(out->u.p);
for (i = 0; i < d->p.count(); i += d->n)
{
}
static void
-evaluate_permute(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_permute(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t * /*p*/, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_permute *d = (t_methoddata_permute *)data;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* externally using _gmx_selelem_set_kwpos_type().
*/
static void
-init_kwpos(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_kwpos(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/*! \brief
* Initializes the \p cog selection method.
*
* \returns 0 on success, a non-zero error code on error.
*/
static void
-init_cog(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_cog(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/*! \brief
* Initializes the \p cog selection method.
*
* \returns 0 on success, a non-zero error code on error.
*/
static void
-init_com(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_com(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/*! \brief
* Initializes output for position evaluation selection methods.
*
* \returns 0 for success.
*/
static void
-init_output_pos(t_topology *top, gmx_ana_selvalue_t *out, void *data);
+init_output_pos(const gmx_mtop_t *top, gmx_ana_selvalue_t *out, void *data);
/** Frees the data allocated for position evaluation selection methods. */
static void
free_data_pos(void *data);
/** Evaluates position evaluation selection methods. */
static void
-evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc, gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
+evaluate_pos(const gmx::SelMethodEvalContext &context,
+ gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data);
/** Parameters for position keyword evaluation. */
static gmx_ana_selparam_t smparams_keyword_pos[] = {
- {NULL, {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
+ {nullptr, {GROUP_VALUE, 1, {nullptr}}, nullptr, SPAR_DYNAMIC},
};
/** Parameters for the \p cog and \p com selection methods. */
static gmx_ana_selparam_t smparams_com[] = {
- {"of", {GROUP_VALUE, 1, {NULL}}, NULL, SPAR_DYNAMIC},
- {"pbc", {NO_VALUE, 0, {NULL}}, NULL, 0},
+ {"of", {GROUP_VALUE, 1, {nullptr}}, nullptr, SPAR_DYNAMIC},
+ {"pbc", {NO_VALUE, 0, {nullptr}}, nullptr, 0},
};
/** Selection method data for position keyword evaluation. */
&init_kwpos,
&init_output_pos,
&free_data_pos,
- NULL,
+ nullptr,
&evaluate_pos,
- NULL,
- {NULL, NULL, 0, NULL},
+ nullptr,
+ {nullptr, nullptr, 0, nullptr},
};
/** Selection method data for the \p cog method. */
&init_cog,
&init_output_pos,
&free_data_pos,
- NULL,
+ nullptr,
&evaluate_pos,
- NULL,
- {"cog of ATOM_EXPR [pbc]", NULL, 0, NULL},
+ nullptr,
+ {"cog of ATOM_EXPR [pbc]", nullptr, 0, nullptr},
};
/** Selection method data for the \p com method. */
gmx_ana_selmethod_t sm_com = {
- "com", POS_VALUE, SMETH_REQTOP | SMETH_DYNAMIC | SMETH_SINGLEVAL,
+ "com", POS_VALUE, SMETH_REQMASS | SMETH_DYNAMIC | SMETH_SINGLEVAL,
asize(smparams_com), smparams_com,
&init_data_pos,
&set_poscoll_pos,
&init_com,
&init_output_pos,
&free_data_pos,
- NULL,
+ nullptr,
&evaluate_pos,
- NULL,
- {"com of ATOM_EXPR [pbc]", NULL, 0, NULL},
+ nullptr,
+ {"com of ATOM_EXPR [pbc]", nullptr, 0, nullptr},
};
/*!
{
param[1].val.u.b = &data->bPBC;
}
- data->pc = NULL;
+ data->pc = nullptr;
data->bPBC = false;
- data->type = NULL;
+ data->type = nullptr;
data->flags = -1;
return data;
}
}
t_methoddata_pos *d = static_cast<t_methoddata_pos *>(sel.u.expr.mdata);
- return d->type == NULL;
+ return d->type == nullptr;
+}
+
+/*! \brief
+ * Updates selection method flags about required topology information.
+ *
+ * Sets the flags to require topology and/or masses if the position calculation
+ * requires them.
+ */
+static void set_pos_method_flags(gmx_ana_selmethod_t *method,
+ t_methoddata_pos *d)
+{
+ const bool forces = (d->flags != -1 && (d->flags & POS_FORCES));
+ switch (gmx::PositionCalculationCollection::requiredTopologyInfoForType(d->type, forces))
+ {
+ case gmx::PositionCalculationCollection::RequiredTopologyInfo::TopologyAndMasses:
+ method->flags |= SMETH_REQMASS;
+ // fallthrough
+ case gmx::PositionCalculationCollection::RequiredTopologyInfo::Topology:
+ method->flags |= SMETH_REQTOP;
+ break;
+ case gmx::PositionCalculationCollection::RequiredTopologyInfo::None:
+ break;
+ }
}
/*!
}
if (!d->type && type)
{
- d->type = gmx_strdup(type);
- /* FIXME: It would be better not to have the string here hardcoded. */
- if (type[0] != 'a')
- {
- sel->u.expr.method->flags |= SMETH_REQTOP;
- }
+ d->type = gmx_strdup(type);
+ set_pos_method_flags(sel->u.expr.method, d);
}
}
}
if (d->flags == -1)
{
+ GMX_RELEASE_ASSERT(d->type != nullptr,
+ "Position type should be set before flags");
d->flags = flags;
+ set_pos_method_flags(sel->u.expr.method, d);
}
}
static void
-init_kwpos(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_kwpos(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_pos *d = (t_methoddata_pos *)data;
}
static void
-init_cog(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_cog(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_pos *d = (t_methoddata_pos *)data;
}
static void
-init_com(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_com(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_pos *d = (t_methoddata_pos *)data;
}
static void
-init_output_pos(t_topology * /* top */, gmx_ana_selvalue_t *out, void *data)
+init_output_pos(const gmx_mtop_t * /* top */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_pos *d = (t_methoddata_pos *)data;
* in \c t_methoddata_pos::g and stores the results in \p out->u.p.
*/
static void
-evaluate_pos(t_topology * /* top */, t_trxframe *fr, t_pbc *pbc,
+evaluate_pos(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_pos *d = (t_methoddata_pos *)data;
- gmx_ana_poscalc_update(d->pc, out->u.p, &d->g, fr, pbc);
+ gmx_ana_poscalc_update(d->pc, out->u.p, &d->g, context.fr, context.pbc);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \returns 0 on success, -1 on failure.
*/
static void
-init_same(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+init_same(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Frees the data allocated for the \p same selection method. */
static void
free_data_same(void *data);
/*! \brief
* Initializes the evaluation of the \p same selection method for a frame.
*
- * \param[in] top Not used.
- * \param[in] fr Current frame.
- * \param[in] pbc PBC structure.
+ * \param[in] context Not used.
* \param data Should point to a \ref t_methoddata_same.
*
* Sorts the \c data->as.i array and removes identical values for faster and
* simpler lookup.
*/
static void
-init_frame_same_int(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
+init_frame_same_int(const gmx::SelMethodEvalContext &context, void *data);
/** Evaluates the \p same selection method. */
static void
-evaluate_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_same_int(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/*! \brief
* Initializes the evaluation of the \p same selection method for a frame.
*
- * \param[in] top Not used.
- * \param[in] fr Current frame.
- * \param[in] pbc PBC structure.
+ * \param[in] context Not used.
* \param data Should point to a \ref t_methoddata_same.
*
* Sorts the \c data->as.s array and removes identical values for faster and
* simpler lookup.
*/
static void
-init_frame_same_str(t_topology *top, t_trxframe *fr, t_pbc *pbc, void *data);
+init_frame_same_str(const gmx::SelMethodEvalContext &context, void *data);
/** Evaluates the \p same selection method. */
static void
-evaluate_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_same_str(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Parameters for the \p same selection method. */
static gmx_ana_selparam_t smparams_same_int[] = {
- {NULL, {INT_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_ATOMVAL},
- {"as", {INT_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
+ {nullptr, {INT_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_ATOMVAL},
+ {"as", {INT_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
};
/** Parameters for the \p same selection method. */
static gmx_ana_selparam_t smparams_same_str[] = {
- {NULL, {STR_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_ATOMVAL},
- {"as", {STR_VALUE, -1, {NULL}}, NULL, SPAR_DYNAMIC | SPAR_VARNUM},
+ {nullptr, {STR_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_ATOMVAL},
+ {"as", {STR_VALUE, -1, {nullptr}}, nullptr, SPAR_DYNAMIC | SPAR_VARNUM},
};
/** Help text for the \p same selection method. */
"same", GROUP_VALUE, 0,
asize(smparams_same_int), smparams_same_int,
&init_data_same,
- NULL,
+ nullptr,
&init_same,
- NULL,
+ nullptr,
&free_data_same,
&init_frame_same_int,
&evaluate_same_int,
- NULL,
+ nullptr,
{"same KEYWORD as ATOM_EXPR",
"Extending selections", asize(help_same), help_same},
};
"same", GROUP_VALUE, SMETH_SINGLEVAL,
asize(smparams_same_str), smparams_same_str,
&init_data_same,
- NULL,
+ nullptr,
&init_same,
- NULL,
+ nullptr,
&free_data_same,
&init_frame_same_str,
&evaluate_same_str,
- NULL,
- {NULL, NULL, 0, NULL},
+ nullptr,
+ {nullptr, nullptr, 0, nullptr},
};
static void *
t_methoddata_same *data;
snew(data, 1);
- data->as_s_sorted = NULL;
+ data->as_s_sorted = nullptr;
param[1].nvalptr = &data->nas;
return data;
}
}
static void
-init_same(t_topology * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
+init_same(const gmx_mtop_t * /* top */, int /* npar */, gmx_ana_selparam_t *param, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
}
static void
-init_frame_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */, void *data)
+init_frame_same_int(const gmx::SelMethodEvalContext & /*context*/, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
int i, j;
* \c data->val.
*/
static void
-evaluate_same_int(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_same_int(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
}
static void
-init_frame_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */, void *data)
+init_frame_same_str(const gmx::SelMethodEvalContext & /*context*/, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
int i, j;
* \c data->val.
*/
static void
-evaluate_same_str(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_same_str(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data)
{
t_methoddata_same *d = (t_methoddata_same *)data;
ptr = bsearch(&d->val.s[j], d->as_s_sorted, d->nas,
sizeof(d->as_s_sorted[0]), &cmp_str);
/* Check whether the value was found in the as list. */
- if (ptr == NULL)
+ if (ptr == nullptr)
{
/* If not, skip all atoms with the same value. */
const char *tmpval = d->val.s[j];
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cctype>
#include "gromacs/selection/position.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
#include "selmethod.h"
/** Evaluates the \p all selection keyword. */
static void
-evaluate_all(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_all(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p none selection keyword. */
static void
-evaluate_none(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_none(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p atomnr selection keyword. */
static void
-evaluate_atomnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_atomnr(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p resnr selection keyword. */
static void
-evaluate_resnr(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_resnr(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p resindex selection keyword. */
static void
-evaluate_resindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_resindex(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/*! \brief
* Checks whether molecule information is present in the topology.
* If molecule information is not found, also prints an error message.
*/
static void
-check_molecules(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+check_molecules(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p molindex selection keyword. */
static void
-evaluate_molindex(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_molindex(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p atomname selection keyword. */
static void
-evaluate_atomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_atomname(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p pdbatomname selection keyword. */
static void
-evaluate_pdbatomname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_pdbatomname(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/*! \brief
* Checks whether atom types are present in the topology.
* \param npar Not used.
* \param param Not used.
* \param data Not used.
- * \returns 0 if atom types are present in the topology, -1 otherwise.
- *
- * If the atom types are not found, also prints an error message.
*/
static void
-check_atomtype(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+check_atomtype(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p atomtype selection keyword. */
static void
-evaluate_atomtype(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_atomtype(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p insertcode selection keyword. */
static void
-evaluate_insertcode(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_insertcode(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p chain selection keyword. */
static void
-evaluate_chain(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_chain(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p mass selection keyword. */
static void
-evaluate_mass(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_mass(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
+/*! \brief
+ * Checks whether charges are present in the topology.
+ *
+ * \param[in] top Topology structure.
+ * \param npar Not used.
+ * \param param Not used.
+ * \param data Not used.
+ */
+static void
+check_charge(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p charge selection keyword. */
static void
-evaluate_charge(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_charge(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/*! \brief
* Checks whether PDB info is present in the topology.
* If PDB info is not found, also prints an error message.
*/
static void
-check_pdbinfo(t_topology *top, int npar, gmx_ana_selparam_t *param, void *data);
+check_pdbinfo(const gmx_mtop_t *top, int npar, gmx_ana_selparam_t *param, void *data);
/** Evaluates the \p altloc selection keyword. */
static void
-evaluate_altloc(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_altloc(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p occupancy selection keyword. */
static void
-evaluate_occupancy(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_occupancy(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p betafactor selection keyword. */
static void
-evaluate_betafactor(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_betafactor(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p resname selection keyword. */
static void
-evaluate_resname(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_resname(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p x selection keyword. */
static void
-evaluate_x(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_x(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p y selection keyword. */
static void
-evaluate_y(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_y(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
/** Evaluates the \p z selection keyword. */
static void
-evaluate_z(t_topology *top, t_trxframe *fr, t_pbc *pbc,
+evaluate_z(const gmx::SelMethodEvalContext &context,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void *data);
//! Help title for atom name selection keywords.
/** Selection method data for \p all selection keyword. */
gmx_ana_selmethod_t sm_all = {
"all", GROUP_VALUE, 0,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_all,
- NULL,
+ nullptr,
};
/** Selection method data for \p none selection keyword. */
gmx_ana_selmethod_t sm_none = {
"none", GROUP_VALUE, 0,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_none,
- NULL,
+ nullptr,
};
/** Selection method data for \p atomnr selection keyword. */
gmx_ana_selmethod_t sm_atomnr = {
"atomnr", INT_VALUE, 0,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_atomnr,
- NULL,
+ nullptr,
};
/** Selection method data for \p resnr selection keyword. */
gmx_ana_selmethod_t sm_resnr = {
"resnr", INT_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_resnr,
- NULL,
- {NULL, helptitle_resindex, asize(help_resindex), help_resindex}
+ nullptr,
+ {nullptr, helptitle_resindex, asize(help_resindex), help_resindex}
};
/** Selection method data for \p resindex selection keyword. */
gmx_ana_selmethod_t sm_resindex = {
"resindex", INT_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_resindex,
- NULL,
- {NULL, helptitle_resindex, asize(help_resindex), help_resindex}
+ nullptr,
+ {nullptr, helptitle_resindex, asize(help_resindex), help_resindex}
};
/** Selection method data for \p molindex selection keyword. */
gmx_ana_selmethod_t sm_molindex = {
"molindex", INT_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
&check_molecules,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_molindex,
- NULL,
+ nullptr,
};
/** Selection method data for \p atomname selection keyword. */
gmx_ana_selmethod_t sm_atomname = {
"atomname", STR_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_atomname,
- NULL,
- {NULL, helptitle_atomname, asize(help_atomname), help_atomname}
+ nullptr,
+ {nullptr, helptitle_atomname, asize(help_atomname), help_atomname}
};
/** Selection method data for \p pdbatomname selection keyword. */
gmx_ana_selmethod_t sm_pdbatomname = {
"pdbatomname", STR_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
&check_pdbinfo,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_pdbatomname,
- NULL,
- {NULL, helptitle_atomname, asize(help_atomname), help_atomname}
+ nullptr,
+ {nullptr, helptitle_atomname, asize(help_atomname), help_atomname}
};
/** Selection method data for \p atomtype selection keyword. */
gmx_ana_selmethod_t sm_atomtype = {
"atomtype", STR_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
&check_atomtype,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_atomtype,
- NULL,
+ nullptr,
};
/** Selection method data for \p resname selection keyword. */
gmx_ana_selmethod_t sm_resname = {
"resname", STR_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_resname,
- NULL,
+ nullptr,
};
/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_insertcode = {
"insertcode", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_insertcode,
- NULL,
+ nullptr,
};
/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_chain = {
"chain", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_chain,
- NULL,
+ nullptr,
};
/** Selection method data for \p mass selection keyword. */
gmx_ana_selmethod_t sm_mass = {
- "mass", REAL_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ "mass", REAL_VALUE, SMETH_REQMASS,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_mass,
- NULL,
+ nullptr,
};
/** Selection method data for \p charge selection keyword. */
gmx_ana_selmethod_t sm_charge = {
"charge", REAL_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ &check_charge,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_charge,
- NULL,
+ nullptr,
};
/** Selection method data for \p chain selection keyword. */
gmx_ana_selmethod_t sm_altloc = {
"altloc", STR_VALUE, SMETH_REQTOP | SMETH_CHARVAL,
- 0, NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
&check_pdbinfo,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_altloc,
- NULL,
+ nullptr,
};
/** Selection method data for \p occupancy selection keyword. */
gmx_ana_selmethod_t sm_occupancy = {
"occupancy", REAL_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
&check_pdbinfo,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_occupancy,
- NULL,
+ nullptr,
};
/** Selection method data for \p betafactor selection keyword. */
gmx_ana_selmethod_t sm_betafactor = {
"betafactor", REAL_VALUE, SMETH_REQTOP,
- 0, NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
&check_pdbinfo,
- NULL,
- NULL,
- NULL,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_betafactor,
- NULL,
+ nullptr,
};
/** Selection method data for \p x selection keyword. */
gmx_ana_selmethod_t sm_x = {
"x", REAL_VALUE, SMETH_DYNAMIC,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_x,
};
/** Selection method data for \p y selection keyword. */
gmx_ana_selmethod_t sm_y = {
"y", REAL_VALUE, SMETH_DYNAMIC,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_y,
};
/** Selection method data for \p z selection keyword. */
gmx_ana_selmethod_t sm_z = {
"z", REAL_VALUE, SMETH_DYNAMIC,
- 0, NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
- NULL,
+ 0, nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
+ nullptr,
&evaluate_z,
};
* Copies \p g to \p out->u.g.
*/
static void
-evaluate_all(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_all(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
gmx_ana_index_copy(out->u.g, g, false);
* Returns an empty \p out->u.g.
*/
static void
-evaluate_none(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_none(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t * /* g */, gmx_ana_selvalue_t *out, void * /* data */)
{
out->u.g->isize = 0;
* Returns the indices for each atom in \p out->u.i.
*/
static void
-evaluate_atomnr(t_topology * /* top */, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_atomnr(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i;
* Returns the residue numbers for each atom in \p out->u.i.
*/
static void
-evaluate_resnr(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_resnr(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
- int resind;
-
- out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ out->nr = g->isize;
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
- out->u.i[i] = top->atoms.resinfo[resind].nr;
+ mtopGetAtomAndResidueName(context.top, g->index[i], &molb,
+ nullptr, &out->u.i[i], nullptr, nullptr);
}
}
* Returns the residue indices for each atom in \p out->u.i.
*/
static void
-evaluate_resindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_resindex(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
- out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ out->nr = g->isize;
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- out->u.i[i] = top->atoms.atom[g->index[i]].resind + 1;
+ int resind;
+ mtopGetAtomAndResidueName(context.top, g->index[i], &molb,
+ nullptr, nullptr, nullptr, &resind);
+ out->u.i[i] = resind + 1;
}
}
static void
-check_molecules(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
+check_molecules(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
bool bOk;
- bOk = (top != NULL && top->mols.nr > 0);
+ bOk = (top != nullptr && top->mols.nr > 0);
if (!bOk)
{
GMX_THROW(gmx::InconsistentInputError("Molecule information not available in topology"));
* Returns the molecule indices for each atom in \p out->u.i.
*/
static void
-evaluate_molindex(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_molindex(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
int i, j;
out->nr = g->isize;
for (i = j = 0; i < g->isize; ++i)
{
- while (top->mols.index[j + 1] <= g->index[i])
+ while (context.top->mols.index[j + 1] <= g->index[i])
{
++j;
}
* Returns the atom name for each atom in \p out->u.s.
*/
static void
-evaluate_atomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_atomname(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- out->u.s[i] = *top->atoms.atomname[g->index[i]];
+ const char *atom_name;
+ mtopGetAtomAndResidueName(context.top, g->index[i], &molb,
+ &atom_name, nullptr, nullptr, nullptr);
+ out->u.s[i] = const_cast<char *>(atom_name);
}
}
* Returns the PDB atom name for each atom in \p out->u.s.
*/
static void
-evaluate_pdbatomname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_pdbatomname(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- char *s = top->atoms.pdbinfo[g->index[i]].atomnm;
+ const char *s = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).atomnm;
while (std::isspace(*s))
{
++s;
}
- out->u.s[i] = s;
+ out->u.s[i] = const_cast<char *>(s);
}
}
static void
-check_atomtype(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
+check_atomtype(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
- bool bOk;
-
- bOk = (top != NULL && top->atoms.atomtype != NULL);
- if (!bOk)
+ if (!gmx_mtop_has_atomtypes(top))
{
GMX_THROW(gmx::InconsistentInputError("Atom types not available in topology"));
}
* Segfaults if atom types are not found in the topology.
*/
static void
-evaluate_atomtype(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_atomtype(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- out->u.s[i] = *top->atoms.atomtype[g->index[i]];
+ int atomIndexInMolecule;
+ mtopGetMolblockIndex(context.top, g->index[i], &molb,
+ nullptr, &atomIndexInMolecule);
+ const gmx_moltype_t &moltype = context.top->moltype[context.top->molblock[molb].type];
+ out->u.s[i] = *moltype.atoms.atomtype[atomIndexInMolecule];
}
}
* Returns the residue name for each atom in \p out->u.s.
*/
static void
-evaluate_resname(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_resname(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
- int resind;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
- out->u.s[i] = *top->atoms.resinfo[resind].name;
+ out->u.s[i] = *mtopGetResidueInfo(context.top, g->index[i], &molb).name;
}
}
* Returns the insertion code for each atom in \p out->u.s.
*/
static void
-evaluate_insertcode(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_insertcode(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
- int resind;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
- out->u.s[i][0] = top->atoms.resinfo[resind].ic;
+ out->u.s[i][0] = mtopGetResidueInfo(context.top, g->index[i], &molb).ic;
}
}
* Returns the chain for each atom in \p out->u.s.
*/
static void
-evaluate_chain(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_chain(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
- int resind;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- resind = top->atoms.atom[g->index[i]].resind;
- out->u.s[i][0] = top->atoms.resinfo[resind].chainid;
+ out->u.s[i][0] = mtopGetResidueInfo(context.top, g->index[i], &molb).chainid;
}
}
* Returns the mass for each atom in \p out->u.r.
*/
static void
-evaluate_mass(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_mass(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
+ GMX_RELEASE_ASSERT(gmx_mtop_has_masses(context.top),
+ "Masses not available for evaluation");
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
+ {
+ out->u.r[i] = mtopGetAtomMass(context.top, g->index[i], &molb);
+ }
+}
+
+
+static void
+check_charge(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
+{
+ if (!gmx_mtop_has_charges(top))
{
- out->u.r[i] = top->atoms.atom[g->index[i]].m;
+ GMX_THROW(gmx::InconsistentInputError("Charges not available in topology"));
}
}
* Returns the charge for each atom in \p out->u.r.
*/
static void
-evaluate_charge(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_charge(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- out->u.r[i] = top->atoms.atom[g->index[i]].q;
+ out->u.r[i] = mtopGetAtomParameters(context.top, g->index[i], &molb).q;
}
}
static void
-check_pdbinfo(t_topology *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
+check_pdbinfo(const gmx_mtop_t *top, int /* npar */, gmx_ana_selparam_t * /* param */, void * /* data */)
{
- bool bOk;
-
- bOk = (top != NULL && top->atoms.pdbinfo != NULL);
- if (!bOk)
+ if (!gmx_mtop_has_pdbinfo(top))
{
GMX_THROW(gmx::InconsistentInputError("PDB info not available in topology"));
}
* Returns the alternate location identifier for each atom in \p out->u.s.
*/
static void
-evaluate_altloc(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_altloc(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- out->u.s[i][0] = top->atoms.pdbinfo[g->index[i]].altloc;
+ out->u.s[i][0] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).altloc;
}
}
* Segfaults if PDB info is not found in the topology.
*/
static void
-evaluate_occupancy(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_occupancy(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- out->u.r[i] = top->atoms.pdbinfo[g->index[i]].occup;
+ out->u.r[i] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).occup;
}
}
* Segfaults if PDB info is not found in the topology.
*/
static void
-evaluate_betafactor(t_topology *top, t_trxframe * /* fr */, t_pbc * /* pbc */,
+evaluate_betafactor(const gmx::SelMethodEvalContext &context,
gmx_ana_index_t *g, gmx_ana_selvalue_t *out, void * /* data */)
{
- int i;
-
out->nr = g->isize;
- for (i = 0; i < g->isize; ++i)
+ int molb = 0;
+ for (int i = 0; i < g->isize; ++i)
{
- out->u.r[i] = top->atoms.pdbinfo[g->index[i]].bfac;
+ out->u.r[i] = mtopGetAtomPdbInfo(context.top, g->index[i], &molb).bfac;
}
}
* Returns the \p x coordinate for each position in \p out->u.r.
*/
static void
-evaluate_x(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
+evaluate_x(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
out->nr = pos->count();
* Returns the \p y coordinate for each position in \p out->u.r.
*/
static void
-evaluate_y(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
+evaluate_y(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
out->nr = pos->count();
* Returns the \p z coordinate for each position in \p out->u.r.
*/
static void
-evaluate_z(t_topology * /*top*/, t_trxframe * /*fr*/, t_pbc * /*pbc*/,
+evaluate_z(const gmx::SelMethodEvalContext & /*context*/,
gmx_ana_pos_t *pos, gmx_ana_selvalue_t *out, void * /*data*/)
{
out->nr = pos->count();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \a var_ members as appropriate.
*/
Impl(SymbolType type, const char *name)
- : name_(name), type_(type), meth_(NULL)
+ : name_(name), type_(type), meth_(nullptr)
{
}
{
const char *const *postypes
= gmx::PositionCalculationCollection::typeEnumValues;
- for (int i = 0; postypes[i] != NULL; ++i)
+ for (int i = 0; postypes[i] != nullptr; ++i)
{
SymbolPointer sym(new SelectionParserSymbol(
new SelectionParserSymbol::Impl(
Impl::SymbolMap::const_iterator sym = impl_->symbols_.lower_bound(name);
if (sym == impl_->symbols_.end())
{
- return NULL;
+ return nullptr;
}
if (sym->second->name() == name)
{
return sym->second.get();
}
- return NULL;
+ return nullptr;
}
SelectionParserSymbolIterator
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
IndexBlockTest::IndexBlockTest()
{
blocka_.nr = 0;
- blocka_.index = NULL;
+ blocka_.index = nullptr;
blocka_.nalloc_index = 0;
blocka_.nra = 0;
- blocka_.a = NULL;
+ blocka_.a = nullptr;
blocka_.nalloc_a = 0;
gmx_ana_index_clear(&g_);
}
for (int i = 0; i < blocka_.nr; ++i)
{
gmx::test::TestReferenceChecker blockCompound(
- compound.checkCompound("Block", NULL));
+ compound.checkCompound("Block", nullptr));
blockCompound.checkSequence(&blocka_.a[blocka_.index[i]],
&blocka_.a[blocka_.index[i+1]],
"Atoms");
TEST_F(IndexBlockTest, CreatesUnknownBlock)
{
- gmx_ana_index_make_block(&blocka_, NULL, NULL, INDEX_UNKNOWN, false);
+ gmx_ana_index_make_block(&blocka_, nullptr, nullptr, INDEX_UNKNOWN, false);
checkBlocka();
done_blocka(&blocka_);
- gmx_ana_index_make_block(&blocka_, NULL, NULL, INDEX_UNKNOWN, false);
+ gmx_ana_index_make_block(&blocka_, nullptr, nullptr, INDEX_UNKNOWN, false);
checkBlocka();
}
{
const int group[] = { 0, 1, 3, 4, 6 };
setGroup(group);
- gmx_ana_index_make_block(&blocka_, NULL, &g_, INDEX_ATOM, false);
+ gmx_ana_index_make_block(&blocka_, nullptr, &g_, INDEX_ATOM, false);
checkBlocka();
done_blocka(&blocka_);
- gmx_ana_index_make_block(&blocka_, NULL, &g_, INDEX_ATOM, true);
+ gmx_ana_index_make_block(&blocka_, nullptr, &g_, INDEX_ATOM, true);
checkBlocka();
}
{
const int group[] = { 0, 1, 3, 4, 6 };
setGroup(group);
- gmx_ana_index_make_block(&blocka_, NULL, &g_, INDEX_ALL, false);
+ gmx_ana_index_make_block(&blocka_, nullptr, &g_, INDEX_ALL, false);
checkBlocka();
done_blocka(&blocka_);
- gmx_ana_index_make_block(&blocka_, NULL, &g_, INDEX_ALL, true);
+ gmx_ana_index_make_block(&blocka_, nullptr, &g_, INDEX_ALL, true);
checkBlocka();
}
{
const int group[] = { 0, 1, 2 };
setGroup(group);
- EXPECT_TRUE(gmx_ana_index_has_complete_elems(&g_, INDEX_ATOM, NULL));
- EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_ALL, NULL));
- EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_UNKNOWN, NULL));
+ EXPECT_TRUE(gmx_ana_index_has_complete_elems(&g_, INDEX_ATOM, nullptr));
+ EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_ALL, nullptr));
+ EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_UNKNOWN, nullptr));
}
TEST_F(IndexBlockTest, ChecksGroupForCompleteResiduesPositive)
topManager_.initAtoms(15);
topManager_.initUniformResidues(3);
- t_topology *top = topManager_.topology();
+ gmx_mtop_t *top = topManager_.topology();
setGroup(group1);
EXPECT_TRUE(gmx_ana_index_has_complete_elems(&g_, INDEX_RES, top));
const int group1[] = { 3, 4, 5, 6, 7, 8, 12, 13 };
const int group2[] = { 3, 4, 5, 6, 7, 12, 13, 14 };
const int group3[] = { 4, 5, 6, 7, 8, 12, 13, 14 };
+ const int group4[] = { 3, 4, 5, 6, 8, 12, 13, 14 };
topManager_.initAtoms(18);
topManager_.initUniformResidues(3);
- t_topology *top = topManager_.topology();
+ gmx_mtop_t *top = topManager_.topology();
setGroup(group1);
EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_RES, top));
setGroup(group3);
EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_RES, top));
+
+ setGroup(group4);
+ EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_RES, top));
}
TEST_F(IndexBlockTest, ChecksGroupForCompleteMoleculesPositive)
topManager_.initAtoms(15);
topManager_.initUniformMolecules(3);
- t_topology *top = topManager_.topology();
+ gmx_mtop_t *top = topManager_.topology();
setGroup(group);
EXPECT_TRUE(gmx_ana_index_has_complete_elems(&g_, INDEX_MOL, top));
topManager_.initAtoms(18);
topManager_.initUniformMolecules(3);
- t_topology *top = topManager_.topology();
+ gmx_mtop_t *top = topManager_.topology();
setGroup(group1);
EXPECT_FALSE(gmx_ana_index_has_complete_elems(&g_, INDEX_MOL, top));
g.isize = atomCount;
g.index = const_cast<int *>(atoms);
gmx_ana_indexmap_update(&map_, &g, bMaskOnly);
- if (name == NULL)
+ if (name == nullptr)
{
name = "Updated";
}
for (int i = 0; i < map_.mapb.nr; ++i)
{
gmx::test::TestReferenceChecker blockCompound(
- compound.checkCompound("Block", NULL));
+ compound.checkCompound("Block", nullptr));
blockCompound.checkSequence(&atoms[map_.mapb.index[i]],
&atoms[map_.mapb.index[i+1]],
"Atoms");
const int maxGroup[] = { 0, 1, 2, 3 };
const int evalGroup[] = { 0, 2 };
testInit(maxGroup, INDEX_ALL);
- testUpdate(evalGroup, false, NULL);
+ testUpdate(evalGroup, false, nullptr);
}
TEST_F(IndexMapTest, MapsResidueBlocks)
topManager_.initAtoms(18);
topManager_.initUniformResidues(3);
testInit(maxGroup, INDEX_RES);
- testUpdate(evalGroup, false, NULL);
+ testUpdate(evalGroup, false, nullptr);
}
TEST_F(IndexMapTest, MapsResidueBlocksWithMask)
topManager_.initAtoms(18);
topManager_.initUniformResidues(3);
testInit(maxGroup, INDEX_RES);
- testUpdate(evalGroup, true, NULL);
+ testUpdate(evalGroup, true, nullptr);
}
TEST_F(IndexMapTest, HandlesMultipleRequests)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include <limits>
+#include <map>
#include <numeric>
#include <vector>
testPos_.reserve(testPositions_.size());
for (size_t i = 0; i < testPositions_.size(); ++i)
{
- testPos_.push_back(testPositions_[i].x);
+ testPos_.emplace_back(testPositions_[i].x);
}
}
return gmx::AnalysisNeighborhoodPositions(testPos_);
{
GMX_RELEASE_ASSERT(testPos_.empty(),
"Cannot add positions after testPositions() call");
- testPositions_.push_back(TestPosition(x));
+ testPositions_.emplace_back(x);
}
gmx::RVec generateRandomPosition();
std::vector<int> generateIndex(int count, gmx_uint64_t seed) const;
void generateRandomRefPositions(int count);
void generateRandomTestPositions(int count);
+ void useRefPositionsAsTestPositions();
void computeReferences(t_pbc *pbc)
{
computeReferencesInternal(pbc, false);
}
}
+void NeighborhoodSearchTestData::useRefPositionsAsTestPositions()
+{
+ testPositions_.reserve(refPosCount_);
+ for (const auto &refPos : refPos_)
+ {
+ addTestPosition(refPos);
+ }
+}
+
void NeighborhoodSearchTestData::computeReferencesInternal(t_pbc *pbc, bool bXY)
{
real cutoff = cutoff_;
{
cutoff = std::numeric_limits<real>::max();
}
- TestPositionList::iterator i;
- for (i = testPositions_.begin(); i != testPositions_.end(); ++i)
+ for (TestPosition &testPos : testPositions_)
{
- i->refMinDist = cutoff;
- i->refNearestPoint = -1;
- i->refPairs.clear();
+ testPos.refMinDist = cutoff;
+ testPos.refNearestPoint = -1;
+ testPos.refPairs.clear();
for (int j = 0; j < refPosCount_; ++j)
{
rvec dx;
- if (pbc != NULL)
+ if (pbc != nullptr)
{
- pbc_dx(pbc, i->x, refPos_[j], dx);
+ pbc_dx(pbc, testPos.x, refPos_[j], dx);
}
else
{
- rvec_sub(i->x, refPos_[j], dx);
+ rvec_sub(testPos.x, refPos_[j], dx);
}
// TODO: This may not work intuitively for 2D with the third box
// vector not parallel to the Z axis, but neither does the actual
// neighborhood search.
const real dist =
!bXY ? norm(dx) : std::hypot(dx[XX], dx[YY]);
- if (dist < i->refMinDist)
+ if (dist < testPos.refMinDist)
{
- i->refMinDist = dist;
- i->refNearestPoint = j;
+ testPos.refMinDist = dist;
+ testPos.refNearestPoint = j;
}
- if (dist <= cutoff)
+ if (dist > 0 && dist <= cutoff)
{
RefPair pair(j, dist);
- GMX_RELEASE_ASSERT(i->refPairs.empty() || i->refPairs.back() < pair,
+ GMX_RELEASE_ASSERT(testPos.refPairs.empty() || testPos.refPairs.back() < pair,
"Reference pairs should be generated in sorted order");
- i->refPairs.push_back(pair);
+ testPos.refPairs.push_back(pair);
}
}
}
exclusionIds_.begin());
excls_.nr = 0;
- excls_.index = NULL;
+ excls_.index = nullptr;
excls_.nra = 0;
- excls_.a = NULL;
+ excls_.a = nullptr;
excls_.nalloc_index = 0;
excls_.nalloc_a = 0;
}
const gmx::AnalysisNeighborhoodPositions &pos,
const t_blocka *excls,
const gmx::ConstArrayRef<int> &refIndices,
- const gmx::ConstArrayRef<int> &testIndices);
+ const gmx::ConstArrayRef<int> &testIndices,
+ bool selfPairs);
gmx::AnalysisNeighborhood nb_;
};
gmx::AnalysisNeighborhoodSearch *search,
const NeighborhoodSearchTestData &data)
{
- testPairSearchFull(search, data, data.testPositions(), NULL,
- gmx::EmptyArrayRef(), gmx::EmptyArrayRef());
+ testPairSearchFull(search, data, data.testPositions(), nullptr,
+ gmx::EmptyArrayRef(), gmx::EmptyArrayRef(), false);
}
void NeighborhoodSearchTest::testPairSearchIndexed(
gmx::AnalysisNeighborhoodSearch search =
nb->initSearch(&data.pbc_,
data.refPositions().indexed(refIndices));
- testPairSearchFull(&search, data, data.testPositions(), NULL,
- refIndices, testIndices);
+ testPairSearchFull(&search, data, data.testPositions(), nullptr,
+ refIndices, testIndices, false);
}
void NeighborhoodSearchTest::testPairSearchFull(
const gmx::AnalysisNeighborhoodPositions &pos,
const t_blocka *excls,
const gmx::ConstArrayRef<int> &refIndices,
- const gmx::ConstArrayRef<int> &testIndices)
+ const gmx::ConstArrayRef<int> &testIndices,
+ bool selfPairs)
{
+ std::map<int, RefPairList> refPairs;
// TODO: Some parts of this code do not work properly if pos does not
// initially contain all the test positions.
- std::set<int> remainingTestPositions;
- gmx::AnalysisNeighborhoodPositions posCopy(pos);
if (testIndices.empty())
{
for (size_t i = 0; i < data.testPositions_.size(); ++i)
{
- remainingTestPositions.insert(i);
+ refPairs[i] = data.testPositions_[i].refPairs;
}
}
else
{
- remainingTestPositions.insert(testIndices.begin(), testIndices.end());
- posCopy.indexed(testIndices);
+ for (int index : testIndices)
+ {
+ refPairs[index] = data.testPositions_[index].refPairs;
+ }
}
-
- gmx::AnalysisNeighborhoodPairSearch pairSearch
- = search->startPairSearch(posCopy);
- gmx::AnalysisNeighborhoodPair pair;
- // There is an ordering assumption here that all pairs for a test position
- // are returned consencutively; with the current optimizations in the
- // search code, this is reasoable, as the set of grid cell pairs searched
- // depends on the test position.
- RefPairList refPairs;
- int prevTestPos = -1;
- while (pairSearch.findNextPair(&pair))
+ if (excls != nullptr)
{
- const int testIndex =
- (testIndices.empty() ? pair.testIndex() : testIndices[pair.testIndex()]);
- const int refIndex =
- (refIndices.empty() ? pair.refIndex() : refIndices[pair.refIndex()]);
- if (testIndex != prevTestPos)
+ GMX_RELEASE_ASSERT(!selfPairs, "Self-pairs testing not implemented with exclusions");
+ for (auto &entry : refPairs)
{
- if (prevTestPos != -1)
- {
- checkAllPairsFound(refPairs, data.refPos_, prevTestPos,
- data.testPositions_[prevTestPos].x);
- }
- if (remainingTestPositions.count(testIndex) == 0)
- {
- ADD_FAILURE()
- << "Pairs for test position " << testIndex
- << " are returned more than once.";
- }
- remainingTestPositions.erase(testIndex);
- refPairs = data.testPositions_[testIndex].refPairs;
- if (excls != NULL)
+ const int testIndex = entry.first;
+ ExclusionsHelper::markExcludedPairs(&entry.second, testIndex, excls);
+ }
+ }
+ if (!refIndices.empty())
+ {
+ GMX_RELEASE_ASSERT(!selfPairs, "Self-pairs testing not implemented with indexing");
+ for (auto &entry : refPairs)
+ {
+ for (auto &refPair : entry.second)
{
- ExclusionsHelper::markExcludedPairs(&refPairs, testIndex, excls);
+ refPair.bIndexed = false;
}
- if (!refIndices.empty())
+ for (int index : refIndices)
{
- RefPairList::iterator refPair;
- for (refPair = refPairs.begin(); refPair != refPairs.end(); ++refPair)
- {
- refPair->bIndexed = false;
- }
- for (size_t i = 0; i < refIndices.size(); ++i)
+ NeighborhoodSearchTestData::RefPair searchPair(index, 0.0);
+ auto refPair = std::lower_bound(entry.second.begin(), entry.second.end(), searchPair);
+ if (refPair != entry.second.end() && refPair->refIndex == index)
{
- NeighborhoodSearchTestData::RefPair searchPair(refIndices[i], 0.0);
- refPair = std::lower_bound(refPairs.begin(), refPairs.end(), searchPair);
- if (refPair != refPairs.end() && refPair->refIndex == refIndices[i])
- {
- refPair->bIndexed = true;
- }
+ refPair->bIndexed = true;
}
- for (refPair = refPairs.begin(); refPair != refPairs.end(); ++refPair)
+ }
+ for (auto &refPair : entry.second)
+ {
+ if (!refPair.bIndexed)
{
- if (!refPair->bIndexed)
- {
- refPair->bFound = true;
- }
+ refPair.bFound = true;
}
}
- prevTestPos = testIndex;
}
+ }
+ gmx::AnalysisNeighborhoodPositions posCopy(pos);
+ if (!testIndices.empty())
+ {
+ posCopy.indexed(testIndices);
+ }
+ gmx::AnalysisNeighborhoodPairSearch pairSearch
+ = selfPairs
+ ? search->startSelfPairSearch()
+ : search->startPairSearch(posCopy);
+ gmx::AnalysisNeighborhoodPair pair;
+ while (pairSearch.findNextPair(&pair))
+ {
+ const int testIndex =
+ (testIndices.empty() ? pair.testIndex() : testIndices[pair.testIndex()]);
+ const int refIndex =
+ (refIndices.empty() ? pair.refIndex() : refIndices[pair.refIndex()]);
+
+ if (refPairs.count(testIndex) == 0)
+ {
+ ADD_FAILURE()
+ << "Expected: No pairs are returned for test position " << testIndex << ".\n"
+ << " Actual: Pair with ref " << refIndex << " is returned.";
+ continue;
+ }
NeighborhoodSearchTestData::RefPair searchPair(refIndex,
std::sqrt(pair.distance2()));
- RefPairList::iterator foundRefPair
- = std::lower_bound(refPairs.begin(), refPairs.end(), searchPair);
- if (foundRefPair == refPairs.end() || foundRefPair->refIndex != refIndex)
+ const auto foundRefPair
+ = std::lower_bound(refPairs[testIndex].begin(), refPairs[testIndex].end(),
+ searchPair);
+ if (foundRefPair == refPairs[testIndex].end() || foundRefPair->refIndex != refIndex)
{
ADD_FAILURE()
<< "Expected: Pair (ref: " << refIndex << ", test: " << testIndex
EXPECT_REAL_EQ_TOL(foundRefPair->distance, searchPair.distance, data.relativeTolerance())
<< "Distance computed by the neighborhood search does not match.";
+ if (selfPairs)
+ {
+ searchPair = NeighborhoodSearchTestData::RefPair(testIndex, 0.0);
+ const auto otherRefPair
+ = std::lower_bound(refPairs[refIndex].begin(), refPairs[refIndex].end(),
+ searchPair);
+ GMX_RELEASE_ASSERT(otherRefPair != refPairs[refIndex].end(),
+ "Precomputed reference data is not symmetric");
+ otherRefPair->bFound = true;
+ }
}
}
- checkAllPairsFound(refPairs, data.refPos_, prevTestPos,
- data.testPositions_[prevTestPos].x);
-
- std::set<int> refPositions(refIndices.begin(), refIndices.end());
-
- for (std::set<int>::const_iterator i = remainingTestPositions.begin();
- i != remainingTestPositions.end(); ++i)
+ for (auto &entry : refPairs)
{
- // Account for the case where the i particle is listed in the testIndex,
- // but none of its ref neighbours were listed in the refIndex.
- if (!refIndices.empty())
- {
- RefPairList::const_iterator refPair;
- bool foundAnyRefInIndex = false;
-
- for (refPair = data.testPositions_[*i].refPairs.begin();
- refPair != data.testPositions_[*i].refPairs.end() && !foundAnyRefInIndex; ++refPair)
- {
- foundAnyRefInIndex = (refPositions.count(refPair->refIndex) > 0);
- }
- if (!foundAnyRefInIndex)
- {
- continue;
- }
- }
- if (!data.testPositions_[*i].refPairs.empty())
- {
- ADD_FAILURE()
- << "Expected: Pairs would be returned for test position " << *i << ".\n"
- << " Actual: None were returned.";
- break;
- }
+ const int testIndex = entry.first;
+ checkAllPairsFound(entry.second, data.refPos_, testIndex,
+ data.testPositions_[testIndex].x);
}
}
NeighborhoodSearchTestData data_;
};
+class TrivialSelfPairsTestData
+{
+ public:
+ static const NeighborhoodSearchTestData &get()
+ {
+ static TrivialSelfPairsTestData singleton;
+ return singleton.data_;
+ }
+
+ TrivialSelfPairsTestData() : data_(12345, 1.0)
+ {
+ data_.box_[XX][XX] = 3.0;
+ data_.box_[YY][YY] = 3.0;
+ data_.box_[ZZ][ZZ] = 3.0;
+ data_.generateRandomRefPositions(20);
+ data_.useRefPositionsAsTestPositions();
+ set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
+ data_.computeReferences(&data_.pbc_);
+ }
+
+ private:
+ NeighborhoodSearchTestData data_;
+};
+
class TrivialNoPBCTestData
{
public:
{
data_.generateRandomRefPositions(10);
data_.generateRandomTestPositions(5);
- data_.computeReferences(NULL);
+ data_.computeReferences(nullptr);
}
private:
NeighborhoodSearchTestData data_;
};
+class RandomBoxSelfPairsData
+{
+ public:
+ static const NeighborhoodSearchTestData &get()
+ {
+ static RandomBoxSelfPairsData singleton;
+ return singleton.data_;
+ }
+
+ RandomBoxSelfPairsData() : data_(12345, 1.0)
+ {
+ data_.box_[XX][XX] = 10.0;
+ data_.box_[YY][YY] = 5.0;
+ data_.box_[ZZ][ZZ] = 7.0;
+ data_.generateRandomRefPositions(1000);
+ data_.useRefPositionsAsTestPositions();
+ set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
+ data_.computeReferences(&data_.pbc_);
+ }
+
+ private:
+ NeighborhoodSearchTestData data_;
+};
+
class RandomBoxXYFullPBCData
{
public:
data_.generateRandomRefPositions(1000);
data_.generateRandomTestPositions(100);
set_pbc(&data_.pbc_, epbcNONE, data_.box_);
- data_.computeReferences(NULL);
+ data_.computeReferences(nullptr);
}
private:
testPairSearch(&search, data);
}
+TEST_F(NeighborhoodSearchTest, SimpleSelfPairsSearch)
+{
+ const NeighborhoodSearchTestData &data = TrivialSelfPairsTestData::get();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Simple);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_, data.refPositions());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
+
+ testPairSearchFull(&search, data, data.testPositions(), nullptr,
+ gmx::EmptyArrayRef(), gmx::EmptyArrayRef(), true);
+}
+
+TEST_F(NeighborhoodSearchTest, GridSelfPairsSearch)
+{
+ const NeighborhoodSearchTestData &data = RandomBoxSelfPairsData::get();
+
+ nb_.setCutoff(data.cutoff_);
+ nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
+ gmx::AnalysisNeighborhoodSearch search =
+ nb_.initSearch(&data.pbc_, data.refPositions());
+ ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
+
+ testPairSearchFull(&search, data, data.testPositions(), nullptr,
+ gmx::EmptyArrayRef(), gmx::EmptyArrayRef(), true);
+}
+
TEST_F(NeighborhoodSearchTest, HandlesConcurrentSearches)
{
const NeighborhoodSearchTestData &data = TrivialTestData::get();
nb_.setCutoff(data.cutoff_);
gmx::AnalysisNeighborhoodSearch search =
- nb_.initSearch(NULL, data.refPositions());
+ nb_.initSearch(nullptr, data.refPositions());
ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
testIsWithin(&search, data);
testPairSearchFull(&search, data,
data.testPositions().exclusionIds(helper.testPosIds()),
- helper.exclusions(), gmx::EmptyArrayRef(), gmx::EmptyArrayRef());
+ helper.exclusions(), gmx::EmptyArrayRef(),
+ gmx::EmptyArrayRef(), false);
}
TEST_F(NeighborhoodSearchTest, GridSearchExclusions)
testPairSearchFull(&search, data,
data.testPositions().exclusionIds(helper.testPosIds()),
- helper.exclusions(), gmx::EmptyArrayRef(), gmx::EmptyArrayRef());
+ helper.exclusions(), gmx::EmptyArrayRef(),
+ gmx::EmptyArrayRef(), false);
}
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void PositionCalculationTest::generateCoordinates()
{
- t_topology *top = topManager_.topology();
+ t_atoms &atoms = topManager_.atoms();
t_trxframe *frame = topManager_.frame();
- for (int i = 0; i < top->atoms.nr; ++i)
+ for (int i = 0; i < atoms.nr; ++i)
{
frame->x[i][XX] = i;
- frame->x[i][YY] = top->atoms.atom[i].resind;
+ frame->x[i][YY] = atoms.atom[i].resind;
frame->x[i][ZZ] = 0.0;
if (frame->bV)
{
posList_.reserve(posList_.size() + 1);
PositionPointer p(new gmx_ana_pos_t());
gmx_ana_pos_t *result = p.get();
- posList_.push_back(PositionTest(std::move(p), pc, name));
+ posList_.emplace_back(std::move(p), pc, name);
gmx_ana_poscalc_init_pos(pc, result);
return result;
}
void PositionCalculationTest::checkInitialized()
{
gmx::test::TestReferenceChecker compound(
- checker_.checkCompound("InitializedPositions", NULL));
+ checker_.checkCompound("InitializedPositions", nullptr));
PositionTestList::const_iterator pi;
for (pi = posList_.begin(); pi != posList_.end(); ++pi)
{
gmx_ana_index_t g;
g.isize = atoms.size();
g.index = const_cast<int *>(atoms.data());
- gmx_ana_poscalc_update(pc, p, &g, topManager_.frame(), NULL);
+ gmx_ana_poscalc_update(pc, p, &g, topManager_.frame(), nullptr);
checkPositions(checker, name, p, true);
}
flags |= POS_FORCES;
}
gmx_ana_poscalc_t *pc = createCalculation(type, flags);
- EXPECT_EQ(bExpectTop, gmx_ana_poscalc_requires_top(pc));
+ const bool requiresTopology
+ = gmx_ana_poscalc_required_topology_info(pc)
+ != gmx::PositionCalculationCollection::RequiredTopologyInfo::None;
+ EXPECT_EQ(bExpectTop, requiresTopology);
setMaximumGroup(pc, atoms);
- gmx_ana_pos_t *p = initPositions(pc, NULL);
+ gmx_ana_pos_t *p = initPositions(pc, nullptr);
checkInitialized();
{
generateCoordinates();
pcc_.initFrame(frame);
gmx::test::TestReferenceChecker frameCompound(
checker_.checkCompound("EvaluatedPositions", "Frame0"));
- updateAndCheck(pc, p, atoms, &frameCompound, NULL);
+ updateAndCheck(pc, p, atoms, &frameCompound, nullptr);
}
}
const gmx::ConstArrayRef<int> &index)
{
gmx_ana_poscalc_t *pc = createCalculation(type, flags | POS_DYNAMIC);
- EXPECT_EQ(bExpectTop, gmx_ana_poscalc_requires_top(pc));
+ const bool requiresTopology
+ = gmx_ana_poscalc_required_topology_info(pc)
+ != gmx::PositionCalculationCollection::RequiredTopologyInfo::None;
+ EXPECT_EQ(bExpectTop, requiresTopology);
setMaximumGroup(pc, initAtoms);
- gmx_ana_pos_t *p = initPositions(pc, NULL);
+ gmx_ana_pos_t *p = initPositions(pc, nullptr);
checkInitialized();
{
generateCoordinates();
pcc_.initFrame(topManager_.frame());
gmx::test::TestReferenceChecker frameCompound(
checker_.checkCompound("EvaluatedPositions", "Frame0"));
- updateAndCheck(pc, p, evalAtoms, &frameCompound, NULL);
+ updateAndCheck(pc, p, evalAtoms, &frameCompound, nullptr);
}
}
std::vector<gmx_ana_poscalc_t *>::const_iterator pci;
for (pci = pcList_.begin(); pci != pcList_.end(); ++pci)
{
- if (gmx_ana_poscalc_requires_top(*pci))
+ const bool requiresTopology
+ = gmx_ana_poscalc_required_topology_info(*pci)
+ != gmx::PositionCalculationCollection::RequiredTopologyInfo::None;
+ if (requiresTopology)
{
bTopSet_ = true;
pcc_.setTopology(topManager_.topology());
for (int i = 0; i < p->count(); ++i)
{
gmx::test::TestReferenceChecker posCompound(
- compound.checkCompound("Position", NULL));
+ compound.checkCompound("Position", nullptr));
posCompound.checkSequence(&p->m.mapb.a[p->m.mapb.index[i]],
&p->m.mapb.a[p->m.mapb.index[i+1]],
"Atoms");
{
posCompound.checkVector(p->x[i], "Coordinates");
}
- if (bCoordinates && p->v != NULL)
+ if (bCoordinates && p->v != nullptr)
{
posCompound.checkVector(p->v[i], "Velocity");
}
- if (bCoordinates && p->f != NULL)
+ if (bCoordinates && p->f != nullptr)
{
posCompound.checkVector(p->f[i], "Force");
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void setAtomCount(int natoms)
{
- ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
+ ASSERT_NO_THROW_GMX(sc_.setTopology(nullptr, natoms));
}
void loadTopology(const char *filename);
void setTopology();
gmx::test::TopologyManager topManager_;
gmx::SelectionCollection sc_;
gmx::SelectionList sel_;
- t_topology *top_;
gmx_ana_indexgrps_t *grps_;
};
#endif
SelectionCollectionTest::SelectionCollectionTest()
- : top_(NULL), grps_(NULL)
+ : grps_(nullptr)
{
topManager_.requestFrame();
sc_.setDebugLevel(s_debugLevel);
SelectionCollectionTest::~SelectionCollectionTest()
{
- if (grps_ != NULL)
+ if (grps_ != nullptr)
{
gmx_ana_indexgrps_free(grps_);
}
void
SelectionCollectionTest::setTopology()
{
- top_ = topManager_.topology();
-
- ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
+ ASSERT_NO_THROW_GMX(sc_.setTopology(topManager_.topology(), -1));
}
void
SelectionCollectionTest::loadIndexGroups(const char *filename)
{
- GMX_RELEASE_ASSERT(grps_ == NULL,
+ GMX_RELEASE_ASSERT(grps_ == nullptr,
"External groups can only be loaded once");
std::string fullpath =
gmx::test::TestFileManager::getInputFilePath(filename);
- gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
+ gmx_ana_indexgrps_init(&grps_, nullptr, fullpath.c_str());
sc_.setIndexGroups(grps_);
}
// TODO: Check something about the returned selections as well.
ASSERT_NO_THROW_GMX(sc_.parseInteractive(
count, &helper_.inputStream(),
- bInteractive ? &helper_.outputStream() : NULL,
+ bInteractive ? &helper_.outputStream() : nullptr,
"for test context"));
helper_.checkSession();
}
checker->checkSequenceCompound("Positions", sel.posCount()));
for (int i = 0; i < sel.posCount(); ++i)
{
- TestReferenceChecker poscompound(compound.checkCompound("Position", NULL));
+ TestReferenceChecker poscompound(compound.checkCompound("Position", nullptr));
const gmx::SelectionPosition &p = sel.position(i);
if (flags.test(efTestPositionAtoms))
{
using gmx::test::TestReferenceChecker;
++framenr_;
- ASSERT_NO_THROW_GMX(sc_.evaluate(topManager_.frame(), NULL));
+ ASSERT_NO_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr));
std::string frame = gmx::formatString("Frame%d", framenr_);
TestReferenceChecker compound(
checker_.checkCompound("EvaluatedSelections", frame.c_str()));
TEST_F(SelectionCollectionTest, HandlesNoSelections)
{
- EXPECT_FALSE(sc_.requiresTopology());
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
EXPECT_NO_THROW_GMX(sc_.compile());
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
+}
+
+TEST_F(SelectionCollectionTest, HandlesNoSelectionsWithDefaultPositionType)
+{
+ EXPECT_NO_THROW_GMX(sc_.setOutputPosType("res_com"));
+ EXPECT_TRUE(sc_.requiredTopologyProperties().needsTopology);
+ EXPECT_TRUE(sc_.requiredTopologyProperties().needsMasses);
+ EXPECT_NO_THROW_GMX(sc_.setOutputPosType("res_cog"));
+ EXPECT_TRUE(sc_.requiredTopologyProperties().needsTopology);
+ EXPECT_FALSE(sc_.requiredTopologyProperties().needsMasses);
+ ASSERT_NO_THROW_GMX(sc_.parseFromString("atom of atomnr 1 to 10"));
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_THROW_GMX(sc_.compile());
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
}
TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
{
ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
ASSERT_EQ(2U, sel_.size());
ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
ASSERT_NO_THROW_GMX(sc_.compile());
+ EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
EXPECT_TRUE(sel_[0].hasVelocities());
EXPECT_TRUE(sel_[1].hasVelocities());
EXPECT_TRUE(sel_[0].hasForces());
EXPECT_TRUE(sel_[1].hasForces());
}
+TEST_F(SelectionCollectionTest, HandlesForceRequestForCenterOfGeometry)
+{
+ ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("res_cog of atomnr 1 to 10"));
+ EXPECT_TRUE(sc_.requiredTopologyProperties().needsTopology);
+ ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_EQ(1U, sel_.size());
+ ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
+ // In principle, the code could know here that the masses are required, but
+ // currently it only knows this after compilation.
+ ASSERT_NO_THROW_GMX(sc_.compile());
+ EXPECT_TRUE(sc_.requiredTopologyProperties().needsMasses);
+ EXPECT_TRUE(sel_[0].hasForces());
+}
+
TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
{
ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
{
- ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
+ ASSERT_NO_THROW_GMX(sc_.setIndexGroups(nullptr));
EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
}
{
ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
- EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
+ EXPECT_THROW_GMX(sc_.setIndexGroups(nullptr), gmx::InconsistentInputError);
EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
}
TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroup)
{
- ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
+ ASSERT_NO_THROW_GMX(sc_.setTopology(nullptr, 5));
ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpB\""), gmx::InconsistentInputError);
}
{
ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
- EXPECT_THROW_GMX(sc_.setTopology(NULL, 5), gmx::InconsistentInputError);
+ EXPECT_THROW_GMX(sc_.setTopology(nullptr, 5), gmx::InconsistentInputError);
}
TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed2)
{
- ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, 5));
+ ASSERT_NO_THROW_GMX(sc_.setTopology(nullptr, 5));
ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
}
ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
ASSERT_NO_THROW_GMX(sc_.compile());
- EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), NULL), gmx::InconsistentInputError);
+ EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
}
TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets)
ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
ASSERT_NO_THROW_GMX(sc_.compile());
topManager_.frame()->natoms = 8;
- EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), NULL), gmx::InconsistentInputError);
+ EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
}
TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets2)
ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
ASSERT_NO_THROW_GMX(sc_.compile());
topManager_.initFrameIndices(index);
- EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), NULL), gmx::InconsistentInputError);
+ EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
}
TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets3)
{
const int index[] = { 0, 1, 2, 3, 4, 5, 6, 9, 10, 11 };
// Evaluating the positions will require atoms 1-3, 7-12.
- ASSERT_NO_THROW_GMX(sc_.parseFromString("whole_res_com of atomnr 2 7 11"));
+ ASSERT_NO_THROW_GMX(sc_.parseFromString("whole_res_cog of atomnr 2 7 11"));
ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
ASSERT_NO_THROW_GMX(sc_.compile());
topManager_.initFrameIndices(index);
- EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), NULL), gmx::InconsistentInputError);
+ EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
}
TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets4)
ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
ASSERT_NO_THROW_GMX(sc_.compile());
topManager_.frame()->natoms = 10;
- EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), NULL), gmx::InconsistentInputError);
+ EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
}
// TODO: Tests for more evaluation errors
"molecule 2 3 5"
};
ASSERT_NO_FATAL_FAILURE(runParser(selections));
- ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
topManager_.initUniformMolecules(3);
+ ASSERT_NO_FATAL_FAILURE(setTopology());
ASSERT_NO_FATAL_FAILURE(runCompiler());
}
"atomtype CA"
};
ASSERT_NO_FATAL_FAILURE(runParser(selections));
- ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
+ ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
const char *const types[] = { "CA", "SA", "SB" };
topManager_.initAtomTypes(types);
+ ASSERT_NO_FATAL_FAILURE(setTopology());
ASSERT_NO_FATAL_FAILURE(runCompiler());
}
"mass > 5"
};
ASSERT_NO_FATAL_FAILURE(runParser(selections));
- ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
- for (int i = 0; i < top_->atoms.nr; ++i)
+ EXPECT_TRUE(sc_.requiredTopologyProperties().needsMasses);
+ ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
+ t_atoms &atoms = topManager_.atoms();
+ for (int i = 0; i < atoms.nr; ++i)
{
- top_->atoms.atom[i].m = 1.0 + i;
+ atoms.atom[i].m = 1.0 + i;
}
+ atoms.haveMass = TRUE;
+ ASSERT_NO_FATAL_FAILURE(setTopology());
ASSERT_NO_FATAL_FAILURE(runCompiler());
}
"charge < 0.5"
};
ASSERT_NO_FATAL_FAILURE(runParser(selections));
- ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
- for (int i = 0; i < top_->atoms.nr; ++i)
+ ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
+ t_atoms &atoms = topManager_.atoms();
+ for (int i = 0; i < atoms.nr; ++i)
{
- top_->atoms.atom[i].q = i / 10.0;
+ atoms.atom[i].q = i / 10.0;
}
- //ensure exact representation of 0.5 is used, so the test is always reproducible
- top_->atoms.atom[5].q = 0.5;
+ // Ensure exact representation of 0.5 is used, so that the test is
+ // reproducible.
+ atoms.atom[5].q = 0.5;
+ atoms.haveCharge = TRUE;
+ ASSERT_NO_FATAL_FAILURE(setTopology());
ASSERT_NO_FATAL_FAILURE(runCompiler());
}
setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
| efTestPositionMasses | efTestPositionCharges);
ASSERT_NO_FATAL_FAILURE(runParser(selections));
- ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
- for (int i = 0; i < top_->atoms.nr; ++i)
+ ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
+ t_atoms &atoms = topManager_.atoms();
+ for (int i = 0; i < atoms.nr; ++i)
{
- top_->atoms.atom[i].m = 1.0 + i / 100.0;
- top_->atoms.atom[i].q = -(1.0 + i / 100.0);
+ atoms.atom[i].m = 1.0 + i / 100.0;
+ atoms.atom[i].q = -(1.0 + i / 100.0);
}
+ atoms.haveMass = TRUE;
+ atoms.haveCharge = TRUE;
+ ASSERT_NO_FATAL_FAILURE(setTopology());
ASSERT_NO_FATAL_FAILURE(runCompiler());
ASSERT_NO_FATAL_FAILURE(runEvaluate());
ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
"charge {0.05 to -0.3 -0.05 to 0.55}"
};
ASSERT_NO_FATAL_FAILURE(runParser(selections));
- ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
- for (int i = 0; i < top_->atoms.nr; ++i)
+ ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
+ t_atoms &atoms = topManager_.atoms();
+ for (int i = 0; i < atoms.nr; ++i)
{
- top_->atoms.atom[i].q = i / 10.0 - 0.5;
+ atoms.atom[i].q = i / 10.0 - 0.5;
}
+ atoms.haveCharge = TRUE;
+ ASSERT_NO_FATAL_FAILURE(setTopology());
ASSERT_NO_FATAL_FAILURE(runCompiler());
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
SelectionOptionTestBase::SelectionOptionTestBase()
- : manager_(&sc_), options_(NULL, NULL)
+ : manager_(&sc_)
{
options_.addManager(&manager_);
sc_.setReferencePosType("atom");
ASSERT_TRUE(sel.isValid());
- EXPECT_NO_THROW_GMX(sc_.setTopology(NULL, 10));
+ EXPECT_NO_THROW_GMX(sc_.setTopology(nullptr, 10));
EXPECT_NO_THROW_GMX(sc_.compile());
EXPECT_STREQ("all", sel.selectionText());
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/vec.h"
#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/arrayref.h"
{
TopologyManager::TopologyManager()
- : top_(NULL), frame_(NULL)
+ : mtop_(nullptr), frame_(nullptr)
{
}
TopologyManager::~TopologyManager()
{
- if (top_ != NULL)
+ if (mtop_ != nullptr)
{
- done_top(top_);
- sfree(top_);
+ done_mtop(mtop_);
+ sfree(mtop_);
}
- if (frame_ != NULL)
+ if (frame_ != nullptr)
{
sfree(frame_->x);
sfree(frame_->v);
sfree(frame_->index);
sfree(frame_);
}
+
+ for (char *atomtype : atomtypes_)
+ {
+ sfree(atomtype);
+ }
}
void TopologyManager::requestFrame()
{
- GMX_RELEASE_ASSERT(top_ == NULL,
+ GMX_RELEASE_ASSERT(mtop_ == nullptr,
"Frame must be requested before initializing topology");
- if (frame_ == NULL)
+ if (frame_ == nullptr)
{
snew(frame_, 1);
}
void TopologyManager::requestVelocities()
{
- GMX_RELEASE_ASSERT(frame_ != NULL,
+ GMX_RELEASE_ASSERT(frame_ != nullptr,
"Velocities requested before requesting a frame");
frame_->bV = TRUE;
if (frame_->natoms > 0)
void TopologyManager::requestForces()
{
- GMX_RELEASE_ASSERT(frame_ != NULL,
+ GMX_RELEASE_ASSERT(frame_ != nullptr,
"Forces requested before requesting a frame");
frame_->bF = TRUE;
if (frame_->natoms > 0)
void TopologyManager::loadTopology(const char *filename)
{
+ bool fullTopology;
int ePBC;
- rvec *xtop = NULL;
+ rvec *xtop = nullptr;
matrix box;
- GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
- snew(top_, 1);
- read_tps_conf(gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
- top_, &ePBC, frame_ != NULL ? &xtop : NULL,
- NULL, box, FALSE);
+ GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
+ snew(mtop_, 1);
+ readConfAndTopology(
+ gmx::test::TestFileManager::getInputFilePath(filename).c_str(),
+ &fullTopology, mtop_, &ePBC, frame_ != nullptr ? &xtop : nullptr,
+ nullptr, box);
- if (frame_ != NULL)
+ if (frame_ != nullptr)
{
- frame_->natoms = top_->atoms.nr;
+ frame_->natoms = mtop_->natoms;
frame_->bX = TRUE;
snew(frame_->x, frame_->natoms);
std::memcpy(frame_->x, xtop, sizeof(*frame_->x) * frame_->natoms);
void TopologyManager::initAtoms(int count)
{
- GMX_RELEASE_ASSERT(top_ == NULL, "Topology initialized more than once");
- snew(top_, 1);
- init_t_atoms(&top_->atoms, count, FALSE);
+ GMX_RELEASE_ASSERT(mtop_ == nullptr, "Topology initialized more than once");
+ snew(mtop_, 1);
+ mtop_->nmoltype = 1;
+ snew(mtop_->moltype, 1);
+ init_t_atoms(&mtop_->moltype[0].atoms, count, FALSE);
+ mtop_->nmolblock = 1;
+ snew(mtop_->molblock, 1);
+ mtop_->molblock[0].type = 0;
+ mtop_->molblock[0].nmol = 1;
+ mtop_->molblock[0].natoms_mol = count;
+ mtop_->natoms = count;
+ mtop_->maxres_renum = 0;
+ gmx_mtop_finalize(mtop_);
+ GMX_RELEASE_ASSERT(mtop_->maxres_renum == 0, "maxres_renum in mtop can be modified by an env.var., that is not supported in this test");
+ t_atoms &atoms = this->atoms();
for (int i = 0; i < count; ++i)
{
- top_->atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
+ atoms.atom[i].m = (i % 3 == 0 ? 2.0 : 1.0);
}
- if (frame_ != NULL)
+ atoms.haveMass = TRUE;
+ if (frame_ != nullptr)
{
frame_->natoms = count;
frame_->bX = TRUE;
void TopologyManager::initAtomTypes(const ConstArrayRef<const char *> &types)
{
- GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
+ GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
atomtypes_.reserve(types.size());
for (const char *type : types)
{
atomtypes_.push_back(gmx_strdup(type));
}
- snew(top_->atoms.atomtype, top_->atoms.nr);
- size_t j = 0;
- for (int i = 0; i < top_->atoms.nr; ++i, ++j)
+ t_atoms &atoms = this->atoms();
+ snew(atoms.atomtype, atoms.nr);
+ size_t j = 0;
+ for (int i = 0; i < atoms.nr; ++i, ++j)
{
if (j == types.size())
{
j = 0;
}
- top_->atoms.atomtype[i] = &atomtypes_[j];
+ atoms.atomtype[i] = &atomtypes_[j];
}
+ atoms.haveType = TRUE;
}
void TopologyManager::initUniformResidues(int residueSize)
{
- GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
- int residueIndex = -1;
- for (int i = 0; i < top_->atoms.nr; ++i)
+ GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
+ t_atoms &atoms = this->atoms();
+ int residueIndex = -1;
+ for (int i = 0; i < atoms.nr; ++i)
{
if (i % residueSize == 0)
{
++residueIndex;
}
- top_->atoms.atom[i].resind = residueIndex;
+ atoms.atom[i].resind = residueIndex;
}
}
void TopologyManager::initUniformMolecules(int moleculeSize)
{
- GMX_RELEASE_ASSERT(top_ != NULL, "Topology not initialized");
+ GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
int index = 0;
- top_->mols.nalloc_index = (top_->atoms.nr + moleculeSize - 1) / moleculeSize + 1;
- snew(top_->mols.index, top_->mols.nalloc_index);
- top_->mols.nr = 0;
- while (index < top_->atoms.nr)
+ mtop_->mols.nalloc_index = (mtop_->natoms + moleculeSize - 1) / moleculeSize + 1;
+ srenew(mtop_->mols.index, mtop_->mols.nalloc_index);
+ mtop_->mols.nr = 0;
+ while (index < mtop_->natoms)
{
- top_->mols.index[top_->mols.nr] = index;
- ++top_->mols.nr;
+ mtop_->mols.index[mtop_->mols.nr] = index;
+ ++mtop_->mols.nr;
index += moleculeSize;
}
- top_->mols.index[top_->mols.nr] = top_->atoms.nr;
+ mtop_->mols.index[mtop_->mols.nr] = mtop_->natoms;
}
void TopologyManager::initFrameIndices(const ConstArrayRef<int> &index)
frame_->natoms = index.size();
}
+t_atoms &TopologyManager::atoms()
+{
+ GMX_RELEASE_ASSERT(mtop_ != nullptr, "Topology not initialized");
+ GMX_RELEASE_ASSERT(mtop_->natoms == mtop_->moltype[0].atoms.nr,
+ "Test setup assumes all atoms in a single molecule type");
+ return mtop_->moltype[0].atoms;
+}
+
} // namespace test
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <vector>
-struct t_topology;
+struct gmx_mtop_t;
+struct t_atoms;
struct t_trxframe;
namespace gmx
void initFrameIndices(const ConstArrayRef<int> &index);
- t_topology *topology() { return top_; }
+ gmx_mtop_t *topology() { return mtop_; }
+ t_atoms &atoms();
t_trxframe *frame() { return frame_; }
private:
- t_topology *top_;
+ gmx_mtop_t *mtop_;
t_trxframe *frame_;
std::vector<char *> atomtypes_;
};
// The result will always be correct since we mask the result with m, but
// for debug builds we also want to make sure not to generate FP exceptions
#ifndef NDEBUG
- x.simdInternal_ = vbslq_f64(m.simdInternal_, x.simdInternal_, vdupq_n_f64(1.0f));
+ x.simdInternal_ = vbslq_f64(m.simdInternal_, x.simdInternal_, vdupq_n_f64(1.0));
#endif
return {
float64x2_t(vandq_u64(uint64x2_t(vrsqrteq_f64(x.simdInternal_)), m.simdInternal_))
// The result will always be correct since we mask the result with m, but
// for debug builds we also want to make sure not to generate FP exceptions
#ifndef NDEBUG
- x.simdInternal_ = vbslq_f64(m.simdInternal_, x.simdInternal_, vdupq_n_f64(1.0f));
+ x.simdInternal_ = vbslq_f64(m.simdInternal_, x.simdInternal_, vdupq_n_f64(1.0));
#endif
return {
float64x2_t(vandq_u64(uint64x2_t(vrecpeq_f64(x.simdInternal_)), m.simdInternal_))
selectByMask(SimdDouble a, SimdDBool m)
{
return {
- float64x2_t(vandq_u64(uint64x2_t(a.simdInternal_), m.simdInternal_))
+ float64x2_t(vandq_u64(uint64x2_t(a.simdInternal_), m.simdInternal_))
};
}
selectByNotMask(SimdDouble a, SimdDBool m)
{
return {
- float64x2_t(vbicq_u64(uint64x2_t(a.simdInternal_), m.simdInternal_))
+ float64x2_t(vbicq_u64(uint64x2_t(a.simdInternal_), m.simdInternal_))
};
}
blend(SimdDouble a, SimdDouble b, SimdDBool sel)
{
return {
- vbslq_f64(sel.simdInternal_, b.simdInternal_, a.simdInternal_)
+ vbslq_f64(sel.simdInternal_, b.simdInternal_, a.simdInternal_)
};
}
operator<<(SimdDInt32 a, int n)
{
return {
- vshl_s32(a.simdInternal_, vdup_n_s32(n >= 32 ? 32 : n))
+ vshl_s32(a.simdInternal_, vdup_n_s32(n >= 32 ? 32 : n))
};
}
operator>>(SimdDInt32 a, int n)
{
return {
- vshl_s32(a.simdInternal_, vdup_n_s32(n >= 32 ? -32 : -n))
+ vshl_s32(a.simdInternal_, vdup_n_s32(n >= 32 ? -32 : -n))
};
}
operator&(SimdDInt32 a, SimdDInt32 b)
{
return {
- vand_s32(a.simdInternal_, b.simdInternal_)
+ vand_s32(a.simdInternal_, b.simdInternal_)
};
}
andNot(SimdDInt32 a, SimdDInt32 b)
{
return {
- vbic_s32(b.simdInternal_, a.simdInternal_)
+ vbic_s32(b.simdInternal_, a.simdInternal_)
};
}
operator|(SimdDInt32 a, SimdDInt32 b)
{
return {
- vorr_s32(a.simdInternal_, b.simdInternal_)
+ vorr_s32(a.simdInternal_, b.simdInternal_)
};
}
operator^(SimdDInt32 a, SimdDInt32 b)
{
return {
- veor_s32(a.simdInternal_, b.simdInternal_)
+ veor_s32(a.simdInternal_, b.simdInternal_)
};
}
operator+(SimdDInt32 a, SimdDInt32 b)
{
return {
- vadd_s32(a.simdInternal_, b.simdInternal_)
+ vadd_s32(a.simdInternal_, b.simdInternal_)
};
}
operator-(SimdDInt32 a, SimdDInt32 b)
{
return {
- vsub_s32(a.simdInternal_, b.simdInternal_)
+ vsub_s32(a.simdInternal_, b.simdInternal_)
};
}
operator*(SimdDInt32 a, SimdDInt32 b)
{
return {
- vmul_s32(a.simdInternal_, b.simdInternal_)
+ vmul_s32(a.simdInternal_, b.simdInternal_)
};
}
operator==(SimdDInt32 a, SimdDInt32 b)
{
return {
- vceq_s32(a.simdInternal_, b.simdInternal_)
+ vceq_s32(a.simdInternal_, b.simdInternal_)
};
}
testBits(SimdDInt32 a)
{
return {
- vtst_s32( a.simdInternal_, a.simdInternal_)
+ vtst_s32( a.simdInternal_, a.simdInternal_)
};
}
operator<(SimdDInt32 a, SimdDInt32 b)
{
return {
- vclt_s32(a.simdInternal_, b.simdInternal_)
+ vclt_s32(a.simdInternal_, b.simdInternal_)
};
}
operator&&(SimdDIBool a, SimdDIBool b)
{
return {
- vand_u32(a.simdInternal_, b.simdInternal_)
+ vand_u32(a.simdInternal_, b.simdInternal_)
};
}
operator||(SimdDIBool a, SimdDIBool b)
{
return {
- vorr_u32(a.simdInternal_, b.simdInternal_)
+ vorr_u32(a.simdInternal_, b.simdInternal_)
};
}
selectByMask(SimdDInt32 a, SimdDIBool m)
{
return {
- vand_s32(a.simdInternal_, vreinterpret_s32_u32(m.simdInternal_))
+ vand_s32(a.simdInternal_, vreinterpret_s32_u32(m.simdInternal_))
};
}
selectByNotMask(SimdDInt32 a, SimdDIBool m)
{
return {
- vbic_s32(a.simdInternal_, vreinterpret_s32_u32(m.simdInternal_))
+ vbic_s32(a.simdInternal_, vreinterpret_s32_u32(m.simdInternal_))
};
}
blend(SimdDInt32 a, SimdDInt32 b, SimdDIBool sel)
{
return {
- vbsl_s32(sel.simdInternal_, b.simdInternal_, a.simdInternal_)
+ vbsl_s32(sel.simdInternal_, b.simdInternal_, a.simdInternal_)
};
}
cvtR2I(SimdDouble a)
{
return {
- vmovn_s64(vcvtnq_s64_f64(a.simdInternal_))
+ vmovn_s64(vcvtnq_s64_f64(a.simdInternal_))
};
}
cvttR2I(SimdDouble a)
{
return {
- vmovn_s64(vcvtq_s64_f64(a.simdInternal_))
+ vmovn_s64(vcvtq_s64_f64(a.simdInternal_))
};
}
cvtI2R(SimdDInt32 a)
{
return {
- vcvtq_f64_s64(vmovl_s32(a.simdInternal_))
+ vcvtq_f64_s64(vmovl_s32(a.simdInternal_))
};
}
cvtB2IB(SimdDBool a)
{
return {
- vqmovn_u64(a.simdInternal_)
+ vqmovn_u64(a.simdInternal_)
};
}
cvtIB2B(SimdDIBool a)
{
return {
- vorrq_u64(vmovl_u32(a.simdInternal_), vshlq_n_u64(vmovl_u32(a.simdInternal_), 32))
+ vorrq_u64(vmovl_u32(a.simdInternal_), vshlq_n_u64(vmovl_u32(a.simdInternal_), 32))
};
}
cvtDD2F(SimdDouble d0, SimdDouble d1)
{
return {
- vcvt_high_f32_f64(vcvt_f32_f64(d0.simdInternal_), d1.simdInternal_)
+ vcvt_high_f32_f64(vcvt_f32_f64(d0.simdInternal_), d1.simdInternal_)
};
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
static inline void
simdPrefetch(const void * m)
{
-#if defined(__ibmxl__) || defined(__xlC__)
- __dcbt(m);
-#elif defined __GNUC__
+#if defined __GNUC__
__builtin_prefetch(m);
#endif
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
// Assert is buggy on xlc with high optimization, so we skip it for QPX
+// TODO Add back the asserts for bgclang
#include <cstddef>
#ifdef __clang__
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* but if the pointer is not aligned the prefetch might start at the
* lower cache line boundary (meaning fewer bytes are prefetched).
*/
-static void
+static inline void
simdPrefetch(void gmx_unused * m)
{
// Do nothing for reference implementation
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_H
+
+#include "impl_x86_avx2_128_definitions.h"
+#include "impl_x86_avx2_128_general.h"
+#include "impl_x86_avx2_128_simd4_double.h"
+#include "impl_x86_avx2_128_simd4_float.h"
+#include "impl_x86_avx2_128_simd_double.h"
+#include "impl_x86_avx2_128_simd_float.h"
+#include "impl_x86_avx2_128_util_double.h"
+#include "impl_x86_avx2_128_util_float.h"
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_DEFINITIONS_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_DEFINITIONS_H
+
+// Capability definitions for (mostly) 128-bit AVX2
+#define GMX_SIMD 1
+#define GMX_SIMD_HAVE_FLOAT 1
+#define GMX_SIMD_HAVE_DOUBLE 1
+#define GMX_SIMD_HAVE_LOADU 1
+#define GMX_SIMD_HAVE_STOREU 1
+#define GMX_SIMD_HAVE_LOGICAL 1
+#define GMX_SIMD_HAVE_FMA 1
+#define GMX_SIMD_HAVE_FINT32_EXTRACT 1
+#define GMX_SIMD_HAVE_FINT32_LOGICAL 1
+#define GMX_SIMD_HAVE_FINT32_ARITHMETICS 1
+#define GMX_SIMD_HAVE_DINT32_EXTRACT 1
+#define GMX_SIMD_HAVE_DINT32_LOGICAL 1
+#define GMX_SIMD_HAVE_DINT32_ARITHMETICS 1
+#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_FLOAT 0
+#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_FLOAT 0
+#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_FLOAT 0
+#define GMX_SIMD_HAVE_NATIVE_LOG_FLOAT 0
+#define GMX_SIMD_HAVE_NATIVE_EXP2_FLOAT 0
+#define GMX_SIMD_HAVE_NATIVE_EXP_FLOAT 0
+#define GMX_SIMD_HAVE_NATIVE_COPYSIGN_DOUBLE 0
+#define GMX_SIMD_HAVE_NATIVE_RSQRT_ITER_DOUBLE 0
+#define GMX_SIMD_HAVE_NATIVE_RCP_ITER_DOUBLE 0
+#define GMX_SIMD_HAVE_NATIVE_LOG_DOUBLE 0
+#define GMX_SIMD_HAVE_NATIVE_EXP2_DOUBLE 0
+#define GMX_SIMD_HAVE_NATIVE_EXP_DOUBLE 0
+#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_FLOAT 1
+#define GMX_SIMD_HAVE_GATHER_LOADU_BYSIMDINT_TRANSPOSE_DOUBLE 1
+#define GMX_SIMD_HAVE_HSIMD_UTIL_FLOAT 0 // No need for half-simd, width is 4
+#define GMX_SIMD_HAVE_HSIMD_UTIL_DOUBLE 0 // No need for half-simd, width is 2
+
+#define GMX_SIMD4_HAVE_FLOAT 1
+#define GMX_SIMD4_HAVE_DOUBLE 1
+
+// Implementation details
+#define GMX_SIMD_FLOAT_WIDTH 4
+#define GMX_SIMD_DOUBLE_WIDTH 2
+#define GMX_SIMD_FINT32_WIDTH 4
+#define GMX_SIMD_DINT32_WIDTH 2
+#define GMX_SIMD4_WIDTH 4
+#define GMX_SIMD_RSQRT_BITS 11
+#define GMX_SIMD_RCP_BITS 11
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_DEFINITIONS_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_GENERAL_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_GENERAL_H
+
+#include "gromacs/simd/impl_x86_avx_256/impl_x86_avx_256_general.h"
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_GENERAL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_SIMD4_DOUBLE_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_SIMD4_DOUBLE_H
+
+#include "gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256_simd4_double.h"
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_SIMD4_DOUBLE_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_SIMD4_FLOAT_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_SIMD4_FLOAT_H
+
+#include "gromacs/simd/impl_x86_avx2_256/impl_x86_avx2_256_simd4_float.h"
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_SIMD4_FLOAT_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_SIMD_DOUBLE_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_SIMD_DOUBLE_H
+
+#include "config.h"
+
+#include <immintrin.h>
+
+#include "gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1_simd_double.h"
+
+namespace gmx
+{
+
+static inline double gmx_simdcall
+reduce(SimdDouble a)
+{
+ __m128d b = _mm_add_sd(a.simdInternal_, _mm_permute_pd(a.simdInternal_, _MM_SHUFFLE2(1, 1)));
+ return *reinterpret_cast<double *>(&b);
+}
+
+static inline SimdDouble gmx_simdcall
+fma(SimdDouble a, SimdDouble b, SimdDouble c)
+{
+ return {
+ _mm_fmadd_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+static inline SimdDouble gmx_simdcall
+fms(SimdDouble a, SimdDouble b, SimdDouble c)
+{
+ return {
+ _mm_fmsub_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+static inline SimdDouble gmx_simdcall
+fnma(SimdDouble a, SimdDouble b, SimdDouble c)
+{
+ return {
+ _mm_fnmadd_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+static inline SimdDouble gmx_simdcall
+fnms(SimdDouble a, SimdDouble b, SimdDouble c)
+{
+ return {
+ _mm_fnmsub_pd(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+} // namespace gmx
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_SIMD_DOUBLE_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_SIMD_FLOAT_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_SIMD_FLOAT_H
+
+#include "config.h"
+
+#include <immintrin.h>
+
+#include "gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1_simd_float.h"
+
+namespace gmx
+{
+
+static inline float gmx_simdcall
+reduce(SimdFloat a)
+{
+ a.simdInternal_ = _mm_add_ps(a.simdInternal_, _mm_permute_ps(a.simdInternal_, _MM_SHUFFLE(1, 0, 3, 2)));
+ a.simdInternal_ = _mm_add_ss(a.simdInternal_, _mm_permute_ps(a.simdInternal_, _MM_SHUFFLE(0, 3, 2, 1)));
+ return *reinterpret_cast<float *>(&a);
+}
+
+static inline SimdFloat gmx_simdcall
+fma(SimdFloat a, SimdFloat b, SimdFloat c)
+{
+ return {
+ _mm_fmadd_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+static inline SimdFloat gmx_simdcall
+fms(SimdFloat a, SimdFloat b, SimdFloat c)
+{
+ return {
+ _mm_fmsub_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+static inline SimdFloat gmx_simdcall
+fnma(SimdFloat a, SimdFloat b, SimdFloat c)
+{
+ return {
+ _mm_fnmadd_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+static inline SimdFloat gmx_simdcall
+fnms(SimdFloat a, SimdFloat b, SimdFloat c)
+{
+ return {
+ _mm_fnmsub_ps(a.simdInternal_, b.simdInternal_, c.simdInternal_)
+ };
+}
+
+} // namespace gmx
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_SIMD_FLOAT_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_UTIL_DOUBLE_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_UTIL_DOUBLE_H
+
+#include "config.h"
+
+#include <immintrin.h>
+
+#include "gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1_util_double.h"
+
+namespace gmx
+{
+
+static inline void gmx_simdcall
+expandScalarsToTriplets(SimdDouble scalar,
+ SimdDouble * triplets0,
+ SimdDouble * triplets1,
+ SimdDouble * triplets2)
+{
+ triplets0->simdInternal_ = _mm_permute_pd(scalar.simdInternal_, _MM_SHUFFLE2(0, 0));
+ triplets1->simdInternal_ = _mm_permute_pd(scalar.simdInternal_, _MM_SHUFFLE2(1, 0));
+ triplets2->simdInternal_ = _mm_permute_pd(scalar.simdInternal_, _MM_SHUFFLE2(1, 1));
+}
+
+static inline double
+reduceIncr4ReturnSum(double * m,
+ SimdDouble v0,
+ SimdDouble v1,
+ SimdDouble v2,
+ SimdDouble v3)
+{
+ __m128d t1, t2, t3, t4;
+
+ t1 = _mm_unpacklo_pd(v0.simdInternal_, v1.simdInternal_);
+ t2 = _mm_unpackhi_pd(v0.simdInternal_, v1.simdInternal_);
+ t3 = _mm_unpacklo_pd(v2.simdInternal_, v3.simdInternal_);
+ t4 = _mm_unpackhi_pd(v2.simdInternal_, v3.simdInternal_);
+
+ t1 = _mm_add_pd(t1, t2);
+ t3 = _mm_add_pd(t3, t4);
+
+ assert(std::size_t(m) % 16 == 0);
+
+ t2 = _mm_add_pd(t1, _mm_load_pd(m));
+ t4 = _mm_add_pd(t3, _mm_load_pd(m + 2));
+ _mm_store_pd(m, t2);
+ _mm_store_pd(m + 2, t4);
+
+ t1 = _mm_add_pd(t1, t3);
+
+ t2 = _mm_add_sd(t1, _mm_permute_pd(t1, _MM_SHUFFLE2(1, 1)));
+ return *reinterpret_cast<double *>(&t2);
+}
+
+} // namespace gmx
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_UTIL_DOUBLE_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+#ifndef GMX_SIMD_IMPL_X86_AVX2_128_UTIL_FLOAT_H
+#define GMX_SIMD_IMPL_X86_AVX2_128_UTIL_FLOAT_H
+
+#include "config.h"
+
+#include <immintrin.h>
+
+#include "gromacs/simd/impl_x86_sse4_1/impl_x86_sse4_1_util_float.h"
+
+namespace gmx
+{
+
+static inline void gmx_simdcall
+expandScalarsToTriplets(SimdFloat scalar,
+ SimdFloat * triplets0,
+ SimdFloat * triplets1,
+ SimdFloat * triplets2)
+{
+ triplets0->simdInternal_ = _mm_permute_ps(scalar.simdInternal_, _MM_SHUFFLE(1, 0, 0, 0));
+ triplets1->simdInternal_ = _mm_permute_ps(scalar.simdInternal_, _MM_SHUFFLE(2, 2, 1, 1));
+ triplets2->simdInternal_ = _mm_permute_ps(scalar.simdInternal_, _MM_SHUFFLE(3, 3, 3, 2));
+}
+
+static inline float gmx_simdcall
+reduceIncr4ReturnSum(float * m,
+ SimdFloat v0,
+ SimdFloat v1,
+ SimdFloat v2,
+ SimdFloat v3)
+{
+ _MM_TRANSPOSE4_PS(v0.simdInternal_, v1.simdInternal_, v2.simdInternal_, v3.simdInternal_);
+ v0.simdInternal_ = _mm_add_ps(v0.simdInternal_, v1.simdInternal_);
+ v2.simdInternal_ = _mm_add_ps(v2.simdInternal_, v3.simdInternal_);
+ v0.simdInternal_ = _mm_add_ps(v0.simdInternal_, v2.simdInternal_);
+
+ assert(std::size_t(m) % 16 == 0);
+
+ v2.simdInternal_ = _mm_add_ps(v0.simdInternal_, _mm_load_ps(m));
+ _mm_store_ps(m, v2.simdInternal_);
+
+ __m128 b = _mm_add_ps(v0.simdInternal_, _mm_permute_ps(v0.simdInternal_, _MM_SHUFFLE(1, 0, 3, 2)));
+ b = _mm_add_ss(b, _mm_permute_ps(b, _MM_SHUFFLE(0, 3, 2, 1)));
+ return *reinterpret_cast<float *>(&b);
+}
+
+} // namespace gmx
+
+#endif // GMX_SIMD_IMPL_X86_AVX2_128_UTIL_FLOAT_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SIMD_IMPL_X86_AVX_128_FMA_DEFINITIONS_H
#define GMX_SIMD_IMPL_X86_AVX_128_FMA_DEFINITIONS_H
-#include "config.h"
-
// Capability definitions for AVX-128-FMA
#define GMX_SIMD 1
#define GMX_SIMD_HAVE_FLOAT 1
#define GMX_SIMD_RSQRT_BITS 11
#define GMX_SIMD_RCP_BITS 11
-// Work around gcc bug with wrong type for mask formal parameter to maskload/maskstore
-#if GMX_SIMD_X86_AVX_GCC_MASKLOAD_BUG
-# define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), _mm_castsi128_ps(mask))
-# define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), _mm_castsi128_ps(mask), (x))
-#else
-# define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), (mask))
-# define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), (mask), (x))
-#endif
+#define gmx_mm_maskload_ps(mem, mask) _mm_maskload_ps((mem), (mask))
+#define gmx_mm_maskstore_ps(mem, mask, x) _mm_maskstore_ps((mem), (mask), (x))
#endif // GMX_SIMD_IMPL_X86_AVX_128_FMA_DEFINITIONS_H
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <immintrin.h>
+#include "gromacs/utility/real.h"
+
#include "impl_x86_avx_512_general.h"
namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-// On MIC it is better to use scatter operations, so we define the load routines
-// that use a SIMD offset variable first.
+static const int c_simdBestPairAlignmentDouble = 2;
-template <int align>
-static inline void gmx_simdcall
-gatherLoadBySimdIntTranspose(const double * base,
- SimdDInt32 simdoffset,
- SimdDouble * v0,
- SimdDouble * v1,
- SimdDouble * v2,
- SimdDouble * v3)
+namespace
{
- assert(std::size_t(base) % 32 == 0);
- assert(align % 4 == 0);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset = simdoffset << 2;
- }
- else if (align == 8)
- {
- simdoffset = simdoffset << 3;
- }
- else
- {
- simdoffset = simdoffset * SimdDInt32(align);
- }
-
- // The 8 corresponds to sizeof(double), but debug builds with gcc require
- // an immediate since sizeof() is taken as a function.
- v0->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base, 8);
- v1->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base+1, 8);
- v2->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base+2, 8);
- v3->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base+3, 8);
-}
-
-template <int align>
-static inline void gmx_simdcall
-gatherLoadUBySimdIntTranspose(const double * base,
- SimdDInt32 simdoffset,
- SimdDouble * v0,
- SimdDouble * v1)
+// Multiply function optimized for powers of 2, for which it is done by
+// shifting. Currently up to 8 is accelerated. Could be accelerated for any
+// number with a constexpr log2 function.
+template<int n>
+SimdDInt32 fastMultiply(SimdDInt32 x)
{
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 2)
+ if (n == 2)
{
- simdoffset = simdoffset << 1;
+ return x << 1;
}
- else if (align == 4)
+ else if (n == 4)
{
- simdoffset = simdoffset << 2;
+ return x << 2;
}
- else if (align == 8)
+ else if (n == 8)
{
- simdoffset = simdoffset << 3;
+ return x << 3;
}
else
{
- simdoffset = simdoffset * SimdDInt32(align);
+ return x * n;
}
-
- v0->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base, 8);
- v1->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base+1, 8);
}
-template <int align>
+template<int align>
static inline void gmx_simdcall
-gatherLoadBySimdIntTranspose(const double * base,
- SimdDInt32 simdoffset,
- SimdDouble * v0,
- SimdDouble * v1)
+gatherLoadBySimdIntTranspose(const double *, SimdDInt32)
{
- assert(std::size_t(base) % 16 == 0);
- assert(align % 2 == 0);
- gatherLoadUBySimdIntTranspose<align>(base, simdoffset, v0, v1);
+ //Nothing to do. Termination of recursion.
+}
}
-
-
-template <int align>
+template <int align, typename ... Targs>
static inline void gmx_simdcall
-gatherLoadTranspose(const double * base,
- const std::int32_t offset[],
- SimdDouble * v0,
- SimdDouble * v1,
- SimdDouble * v2,
- SimdDouble * v3)
+gatherLoadBySimdIntTranspose(const double * base, SimdDInt32 offset, SimdDouble *v, Targs... Fargs)
{
- assert(std::size_t(offset) % 64 == 0);
- gatherLoadBySimdIntTranspose<align>(base, simdLoadDI(offset), v0, v1, v2, v3);
+ if (align > 1)
+ {
+ offset = fastMultiply<align>(offset);
+ }
+ v->simdInternal_ = _mm512_i32gather_pd(offset.simdInternal_, base, sizeof(double));
+ gatherLoadBySimdIntTranspose<1>(base+1, offset, Fargs ...);
}
-template <int align>
+template <int align, typename ... Targs>
static inline void gmx_simdcall
-gatherLoadTranspose(const double * base,
- const std::int32_t offset[],
- SimdDouble * v0,
- SimdDouble * v1)
+gatherLoadUBySimdIntTranspose(const double *base, SimdDInt32 offset, Targs... Fargs)
{
- assert(std::size_t(offset) % 64 == 0);
- gatherLoadBySimdIntTranspose<align>(base, simdLoadDI(offset), v0, v1);
+ gatherLoadBySimdIntTranspose<align>(base, offset, Fargs ...);
}
-static const int c_simdBestPairAlignmentDouble = 2;
-
-template <int align>
+template <int align, typename ... Targs>
static inline void gmx_simdcall
-gatherLoadUTranspose(const double * base,
- const std::int32_t offset[],
- SimdDouble * v0,
- SimdDouble * v1,
- SimdDouble * v2)
+gatherLoadTranspose(const double *base, const std::int32_t offset[], Targs... Fargs)
{
- SimdDInt32 simdoffset;
-
- assert(std::size_t(offset) % 32 == 0);
-
- simdoffset = simdLoadDI(offset);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset = simdoffset << 2;
- }
- else if (align == 8)
- {
- simdoffset = simdoffset << 3;
- }
- else
- {
- simdoffset = simdoffset * SimdDInt32(align);
- }
+ gatherLoadBySimdIntTranspose<align>(base, simdLoadDI(offset), Fargs ...);
+}
- v0->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base, 8);
- v1->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base+1, 8);
- v2->simdInternal_ = _mm512_i32gather_pd(simdoffset.simdInternal_, base+2, 8);
+template <int align, typename ... Targs>
+static inline void gmx_simdcall
+gatherLoadUTranspose(const double *base, const std::int32_t offset[], Targs... Fargs)
+{
+ gatherLoadTranspose<align>(base, offset, Fargs ...);
}
template <int align>
static inline void gmx_simdcall
-transposeScatterStoreU(double * base,
- const std::int32_t offset[],
- SimdDouble v0,
- SimdDouble v1,
- SimdDouble v2)
+transposeScatterStoreU(double * base,
+ const std::int32_t offset[],
+ SimdDouble v0,
+ SimdDouble v1,
+ SimdDouble v2)
{
- SimdDInt32 simdoffset;
-
- assert(std::size_t(offset) % 32 == 0);
-
- simdoffset = simdLoadDI(offset);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset = simdoffset << 2;
- }
- else if (align == 8)
- {
- simdoffset = simdoffset << 3;
- }
- else
+ SimdDInt32 simdoffset = simdLoadDI(offset);
+ if (align > 1)
{
- simdoffset = simdoffset * SimdDInt32(align);
+ simdoffset = fastMultiply<align>(simdoffset);;
}
-
- _mm512_i32scatter_pd(base, simdoffset.simdInternal_, v0.simdInternal_, 8);
- _mm512_i32scatter_pd(base+1, simdoffset.simdInternal_, v1.simdInternal_, 8);
- _mm512_i32scatter_pd(base+2, simdoffset.simdInternal_, v2.simdInternal_, 8);
+ _mm512_i32scatter_pd(base, simdoffset.simdInternal_, v0.simdInternal_, sizeof(double));
+ _mm512_i32scatter_pd(base+1, simdoffset.simdInternal_, v1.simdInternal_, sizeof(double));
+ _mm512_i32scatter_pd(base+2, simdoffset.simdInternal_, v2.simdInternal_, sizeof(double));
}
template <int align>
{
__m512d t[4], t5, t6, t7, t8;
GMX_ALIGNED(std::int64_t, 8) o[8];
+ //TODO: should use fastMultiply
_mm512_store_epi64(o, _mm512_cvtepi32_epi64(_mm256_mullo_epi32(_mm256_load_si256((const __m256i*)(offset )), _mm256_set1_epi32(align))));
t5 = _mm512_unpacklo_pd(v0.simdInternal_, v1.simdInternal_);
t6 = _mm512_unpackhi_pd(v0.simdInternal_, v1.simdInternal_);
{
__m512d t[4], t5, t6, t7, t8;
GMX_ALIGNED(std::int64_t, 8) o[8];
+ //TODO: should use fastMultiply
_mm512_store_epi64(o, _mm512_cvtepi32_epi64(_mm256_mullo_epi32(_mm256_load_si256((const __m256i*)(offset )), _mm256_set1_epi32(align))));
t5 = _mm512_unpacklo_pd(v0.simdInternal_, v1.simdInternal_);
t6 = _mm512_unpackhi_pd(v0.simdInternal_, v1.simdInternal_);
load1DualHsimd(const double * m)
{
return {
- _mm512_insertf64x4(_mm512_broadcastsd_pd(_mm_loadu_pd(m)), //note: this does not load 128bit each
- _mm256_broadcastsd_pd(_mm_loadu_pd(m+1)), 1) //because both intriniscs get combined
+ _mm512_insertf64x4(_mm512_broadcastsd_pd(_mm_load_sd(m)),
+ _mm256_broadcastsd_pd(_mm_load_sd(m+1)), 1)
};
}
assert(std::size_t(offset) % 16 == 0);
assert(std::size_t(base0) % 16 == 0);
assert(std::size_t(base1) % 16 == 0);
- assert(std::size_t(align) % 2 == 0);
idx0 = _mm_load_si128(reinterpret_cast<const __m128i*>(offset));
- idx0 = _mm_mullo_epi32(idx0, _mm_set1_epi32(align));
+ static_assert(align == 2 || align == 4, "If more are needed use fastMultiply");
+ idx0 = _mm_slli_epi32(idx0, align == 2 ? 1 : 2);
+
idx1 = _mm_add_epi32(idx0, _mm_set1_epi32(1));
idx = _mm256_inserti128_si256(_mm256_castsi128_si256(idx0), idx1, 1);
- tmp1 = _mm512_i32gather_pd(idx, base0, 8);
- tmp2 = _mm512_i32gather_pd(idx, base1, 8);
+ tmp1 = _mm512_i32gather_pd(idx, base0, sizeof(double)); //TODO: Might be faster to use invidual loads
+ tmp2 = _mm512_i32gather_pd(idx, base1, sizeof(double));
v0->simdInternal_ = _mm512_shuffle_f64x2(tmp1, tmp2, 0x44 );
v1->simdInternal_ = _mm512_shuffle_f64x2(tmp1, tmp2, 0xEE );
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace gmx
{
-// On MIC it is better to use scatter operations, so we define the load routines
-// that use a SIMD offset variable first.
+static const int c_simdBestPairAlignmentFloat = 2;
-template <int align>
-static inline void gmx_simdcall
-gatherLoadBySimdIntTranspose(const float * base,
- SimdFInt32 simdoffset,
- SimdFloat * v0,
- SimdFloat * v1,
- SimdFloat * v2,
- SimdFloat * v3)
+namespace
{
- assert(std::size_t(base) % 16 == 0);
- assert(align % 4 == 0);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
+// Multiply function optimized for powers of 2, for which it is done by
+// shifting. Currently up to 8 is accelerated. Could be accelerated for any
+// number with a constexpr log2 function.
+template<int n>
+SimdFInt32 fastMultiply(SimdFInt32 x)
+{
+ if (n == 2)
+ {
+ return x << 1;
+ }
+ else if (n == 4)
{
- simdoffset = simdoffset << 2;
+ return x << 2;
}
- else if (align == 8)
+ else if (n == 8)
{
- simdoffset = simdoffset << 3;
+ return x << 3;
}
else
{
- simdoffset = simdoffset * SimdFInt32(align);
+ return x * n;
}
-
- // The 4 corresponds to sizeof(float), but it must be an immediate, and with debug builds
- // gcc will not evaluate the sizeof() function at compile time.
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, 4);
- v1->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base+1, 4);
- v2->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base+2, 4);
- v3->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base+3, 4);
}
-template <int align>
+template<int align>
static inline void gmx_simdcall
-gatherLoadUBySimdIntTranspose(const float * base,
- SimdFInt32 simdoffset,
- SimdFloat * v0,
- SimdFloat * v1)
+gatherLoadBySimdIntTranspose(const float *, SimdFInt32)
{
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- // For align == 2 we can merge the constant into the scale parameter,
- // which can take constants up to 8 in total.
- if (align == 2)
- {
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, align * 4);
- v1->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base+1, align * 4);
- }
- else
- {
- if (align == 4)
- {
- simdoffset = simdoffset << 2;
- }
- else if (align == 8)
- {
- simdoffset = simdoffset << 3;
- }
- else
- {
- simdoffset = simdoffset * SimdFInt32(align);
- }
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, 4);
- v1->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base+1, 4);
- }
+ //Nothing to do. Termination of recursion.
+}
}
-template <int align>
+template <int align, typename ... Targs>
static inline void gmx_simdcall
-gatherLoadBySimdIntTranspose(const float * base,
- SimdFInt32 simdoffset,
- SimdFloat * v0,
- SimdFloat * v1)
+gatherLoadBySimdIntTranspose(const float *base, SimdFInt32 offset, SimdFloat *v, Targs... Fargs)
{
- assert(std::size_t(base) % 8 == 0);
- assert(align % 2 == 0);
- gatherLoadUBySimdIntTranspose<align>(base, simdoffset.simdInternal_, v0, v1);
+ // For align 1 or 2: No multiplication of offset is needed
+ if (align > 2)
+ {
+ offset = fastMultiply<align>(offset);
+ }
+ // For align 2: Scale of 2*sizeof(float) is used (maximum supported scale)
+ constexpr int align_ = (align > 2) ? 1 : align;
+ v->simdInternal_ = _mm512_i32gather_ps(offset.simdInternal_, base, sizeof(float)*align_);
+ // Gather remaining elements. Avoid extra multiplication (new align is 1 or 2).
+ gatherLoadBySimdIntTranspose<align_>(base+1, offset, Fargs ...);
}
-template <int align>
+template <int align, typename ... Targs>
static inline void gmx_simdcall
-gatherLoadTranspose(const float * base,
- const std::int32_t offset[],
- SimdFloat * v0,
- SimdFloat * v1,
- SimdFloat * v2,
- SimdFloat * v3)
+gatherLoadUBySimdIntTranspose(const float *base, SimdFInt32 offset, Targs... Fargs)
{
- gatherLoadBySimdIntTranspose<align>(base, simdLoadFI(offset), v0, v1, v2, v3);
+ gatherLoadBySimdIntTranspose<align>(base, offset, Fargs ...);
}
-template <int align>
+template <int align, typename ... Targs>
static inline void gmx_simdcall
-gatherLoadTranspose(const float * base,
- const std::int32_t offset[],
- SimdFloat * v0,
- SimdFloat * v1)
+gatherLoadTranspose(const float *base, const std::int32_t offset[], Targs... Fargs)
{
- gatherLoadBySimdIntTranspose<align>(base, simdLoadFI(offset), v0, v1);
+ gatherLoadBySimdIntTranspose<align>(base, simdLoadFI(offset), Fargs ...);
}
-static const int c_simdBestPairAlignmentFloat = 2;
-
-template <int align>
+template <int align, typename ... Targs>
static inline void gmx_simdcall
-gatherLoadUTranspose(const float * base,
- const std::int32_t offset[],
- SimdFloat * v0,
- SimdFloat * v1,
- SimdFloat * v2)
+gatherLoadUTranspose(const float *base, const std::int32_t offset[], Targs... Fargs)
{
- SimdFInt32 simdoffset;
-
- assert(std::size_t(offset) % 64 == 0);
-
- simdoffset = simdLoadFI(offset);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset = simdoffset << 2;
- }
- else if (align == 8)
- {
- simdoffset = simdoffset << 3;
- }
- else
- {
- simdoffset = simdoffset * SimdFInt32(align);
- }
-
- v0->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base, 4);
- v1->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base+1, 4);
- v2->simdInternal_ = _mm512_i32gather_ps(simdoffset.simdInternal_, base+2, 4);
+ gatherLoadTranspose<align>(base, offset, Fargs ...);
}
-
template <int align>
static inline void gmx_simdcall
transposeScatterStoreU(float * base,
SimdFloat v1,
SimdFloat v2)
{
- SimdFInt32 simdoffset;
-
- assert(std::size_t(offset) % 64 == 0);
-
- simdoffset = simdLoadFI(offset);
-
- // All instructions might be latency ~4 on MIC, so we use shifts where we
- // only need a single instruction (since the shift parameter is an immediate),
- // but multiplication otherwise.
- if (align == 4)
- {
- simdoffset = simdoffset << 2;
- }
- else if (align == 8)
+ SimdFInt32 simdoffset = simdLoadFI(offset);
+ if (align > 2)
{
- simdoffset = simdoffset << 3;
+ simdoffset = fastMultiply<align>(simdoffset);
}
- else
- {
- simdoffset = simdoffset * SimdFInt32(align);
- }
-
- _mm512_i32scatter_ps(base, simdoffset.simdInternal_, v0.simdInternal_, 4);
- _mm512_i32scatter_ps(base+1, simdoffset.simdInternal_, v1.simdInternal_, 4);
- _mm512_i32scatter_ps(base+2, simdoffset.simdInternal_, v2.simdInternal_, 4);
+ constexpr int align_ = (align > 2) ? 1 : align;
+ _mm512_i32scatter_ps(base, simdoffset.simdInternal_, v0.simdInternal_, sizeof(float)*align_);
+ _mm512_i32scatter_ps(base+1, simdoffset.simdInternal_, v1.simdInternal_, sizeof(float)*align_);
+ _mm512_i32scatter_ps(base+2, simdoffset.simdInternal_, v2.simdInternal_, sizeof(float)*align_);
}
{
__m512 t[4], t5, t6, t7, t8;
int i;
- GMX_ALIGNED(std::int32_t, 8) o[16];
- _mm512_store_epi32(o, _mm512_mullo_epi32(_mm512_load_epi32(offset), _mm512_set1_epi32(align)));
+ GMX_ALIGNED(std::int32_t, 16) o[16];
+ store(o, fastMultiply<align>(simdLoadFI(offset)));
if (align < 4)
{
t5 = _mm512_unpacklo_ps(v0.simdInternal_, v1.simdInternal_);
{
__m512 t[4], t5, t6, t7, t8;
int i;
- GMX_ALIGNED(std::int32_t, 8) o[16];
- _mm512_store_epi32(o, _mm512_mullo_epi32(_mm512_load_epi32(offset), _mm512_set1_epi32(align)));
+ GMX_ALIGNED(std::int32_t, 16) o[16];
+ store(o, fastMultiply<align>(simdLoadFI(offset)));
if (align < 4)
{
t5 = _mm512_unpacklo_ps(v0.simdInternal_, v1.simdInternal_);
SimdFloat * triplets1,
SimdFloat * triplets2)
{
- triplets0->simdInternal_ = _mm512_castsi512_ps(_mm512_permutexvar_epi32(_mm512_set_epi32(5, 4, 4, 4, 3, 3, 3, 2, 2, 2, 1, 1, 1, 0, 0, 0),
- _mm512_castps_si512(scalar.simdInternal_)));
- triplets1->simdInternal_ = _mm512_castsi512_ps(_mm512_permutexvar_epi32(_mm512_set_epi32(10, 10, 9, 9, 9, 8, 8, 8, 7, 7, 7, 6, 6, 6, 5, 5),
- _mm512_castps_si512(scalar.simdInternal_)));
- triplets2->simdInternal_ = _mm512_castsi512_ps(_mm512_permutexvar_epi32(_mm512_set_epi32(15, 15, 15, 14, 14, 14, 13, 13, 13, 12, 12, 12, 11, 11, 11, 10),
- _mm512_castps_si512(scalar.simdInternal_)));
+ triplets0->simdInternal_ = _mm512_permutexvar_ps(_mm512_set_epi32(5, 4, 4, 4, 3, 3, 3, 2, 2, 2, 1, 1, 1, 0, 0, 0),
+ scalar.simdInternal_);
+ triplets1->simdInternal_ = _mm512_permutexvar_ps(_mm512_set_epi32(10, 10, 9, 9, 9, 8, 8, 8, 7, 7, 7, 6, 6, 6, 5, 5),
+ scalar.simdInternal_);
+ triplets2->simdInternal_ = _mm512_permutexvar_ps(_mm512_set_epi32(15, 15, 15, 14, 14, 14, 13, 13, 13, 12, 12, 12, 11, 11, 11, 10),
+ scalar.simdInternal_);
}
load1DualHsimd(const float * m)
{
return {
- _mm512_shuffle_f32x4(_mm512_broadcastss_ps(_mm_loadu_ps(m)),
- _mm512_broadcastss_ps(_mm_loadu_ps(m+1)), 0x44)
+ _mm512_shuffle_f32x4(_mm512_broadcastss_ps(_mm_load_ss(m)),
+ _mm512_broadcastss_ps(_mm_load_ss(m+1)), 0x44)
};
}
SimdFloat * v0,
SimdFloat * v1)
{
- __m256i idx0, idx1;
- __m512i idx;
+ __m256i idx;
__m512 tmp1, tmp2;
assert(std::size_t(offset) % 32 == 0);
assert(std::size_t(base0) % 8 == 0);
assert(std::size_t(base1) % 8 == 0);
- assert(std::size_t(align) % 2 == 0);
- idx0 = _mm256_load_si256(reinterpret_cast<const __m256i*>(offset));
+ idx = _mm256_load_si256(reinterpret_cast<const __m256i*>(offset));
- idx0 = _mm256_mullo_epi32(idx0, _mm256_set1_epi32(align));
- idx1 = _mm256_add_epi32(idx0, _mm256_set1_epi32(1));
+ static_assert(align == 2 || align == 4, "If more are needed use fastMultiply");
+ if (align == 4)
+ {
+ idx = _mm256_slli_epi32(idx, 1);
+ }
- idx = _mm512_inserti64x4(_mm512_castsi256_si512(idx0), idx1, 1);
+ tmp1 = _mm512_castpd_ps(_mm512_i32gather_pd(idx, reinterpret_cast<const double *>(base0), sizeof(double)));
+ tmp2 = _mm512_castpd_ps(_mm512_i32gather_pd(idx, reinterpret_cast<const double *>(base1), sizeof(double)));
- tmp1 = _mm512_i32gather_ps(idx, base0, 4);
- tmp2 = _mm512_i32gather_ps(idx, base1, 4);
+ v0->simdInternal_ = _mm512_mask_moveldup_ps(tmp1, 0xAAAA, tmp2);
+ v1->simdInternal_ = _mm512_mask_movehdup_ps(tmp2, 0x5555, tmp1);
- v0->simdInternal_ = _mm512_shuffle_f32x4(tmp1, tmp2, 0x44 );
- v1->simdInternal_ = _mm512_shuffle_f32x4(tmp1, tmp2, 0xEE );
+ v0->simdInternal_ = _mm512_permutexvar_ps(_mm512_set_epi32(15, 13, 11, 9, 7, 5, 3, 1, 14, 12, 10, 8, 6, 4, 2, 0), v0->simdInternal_);
+ v1->simdInternal_ = _mm512_permutexvar_ps(_mm512_set_epi32(15, 13, 11, 9, 7, 5, 3, 1, 14, 12, 10, 8, 6, 4, 2, 0), v1->simdInternal_);
}
static inline float gmx_simdcall
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <immintrin.h>
+#include "gromacs/math/utilities.h"
#include "gromacs/simd/impl_x86_avx_512/impl_x86_avx_512_simd_float.h"
namespace gmx
};
}
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
exp2(SimdFloat x)
{
};
}
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
exp(SimdFloat x)
{
const __m512 argscale = _mm512_set1_ps(1.44269504088896341f);
const __m512 invargscale = _mm512_set1_ps(-0.69314718055994528623f);
- __m512 xscaled = _mm512_mul_ps(x.simdInternal_, argscale);
- __m512 r = _mm512_exp2a23_ps(xscaled);
+ if (opt == MathOptimization::Safe)
+ {
+ // Set the limit to gurantee flush to zero
+ const SimdFloat smallArgLimit(-88.f);
+ // Since we multiply the argument by 1.44, for the safe version we need to make
+ // sure this doesn't result in overflow
+ x = max(x, smallArgLimit);
+ }
+
+ __m512 xscaled = _mm512_mul_ps(x.simdInternal_, argscale);
+ __m512 r = _mm512_exp2a23_ps(xscaled);
// exp2a23_ps provides 23 bits of accuracy, but we ruin some of that with our argument
// scaling. To correct this, we find the difference between the scaled argument and
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <immintrin.h>
+#include "gromacs/math/utilities.h"
+
namespace gmx
{
};
}
+
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
exp2(SimdFloat x)
{
};
}
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
exp(SimdFloat x)
{
const __m512 argscale = _mm512_set1_ps(1.44269504088896341f);
const __m512 invargscale = _mm512_set1_ps(-0.69314718055994528623f);
- __m512 xscaled = _mm512_mul_ps(x.simdInternal_, argscale);
- __m512 r = _mm512_exp223_ps(_mm512_cvtfxpnt_round_adjustps_epi32(xscaled, _MM_ROUND_MODE_NEAREST, _MM_EXPADJ_24));
+ if (opt == MathOptimization::Safe)
+ {
+ // Set the limit to gurantee flush to zero
+ const SimdFloat smallArgLimit(-88.f);
+ // Since we multiply the argument by 1.44, for the safe version we need to make
+ // sure this doesn't result in overflow
+ x = max(x, smallArgLimit);
+ }
+
+ __m512 xscaled = _mm512_mul_ps(x.simdInternal_, argscale);
+ __m512 r = _mm512_exp223_ps(_mm512_cvtfxpnt_round_adjustps_epi32(xscaled, _MM_ROUND_MODE_NEAREST, _MM_EXPADJ_24));
// exp2a23_ps provides 23 bits of accuracy, but we ruin some of that with our argument
// scaling. To correct this, we find the difference between the scaled argument and
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
SimdFInt32 simdoffset;
- assert(sdt::size_t(offset) % 64 == 0);
+ assert(std::size_t(offset) % 64 == 0);
simdoffset = simdLoadFI(offset);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* write templated SIMD/non-SIMD code. For clarity it should not be used
* outside such code.
*/
-static inline float
+static inline double
reduceIncr4ReturnSum(double * m,
double v0,
double v1,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstddef>
#include <cstdint>
+#include <array>
+
#include "gromacs/utility/classhelpers.h"
#include "gromacs/utility/real.h"
# include "impl_x86_avx_256/impl_x86_avx_256.h"
#elif GMX_SIMD_X86_AVX2_256
# include "impl_x86_avx2_256/impl_x86_avx2_256.h"
+#elif GMX_SIMD_X86_AVX2_128
+# include "impl_x86_avx2_128/impl_x86_avx2_128.h"
#elif GMX_SIMD_X86_MIC
# include "impl_x86_mic/impl_x86_mic.h"
#elif GMX_SIMD_X86_AVX_512
namespace gmx
{
+template<class T, size_t N>
+struct AlignedArray;
+
+#if GMX_SIMD_HAVE_FLOAT
+/*! \libinternal \brief Identical to std::array with GMX_SIMD_FLOAT_WIDTH alignment.
+ * Should not be deleted through base pointer (destructor is non-virtual).
+ */
+template<size_t N>
+struct alignas(GMX_SIMD_FLOAT_WIDTH*sizeof(float))AlignedArray<float, N> : public std::array<float, N>
+{
+};
+#endif
+
+#if GMX_SIMD_HAVE_DOUBLE
+/*! \libinternal \brief Identical to std::array with GMX_SIMD_DOUBLE_WIDTH alignment.
+ * Should not be deleted through base pointer (destructor is non-virtual).
+ */
+template<size_t N>
+struct alignas(GMX_SIMD_DOUBLE_WIDTH*sizeof(double))AlignedArray<double, N> : public std::array<double, N>
+{
+};
+#endif
+
#if GMX_SIMD_HAVE_REAL
/*! \name SIMD data types
static inline const SimdLoadFProxyInternal gmx_simdcall
load(const float *m);
+template <size_t N>
+static inline const SimdLoadFProxyInternal gmx_simdcall
+load(const AlignedArray<float, N> &m);
+
/*! \libinternal \brief Proxy object to enable load() for SIMD and float types
*
* This object is returned by the load() function that takes a single pointer
friend const SimdLoadFProxyInternal gmx_simdcall
load(const float *m);
+ template <size_t N>
+ friend const SimdLoadFProxyInternal gmx_simdcall
+ load(const AlignedArray<float, N> &m);
const float * const m_; //!< The pointer used to load memory
};
}
+template <size_t N>
+static inline const SimdLoadFProxyInternal gmx_simdcall
+load(const AlignedArray<float, N> &m)
+{
+ return {
+ m.data()
+ };
+}
class SimdLoadUFProxyInternal;
static inline const SimdLoadDProxyInternal gmx_simdcall
load(const double *m);
+template <size_t N>
+static inline const SimdLoadDProxyInternal gmx_simdcall
+load(const AlignedArray<double, N> &m);
+
/*! \libinternal \brief Proxy object to enable load() for SIMD and double types
*
* This object is returned by the load() function that takes a single pointer
friend const SimdLoadDProxyInternal gmx_simdcall
load(const double *m);
-
+ template <size_t N>
+ friend const SimdLoadDProxyInternal gmx_simdcall
+ load(const AlignedArray<double, N> &m);
const double * const m_; //!< The pointer used to load memory
GMX_DISALLOW_COPY_AND_ASSIGN(SimdLoadDProxyInternal);
};
}
+template <size_t N>
+static inline const SimdLoadDProxyInternal gmx_simdcall
+load(const AlignedArray<double, N> &m)
+{
+ return {
+ m.data()
+ };
+}
+
class SimdLoadUDProxyInternal;
static inline const SimdLoadUDProxyInternal gmx_simdcall
/*! \brief Calculate 1/sqrt(x) for SIMD float.
*
- * \param x Argument that must be >0. This routine does not check arguments.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline SimdFloat gmx_simdcall
/*! \brief Calculate 1/sqrt(x) for two SIMD floats.
*
- * \param x0 First set of arguments, x0 must be positive - no argument checking.
- * \param x1 Second set of arguments, x1 must be positive - no argument checking.
+ * \param x0 First set of arguments, x0 must be in single range (see below).
+ * \param x1 Second set of arguments, x1 must be in single range (see below).
* \param[out] out0 Result 1/sqrt(x0)
* \param[out] out1 Result 1/sqrt(x1)
*
* In particular for double precision we can sometimes calculate square root
* pairs slightly faster by using single precision until the very last step.
+ *
+ * \note Both arguments must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
*/
static inline void gmx_simdcall
invsqrtPair(SimdFloat x0, SimdFloat x1,
/*! \brief Calculate 1/x for SIMD float.
*
- * \param x Argument that must be nonzero. This routine does not check arguments.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \return 1/x. Result is undefined if your argument was invalid.
*/
static inline SimdFloat gmx_simdcall
/*! \brief Division for SIMD floats
*
* \param nom Nominator
- * \param denom Denominator
+ * \param denom Denominator, with magnitude in range (GMX_FLOAT_MIN,GMX_FLOAT_MAX).
+ * For single precision this is equivalent to a nonzero argument,
+ * but in double precision it adds an extra restriction since
+ * the first lookup step might have to be performed in single
+ * precision on some architectures. Note that the responsibility
+ * for checking falls on you - this routine does not check arguments.
*
* \return nom/denom
*
* Illegal values in the masked-out elements will not lead to
* floating-point exceptions.
*
- * \param x Argument that must be >0 for masked-in entries
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX for masked-in entries.
+ * See \ref invsqrt for the discussion about argument restrictions.
* \param m Mask
* \return 1/sqrt(x). Result is undefined if your argument was invalid or
* entry was not masked, and 0.0 for masked-out entries.
/*! \brief Calculate 1/x for SIMD float, masked version.
*
- * \param x Argument that must be nonzero for non-masked entries.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX for masked-in entries.
+ * See \ref invsqrt for the discussion about argument restrictions.
* \param m Mask
* \return 1/x for elements where m is true, or 0.0 for masked-out entries.
*/
return lu;
}
-/*! \brief Calculate sqrt(x) correctly for SIMD floats, including argument 0.0.
+/*! \brief Calculate sqrt(x) for SIMD floats
+ *
+ * \tparam opt By default, this function checks if the input value is 0.0
+ * and masks this to return the correct result. If you are certain
+ * your argument will never be zero, and you know you need to save
+ * every single cycle you can, you can alternatively call the
+ * function as sqrt<MathOptimization::Unsafe>(x).
+ *
+ * \param x Argument that must be in range 0 <=x <= GMX_FLOAT_MAX, since the
+ * lookup step often has to be implemented in single precision.
+ * Arguments smaller than GMX_FLOAT_MIN will always lead to a zero
+ * result, even in double precision. If you are using the unsafe
+ * math optimization parameter, the argument must be in the range
+ * GMX_FLOAT_MIN <= x <= GMX_FLOAT_MAX.
*
- * \param x Argument that must be >=0.
- * \return sqrt(x). If x=0, the result will correctly be set to 0.
- * The result is undefined if the input value is negative.
+ * \return sqrt(x). The result is undefined if the input value does not fall
+ * in the allowed range specified for the argument.
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
sqrt(SimdFloat x)
{
- SimdFloat res = maskzInvsqrt(x, setZero() < x);
- return res*x;
+ if (opt == MathOptimization::Safe)
+ {
+ SimdFloat res = maskzInvsqrt(x, setZero() < x);
+ return res*x;
+ }
+ else
+ {
+ return x * invsqrt(x);
+ }
}
#if !GMX_SIMD_HAVE_NATIVE_LOG_FLOAT
#endif
#if !GMX_SIMD_HAVE_NATIVE_EXP2_FLOAT
-/*! \brief SIMD float 2^x.
- *
- * \param x Argument.
- * \result 2^x. Undefined if input argument caused overflow.
+/*! \brief SIMD float 2^x
+ *
+ * \tparam opt If this is changed from the default (safe) into the unsafe
+ * option, input values that would otherwise lead to zero-clamped
+ * results are not allowed and will lead to undefined results.
+ *
+ * \param x Argument. For the default (safe) function version this can be
+ * arbitrarily small value, but the routine might clamp the result to
+ * zero for arguments that would produce subnormal IEEE754-2008 results.
+ * This corresponds to inputs below -126 in single or -1022 in double,
+ * and it might overflow for arguments reaching 127 (single) or
+ * 1023 (double). If you enable the unsafe math optimization,
+ * very small arguments will not necessarily be zero-clamped, but
+ * can produce undefined results.
+ *
+ * \result 2^x. The result is undefined for very large arguments that cause
+ * internal floating-point overflow. If unsafe optimizations are enabled,
+ * this is also true for very small values.
+ *
+ * \note The definition range of this function is just-so-slightly smaller
+ * than the allowed IEEE exponents for many architectures. This is due
+ * to the implementation, which will hopefully improve in the future.
+ *
+ * \warning You cannot rely on this implementation returning inf for arguments
+ * that cause overflow. If you have some very large
+ * values and need to rely on getting a valid numerical output,
+ * take the minimum of your variable and the largest valid argument
+ * before calling this routine.
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
exp2(SimdFloat x)
{
- // Lower bound: Disallow numbers that would lead to an IEEE fp exponent reaching +-127.
- const SimdFloat arglimit(126.0f);
+ // Lower bound: Clamp args that would lead to an IEEE fp exponent below -127.
+ // Note that we use a slightly wider range inside this *implementation* compared
+ // to that guaranteed by the API documentation in the comment above (which has
+ // to cover all architectures).
+ const SimdFloat smallArgLimit(-127.0f);
const SimdFloat CC6(0.0001534581200287996416911311f);
const SimdFloat CC5(0.001339993121934088894618990f);
const SimdFloat CC4(0.009618488957115180159497841f);
SimdFloat intpart;
SimdFloat fexppart;
SimdFloat p;
- SimdFBool m;
+
+ // Large negative values are valid arguments to exp2(), so there are two
+ // things we need to account for:
+ // 1. When the exponents reaches -127, the (biased) exponent field will be
+ // zero and we can no longer multiply with it. There are special IEEE
+ // formats to handle this range, but for now we have to accept that
+ // we cannot handle those arguments. If input value becomes even more
+ // negative, it will start to loop and we would end up with invalid
+ // exponents. Thus, we need to limit or mask this.
+ // 2. For VERY large negative values, we will have problems that the
+ // subtraction to get the fractional part loses accuracy, and then we
+ // can end up with overflows in the polynomial.
+ //
+ // For now, we handle this by clamping smaller arguments to -127. At this
+ // point we will already return zero, so we don't need to do anything
+ // extra for the exponent.
+
+ if (opt == MathOptimization::Safe)
+ {
+ x = max(x, smallArgLimit);
+ }
fexppart = ldexp(one, cvtR2I(x));
intpart = round(x);
- m = abs(x) <= arglimit;
- fexppart = selectByMask(fexppart, m);
x = x - intpart;
p = fma(CC6, x, CC5);
* In addition to scaling the argument for 2^x this routine correctly does
* extended precision arithmetics to improve accuracy.
*
- * \param x Argument.
- * \result exp(x). Undefined if input argument caused overflow,
- * which can happen if abs(x) \> 7e13.
+ * \tparam opt If this is changed from the default (safe) into the unsafe
+ * option, input values that would otherwise lead to zero-clamped
+ * results are not allowed and will lead to undefined results.
+ *
+ * \param x Argument. For the default (safe) function version this can be
+ * arbitrarily small value, but the routine might clamp the result to
+ * zero for arguments that would produce subnormal IEEE754-2008 results.
+ * This corresponds to input arguments reaching
+ * -126*ln(2)=-87.3 in single, or -1022*ln(2)=-708.4 (double).
+ * Similarly, it might overflow for arguments reaching
+ * 127*ln(2)=88.0 (single) or 1023*ln(2)=709.1 (double). If the
+ * unsafe math optimizations are enabled, small input values that would
+ * result in zero-clamped output are not allowed.
+ *
+ * \result exp(x). Overflowing arguments are likely to either return 0 or inf,
+ * depending on the underlying implementation. If unsafe optimizations
+ * are enabled, this is also true for very small values.
+ *
+ * \note The definition range of this function is just-so-slightly smaller
+ * than the allowed IEEE exponents for many architectures. This is due
+ * to the implementation, which will hopefully improve in the future.
+ *
+ * \warning You cannot rely on this implementation returning inf for arguments
+ * that cause overflow. If you have some very large
+ * values and need to rely on getting a valid numerical output,
+ * take the minimum of your variable and the largest valid argument
+ * before calling this routine.
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
exp(SimdFloat x)
{
const SimdFloat argscale(1.44269504088896341f);
- // Lower bound: Disallow numbers that would lead to an IEEE fp exponent reaching +-127.
- const SimdFloat arglimit(126.0f);
+ // Lower bound: Clamp args that would lead to an IEEE fp exponent below -127.
+ // Note that we use a slightly wider range inside this *implementation* compared
+ // to that guaranteed by the API documentation in the comment above (which has
+ // to cover all architectures).
+ const SimdFloat smallArgLimit(-88.0296919311f);
const SimdFloat invargscale0(-0.693145751953125f);
const SimdFloat invargscale1(-1.428606765330187045e-06f);
const SimdFloat CC4(0.00136324646882712841033936f);
SimdFloat fexppart;
SimdFloat intpart;
SimdFloat y, p;
- SimdFBool m;
+
+ // Large negative values are valid arguments to exp2(), so there are two
+ // things we need to account for:
+ // 1. When the IEEE exponents reaches -127, the (biased) exponent field will be
+ // zero and we can no longer multiply with it. There are special IEEE
+ // formats to handle this range, but for now we have to accept that
+ // we cannot handle those arguments. If input value becomes even more
+ // negative, it will start to loop and we would end up with invalid
+ // exponents. Thus, we need to limit or mask this.
+ // 2. For VERY large negative values, we will have problems that the
+ // subtraction to get the fractional part loses accuracy, and then we
+ // can end up with overflows in the polynomial.
+ //
+ // For now, we handle this by clamping smaller arguments to -127*ln(2). At this
+ // point we will already return zero, so we don't need to do anything
+ // extra for the exponent.
+
+ if (opt == MathOptimization::Safe)
+ {
+ x = max(x, smallArgLimit);
+ }
y = x * argscale;
fexppart = ldexp(one, cvtR2I(y));
intpart = round(y);
- m = (abs(y) <= arglimit);
- fexppart = selectByMask(fexppart, m);
// Extended precision arithmetics
x = fma(invargscale0, intpart, x);
/*! \brief Calculate 1/sqrt(x) for SIMD double.
*
- * \param x Argument that must be >0. This routine does not check arguments.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline SimdDouble gmx_simdcall
/*! \brief Calculate 1/sqrt(x) for two SIMD doubles.
*
- * \param x0 First set of arguments, x0 must be positive - no argument checking.
- * \param x1 Second set of arguments, x1 must be positive - no argument checking.
+ * \param x0 First set of arguments, x0 must be in single range (see below).
+ * \param x1 Second set of arguments, x1 must be in single range (see below).
* \param[out] out0 Result 1/sqrt(x0)
* \param[out] out1 Result 1/sqrt(x1)
*
* In particular for double precision we can sometimes calculate square root
* pairs slightly faster by using single precision until the very last step.
+ *
+ * \note Both arguments must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
*/
static inline void gmx_simdcall
invsqrtPair(SimdDouble x0, SimdDouble x1,
/*! \brief Calculate 1/x for SIMD double.
*
- * \param x Argument that must be nonzero. This routine does not check arguments.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \return 1/x. Result is undefined if your argument was invalid.
*/
static inline SimdDouble gmx_simdcall
/*! \brief Division for SIMD doubles
*
* \param nom Nominator
- * \param denom Denominator
+ * \param denom Denominator, with magnitude in range (GMX_FLOAT_MIN,GMX_FLOAT_MAX).
+ * For single precision this is equivalent to a nonzero argument,
+ * but in double precision it adds an extra restriction since
+ * the first lookup step might have to be performed in single
+ * precision on some architectures. Note that the responsibility
+ * for checking falls on you - this routine does not check arguments.
*
* \return nom/denom
*
* Illegal values in the masked-out elements will not lead to
* floating-point exceptions.
*
- * \param x Argument that must be >0 for masked-in entries
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX for masked-in entries.
+ * See \ref invsqrt for the discussion about argument restrictions.
* \param m Mask
* \return 1/sqrt(x). Result is undefined if your argument was invalid or
* entry was not masked, and 0.0 for masked-out entries.
/*! \brief Calculate 1/x for SIMD double, masked version.
*
- * \param x Argument that must be nonzero for non-masked entries.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX for masked-in entries.
+ * See \ref invsqrt for the discussion about argument restrictions.
* \param m Mask
* \return 1/x for elements where m is true, or 0.0 for masked-out entries.
*/
}
-/*! \brief Calculate sqrt(x) correctly for SIMD doubles, including argument 0.0.
+/*! \brief Calculate sqrt(x) for SIMD doubles.
*
- * \param x Argument that must be >=0.
- * \return sqrt(x). If x=0, the result will correctly be set to 0.
- * if x>0 && x<float_min, the result will incorrectly be set to 0.
- * The result is undefined if the input value is negative.
+ * \copydetails sqrt(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdDouble gmx_simdcall
sqrt(SimdDouble x)
{
- // As we might use a float version of rsqrt, we mask out small values
- return x * maskzInvsqrt(x, SimdDouble(GMX_FLOAT_MIN) <= x);
+ if (opt == MathOptimization::Safe)
+ {
+ // As we might use a float version of rsqrt, we mask out small values
+ SimdDouble res = maskzInvsqrt(x, SimdDouble(GMX_FLOAT_MIN) < x);
+ return res*x;
+ }
+ else
+ {
+ return x * invsqrt(x);
+ }
}
#if !GMX_SIMD_HAVE_NATIVE_LOG_DOUBLE
#if !GMX_SIMD_HAVE_NATIVE_EXP2_DOUBLE
/*! \brief SIMD double 2^x.
*
- * \param x Argument.
- * \result 2^x. Undefined if input argument caused overflow.
+ * \copydetails exp2(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdDouble gmx_simdcall
exp2(SimdDouble x)
{
- const SimdDouble arglimit(1022.0);
+ // Lower bound: Clamp args that would lead to an IEEE fp exponent below -1023.
+ const SimdDouble smallArgLimit(-1023.0);
const SimdDouble CE11(4.435280790452730022081181e-10);
const SimdDouble CE10(7.074105630863314448024247e-09);
const SimdDouble CE9(1.017819803432096698472621e-07);
SimdDouble intpart;
SimdDouble fexppart;
SimdDouble p;
- SimdDBool m;
+
+ // Large negative values are valid arguments to exp2(), so there are two
+ // things we need to account for:
+ // 1. When the exponents reaches -1023, the (biased) exponent field will be
+ // zero and we can no longer multiply with it. There are special IEEE
+ // formats to handle this range, but for now we have to accept that
+ // we cannot handle those arguments. If input value becomes even more
+ // negative, it will start to loop and we would end up with invalid
+ // exponents. Thus, we need to limit or mask this.
+ // 2. For VERY large negative values, we will have problems that the
+ // subtraction to get the fractional part loses accuracy, and then we
+ // can end up with overflows in the polynomial.
+ //
+ // For now, we handle this by clamping smaller arguments to -1023. At this
+ // point we will already return zero, so we don't need to do anything
+ // extra for the exponent.
+
+ if (opt == MathOptimization::Safe)
+ {
+ x = max(x, smallArgLimit);
+ }
fexppart = ldexp(one, cvtR2I(x));
intpart = round(x);
- m = abs(x) <= arglimit;
- fexppart = selectByMask(fexppart, m);
x = x - intpart;
p = fma(CE11, x, CE10);
#if !GMX_SIMD_HAVE_NATIVE_EXP_DOUBLE
/*! \brief SIMD double exp(x).
*
- * In addition to scaling the argument for 2^x this routine correctly does
- * extended precision arithmetics to improve accuracy.
- *
- * \param x Argument.
- * \result exp(x). Undefined if input argument caused overflow,
- * which can happen if abs(x) \> 7e13.
+ * \copydetails exp(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdDouble gmx_simdcall
exp(SimdDouble x)
{
const SimdDouble argscale(1.44269504088896340735992468100);
- const SimdDouble arglimit(1022.0);
+ // Lower bound: Clamp args that would lead to an IEEE fp exponent below -1023.
+ const SimdDouble smallArgLimit(-709.0895657128);
const SimdDouble invargscale0(-0.69314718055966295651160180568695068359375);
const SimdDouble invargscale1(-2.8235290563031577122588448175013436025525412068e-13);
const SimdDouble CE12(2.078375306791423699350304e-09);
SimdDouble fexppart;
SimdDouble intpart;
SimdDouble y, p;
- SimdDBool m;
+
+ // Large negative values are valid arguments to exp2(), so there are two
+ // things we need to account for:
+ // 1. When the exponents reaches -1023, the (biased) exponent field will be
+ // zero and we can no longer multiply with it. There are special IEEE
+ // formats to handle this range, but for now we have to accept that
+ // we cannot handle those arguments. If input value becomes even more
+ // negative, it will start to loop and we would end up with invalid
+ // exponents. Thus, we need to limit or mask this.
+ // 2. For VERY large negative values, we will have problems that the
+ // subtraction to get the fractional part loses accuracy, and then we
+ // can end up with overflows in the polynomial.
+ //
+ // For now, we handle this by clamping smaller arguments to -1023*ln(2). At this
+ // point we will already return zero, so we don't need to do anything
+ // extra for the exponent.
+
+ if (opt == MathOptimization::Safe)
+ {
+ x = max(x, smallArgLimit);
+ }
y = x * argscale;
fexppart = ldexp(one, cvtR2I(y));
intpart = round(y);
- m = (abs(y) <= arglimit);
- fexppart = selectByMask(fexppart, m);
// Extended precision arithmetics
x = fma(invargscale0, intpart, x);
/*! \brief Calculate 1/sqrt(x) for SIMD double, but in single accuracy.
*
- * \param x Argument that must be >0. This routine does not check arguments.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline SimdDouble gmx_simdcall
* Illegal values in the masked-out elements will not lead to
* floating-point exceptions.
*
- * \param x Argument that must be >0 for masked-in entries
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \param m Mask
* \return 1/sqrt(x). Result is undefined if your argument was invalid or
* entry was not masked, and 0.0 for masked-out entries.
/*! \brief Calculate 1/sqrt(x) for two SIMD doubles, but single accuracy.
*
- * \param x0 First set of arguments, x0 must be positive - no argument checking.
- * \param x1 Second set of arguments, x1 must be positive - no argument checking.
+ * \param x0 First set of arguments, x0 must be in single range (see below).
+ * \param x1 Second set of arguments, x1 must be in single range (see below).
* \param[out] out0 Result 1/sqrt(x0)
* \param[out] out1 Result 1/sqrt(x1)
*
* In particular for double precision we can sometimes calculate square root
* pairs slightly faster by using single precision until the very last step.
+ *
+ * \note Both arguments must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
*/
static inline void gmx_simdcall
invsqrtPairSingleAccuracy(SimdDouble x0, SimdDouble x1,
/*! \brief Calculate 1/x for SIMD double, but in single accuracy.
*
- * \param x Argument that must be nonzero. This routine does not check arguments.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \return 1/x. Result is undefined if your argument was invalid.
*/
static inline SimdDouble gmx_simdcall
/*! \brief 1/x for masked entries of SIMD double, single accuracy.
*
- * \param x Argument that must be nonzero for non-masked entries.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ *
* \param m Mask
* \return 1/x for elements where m is true, or 0.0 for masked-out entries.
*/
}
-/*! \brief Calculate sqrt(x) (correct for 0.0) for SIMD double, single accuracy.
+/*! \brief Calculate sqrt(x) (correct for 0.0) for SIMD double, with single accuracy.
*
- * \param x Argument that must be >=0.
- * \return sqrt(x). If x<float_min, the result will correctly be set to 0.
- * The result is undefined if the input value is negative.
+ * \copydetails sqrt(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdDouble gmx_simdcall
sqrtSingleAccuracy(SimdDouble x)
{
- return x * maskzInvsqrtSingleAccuracy(x, SimdDouble(GMX_FLOAT_MIN) <= x);
+ if (opt == MathOptimization::Safe)
+ {
+ SimdDouble res = maskzInvsqrt(x, SimdDouble(GMX_FLOAT_MIN) < x);
+ return res*x;
+ }
+ else
+ {
+ return x * invsqrtSingleAccuracy(x);
+ }
}
+
/*! \brief SIMD log(x). Double precision SIMD data, single accuracy.
*
* \param x Argument, should be >0.
return p;
}
-/*! \brief SIMD 2^x. Double precision SIMD data, single accuracy.
+/*! \brief SIMD 2^x. Double precision SIMD, single accuracy.
*
- * \param x Argument.
- * \result 2^x. Undefined if input argument caused overflow.
+ * \copydetails exp2(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdDouble gmx_simdcall
exp2SingleAccuracy(SimdDouble x)
{
- // Lower bound: Disallow numbers that would lead to an IEEE fp exponent reaching +-127.
- const SimdDouble arglimit = SimdDouble(126.0);
+ // Lower bound: Clamp args that would lead to an IEEE fp exponent below -1023.
+ const SimdDouble smallArgLimit(-1023.0);
const SimdDouble CC6(0.0001534581200287996416911311);
const SimdDouble CC5(0.001339993121934088894618990);
const SimdDouble CC4(0.009618488957115180159497841);
SimdDouble intpart;
SimdDouble p;
- SimdDBool valuemask;
SimdDInt32 ix;
+ // Large negative values are valid arguments to exp2(), so there are two
+ // things we need to account for:
+ // 1. When the exponents reaches -1023, the (biased) exponent field will be
+ // zero and we can no longer multiply with it. There are special IEEE
+ // formats to handle this range, but for now we have to accept that
+ // we cannot handle those arguments. If input value becomes even more
+ // negative, it will start to loop and we would end up with invalid
+ // exponents. Thus, we need to limit or mask this.
+ // 2. For VERY large negative values, we will have problems that the
+ // subtraction to get the fractional part loses accuracy, and then we
+ // can end up with overflows in the polynomial.
+ //
+ // For now, we handle this by clamping smaller arguments to -1023. At this
+ // point we will already return zero, so we don't need to do anything
+ // extra for the exponent.
+
+ if (opt == MathOptimization::Safe)
+ {
+ x = max(x, smallArgLimit);
+ }
+
ix = cvtR2I(x);
intpart = round(x);
- valuemask = (abs(x) <= arglimit);
x = x - intpart;
p = fma(CC6, x, CC5);
p = fma(p, x, CC1);
p = fma(p, x, one);
x = ldexp(p, ix);
- x = selectByMask(x, valuemask);
return x;
}
-/*! \brief SIMD exp(x). Double precision SIMD data, single accuracy.
+
+
+/*! \brief SIMD exp(x). Double precision SIMD, single accuracy.
*
- * \param x Argument.
- * \result exp(x). Undefined if input argument caused overflow.
+ * \copydetails exp(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdDouble gmx_simdcall
expSingleAccuracy(SimdDouble x)
{
const SimdDouble argscale(1.44269504088896341);
- // Lower bound: Disallow numbers that would lead to an IEEE fp exponent reaching +-127
- const SimdDouble arglimit(126.0);
+ // Lower bound: Clamp args that would lead to an IEEE fp exponent below -1023.
+ const SimdDouble smallArgLimit(-709.0895657128);
const SimdDouble invargscale(-0.69314718055994528623);
const SimdDouble CC4(0.00136324646882712841033936);
const SimdDouble CC3(0.00836596917361021041870117);
const SimdDouble one(1.0);
SimdDouble intpart;
SimdDouble y, p;
- SimdDBool valuemask;
SimdDInt32 iy;
+ // Large negative values are valid arguments to exp2(), so there are two
+ // things we need to account for:
+ // 1. When the exponents reaches -127, the (biased) exponent field will be
+ // zero and we can no longer multiply with it. There are special IEEE
+ // formats to handle this range, but for now we have to accept that
+ // we cannot handle those arguments. If input value becomes even more
+ // negative, it will start to loop and we would end up with invalid
+ // exponents. Thus, we need to limit or mask this.
+ // 2. For VERY large negative values, we will have problems that the
+ // subtraction to get the fractional part loses accuracy, and then we
+ // can end up with overflows in the polynomial.
+ //
+ // For now, we handle this by clamping smaller arguments to -127. At this
+ // point we will already return zero, so we don't need to do anything
+ // extra for the exponent.
+
+ if (opt == MathOptimization::Safe)
+ {
+ x = max(x, smallArgLimit);
+ }
+
y = x * argscale;
iy = cvtR2I(y);
intpart = round(y); // use same rounding algorithm here
- valuemask = (abs(y) <= arglimit);
// Extended precision arithmetics not needed since
// we have double precision and only need single accuracy.
p = fma(x*x, p, x);
p = p + one;
x = ldexp(p, iy);
- x = selectByMask(x, valuemask);
return x;
}
+
/*! \brief SIMD erf(x). Double precision SIMD data, single accuracy.
*
* \param x The value to calculate erf(x) for.
* added to \f$1/r\f$ the error will be insignificant.
*
*/
-static SimdDouble gmx_simdcall
+static inline SimdDouble gmx_simdcall
pmeForceCorrectionSingleAccuracy(SimdDouble z2)
{
const SimdDouble FN6(-1.7357322914161492954e-8);
* This approximation achieves an accuracy slightly lower than 1e-6; when
* added to \f$1/r\f$ the error will be insignificant.
*/
-static SimdDouble gmx_simdcall
+static inline SimdDouble gmx_simdcall
pmePotentialCorrectionSingleAccuracy(SimdDouble z2)
{
const SimdDouble VN6(1.9296833005951166339e-8);
/*! \brief Calculate 1/sqrt(x) for SIMD4 float.
*
- * \param x Argument that must be >0. This routine does not check arguments.
- * \return 1/sqrt(x). Result is undefined if your argument was invalid.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ * \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline Simd4Float gmx_simdcall
invsqrt(Simd4Float x)
/*! \brief Calculate 1/sqrt(x) for SIMD4 double.
*
- * \param x Argument that must be >0. This routine does not check arguments.
- * \return 1/sqrt(x). Result is undefined if your argument was invalid.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ * \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline Simd4Double gmx_simdcall
invsqrt(Simd4Double x)
/*! \brief Calculate 1/sqrt(x) for SIMD4 double, but in single accuracy.
*
- * \param x Argument that must be >0. This routine does not check arguments.
- * \return 1/sqrt(x). Result is undefined if your argument was invalid.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ * \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline Simd4Double gmx_simdcall
invsqrtSingleAccuracy(Simd4Double x)
#if GMX_SIMD_HAVE_FLOAT
/*! \brief Calculate 1/sqrt(x) for SIMD float, only targeting single accuracy.
*
- * \param x Argument that must be >0. This routine does not check arguments.
- * \return 1/sqrt(x). Result is undefined if your argument was invalid.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ * \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline SimdFloat gmx_simdcall
invsqrtSingleAccuracy(SimdFloat x)
* Illegal values in the masked-out elements will not lead to
* floating-point exceptions.
*
- * \param x Argument that must be >0 for masked-in entries
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
* \param m Mask
- * \return 1/sqrt(x). Result is undefined if your argument was invalid or
- * entry was not masked, and 0.0 for masked-out entries.
+ * \return 1/sqrt(x). Result is undefined if your argument was invalid or
+ * entry was not masked, and 0.0 for masked-out entries.
*/
static inline SimdFloat
maskzInvsqrtSingleAccuracy(SimdFloat x, SimdFBool m)
/*! \brief Calculate 1/sqrt(x) for two SIMD floats, only targeting single accuracy.
*
- * \param x0 First set of arguments, x0 must be positive - no argument checking.
- * \param x1 Second set of arguments, x1 must be positive - no argument checking.
+ * \param x0 First set of arguments, x0 must be in single range (see below).
+ * \param x1 Second set of arguments, x1 must be in single range (see below).
* \param[out] out0 Result 1/sqrt(x0)
* \param[out] out1 Result 1/sqrt(x1)
*
* In particular for double precision we can sometimes calculate square root
* pairs slightly faster by using single precision until the very last step.
+ *
+ * \note Both arguments must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
*/
static inline void gmx_simdcall
invsqrtPairSingleAccuracy(SimdFloat x0, SimdFloat x1,
/*! \brief Calculate 1/x for SIMD float, only targeting single accuracy.
*
- * \param x Argument that must be nonzero. This routine does not check arguments.
- * \return 1/x. Result is undefined if your argument was invalid.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
+ * \return 1/x. Result is undefined if your argument was invalid.
*/
static inline SimdFloat gmx_simdcall
invSingleAccuracy(SimdFloat x)
/*! \brief Calculate 1/x for masked SIMD floats, only targeting single accuracy.
*
- * \param x Argument that must be nonzero for non-masked entries.
+ * \param x Argument with magnitude larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
* \param m Mask
- * \return 1/x for elements where m is true, or 0.0 for masked-out entries.
+ * \return 1/x for elements where m is true, or 0.0 for masked-out entries.
*/
static inline SimdFloat
maskzInvSingleAccuracy(SimdFloat x, SimdFBool m)
return maskzInv(x, m);
}
-/*! \brief Calculate sqrt(x) for SIMD float, only targeting single accuracy.
+/*! \brief Calculate sqrt(x) for SIMD float, always targeting single accuracy.
*
- * \param x Argument that must be >=0.
- * \return sqrt(x). If x=0, the result will correctly be set to 0.
- * The result is undefined if the input value is negative.
+ * \copydetails sqrt(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
sqrtSingleAccuracy(SimdFloat x)
{
- return sqrt(x);
+ return sqrt<opt>(x);
}
/*! \brief SIMD float log(x), only targeting single accuracy. This is the natural logarithm.
/*! \brief SIMD float 2^x, only targeting single accuracy.
*
- * \param x Argument.
- * \result 2^x. Undefined if input argument caused overflow.
+ * \copydetails exp2(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
exp2SingleAccuracy(SimdFloat x)
{
- return exp2(x);
+ return exp2<opt>(x);
}
/*! \brief SIMD float e^x, only targeting single accuracy.
*
- * \param x Argument.
- * \result exp(x). Undefined if input argument caused overflow.
+ * \copydetails exp(SimdFloat)
*/
+template <MathOptimization opt = MathOptimization::Safe>
static inline SimdFloat gmx_simdcall
expSingleAccuracy(SimdFloat x)
{
- return exp(x);
+ return exp<opt>(x);
}
+
/*! \brief SIMD float erf(x), only targeting single accuracy.
*
* \param x The value to calculate erf(x) for.
#if GMX_SIMD4_HAVE_FLOAT
/*! \brief Calculate 1/sqrt(x) for SIMD4 float, only targeting single accuracy.
*
- * \param x Argument that must be >0. This routine does not check arguments.
+ * \param x Argument that must be larger than GMX_FLOAT_MIN and smaller than
+ * GMX_FLOAT_MAX, i.e. within the range of single precision.
+ * For the single precision implementation this is obviously always
+ * true for positive values, but for double precision it adds an
+ * extra restriction since the first lookup step might have to be
+ * performed in single precision on some architectures. Note that the
+ * responsibility for checking falls on you - this routine does not
+ * check arguments.
* \return 1/sqrt(x). Result is undefined if your argument was invalid.
*/
static inline Simd4Float gmx_simdcall
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{ SimdType::X86_Avx128Fma, "AVX_128_FMA" },
{ SimdType::X86_Avx, "AVX_256" },
{ SimdType::X86_Avx2, "AVX2_256" },
+ { SimdType::X86_Avx2_128, "AVX2_128" },
{ SimdType::X86_Avx512, "AVX_512" },
{ SimdType::X86_Avx512Knl, "AVX_512_KNL" },
{ SimdType::X86_Mic, "X86_MIC" },
case CpuInfo::Vendor::Amd:
if (c.feature(CpuInfo::Feature::X86_Avx2))
{
- // When Amd starts supporting Avx2 we assume it will be 256 bits
- suggested = SimdType::X86_Avx2;
+ // AMD Ryzen supports 256-bit AVX2, but performs better with 128-bit
+ // since it can execute two independent such instructions per cycle,
+ // and wider SIMD has slightly lower efficiency in GROMACS.
+ suggested = SimdType::X86_Avx2_128;
}
else if (c.feature(CpuInfo::Feature::X86_Avx))
{
return SimdType::X86_Mic;
#elif GMX_SIMD_X86_AVX2_256
return SimdType::X86_Avx2;
+#elif GMX_SIMD_X86_AVX2_128
+ return SimdType::X86_Avx2_128;
#elif GMX_SIMD_X86_AVX_256
return SimdType::X86_Avx;
#elif GMX_SIMD_X86_AVX_128_FMA
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
X86_Avx128Fma, //!< 128-bit Avx with FMA (Amd)
X86_Avx, //!< 256-bit Avx
X86_Avx2, //!< AVX2
+ X86_Avx2_128, //!< 128-bit AVX2, better than 256-bit for AMD Ryzen
X86_Avx512, //!< AVX_512
X86_Avx512Knl, //!< AVX_512_KNL
X86_Mic, //!< Knight's corner
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test(SimdUnitTests simd-test
bootstrap_loadstore.cpp
base.cpp
+ data.cpp
simd.cpp
simd_floatingpoint.cpp
simd_floatingpoint_util.cpp
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "data.h"
+
+#include "gromacs/utility/real.h"
+
+
+namespace gmx
+{
+namespace test
+{
+
+/*! \cond internal */
+/*! \addtogroup module_simd */
+/*! \{ */
+
+// Common test data constants used both for SIMD, SIMD4, and scalar tests.
+// We both want numbers that are easy to identify with integer part from 0 to 9,
+// and to fill all digits in the mantissa and avoid identical differences
+// between adjacent numbers we add a fraction of primes.
+const real czero = 0.0;
+const real c0 = 0.0 + 1.0/3.0;
+const real c1 = 1.0 + 5.0/7.0;
+const real c2 = 2.0 + 9.0/13.0;
+const real c3 = 3.0 + 17.0/19.0;
+const real c4 = 4.0 + 23.0/29.0;
+const real c5 = 5.0 + 31.0/37.0;
+const real c6 = 6.0 + 41.0/43.0;
+const real c7 = 7.0 + 47.0/53.0;
+const real c8 = 8.0 + 59.0/61.0;
+
+/*! \} */
+/*! \endcond */
+
+} // namespace test
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#ifndef GMX_SIMD_TESTS_DATA_H
+#define GMX_SIMD_TESTS_DATA_H
+
+/*! \internal \file
+ * \brief Common test data constants for SIMD, SIMD4 and scalar tests
+ *
+ * To avoid silent bugs due to double/float truncation if we ever use the
+ * wrong return type of routines, we want to use test data that fills all
+ * available bits in either single or double precision. The values themselves
+ * are meaningless.
+ * Note that the data is used to initialize the SIMD constants, which for
+ * technical (alignment) reasons in some compilers cannot be placed inside
+ * the text fixture classes. For that reason this data cannot go in the
+ * fixtures either.
+ *
+ * \author Erik Lindahl <erik.lindahl@scilifelab.se>
+ * \ingroup module_simd
+ */
+
+#include "gromacs/utility/real.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/*! \cond internal */
+/*! \addtogroup module_simd */
+/*! \{ */
+extern const real czero; //!< Value 0.0 in real precision
+extern const real c0; //!< Random fp value using entire mantissa
+extern const real c1; //!< Random fp value using entire mantissa
+extern const real c2; //!< Random fp value using entire mantissa
+extern const real c3; //!< Random fp value using entire mantissa
+extern const real c4; //!< Random fp value using entire mantissa
+extern const real c5; //!< Random fp value using entire mantissa
+extern const real c5; //!< Random fp value using entire mantissa
+extern const real c6; //!< Random fp value using entire mantissa
+extern const real c7; //!< Random fp value using entire mantissa
+extern const real c8; //!< Random fp value using entire mantissa
+extern const real c9; //!< Random fp value using entire mantissa
+
+/*! \} */
+/*! \endcond */
+
+} // namespace test
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
+#include "data.h"
+
namespace gmx
{
namespace test
TEST(SimdScalarTest, load)
{
- real ref = 1.234;
- real val = load(&ref);
+ real val = load(&c1);
- EXPECT_EQ(ref, val);
+ EXPECT_EQ(c1, val);
}
TEST(SimdScalarTest, loadU)
{
- real ref = 1.234;
- real val = loadU(&ref);
+ real val = loadU(&c1);
- EXPECT_EQ(ref, val);
+ EXPECT_EQ(c1, val);
}
TEST(SimdScalarTest, store)
{
- real ref = 1.234;
real val;
- store(&val, ref);
+ store(&val, c1);
- EXPECT_EQ(ref, val);
+ EXPECT_EQ(c1, val);
}
TEST(SimdScalarTest, storeU)
{
- real ref = 1.234;
real val;
- store(&val, ref);
+ store(&val, c1);
- EXPECT_EQ(ref, val);
+ EXPECT_EQ(c1, val);
}
TEST(SimdScalarTest, setZero)
{
real signBit = GMX_REAL_NEGZERO;
- EXPECT_EQ(real(1), andNot(signBit, real(-1)));
- EXPECT_EQ(real(2), andNot(signBit, real(2)));
+ EXPECT_EQ(c1, andNot(signBit, -c1));
+ EXPECT_EQ(c2, andNot(signBit, c2));
}
TEST(SimdScalarTest, fma)
{
- EXPECT_EQ(real(27), fma(real(3), real(6), real(9))); // 3*6+9=27
+ EXPECT_EQ(c1*c2+c3, fma(real(c1), real(c2), real(c3)));
}
TEST(SimdScalarTest, fms)
{
- EXPECT_EQ(real(9), fms(real(3), real(6), real(9))); // 3*6-9=9
+ EXPECT_EQ(c1*c2-c3, fms(c1, c2, c3));
}
TEST(SimdScalarTest, fnma)
{
- EXPECT_EQ(real(-9), fnma(real(3), real(6), real(9))); // -3*6+9=-9
+ EXPECT_EQ(-c1*c2+c3, fnma(c1, c2, c3));
}
TEST(SimdScalarTest, fnms)
{
- EXPECT_EQ(real(-27), fnms(real(3), real(6), real(9))); // -3*6-9=-27
+ EXPECT_EQ(-c1*c2-c3, fnms(c1, c2, c3));
}
TEST(SimdScalarTest, maskAdd)
{
- EXPECT_EQ(real(3), maskAdd(real(3), real(6), false));
- EXPECT_EQ(real(9), maskAdd(real(3), real(6), true));
+ EXPECT_EQ(c1, maskAdd(c1, c2, false));
+ EXPECT_EQ(c1+c2, maskAdd(c1, c2, true));
}
TEST(SimdScalarTest, maskzMul)
{
- EXPECT_EQ(real(0), maskzMul(real(3), real(6), false));
- EXPECT_EQ(real(18), maskzMul(real(3), real(6), true));
+ EXPECT_EQ(czero, maskzMul(c1, c2, false));
+ EXPECT_EQ(c1*c2, maskzMul(c1, c2, true));
}
TEST(SimdScalarTest, maskzFma)
{
- EXPECT_EQ(real(0), maskzFma(real(3), real(6), real(9), false));
- EXPECT_EQ(real(27), maskzFma(real(3), real(6), real(9), true));
+ EXPECT_EQ(czero, maskzFma(c1, c2, c3, false));
+ EXPECT_EQ(c1*c2+c3, maskzFma(c1, c2, c3, true));
}
TEST(SimdScalarTest, abs)
{
- EXPECT_EQ(real(3), abs(real(-3)));
+ EXPECT_EQ(c1, abs(-c1));
}
TEST(SimdScalarTest, max)
{
- EXPECT_EQ(real(3), max(real(1), real(3)));
+ EXPECT_EQ(c3, max(c1, c3));
}
TEST(SimdScalarTest, min)
{
- EXPECT_EQ(real(1), min(real(1), real(3)));
+ EXPECT_EQ(c1, min(c1, c3));
}
TEST(SimdScalarTest, round)
TEST(SimdScalarTest, reduce)
{
- EXPECT_EQ(real(5), reduce(real(5)));
+ EXPECT_EQ(c1, reduce(c1));
}
TEST(SimdScalarTest, testBits)
{
- EXPECT_TRUE(testBits(real(1)));
+ EXPECT_TRUE(testBits(c1));
EXPECT_TRUE(testBits(GMX_REAL_NEGZERO));
- EXPECT_FALSE(testBits(real(0)));
+ EXPECT_FALSE(testBits(czero));
}
TEST(SimdScalarTest, anyTrue)
TEST(SimdScalarTest, selectByMask)
{
- EXPECT_EQ(real(5.0), selectByMask(real(5.0), true));
- EXPECT_EQ(real(0.0), selectByMask(real(5.0), false));
+ EXPECT_EQ(c1, selectByMask(c1, true));
+ EXPECT_EQ(czero, selectByMask(c1, false));
}
TEST(SimdScalarTest, selectByNotMask)
{
- EXPECT_EQ(real(0.0), selectByNotMask(real(5.0), true));
- EXPECT_EQ(real(5.0), selectByNotMask(real(5.0), false));
+ EXPECT_EQ(czero, selectByNotMask(c1, true));
+ EXPECT_EQ(c1, selectByNotMask(c1, false));
}
TEST(SimdScalarTest, blend)
{
- EXPECT_EQ(real(5.0), blend(real(3.0), real(5.0), true));
- EXPECT_EQ(real(3.0), blend(real(3.0), real(5.0), false));
+ EXPECT_EQ(c2, blend(c1, c2, true));
+ EXPECT_EQ(c1, blend(c1, c2, false));
}
TEST(SimdScalarTest, cvtR2I)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "testutils/testasserts.h"
+#include "data.h"
+
namespace gmx
{
namespace test
TEST(SimdScalarMathTest, copysign)
{
- EXPECT_EQ(real(-4), copysign(real(4), real(-5)));
- EXPECT_EQ(real(5), copysign(real(5), real(2)));
+ EXPECT_EQ(real(-c1), copysign(real(c1), real(-c2)));
+ EXPECT_EQ(real(c2), copysign(real(c2), real(c3)));
}
TEST(SimdScalarMathTest, invsqrtPair)
{
- real x0 = 1.2345;
- real x1 = 9.8765;
+ real x0 = c1;
+ real x1 = c2;
real out0, out1;
TEST(SimdScalarMathTest, inv)
{
- real x0 = 1.2345;
+ real x0 = c0;
EXPECT_EQ(real(1.0)/x0, inv(x0));
}
TEST(SimdScalarMathTest, maskzInvsqrt)
{
- real x0 = 1.2345;
+ real x0 = c0;
EXPECT_EQ(invsqrt(x0), maskzInvsqrt(x0, true));
EXPECT_EQ(real(0), maskzInvsqrt(x0, false));
TEST(SimdScalarMathTest, log)
{
- real x0 = 1.2345;
+ real x0 = c0;
EXPECT_EQ(std::log(x0), log(x0));
}
TEST(SimdScalarMathTest, exp2)
{
- real x0 = 1.2345;
+ real x0 = c0;
EXPECT_EQ(std::exp2(x0), exp2(x0));
}
TEST(SimdScalarMathTest, exp)
{
- real x0 = 1.2345;
+ real x0 = c0;
EXPECT_EQ(std::exp(x0), exp(x0));
}
TEST(SimdScalarMathTest, erf)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::erf(x0), erf(x0));
}
TEST(SimdScalarMathTest, erfc)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::erfc(x0), erfc(x0));
}
TEST(SimdScalarMathTest, sincos)
{
- real x0 = 0.51256;
+ real x0 = c0;
real s, c;
sincos(x0, &s, &c);
TEST(SimdScalarMathTest, sin)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::sin(x0), sin(x0));
}
TEST(SimdScalarMathTest, cos)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::cos(x0), cos(x0));
}
TEST(SimdScalarMathTest, tan)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::tan(x0), tan(x0));
}
TEST(SimdScalarMathTest, asin)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::asin(x0), asin(x0));
}
TEST(SimdScalarMathTest, acos)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::acos(x0), acos(x0));
}
TEST(SimdScalarMathTest, atan)
{
- real x0 = 0.51256;
+ real x0 = c0;
EXPECT_EQ(std::atan(x0), atan(x0));
}
TEST(SimdScalarMathTest, atan2)
{
- real x = 0.5;
- real y = std::sqrt(0.75);
+ real x = c0;
+ real y = std::sqrt(c0);
EXPECT_EQ(std::atan2(y, x), atan2(y, x));
TEST(SimdScalarMathTest, pmeForceCorrection)
{
- real z2 = 0.51256;
+ real z2 = c0;
// Calculate reference value for z2!=0
real z = std::sqrt(z2);
TEST(SimdScalarMathTest, pmePotentialCorrection)
{
- real z2 = 0.51256;
+ real z2 = c0;
// Calculate reference value for z2!=0
real z = std::sqrt(z2);
TEST(SimdScalarMathTest, invsqrtPairSingleAccuracy)
{
- double x0 = 1.2345;
- double x1 = 9.8765;
+ double x0 = c1;
+ double x1 = c2;
double out0, out1;
TEST(SimdScalarMathTest, invSingleAccuracy)
{
- double x0 = 1.2345;
+ double x0 = c1;
EXPECT_EQ(1.0f/static_cast<float>(x0),
static_cast<float>(invSingleAccuracy(x0)));
TEST(SimdScalarMathTest, maskzInvsqrtSingleAccuracy)
{
- double x0 = 1.2345;
+ double x0 = c1;
EXPECT_EQ(invsqrt(static_cast<float>(x0)),
static_cast<float>(maskzInvsqrtSingleAccuracy(x0, true)));
TEST(SimdScalarMathTest, logSingleAccuracy)
{
- double x0 = 1.2345;
+ double x0 = c1;
EXPECT_EQ(std::log(static_cast<float>(x0)),
static_cast<float>(logSingleAccuracy(x0)));
TEST(SimdScalarMathTest, exp2SingleAccuracy)
{
- double x0 = 1.2345;
+ double x0 = c1;
EXPECT_EQ(std::exp2(static_cast<float>(x0)),
static_cast<float>(exp2SingleAccuracy(x0)));
TEST(SimdScalarMathTest, expSingleAccuracy)
{
- double x0 = 1.2345;
+ double x0 = c1;
EXPECT_EQ(std::exp(static_cast<float>(x0)),
static_cast<float>(expSingleAccuracy(x0)));
TEST(SimdScalarMathTest, erfSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::erf(static_cast<float>(x0)), static_cast<float>(erfSingleAccuracy(x0)));
}
TEST(SimdScalarMathTest, erfcSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::erfc(static_cast<float>(x0)), static_cast<float>(erfcSingleAccuracy(x0)));
}
TEST(SimdScalarMathTest, sincosSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
double s, c;
sincosSingleAccuracy(x0, &s, &c);
TEST(SimdScalarMathTest, sinSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::sin(static_cast<float>(x0)),
static_cast<float>(sinSingleAccuracy(x0)));
TEST(SimdScalarMathTest, cosSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::cos(static_cast<float>(x0)),
static_cast<float>(cosSingleAccuracy(x0)));
TEST(SimdScalarMathTest, tanSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::tan(static_cast<float>(x0)),
static_cast<float>(tanSingleAccuracy(x0)));
TEST(SimdScalarMathTest, asinSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::asin(static_cast<float>(x0)),
static_cast<float>(asinSingleAccuracy(x0)));
TEST(SimdScalarMathTest, acosSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::acos(static_cast<float>(x0)),
static_cast<float>(acosSingleAccuracy(x0)));
TEST(SimdScalarMathTest, atanSingleAccuracy)
{
- double x0 = 0.51256;
+ double x0 = c0;
EXPECT_EQ(std::atan(static_cast<float>(x0)),
static_cast<float>(atanSingleAccuracy(x0)));
TEST(SimdScalarMathTest, atan2SingleAccuracy)
{
- double x = 0.5;
- double y = std::sqrt(0.75);
+ double x = c0;
+ double y = std::sqrt(c0);
EXPECT_EQ(std::atan2(static_cast<float>(y), static_cast<float>(x)),
TEST(SimdScalarMathTest, pmeForceCorrectionSingleAccuracy)
{
- double z2 = 0.51256;
+ double z2 = c0;
// Calculate reference value for z2!=0 in single precision
float z = std::sqrt(static_cast<float>(z2));
TEST(SimdScalarMathTest, pmePotentialCorrectionSingleAccuracy)
{
- double z2 = 0.51256;
+ double z2 = c0;
// Calculate reference value for z2!=0 in single precision
float z = std::sqrt(static_cast<float>(z2));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
+#include "testutils/testasserts.h"
+
+#include "data.h"
+
namespace gmx
{
namespace test
TEST(SimdScalarUtilTest, gatherLoadTranspose)
{
- real data[8] = {1, 2, 3, 4, 5, 6, 7, 8};
+ real data[8] = {c0, c1, c2, c3, c4, c5, c6, c7};
std::int32_t offset = 1;
real v0, v1, v2, v3;
TEST(SimdScalarUtilTest, gatherLoadUTranspose)
{
- real data[6] = {1, 2, 3, 4, 5, 6};
+ real data[6] = {c0, c1, c2, c3, c4, c5};
std::int32_t offset = 1;
real v0, v1, v2;
transposeScatterStoreU<3>(data, &offset, v0, v1, v2);
- EXPECT_EQ(real(0.0), data[0]);
- EXPECT_EQ(real(0.0), data[1]);
- EXPECT_EQ(real(0.0), data[2]);
+ EXPECT_EQ(czero, data[0]);
+ EXPECT_EQ(czero, data[1]);
+ EXPECT_EQ(czero, data[2]);
EXPECT_EQ(v0, data[3]);
EXPECT_EQ(v1, data[4]);
EXPECT_EQ(v2, data[5]);
- EXPECT_EQ(real(0.0), data[6]);
- EXPECT_EQ(real(0.0), data[7]);
- EXPECT_EQ(real(0.0), data[8]);
+ EXPECT_EQ(czero, data[6]);
+ EXPECT_EQ(czero, data[7]);
+ EXPECT_EQ(czero, data[8]);
}
TEST(SimdScalarUtilTest, transposeScatterIncrU)
{
real data[9] = {10, 20, 30, 40, 50, 60, 70, 80, 90};
std::int32_t offset = 1;
- real v0 = 1;
- real v1 = 2;
- real v2 = 3;
+ real v0 = c1;
+ real v1 = c2;
+ real v2 = c3;
transposeScatterIncrU<3>(data, &offset, v0, v1, v2);
EXPECT_EQ(real(10), data[0]);
EXPECT_EQ(real(20), data[1]);
EXPECT_EQ(real(30), data[2]);
- EXPECT_EQ(real(41), data[3]);
- EXPECT_EQ(real(52), data[4]);
- EXPECT_EQ(real(63), data[5]);
+ EXPECT_EQ(real(40+c1), data[3]);
+ EXPECT_EQ(real(50+c2), data[4]);
+ EXPECT_EQ(real(60+c3), data[5]);
EXPECT_EQ(real(70), data[6]);
EXPECT_EQ(real(80), data[7]);
EXPECT_EQ(real(90), data[8]);
{
real data[9] = {10, 20, 30, 40, 50, 60, 70, 80, 90};
std::int32_t offset = 1;
- real v0 = 1;
- real v1 = 2;
- real v2 = 3;
+ real v0 = c1;
+ real v1 = c2;
+ real v2 = c3;
transposeScatterDecrU<3>(data, &offset, v0, v1, v2);
EXPECT_EQ(real(10), data[0]);
EXPECT_EQ(real(20), data[1]);
EXPECT_EQ(real(30), data[2]);
- EXPECT_EQ(real(39), data[3]);
- EXPECT_EQ(real(48), data[4]);
- EXPECT_EQ(real(57), data[5]);
+ EXPECT_EQ(real(40-c1), data[3]);
+ EXPECT_EQ(real(50-c2), data[4]);
+ EXPECT_EQ(real(60-c3), data[5]);
EXPECT_EQ(real(70), data[6]);
EXPECT_EQ(real(80), data[7]);
EXPECT_EQ(real(90), data[8]);
TEST(SimdScalarTest, expandScalarsToTriplets)
{
- real scalar = 1.234;
+ real scalar = c1;
real t0, t1, t2;
expandScalarsToTriplets(scalar, &t0, &t1, &t2);
TEST(SimdScalarUtilTest, gatherLoadBySimdIntTranspose)
{
- real data[8] = {1, 2, 3, 4, 5, 6, 7, 8};
+ real data[8] = {c0, c1, c2, c3, c4, c5, c6, c7};
std::int32_t offset = 1;
real v0, v1, v2, v3;
TEST(SimdScalarUtilTest, gatherLoadUBySimdIntTranspose)
{
- real data[8] = {1, 2, 3, 4, 5, 6, 7, 8};
+ real data[8] = {c0, c1, c2, c3, c4, c5, c6, c7};
std::int32_t offset = 1;
real v0, v1;
TEST(SimdScalarUtilTest, reduceIncr4ReturnSum)
{
real data[6] = {0, 0, 0, 0, 0, 0};
- real v0 = 1;
- real v1 = 2;
- real v2 = 3;
- real v3 = 4;
+ real v0 = c1;
+ real v1 = c2;
+ real v2 = c3;
+ real v3 = c4;
real sum;
sum = reduceIncr4ReturnSum(data+1, v0, v1, v2, v3);
- EXPECT_EQ(real(0.0), data[0]);
+ EXPECT_EQ(czero, data[0]);
EXPECT_EQ(v0, data[1]);
EXPECT_EQ(v1, data[2]);
EXPECT_EQ(v2, data[3]);
EXPECT_EQ(v3, data[4]);
- EXPECT_EQ(real(0.0), data[5]);
+ EXPECT_EQ(czero, data[5]);
- EXPECT_EQ(real(v0+v1+v2+v3), sum);
+ EXPECT_REAL_EQ_TOL(real(v0+v1+v2+v3), sum, defaultRealTolerance());
}
/*! \} */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* them in a single place makes sure they are consistent.
*/
#if GMX_SIMD_HAVE_REAL
-const SimdReal rSimd_1_2_3 = setSimdRealFrom3R(1, 2, 3);
-const SimdReal rSimd_4_5_6 = setSimdRealFrom3R(4, 5, 6);
-const SimdReal rSimd_7_8_9 = setSimdRealFrom3R(7, 8, 9);
-const SimdReal rSimd_5_7_9 = setSimdRealFrom3R(5, 7, 9);
-const SimdReal rSimd_m1_m2_m3 = setSimdRealFrom3R(-1, -2, -3);
-const SimdReal rSimd_3_1_4 = setSimdRealFrom3R(3, 1, 4);
-const SimdReal rSimd_m3_m1_m4 = setSimdRealFrom3R(-3, -1, -4);
-const SimdReal rSimd_2p25 = setSimdRealFrom1R(2.25);
-const SimdReal rSimd_3p25 = setSimdRealFrom1R(3.25);
-const SimdReal rSimd_3p75 = setSimdRealFrom1R(3.75);
+const SimdReal rSimd_c0c1c2 = setSimdRealFrom3R( c0, c1, c2);
+const SimdReal rSimd_c3c4c5 = setSimdRealFrom3R( c3, c4, c5);
+const SimdReal rSimd_c6c7c8 = setSimdRealFrom3R( c6, c7, c8);
+const SimdReal rSimd_c3c0c4 = setSimdRealFrom3R( c3, c0, c4);
+const SimdReal rSimd_c4c6c8 = setSimdRealFrom3R( c4, c6, c8);
+const SimdReal rSimd_c7c2c3 = setSimdRealFrom3R( c7, c2, c3);
+const SimdReal rSimd_m0m1m2 = setSimdRealFrom3R(-c0, -c1, -c2);
+const SimdReal rSimd_m3m0m4 = setSimdRealFrom3R(-c3, -c0, -c4);
+
+const SimdReal rSimd_2p25 = setSimdRealFrom1R( 2.25);
+const SimdReal rSimd_3p25 = setSimdRealFrom1R( 3.25);
+const SimdReal rSimd_3p75 = setSimdRealFrom1R( 3.75);
const SimdReal rSimd_m2p25 = setSimdRealFrom1R(-2.25);
const SimdReal rSimd_m3p25 = setSimdRealFrom1R(-3.25);
const SimdReal rSimd_m3p75 = setSimdRealFrom1R(-3.75);
const SimdReal rSimd_Exp = setSimdRealFrom3R( 1.4055235171027452623914516e+18,
5.3057102734253445623914516e-13,
-2.1057102745623934534514516e+16);
-# if GMX_SIMD_HAVE_DOUBLE && GMX_DOUBLE
+#if GMX_SIMD_HAVE_DOUBLE && GMX_DOUBLE
// Make sure we also test exponents outside single precision when we use double
const SimdReal rSimd_ExpDouble = setSimdRealFrom3R( 6.287393598732017379054414e+176,
8.794495252903116023030553e-140,
-3.637060701570496477655022e+202);
-# endif
-#endif // GMX_SIMD_HAVE_REAL
+#endif // GMX_SIMD_HAVE_DOUBLE && GMX_DOUBLE
+
+#if GMX_SIMD_HAVE_LOGICAL
+// The numbers below all have exponent (2^0), which will not change with AND/OR operations.
+// We also leave the last part of the mantissa as zeros, to avoid rounding issues in the compiler
+#if GMX_DOUBLE
+const SimdReal rSimd_logicalA = setSimdRealFrom1R(1.3333333332557231188); // mantissa 01010101010101010101010101010101
+const SimdReal rSimd_logicalB = setSimdRealFrom1R(1.7999999998137354851); // mantissa 11001100110011001100110011001100
+const SimdReal rSimd_logicalResultAnd = setSimdRealFrom1R(1.266666666604578495); // mantissa 01000100010001000100010001000100
+const SimdReal rSimd_logicalResultOr = setSimdRealFrom1R(1.8666666664648801088); // mantissa 11011101110111011101110111011101
+#else // GMX_DOUBLE
+const SimdReal rSimd_logicalA = setSimdRealFrom1R(1.3333282470703125); // mantissa 0101010101010101
+const SimdReal rSimd_logicalB = setSimdRealFrom1R(1.79998779296875); // mantissa 1100110011001100
+const SimdReal rSimd_logicalResultAnd = setSimdRealFrom1R(1.26666259765625); // mantissa 0100010001000100
+const SimdReal rSimd_logicalResultOr = setSimdRealFrom1R(1.8666534423828125); // mantissa 1101110111011101
+#endif // GMX_DOUBLE
+#endif // GMX_SIMD_HAVE_LOGICAL
+
+#endif // GMX_SIMD_HAVE_REAL
#if GMX_SIMD_HAVE_INT32_ARITHMETICS
const SimdInt32 iSimd_1_2_3 = setSimdIntFrom3I(1, 2, 3);
const SimdInt32 iSimd_4_5_6 = setSimdIntFrom3I(4, 5, 6);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "base.h"
+#include "data.h"
#if GMX_SIMD
* them in a single place makes sure they are consistent.
*/
#if GMX_SIMD_HAVE_REAL
-extern const SimdReal rSimd_1_2_3; //!< Generic (different) fp values.
-extern const SimdReal rSimd_4_5_6; //!< Generic (different) fp values.
-extern const SimdReal rSimd_7_8_9; //!< Generic (different) fp values.
-extern const SimdReal rSimd_5_7_9; //!< rSimd_1_2_3 + rSimd_4_5_6.
-extern const SimdReal rSimd_m1_m2_m3; //!< Generic negative floating-point values.
-extern const SimdReal rSimd_3_1_4; //!< Used to test min/max.
-extern const SimdReal rSimd_m3_m1_m4; //!< negative rSimd_3_1_4.
+extern const SimdReal rSimd_c0c1c2; //!< c0,c1,c2 repeated
+extern const SimdReal rSimd_c3c4c5; //!< c3,c4,c5 repeated
+extern const SimdReal rSimd_c6c7c8; //!< c6,c7,c8 repeated
+extern const SimdReal rSimd_c3c0c4; //!< c3,c0,c4 repeated
+extern const SimdReal rSimd_c4c6c8; //!< c4,c6,c8 repeated
+extern const SimdReal rSimd_c7c2c3; //!< c7,c2,c3 repeated
+extern const SimdReal rSimd_m0m1m2; //!< -c0,-c1,-c2 repeated
+extern const SimdReal rSimd_m3m0m4; //!< -c3,-c0,-c4 repeated
+
extern const SimdReal rSimd_2p25; //!< Value that rounds down.
extern const SimdReal rSimd_3p25; //!< Value that rounds down.
extern const SimdReal rSimd_3p75; //!< Value that rounds up.
extern const SimdReal rSimd_m3p75; //!< Negative value that rounds down.
//! Three large floating-point values whose exponents are >32.
extern const SimdReal rSimd_Exp;
+
+#if GMX_SIMD_HAVE_LOGICAL
+extern const SimdReal rSimd_logicalA; //!< Bit pattern to test logical ops
+extern const SimdReal rSimd_logicalB; //!< Bit pattern to test logical ops
+extern const SimdReal rSimd_logicalResultOr; //!< Result or bitwise 'or' of A and B
+extern const SimdReal rSimd_logicalResultAnd; //!< Result or bitwise 'and' of A and B
+#endif // GMX_SIMD_HAVE_LOGICAL
+
# if GMX_SIMD_HAVE_DOUBLE && GMX_DOUBLE
// Make sure we also test exponents outside single precision when we use double
extern const SimdReal rSimd_ExpDouble;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
+#include "data.h"
+
#if GMX_SIMD
namespace gmx
#if GMX_SIMD4_HAVE_REAL
-const Simd4Real rSimd4_1_2_3 = setSimd4RealFrom3R(1, 2, 3);
-const Simd4Real rSimd4_4_5_6 = setSimd4RealFrom3R(4, 5, 6);
-const Simd4Real rSimd4_7_8_9 = setSimd4RealFrom3R(7, 8, 9);
-const Simd4Real rSimd4_5_7_9 = setSimd4RealFrom3R(5, 7, 9);
-const Simd4Real rSimd4_m1_m2_m3 = setSimd4RealFrom3R(-1, -2, -3);
-const Simd4Real rSimd4_3_1_4 = setSimd4RealFrom3R(3, 1, 4);
-const Simd4Real rSimd4_m3_m1_m4 = setSimd4RealFrom3R(-3, -1, -4);
+const Simd4Real rSimd4_c0c1c2 = setSimd4RealFrom3R( c0, c1, c2);
+const Simd4Real rSimd4_c3c4c5 = setSimd4RealFrom3R( c3, c4, c5);
+const Simd4Real rSimd4_c6c7c8 = setSimd4RealFrom3R( c6, c7, c8);
+const Simd4Real rSimd4_c3c0c4 = setSimd4RealFrom3R( c3, c0, c4);
+const Simd4Real rSimd4_c4c6c8 = setSimd4RealFrom3R( c4, c6, c8);
+const Simd4Real rSimd4_c7c2c3 = setSimd4RealFrom3R( c7, c2, c3);
+const Simd4Real rSimd4_m0m1m2 = setSimd4RealFrom3R(-c0, -c1, -c2);
+const Simd4Real rSimd4_m3m0m4 = setSimd4RealFrom3R(-c3, -c0, -c4);
const Simd4Real rSimd4_2p25 = setSimd4RealFrom1R(2.25);
const Simd4Real rSimd4_3p75 = setSimd4RealFrom1R(3.75);
const Simd4Real rSimd4_m2p25 = setSimd4RealFrom1R(-2.25);
const Simd4Real rSimd4_m3p75 = setSimd4RealFrom1R(-3.75);
-const Simd4Real rSimd4_Exp = setSimd4RealFrom3R( 1.4055235171027452623914516e+18,
- 5.3057102734253445623914516e-13,
- -2.1057102745623934534514516e+16);
-# if GMX_SIMD_HAVE_DOUBLE && GMX_DOUBLE
-// Make sure we also test exponents outside single precision when we use double
-const Simd4Real rSimd_ExpDouble = setSimd4RealFrom3R( 6.287393598732017379054414e+176,
- 8.794495252903116023030553e-140,
- -3.637060701570496477655022e+202);
-# endif
+
+#if GMX_SIMD_HAVE_LOGICAL
+// The numbers below all have exponent (2^0), which will not change with AND/OR operations.
+// We also leave the last part of the mantissa as zeros, to avoid rounding issues in the compiler
+#if GMX_DOUBLE
+const Simd4Real rSimd4_logicalA = setSimd4RealFrom1R(1.3333333332557231188); // mantissa 01010101010101010101010101010101
+const Simd4Real rSimd4_logicalB = setSimd4RealFrom1R(1.7999999998137354851); // mantissa 11001100110011001100110011001100
+const Simd4Real rSimd4_logicalResultAnd = setSimd4RealFrom1R(1.266666666604578495); // mantissa 01000100010001000100010001000100
+const Simd4Real rSimd4_logicalResultOr = setSimd4RealFrom1R(1.8666666664648801088); // mantissa 11011101110111011101110111011101
+#else // GMX_DOUBLE
+const Simd4Real rSimd4_logicalA = setSimd4RealFrom1R(1.3333282470703125); // mantissa 0101010101010101
+const Simd4Real rSimd4_logicalB = setSimd4RealFrom1R(1.79998779296875); // mantissa 1100110011001100
+const Simd4Real rSimd4_logicalResultAnd = setSimd4RealFrom1R(1.26666259765625); // mantissa 0100010001000100
+const Simd4Real rSimd4_logicalResultOr = setSimd4RealFrom1R(1.8666534423828125); // mantissa 1101110111011101
+#endif // GMX_DOUBLE
+#endif // GMX_SIMD_HAVE_LOGICAL
::std::vector<real>
simd4Real2Vector(const Simd4Real simd4)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "base.h"
+#include "data.h"
#if GMX_SIMD
/*! \{ */
#if GMX_SIMD4_HAVE_REAL
-extern const Simd4Real rSimd4_1_2_3; //!< Generic (different) fp values.
-extern const Simd4Real rSimd4_4_5_6; //!< Generic (different) fp values.
-extern const Simd4Real rSimd4_7_8_9; //!< Generic (different) fp values.
-extern const Simd4Real rSimd4_5_7_9; //!< rSimd_1_2_3 + rSimd_4_5_6.
-extern const Simd4Real rSimd4_m1_m2_m3; //!< Generic negative fp values.
-extern const Simd4Real rSimd4_3_1_4; //!< Used to test min/max.
-extern const Simd4Real rSimd4_m3_m1_m4; //!< negative rSimd_3_1_4.
+extern const Simd4Real rSimd4_c0c1c2; //!< c0,c1,c2 repeated
+extern const Simd4Real rSimd4_c3c4c5; //!< c3,c4,c5 repeated
+extern const Simd4Real rSimd4_c6c7c8; //!< c6,c7,c8 repeated
+extern const Simd4Real rSimd4_c3c0c4; //!< c3,c0,c4 repeated
+extern const Simd4Real rSimd4_c4c6c8; //!< c4,c6,c8 repeated
+extern const Simd4Real rSimd4_c7c2c3; //!< c7,c2,c3 repeated
+extern const Simd4Real rSimd4_m0m1m2; //!< -c0,-c1,-c2 repeated
+extern const Simd4Real rSimd4_m3m0m4; //!< -c3,-c0,-c4 repeated
extern const Simd4Real rSimd4_2p25; //!< Value that rounds down.
extern const Simd4Real rSimd4_3p75; //!< Value that rounds up.
extern const Simd4Real rSimd4_m2p25; //!< Negative value that rounds up.
extern const Simd4Real rSimd4_m3p75; //!< Negative value that rounds down.
//! Three large floating-point values whose exponents are >32.
extern const Simd4Real rSimd4_Exp;
-# if GMX_SIMD_HAVE_DOUBLE && GMX_DOUBLE
-// Make sure we also test exponents outside single precision when we use double
-extern const Simd4Real rSimd4_ExpDouble;
-# endif
-extern const Simd4Real rSimd4_Bits1; //!< Pattern F0 repeated to fill single/double.
-extern const Simd4Real rSimd4_Bits2; //!< Pattern CC repeated to fill single/double.
-extern const Simd4Real rSimd4_Bits3; //!< Pattern C0 repeated to fill single/double.
-extern const Simd4Real rSimd4_Bits4; //!< Pattern 0C repeated to fill single/double.
-extern const Simd4Real rSimd4_Bits5; //!< Pattern FC repeated to fill single/double.
-extern const Simd4Real rSimd4_Bits6; //!< Pattern 3C repeated to fill single/double.
+
+#if GMX_SIMD_HAVE_LOGICAL
+extern const Simd4Real rSimd4_logicalA; //!< Bit pattern to test logical ops
+extern const Simd4Real rSimd4_logicalB; //!< Bit pattern to test logical ops
+extern const Simd4Real rSimd4_logicalResultOr; //!< Result or bitwise 'or' of A and B
+extern const Simd4Real rSimd4_logicalResultAnd; //!< Result or bitwise 'and' of A and B
+#endif // GMX_SIMD_HAVE_LOGICAL
+
+extern const Simd4Real rSimd4_Bits1; //!< Pattern F0 repeated to fill single/double.
+extern const Simd4Real rSimd4_Bits2; //!< Pattern CC repeated to fill single/double.
+extern const Simd4Real rSimd4_Bits3; //!< Pattern C0 repeated to fill single/double.
+extern const Simd4Real rSimd4_Bits4; //!< Pattern 0C repeated to fill single/double.
+extern const Simd4Real rSimd4_Bits5; //!< Pattern FC repeated to fill single/double.
+extern const Simd4Real rSimd4_Bits6; //!< Pattern 3C repeated to fill single/double.
/*! \internal
* \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "gromacs/utility/basedefinitions.h"
+#include "testutils/testasserts.h"
+
+#include "data.h"
#include "simd4.h"
#if GMX_SIMD
TEST_F(Simd4FloatingpointTest, set)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom1R(1.0), Simd4Real(1.0));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom1R(c1), Simd4Real(c1));
}
TEST_F(Simd4FloatingpointTest, add)
{
- GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_5_7_9, rSimd4_1_2_3 + rSimd4_4_5_6); // 1+4=5, 2+5=7, 3+6=9
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c0 + c3, c1 + c4, c2 + c5 ),
+ rSimd4_c0c1c2 + rSimd4_c3c4c5);
+
}
TEST_F(Simd4FloatingpointTest, sub)
{
- GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_4_5_6, rSimd4_5_7_9 - rSimd4_1_2_3); // 5-1=4, 7-2=5, 9-3=6
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c0 - c3, c1 - c4, c2 - c5 ),
+ rSimd4_c0c1c2 - rSimd4_c3c4c5);
}
TEST_F(Simd4FloatingpointTest, mul)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(4, 10, 18), rSimd4_1_2_3 * rSimd4_4_5_6);
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c0 * c3, c1 * c4, c2 * c5 ),
+ rSimd4_c0c1c2 * rSimd4_c3c4c5);
}
TEST_F(Simd4FloatingpointTest, fma)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(11, 18, 27), fma(rSimd4_1_2_3, rSimd4_4_5_6, rSimd4_7_8_9)); // 1*4+7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD4_REAL_NEAR(setSimd4RealFrom3R(c0 * c3 + c6, c1 * c4 + c7, c2 * c5 + c8),
+ fma(rSimd4_c0c1c2, rSimd4_c3c4c5, rSimd4_c6c7c8));
}
TEST_F(Simd4FloatingpointTest, fms)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-3, 2, 9), fms(rSimd4_1_2_3, rSimd4_4_5_6, rSimd4_7_8_9)); // 1*4-7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD4_REAL_NEAR(setSimd4RealFrom3R(c0 * c3 - c6, c1 * c4 - c7, c2 * c5 - c8),
+ fms(rSimd4_c0c1c2, rSimd4_c3c4c5, rSimd4_c6c7c8));
}
TEST_F(Simd4FloatingpointTest, fnma)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(3, -2, -9), fnma(rSimd4_1_2_3, rSimd4_4_5_6, rSimd4_7_8_9)); // -1*4+7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD4_REAL_NEAR(setSimd4RealFrom3R(c6 - c0 * c3, c7 - c1 * c4, c8 - c2 * c5),
+ fnma(rSimd4_c0c1c2, rSimd4_c3c4c5, rSimd4_c6c7c8));
}
TEST_F(Simd4FloatingpointTest, fnms)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-11, -18, -27), fnms(rSimd4_1_2_3, rSimd4_4_5_6, rSimd4_7_8_9)); // -1*4-7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD4_REAL_NEAR(setSimd4RealFrom3R(-c0 * c3 - c6, -c1 * c4 - c7, -c2 * c5 - c8),
+ fnms(rSimd4_c0c1c2, rSimd4_c3c4c5, rSimd4_c6c7c8));
}
TEST_F(Simd4FloatingpointTest, abs)
{
- GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_1_2_3, abs(rSimd4_1_2_3)); // fabs(x)=x
- GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_1_2_3, abs(rSimd4_m1_m2_m3)); // fabs(-x)=x
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_c0c1c2, abs(rSimd4_c0c1c2)); // fabs(x)=x
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_c0c1c2, abs(rSimd4_m0m1m2)); // fabs(-x)=x
}
TEST_F(Simd4FloatingpointTest, neg)
{
- GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_m1_m2_m3, -rSimd4_1_2_3); // fneg(x)=-x
- GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_1_2_3, -rSimd4_m1_m2_m3); // fneg(-x)=x
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_m0m1m2, -(rSimd4_c0c1c2)); // fneg(x)=-x
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_c0c1c2, -(rSimd4_m0m1m2)); // fneg(-x)=x
}
#if GMX_SIMD_HAVE_LOGICAL
-/* 1.3333282470703125 has mantissa 0101010101010101 (followed by zeros)
- * 1.79998779296875 has mantissa 1100110011001100 (followed by zeros)
- * 1.26666259765625 has mantissa 0100010001000100 (followed by zeros)
- * 1.8666534423828125 has mantissa 1101110111011101 (followed by zeros)
- *
- * Since all of them have the same exponent (2^0), the exponent will
- * not change with AND or OR operations.
- */
TEST_F(Simd4FloatingpointTest, and)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom1R(1.26666259765625),
- Simd4Real(1.3333282470703125) & Simd4Real(1.79998779296875));
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_logicalResultAnd,
+ (rSimd4_logicalA & rSimd4_logicalB));
}
TEST_F(Simd4FloatingpointTest, or)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom1R(1.8666534423828125),
- Simd4Real(1.3333282470703125) | Simd4Real(1.79998779296875));
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_logicalResultOr,
+ (rSimd4_logicalA | rSimd4_logicalB));
}
TEST_F(Simd4FloatingpointTest, xor)
* in only the sign bit being set. We then use this bit change the sign of
* different numbers.
*/
- Simd4Real signbit = Simd4Real(1.5) ^ Simd4Real(-1.5);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-1, 2, -3), signbit ^ setSimd4RealFrom3R(1, -2, 3));
+ Simd4Real signbit = Simd4Real(c1) ^ Simd4Real(-c1);
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-c2, c3, -c4), signbit ^ setSimd4RealFrom3R(c2, -c3, c4));
}
TEST_F(Simd4FloatingpointTest, andNot)
/* Use xor (which we already tested, so fix that first if both tests fail)
* to extract the sign bit, and then use andnot to take absolute values.
*/
- Simd4Real signbit = Simd4Real(1.5) ^ Simd4Real(-1.5);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(1, 2, 3), andNot(signbit, setSimd4RealFrom3R(-1, 2, -3)));
+ Simd4Real signbit = Simd4Real(c1) ^ Simd4Real(-c1);
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c2, c3, c4), andNot(signbit, setSimd4RealFrom3R(-c2, c3, -c4)));
}
#endif
TEST_F(Simd4FloatingpointTest, max)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(3, 2, 4), max(rSimd4_1_2_3, rSimd4_3_1_4));
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(3, 2, 4), max(rSimd4_3_1_4, rSimd4_1_2_3));
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-1, -1, -3), max(rSimd4_m1_m2_m3, rSimd4_m3_m1_m4));
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-1, -1, -3), max(rSimd4_m3_m1_m4, rSimd4_m1_m2_m3));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R( c3, c1, c4), max(rSimd4_c0c1c2, rSimd4_c3c0c4));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R( c3, c1, c4), max(rSimd4_c3c0c4, rSimd4_c0c1c2));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-c0, -c0, -c2), max(rSimd4_m0m1m2, rSimd4_m3m0m4));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-c0, -c0, -c2), max(rSimd4_m3m0m4, rSimd4_m0m1m2));
}
TEST_F(Simd4FloatingpointTest, min)
{
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(1, 1, 3), min(rSimd4_1_2_3, rSimd4_3_1_4));
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(1, 1, 3), min(rSimd4_3_1_4, rSimd4_1_2_3));
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-3, -2, -4), min(rSimd4_m1_m2_m3, rSimd4_m3_m1_m4));
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-3, -2, -4), min(rSimd4_m3_m1_m4, rSimd4_m1_m2_m3));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R( c0, c0, c2), min(rSimd4_c0c1c2, rSimd4_c3c0c4));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R( c0, c0, c2), min(rSimd4_c3c0c4, rSimd4_c0c1c2));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-c3, -c1, -c4), min(rSimd4_m0m1m2, rSimd4_m3m0m4));
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(-c3, -c1, -c4), min(rSimd4_m3m0m4, rSimd4_m0m1m2));
}
TEST_F(Simd4FloatingpointTest, round)
TEST_F(Simd4FloatingpointTest, cmpEqAndSelectByMask)
{
- Simd4Bool eq = (rSimd4_5_7_9 == rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(0, 0, 3), selectByMask(rSimd4_1_2_3, eq));
+ Simd4Bool eq = rSimd4_c4c6c8 == rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(0, 0, c2), selectByMask(rSimd4_c0c1c2, eq));
}
TEST_F(Simd4FloatingpointTest, selectByNotMask)
{
- Simd4Bool eq = (rSimd4_5_7_9 == rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(1, 2, 0), selectByNotMask(rSimd4_1_2_3, eq));
+ Simd4Bool eq = rSimd4_c4c6c8 == rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c0, c1, 0), selectByNotMask(rSimd4_c0c1c2, eq));
}
TEST_F(Simd4FloatingpointTest, cmpNe)
{
- Simd4Bool eq = (rSimd4_5_7_9 != rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(1, 2, 0), selectByMask(rSimd4_1_2_3, eq));
+ Simd4Bool eq = rSimd4_c4c6c8 != rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c0, c1, 0), selectByMask(rSimd4_c0c1c2, eq));
}
TEST_F(Simd4FloatingpointTest, cmpLe)
{
- Simd4Bool le = (rSimd4_5_7_9 <= rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_1_2_3, selectByMask(rSimd4_1_2_3, le));
+ Simd4Bool le = rSimd4_c4c6c8 <= rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_c0c1c2, selectByMask(rSimd4_c0c1c2, le));
}
TEST_F(Simd4FloatingpointTest, cmpLt)
{
- Simd4Bool lt = (rSimd4_5_7_9 < rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(1, 2, 0), selectByMask(rSimd4_1_2_3, lt));
+ Simd4Bool lt = rSimd4_c4c6c8 < rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c0, c1, 0), selectByMask(rSimd4_c0c1c2, lt));
}
TEST_F(Simd4FloatingpointTest, andB)
{
- Simd4Bool eq = (rSimd4_5_7_9 == rSimd4_7_8_9);
- Simd4Bool le = (rSimd4_5_7_9 <= rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(0, 0, 3), selectByMask(rSimd4_1_2_3, eq && le));
+ Simd4Bool eq = rSimd4_c4c6c8 == rSimd4_c6c7c8;
+ Simd4Bool le = rSimd4_c4c6c8 <= rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(0, 0, c2), selectByMask(rSimd4_c0c1c2, (eq && le)));
}
TEST_F(Simd4FloatingpointTest, orB)
{
- Simd4Bool eq = (rSimd4_5_7_9 == rSimd4_7_8_9);
- Simd4Bool lt = (rSimd4_5_7_9 < rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(1, 2, 3), selectByMask(rSimd4_1_2_3, eq || lt));
+ Simd4Bool eq = rSimd4_c4c6c8 == rSimd4_c6c7c8;
+ Simd4Bool lt = rSimd4_c4c6c8 < rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(rSimd4_c0c1c2, selectByMask(rSimd4_c0c1c2, (eq || lt)));
}
TEST_F(Simd4FloatingpointTest, anyTrue)
* We cannot check for truth values for "any" element beyond the first,
* since that part of the data will not be used if simd width is 1.
*/
- eq = (rSimd4_5_7_9 == setSimd4RealFrom3R(5, 0, 0));
+ eq = (rSimd4_c4c6c8 == setSimd4RealFrom3R(c4, 0, 0));
EXPECT_TRUE(anyTrue(eq));
- eq = (rSimd4_1_2_3 == rSimd4_4_5_6);
+ eq = (rSimd4_c0c1c2 == rSimd4_c3c4c5);
EXPECT_FALSE(anyTrue(eq));
}
TEST_F(Simd4FloatingpointTest, blend)
{
- Simd4Bool lt = (rSimd4_5_7_9 < rSimd4_7_8_9);
- GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(4, 5, 3), blend(rSimd4_1_2_3, rSimd4_4_5_6, lt));
+ Simd4Bool lt = rSimd4_c4c6c8 < rSimd4_c6c7c8;
+ GMX_EXPECT_SIMD4_REAL_EQ(setSimd4RealFrom3R(c3, c4, c2), blend(rSimd4_c0c1c2, rSimd4_c3c4c5, lt));
}
TEST_F(Simd4FloatingpointTest, reduce)
{
// The horizontal sum of the SIMD variable depends on the width, so
// simply store it an extra time and calculate what the sum should be
- std::vector<real> v = simd4Real2Vector(rSimd4_1_2_3);
+ std::vector<real> v = simd4Real2Vector(rSimd4_c3c4c5);
real sum = 0.0;
for (int i = 0; i < GMX_SIMD4_WIDTH; i++)
sum += v[i];
}
- EXPECT_EQ(sum, reduce(rSimd4_1_2_3));
+ EXPECT_REAL_EQ_TOL(sum, reduce(rSimd4_c3c4c5), defaultRealTolerance() );
}
TEST_F(Simd4FloatingpointTest, dotProduct)
{
- Simd4Real v1 = setSimd4RealFrom3R(1, 4, 5);
- Simd4Real v2 = setSimd4RealFrom3R(3, 8, 2);
-# if GMX_DOUBLE
- EXPECT_DOUBLE_EQ(45.0, dotProduct(v1, v2));
-# else
- EXPECT_FLOAT_EQ(45.0, dotProduct(v1, v2));
-# endif
+ real res = c0*c3 + c1*c4 + c2*c5;
+
+ EXPECT_REAL_EQ_TOL(res, dotProduct(rSimd4_c0c1c2, rSimd4_c3c4c5), defaultRealTolerance());
}
TEST_F(Simd4FloatingpointTest, transpose)
// Assign data with tens as row, single-digit as column
for (i = 0; i < 4; i++)
{
- p0[i] = 0*10 + i*1;
- p1[i] = 1*10 + i*1;
- p2[i] = 2*10 + i*1;
- p3[i] = 3*10 + i*1;
+ // Scale by 1+100*eps to use low bits tii
+ p0[i] = (0*10 + i*1) * (1.0 + 100*GMX_REAL_EPS);
+ p1[i] = (1*10 + i*1) * (1.0 + 100*GMX_REAL_EPS);
+ p2[i] = (2*10 + i*1) * (1.0 + 100*GMX_REAL_EPS);
+ p3[i] = (3*10 + i*1) * (1.0 + 100*GMX_REAL_EPS);
}
v0 = load4(p0);
for (i = 0; i < 4; i++)
{
- EXPECT_EQ(i*10+0, p0[i]);
- EXPECT_EQ(i*10+1, p1[i]);
- EXPECT_EQ(i*10+2, p2[i]);
- EXPECT_EQ(i*10+3, p3[i]);
+ EXPECT_REAL_EQ_TOL( (i*10+0) * (1.0 + 100*GMX_REAL_EPS), p0[i], defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL( (i*10+1) * (1.0 + 100*GMX_REAL_EPS), p1[i], defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL( (i*10+2) * (1.0 + 100*GMX_REAL_EPS), p2[i], defaultRealTolerance());
+ EXPECT_REAL_EQ_TOL( (i*10+3) * (1.0 + 100*GMX_REAL_EPS), p3[i], defaultRealTolerance());
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "gromacs/simd/vector_operations.h"
+#include "data.h"
#include "simd4.h"
#if GMX_SIMD
TEST_F(Simd4VectorOperationsTest, norm2)
{
- Simd4Real simdX = setSimd4RealFrom3R(1, 2, 3);
- Simd4Real simdY = setSimd4RealFrom3R(3, 0, 5);
- Simd4Real simdZ = setSimd4RealFrom3R(4, 1, 8);
- Simd4Real simdR2 = setSimd4RealFrom3R(26, 5, 98);
+ Simd4Real simdX = rSimd4_c0c1c2;
+ Simd4Real simdY = rSimd4_c3c4c5;
+ Simd4Real simdZ = rSimd4_c6c7c8;
+ Simd4Real simdR2 = setSimd4RealFrom3R(c0*c0 + c3*c3 + c6*c6,
+ c1*c1 + c4*c4 + c7*c7,
+ c2*c2 + c5*c5 + c8*c8);
setUlpTol(2);
GMX_EXPECT_SIMD4_REAL_NEAR(simdR2, norm2(simdX, simdY, simdZ));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "testutils/testasserts.h"
+#include "data.h"
#include "simd.h"
#if GMX_SIMD
TEST_F(SimdFloatingpointTest, set)
{
- real r = 2.0;
- real *p = &r;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(1.0), SimdReal(1.0));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(r), SimdReal(*p));
+ const real *p = &c0;
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(c1), SimdReal(c1));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(c0), SimdReal(*p));
}
TEST_F(SimdFloatingpointTest, add)
{
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_5_7_9,
- (rSimd_1_2_3 + rSimd_4_5_6)); // 1+4=5, 2+5=7, 3+6=9
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 + c3, c1 + c4, c2 + c5 ),
+ rSimd_c0c1c2 + rSimd_c3c4c5);
}
TEST_F(SimdFloatingpointTest, maskAdd)
{
- SimdBool m = setSimdRealFrom3R(1, 0, 1) != setZero();
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(5, 2, 9),
- maskAdd(rSimd_1_2_3, rSimd_4_5_6, m));
+ SimdBool m = setSimdRealFrom3R(c6, 0, c7) != setZero();
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 + c3, c1 + 0.0, c2 + c5 ),
+ maskAdd(rSimd_c0c1c2, rSimd_c3c4c5, m));
}
TEST_F(SimdFloatingpointTest, sub)
{
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_4_5_6,
- (rSimd_5_7_9 - rSimd_1_2_3)); // 5-1=4, 7-2=5, 9-3=6
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 - c3, c1 - c4, c2 - c5 ),
+ rSimd_c0c1c2 - rSimd_c3c4c5);
}
TEST_F(SimdFloatingpointTest, mul)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(4, 10, 18),
- (rSimd_1_2_3 * rSimd_4_5_6));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 * c3, c1 * c4, c2 * c5 ),
+ rSimd_c0c1c2 * rSimd_c3c4c5);
}
TEST_F(SimdFloatingpointTest, maskzMul)
{
- SimdBool m = setSimdRealFrom3R(1, 0, 1) != setZero();
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(4, 0, 18),
- maskzMul(rSimd_1_2_3, rSimd_4_5_6, m));
+ SimdBool m = setSimdRealFrom3R(c1, 0, c1) != setZero();
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 * c3, 0.0, c2 * c5 ),
+ maskzMul(rSimd_c0c1c2, rSimd_c3c4c5, m));
}
TEST_F(SimdFloatingpointTest, fma)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(11, 18, 27),
- fma(rSimd_1_2_3, rSimd_4_5_6, rSimd_7_8_9)); // 1*4+7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 * c3 + c6, c1 * c4 + c7, c2 * c5 + c8),
+ fma(rSimd_c0c1c2, rSimd_c3c4c5, rSimd_c6c7c8));
}
+
TEST_F(SimdFloatingpointTest, maskzFma)
{
- SimdBool m = setSimdRealFrom3R(1, 0, 1) != setZero();
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(11, 0, 27),
- maskzFma(rSimd_1_2_3, rSimd_4_5_6, rSimd_7_8_9, m)); // 1*4+7, etc.
+ SimdBool m = setSimdRealFrom3R(c2, 0, c3) != setZero();
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 * c3 + c6, 0.0, c2 * c5 + c8),
+ maskzFma(rSimd_c0c1c2, rSimd_c3c4c5, rSimd_c6c7c8, m));
}
TEST_F(SimdFloatingpointTest, fms)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-3, 2, 9),
- fms(rSimd_1_2_3, rSimd_4_5_6, rSimd_7_8_9)); // 1*4-7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c0 * c3 - c6, c1 * c4 - c7, c2 * c5 - c8),
+ fms(rSimd_c0c1c2, rSimd_c3c4c5, rSimd_c6c7c8));
}
TEST_F(SimdFloatingpointTest, fnma)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(3, -2, -9),
- fnma(rSimd_1_2_3, rSimd_4_5_6, rSimd_7_8_9)); // -1*4+7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(c6 - c0 * c3, c7 - c1 * c4, c8 - c2 * c5),
+ fnma(rSimd_c0c1c2, rSimd_c3c4c5, rSimd_c6c7c8));
}
TEST_F(SimdFloatingpointTest, fnms)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-11, -18, -27),
- fnms(rSimd_1_2_3, rSimd_4_5_6, rSimd_7_8_9)); // -1*4-7, etc.
+ // The last bit of FMA operations depends on hardware, so we don't require exact match
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(-c0 * c3 - c6, -c1 * c4 - c7, -c2 * c5 - c8),
+ fnms(rSimd_c0c1c2, rSimd_c3c4c5, rSimd_c6c7c8));
}
TEST_F(SimdFloatingpointTest, abs)
{
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_1_2_3, abs(rSimd_1_2_3)); // fabs(x)=x
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_1_2_3, abs(rSimd_m1_m2_m3)); // fabs(-x)=x
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_c0c1c2, abs(rSimd_c0c1c2)); // fabs(x)=x
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_c0c1c2, abs(rSimd_m0m1m2)); // fabs(-x)=x
}
TEST_F(SimdFloatingpointTest, neg)
{
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_m1_m2_m3, -(rSimd_1_2_3)); // fneg(x)=-x
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_1_2_3, -(rSimd_m1_m2_m3)); // fneg(-x)=x
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_m0m1m2, -(rSimd_c0c1c2)); // fneg(x)=-x
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_c0c1c2, -(rSimd_m0m1m2)); // fneg(-x)=x
}
#if GMX_SIMD_HAVE_LOGICAL
-/* 1.3333282470703125 has mantissa 0101010101010101 (followed by zeros)
- * 1.79998779296875 has mantissa 1100110011001100 (followed by zeros)
- * 1.26666259765625 has mantissa 0100010001000100 (followed by zeros)
- * 1.8666534423828125 has mantissa 1101110111011101 (followed by zeros)
- *
- * Since all of them have the same exponent (2^0), the exponent will
- * not change with AND or OR operations.
- */
TEST_F(SimdFloatingpointTest, and)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(1.26666259765625),
- (SimdReal(1.3333282470703125) & SimdReal(1.79998779296875)));
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_logicalResultAnd,
+ (rSimd_logicalA & rSimd_logicalB));
}
TEST_F(SimdFloatingpointTest, or)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(1.8666534423828125),
- (SimdReal(1.3333282470703125) | SimdReal(1.79998779296875)));
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_logicalResultOr,
+ (rSimd_logicalA | rSimd_logicalB));
}
TEST_F(SimdFloatingpointTest, xor)
* in only the sign bit being set. We then use this bit change the sign of
* different numbers.
*/
- SimdReal signbit = SimdReal(1.5) ^ SimdReal(-1.5);
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-1, 2, -3), (signbit ^ setSimdRealFrom3R(1, -2, 3)));
+ SimdReal signbit = SimdReal(c1) ^ SimdReal(-c1);
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-c2, c3, -c4), (signbit ^ setSimdRealFrom3R(c2, -c3, c4)));
}
TEST_F(SimdFloatingpointTest, andNot)
/* Use xor (which we already tested, so fix that first if both tests fail)
* to extract the sign bit, and then use andnot to take absolute values.
*/
- SimdReal signbit = SimdReal(1.5) ^ SimdReal(-1.5);
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 2, 3), andNot(signbit, setSimdRealFrom3R(-1, 2, -3)));
+ SimdReal signbit = SimdReal(c1) ^ SimdReal(-c1);
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(c2, c3, c4), andNot(signbit, setSimdRealFrom3R(-c2, c3, -c4)));
}
#endif
TEST_F(SimdFloatingpointTest, max)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(3, 2, 4), max(rSimd_1_2_3, rSimd_3_1_4));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(3, 2, 4), max(rSimd_3_1_4, rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-1, -1, -3), max(rSimd_m1_m2_m3, rSimd_m3_m1_m4));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-1, -1, -3), max(rSimd_m3_m1_m4, rSimd_m1_m2_m3));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R( c3, c1, c4), max(rSimd_c0c1c2, rSimd_c3c0c4));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R( c3, c1, c4), max(rSimd_c3c0c4, rSimd_c0c1c2));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-c0, -c0, -c2), max(rSimd_m0m1m2, rSimd_m3m0m4));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-c0, -c0, -c2), max(rSimd_m3m0m4, rSimd_m0m1m2));
}
TEST_F(SimdFloatingpointTest, min)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 1, 3), min(rSimd_1_2_3, rSimd_3_1_4));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 1, 3), min(rSimd_3_1_4, rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-3, -2, -4), min(rSimd_m1_m2_m3, rSimd_m3_m1_m4));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-3, -2, -4), min(rSimd_m3_m1_m4, rSimd_m1_m2_m3));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R( c0, c0, c2), min(rSimd_c0c1c2, rSimd_c3c0c4));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R( c0, c0, c2), min(rSimd_c3c0c4, rSimd_c0c1c2));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-c3, -c1, -c4), min(rSimd_m0m1m2, rSimd_m3m0m4));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-c3, -c1, -c4), min(rSimd_m3m0m4, rSimd_m0m1m2));
}
TEST_F(SimdFloatingpointTest, round)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(2), round(SimdReal(2.25)));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(4), round(SimdReal(3.75)));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(-2), round(SimdReal(-2.25)));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(-4), round(SimdReal(-3.75)));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(2), round(rSimd_2p25));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(4), round(rSimd_3p75));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(-2), round(rSimd_m2p25));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom1R(-4), round(rSimd_m3p75));
}
TEST_F(SimdFloatingpointTest, trunc)
TEST_F(SimdFloatingpointTest, cmpEqAndSelectByMask)
{
- SimdBool eq = rSimd_5_7_9 == rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0, 0, 3), selectByMask(rSimd_1_2_3, eq));
+ SimdBool eq = rSimd_c4c6c8 == rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0, 0, c2), selectByMask(rSimd_c0c1c2, eq));
}
TEST_F(SimdFloatingpointTest, selectByNotMask)
{
- SimdBool eq = rSimd_5_7_9 == rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 2, 0), selectByNotMask(rSimd_1_2_3, eq));
+ SimdBool eq = rSimd_c4c6c8 == rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(c0, c1, 0), selectByNotMask(rSimd_c0c1c2, eq));
}
TEST_F(SimdFloatingpointTest, cmpNe)
{
- SimdBool eq = rSimd_5_7_9 != rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 2, 0), selectByMask(rSimd_1_2_3, eq));
+ SimdBool eq = rSimd_c4c6c8 != rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(c0, c1, 0), selectByMask(rSimd_c0c1c2, eq));
}
TEST_F(SimdFloatingpointTest, cmpLe)
{
- SimdBool le = rSimd_5_7_9 <= rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_1_2_3, selectByMask(rSimd_1_2_3, le));
+ SimdBool le = rSimd_c4c6c8 <= rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_c0c1c2, selectByMask(rSimd_c0c1c2, le));
}
TEST_F(SimdFloatingpointTest, cmpLt)
{
- SimdBool lt = rSimd_5_7_9 < rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 2, 0), selectByMask(rSimd_1_2_3, lt));
+ SimdBool lt = rSimd_c4c6c8 < rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(c0, c1, 0), selectByMask(rSimd_c0c1c2, lt));
}
#if GMX_SIMD_HAVE_INT32_LOGICAL || GMX_SIMD_HAVE_LOGICAL
TEST_F(SimdFloatingpointTest, testBits)
{
- SimdBool eq = testBits(setSimdRealFrom3R(1, 0, 2));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 0, 3), selectByMask(rSimd_1_2_3, eq));
+ SimdBool eq = testBits(setSimdRealFrom3R(c1, 0, c1));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(c0, 0, c2), selectByMask(rSimd_c0c1c2, eq));
// Test if we detect only the sign bit being set
eq = testBits(setSimdRealFrom1R(GMX_REAL_NEGZERO));
- GMX_EXPECT_SIMD_REAL_EQ(rSimd_1_2_3, selectByMask(rSimd_1_2_3, eq));
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_c0c1c2, selectByMask(rSimd_c0c1c2, eq));
}
#endif
TEST_F(SimdFloatingpointTest, andB)
{
- SimdBool eq = rSimd_5_7_9 == rSimd_7_8_9;
- SimdBool le = rSimd_5_7_9 <= rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0, 0, 3), selectByMask(rSimd_1_2_3, (eq && le)));
+ SimdBool eq = rSimd_c4c6c8 == rSimd_c6c7c8;
+ SimdBool le = rSimd_c4c6c8 <= rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(0, 0, c2), selectByMask(rSimd_c0c1c2, (eq && le)));
}
TEST_F(SimdFloatingpointTest, orB)
{
- SimdBool eq = rSimd_5_7_9 == rSimd_7_8_9;
- SimdBool lt = rSimd_5_7_9 < rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1, 2, 3), selectByMask(rSimd_1_2_3, (eq || lt)));
+ SimdBool eq = rSimd_c4c6c8 == rSimd_c6c7c8;
+ SimdBool lt = rSimd_c4c6c8 < rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(rSimd_c0c1c2, selectByMask(rSimd_c0c1c2, (eq || lt)));
}
TEST_F(SimdFloatingpointTest, anyTrueB)
* We cannot check for truth values for "any" element beyond the first,
* since that part of the data will not be used if simd width is 1.
*/
- eq = rSimd_5_7_9 == setSimdRealFrom3R(5, 0, 0);
+ eq = rSimd_c4c6c8 == setSimdRealFrom3R(c4, 0, 0);
EXPECT_TRUE(anyTrue(eq));
- eq = rSimd_1_2_3 == rSimd_4_5_6;
+ eq = rSimd_c0c1c2 == rSimd_c3c4c5;
EXPECT_FALSE(anyTrue(eq));
}
TEST_F(SimdFloatingpointTest, blend)
{
- SimdBool lt = rSimd_5_7_9 < rSimd_7_8_9;
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(4, 5, 3), blend(rSimd_1_2_3, rSimd_4_5_6, lt));
+ SimdBool lt = rSimd_c4c6c8 < rSimd_c6c7c8;
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(c3, c4, c2), blend(rSimd_c0c1c2, rSimd_c3c4c5, lt));
}
TEST_F(SimdFloatingpointTest, reduce)
{
// The horizontal sum of the SIMD variable depends on the width, so
// simply store it an extra time and calculate what the sum should be
- std::vector<real> v = simdReal2Vector(rSimd_4_5_6);
+ std::vector<real> v = simdReal2Vector(rSimd_c3c4c5);
real sum = 0.0;
for (int i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
sum += v[i];
}
- EXPECT_EQ(sum, reduce(rSimd_4_5_6));
+ EXPECT_REAL_EQ_TOL(sum, reduce(rSimd_c3c4c5), defaultRealTolerance() );
}
#endif // GMX_SIMD_HAVE_REAL
for (i = 0; i < GMX_SIMD_FLOAT_WIDTH; i++)
{
- f[i] = i;
+ // Scale by 1+100*eps to use low bits too.
+ // Due to the conversions we want to avoid being too sensitive to fluctuations in last bit
+ f[i] = i * (1.0 + 100*GMX_FLOAT_EPS);
}
vf = load(f);
// This fills elements for pd1 too when double width is 2*single width
for (i = 0; i < GMX_SIMD_FLOAT_WIDTH; i++)
{
- d[i] = i;
+ // Scale by 1+eps to use low bits too.
+ // Due to the conversions we want to avoid being too sensitive to fluctuations in last bit
+ d[i] = i * (1.0 + 100*GMX_FLOAT_EPS);
}
vd0 = load(d);
// This will check elements in pd1 too when double width is 2*single width
for (i = 0; i < GMX_SIMD_FLOAT_WIDTH; i++)
{
- EXPECT_REAL_EQ_TOL(d[i], f[i], tolerance);
+ EXPECT_FLOAT_EQ_TOL(d[i], f[i], tolerance);
}
}
#endif // GMX_SIMD_HAVE_FLOAT && GMX_SIMD_HAVE_DOUBLE
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
// Use every third point to avoid a continguous access pattern
offset_[i] = 3 * i;
- val0_[i] = i;
- val1_[i] = i + 0.1;
- val2_[i] = i + 0.2;
- val3_[i] = i + 0.3;
+ // Multiply numbers by 1+100*GMX_REAL_EPS ensures some low bits are
+ // set too, so the tests make sure we read all bits correctly.
+ val0_[i] = (i ) * (1.0 + 100*GMX_REAL_EPS);
+ val1_[i] = (i + 0.1) * (1.0 + 100*GMX_REAL_EPS);
+ val2_[i] = (i + 0.2) * (1.0 + 100*GMX_REAL_EPS);
+ val3_[i] = (i + 0.3) * (1.0 + 100*GMX_REAL_EPS);
}
}
// Set test and reference memory to background value
for (std::size_t j = 0; j < s_workMemSize_; j++)
{
- mem0_[j] = refmem[j] = 1000.0 + j;
+ // Multiply by 1+100*eps to make sure low bits are also used
+ mem0_[j] = refmem[j] = (1000.0 + j) * (1.0 + 100*GMX_REAL_EPS);
}
for (std::size_t j = 0; j < GMX_SIMD_REAL_WIDTH; j++)
// Set test and reference memory to background value
for (std::size_t j = 0; j < s_workMemSize_; j++)
{
- mem0_[j] = refmem[j] = 1000.0 + j;
+ // Multiply by 1+100*eps to make sure low bits are also used
+ mem0_[j] = refmem[j] = (1000.0 + j) * (1.0 + 100*GMX_REAL_EPS);
}
for (std::size_t j = 0; j < GMX_SIMD_REAL_WIDTH; j++)
// Set test and reference memory to background value
for (std::size_t j = 0; j < s_workMemSize_; j++)
{
- mem0_[j] = refmem[j] = 1000.0 + j;
+ // Multiply by 1+100*eps to make sure low bits are also used
+ mem0_[j] = refmem[j] = (1000.0 + j) * (1.0 + 100*GMX_REAL_EPS);
}
for (std::size_t j = 0; j < GMX_SIMD_REAL_WIDTH; j++)
// Set test and reference memory to background value
for (std::size_t j = 0; j < s_workMemSize_; j++)
{
- mem0_[j] = refmem[j] = 1000.0 + j;
+ // Multiply by 1+100*eps to make sure low bits are also used
+ mem0_[j] = refmem[j] = (1000.0 + j) * (1.0 + 100*GMX_REAL_EPS);
}
for (std::size_t j = 0; j < GMX_SIMD_REAL_WIDTH; j++)
// Set test and reference memory to background value
for (std::size_t j = 0; j < s_workMemSize_; j++)
{
- mem0_[j] = refmem[j] = 1000.0 + j;
+ // Multiply by 1+100*eps to make sure low bits are also used
+ mem0_[j] = refmem[j] = (1000.0 + j) * (1.0 + 100*GMX_REAL_EPS);
}
for (std::size_t j = 0; j < GMX_SIMD_REAL_WIDTH; j++)
}
// Just put some numbers in memory so we check the addition is correct
- mem0_[0] = 5.0;
- mem0_[1] = 15.0;
- mem0_[2] = 25.0;
- mem0_[3] = 35.0;
+ mem0_[0] = c0;
+ mem0_[1] = c1;
+ mem0_[2] = c2;
+ mem0_[3] = c3;
tstsum = reduceIncr4ReturnSum(mem0_, v0, v1, v2, v3);
- EXPECT_REAL_EQ_TOL( 5.0 + sum0, mem0_[0], tolerance);
- EXPECT_REAL_EQ_TOL(15.0 + sum1, mem0_[1], tolerance);
- EXPECT_REAL_EQ_TOL(25.0 + sum2, mem0_[2], tolerance);
- EXPECT_REAL_EQ_TOL(35.0 + sum3, mem0_[3], tolerance);
+ EXPECT_REAL_EQ_TOL(c0 + sum0, mem0_[0], tolerance);
+ EXPECT_REAL_EQ_TOL(c1 + sum1, mem0_[1], tolerance);
+ EXPECT_REAL_EQ_TOL(c2 + sum2, mem0_[2], tolerance);
+ EXPECT_REAL_EQ_TOL(c3 + sum3, mem0_[3], tolerance);
EXPECT_REAL_EQ_TOL(sum0 + sum1 + sum2 + sum3, tstsum, tolerance);
}
}
// Just put some numbers in memory so we check the addition is correct
- mem0_[0] = 5.0;
- mem0_[1] = 15.0;
- mem0_[2] = 25.0;
- mem0_[3] = 35.0;
+ mem0_[0] = c0;
+ mem0_[1] = c1;
+ mem0_[2] = c2;
+ mem0_[3] = c3;
tstsum = reduceIncr4ReturnSumHsimd(mem0_, v0, v1);
- EXPECT_REAL_EQ_TOL( 5.0 + sum0, mem0_[0], tolerance);
- EXPECT_REAL_EQ_TOL(15.0 + sum1, mem0_[1], tolerance);
- EXPECT_REAL_EQ_TOL(25.0 + sum2, mem0_[2], tolerance);
- EXPECT_REAL_EQ_TOL(35.0 + sum3, mem0_[3], tolerance);
+ EXPECT_REAL_EQ_TOL(c0 + sum0, mem0_[0], tolerance);
+ EXPECT_REAL_EQ_TOL(c1 + sum1, mem0_[1], tolerance);
+ EXPECT_REAL_EQ_TOL(c2 + sum2, mem0_[2], tolerance);
+ EXPECT_REAL_EQ_TOL(c3 + sum3, mem0_[3], tolerance);
EXPECT_REAL_EQ_TOL(sum0 + sum1 + sum2 + sum3, tstsum, tolerance);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#if GMX_SIMD_HAVE_REAL && GMX_SIMD_HAVE_INT32_ARITHMETICS
TEST_F(SimdIntegerTest, cvtB2IB)
{
- SimdBool eq = (rSimd_5_7_9 == setSimdRealFrom3R(5, 0, 0)); // eq should be T,F,F
+ SimdBool eq = (rSimd_c3c4c5 == rSimd_c3c0c4); // eq should be T,F,F
SimdIBool eqi = cvtB2IB(eq);
GMX_EXPECT_SIMD_INT_EQ(setSimdIntFrom3I(1, 0, 0), selectByMask(iSimd_1_2_3, eqi));
{
SimdIBool eqi = (iSimd_5_7_9 == setSimdIntFrom3I(5, 0, 0)); // eq should be T,F,F
SimdBool eq = cvtIB2B(eqi);
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(1.0, 0, 0), selectByMask(rSimd_1_2_3, eq));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(c0, 0, 0), selectByMask(rSimd_c0c1c2, eq));
}
#endif // GMX_SIMD_HAVE_REAL && GMX_SIMD_HAVE_INT32_ARITHMETICS
{
public:
::testing::AssertionResult
- compareSimdMathFunction(const char * refFuncExpr, const char *simdFuncExpr,
- real refFunc(real x), SimdReal gmx_simdcall simdFunc(SimdReal x));
+ compareSimdMathFunction(const char * refFuncExpr,
+ const char * simdFuncExpr,
+ const char * denormalsToZeroExpr,
+ real refFunc(real x),
+ SimdReal gmx_simdcall simdFunc(SimdReal x),
+ bool denormalsToZero);
};
/*! \brief Test approximate equality of SIMD vs reference version of a function.
* the number of points, range, and tolerances specified by the test fixture class.
*/
#define GMX_EXPECT_SIMD_FUNC_NEAR(refFunc, tstFunc) \
- EXPECT_PRED_FORMAT2(compareSimdMathFunction, refFunc, tstFunc)
+ EXPECT_PRED_FORMAT3(compareSimdMathFunction, refFunc, tstFunc, false)
+
+/*! \brief Test approximate equality of SIMD vs reference function, denormals can be zero.
+ *
+ * This macro takes vanilla C and SIMD flavors of a function and tests it with
+ * the number of points, range, and tolerances specified by the test fixture class.
+ *
+ * This version of the function will also return success if the test function
+ * returns zero where the reference function returns a denormal value.
+ */
+#define GMX_EXPECT_SIMD_FUNC_NEAR_DTZ(refFunc, tstFunc) \
+ EXPECT_PRED_FORMAT3(compareSimdMathFunction, refFunc, tstFunc, true)
/*! \brief Implementation routine to compare SIMD vs reference functions.
*
- * \param refFuncExpr Description of reference function expression
- * \param simdFuncExpr Description of SIMD function expression
- * \param refFunc Reference math function pointer
- * \param simdFunc SIMD math function pointer
+ * \param refFuncExpr Description of reference function expression
+ * \param simdFuncExpr Description of SIMD function expression
+ * \param denormalsToZeroExpr Description of denormal-to-zero setting
+ * \param refFunc Reference math function pointer
+ * \param simdFunc SIMD math function pointer
+ * \param denormalsToZero If true, the function will consider denormal
+ * values equivalent to 0.0.
*
* The function will be tested with the range and tolerances specified in
* the SimdBaseTest class. You should not never call this function directly,
* but use the macro GMX_EXPECT_SIMD_FUNC_NEAR(refFunc,tstFunc) instead.
*/
::testing::AssertionResult
-SimdMathTest::compareSimdMathFunction(const char * refFuncExpr, const char *simdFuncExpr,
- real refFunc(real x), SimdReal gmx_simdcall simdFunc(SimdReal x))
+SimdMathTest::compareSimdMathFunction(const char * refFuncExpr,
+ const char * simdFuncExpr,
+ const char * denormalsToZeroExpr,
+ real refFunc(real x),
+ SimdReal gmx_simdcall simdFunc(SimdReal x),
+ bool denormalsToZero)
{
std::vector<real> vx(GMX_SIMD_REAL_WIDTH);
std::vector<real> vref(GMX_SIMD_REAL_WIDTH);
for (i = 0, signOk = true, absOk = true; i < GMX_SIMD_REAL_WIDTH; i++)
{
+ if (denormalsToZero)
+ {
+ // Clamp denormal values to zero if requested
+ if (std::abs(vref[i]) < GMX_REAL_MIN)
+ {
+ vref[i] = 0.0;
+ }
+ if (std::abs(vtst[i]) < GMX_REAL_MIN)
+ {
+ vtst[i] = 0.0;
+ }
+ }
+
absDiff = fabs(vref[i]-vtst[i]);
absOk = absOk && ( absDiff < absTol_ );
signOk = signOk && ( (vref[i] >= 0 && vtst[i] >= 0) ||
<< "Reference function: " << refFuncExpr << std::endl
<< "Simd function: " << simdFuncExpr << std::endl
<< "Test range is ( " << range_.first << " , " << range_.second << " ) " << std::endl
+ << "Denormals can be 0: " << denormalsToZeroExpr << std::endl
<< "First sign difference around x=" << std::setprecision(20) << ::testing::PrintToString(vx) << std::endl
<< "Ref values: " << std::setprecision(20) << ::testing::PrintToString(vref) << std::endl
<< "SIMD values: " << std::setprecision(20) << ::testing::PrintToString(vtst) << std::endl;
<< "Failing SIMD math function ulp comparison between " << refFuncExpr << " and " << simdFuncExpr << std::endl
<< "Requested ulp tolerance: " << ulpTol_ << std::endl
<< "Requested abs tolerance: " << absTol_ << std::endl
+ << "Denormals can be 0: " << denormalsToZeroExpr << std::endl
<< "Largest Ulp difference occurs for x=" << std::setprecision(20) << maxUlpDiffPos << std::endl
<< "Ref values: " << std::setprecision(20) << refValMaxUlpDiff << std::endl
<< "SIMD values: " << std::setprecision(20) << simdValMaxUlpDiff << std::endl
TEST_F(SimdMathTest, copysign)
{
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-4, 5, 6), copysign(setSimdRealFrom3R(4, 5, 6), setSimdRealFrom3R(-5, 2, 0)));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-4, 5, 6), copysign(setSimdRealFrom3R(-4, -5, -6), setSimdRealFrom3R(-5, 2, 0)));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(4, -5, 6), copysign(setSimdRealFrom3R(4, 5, 6), setSimdRealFrom3R(5, -2, 0)));
- GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(4, -5, 6), copysign(setSimdRealFrom3R(-4, -5, -6), setSimdRealFrom3R(5, -2, 0)));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-c0, c1, c2), copysign(setSimdRealFrom3R( c0, c1, c2), setSimdRealFrom3R(-c3, c4, 0)));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R(-c0, c1, c2), copysign(setSimdRealFrom3R(-c0, -c1, -c2), setSimdRealFrom3R(-c3, c4, 0)));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R( c0, -c1, c2), copysign(setSimdRealFrom3R( c0, c1, c2), setSimdRealFrom3R( c3, -c4, 0)));
+ GMX_EXPECT_SIMD_REAL_EQ(setSimdRealFrom3R( c0, -c1, c2), copysign(setSimdRealFrom3R(-c0, -c1, -c2), setSimdRealFrom3R( c3, -c4, 0)));
}
/*! \brief Function wrapper to evaluate reference 1/sqrt(x) */
TEST_F(SimdMathTest, invsqrt)
{
- setRange(1e-10, 1e10);
+ setRange(1.01*GMX_FLOAT_MIN, GMX_FLOAT_MAX);
GMX_EXPECT_SIMD_FUNC_NEAR(refInvsqrt, invsqrt);
}
TEST_F(SimdMathTest, maskzInvsqrt)
{
- SimdReal x = setSimdRealFrom3R(1.0, 0.0, 3.0);
+ SimdReal x = setSimdRealFrom3R(c1, 0.0, c2);
SimdBool m = (setZero() < x);
- SimdReal ref = setSimdRealFrom3R(1.0/std::sqrt(1.0), 0.0, 1.0/std::sqrt(3.0));
+ SimdReal ref = setSimdRealFrom3R(1.0/std::sqrt(c1), 0.0, 1.0/std::sqrt(c2));
GMX_EXPECT_SIMD_REAL_NEAR(ref, maskzInvsqrt(x, m));
}
TEST_F(SimdMathTest, invsqrtPair)
{
- setRange(1e-10, 1e10);
+ setRange(1.01*GMX_FLOAT_MIN, GMX_FLOAT_MAX);
// The accuracy conversions lose a bit of extra accuracy compared to
// doing the iterations in all-double.
setUlpTol(4*ulpTol_);
GMX_EXPECT_SIMD_FUNC_NEAR(refInvsqrt, tstInvsqrtPair1);
}
+/*! \brief Function wrapper to evaluate reference sqrt(x) */
+static real
+refSqrt(real x)
+{
+ return std::sqrt(x);
+}
+
+/*! \brief Dummy function returning 0.0 to test function ranges that should be zero */
+gmx_unused static real
+refZero(real gmx_unused x)
+{
+ return 0.0;
+}
+
+
TEST_F(SimdMathTest, sqrt)
{
- // Make sure sqrt(0)=0 works and isn't evaluated as 0*1/sqrt(0)=NaN
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(0, std::sqrt(3), 2), sqrt(setSimdRealFrom3R(0, 3, 4)));
+ // The accuracy conversions lose a bit of extra accuracy compared to
+ // doing the iterations in all-double.
+ setUlpTol(4*ulpTol_);
+
+ // First test that 0.0 and a few other values works
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(0, std::sqrt(c1), std::sqrt(c2)), sqrt(setSimdRealFrom3R(0, c1, c2)));
+
+ // Values smaller-than-or-equal to GMX_FLOAT_MIN will be clamped to 0.0,
+ // so only test larger values
+ setRange(1.01*GMX_FLOAT_MIN, GMX_FLOAT_MAX);
+ GMX_EXPECT_SIMD_FUNC_NEAR(refSqrt, sqrt);
#if GMX_DOUBLE
- // Test arguments in the problematic range 0 < x <= GMX_FLOAT_MIN
- double x0 = GMX_FLOAT_MIN;
- double x1 = GMX_FLOAT_MIN*0.5;
- double x2 = GMX_DOUBLE_MIN;
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::sqrt(x0), 0, 0), sqrt(setSimdRealFrom3R(x0, x1, x2)));
+ // Make sure that values smaller than GMX_FLOAT_MIN lead to result 0.0
+ setRange(0.0, 0.99*GMX_FLOAT_MIN);
+ GMX_EXPECT_SIMD_FUNC_NEAR(refZero, sqrt);
#endif
}
+TEST_F(SimdMathTest, sqrtUnsafe)
+{
+ // The accuracy conversions lose a bit of extra accuracy compared to
+ // doing the iterations in all-double.
+ setUlpTol(4*ulpTol_);
+
+ setRange(GMX_FLOAT_MIN, GMX_FLOAT_MAX);
+ GMX_EXPECT_SIMD_FUNC_NEAR(refSqrt, sqrt<MathOptimization::Unsafe>);
+}
+
/*! \brief Function wrapper to evaluate reference 1/x */
real refInv(real x)
{
TEST_F(SimdMathTest, maskzInv)
{
- SimdReal x = setSimdRealFrom3R(2.0, 0.0, 3.0);
+ SimdReal x = setSimdRealFrom3R(c1, 0.0, c2);
SimdBool m = (setZero() < x);
- SimdReal ref = setSimdRealFrom3R(0.5, 0.0, 1.0/3.0);
+ SimdReal ref = setSimdRealFrom3R(1.0/c1, 0.0, 1.0/c2);
GMX_EXPECT_SIMD_REAL_NEAR(ref, maskzInv(x, m));
}
TEST_F(SimdMathTest, exp2)
{
- setRange(-100, 100);
+ // Test normal/denormal/zero range separately to make errors clearer
+
+ // First test the range where we get normalized (non-denormal) results,
+ // since we don't require denormal results to be reproduced correctly.
+#if GMX_DOUBLE
+ setRange(-1022, 1023);
+#else
+ setRange(-126, 127);
+#endif
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2);
- // We do not care about the SIMD implementation getting denormal values right,
- // but they must be clamped to zero rather than producing garbage.
- // Check by setting the absolute tolerance to machine precision.
- setAbsTol(GMX_REAL_EPS);
+ // Some implementations might have denormal support, in which case they
+ // support an extended range, adding roughly the number of bits in the
+ // mantissa to the smallest allowed arg (1023+52 in double, 127+23 single).
+ // In this range we allow the value to be either correct (denormal) or 0.0
+#if GMX_DOUBLE
+ setRange(-1075, -1022);
+#else
+ setRange(-150, -126);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR_DTZ(std::exp2, exp2);
- // First two values will have denormal results in single, third value in double too.
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp2(-150.0), std::exp2(-300.0), std::exp2(-1050.0)),
- exp2(setSimdRealFrom3R(-150.0, -300.0, -1050.0)));
+ // For arguments smaller than the subnormal the result should be zero
+ // both in the reference and our implementations.
+#if GMX_DOUBLE
+ setRange(-1000000.0, -1075.0);
+#else
+ setRange(-100000.0, -150.0);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2);
- // Reset absolute tolerance to enforce ULP checking
- setAbsTol(0.0);
+ // Test a few very negative values, including values so small that they
+ // will start to cause inf values in the polynomial interpolations
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp2(-GMX_FLOAT_MAX), std::exp2(-0.1*GMX_REAL_MAX), std::exp2(-GMX_REAL_MAX)),
+ exp2(setSimdRealFrom3R(-GMX_FLOAT_MAX, -0.1*GMX_REAL_MAX, -GMX_REAL_MAX)));
+}
- // Make sure that underflowing values are set to zero.
- // First two values underflow in single, third value in double too.
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp2(-200.0), std::exp2(-600.0), std::exp2(-1500.0)),
- exp2(setSimdRealFrom3R(-200.0, -600.0, -1500.0)));
+TEST_F(SimdMathTest, exp2Unsafe)
+{
+ // The unsafe version is only defined in this range
+#if GMX_DOUBLE
+ setRange(-1022, 1023);
+#else
+ setRange(-126, 127);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2<MathOptimization::Unsafe>);
}
TEST_F(SimdMathTest, exp)
{
- setRange(-75, 75);
+ // Test normal/denormal/zero range separately to make errors clearer
+
+ // First test the range where we get normalized (non-denormal) results,
+ // since we don't require denormal results to be reproduced correctly.
+#if GMX_DOUBLE
+ setRange(-708.4, 709.1);
+#else
+ setRange(-87.3, 88.0);
+#endif
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, exp);
- // We do not care about the SIMD implementation getting denormal values right,
- // but they must be clamped to zero rather than producing garbage.
- // Check by setting the absolute tolerance to machine precision.
- setAbsTol(GMX_REAL_EPS);
- // First two values will have denormal results in single, third value in double too.
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp(-90.0), std::exp(-100.0), std::exp(-725.0)),
- exp(setSimdRealFrom3R(-90.0, -100.0, -725.0)));
+ // Some implementations might have denormal support, in which case they
+ // support an extended range, adding roughly the number of bits in the
+ // mantissa to the smallest allowed arg (1023+52 in double, 127+23 single).
+ // Then multiply with ln(2) to get our limit for exp().
+ // In this range we allow the value to be either correct (denormal) or 0.0
+#if GMX_DOUBLE
+ setRange(-746.0, -708.4);
+#else
+ setRange(-104.0, -87.3);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR_DTZ(std::exp, exp);
- // Reset absolute tolerance to enforce ULP checking
- setAbsTol(0.0);
+ // For arguments smaller than the subnormal the result should be zero
+ // both in the reference and our implementations.
+#if GMX_DOUBLE
+ setRange(-1000000.0, -746.0);
+#else
+ setRange(-100000.0, -104.0);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, exp);
- // Make sure that underflowing values are set to zero.
- // First two values underflow in single, third value in double too.
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp(-150.0), std::exp(-300.0), std::exp(-800.0)),
- exp(setSimdRealFrom3R(-150.0, -300.0, -800.0)));
+ // Test a few very negative values, including values so small that they
+ // will start to cause inf values in the polynomial interpolations
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp(-GMX_FLOAT_MAX), std::exp(-0.1*GMX_REAL_MAX), std::exp(-GMX_REAL_MAX)),
+ exp(setSimdRealFrom3R(-GMX_FLOAT_MAX, -0.1*GMX_REAL_MAX, -GMX_REAL_MAX)));
+}
+
+TEST_F(SimdMathTest, expUnsafe)
+{
+#if GMX_DOUBLE
+ setRange(-708.4, 709.1);
+#else
+ setRange(-87.3, 88.0);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, exp<MathOptimization::Unsafe>);
}
/*! \brief Function wrapper for erf(x), with argument/return in default Gromacs precision.
TEST_F(SimdMathTest, atan2)
{
// test each quadrant
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, 1.0)), atan2(rSimd_1_2_3, rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, 1.0)), atan2(rSimd_m1_m2_m3, rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, -1.0)), atan2(rSimd_m1_m2_m3, rSimd_m1_m2_m3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, -1.0)), atan2(rSimd_1_2_3, rSimd_m1_m2_m3));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(c0, c3), std::atan2(c1, c4), std::atan2(c2, c5)),
+ atan2(rSimd_c0c1c2, rSimd_c3c4c5));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(-c0, c3), std::atan2(-c1, c4), std::atan2(-c2, c5)),
+ atan2(rSimd_m0m1m2, rSimd_c3c4c5));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(-c0, -c3), std::atan2(-c1, -c0), std::atan2(-c2, -c4)),
+ atan2(rSimd_m0m1m2, rSimd_m3m0m4));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(c0, -c3), std::atan2(c1, -c0), std::atan2(c2, -c4)),
+ atan2(rSimd_c0c1c2, rSimd_m3m0m4));
+
// cases important for calculating angles
// values on coordinate axes
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, 1.0)), atan2(setZero(), rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, 0.0)), atan2(rSimd_1_2_3, setZero()));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, -1.0)), atan2(setZero(), rSimd_m1_m2_m3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, 0.0)), atan2(rSimd_m1_m2_m3, setZero()));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(0, c0), std::atan2(0, c1), std::atan2(0, c2)),
+ atan2(setZero(), rSimd_c0c1c2));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(c0, 0), std::atan2(c1, 0), std::atan2(c2, 0)),
+ atan2(rSimd_c0c1c2, setZero()));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(0, -c0), std::atan2(0, -c1), std::atan2(0, -c2)),
+ atan2(setZero(), rSimd_m0m1m2));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(-c0, 0), std::atan2(-c1, 0), std::atan2(-c2, 0)),
+ atan2(rSimd_m0m1m2, setZero()));
// degenerate value (origin) should return 0.0. At least IBM xlc 13.1.5 gets the reference
// value wrong (-nan) at -O3 optimization, so we compare to the correct value (0.0) instead.
GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(0.0), atan2(setSimdRealFrom3R(0.0, 0.0, 0.0), setZero()));
/* Increase the allowed error by the difference between the actual precision and single */
setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
- setRange(1e-10, 1e10);
+ setRange(1.01*GMX_FLOAT_MIN, GMX_FLOAT_MAX);
GMX_EXPECT_SIMD_FUNC_NEAR(refInvsqrt, invsqrtSingleAccuracy);
}
/* Increase the allowed error by the difference between the actual precision and single */
setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
- setRange(1e-10, 1e10);
+ setRange(1.01*GMX_FLOAT_MIN, GMX_FLOAT_MAX);
GMX_EXPECT_SIMD_FUNC_NEAR(refInvsqrt, tst_invsqrt_SingleAccuracy_pair0);
GMX_EXPECT_SIMD_FUNC_NEAR(refInvsqrt, tst_invsqrt_SingleAccuracy_pair1);
}
/* Increase the allowed error by the difference between the actual precision and single */
setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
- // Just make sure sqrt(0)=0 works and isn't evaluated as 0*1/sqrt(0)=NaN
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(0, std::sqrt(3), 2), sqrtSingleAccuracy(setSimdRealFrom3R(0, 3, 4)));
+ // First test that 0.0 and a few other values works
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(0, std::sqrt(c0), std::sqrt(c1)), sqrtSingleAccuracy(setSimdRealFrom3R(0, c0, c1)));
+
+ // Values smaller-than-or-equal to GMX_FLOAT_MIN will be clamped to 0.0,
+ // so only test larger values
+ setRange(1.01*GMX_FLOAT_MIN, GMX_FLOAT_MAX);
+ GMX_EXPECT_SIMD_FUNC_NEAR(refSqrt, sqrtSingleAccuracy);
+
+#if GMX_DOUBLE
+ // Make sure that values smaller than GMX_FLOAT_MIN lead to result 0.0
+ setRange(0.0, 0.99*GMX_FLOAT_MIN);
+ GMX_EXPECT_SIMD_FUNC_NEAR(refZero, sqrtSingleAccuracy);
+#endif
+}
+
+TEST_F(SimdMathTest, sqrtSingleAccuracyUnsafe)
+{
+ /* Increase the allowed error by the difference between the actual precision and single */
+ setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
+
+ // Test the full range
+ setRange(GMX_FLOAT_MIN, GMX_FLOAT_MAX);
+ GMX_EXPECT_SIMD_FUNC_NEAR(refSqrt, sqrtSingleAccuracy<MathOptimization::Unsafe>);
}
TEST_F(SimdMathTest, invSingleAccuracy)
/* Increase the allowed error by the difference between the actual precision and single */
setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
- setRange(-100, 100);
+#if GMX_DOUBLE
+ setRange(-1022.49, 1023.49);
+#else
+ setRange(-126, 127.49);
+#endif
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2SingleAccuracy);
+
+ // Test a range that should be zero both for reference and simd versions.
+ // Some implementations might have subnormal support, in which case they
+ // support an extended range, adding roughly the number of bits in the
+ // mantissa to the smallest allowed arg (1023+52 in double, 127+23 single).
+#if GMX_DOUBLE
+ setRange(-1000000.0, -1075.0);
+#else
+ setRange(-100000.0, -150.0);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR_DTZ(std::exp2, exp2SingleAccuracy);
+
+ // Test a few very negative values
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp2(-GMX_FLOAT_MAX), std::exp2(-0.1*GMX_REAL_MAX), std::exp2(-GMX_REAL_MAX)),
+ exp2SingleAccuracy(setSimdRealFrom3R(-GMX_FLOAT_MAX, -0.1*GMX_REAL_MAX, -GMX_REAL_MAX)));
+}
+
+TEST_F(SimdMathTest, exp2SingleAccuracyUnsafe)
+{
+ /* Increase the allowed error by the difference between the actual precision and single */
+ setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
+
+#if GMX_DOUBLE
+ setRange(-1022.49, 1023.49);
+#else
+ setRange(-126, 127.49);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp2, exp2SingleAccuracy<MathOptimization::Unsafe>);
}
TEST_F(SimdMathTest, expSingleAccuracy)
/* Increase the allowed error by the difference between the actual precision and single */
setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
- setRange(-75, 75);
+#if GMX_DOUBLE
+ setRange(-708.7, 709.4);
+#else
+ setRange(-87.3, 88.3);
+#endif
GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, expSingleAccuracy);
+
+ // Test a range that should be zero both for reference and simd versions.
+ // Some implementations might have subnormal support, in which case they
+ // support an extended range, adding roughly the number of bits in the
+ // mantissa to the smallest result exponent (1023+52 in double, 127+23 single).
+ // Then multiply with ln(2) to get our limit for exp().
+#if GMX_DOUBLE
+ setRange(-1000000.0, -746.0);
+#else
+ setRange(-100000.0, -104.0);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR_DTZ(std::exp, expSingleAccuracy);
+
+ // Test a few very negative values, including values so small that they
+ // will start to cause inf values in the polynomial interpolations
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::exp(-GMX_FLOAT_MAX), std::exp(-0.1*GMX_REAL_MAX), std::exp(-GMX_REAL_MAX)),
+ expSingleAccuracy(setSimdRealFrom3R(-GMX_FLOAT_MAX, -0.1*GMX_REAL_MAX, -GMX_REAL_MAX)));
+}
+
+TEST_F(SimdMathTest, expSingleAccuracyUnsafe)
+{
+ /* Increase the allowed error by the difference between the actual precision and single */
+ setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
+
+#if GMX_DOUBLE
+ setRange(-708.7, 709.4);
+#else
+ setRange(-87.3, 88.3);
+#endif
+ GMX_EXPECT_SIMD_FUNC_NEAR(std::exp, expSingleAccuracy<MathOptimization::Unsafe>);
}
TEST_F(SimdMathTest, erfSingleAccuracy)
setUlpTol(ulpTol_ * (1LL << (std::numeric_limits<real>::digits-std::numeric_limits<float>::digits)));
// test each quadrant
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, 1.0)), atan2SingleAccuracy(rSimd_1_2_3, rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, 1.0)), atan2SingleAccuracy(rSimd_m1_m2_m3, rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, -1.0)), atan2SingleAccuracy(rSimd_m1_m2_m3, rSimd_m1_m2_m3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, -1.0)), atan2SingleAccuracy(rSimd_1_2_3, rSimd_m1_m2_m3));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(c0, c3), std::atan2(c1, c4), std::atan2(c2, c5)),
+ atan2SingleAccuracy(rSimd_c0c1c2, rSimd_c3c4c5));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(-c0, c3), std::atan2(-c1, c4), std::atan2(-c2, c5)),
+ atan2SingleAccuracy(rSimd_m0m1m2, rSimd_c3c4c5));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(-c0, -c3), std::atan2(-c1, -c0), std::atan2(-c2, -c4)),
+ atan2SingleAccuracy(rSimd_m0m1m2, rSimd_m3m0m4));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(c0, -c3), std::atan2(c1, -c0), std::atan2(c2, -c4)),
+ atan2SingleAccuracy(rSimd_c0c1c2, rSimd_m3m0m4));
// cases important for calculating angles
// values on coordinate axes
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, 1.0)), atan2SingleAccuracy(setZero(), rSimd_1_2_3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(1.0, 0.0)), atan2SingleAccuracy(rSimd_1_2_3, setZero()));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(0.0, -1.0)), atan2SingleAccuracy(setZero(), rSimd_m1_m2_m3));
- GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(std::atan2(-1.0, 0.0)), atan2SingleAccuracy(rSimd_m1_m2_m3, setZero()));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(0, c0), std::atan2(0, c1), std::atan2(0, c2)),
+ atan2SingleAccuracy(setZero(), rSimd_c0c1c2));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(c0, 0), std::atan2(c1, 0), std::atan2(c2, 0)),
+ atan2SingleAccuracy(rSimd_c0c1c2, setZero()));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(0, -c0), std::atan2(0, -c1), std::atan2(0, -c2)),
+ atan2SingleAccuracy(setZero(), rSimd_m0m1m2));
+ GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom3R(std::atan2(-c0, 0), std::atan2(-c1, 0), std::atan2(-c2, 0)),
+ atan2SingleAccuracy(rSimd_m0m1m2, setZero()));
+
// degenerate value (origin) should return 0.0. At least IBM xlc 13.1.5 gets the reference
// value wrong (-nan) at -O3 optimization, so we compare to the correct value (0.0) instead.
GMX_EXPECT_SIMD_REAL_NEAR(setSimdRealFrom1R(0.0), atan2SingleAccuracy(setSimdRealFrom3R(0.0, 0.0, 0.0), setZero()));
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/simd/simd.h"
#include "gromacs/simd/vector_operations.h"
+#include "data.h"
#include "simd.h"
#if GMX_SIMD
TEST_F(SimdVectorOperationsTest, iprod)
{
- SimdReal aX = setSimdRealFrom3R(1, 2, 3);
- SimdReal aY = setSimdRealFrom3R(3, 0, 5);
- SimdReal aZ = setSimdRealFrom3R(4, 1, 8);
- SimdReal bX = setSimdRealFrom3R(8, 3, 6);
- SimdReal bY = setSimdRealFrom3R(2, 3, 1);
- SimdReal bZ = setSimdRealFrom3R(5, 7, 9);
- SimdReal iprodRef = setSimdRealFrom3R(34, 13, 95);
+ SimdReal aX = rSimd_c0c1c2;
+ SimdReal aY = rSimd_c3c4c5;
+ SimdReal aZ = rSimd_c6c7c8;
+ SimdReal bX = rSimd_c3c0c4;
+ SimdReal bY = rSimd_c4c6c8;
+ SimdReal bZ = rSimd_c7c2c3;
+ SimdReal iprodRef = setSimdRealFrom3R(c0*c3 + c3*c4 + c6*c7,
+ c1*c0 + c4*c6 + c7*c2,
+ c2*c4 + c5*c8 + c8*c3);
setUlpTol(2);
GMX_EXPECT_SIMD_REAL_NEAR(iprodRef, iprod(aX, aY, aZ, bX, bY, bZ));
TEST_F(SimdVectorOperationsTest, norm2)
{
- SimdReal simdX = setSimdRealFrom3R(1, 2, 3);
- SimdReal simdY = setSimdRealFrom3R(3, 0, 5);
- SimdReal simdZ = setSimdRealFrom3R(4, 1, 8);
- SimdReal norm2Ref = setSimdRealFrom3R(26, 5, 98);
+ SimdReal simdX = rSimd_c0c1c2;
+ SimdReal simdY = rSimd_c3c4c5;
+ SimdReal simdZ = rSimd_c6c7c8;
+ SimdReal norm2Ref = setSimdRealFrom3R(c0*c0 + c3*c3 + c6*c6,
+ c1*c1 + c4*c4 + c7*c7,
+ c2*c2 + c5*c5 + c8*c8);
setUlpTol(2);
GMX_EXPECT_SIMD_REAL_NEAR(norm2Ref, norm2(simdX, simdY, simdZ));
TEST_F(SimdVectorOperationsTest, cprod)
{
- SimdReal aX = setSimdRealFrom3R(1, 2, 3);
- SimdReal aY = setSimdRealFrom3R(3, 0, 5);
- SimdReal aZ = setSimdRealFrom3R(4, 1, 8);
- SimdReal bX = setSimdRealFrom3R(8, 3, 6);
- SimdReal bY = setSimdRealFrom3R(2, 3, 1);
- SimdReal bZ = setSimdRealFrom3R(5, 7, 9);
- SimdReal refcX = setSimdRealFrom3R(7, -3, 37);
- SimdReal refcY = setSimdRealFrom3R(27, -11, 21);
- SimdReal refcZ = setSimdRealFrom3R(-22, 6, -27);
+ SimdReal aX = rSimd_c0c1c2;
+ SimdReal aY = rSimd_c3c4c5;
+ SimdReal aZ = rSimd_c6c7c8;
+ SimdReal bX = rSimd_c3c0c4;
+ SimdReal bY = rSimd_c4c6c8;
+ SimdReal bZ = rSimd_c7c2c3;
+ //The SIMD version might use FMA. If we don't force FMA for the reference value, the compiler is free to use FMA
+ //for either product. If the compiler uses FMA for one product and the SIMD version uses FMA for the other, the
+ //rounding error of each product adds up and the total possible ulp-error is 12.
+ SimdReal refcX = setSimdRealFrom3R( std::fma(-c6, c4, c3*c7), std::fma(-c7, c6, c4*c2), std::fma(-c8, c8, c5*c3));
+ SimdReal refcY = setSimdRealFrom3R( std::fma(-c0, c7, c6*c3), std::fma(-c1, c2, c7*c0), std::fma(-c2, c3, c8*c4));
+ SimdReal refcZ = setSimdRealFrom3R( std::fma(-c3, c3, c0*c4), std::fma(-c4, c0, c1*c6), std::fma(-c5, c4, c2*c8));
SimdReal cX, cY, cZ;
+ //The test assumes that cprod uses FMA on architectures which have FMA so that the compiler can't choose which
+ //product is computed with FMA.
cprod(aX, aY, aZ, bX, bY, bZ, &cX, &cY, &cZ);
- setUlpTol(2);
+ //The test values cannot be computed without FMA for the case that SIMD has no FMA. Even if no explicit FMA were
+ //used, the compiler could choose to use FMA. This causes up to 6upl error because of the product is up to 6 times
+ //larger than the final result after the difference.
+ setUlpTol(GMX_SIMD_HAVE_FMA ? 0 : 6);
+
GMX_EXPECT_SIMD_REAL_NEAR(refcX, cX);
GMX_EXPECT_SIMD_REAL_NEAR(refcY, cY);
GMX_EXPECT_SIMD_REAL_NEAR(refcZ, cZ);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
SimdFloat *cx, SimdFloat *cy, SimdFloat *cz)
{
*cx = ay * bz;
- *cx = *cx - az * by;
+ *cx = fnma(az, by, *cx);
*cy = az * bx;
- *cy = *cy - ax * bz;
+ *cy = fnma(ax, bz, *cy);
*cz = ax * by;
- *cz = *cz - ay * bx;
+ *cz = fnma(ay, bx, *cz);
}
#endif // GMX_SIMD_HAVE_FLOAT
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
outlier = (r > rmsd*level);
if (outlier)
{
- if (NULL != x)
+ if (nullptr != x)
{
*x = stats->x[stats->np_c];
}
- if (NULL != y)
+ if (nullptr != y)
{
*y = stats->y[stats->np_c];
}
- if (NULL != dx)
+ if (nullptr != dx)
{
*dx = stats->dx[stats->np_c];
}
- if (NULL != dy)
+ if (nullptr != dy)
{
*dy = stats->dy[stats->np_c];
}
{
int ok;
if ((ok = gmx_stats_add_point(gstats, x[i], y[i],
- (NULL != dx) ? dx[i] : 0,
- (NULL != dy) ? dy[i] : 0)) != estatsOK)
+ (nullptr != dx) ? dx[i] : 0,
+ (nullptr != dy) ? dy[i] : 0)) != estatsOK)
{
return ok;
}
{
return ok;
}
- if (NULL != a)
+ if (nullptr != a)
{
*a = stats->a;
}
- if (NULL != b)
+ if (nullptr != b)
{
*b = stats->b;
}
- if (NULL != da)
+ if (nullptr != da)
{
*da = stats->sigma_a;
}
- if (NULL != db)
+ if (nullptr != db)
{
*db = stats->sigma_b;
}
- if (NULL != chi2)
+ if (nullptr != chi2)
{
*chi2 = stats->chi2;
}
- if (NULL != Rfit)
+ if (nullptr != Rfit)
{
*Rfit = stats->Rfit;
}
{
return ok;
}
- if (NULL != a)
+ if (nullptr != a)
{
*a = stats->aa;
}
- if (NULL != da)
+ if (nullptr != da)
{
*da = stats->sigma_aa;
}
- if (NULL != chi2)
+ if (nullptr != chi2)
{
*chi2 = stats->chi2aa;
}
- if (NULL != Rfit)
+ if (nullptr != Rfit)
{
*Rfit = stats->Rfitaa;
}
return ok;
}
- if (NULL != aver)
+ if (nullptr != aver)
{
*aver = stats->aver;
}
- if (NULL != sigma)
+ if (nullptr != sigma)
{
*sigma = stats->sigma_aver;
}
- if (NULL != error)
+ if (nullptr != error)
{
*error = stats->error;
}
int ok;
real da, chi2, Rfit;
- gmx_stats_add_points(lsq, n, x, y, 0, 0);
+ gmx_stats_add_points(lsq, n, x, y, nullptr, nullptr);
ok = gmx_stats_get_a(lsq, elsqWEIGHT_NONE, a, &da, &chi2, &Rfit);
gmx_stats_free(lsq);
{
double pt;
- if (xd != NULL)
+ if (xd != nullptr)
{
pt = xd[i];
}
- else if (xr != NULL)
+ else if (xr != nullptr)
{
pt = xr[i];
}
return ok;
}
}
- ok = gmx_stats_get_ab(lsq, elsqWEIGHT_NONE, a, b, NULL, NULL, chi2, r);
+ ok = gmx_stats_get_ab(lsq, elsqWEIGHT_NONE, a, b, nullptr, nullptr, chi2, r);
gmx_stats_free(lsq);
return ok;
int lsq_y_ax_b(int n, real x[], real y[], real *a, real *b, real *r, real *chi2)
{
- return low_lsq_y_ax_b(n, x, NULL, y, a, b, r, chi2);
+ return low_lsq_y_ax_b(n, x, nullptr, y, a, b, r, chi2);
}
int lsq_y_ax_b_xdouble(int n, double x[], real y[], real *a, real *b,
real *r, real *chi2)
{
- return low_lsq_y_ax_b(n, NULL, x, y, a, b, r, chi2);
+ return low_lsq_y_ax_b(n, nullptr, x, y, a, b, r, chi2);
}
int lsq_y_ax_b_error(int n, real x[], real y[], real dy[],
#include "gromacs/mdlib/groupcoord.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/observableshistory.h"
+#include "gromacs/mdtypes/swaphistory.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
-#include "gromacs/topology/mtop_util.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
static const char *SwS = {"SWAP:"}; /**< For output that comes from the swap module */
static const char *SwSEmpty = {" "}; /**< Placeholder for multi-line output */
static const char* CompStr[eCompNR] = {"A", "B" }; /**< Compartment name */
-static const char *SwapStr[eSwapTypesNR+1] = { "", "X-", "Y-", "Z-", NULL}; /**< Name for the swap types. */
-static const char *DimStr[DIM+1] = { "X", "Y", "Z", NULL}; /**< Name for the swap dimension. */
+static const char *SwapStr[eSwapTypesNR+1] = { "", "X-", "Y-", "Z-", nullptr}; /**< Name for the swap types. */
+static const char *DimStr[DIM+1] = { "X", "Y", "Z", nullptr}; /**< Name for the swap dimension. */
/** Keep track of through which channel the ions have passed */
enum eChannelHistory {
rvec_add(reference, dx, correctPBCimage);
/* Take weight into account */
- if (NULL == weights)
+ if (nullptr == weights)
{
wi = 1.0;
}
add_to_list(iAtom, &g->comp[comp], dist);
/* Master also checks for ion groups through which channel each ion has passed */
- if (MASTER(cr) && (g->comp_now != NULL) && !bIsSolvent)
+ if (MASTER(cr) && (g->comp_now != nullptr) && !bIsSolvent)
{
int globalAtomNr = g->ind[iAtom] + 1; /* PDB index starts at 1 ... */
detect_flux_per_channel(g, globalAtomNr, comp, g->xc[iAtom],
}
}
- if (bIsSolvent && NULL != fpout)
+ if (bIsSolvent && nullptr != fpout)
{
fprintf(fpout, "# Solv. molecules in comp.%s: %d comp.%s: %d\n",
CompStr[eCompA], g->comp[eCompA].nMol,
* over the values from .cpt file to the swap data structure.
*/
static void get_initial_ioncounts_from_cpt(
- t_inputrec *ir, swapstate_t *swapstate,
+ t_inputrec *ir, swaphistory_t *swapstate,
t_commrec *cr, gmx_bool bVerbose)
{
t_swapcoords *sc;
/*! \brief Ensure that each atom belongs to at most one of the swap groups. */
static void check_swap_groups(t_swap *s, int nat, gmx_bool bVerbose)
{
- int *nGroup = NULL; /* This array counts for each atom in the MD system to
- how many swap groups it belongs (should be 0 or 1!) */
+ int *nGroup = nullptr; /* This array counts for each atom in the MD system to
+ how many swap groups it belongs (should be 0 or 1!) */
int ind = -1;
- int nMultiple = 0; /* Number of atoms belonging to multiple groups */
+ int nMultiple = 0; /* Number of atoms belonging to multiple groups */
if (bVerbose)
int igroup,
t_swap *s,
gmx_bool bVerbose,
- const gmx_mtop_atomlookup_t alook,
gmx_mtop_t *mtop)
{
- int molb, molnr, atnr_mol;
t_swapgrp *g = &s->group[igroup];
int *ind = s->group[igroup].ind;
int nat = s->group[igroup].nat;
/* Determine the number of solvent atoms per solvent molecule from the
* first solvent atom: */
- gmx_mtop_atomnr_to_molblock_ind(alook, ind[0], &molb, &molnr, &atnr_mol);
+ int molb = 0;
+ mtopGetMolblockIndex(mtop, ind[0], &molb, nullptr, nullptr);
int apm = mtop->molblock[molb].natoms_mol;
if (bVerbose)
/* Check whether this is also true for all other solvent atoms */
for (int i = 1; i < nat; i++)
{
- gmx_mtop_atomnr_to_molblock_ind(alook, ind[i], &molb, &molnr, &atnr_mol);
+ mtopGetMolblockIndex(mtop, ind[i], &molb, nullptr, nullptr);
if (apm != mtop->molblock[molb].natoms_mol)
{
gmx_fatal(FARGS, "Not all molecules of swap group %d consist of %d atoms.",
}
// Center of split groups
- snprintf(buf, STRLEN, "%scenter of %s of split group 0", SwapStr[ir->eSwapCoords], (NULL != s->group[eGrpSplit0].m) ? "mass" : "geometry");
+ snprintf(buf, STRLEN, "%scenter of %s of split group 0", SwapStr[ir->eSwapCoords], (nullptr != s->group[eGrpSplit0].m) ? "mass" : "geometry");
legend[count++] = gmx_strdup(buf);
- snprintf(buf, STRLEN, "%scenter of %s of split group 1", SwapStr[ir->eSwapCoords], (NULL != s->group[eGrpSplit1].m) ? "mass" : "geometry");
+ snprintf(buf, STRLEN, "%scenter of %s of split group 1", SwapStr[ir->eSwapCoords], (nullptr != s->group[eGrpSplit1].m) ? "mass" : "geometry");
legend[count++] = gmx_strdup(buf);
// Ion flux for each channel and ion type
* they go.
*/
static void detect_flux_per_channel_init(
- t_commrec *cr,
- t_swap *s,
- swapstate_t *swapstate,
- gmx_bool bStartFromCpt)
+ t_swap *s,
+ swaphistory_t *swapstate,
+ gmx_bool bStartFromCpt)
{
t_swapgrp *g;
swapstateIons_t *gs;
+ /* All these flux detection routines run on the master only */
+ if (swapstate == nullptr)
+ {
+ return;
+ }
for (int ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
{
g = &s->group[ig];
gs = &swapstate->ionType[ig - eSwapFixedGrpNR];
- /* All these flux detection routines run on the master only */
- if (!MASTER(cr))
- {
- g->comp_now = NULL;
- g->comp_from = NULL;
- g->channel_label = NULL;
-
- return;
- }
-
/******************************************************/
/* Channel and domain history for the individual ions */
/******************************************************/
{
char *env = getenv("GMX_COMPELDUMP");
- if (env != NULL)
+ if (env != nullptr)
{
fprintf(stderr, "\n%s Found env.var. GMX_COMPELDUMP, will output CompEL starting structure made whole.\n"
"%s In case of multimeric channels, please check whether they have the correct PBC representation.\n",
SwS, SwSEmpty);
- write_sto_conf_mtop("CompELAssumedWholeConfiguration.pdb", *mtop->name, mtop, x, NULL, ePBC, box);
+ write_sto_conf_mtop("CompELAssumedWholeConfiguration.pdb", *mtop->name, mtop, x, nullptr, ePBC, box);
}
}
* multimeric channels at the last time step.
*/
static void init_swapstate(
- swapstate_t *swapstate,
+ swaphistory_t *swapstate,
t_swapcoords *sc,
gmx_mtop_t *mtop,
rvec x[], /* the initial positions */
matrix box,
- int ePBC)
+ t_inputrec *ir)
{
- rvec *x_pbc = NULL; /* positions of the whole MD system with molecules made whole */
+ rvec *x_pbc = nullptr; /* positions of the whole MD system with molecules made whole */
t_swapgrp *g;
t_swap *s;
}
else
{
+ swapstate->eSwapCoords = ir->eSwapCoords;
+
/* Set the number of ion types and allocate memory for checkpointing */
swapstate->nIonTypes = s->ngrp - eSwapFixedGrpNR;
snew(swapstate->ionType, swapstate->nIonTypes);
copy_rvecn(x, x_pbc, 0, mtop->natoms);
/* This can only make individual molecules whole, not multimers */
- do_pbc_mtop(NULL, ePBC, box, mtop, x_pbc);
+ do_pbc_mtop(nullptr, ir->ePBC, box, mtop, x_pbc);
/* Output the starting structure? */
- outputStartStructureIfWanted(mtop, x_pbc, ePBC, box);
+ outputStartStructureIfWanted(mtop, x_pbc, ir->ePBC, box);
/* If this is the first run (i.e. no checkpoint present) we assume
* that the starting positions give us the correct PBC representation */
* This routine should be called for the 'anions' and 'cations' group,
* of which the indices were lumped together in the older version of the code.
*/
-void copyIndicesToGroup(
+static void copyIndicesToGroup(
int *indIons,
int nIons,
t_swapGroup *g,
* #4 cations - empty before conversion
*
*/
-void convertOldToNewGroupFormat(
+static void convertOldToNewGroupFormat(
t_swapcoords *sc,
gmx_mtop_t *mtop,
gmx_bool bVerbose,
t_commrec *cr)
{
- t_atom *atom;
- gmx_mtop_atomlookup_t alook = gmx_mtop_atomlookup_init(mtop);
t_swapGroup *g = &sc->grp[3];
/* Loop through the atom indices of group #3 (anions) and put all indices
*/
int nAnions = 0;
int nCations = 0;
- int *indAnions = NULL;
- int *indCations = NULL;
+ int *indAnions = nullptr;
+ int *indCations = nullptr;
snew(indAnions, g->nat);
snew(indCations, g->nat);
+ int molb = 0;
for (int i = 0; i < g->nat; i++)
{
- gmx_mtop_atomnr_to_atom(alook, g->ind[i], &atom);
- if (atom->q < 0)
+ const t_atom &atom = mtopGetAtomParameters(mtop, g->ind[i], &molb);
+ if (atom.q < 0)
{
// This is an anion, add it to the list of anions
indAnions[nAnions++] = g->ind[i];
/*! \brief Returns TRUE if we started from an old .tpr
*
* Then we need to re-sort anions and cations into separate groups */
-gmx_bool bConvertFromOldTpr(t_swapcoords *sc)
+static gmx_bool bConvertFromOldTpr(t_swapcoords *sc)
{
// If the last group has no atoms it means we need to convert!
if ( (sc->ngrp >= 5) && (0 == sc->grp[4].nat) )
void init_swapcoords(
FILE *fplog,
- gmx_bool bVerbose,
t_inputrec *ir,
const char *fn,
gmx_mtop_t *mtop,
rvec x[],
matrix box,
- swapstate_t *swapstate,
+ ObservablesHistory *oh,
t_commrec *cr,
const gmx_output_env_t *oenv,
- unsigned long Flags)
+ const MdrunOptions &mdrunOptions)
{
t_swapcoords *sc;
t_swap *s;
- t_atom *atom;
t_swapgrp *g;
swapstateIons_t *gs;
- gmx_bool bAppend, bStartFromCpt, bRerun;
- gmx_mtop_atomlookup_t alook = NULL;
-
- alook = gmx_mtop_atomlookup_init(mtop);
+ gmx_bool bAppend, bStartFromCpt;
+ swaphistory_t *swapstate = nullptr;
if ( (PAR(cr)) && !DOMAINDECOMP(cr) )
{
gmx_fatal(FARGS, "Position swapping is only implemented for domain decomposition!");
}
- bAppend = Flags & MD_APPENDFILES;
- bStartFromCpt = Flags & MD_STARTFROMCPT;
- bRerun = Flags & MD_RERUN;
+ bAppend = mdrunOptions.continuationOptions.appendFiles;
+ bStartFromCpt = mdrunOptions.continuationOptions.startedFromCheckpoint;
sc = ir->swap;
snew(sc->si_priv, 1);
s = sc->si_priv;
- if (bRerun)
+ if (mdrunOptions.rerun)
{
if (PAR(cr))
{
break;
}
+ const gmx_bool bVerbose = mdrunOptions.verbose;
+
// For compatibility with old .tpr files
if (bConvertFromOldTpr(sc) )
{
if (MASTER(cr))
{
- init_swapstate(swapstate, sc, mtop, x, box, ir->ePBC);
+ if (oh->swapHistory == nullptr)
+ {
+ oh->swapHistory = std::unique_ptr<swaphistory_t>(new swaphistory_t {});
+ }
+ swapstate = oh->swapHistory.get();
+
+ init_swapstate(swapstate, sc, mtop, x, box, ir);
}
/* After init_swapstate we have a set of (old) whole positions for our
real charge;
g = &(s->group[ig]);
- g->apm = get_group_apm_check(ig, s, MASTER(cr) && bVerbose, alook, mtop);
+ g->apm = get_group_apm_check(ig, s, MASTER(cr) && bVerbose, mtop);
/* Since all molecules of a group are equal, we only need enough space
* to determine properties of a single molecule at at time */
snew(g->m, g->apm); /* For the center of mass */
charge = 0; /* To determine the charge imbalance */
+ int molb = 0;
for (int j = 0; j < g->apm; j++)
{
- gmx_mtop_atomnr_to_atom(alook, g->ind[j], &atom);
- g->m[j] = atom->m;
- charge += atom->q;
+ const t_atom &atom = mtopGetAtomParameters(mtop, g->ind[j], &molb);
+ g->m[j] = atom.m;
+ charge += atom.q;
}
/* Total charge of one molecule of this group: */
g->q = charge;
{
/* Save the split group masses if mass-weighting is requested */
snew(g->m, g->nat);
+ int molb = 0;
for (int i = 0; i < g->nat; i++)
{
- gmx_mtop_atomnr_to_atom(alook, g->ind[i], &atom);
- g->m[i] = atom->m;
+ g->m[i] = mtopGetAtomMass(mtop, g->ind[i], &molb);
}
}
}
sc->cyl1r, sc->cyl1u, sc->cyl1l);
fprintf(s->fpout, "#\n");
- if (!bRerun)
+ if (!mdrunOptions.rerun)
{
fprintf(s->fpout, "# Coupling constant (number of swap attempt steps to average over): %d (translates to %f ps).\n",
sc->nAverage, sc->nAverage*sc->nstswap*ir->delta_t);
}
else
{
- s->fpout = NULL;
+ s->fpout = nullptr;
}
/* Prepare for parallel or serial run */
g = &(s->group[ig]);
g->nat_loc = 0;
g->nalloc_loc = 0;
- g->ind_loc = NULL;
+ g->ind_loc = nullptr;
}
}
else
else
{
fprintf(stderr, "%s Determining initial numbers of ions per compartment.\n", SwS);
- get_initial_ioncounts(ir, x, box, cr, bRerun);
+ get_initial_ioncounts(ir, x, box, cr, mdrunOptions.rerun);
}
/* Prepare (further) checkpoint writes ... */
}
/* Initialize arrays that keep track of through which channel the ions go */
- detect_flux_per_channel_init(cr, s, swapstate, bStartFromCpt);
+ detect_flux_per_channel_init(s, swapstate, bStartFromCpt);
/* We need to print the legend if we open this file for the first time. */
if (MASTER(cr) && !bAppend)
gmx_int64_t step,
double t,
t_inputrec *ir,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle *wcycle,
rvec x[],
matrix box,
- gmx_mtop_t *mtop,
gmx_bool bVerbose,
gmx_bool bRerun)
{
t_swapgrp *g, *gsol;
int isol, iion;
rvec com_solvent, com_particle; /* solvent and swap molecule's center of mass */
- gmx_mtop_atomlookup_t alook = NULL;
wallcycle_start(wcycle, ewcSWAP);
for (ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
{
g = &(s->group[ig]);
- communicate_group_positions(cr, g->xc, NULL, NULL, FALSE,
- x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, NULL, NULL);
+ communicate_group_positions(cr, g->xc, nullptr, nullptr, FALSE,
+ x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, nullptr, nullptr);
/* Determine how many ions of this type each compartment contains */
sortMoleculesIntoCompartments(g, cr, sc, box, step, s->fpout, bRerun, FALSE);
/* Since we here know that we have to perform ion/water position exchanges,
* we now assemble the solvent positions */
g = &(s->group[eGrpSolvent]);
- communicate_group_positions(cr, g->xc, NULL, NULL, FALSE,
- x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, NULL, NULL);
+ communicate_group_positions(cr, g->xc, nullptr, nullptr, FALSE,
+ x, g->nat, g->nat_loc, g->ind_loc, g->c_ind_loc, nullptr, nullptr);
/* Determine how many molecules of solvent each compartment contains */
sortMoleculesIntoCompartments(g, cr, sc, box, step, s->fpout, bRerun, TRUE);
}
/* Now actually perform the particle exchanges, one swap group after another */
- alook = gmx_mtop_atomlookup_init(mtop);
gsol = &s->group[eGrpSolvent];
for (ig = eSwapFixedGrpNR; ig < s->ngrp; ig++)
{
SwS, nswaps, nswaps > 1 ? "s" : "", step, g->molname);
}
}
- gmx_mtop_atomlookup_destroy(alook);
- if (s->fpout != NULL)
+ if (s->fpout != nullptr)
{
print_ionlist(s, t, " # after swap");
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_SWAP_SWAPCOORDS_H
#define GMX_SWAP_SWAPCOORDS_H
-#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/timing/wallcycle.h"
+#include <cstdio>
+#include "gromacs/math/vectypes.h"
+#include "gromacs/utility/basedefinitions.h"
+
+struct gmx_domdec_t;
struct gmx_mtop_t;
struct gmx_output_env_t;
-struct swapstate_t;
+struct gmx_wallcycle;
+struct MdrunOptions;
+struct swaphistory_t;
+struct t_commrec;
struct t_inputrec;
struct t_swapcoords;
+struct ObservablesHistory;
+
/*! \brief Initialize ion / water position swapping ("Computational Electrophysiology").
*
* the output file, sets up swap data checkpoint writing, etc.
*
* \param[in] fplog General output file, normally md.log.
- * \param[in] bVerbose Should we be quiet or verbose?
* \param[in] ir Structure containing MD input parameters, among those
* also the structure needed for position swapping.
* \param[in] fn Output file name for swap data.
* \param[in] mtop Molecular topology.
* \param[in] x The initial positions of all particles.
* \param[in] box The simulation box.
- * \param[in] swapstate Swap-related data that is read from or written to checkpoint.
+ * \param[in] oh Contains struct with swap data that is read from or written to checkpoint.
* \param[in] cr Pointer to MPI communication data.
* \param[in] oenv Needed to open the swap output XVGR file.
- * \param[in] Flags Flags passed over from main, used to determine
- * whether we are doing a rerun, appending, etc.
+ * \param[in] mdrunOptions Options for mdrun.
*/
void init_swapcoords(
FILE *fplog,
- gmx_bool bVerbose,
t_inputrec *ir,
const char *fn,
gmx_mtop_t *mtop,
rvec x[],
matrix box,
- swapstate_t *swapstate,
+ ObservablesHistory *oh,
t_commrec *cr,
const gmx_output_env_t *oenv,
- unsigned long Flags);
+ const MdrunOptions &mdrunOptions);
/*! \brief Finalizes ion / water position swapping.
* \param[in] wcycle Count wallcycles of swap routines for diagnostic output.
* \param[in] x Positions of home particles this node owns.
* \param[in] box The simulation box.
- * \param[in] mtop Molecular topology.
* \param[in] bVerbose Should we be quiet or verbose?
* \param[in] bRerun Are we doing a rerun?
*
gmx_int64_t step,
double t,
t_inputrec *ir,
- gmx_wallcycle_t wcycle,
+ gmx_wallcycle *wcycle,
rvec x[],
matrix box,
- gmx_mtop_t *mtop,
gmx_bool bVerbose,
gmx_bool bRerun);
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015, by the GROMACS development team, led by
+# Copyright (c) 2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${TABLE_SOURCES} PARENT_SCOPE)
if (BUILD_TESTING)
-# add_subdirectory(tests)
+ add_subdirectory(tests)
endif()
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Implements classes for cubic spline table functions
+ *
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+#include "gmxpre.h"
+
+#include "cubicsplinetable.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <functional>
+#include <initializer_list>
+#include <utility>
+#include <vector>
+
+#include "gromacs/tables/tableinput.h"
+#include "gromacs/utility/alignedallocator.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/real.h"
+
+#include "splineutil.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+/*! \brief Calculate table elements from function/derivative data
+ *
+ * \param functionValue0 Function value for the present table index
+ * \param functionValue1 Function value for the next table index
+ * \param derivativeValue0 Derivative value for the present table index
+ * \param derivativeValue1 Derivative value for the next table index
+ * \param spacing Distance between table points
+ * \param Y Function value for table index
+ * \param F Component to multiply with offset eps
+ * \param G Component to multiply with eps^2
+ * \param H Component to multiply with eps^3
+ */
+void
+calculateCubicSplineCoefficients(double functionValue0,
+ double functionValue1,
+ double derivativeValue0,
+ double derivativeValue1,
+ double spacing,
+ double *Y,
+ double *F,
+ double *G,
+ double *H)
+{
+ *Y = functionValue0;
+ *F = spacing * derivativeValue0;
+ *G = 3.0*( functionValue1 - functionValue0) - spacing * (derivativeValue1 + 2.0 * derivativeValue0);
+ *H = -2.0*( functionValue1 - functionValue0) + spacing * (derivativeValue1 + derivativeValue0);
+}
+
+/*! \brief Perform cubic spline interpolation in interval from function/derivative
+ *
+ * \param functionValue0 Function value for the present table index
+ * \param functionValue1 Function value for the next table index
+ * \param derivativeValue0 Derivative value for the present table index
+ * \param derivativeValue1 Derivative value for the next table index
+ * \param spacing Distance between table points
+ * \param eps Offset from lower table point for evaluation
+ * \param[out] interpolatedFunctionValue Output function value
+ * \param[out] interpolatedDerivativeValue Output derivative value
+ */
+void
+cubicSplineInterpolationFromFunctionAndDerivative(double functionValue0,
+ double functionValue1,
+ double derivativeValue0,
+ double derivativeValue1,
+ double spacing,
+ double eps,
+ double *interpolatedFunctionValue,
+ double *interpolatedDerivativeValue)
+{
+ double Y, F, G, H;
+
+ calculateCubicSplineCoefficients(functionValue0, functionValue1,
+ derivativeValue0, derivativeValue1,
+ spacing,
+ &Y, &F, &G, &H);
+
+ double Fp = fma(fma(H, eps, G), eps, F);
+
+ *interpolatedFunctionValue = fma(Fp, eps, Y);
+ *interpolatedDerivativeValue = fma(eps, fma(2.0*eps, H, G), Fp)/spacing;
+}
+
+
+
+/*! \brief Construct the data for a single cubic table from analytical functions
+ *
+ * \param[in] function Analytical functiojn
+ * \param[in] derivative Analytical derivative
+ * \param[in] range Upper/lower limit of region to tabulate
+ * \param[in] spacing Distance between table points
+ * \param[out] yfghTableData Output cubic spline table with Y,F,G,H entries
+ */
+void
+fillSingleCubicSplineTableData(const std::function<double(double)> &function,
+ const std::function<double(double)> &derivative,
+ const std::pair<real, real> &range,
+ double spacing,
+ std::vector<real> *yfghTableData)
+{
+ int endIndex = range.second / spacing + 2;
+
+ yfghTableData->resize(4*endIndex);
+
+ double maxMagnitude = 0.0001*GMX_REAL_MAX;
+ bool functionIsInRange = true;
+ std::size_t lastIndexInRange = endIndex - 1;
+
+ for (int i = endIndex - 1; i >= 0; i--)
+ {
+ double x = i * spacing;
+ double tmpFunctionValue;
+ double tmpDerivativeValue;
+ double nextHigherFunction;
+ double nextHigherDerivative;
+ double Y, F, G, H;
+
+ if (range.first > 0 && i == 0)
+ {
+ // Avoid x==0 if it is not in the range, since it can lead to
+ // singularities even if the value for i==1 was within or required magnitude
+ functionIsInRange = false;
+ }
+
+ if (functionIsInRange)
+ {
+ tmpFunctionValue = function(x);
+ tmpDerivativeValue = derivative(x);
+ nextHigherFunction = ((i+1) < endIndex) ? function(x+spacing) : 0.0;
+ nextHigherDerivative = ((i+1) < endIndex) ? derivative(x+spacing) : 0.0;
+
+ if (std::abs(tmpFunctionValue) > maxMagnitude || std::abs(tmpDerivativeValue) > maxMagnitude)
+ {
+ functionIsInRange = false; // Once this happens, it never resets to true again
+ }
+ }
+
+ if (functionIsInRange)
+ {
+ calculateCubicSplineCoefficients(tmpFunctionValue, nextHigherFunction,
+ tmpDerivativeValue, nextHigherDerivative,
+ spacing,
+ &Y, &F, &G, &H);
+ lastIndexInRange--;
+ }
+ else
+ {
+ double lastIndexY = (*yfghTableData)[4*lastIndexInRange];
+ double lastIndexF = (*yfghTableData)[4*lastIndexInRange + 1];
+
+ Y = lastIndexY + lastIndexF * (i - lastIndexInRange);
+ F = lastIndexF;
+ G = 0.0;
+ H = 0.0;
+ }
+
+ (*yfghTableData)[4*i ] = Y;
+ (*yfghTableData)[4*i+1] = F;
+ (*yfghTableData)[4*i+2] = G;
+ (*yfghTableData)[4*i+3] = H;
+ }
+}
+
+
+/*! \brief Construct the data for a single cubic table from vector data
+ *
+ * \param[in] function Input vector with function data
+ * \param[in] derivative Input vector with derivative data
+ * \param[in] inputSpacing Distance between points in input vectors
+ * \param[in] range Upper/lower limit of region to tabulate
+ * \param[in] spacing Distance between table points
+ * \param[out] yfghTableData Output cubic spline table with Y,F,G,H entries
+ */
+void
+fillSingleCubicSplineTableData(ConstArrayRef<double> function,
+ ConstArrayRef<double> derivative,
+ double inputSpacing,
+ const std::pair<real, real> &range,
+ double spacing,
+ std::vector<real> *yfghTableData)
+{
+ int endIndex = range.second / spacing + 2;
+
+ std::vector<double> tmpFunction(endIndex);
+ std::vector<double> tmpDerivative(endIndex);
+
+ double maxMagnitude = 0.0001*GMX_REAL_MAX;
+ bool functionIsInRange = true;
+ std::size_t lastIndexInRange = endIndex - 1;
+
+ // Interpolate function and derivative values in positions needed for output
+ for (int i = endIndex - 1; i >= 0; i--)
+ {
+ double x = i * spacing;
+ double xtab = x / inputSpacing;
+ int index = xtab;
+ double eps = xtab - index;
+
+ if (range.first > 0 && i == 0)
+ {
+ // Avoid x==0 if it is not in the range, since it can lead to
+ // singularities even if the value for i==1 was within or required magnitude
+ functionIsInRange = false;
+ }
+
+ if (functionIsInRange && (std::abs(function[index]) > maxMagnitude || std::abs(derivative[index]) > maxMagnitude))
+ {
+ functionIsInRange = false; // Once this happens, it never resets to true again
+ }
+
+ if (functionIsInRange)
+ {
+ cubicSplineInterpolationFromFunctionAndDerivative(function[index],
+ function[index+1],
+ derivative[index],
+ derivative[index+1],
+ inputSpacing,
+ eps,
+ &(tmpFunction[i]),
+ &(tmpDerivative[i]));
+ lastIndexInRange--;
+ }
+ else
+ {
+ double lastIndexFunction = tmpFunction[lastIndexInRange];
+ double lastIndexDerivative = tmpDerivative[lastIndexInRange];
+ tmpFunction[i] = lastIndexFunction + lastIndexDerivative * (i - lastIndexInRange) * spacing;
+ tmpDerivative[i] = lastIndexDerivative;
+ }
+ }
+
+ yfghTableData->resize(4*endIndex);
+
+ for (int i = 0; i < endIndex; i++)
+ {
+ double Y, F, G, H;
+
+ double nextFunction = ((i+1) < endIndex) ? tmpFunction[i+1] : 0.0;
+ double nextDerivative = ((i+1) < endIndex) ? tmpDerivative[i+1] : 0.0;
+
+ calculateCubicSplineCoefficients(tmpFunction[i], nextFunction,
+ tmpDerivative[i], nextDerivative,
+ spacing,
+ &Y, &F, &G, &H);
+ (*yfghTableData)[4*i ] = Y;
+ (*yfghTableData)[4*i+1] = F;
+ (*yfghTableData)[4*i+2] = G;
+ (*yfghTableData)[4*i+3] = H;
+ }
+
+}
+
+} // namespace anonymous
+
+
+
+#if GMX_DOUBLE
+const real
+CubicSplineTable::defaultTolerance = 1e-10;
+#else
+const real
+CubicSplineTable::defaultTolerance = 10.0 * GMX_FLOAT_EPS;
+#endif
+
+CubicSplineTable::CubicSplineTable(std::initializer_list<AnalyticalSplineTableInput> analyticalInputList,
+ const std::pair<real, real> &range,
+ real tolerance)
+ : numFuncInTable_(analyticalInputList.size()), range_(range)
+{
+ // Sanity check on input values
+ if (range_.first < 0.0 || (range_.second-range_.first) < 0.001)
+ {
+ GMX_THROW(InvalidInputError("Range to tabulate cannot include negative values and must span at least 0.001"));
+ }
+
+ if (tolerance < GMX_REAL_EPS)
+ {
+ GMX_THROW(ToleranceError("Table tolerance cannot be smaller than GMX_REAL_EPS"));
+ }
+
+ double minQuotient = GMX_REAL_MAX;
+
+ // loop over all functions to find smallest spacing
+ for (auto thisFuncInput : analyticalInputList)
+ {
+ try
+ {
+ internal::throwUnlessDerivativeIsConsistentWithFunction(thisFuncInput.function, thisFuncInput.derivative, range_);
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating cubic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ // Calculate the required table spacing h. The error we make with linear interpolation
+ // of the derivative will be described by the third-derivative correction term.
+ // This means we can compute the required spacing as h = sqrt(12*tolerance*min(f'/f''')),
+ // where f'/f''' is the first and third derivative of the function, respectively.
+
+ double thisMinQuotient = internal::findSmallestQuotientOfFunctionAndThirdDerivative(thisFuncInput.derivative, range_);
+
+ minQuotient = std::min(minQuotient, thisMinQuotient);
+ }
+
+ double spacing = 0.5 * std::cbrt(72.0 * std::sqrt(3.0) * tolerance * minQuotient);
+
+ tableScale_ = 1.0 / spacing;
+
+ if (range_.second * tableScale_ > 2e6)
+ {
+ GMX_THROW(ToleranceError("Over a million points would be required for table; decrease range or increase tolerance"));
+ }
+
+ // Loop over all tables again.
+ // Here we create the actual table for each function, and then
+ // combine them into a multiplexed table function.
+ std::size_t funcIndex = 0;
+
+ for (auto thisFuncInput : analyticalInputList)
+ {
+ try
+ {
+ std::vector<real> tmpYfghTableData;
+
+ fillSingleCubicSplineTableData(thisFuncInput.function,
+ thisFuncInput.derivative,
+ range_,
+ spacing,
+ &tmpYfghTableData);
+
+ internal::fillMultiplexedTableData(tmpYfghTableData, &yfghMultiTableData_,
+ 4, numFuncInTable_, funcIndex);
+
+ funcIndex++;
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating cubic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ }
+}
+
+
+CubicSplineTable::CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
+ const std::pair<real, real> &range,
+ real tolerance)
+ : numFuncInTable_(numericalInputList.size()), range_(range)
+{
+ // Sanity check on input values
+ if (range.first < 0.0 || (range.second-range.first) < 0.001)
+ {
+ GMX_THROW(InvalidInputError("Range to tabulate cannot include negative values and must span at least 0.001"));
+ }
+
+ if (tolerance < GMX_REAL_EPS)
+ {
+ GMX_THROW(ToleranceError("Table tolerance cannot be smaller than GMX_REAL_EPS"));
+ }
+
+ double minQuotient = GMX_REAL_MAX;
+
+ // loop over all functions to find smallest spacing
+ for (auto thisFuncInput : numericalInputList)
+ {
+ try
+ {
+ // We do not yet know what the margin is, but we need to test that we at least cover
+ // the requested range before starting to calculate derivatives
+ if (thisFuncInput.function.size() < range_.second / thisFuncInput.spacing + 1)
+ {
+ GMX_THROW(InconsistentInputError("Table input vectors must cover requested range, and a margin beyond the upper endpoint"));
+ }
+
+ if (thisFuncInput.function.size() != thisFuncInput.derivative.size())
+ {
+ GMX_THROW(InconsistentInputError("Function and derivative vectors have different lengths"));
+ }
+
+ internal::throwUnlessDerivativeIsConsistentWithFunction(thisFuncInput.function, thisFuncInput.derivative, thisFuncInput.spacing, range_);
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating cubic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ // Calculate the required table spacing h. The error we make with linear interpolation
+ // of the derivative will be described by the third-derivative correction term.
+ // This means we can compute the required spacing as h = sqrt(12*tolerance*min(f'/f''')),
+ // where f'/f''' is the first and third derivative of the function, respectively.
+
+ double thisMinQuotient = internal::findSmallestQuotientOfFunctionAndThirdDerivative(thisFuncInput.derivative, thisFuncInput.spacing, range_);
+
+ minQuotient = std::min(minQuotient, thisMinQuotient);
+ }
+
+ double spacing = std::cbrt(72.0 * std::sqrt(3.0) * tolerance * minQuotient);
+
+ tableScale_ = 1.0 / spacing;
+
+ if (range_.second * tableScale_ > 1e6)
+ {
+ GMX_THROW(ToleranceError("Requested tolerance would require over a million points in table"));
+ }
+
+ // Loop over all tables again.
+ // Here we create the actual table for each function, and then
+ // combine them into a multiplexed table function.
+ std::size_t funcIndex = 0;
+
+ for (auto thisFuncInput : numericalInputList)
+ {
+ try
+ {
+ if (spacing < thisFuncInput.spacing)
+ {
+ GMX_THROW(ToleranceError("Input vector spacing cannot achieve tolerance requested"));
+ }
+
+ std::vector<real> tmpYfghTableData;
+
+ fillSingleCubicSplineTableData(thisFuncInput.function,
+ thisFuncInput.derivative,
+ thisFuncInput.spacing,
+ range,
+ spacing,
+ &tmpYfghTableData);
+
+ internal::fillMultiplexedTableData(tmpYfghTableData, &yfghMultiTableData_,
+ 4, numFuncInTable_, funcIndex);
+
+ funcIndex++;
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating cubic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ }
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ * \brief
+ * Declares classes for cubic spline table
+ *
+ * \inlibraryapi
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+#ifndef GMX_TABLES_CUBICSPLINETABLE_H
+#define GMX_TABLES_CUBICSPLINETABLE_H
+
+#include <initializer_list>
+#include <vector>
+
+#include "gromacs/simd/simd.h"
+#include "gromacs/tables/tableinput.h"
+#include "gromacs/utility/alignedallocator.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
+
+namespace gmx
+{
+
+/*! \libinternal \brief Cubic spline interpolation table.
+ *
+ * This class interpolates a function specified either as an analytical
+ * expression or from user-provided table data.
+ *
+ * At initialization, you provide the reference function of vectors
+ * as a list of tuples that contain a brief name, the function, and
+ * derivative for each function to tabulate. To create a table with
+ * two functions this initializer list can for instance look like
+ *
+ * { {"LJ6", lj6Func, lj6Der}, {"LJ12", lj12Func, lj12Der} }
+ *
+ * The names are only used so exceptions during initialization can
+ * be traced to a specific table.
+ *
+ * When interpolating, there are methods to interpolate either 1, 2, or 3
+ * functions in one go. By default these interpolation routines will
+ * operate on tables with the same number of functions as specified in
+ * the interpolation method (debug builds check that this is consistent with
+ * the table). However, it is also possible to use optional template
+ * parameters that specify the total number of functions in a table, and
+ * what function index to interpolate. For instance, to interpolate the
+ * derivative of the second function (i.e., index 1) in a
+ * multi-function-table with three functions in total, you can write
+ *
+ * table.evaluateDerivative<3,1>(x,&der);
+ *
+ * Here too, debug builds will check that the template parameters are
+ * consistent with the table.
+ *
+ * This class interpolates a function specified either as an analytical
+ * expression or from user-provided table data. The coefficients for each
+ * table point are precalculated such that we simply evaluate
+ *
+ * \f{eqnarray*}{
+ * V(x) = Y + F \epsilon + G \epsilon^2 + H \epsilon^3
+ * V'(x) = (F + 2 G \epsilon + 3 H \epsilon^2)/h
+ * \f}
+ *
+ * Where h is the spacing and epsilon the fractional offset from table point.
+ *
+ * While it is possible to create tables only from function values
+ * (i.e., no derivatives), it is recommended to provide derivatives for higher
+ * accuracy and to avoid issues with numerical differentiation. Note that the
+ * table input should be smooth, i.e. it should not contain noise e.g. from an
+ * (iterative) Boltzmann inversion procedure - you have been warned.
+ *
+ * \note This class is responsible for fundamental interpolation of any function,
+ * which might or might not correspond to a potential. For this reason
+ * both input and output derivatives are proper function derivatives, and
+ * we do not swap any signs to get forces directly from the table.
+ *
+ * \note There will be a small additional accuracy loss from the internal
+ * operation where we calculate the epsilon offset from the nearest table
+ * point, since the integer part we subtract can get large in those cases.
+ *
+ * While this is technically possible to solve with extended precision
+ * arithmetics, that would introduce extra instructions in some highly
+ * performance-sensitive code parts. For typical GROMACS interaction
+ * functions the derivatives will decay faster than the potential, which
+ * means it will never play any role. For other functions it will only
+ * cause a small increase in the relative error for arguments where the
+ * magnitude of the function or derivative is very small.
+ * Since we typically sum several results in GROMACS, this should never
+ * show up in any real cases, and for this reason we choose not to do
+ * the extended precision arithmetics.
+ *
+ * \note These routines are not suitable for table ranges starting far away
+ * from zero, since we allocate memory and calculate indices starting from
+ * range zero for efficiency reasons.
+ */
+class CubicSplineTable
+{
+ private:
+ /*! \brief Change that function value falls inside range when debugging
+ *
+ * \tparam T Lookup argument floating-point type, typically SimdReal or real.
+ * \param r Lookup argument to test
+ *
+ * \throws Debug builds will throw gmx::RangeError for values that are
+ * larger than the upper limit of the range, or smaller than 0.
+ * We allow the table to be called with arguments between 0 and
+ * the lower limit of the range, since this might in theory occur
+ * once-in-a-blue-moon with some algorithms.
+ */
+ template <typename T>
+ void
+ rangeCheck(T gmx_unused r) const
+ {
+#ifndef NDEBUG
+ // Check that all values fall in range when debugging
+ if (anyTrue( r < T(0.0) || T(range_.second) <= r ) )
+ {
+ GMX_THROW(RangeError("Interpolation input value falls outside table definition range"));
+ }
+#endif
+ }
+
+ public:
+
+ /*! \brief Default tolerance for cubic spline tables
+ *
+ * This is 10*GMX_FLOAT_EPS in single precision, and
+ * 1e-10 for double precision. It might not be worth setting
+ * this tolerance lower than 1e-10 in double precision, both because
+ * you will end up with very large tables, and because
+ * functions like r^-12 become so large for small values of r the
+ * table generation code will lead to some precision loss even
+ * in double precision.
+ */
+ static const real defaultTolerance;
+
+ /*! \brief Initialize table data from function
+ *
+ * \param analyticalInputList Initializer list with one or more functions to tabulate,
+ * specified as elements with a string description and
+ * the function as well as derivative. The function will also
+ * be called for values smaller than the lower limit of the
+ * range, but we avoid calling it for 0.0 if that value
+ * is not included in the range.
+ * Constructor will throw gmx::APIError for negative values.
+ * Due to the way the numerical derivative evaluation depends
+ * on machine precision internally, this range must be
+ * at least 0.001, or the constructor throws gmx::APIError.
+ * \param range Range over which the function will be tabulated.
+ * Constructor will throw gmx::APIError for negative values,
+ * or if the value/derivative vector does not cover the
+ * range.
+ * \param tolerance Requested accuracy of the table. This will be used to
+ * calculate the required internal spacing. If this cannot
+ * be achieved (for instance because the table would require
+ * too much memory) the constructor will throw gmx::ToleranceError.
+ *
+ * \note The functions are always defined in double precision to avoid
+ * losing accuracy when constructing tables.
+ *
+ * \note Since we fill the table for values below range.first, you can achieve
+ * a smaller table by using a smaller range where the tolerance has to be
+ * met, and accept that a few function calls below range.first do not
+ * quite reach the tolerance.
+ *
+ * \warning For efficiency reasons (since this code is used in some inner
+ * (kernels), we always allocate memory and calculate table indices
+ * for the complete interval [0,range.second], although the data will
+ * not be valid outside the definition range to avoid calling the
+ * function there. This means you should \a not use this class
+ * to tabulate functions for small ranges very far away from zero,
+ * since you would both waste a huge amount of memory and incur
+ * truncation errors when calculating the index.
+ *
+ * \throws gmx::ToleranceError if the requested tolerance cannot be achieved,
+ * and gmx::APIError for other incorrect input.
+ */
+ CubicSplineTable(std::initializer_list<AnalyticalSplineTableInput> analyticalInputList,
+ const std::pair<real, real> &range,
+ real tolerance = defaultTolerance);
+
+ /*! \brief Initialize table data from tabulated values and derivatives
+ *
+ * \param numericalInputList Initializer list with one or more functions to tabulate,
+ * specified as a string description, vectors with function and
+ * derivative values, and the input spacing. Data points are
+ * separated by the spacing parameter, starting from 0.
+ * Values below the lower limit of the range will be used to
+ * attempt defining the table, but we avoid using index 0
+ * unless 0.0 is included in the range. Some extra points beyond
+ * range.second are required to re-interpolate values, so add
+ * some margin. The constructor will throw gmx::APIError if the
+ * input vectors are too short to cover the requested range
+ * (and they must always be at least five points).
+ * \param range Range over which the function will be tabulated.
+ * Constructor will throw gmx::APIError for negative values,
+ * or if the value/derivative vector does not cover the
+ * range.
+ * \param tolerance Requested accuracy of the table. This will be used to
+ * calculate the required internal spacing and possibly
+ * re-interpolate. The constructor will throw
+ * gmx::ToleranceError if the input spacing is too coarse
+ * to achieve this accuracy.
+ *
+ * \note The input data vectors are always double precision to avoid
+ * losing accuracy when constructing tables.
+ *
+ * \note Since we fill the table for values below range.first, you can achieve
+ * a smaller table by using a smaller range where the tolerance has to be
+ * met, and accept that a few function calls below range.first do not
+ * quite reach the tolerance.
+ *
+ * \warning For efficiency reasons (since this code is used in some inner
+ * (kernels), we always allocate memory and calculate table indices
+ * for the complete interval [0,range.second], although the data will
+ * not be valid outside the definition range to avoid calling the
+ * function there. This means you should \a not use this class
+ * to tabulate functions for small ranges very far away from zero,
+ * since you would both waste a huge amount of memory and incur
+ * truncation errors when calculating the index.
+ */
+ CubicSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
+ const std::pair<real, real> &range,
+ real tolerance = defaultTolerance);
+
+
+ /************************************************************
+ * Evaluation methods for single functions *
+ ************************************************************/
+
+ /*! \brief Evaluate both function and derivative, single table function
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 1
+ * \tparam funcIndex Index of function to evaluate in table, default is 0
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function and derivative
+ * \param[out] functionValue Function value
+ * \param[out] derivativeValue Function derivative
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 1, int funcIndex = 0, typename T>
+ void
+ evaluateFunctionAndDerivative(T r,
+ T * functionValue,
+ T * derivativeValue) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T Y, F, G, H;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4*funcIndex, tabIndex, &Y, &F, &G, &H);
+ *functionValue = fma(fma(fma(H, eps, G), eps, F), eps, Y);
+ *derivativeValue = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+ }
+
+ /*! \brief Evaluate function value only, single table function
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 1
+ * \tparam funcIndex Index of function to evaluate in table, default is 0
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function value
+ * \param[out] functionValue Function value
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 1, int funcIndex = 0, typename T>
+ void
+ evaluateFunction(T r,
+ T * functionValue) const
+ {
+ T der gmx_unused;
+
+ evaluateFunctionAndDerivative<numFuncInTable, funcIndex>(r, functionValue, &der);
+ }
+
+ /*! \brief Evaluate function derivative only, single table function
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 1
+ * \tparam funcIndex Index of function to evaluate in table, default is 0
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function derivative
+ * \param[out] derivativeValue Function derivative
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 1, int funcIndex = 0, typename T>
+ void
+ evaluateDerivative(T r,
+ T * derivativeValue) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T Y, F, G, H;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex, tabIndex, &Y, &F, &G, &H);
+ *derivativeValue = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+ }
+
+ /************************************************************
+ * Evaluation methods for two functions *
+ ************************************************************/
+
+ /*! \brief Evaluate both function and derivative, two table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 2
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function and derivative
+ * \param[out] functionValue0 Interpolated value for first function
+ * \param[out] derivativeValue0 Interpolated derivative for first function
+ * \param[out] functionValue1 Interpolated value for second function
+ * \param[out] derivativeValue1 Interpolated derivative for second function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 2, int funcIndex0 = 0, int funcIndex1 = 1, typename T>
+ void
+ evaluateFunctionAndDerivative(T r,
+ T * functionValue0,
+ T * derivativeValue0,
+ T * functionValue1,
+ T * derivativeValue1) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T Y, F, G, H;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4*funcIndex0, tabIndex, &Y, &F, &G, &H);
+ *functionValue0 = fma(fma(fma(H, eps, G), eps, F), eps, Y);
+ *derivativeValue0 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4*funcIndex1, tabIndex, &Y, &F, &G, &H);
+ *functionValue1 = fma(fma(fma(H, eps, G), eps, F), eps, Y);
+ *derivativeValue1 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+ }
+
+ /*! \brief Evaluate function value only, two table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 2
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function value
+ * \param[out] functionValue0 Interpolated value for first function
+ * \param[out] functionValue1 Interpolated value for second function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 2, int funcIndex0 = 0, int funcIndex1 = 1, typename T>
+ void
+ evaluateFunction(T r,
+ T * functionValue0,
+ T * functionValue1) const
+ {
+ T der0 gmx_unused;
+ T der1 gmx_unused;
+
+ evaluateFunctionAndDerivative<numFuncInTable, funcIndex0, funcIndex1>(r, functionValue0, &der0, functionValue1, &der1);
+ }
+
+ /*! \brief Evaluate function derivative only, two table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 2
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function derivative
+ * \param[out] derivativeValue0 Interpolated derivative for first function
+ * \param[out] derivativeValue1 Interpolated derivative for second function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 2, int funcIndex0 = 0, int funcIndex1 = 1, typename T>
+ void
+ evaluateDerivative(T r,
+ T * derivativeValue0,
+ T * derivativeValue1) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T Y, F, G, H;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex0, tabIndex, &Y, &F, &G, &H);
+ *derivativeValue0 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex1, tabIndex, &Y, &F, &G, &H);
+ *derivativeValue1 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+ }
+
+ /************************************************************
+ * Evaluation methods for three functions *
+ ************************************************************/
+
+
+ /*! \brief Evaluate both function and derivative, three table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 3
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam funcIndex2 Index of 3rd function to evaluate in table, default is 2
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function and derivative
+ * \param[out] functionValue0 Interpolated value for first function
+ * \param[out] derivativeValue0 Interpolated derivative for first function
+ * \param[out] functionValue1 Interpolated value for second function
+ * \param[out] derivativeValue1 Interpolated derivative for second function
+ * \param[out] functionValue2 Interpolated value for third function
+ * \param[out] derivativeValue2 Interpolated derivative for third function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 3, int funcIndex0 = 0, int funcIndex1 = 1, int funcIndex2 = 2, typename T>
+ void
+ evaluateFunctionAndDerivative(T r,
+ T * functionValue0,
+ T * derivativeValue0,
+ T * functionValue1,
+ T * derivativeValue1,
+ T * functionValue2,
+ T * derivativeValue2) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable && funcIndex2 < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T Y, F, G, H;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4*funcIndex0, tabIndex, &Y, &F, &G, &H);
+ *functionValue0 = fma(fma(fma(H, eps, G), eps, F), eps, Y);
+ *derivativeValue0 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4*funcIndex1, tabIndex, &Y, &F, &G, &H);
+ *functionValue1 = fma(fma(fma(H, eps, G), eps, F), eps, Y);
+ *derivativeValue1 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4*funcIndex2, tabIndex, &Y, &F, &G, &H);
+ *functionValue2 = fma(fma(fma(H, eps, G), eps, F), eps, Y);
+ *derivativeValue2 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+ }
+
+ /*! \brief Evaluate function value only, three table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 3
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam funcIndex2 Index of 3rd function to evaluate in table, default is 2
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function value
+ * \param[out] functionValue0 Interpolated value for first function
+ * \param[out] functionValue1 Interpolated value for second function
+ * \param[out] functionValue2 Interpolated value for third function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 3, int funcIndex0 = 0, int funcIndex1 = 1, int funcIndex2 = 2, typename T>
+ void
+ evaluateFunction(T r,
+ T * functionValue0,
+ T * functionValue1,
+ T * functionValue2) const
+ {
+ T der0 gmx_unused;
+ T der1 gmx_unused;
+ T der2 gmx_unused;
+
+ evaluateFunctionAndDerivative<numFuncInTable, funcIndex0, funcIndex1, funcIndex2>(r, functionValue0, &der0, functionValue1, &der1, functionValue2, &der2);
+ }
+
+ /*! \brief Evaluate function derivative only, three table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 3
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam funcIndex2 Index of 3rd function to evaluate in table, default is 2
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function derivative
+ * \param[out] derivativeValue0 Interpolated derivative for first function
+ * \param[out] derivativeValue1 Interpolated derivative for second function
+ * \param[out] derivativeValue2 Interpolated derivative for third function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 3, int funcIndex0 = 0, int funcIndex1 = 1, int funcIndex2 = 2, typename T>
+ void
+ evaluateDerivative(T r,
+ T * derivativeValue0,
+ T * derivativeValue1,
+ T * derivativeValue2) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable && funcIndex2 < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T Y, F, G, H;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex0, tabIndex, &Y, &F, &G, &H);
+ *derivativeValue0 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex1, tabIndex, &Y, &F, &G, &H);
+ *derivativeValue1 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(yfghMultiTableData_.data() + 4 * funcIndex2, tabIndex, &Y, &F, &G, &H);
+ *derivativeValue2 = tableScale_ * fma(fma(T(3.0)*H, eps, T(2.0)*G), eps, F);
+ }
+
+ /*! \brief Return the table spacing (distance between points)
+ *
+ * You should never have to use this for normal code, but due to the
+ * way tables are constructed internally we need this in the unit tests
+ * to check relative tolerances over each interval.
+ *
+ * \return table spacing.
+ */
+ real
+ tableSpacing() const { return 1.0 / tableScale_; }
+
+ private:
+
+ std::size_t numFuncInTable_; //!< Number of separate tabluated functions
+ std::pair<real, real> range_; //!< Range for which table evaluation is allowed
+ real tableScale_; //!< Table scale (inverse of spacing between points)
+
+ /*! \brief Vector with combined table data to save calculations after lookup.
+ *
+ * For table point i, this vector contains the four coefficients
+ * Y,F,G,H that we use to express the function value as
+ * V(x) = Y + F e + G e^2 + H e^3, where e is the epsilon offset from
+ * the nearest table point.
+ *
+ * To allow aligned SIMD loads we need to use an aligned allocator for
+ * this container.
+ */
+ std::vector<real, AlignedAllocator<real> > yfghMultiTableData_;
+
+ // There should never be any reason to copy the table since it is read-only
+ GMX_DISALLOW_COPY_AND_ASSIGN(CubicSplineTable);
+};
+
+
+} // namespace gmx
+
+#endif // GMX_TABLES_CUBICSPLINETABLE_H
vi = v_inrange - dc*(i - i_inrange)*dx;
}
- if (table_v != NULL)
+ if (table_v != nullptr)
{
table_v[i] = vi;
}
/* Currently the last value only contains half the force: double it */
table_f[0] *= 2;
- if (table_v != NULL && table_fdv0 != NULL)
+ if (table_v != nullptr && table_fdv0 != nullptr)
{
/* Copy to FDV0 table too. Allocation occurs in forcerec.c,
* init_ewald_f_table().
return sc;
}
-/* Calculate the potential and force for an r value
- * in exactly the same way it is done in the inner loop.
- * VFtab is a pointer to the table data, offset is
- * the point where we should begin and stride is
- * 4 if we have a buckingham table, 3 otherwise.
- * If you want to evaluate table no N, set offset to 4*N.
- *
- * We use normal precision here, since that is what we
- * will use in the inner loops.
- */
-static void evaluate_table(real VFtab[], int offset, int stride,
- real tabscale, real r, real *y, real *yp)
-{
- int n;
- real rt, eps, eps2;
- real Y, F, Geps, Heps2, Fp;
-
- rt = r*tabscale;
- n = (int)rt;
- eps = rt - n;
- eps2 = eps*eps;
- n = offset+stride*n;
- Y = VFtab[n];
- F = VFtab[n+1];
- Geps = eps*VFtab[n+2];
- Heps2 = eps2*VFtab[n+3];
- Fp = F+Geps+Heps2;
- *y = Y+eps*Fp;
- *yp = (Fp+Geps+2.0*Heps2)*tabscale;
-}
-
static void copy2table(int n, int offset, int stride,
double x[], double Vtab[], double Ftab[], real scalefactor,
real dest[])
{
char *libfn;
char buf[STRLEN];
- double **yy = NULL, start, end, dx0, dx1, ssd, vm, vp, f, numf;
+ double **yy = nullptr, start, end, dx0, dx1, ssd, vm, vp, f, numf;
int k, i, nx, nx0 = 0, ny, nny, ns;
gmx_bool bAllZero, bZeroV, bZeroF;
double tabscale;
t_forcerec *fr, real rtab,
const char *tabfn)
{
- t_forcetable *dispersionCorrectionTable = NULL;
+ t_forcetable *dispersionCorrectionTable = nullptr;
- if (tabfn == NULL)
+ if (tabfn == nullptr)
{
if (debug)
{
#ifndef GMX_TABLES_FORCETABLE_H
#define GMX_TABLES_FORCETABLE_H
+/*! \libinternal \file
+ * \brief
+ * Old routines for table generation (will eventually be replaced)
+ *
+ * \inlibraryapi
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+
#include <cstdio>
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/utility/real.h"
+/*! \brief Flag to select user tables for make_tables */
#define GMX_MAKETABLES_FORCEUSER (1<<0)
+/*! \brief Flag to only make 1,4 pair tables for make_tables */
#define GMX_MAKETABLES_14ONLY (1<<1)
-/* Index in the tables that says which function to use */
+/*! \brief Enumerated type to describe the interaction types in a table */
enum {
- etiCOUL, etiLJ6, etiLJ12, etiNR
+ etiCOUL, //!< Coulomb
+ etiLJ6, //!< Dispersion
+ etiLJ12, //!< Repulsion
+ etiNR //!< Total number of interaction types
};
-typedef double (*real_space_grid_contribution_computer)(double, double);
-/* Function pointer used to tell table_spline3_fill_ewald_lr whether it
+/*! \brief Function pointer to calculate the grid contribution for coulomb/LJ
+ *
+ * Used to tell table_spline3_fill_ewald_lr whether it
* should calculate the grid contribution for electrostatics or LJ.
*/
+typedef double (*real_space_grid_contribution_computer)(double, double);
+
+/*! \brief Fill tables with the Ewald long-range force interaction
+ *
+ * Fill tables of ntab points with spacing dr with the ewald long-range
+ * (mesh) force.
+ * There are three separate tables with format FDV0, F, and V.
+ * This function interpolates the Ewald mesh potential contribution
+ * with coefficient beta using a quadratic spline.
+ * The force can then be interpolated linearly.
+ *
+ * \param table_F Force table
+ * \param table_V Potential table
+ * \param table_FDV0 Combined table optimized for SIMD loads
+ * \param ntab Number of points in tables
+ * \param dx Spacing
+ * \param beta Ewald splitting paramter
+ * \param v_lr Pointer to function calculating real-space grid contribution
+ */
void table_spline3_fill_ewald_lr(real *table_F,
real *table_V,
real *table_FDV0,
double dx,
real beta,
real_space_grid_contribution_computer v_lr);
-/* Fill tables of ntab points with spacing dr with the ewald long-range
- * (mesh) force.
- * There are three separate tables with format FDV0, F, and V.
- * This function interpolates the Ewald mesh potential contribution
- * with coefficient beta using a quadratic spline.
- * The force can then be interpolated linearly.
- */
+/*! \brief Compute scaling for the Ewald quadratic spline tables.
+ *
+ * \param ic Pointer to interaction constant structure
+ * \return The scaling factor
+ */
real ewald_spline3_table_scale(const interaction_const_t *ic);
-/* Return the scaling for the Ewald quadratic spline tables. */
+/*! \brief Return the real space grid contribution for Ewald
+ *
+ * \param beta Ewald splitting parameter
+ * \param r Distance for which to calculate the real-space contrib
+ * \return Real space grid contribution for Ewald electrostatics
+ */
double v_q_ewald_lr(double beta, double r);
-/* Return the real space grid contribution for Ewald*/
+/*! \brief Return the real space grid contribution for LJ-Ewald
+ *
+ * \param beta Ewald splitting parameter
+ * \param r Distance for which to calculate the real-space contrib
+ * \return Real space grid contribution for Ewald Lennard-Jones interaction
+ */
double v_lj_ewald_lr(double beta, double r);
-/* Return the real space grid contribution for LJ-Ewald*/
+/*! \brief Return tables for inner loops.
+ *
+ * \param fp Log file pointer
+ * \param fr Force record
+ * \param fn File name from which to read user tables
+ * \param rtab Largest interaction distance to tabulate
+ * \param flags Flags to select table settings
+ *
+ * \return Pointer to inner loop table structure
+ */
t_forcetable *make_tables(FILE *fp,
const t_forcerec *fr,
const char *fn, real rtab, int flags);
-/* Return tables for inner loops. */
-bondedtable_t make_bonded_table(FILE *fplog, const char *fn, int angle);
-/* Return a table for bonded interactions,
- * angle should be: bonds 0, angles 1, dihedrals 2
+/*! \brief Return a table for bonded interactions,
+ *
+ * \param fplog Pointer to log file
+ * \param fn File name
+ * \param angle Type of angle: bonds 0, angles 1, dihedrals 2
+ * \return New bonded table datatype
*/
+bondedtable_t make_bonded_table(FILE *fplog, const char *fn, int angle);
-/* Return a table for GB calculations */
+/*! \brief Return a table for GB calculations
+ *
+ * \param fr Force record
+ * \return Pointer to new gb table structure
+ */
t_forcetable *make_gb_table(const t_forcerec *fr);
/*! \brief Construct and return tabulated dispersion and repulsion interactions
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Implements classes for quadratic spline table functions
+ *
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+#include "gmxpre.h"
+
+#include "quadraticsplinetable.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <functional>
+#include <initializer_list>
+#include <utility>
+#include <vector>
+
+#include "gromacs/tables/tableinput.h"
+#include "gromacs/utility/alignedallocator.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/real.h"
+
+#include "splineutil.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+/*! \brief Construct the data for a single quadratic table from analytical functions
+ *
+ * \param[in] function Analytical functiojn
+ * \param[in] derivative Analytical derivative
+ * \param[in] range Upper/lower limit of region to tabulate
+ * \param[in] spacing Distance between table points
+ * \param[out] functionTableData Output table with function data
+ * \param[out] derivativeTableData OUtput table with (adjusted) derivative data
+ */
+void
+fillSingleQuadraticSplineTableData(const std::function<double(double)> &function,
+ const std::function<double(double)> &derivative,
+ const std::pair<real, real> &range,
+ double spacing,
+ std::vector<real> *functionTableData,
+ std::vector<real> *derivativeTableData)
+{
+ std::size_t endIndex = range.second / spacing + 2;
+
+ functionTableData->resize(endIndex);
+ derivativeTableData->resize(endIndex);
+
+ double maxMagnitude = 0.0001*GMX_REAL_MAX;
+ bool functionIsInRange = true;
+ std::size_t lastIndexInRange = endIndex - 1;
+
+ for (int i = endIndex - 1; i >= 0; i--)
+ {
+ double x = i * spacing;
+ double tmpFunctionValue;
+ double tmpDerivativeValue;
+
+ if (range.first > 0 && i == 0)
+ {
+ // Avoid x==0 if it is not in the range, since it can lead to
+ // singularities even if the value for i==1 was within or required magnitude
+ functionIsInRange = false;
+ }
+
+ if (functionIsInRange)
+ {
+ tmpFunctionValue = function(x);
+
+ // Calculate third derivative term (2nd derivative of the derivative)
+ // Make sure we stay in range. In practice this means we use one-sided
+ // interpolation at the interval endpoints (indentical to an offset for 3-point formula)
+ const double h = std::pow( GMX_DOUBLE_EPS, 0.25 );
+ double y = std::min( std::max(x, range.first + h), range.second - h);
+ double thirdDerivativeValue = ( derivative(y+h) - 2.0 * derivative(y) + derivative(y-h) ) / ( h * h );
+
+ tmpDerivativeValue = derivative(x) - spacing * spacing * thirdDerivativeValue / 12.0;
+
+ if (std::abs(tmpFunctionValue) > maxMagnitude || std::abs(tmpDerivativeValue) > maxMagnitude)
+ {
+ functionIsInRange = false; // Once this happens, it never resets to true again
+ }
+ }
+
+ if (functionIsInRange)
+ {
+ (*functionTableData)[i] = tmpFunctionValue;
+ (*derivativeTableData)[i] = tmpDerivativeValue;
+ lastIndexInRange--;
+ }
+ else
+ {
+ // Once the function or derivative (more likely) has reached very large values,
+ // we simply make a linear function from the last in-range value of the derivative.
+ double lastIndexFunction = (*functionTableData)[lastIndexInRange];
+ double lastIndexDerivative = (*derivativeTableData)[lastIndexInRange];
+ (*functionTableData)[i] = lastIndexFunction + lastIndexDerivative * (i - lastIndexInRange) * spacing;
+ (*derivativeTableData)[i] = lastIndexDerivative;
+ }
+ }
+}
+
+
+/*! \brief Construct the data for a single quadratic table from vector data
+ *
+ * \param[in] function Input vector with function data
+ * \param[in] derivative Input vector with derivative data
+ * \param[in] inputSpacing Distance between points in input vectors
+ * \param[in] range Upper/lower limit of region to tabulate
+ * \param[in] spacing Distance between table points
+ * \param[out] functionTableData Output table with function data
+ * \param[out] derivativeTableData OUtput table with (adjusted) derivative data
+ */
+void
+fillSingleQuadraticSplineTableData(ConstArrayRef<double> function,
+ ConstArrayRef<double> derivative,
+ double inputSpacing,
+ const std::pair<real, real> &range,
+ double spacing,
+ std::vector<real> *functionTableData,
+ std::vector<real> *derivativeTableData)
+{
+ std::size_t endIndex = range.second / spacing + 2;
+
+ functionTableData->resize(endIndex);
+ derivativeTableData->resize(endIndex);
+
+ std::vector<double> thirdDerivative(internal::vectorSecondDerivative(derivative, inputSpacing));
+
+ double maxMagnitude = 0.0001*GMX_REAL_MAX;
+ bool functionIsInRange = true;
+ std::size_t lastIndexInRange = endIndex - 1;
+
+ for (int i = endIndex - 1; i >= 0; i--)
+ {
+ double x = i * spacing;
+ double tmpFunctionValue;
+ double tmpDerivativeValue;
+
+ if (range.first > 0 && i == 0)
+ {
+ // Avoid x==0 if it is not in the range, since it can lead to
+ // singularities even if the value for i==1 was within or required magnitude
+ functionIsInRange = false;
+ }
+
+ if (functionIsInRange)
+ {
+ // Step 1: Interpolate the function value at x from input table.
+ double inputXTab = x / inputSpacing;
+ int inputIndex = inputXTab;
+ double inputEps = inputXTab - inputIndex;
+
+ // Linear interpolation of input derivative and third derivative
+ double thirdDerivativeValue = (1.0 - inputEps) * thirdDerivative[inputIndex] + inputEps * thirdDerivative[inputIndex+1];
+ double derivativeValue = (1.0 - inputEps) * derivative[inputIndex] + inputEps * derivative[inputIndex+1];
+
+ // Quadratic interpolation for function value
+ tmpFunctionValue = function[inputIndex] + 0.5 * (derivative[inputIndex] + derivativeValue) * inputEps * inputSpacing;
+ tmpDerivativeValue = derivativeValue - spacing * spacing * thirdDerivativeValue / 12.0;
+
+ if (std::abs(tmpFunctionValue) > maxMagnitude || std::abs(tmpDerivativeValue) > maxMagnitude)
+ {
+ functionIsInRange = false; // Once this happens, it never resets to true again
+ }
+ }
+
+ if (functionIsInRange)
+ {
+ (*functionTableData)[i] = tmpFunctionValue;
+ (*derivativeTableData)[i] = tmpDerivativeValue;
+ lastIndexInRange--;
+ }
+ else
+ {
+ // Once the function or derivative (more likely) has reached very large values,
+ // we simply make a linear function from the last in-range value of the derivative.
+ double lastIndexFunction = (*functionTableData)[lastIndexInRange];
+ double lastIndexDerivative = (*derivativeTableData)[lastIndexInRange];
+ (*functionTableData)[i] = lastIndexFunction + lastIndexDerivative * (i - lastIndexInRange) * spacing;
+ (*derivativeTableData)[i] = lastIndexDerivative;
+ }
+ }
+}
+
+/*! \brief Create merged DDFZ vector from function & derivative data
+ *
+ * \param functionTableData Function values
+ * \param derivativeTableData Derivative values. We have already subtracted the
+ * small third derivative component when calling this
+ * function, but in practice it is just an arbitrary
+ * vector here.
+ * \param ddfzTableData Vector four times longer, filled with
+ * the derivative, the difference to the next derivative
+ * point, the function value, and zero.
+ *
+ * \throws If the vector lengths do not match.
+ */
+void
+fillDdfzTableData(const std::vector<real> &functionTableData,
+ const std::vector<real> &derivativeTableData,
+ std::vector<real> *ddfzTableData)
+{
+ GMX_ASSERT(functionTableData.size() == derivativeTableData.size(), "Mismatching vector lengths");
+
+ std::size_t points = functionTableData.size();
+
+ ddfzTableData->resize(4 * points);
+
+ for (std::size_t i = 0; i < points; i++)
+ {
+ (*ddfzTableData)[4*i] = derivativeTableData[i];
+
+ double nextDerivative = ( i < functionTableData.size() - 1 ) ? derivativeTableData[i+1] : 0.0;
+
+ (*ddfzTableData)[4*i + 1] = nextDerivative - derivativeTableData[i];
+ (*ddfzTableData)[4*i + 2] = functionTableData[i];
+ (*ddfzTableData)[4*i + 3] = 0.0;
+ }
+}
+
+} // namespace anonymous
+
+
+
+const real
+QuadraticSplineTable::defaultTolerance = 10.0 * GMX_FLOAT_EPS;
+
+
+QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<AnalyticalSplineTableInput> analyticalInputList,
+ const std::pair<real, real> &range,
+ real tolerance)
+ : numFuncInTable_(analyticalInputList.size()), range_(range)
+{
+ // Sanity check on input values
+ if (range_.first < 0.0 || (range_.second-range_.first) < 0.001)
+ {
+ GMX_THROW(InvalidInputError("Range to tabulate cannot include negative values and must span at least 0.001"));
+ }
+
+ if (tolerance < GMX_REAL_EPS)
+ {
+ GMX_THROW(ToleranceError("Table tolerance cannot be smaller than GMX_REAL_EPS"));
+ }
+
+ double minQuotient = GMX_REAL_MAX;
+
+ // loop over all functions to find smallest spacing
+ for (auto thisFuncInput : analyticalInputList)
+ {
+ try
+ {
+ internal::throwUnlessDerivativeIsConsistentWithFunction(thisFuncInput.function, thisFuncInput.derivative, range_);
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating quadratic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ // Calculate the required table spacing h. The error we make with linear interpolation
+ // of the derivative will be described by the third-derivative correction term.
+ // This means we can compute the required spacing as h = sqrt(12*tolerance*min(f'/f''')),
+ // where f'/f''' is the first and third derivative of the function, respectively.
+
+ double thisMinQuotient = internal::findSmallestQuotientOfFunctionAndSecondDerivative(thisFuncInput.derivative, range_);
+
+ minQuotient = std::min(minQuotient, thisMinQuotient);
+ }
+
+ double spacing = std::sqrt(12.0 * tolerance * minQuotient);
+
+ halfSpacing_ = 0.5 * spacing;
+ tableScale_ = 1.0 / spacing;
+
+ if (range_.second * tableScale_ > 1e6)
+ {
+ GMX_THROW(ToleranceError("Over a million points would be required for table; decrease range or increase tolerance"));
+ }
+
+ // Loop over all tables again.
+ // Here we create the actual table for each function, and then
+ // combine them into a multiplexed table function.
+ std::size_t funcIndex = 0;
+
+ for (auto thisFuncInput : analyticalInputList)
+ {
+ try
+ {
+ std::vector<real> tmpFuncTableData;
+ std::vector<real> tmpDerTableData;
+ std::vector<real> tmpDdfzTableData;
+
+ fillSingleQuadraticSplineTableData(thisFuncInput.function,
+ thisFuncInput.derivative,
+ range_,
+ spacing,
+ &tmpFuncTableData,
+ &tmpDerTableData);
+
+ fillDdfzTableData(tmpFuncTableData, tmpDerTableData, &tmpDdfzTableData);
+
+ internal::fillMultiplexedTableData(tmpDerTableData, &derivativeMultiTableData_,
+ 1, numFuncInTable_, funcIndex);
+
+ internal::fillMultiplexedTableData(tmpDdfzTableData, &ddfzMultiTableData_,
+ 4, numFuncInTable_, funcIndex);
+
+ funcIndex++;
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating quadratic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ }
+}
+
+
+QuadraticSplineTable::QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
+ const std::pair<real, real> &range,
+ real tolerance)
+ : numFuncInTable_(numericalInputList.size()), range_(range)
+{
+ // Sanity check on input values
+ if (range.first < 0.0 || (range.second-range.first) < 0.001)
+ {
+ GMX_THROW(InvalidInputError("Range to tabulate cannot include negative values and must span at least 0.001"));
+ }
+
+ if (tolerance < GMX_REAL_EPS)
+ {
+ GMX_THROW(ToleranceError("Table tolerance cannot be smaller than GMX_REAL_EPS"));
+ }
+
+ double minQuotient = GMX_REAL_MAX;
+
+ // loop over all functions to find smallest spacing
+ for (auto thisFuncInput : numericalInputList)
+ {
+ try
+ {
+ // We do not yet know what the margin is, but we need to test that we at least cover
+ // the requested range before starting to calculate derivatives
+ if (thisFuncInput.function.size() < range_.second / thisFuncInput.spacing + 1)
+ {
+ GMX_THROW(InconsistentInputError("Table input vectors must cover requested range, and a margin beyond the upper endpoint"));
+ }
+
+ if (thisFuncInput.function.size() != thisFuncInput.derivative.size())
+ {
+ GMX_THROW(InconsistentInputError("Function and derivative vectors have different lengths"));
+ }
+
+ internal::throwUnlessDerivativeIsConsistentWithFunction(thisFuncInput.function, thisFuncInput.derivative, thisFuncInput.spacing, range_);
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating quadratic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ // Calculate the required table spacing h. The error we make with linear interpolation
+ // of the derivative will be described by the third-derivative correction term.
+ // This means we can compute the required spacing as h = sqrt(12*tolerance*min(f'/f''')),
+ // where f'/f''' is the first and third derivative of the function, respectively.
+
+ double thisMinQuotient = internal::findSmallestQuotientOfFunctionAndSecondDerivative(thisFuncInput.derivative, thisFuncInput.spacing, range_);
+
+ minQuotient = std::min(minQuotient, thisMinQuotient);
+ }
+
+ double spacing = std::sqrt(12.0 * tolerance * minQuotient);
+
+ halfSpacing_ = 0.5 * spacing;
+ tableScale_ = 1.0 / spacing;
+
+ if (range_.second * tableScale_ > 1e6)
+ {
+ GMX_THROW(ToleranceError("Requested tolerance would require over a million points in table"));
+ }
+
+ // Loop over all tables again.
+ // Here we create the actual table for each function, and then
+ // combine them into a multiplexed table function.
+ std::size_t funcIndex = 0;
+
+ for (auto thisFuncInput : numericalInputList)
+ {
+ try
+ {
+ if (spacing < thisFuncInput.spacing)
+ {
+ GMX_THROW(ToleranceError("Input vector spacing cannot achieve tolerance requested"));
+ }
+
+ std::vector<real> tmpFuncTableData;
+ std::vector<real> tmpDerTableData;
+ std::vector<real> tmpDdfzTableData;
+
+ fillSingleQuadraticSplineTableData(thisFuncInput.function,
+ thisFuncInput.derivative,
+ thisFuncInput.spacing,
+ range,
+ spacing,
+ &tmpFuncTableData,
+ &tmpDerTableData);
+
+ fillDdfzTableData(tmpFuncTableData, tmpDerTableData, &tmpDdfzTableData);
+
+ internal::fillMultiplexedTableData(tmpDerTableData, &derivativeMultiTableData_,
+ 1, numFuncInTable_, funcIndex);
+
+ internal::fillMultiplexedTableData(tmpDdfzTableData, &ddfzMultiTableData_,
+ 4, numFuncInTable_, funcIndex);
+
+ funcIndex++;
+ }
+ catch (gmx::GromacsException &ex)
+ {
+ ex.prependContext("Error generating quadratic spline table for function '" + thisFuncInput.desc + "'");
+ throw;
+ }
+ }
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal
+ * \defgroup module_tables Classes for table interpolation
+ * \ingroup group_utilitymodules
+ *
+ * \brief Table interpolation from analytical or numerical input
+ *
+ * This module provides quadratic spline interpolation tables used
+ * both for the nonbonded kernels and listed interactions.
+ *
+ * \author Erik Lindahl <erik.lindahl@scilifelab.se>
+ */
+
+
+/*! \libinternal \file
+ * \brief
+ * Declares classes for quadratic spline table
+ *
+ * \inlibraryapi
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+#ifndef GMX_TABLES_QUADRATICSPLINETABLE_H
+#define GMX_TABLES_QUADRATICSPLINETABLE_H
+
+#include <functional>
+#include <initializer_list>
+#include <vector>
+
+#include "gromacs/simd/simd.h"
+#include "gromacs/tables/tableinput.h"
+#include "gromacs/utility/alignedallocator.h"
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
+
+namespace gmx
+{
+
+/*! \libinternal \brief Quadratic spline interpolation table.
+ *
+ * This class interpolates a function specified either as an analytical
+ * expression or from user-provided table data.
+ *
+ * At initialization, you provide the reference function of vectors
+ * as a list of tuples that contain a brief name, the function, and
+ * derivative for each function to tabulate. To create a table with
+ * two functions this initializer list can for instance look like
+ *
+ * { {"LJ6", lj6Func, lj6Der}, {"LJ12", lj12Func, lj12Der} }
+ *
+ * The names are only used so exceptions during initialization can
+ * be traced to a specific table.
+ *
+ * When interpolating, there are methods to interpolate either 1, 2, or 3
+ * functions in one go. By default these interpolation routines will
+ * operate on tables with the same number of functions as specified in
+ * the interpolation method (debug builds check that this is consistent with
+ * the table). However, it is also possible to use optional template
+ * parameters that specify the total number of functions in a table, and
+ * what function index to interpolate. For instance, to interpolate the
+ * derivative of the second function (i.e., index 1) in a
+ * multi-function-table with three functions in total, you can write
+ *
+ * table.evaluateDerivative<3,1>(x,&der);
+ *
+ * Here too, debug builds will check that the template parameters are
+ * consistent with the table.
+ *
+ * The table data is internally adjusted to guarantee that the interpolated
+ * derivative is the true derivative of the interpolated potential, which is
+ * important to avoid systematic errors for the common case when the derivative
+ * is concave/convex in the entire interval.
+ * We do this by expressing the difference in the function value
+ * at a small offset h relative to a reference value in position 0 with a forward
+ * Taylor series expanded around 0, and then doing the opposite of expressing
+ * difference in the function at position 0 relative to a reference value in
+ * position h when using a backward Taylor expansion:
+ *
+ * \f{eqnarray*}{
+ * \Delta V & = & hV'(0) + \frac{1}{2} h^2 V''(0) + \frac{1}{6} h^3 V'''(0) + O(h^4) \\
+ * \Delta V & = & hV'(h) - \frac{1}{2} h^2 V''(h) + \frac{1}{6} h^3 V'''(h) + O(h^4)
+ * \f}
+ *
+ * Summing the equations leads to
+ *
+ * \f[
+ * 2 \Delta V = h(V'(0) + V'(h)) + \frac{1}{2} h^2 (V''(0)-V''(h)) + \frac{1}{6}h^3(V'''(0)+V'''(h)) + O(h^4)
+ * \f]
+ *
+ * To make the second term symmetric too, we can replace it with the average of
+ * the Taylor expansion at 0 and h (i.e., using the third derivative). This gives
+ *
+ * \f[
+ * 2 \Delta V = h(V'(0) + V'(h)) - \frac{1}{12} h^3 (V'''(0)+V'''(h)) + O(h^4)
+ * \f]
+ *
+ * Thus, if we replace the derivative in the internal quadratic table data with
+ *
+ * \f[
+ * V' - \frac{1}{12}h^2 V'''
+ * \f]
+ *
+ * we will cancel the h^3 term in the error. This will make the integral of the
+ * forces match the potential much better (The h^4 term actually disappears, so
+ * when summing over 1/h points the remaining error will be O(h^4).
+ *
+ * While it is possible to create tables only from function values
+ * (i.e., no derivatives), it is recommended to provide derivatives for higher
+ * accuracy and to avoid issues with numerical differentiation. Note that the
+ * table input should be smooth, i.e. it should not contain noise e.g. from an
+ * (iterative) Boltzmann inversion procedure - you have been warned.
+ *
+ * \note This class is responsible for fundamental interpolation of any function,
+ * which might or might not correspond to a potential. For this reason
+ * both input and output derivatives are proper function derivatives, and
+ * we do not swap any signs to get forces directly from the table.
+ *
+ * \note There will be a small additional accuracy loss from the internal
+ * operation where we calculate the epsilon offset from the nearest table
+ * point, since the integer part we subtract can get large in those cases.
+ * The absolute such error both in the function and derivative value will
+ * be roughly f''*x*GMX_REAL_EPS, where x is the argument and f'' the
+ * second derivative.
+ * While this is technically possible to solve with extended precision
+ * arithmetics, that would introduce extra instructions in some highly
+ * performance-sensitive code parts. For typical GROMACS interaction
+ * functions the derivatives will decay faster than the potential, which
+ * means it will never play any role. For other functions it will only
+ * cause a small increase in the relative error for arguments where the
+ * magnitude of the function or derivative is very small.
+ * Since we typically sum several results in GROMACS, this should never
+ * show up in any real cases, and for this reason we choose not to do
+ * the extended precision arithmetics.
+ *
+ * \note These routines are not suitable for table ranges starting far away
+ * from zero, since we allocate memory and calculate indices starting from
+ * range zero for efficiency reasons.
+ */
+class QuadraticSplineTable
+{
+ private:
+ /*! \brief Change that function value falls inside range when debugging
+ *
+ * \tparam T Lookup argument floating-point type, typically SimdReal or real.
+ * \param r Lookup argument to test
+ *
+ * \throws Debug builds will throw gmx::RangeError for values that are
+ * larger than the upper limit of the range, or smaller than 0.
+ * We allow the table to be called with arguments between 0 and
+ * the lower limit of the range, since this might in theory occur
+ * once-in-a-blue-moon with some algorithms.
+ */
+ template <typename T>
+ void
+ rangeCheck(T gmx_unused r) const
+ {
+#ifndef NDEBUG
+ // Check that all values fall in range when debugging
+ if (anyTrue( r < T(0.0) || T(range_.second) <= r ) )
+ {
+ GMX_THROW(RangeError("Interpolation input value falls outside table definition range"));
+ }
+#endif
+ }
+
+ public:
+
+ /*! \brief Default tolerance for tables is 10*GMX_FLOAT_EPS
+ *
+ * \note Even for double precision builds we set the tolerance to
+ * one order of magnitude above the single precision epsilon.
+ */
+ static const real defaultTolerance;
+
+ /*! \brief Initialize table data from function
+ *
+ * \param analyticalInputList Initializer list with one or more functions to tabulate,
+ * specified as pairs containing analytical
+ * functions and their derivatives. The function will also
+ * be called for values smaller than the lower limit of the
+ * range, but we avoid calling it for 0.0 if that value
+ * is not included in the range.
+ * \param range Range over which the function will be tabulated.
+ * Constructor will throw gmx::APIError for negative values.
+ * Due to the way the numerical derivative evaluation depends
+ * on machine precision internally, this range must be
+ * at least 0.001, or the constructor throws gmx::APIError.
+ * \param tolerance Requested accuracy of the table. This will be used to
+ * calculate the required internal spacing. If this cannot
+ * be achieved (for instance because the table would require
+ * too much memory) the constructor will throw gmx::ToleranceError.
+ *
+ * \note The functions are always defined in double precision to avoid
+ * losing accuracy when constructing tables.
+ *
+ * \note Since we fill the table for values below range.first, you can achieve
+ * a smaller table by using a smaller range where the tolerance has to be
+ * met, and accept that a few function calls below range.first do not
+ * quite reach the tolerance.
+ *
+ * \warning For efficiency reasons (since this code is used in some inner
+ * (kernels), we always allocate memory and calculate table indices
+ * for the complete interval [0,range.second], although the data will
+ * not be valid outside the definition range to avoid calling the
+ * function there. This means you should \a not use this class
+ * to tabulate functions for small ranges very far away from zero,
+ * since you would both waste a huge amount of memory and incur
+ * truncation errors when calculating the index.
+ *
+ * \throws gmx::ToleranceError if the requested tolerance cannot be achieved,
+ * and gmx::APIError for other incorrect input.
+ */
+ QuadraticSplineTable(std::initializer_list<AnalyticalSplineTableInput> analyticalInputList,
+ const std::pair<real, real> &range,
+ real tolerance = defaultTolerance);
+
+ /*! \brief Initialize table data from tabulated values and derivatives
+ *
+ * \param numericalInputList Initializer list with one or more functions to tabulate,
+ * specified as pairs containing containing vectors for the
+ * function values and their derivatives. Data points are
+ * separated by the spacing parameter, starting from 0.
+ * Values below the lower limit of the range will be used to
+ * attempt defining the table, but we avoid using index 0
+ * unless 0.0 is included in the range. Some extra points beyond
+ * range.second are required to re-interpolate values, so add
+ * some margin. The constructor will throw gmx::APIError if the
+ * input vectors are too short to cover the requested range
+ * (and they must always be at least five points).
+ * \param range Range over which the function will be tabulated.
+ * Constructor will throw gmx::APIError for negative values,
+ * or if the value/derivative vector does not cover the
+ * range.
+ * \param tolerance Requested accuracy of the table in the range. This will be
+ * used to calculate the required internal spacing and possibly
+ * re-interpolate. The constructor will throw
+ * gmx::ToleranceError if the input spacing is too coarse
+ * to achieve this accuracy.
+ *
+ * \note The input data vectors are always double precision to avoid
+ * losing accuracy when constructing tables.
+ *
+ * \note Since we fill the table for values below range.first, you can achieve
+ * a smaller table by using a smaller range where the tolerance has to be
+ * met, and accept that a few function calls below range.first do not
+ * quite reach the tolerance.
+ *
+ * \warning For efficiency reasons (since this code is used in some inner
+ * (kernels), we always allocate memory and calculate table indices
+ * for the complete interval [0,range.second], although the data will
+ * not be valid outside the definition range to avoid calling the
+ * function there. This means you should \a not use this class
+ * to tabulate functions for small ranges very far away from zero,
+ * since you would both waste a huge amount of memory and incur
+ * truncation errors when calculating the index.
+ */
+ QuadraticSplineTable(std::initializer_list<NumericalSplineTableInput> numericalInputList,
+ const std::pair<real, real> &range,
+ real tolerance = defaultTolerance);
+
+
+ /************************************************************
+ * Evaluation methods for single functions *
+ ************************************************************/
+
+ /*! \brief Evaluate both function and derivative, single table function
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 1
+ * \tparam funcIndex Index of function to evaluate in table, default is 0
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function and derivative
+ * \param[out] functionValue Function value
+ * \param[out] derivativeValue Function derivative
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 1, int funcIndex = 0, typename T>
+ void
+ evaluateFunctionAndDerivative(T r,
+ T * functionValue,
+ T * derivativeValue) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T t0;
+ T t1;
+ T t2;
+ T t3 gmx_unused;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(ddfzMultiTableData_.data() + 4 * funcIndex, tabIndex, &t0, &t1, &t2, &t3);
+
+ t1 = t0 + eps * t1;
+ *functionValue = fma( eps * T(halfSpacing_), t0 + t1, t2);
+ *derivativeValue = t1;
+ }
+
+ /*! \brief Evaluate function value only, single table function
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 1
+ * \tparam funcIndex Index of function to evaluate in table, default is 0
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function value
+ * \param[out] functionValue Function value
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 1, int funcIndex = 0, typename T>
+ void
+ evaluateFunction(T r,
+ T * functionValue) const
+ {
+ T der gmx_unused;
+
+ evaluateFunctionAndDerivative<numFuncInTable, funcIndex>(r, functionValue, &der);
+ }
+
+ /*! \brief Evaluate function derivative only, single table function
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 1
+ * \tparam funcIndex Index of function to evaluate in table, default is 0
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function derivative
+ * \param[out] derivativeValue Function derivative
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 1, int funcIndex = 0, typename T>
+ void
+ evaluateDerivative(T r,
+ T * derivativeValue) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T t0;
+ T t1;
+ T t2 gmx_unused;
+
+ if (numFuncInTable == 1)
+ {
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex, tabIndex, &t0, &t1); // works for scalar T too
+ }
+ else
+ {
+ // This is not ideal, but we need a version of gatherLoadUBySimdIntTranspose that
+ // only loads a single value from memory to implement it better (will be written)
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex, tabIndex, &t0, &t2); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex, tabIndex + T(1), &t1, &t2); // works for scalar T too
+ }
+
+ // (1-eps)*t0 + eps*t1
+ *derivativeValue = fma(t1-t0, eps, t0);
+ }
+
+ /************************************************************
+ * Evaluation methods for two functions *
+ ************************************************************/
+
+ /*! \brief Evaluate both function and derivative, two table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 2
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function and derivative
+ * \param[out] functionValue1 Interpolated value for first function
+ * \param[out] derivativeValue1 Interpolated derivative for first function
+ * \param[out] functionValue2 Interpolated value for second function
+ * \param[out] derivativeValue2 Interpolated derivative for second function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 2, int funcIndex0 = 0, int funcIndex1 = 1, typename T>
+ void
+ evaluateFunctionAndDerivative(T r,
+ T * functionValue1,
+ T * derivativeValue1,
+ T * functionValue2,
+ T * derivativeValue2) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T t0;
+ T t1;
+ T t2;
+ T t3 gmx_unused;
+
+ // Load Derivative, Delta, Function, and Zero values for each table point.
+ // The 4 refers to these four values - not any SIMD width.
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(ddfzMultiTableData_.data() + 4*funcIndex0, tabIndex, &t0, &t1, &t2, &t3);
+ t1 = t0 + eps * t1;
+ *functionValue1 = fma( eps * T(halfSpacing_), t0 + t1, t2);
+ *derivativeValue1 = t1;
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(ddfzMultiTableData_.data() + 4*funcIndex1, tabIndex, &t0, &t1, &t2, &t3);
+ t1 = t0 + eps * t1;
+ *functionValue2 = fma( eps * T(halfSpacing_), t0 + t1, t2);
+ *derivativeValue2 = t1;
+ }
+
+ /*! \brief Evaluate function value only, two table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 2
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function value
+ * \param[out] functionValue1 Interpolated value for first function
+ * \param[out] functionValue2 Interpolated value for second function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 2, int funcIndex0 = 0, int funcIndex1 = 1, typename T>
+ void
+ evaluateFunction(T r,
+ T * functionValue1,
+ T * functionValue2) const
+ {
+ T der1 gmx_unused;
+ T der2 gmx_unused;
+
+ evaluateFunctionAndDerivative<numFuncInTable, funcIndex0, funcIndex1>(r, functionValue1, &der1, functionValue2, &der2);
+ }
+
+ /*! \brief Evaluate function derivative only, two table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 2
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function derivative
+ * \param[out] derivativeValue1 Interpolated derivative for first function
+ * \param[out] derivativeValue2 Interpolated derivative for second function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 2, int funcIndex0 = 0, int funcIndex1 = 1, typename T>
+ void
+ evaluateDerivative(T r,
+ T * derivativeValue1,
+ T * derivativeValue2) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable, "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+
+ if (numFuncInTable == 2 && funcIndex0 == 0 && funcIndex1 == 1)
+ {
+ T t0A, t0B, t1A, t1B;
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data(), tabIndex, &t0A, &t0B); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + 2, tabIndex, &t1A, &t1B); // works for scalar T too
+ *derivativeValue1 = fma(t1A-t0A, eps, t0A);
+ *derivativeValue2 = fma(t1B-t0B, eps, t0B);
+ }
+ else
+ {
+ T t0, t1, t2;
+ // This is not ideal, but we need a version of gatherLoadUBySimdIntTranspose that
+ // only loads a single value from memory to implement it better (will be written)
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0, tabIndex, &t0, &t2); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0, tabIndex + T(1), &t1, &t2); // works for scalar T too
+ *derivativeValue1 = fma(t1-t0, eps, t0);
+
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1, tabIndex, &t0, &t2); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1, tabIndex + T(1), &t1, &t2); // works for scalar T too
+ *derivativeValue2 = fma(t1-t0, eps, t0);
+ }
+ }
+
+ /************************************************************
+ * Evaluation methods for three functions *
+ ************************************************************/
+
+
+ /*! \brief Evaluate both function and derivative, three table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 3
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam funcIndex2 Index of 3rd function to evaluate in table, default is 2
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function and derivative
+ * \param[out] functionValue1 Interpolated value for first function
+ * \param[out] derivativeValue1 Interpolated derivative for first function
+ * \param[out] functionValue2 Interpolated value for second function
+ * \param[out] derivativeValue2 Interpolated derivative for second function
+ * \param[out] functionValue3 Interpolated value for third function
+ * \param[out] derivativeValue3 Interpolated derivative for third function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 3, int funcIndex0 = 0, int funcIndex1 = 1, int funcIndex2 = 2, typename T>
+ void
+ evaluateFunctionAndDerivative(T r,
+ T * functionValue1,
+ T * derivativeValue1,
+ T * functionValue2,
+ T * derivativeValue2,
+ T * functionValue3,
+ T * derivativeValue3) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable && funcIndex2 < numFuncInTable,
+ "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+ T t0;
+ T t1;
+ T t2;
+ T t3 gmx_unused;
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(ddfzMultiTableData_.data() + 4*funcIndex0, tabIndex, &t0, &t1, &t2, &t3);
+ t1 = t0 + eps * t1;
+ *functionValue1 = fma( eps * T(halfSpacing_), t0 + t1, t2);
+ *derivativeValue1 = t1;
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(ddfzMultiTableData_.data() + 4*funcIndex1, tabIndex, &t0, &t1, &t2, &t3);
+ t1 = t0 + eps * t1;
+ *functionValue2 = fma( eps * T(halfSpacing_), t0 + t1, t2);
+ *derivativeValue2 = t1;
+
+ gatherLoadBySimdIntTranspose<4*numFuncInTable>(ddfzMultiTableData_.data() + 4*funcIndex2, tabIndex, &t0, &t1, &t2, &t3);
+ t1 = t0 + eps * t1;
+ *functionValue3 = fma( eps * T(halfSpacing_), t0 + t1, t2);
+ *derivativeValue3 = t1;
+ }
+
+ /*! \brief Evaluate function value only, three table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 3
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam funcIndex2 Index of 3rd function to evaluate in table, default is 2
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function value
+ * \param[out] functionValue1 Interpolated value for first function
+ * \param[out] functionValue2 Interpolated value for second function
+ * \param[out] functionValue3 Interpolated value for third function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 3, int funcIndex0 = 0, int funcIndex1 = 1, int funcIndex2 = 2, typename T>
+ void
+ evaluateFunction(T r,
+ T * functionValue1,
+ T * functionValue2,
+ T * functionValue3) const
+ {
+ T der1 gmx_unused;
+ T der2 gmx_unused;
+ T der3 gmx_unused;
+
+ evaluateFunctionAndDerivative<numFuncInTable, funcIndex0, funcIndex1, funcIndex2>(r, functionValue1, &der1, functionValue2, &der2, functionValue3, &der3);
+ }
+
+ /*! \brief Evaluate function derivative only, three table functions
+ *
+ * This is a templated method where the template can be either real or SimdReal.
+ *
+ * \tparam numFuncInTable Number of separate functions in table, default is 3
+ * \tparam funcIndex0 Index of 1st function to evaluate in table, default is 0
+ * \tparam funcIndex1 Index of 2nd function to evaluate in table, default is 1
+ * \tparam funcIndex2 Index of 3rd function to evaluate in table, default is 2
+ * \tparam T Type (SimdReal or real) of lookup and result
+ * \param r Points for which to evaluate function derivative
+ * \param[out] derivativeValue1 Interpolated derivative for first function
+ * \param[out] derivativeValue2 Interpolated derivative for second function
+ * \param[out] derivativeValue3 Interpolated derivative for third function
+ *
+ * For debug builds we assert that the input values fall in the range
+ * specified when constructing the table.
+ */
+ template <int numFuncInTable = 3, int funcIndex0 = 0, int funcIndex1 = 1, int funcIndex2 = 2, typename T>
+ void
+ evaluateDerivative(T r,
+ T * derivativeValue1,
+ T * derivativeValue2,
+ T * derivativeValue3) const
+ {
+ rangeCheck(r);
+ GMX_ASSERT(numFuncInTable == numFuncInTable_, "Evaluation method not matching number of functions in table");
+ GMX_ASSERT(funcIndex0 < numFuncInTable && funcIndex1 < numFuncInTable && funcIndex2 < numFuncInTable,
+ "Function index not in range of the number of tables");
+
+ T rTable = r * T(tableScale_);
+ auto tabIndex = cvttR2I(rTable); // type is either std::int32_t or SimdInt32
+ T eps = rTable - trunc(rTable);
+
+ if (numFuncInTable == 3 && funcIndex0 == 0 && funcIndex1 == 1 && funcIndex2 == 2)
+ {
+ T t0A, t0B, t0C, t1A, t1B, t1C;
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data(), tabIndex, &t0A, &t0B);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + 2, tabIndex, &t0C, &t1A);
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + 4, tabIndex, &t1B, &t1C);
+ *derivativeValue1 = fma(t1A-t0A, eps, t0A);
+ *derivativeValue2 = fma(t1B-t0B, eps, t0B);
+ *derivativeValue3 = fma(t1C-t0C, eps, t0C);
+ }
+ else
+ {
+ T t0, t1, t2;
+ // This is not ideal, but we need a version of gatherLoadUBySimdIntTranspose that
+ // only loads a single value from memory to implement it better (will be written)
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0, tabIndex, &t0, &t2); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex0, tabIndex + T(1), &t1, &t2); // works for scalar T too
+ *derivativeValue1 = fma(t1-t0, eps, t0);
+
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1, tabIndex, &t0, &t2); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex1, tabIndex + T(1), &t1, &t2); // works for scalar T too
+ *derivativeValue2 = fma(t1-t0, eps, t0);
+
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex2, tabIndex, &t0, &t2); // works for scalar T too
+ gatherLoadUBySimdIntTranspose<numFuncInTable>(derivativeMultiTableData_.data() + funcIndex2, tabIndex + T(1), &t1, &t2); // works for scalar T too
+ *derivativeValue3 = fma(t1-t0, eps, t0);
+ }
+ }
+
+ /*! \brief Return the table spacing (distance between points)
+ *
+ * You should never have to use this for normal code, but due to the
+ * way tables are constructed internally we need this in the unit tests
+ * to check relative tolerances over each interval.
+ *
+ * \return table spacing.
+ */
+ real
+ tableSpacing() const { return 1.0 / tableScale_; }
+
+ private:
+
+ std::size_t numFuncInTable_; //!< Number of separate tabluated functions
+ std::pair<real, real> range_; //!< Range for which table evaluation is allowed
+ real tableScale_; //!< Table scale (inverse of spacing between points)
+ real halfSpacing_; //!< 0.5*spacing (used for DDFZ table data)
+
+ //!< Derivative values only, with the third-derivative subtraction described in the class documentation.
+ std::vector<real> derivativeMultiTableData_;
+
+ /*! \brief Combined derivative, difference to next derivative, value, and zero.
+ *
+ * For table point i, this vector contains the four values:
+ * - derivative[i]
+ * - (derivative[i+1]-derivative[i])
+ * - value[i]
+ * - 0.0
+ *
+ * For the derivative terms we have subtracted the third-derivative term described
+ * in the main class documentation.
+ *
+ * This is typically more efficient than the individual tables, in particular
+ * when using SIMD. The result should be identical outside the class, so this
+ * is merely an internal implementation optimization. However, to allow
+ * aligned SIMD loads we need to use an aligned allocator for this container.
+ * We occasionally abbreviate this data as DDFZ.
+ */
+ std::vector<real, AlignedAllocator<real> > ddfzMultiTableData_;
+
+ // There should never be any reason to copy the table since it is read-only
+ GMX_DISALLOW_COPY_AND_ASSIGN(QuadraticSplineTable);
+};
+
+
+} // namespace gmx
+
+#endif // GMX_TABLES_QUADRATICSPLINETABLE_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Implements internal utility functions for spline tables
+ *
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+#include "gmxpre.h"
+
+#include "splineutil.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <functional>
+#include <utility>
+#include <vector>
+
+#include "gromacs/utility/alignedallocator.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace internal
+{
+
+void
+throwUnlessDerivativeIsConsistentWithFunction(const std::function<double(double)> &function,
+ const std::function<double(double)> &derivative,
+ const std::pair<real, real> &range)
+{
+ // Since the numerical derivative will evaluate extra points
+ // we shrink the interval slightly to avoid calling the function with values
+ // outside the range specified.
+ double h = std::cbrt(GMX_DOUBLE_EPS); // ideal spacing
+ std::pair<double, double> newRange(range.first + h, range.second - h);
+ const int points = 1000; // arbitrary
+ double dx = (newRange.second - newRange.first) / points;
+ bool isConsistent = true;
+ double minFail = newRange.second;
+ double maxFail = newRange.first;
+
+ for (double x = newRange.first; x <= newRange.second; x += dx)
+ {
+ double analyticalDerivative = derivative(x);
+ double numericalDerivative = (function(x+h)-function(x-h))/(2*h);
+ double thirdDerivative = (derivative(x+h)-2.0*derivative(x)+derivative(x-h))/(h*h);
+
+ // We make two types of errors in numerical calculation of the derivative:
+ // - The truncation error: eps * |f| / h
+ // - The rounding error: h * h * |f'''| / 6.0
+ double expectedErr = GMX_DOUBLE_EPS*std::abs(function(x))/h + h*h*std::abs(thirdDerivative)/6.0;
+
+ // To avoid triggering false errors because of compiler optimization or numerical issues
+ // in the function evalulation we allow an extra factor of 10 in the expected error
+ if (std::abs(analyticalDerivative-numericalDerivative) > 10.0*expectedErr)
+ {
+ isConsistent = false;
+ minFail = std::min(minFail, x);
+ maxFail = std::max(maxFail, x);
+ }
+ }
+
+ if (!isConsistent)
+ {
+ GMX_THROW(InconsistentInputError(formatString("Derivative inconsistent with analytical function in range [%d,%d]", minFail, maxFail)));
+ }
+}
+
+
+void
+throwUnlessDerivativeIsConsistentWithFunction(ConstArrayRef<double> function,
+ ConstArrayRef<double> derivative,
+ double inputSpacing,
+ const std::pair<real, real> &range)
+{
+ std::size_t firstIndex = range.first / inputSpacing;
+ std::size_t lastIndex = range.second / inputSpacing;
+ bool isConsistent = true;
+ std::size_t minFail = lastIndex;
+ std::size_t maxFail = firstIndex;
+
+ // The derivative will access one extra point before/after each point, so reduce interval
+ for (std::size_t i = firstIndex + 1; (i + 1) < lastIndex; i++)
+ {
+ double inputDerivative = derivative[i];
+ double numericalDerivative = (function[i+1] - function[i-1]) / (2.0 * inputSpacing);
+ double thirdDerivative = (derivative[i+1] - 2.0*derivative[i] + derivative[i-1])/(inputSpacing * inputSpacing);
+
+ // We make two types of errors in numerical calculation of the derivative:
+ // - The truncation error: eps * |f| / h
+ // - The rounding error: h * h * |f'''| / 6.0
+ double expectedErr = GMX_DOUBLE_EPS*std::abs(function[i])/inputSpacing + inputSpacing*inputSpacing*std::abs(thirdDerivative)/6.0;
+
+ // To avoid triggering false errors because of compiler optimization or numerical issues
+ // in the function evalulation we allow an extra factor of 10 in the expected error
+ if (std::abs(inputDerivative-numericalDerivative) > 10.0*expectedErr)
+ {
+ isConsistent = false;
+ minFail = std::min(minFail, i);
+ maxFail = std::max(maxFail, i);
+ }
+ }
+ if (!isConsistent)
+ {
+ GMX_THROW(InconsistentInputError(formatString("Derivative inconsistent with numerical vector for elements %d-%d", minFail+1, maxFail+1)));
+ }
+}
+
+
+/*! \brief Update minQuotient if the ratio of this function value and its second derivative is smaller
+ *
+ * This is a utility function used in the functions to find the smallest quotient
+ * in a range.
+ *
+ * \param[in] previousPoint Value of function at x-h.
+ * \param[in] thisPoint Value of function at x.
+ * \param[in] nextPoint Value of function at x+h.
+ * \param[in] spacing Value of h.
+ * \param[inout] minQuotient Current minimum of such quotients, updated if this quotient is smaller.
+ */
+static void
+updateMinQuotientOfFunctionAndSecondDerivative(double previousPoint,
+ double thisPoint,
+ double nextPoint,
+ double spacing,
+ double * minQuotient)
+{
+ double value = std::abs( thisPoint );
+ double secondDerivative = std::abs( (previousPoint - 2.0 * thisPoint + nextPoint) / (spacing * spacing ) );
+
+ // Make sure we do not divide by zero. This limit is arbitrary,
+ // but it doesnt matter since this point will have a very large value,
+ // and the whole routine is searching for the smallest value.
+ secondDerivative = std::max(secondDerivative, static_cast<double>(std::sqrt(GMX_REAL_MIN)));
+
+ *minQuotient = std::min(*minQuotient, value / secondDerivative);
+}
+
+
+real
+findSmallestQuotientOfFunctionAndSecondDerivative(const std::function<double(double)> &f,
+ const std::pair<real, real> &range)
+{
+ // Since the numerical second derivative will evaluate extra points
+ // we shrink the interval slightly to avoid calling the function with values
+ // outside the range specified.
+ double h = std::pow( GMX_DOUBLE_EPS, 0.25 );
+ std::pair<double, double> newRange(range.first + h, range.second - h);
+ const int points = 1000; // arbitrary
+ double dx = (newRange.second - newRange.first) / points;
+ double minQuotient = GMX_REAL_MAX;
+
+ for (double x = newRange.first; x <= newRange.second; x += dx)
+ {
+ updateMinQuotientOfFunctionAndSecondDerivative(f(x-h), f(x), f(x+h), h, &minQuotient);
+ }
+ return static_cast<real>(minQuotient);
+}
+
+
+
+
+
+
+real
+findSmallestQuotientOfFunctionAndSecondDerivative(ConstArrayRef<double> function,
+ double inputSpacing,
+ const std::pair<real, real> &range)
+{
+
+ std::size_t firstIndex = range.first / inputSpacing;
+ std::size_t lastIndex = range.second / inputSpacing;
+ double minQuotient = GMX_REAL_MAX;
+
+ for (std::size_t i = firstIndex + 1; (i + 1) < lastIndex; i++)
+ {
+ updateMinQuotientOfFunctionAndSecondDerivative(function[i-1], function[i], function[i+1], inputSpacing, &minQuotient);
+ }
+ return static_cast<real>(minQuotient);
+}
+
+
+
+/*! \brief Update minQuotient if the ratio of this function value and its third derivative is smaller
+ *
+ * This is a utility function used in the functions to find the smallest quotient
+ * in a range.
+ *
+ * \param[in] previousPreviousPoint Value of function at x-2h.
+ * \param[in] previousPoint Value of function at x-h.
+ * \param[in] thisPoint Value of function at x.
+ * \param[in] nextPoint Value of function at x+h.
+ * \param[in] nextNextPoint Value of function at x+2h.
+ * \param[in] spacing Value of h.
+ * \param[inout] minQuotient Current minimum of such quotients, updated if this quotient is smaller.
+ */
+static void
+updateMinQuotientOfFunctionAndThirdDerivative(double previousPreviousPoint,
+ double previousPoint,
+ double thisPoint,
+ double nextPoint,
+ double nextNextPoint,
+ double spacing,
+ double * minQuotient)
+{
+ double value = std::abs( thisPoint );
+ double thirdDerivative = std::abs((nextNextPoint - 2 * nextPoint + 2 * previousPoint - previousPreviousPoint) / (2 * spacing * spacing * spacing));
+
+ // Make sure we do not divide by zero. This limit is arbitrary,
+ // but it doesnt matter since this point will have a very large value,
+ // and the whole routine is searching for the smallest value.
+ thirdDerivative = std::max(thirdDerivative, static_cast<double>(std::sqrt(GMX_REAL_MIN)));
+
+ *minQuotient = std::min(*minQuotient, value / thirdDerivative);
+}
+
+
+real
+findSmallestQuotientOfFunctionAndThirdDerivative(const std::function<double(double)> &f,
+ const std::pair<real, real> &range)
+{
+ // Since the numerical second derivative will evaluate extra points
+ // we shrink the interval slightly to avoid calling the function with values
+ // outside the range specified.
+ double h = std::pow( GMX_DOUBLE_EPS, 0.2 ); // optimal spacing for 3rd derivative
+ std::pair<double, double> newRange(range.first + 2*h, range.second - 2*h);
+ const int points = 1000; // arbitrary
+ double dx = (newRange.second - newRange.first) / points;
+ double minQuotient = GMX_REAL_MAX;
+
+ for (double x = newRange.first; x <= newRange.second; x += dx)
+ {
+ updateMinQuotientOfFunctionAndThirdDerivative(f(x-2*h), f(x-h), f(x), f(x+h), f(x+2*h), h, &minQuotient);
+ }
+ return static_cast<real>(minQuotient);
+}
+
+
+real
+findSmallestQuotientOfFunctionAndThirdDerivative(ConstArrayRef<double> function,
+ double inputSpacing,
+ const std::pair<real, real> &range)
+{
+
+ std::size_t firstIndex = range.first / inputSpacing;
+ std::size_t lastIndex = range.second / inputSpacing;
+ double minQuotient = GMX_REAL_MAX;
+
+ for (std::size_t i = firstIndex + 2; (i + 2) < lastIndex; i++)
+ {
+ updateMinQuotientOfFunctionAndThirdDerivative(function[i-2], function[i-1], function[i], function[i+1], function[i+2], inputSpacing, &minQuotient);
+ }
+ return static_cast<real>(minQuotient);
+}
+
+
+
+std::vector<double>
+vectorSecondDerivative(ConstArrayRef<double> f, double spacing)
+{
+ if (f.size() < 5)
+ {
+ GMX_THROW(APIError("Too few points in vector for 5-point differentiation"));
+ }
+
+ std::vector<double> d(f.size());
+ std::size_t i;
+
+ // 5-point formula evaluated for points 0,1
+ i = 0;
+ d[i] = (11 * f[i+4] - 56 * f[i+3] + 114 * f[i+2] - 104 * f[i+1] + 35 * f[i]) / ( 12 * spacing * spacing);
+ i = 1;
+ d[i] = (-f[i+3] + 4 * f[i+2] + 6 * f[i+1] - 20 * f[i] + 11 * f[i-1]) / ( 12 * spacing * spacing);
+
+ for (std::size_t i = 2; i < d.size() - 2; i++)
+ {
+ // 5-point formula evaluated for central point (2)
+ d[i] = (-f[i+2] + 16 * f[i+1] - 30 * f[i] + 16 * f[i-1] - f[i-2]) / (12 * spacing * spacing);
+ }
+
+ // 5-point formula evaluated for points 3,4
+ i = d.size() - 2;
+ d[i] = (11 * f[i+1] - 20 * f[i] + 6 * f[i-1] + 4 * f[i-2] - f[i-3]) / ( 12 * spacing * spacing);
+ i = d.size() - 1;
+ d[i] = (35 * f[i] - 104 * f[i-1] + 114 * f[i-2] - 56 * f[i-3] + 11 * f[i-4]) / ( 12 * spacing * spacing);
+
+ return d;
+}
+
+
+
+} // namespace internal
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \internal \file
+ * \brief
+ * Declares internal utility functions for spline tables
+ *
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+#ifndef GMX_TABLES_SPLINEUTIL_H
+#define GMX_TABLES_SPLINEUTIL_H
+
+#include <functional>
+#include <utility>
+#include <vector>
+
+#include "gromacs/utility/alignedallocator.h"
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/real.h"
+
+namespace gmx
+{
+
+namespace internal
+{
+
+/*! \brief Ensure analytical derivative is the derivative of analytical function.
+ *
+ * This routine evaluates the numerical derivative of the function for
+ * a few (1000) points in the interval and checks that the relative difference
+ * between numerical and analytical derivative is within the expected error
+ * for the numerical derivative approximation we use.
+ *
+ * The main point of this routine is to make sure the user has not made a
+ * mistake or sign error when defining the functions.
+ *
+ * \param function Analytical function to differentiate
+ * \param derivative Analytical derivative to compare with
+ * \param range Range to test
+ *
+ * \throws If the provided derivative does not seem to match the function.
+ *
+ * \note The function/derivative are always double-valued to avoid accuracy loss.
+ */
+void
+throwUnlessDerivativeIsConsistentWithFunction(const std::function<double(double)> &function,
+ const std::function<double(double)> &derivative,
+ const std::pair<real, real> &range);
+
+/*! \brief Ensure vector of derivative values is the derivative of function vector.
+ *
+ * This routine differentiates a vector of numerical values and checks
+ * that the relative difference to a provided vector of numerical derivatives
+ * is smaller than the expected error from the numerical differentiation.
+ *
+ * The main point of this routine is to make sure the user has not made a
+ * mistake or sign error when defining the functions.
+ *
+ * To avoid problems if the vectors change from zero to finite values at the
+ * start/end of the interval, we only check inside the range requested.
+ *
+ * \param function Numerical function value vector to differentiate
+ * \param derivative Numerical derivative vector to compare with
+ * \param inputSpacing Distance between input points
+ * \param range Range to test
+ *
+ * \throws If the provided derivative does not seem to match the function.
+ *
+ * \note The function/derivative vectors and spacing are always double-valued
+ * to avoid accuracy loss.
+ */
+void
+throwUnlessDerivativeIsConsistentWithFunction(ConstArrayRef<double> function,
+ ConstArrayRef<double> derivative,
+ double inputSpacing,
+ const std::pair<real, real> &range);
+
+
+
+
+/*! \brief Find smallest quotient between analytical function and its 2nd derivative
+ *
+ * Used to calculate spacing for quadratic spline tables. This function divides the
+ * function value by the second derivative (or a very small number when that is zero),
+ * and returns the smallest such quotient found in the range.
+ *
+ * Our quadratic tables corresponds to linear interpolation of the derivative,
+ * which means the derivative will typically have larger error than the value
+ * when interpolating. The spacing required to reach a particular relative
+ * tolerance in the derivative depends on the quotient between the first
+ * derivative and the third derivative of the function itself.
+ *
+ * You should call this routine with the analytical derivative as the "function"
+ * parameter, and the quotient between "function and second derivative" will
+ * then correspond to the quotient bewteen the derivative and the third derivative
+ * of the actual function we want to tabulate.
+ *
+ * Since all functions that can be tabulated efficiently are reasonably smooth,
+ * we simply check 1,000 points in the interval rather than bother about
+ * implementing any complicated global optimization scheme.
+ *
+ * \param f Analytical function
+ * \param range Interval
+ *
+ * \return Smallest quotient found in range.
+ *
+ * \note The function is always double-valued to avoid accuracy loss.
+ */
+real
+findSmallestQuotientOfFunctionAndSecondDerivative(const std::function<double(double)> &f,
+ const std::pair<real, real> &range);
+
+
+
+
+
+/*! \brief Find smallest quotient between vector of values and its 2nd derivative
+ *
+ * Used to calculate spacing for quadratic spline tables. This function divides the
+ * function value by the second derivative (or a very small number when that is zero),
+ * and returns the smallest such quotient found in the range.
+ *
+ * Our quadratic tables corresponds to linear interpolation of the derivative,
+ * which means the derivative will typically have larger error than the value
+ * when interpolating. The spacing required to reach a particular relative
+ * tolerance in the derivative depends on the quotient between the first
+ * derivative and the third derivative of the function itself.
+ *
+ * You should call this routine with the analytical derivative as the "function"
+ * parameter, and the quotient between "function and second derivative" will
+ * then correspond to the quotient bewteen the derivative and the third derivative
+ * of the actual function we want to tabulate.
+ *
+ * \param function Vector with function values
+ * \param inputSpacing Spacing between function values
+ * \param range Interval to check
+ *
+ * \return Smallest quotient found in range.
+ *
+ * \note The function vector and input spacing are always double-valued to
+ * avoid accuracy loss.
+ */
+real
+findSmallestQuotientOfFunctionAndSecondDerivative(ConstArrayRef<double> function,
+ double inputSpacing,
+ const std::pair<real, real> &range);
+
+
+
+
+
+/*! \brief Find smallest quotient between analytical function and its 3rd derivative
+ *
+ * Used to calculate table spacing. This function divides the function value
+ * by the second derivative (or a very small number when that is zero), and
+ * returns the smallest such quotient found in the range.
+ *
+ * Our quadratic tables corresponds to linear interpolation of the derivative,
+ * which means the derivative will typically have larger error than the value
+ * when interpolating. The spacing required to reach a particular relative
+ * tolerance in the derivative depends on the quotient between the first
+ * derivative and the third derivative of the function itself.
+ *
+ * You should call this routine with the analytical derivative as the "function"
+ * parameter, and the quotient between "function and second derivative" will
+ * then correspond to the quotient bewteen the derivative and the third derivative
+ * of the actual function we want to tabulate.
+ *
+ * Since all functions that can be tabulated efficiently are reasonably smooth,
+ * we simply check 1,000 points in the interval rather than bother about
+ * implementing any complicated global optimization scheme.
+ *
+ * \param f Analytical function
+ * \param range Interval
+ *
+ * \return Smallest quotient found in range.
+ *
+ * \note The function is always double-valued to avoid accuracy loss.
+ */
+real
+findSmallestQuotientOfFunctionAndThirdDerivative(const std::function<double(double)> &f,
+ const std::pair<real, real> &range);
+
+
+
+
+/*! \brief Find smallest quotient between function and 2nd derivative (vectors)
+ *
+ * Used to calculate table spacing. This function divides the function value
+ * by the second derivative (or a very small number when that is zero), and
+ * returns the smallest such quotient found in the range.
+ *
+ * Our quadratic tables corresponds to linear interpolation of the derivative,
+ * which means the derivative will typically have larger error than the value
+ * when interpolating. The spacing required to reach a particular relative
+ * tolerance in the derivative depends on the quotient between the first
+ * derivative and the third derivative of the function itself.
+ *
+ * You should call this routine with the analytical derivative as the "function"
+ * parameter, and the quotient between "function and second derivative" will
+ * then correspond to the quotient bewteen the derivative and the third derivative
+ * of the actual function we want to tabulate.
+ *
+ * \param function Vector with function values
+ * \param inputSpacing Spacing between function values
+ * \param range Interval to check
+ *
+ * \return Smallest quotient found in range.
+ *
+ * \note The function vector and input spacing are always double-valued to
+ * avoid accuracy loss.
+ */
+real
+findSmallestQuotientOfFunctionAndThirdDerivative(ConstArrayRef<double> function,
+ double inputSpacing,
+ const std::pair<real, real> &range);
+
+
+/*! \brief Calculate second derivative of vector and return vector of same length
+ *
+ * 5-point approximations are used, with endpoints using non-center interpolation.
+ *
+ * \param f Vector (function) for which to calculate second derivative
+ * \param spacing Spacing of input data.
+ *
+ * \throws If the input vector has fewer than five data points.
+ *
+ * \note This function always uses double precision arguments since it is meant
+ * to be used on raw user input data for tables, where we want to avoid
+ * accuracy loss (since differentiation can be numerically fragile).
+ */
+std::vector<double>
+vectorSecondDerivative(ConstArrayRef<double> f,
+ double spacing);
+
+
+/*! \brief Copy (temporary) table data into aligned multiplexed vector
+ *
+ * This routine takes the temporary data generated for a single table
+ * and writes multiplexed output into a multiple-table-data vector.
+ * If the output vector is empty we will resize it to fit the data, and
+ * otherwise we assert the size is correct to add out input data.
+ *
+ * \tparam T Type of container for input data
+ * \tparam U Type of container for output data
+ *
+ * \param[in] inputData Input data for single table
+ * \param[inout] multiplexedOutputData Multiplexed output vector, many tables.
+ * \param[in] valuesPerTablePoint Number of real values for each table point,
+ * for instance 4 in DDFZ tables.
+ * \param[in] numTables Number of tables mixed into multiplexed output
+ * \param[in] thisTableIndex Index of this table in multiplexed output
+ *
+ * \note The output container type can be different from the input since the latter
+ * sometimes uses an aligned allocator so the data can be loaded efficiently
+ * in the GROMACS nonbonded kernels.
+ */
+template<class T, class U>
+void
+fillMultiplexedTableData(const T inputData,
+ U * multiplexedOutputData,
+ std::size_t valuesPerTablePoint,
+ std::size_t numTables,
+ std::size_t thisTableIndex)
+{
+ if (multiplexedOutputData->size() == 0)
+ {
+ multiplexedOutputData->resize( inputData.size() * numTables );
+ }
+ else
+ {
+ GMX_ASSERT(inputData.size() * numTables == multiplexedOutputData->size(),
+ "Size mismatch when multiplexing table data");
+ }
+
+ GMX_ASSERT(inputData.size() % valuesPerTablePoint == 0,
+ "Input table size must be a multiple of valuesPerTablePoint");
+
+ std::size_t points = inputData.size() / valuesPerTablePoint;
+
+ for (std::size_t i = 0; i < points; i++)
+ {
+ std::size_t inputOffset = valuesPerTablePoint * i;
+ std::size_t outputOffset = valuesPerTablePoint * ( numTables * i + thisTableIndex );
+
+ for (std::size_t j = 0; j < valuesPerTablePoint; j++)
+ {
+ (*multiplexedOutputData)[outputOffset + j] = inputData[inputOffset + j];
+ }
+ }
+}
+
+
+} // namespace internal
+
+} // namespace gmx
+
+#endif // GMX_TABLES_SPLINEUTIL_H
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+
+/*! \libinternal \file
+ * \brief
+ * Declares structures for analytical or numerical input data to construct tables
+ *
+ * \inlibraryapi
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+
+#ifndef GMX_TABLES_TABLEINPUT_H
+#define GMX_TABLES_TABLEINPUT_H
+
+#include <functional>
+#include <vector>
+
+#include "gromacs/utility/arrayref.h"
+
+namespace gmx
+{
+
+/*! \libinternal \brief Specification for analytical table function (name, function, derivative)
+ */
+struct
+AnalyticalSplineTableInput
+{
+ const std::string &desc; //!< \libinternal Brief description of function
+ std::function<double(double)> function; //!< \libinternal Analytical form of function
+ std::function<double(double)> derivative; //!< \libinternal Analytical derivative
+};
+
+/*! \libinternal \brief Specification for vector table function (name, function, derivative, spacing)
+ */
+struct
+NumericalSplineTableInput
+{
+ const std::string &desc; //!< \libinternal Brief description of function
+ ConstArrayRef<double> function; //!< \libinternal Vector with function values
+ ConstArrayRef<double> derivative; //!< \libinternal Vector with derivative values
+ double spacing; //!< \libinternal Distance between data points
+};
+
+
+} // namespace gmx
+
+
+#endif // GMX_TABLES_TABLEINPUT_H
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2016, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+gmx_add_unit_test(TableUnitTests table-test
+ splinetable.cpp
+ )
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for simple math functions.eval
+ *
+ * \author Erik Lindahl <erik.lindahl@gmail.com>
+ * \ingroup module_tables
+ */
+#include "gmxpre.h"
+
+#include <cmath>
+
+#include <algorithm>
+#include <functional>
+#include <utility>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/utilities.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/ioptionscontainer.h"
+#include "gromacs/simd/simd.h"
+#include "gromacs/tables/cubicsplinetable.h"
+#include "gromacs/tables/quadraticsplinetable.h"
+
+#include "testutils/testasserts.h"
+#include "testutils/testoptions.h"
+
+
+namespace gmx
+{
+
+namespace test
+{
+
+namespace
+{
+
+class SplineTableTestBase : public ::testing::Test
+{
+ public:
+ static int s_testPoints_; //!< Number of points to use. Public so we can set it as option
+};
+
+int
+SplineTableTestBase::s_testPoints_ = 100;
+
+/*! \cond */
+/*! \brief Command-line option to adjust the number of points used to test SIMD math functions. */
+GMX_TEST_OPTIONS(SplineTableTestOptions, options)
+{
+ options->addOption(::gmx::IntegerOption("npoints")
+ .store(&SplineTableTestBase::s_testPoints_)
+ .description("Number of points to test for spline table functions"));
+}
+/*! \endcond */
+
+
+
+
+/*! \brief Test fixture for table comparision with analytical/numerical functions */
+template <typename T>
+class SplineTableTest : public SplineTableTestBase
+{
+ public:
+ SplineTableTest() : tolerance_(T::defaultTolerance) {}
+
+ /*! \brief Set a new tolerance to be used in table function comparison
+ *
+ * \param tol New tolerance to use
+ */
+ void
+ setTolerance(real tol) { tolerance_ = tol; }
+
+ //! \cond internal
+ /*! \internal \brief
+ * Assertion predicate formatter for comparing table with function/derivative
+ */
+ template<int numFuncInTable = 1, int funcIndex = 0>
+ void
+ testSplineTableAgainstFunctions(const std::string &desc,
+ const std::function<double(double)> &refFunc,
+ const std::function<double(double)> &refDer,
+ const T &table,
+ const std::pair<real, real> &testRange);
+ //! \endcond
+
+ private:
+ real tolerance_; //!< Tolerance to use
+};
+
+template <class T>
+template<int numFuncInTable, int funcIndex>
+void
+SplineTableTest<T>::testSplineTableAgainstFunctions(const std::string &desc,
+ const std::function<double(double)> &refFunc,
+ const std::function<double(double)> &refDer,
+ const T &table,
+ const std::pair<real, real> &testRange)
+{
+ real dx = (testRange.second - testRange.first) / s_testPoints_;
+
+ FloatingPointTolerance funcTolerance(relativeToleranceAsFloatingPoint(0.0, tolerance_));
+
+ for (real x = testRange.first; x < testRange.second; x += dx)
+ {
+ real h = std::sqrt(GMX_REAL_EPS);
+ real secondDerivative = (refDer(x+h)-refDer(x))/h;
+
+ real testFuncValue;
+ real testDerValue;
+
+ table.template evaluateFunctionAndDerivative<numFuncInTable, funcIndex>(x, &testFuncValue, &testDerValue);
+
+ // Check that we get the same values from function/derivative-only methods
+ real tmpFunc, tmpDer;
+
+ table.template evaluateFunction<numFuncInTable, funcIndex>(x, &tmpFunc);
+
+ table.template evaluateDerivative<numFuncInTable, funcIndex>(x, &tmpDer);
+
+ if (testFuncValue != tmpFunc)
+ {
+ ADD_FAILURE()
+ << "Interpolation inconsistency for table " << desc << std::endl
+ << numFuncInTable << " function(s) in table, testing index " << funcIndex << std::endl
+ << "First failure at x = " << x << std::endl
+ << "Function value when evaluating function & derivative: " << testFuncValue << std::endl
+ << "Function value when evaluating only function: " << tmpFunc << std::endl;
+ return;
+ }
+ if (testDerValue != tmpDer)
+ {
+ ADD_FAILURE()
+ << "Interpolation inconsistency for table " << desc << std::endl
+ << numFuncInTable << " function(s) in table, testing index " << funcIndex << std::endl
+ << "First failure at x = " << x << std::endl
+ << "Derivative value when evaluating function & derivative: " << testDerValue << std::endl
+ << "Derivative value when evaluating only derivative: " << tmpDer << std::endl;
+ return;
+ }
+
+ // There are two sources of errors that we need to account for when checking the values,
+ // and we only fail the test if both of these tolerances are violated:
+ //
+ // 1) First, we have the normal relative error of the test vs. reference value. For this
+ // we use the normal testutils relative tolerance checking.
+ // However, there is an additional source of error: When we calculate the forces we
+ // use average higher derivatives over the interval to improve accuracy, but this
+ // also means we won't reproduce values at table points exactly. This is usually not
+ // an issue since the tolerances we have are much larger, but when the reference derivative
+ // value is exactly zero the relative error will be infinite. To account for this, we
+ // extract the spacing from the table and evaluate the reference derivative at a point
+ // this much larger too, and use the largest of the two values as the reference
+ // magnitude for the derivative when setting the relative tolerance.
+ // Note that according to the table function definitions, we should be allowed to evaluate
+ // it one table point beyond the range (this is done already for construction).
+ //
+ // 2) Second, due to the loss-of-accuracy when calculating the index through rtable
+ // there is an internal absolute tolerance that we can calculate.
+ // The source of this error is the subtraction eps=rtab-[rtab], which leaves an
+ // error proportional to eps_machine*rtab=eps_machine*x*tableScale.
+ // To lowest order, the term in the function and derivative values (respectively) that
+ // are proportional to eps will be the next-higher derivative multiplied by the spacing.
+ // This means the truncation error in the value is derivative*x*eps_machine, and in the
+ // derivative the error is 2nd_derivative*x*eps_machine.
+
+ real refFuncValue = refFunc(x);
+ real refDerValue = refDer(x);
+ real nextRefDerValue = refDer(x + table.tableSpacing());
+
+ real derMagnitude = std::max( std::abs(refDerValue), std::abs(nextRefDerValue));
+
+ // Since the reference magnitude will change over each interval we need to re-evaluate
+ // the derivative tolerance inside the loop.
+ FloatingPointTolerance derTolerance(relativeToleranceAsFloatingPoint(derMagnitude, tolerance_));
+
+ FloatingPointDifference funcDiff(refFuncValue, testFuncValue);
+ FloatingPointDifference derDiff(refDerValue, testDerValue);
+
+ real allowedAbsFuncErr = std::abs(refDerValue) * x * GMX_REAL_EPS;
+ real allowedAbsDerErr = std::abs(secondDerivative) * x * GMX_REAL_EPS;
+
+ if ((!funcTolerance.isWithin(funcDiff) && funcDiff.asAbsolute() > allowedAbsFuncErr) ||
+ (!derTolerance.isWithin(derDiff) && derDiff.asAbsolute() > allowedAbsDerErr))
+ {
+ ADD_FAILURE()
+ << "Failing comparison with function for table " << desc << std::endl
+ << numFuncInTable << " function(s) in table, testing index " << funcIndex << std::endl
+ << "Test range is ( " << testRange.first << " , " << testRange.second << " ) " << std::endl
+ << "Tolerance = " << tolerance_ << std::endl
+ << "First failure at x = " << x << std::endl
+ << "Reference function = " << refFuncValue << std::endl
+ << "Test table function = " << testFuncValue << std::endl
+ << "Reference derivative = " << refDerValue << std::endl
+ << "Test table derivative = " << testDerValue << std::endl;
+ return;
+ }
+ }
+}
+
+
+/*! \brief Function similar to coulomb electrostatics
+ *
+ * \param r argument
+ * \return r^-1
+ */
+double
+coulombFunction(double r)
+{
+ return 1.0/r;
+}
+
+/*! \brief Derivative (not force) of coulomb electrostatics
+ *
+ * \param r argument
+ * \return -r^-2
+ */
+double
+coulombDerivative(double r)
+{
+ return -1.0/(r*r);
+}
+
+/*! \brief Function similar to power-6 Lennard-Jones dispersion
+ *
+ * \param r argument
+ * \return r^-6
+ */
+double
+lj6Function(double r)
+{
+ return std::pow(r, -6.0);
+}
+
+/*! \brief Derivative (not force) of the power-6 Lennard-Jones dispersion
+ *
+ * \param r argument
+ * \return -6.0*r^-7
+ */
+double
+lj6Derivative(double r)
+{
+ return -6.0*std::pow(r, -7.0);
+}
+
+/*! \brief Function similar to power-12 Lennard-Jones repulsion
+ *
+ * \param r argument
+ * \return r^-12
+ */
+double
+lj12Function(double r)
+{
+ return std::pow(r, -12.0);
+}
+
+/*! \brief Derivative (not force) of the power-12 Lennard-Jones repulsion
+ *
+ * \param r argument
+ * \return -12.0*r^-13
+ */
+double
+lj12Derivative(double r)
+{
+ return -12.0*std::pow(r, -13.0);
+}
+
+/*! \brief The sinc function, sin(r)/r
+ *
+ * \param r argument
+ * \return sin(r)/r
+ */
+double
+sincFunction(double r)
+{
+ return std::sin(r)/r;
+}
+
+/*! \brief Derivative of the sinc function
+ *
+ * \param r argument
+ * \return derivative of sinc, (r*cos(r)-sin(r))/r^2
+ */
+double
+sincDerivative(double r)
+{
+ return (r*std::cos(r)-std::sin(r))/(r*r);
+}
+
+/*! \brief Function for the direct-space PME correction to 1/r
+ *
+ * \param r argument
+ * \return PME correction function, erf(r)/r
+ */
+double
+pmeCorrFunction(double r)
+{
+ if (r == 0)
+ {
+ return 2.0/std::sqrt(M_PI);
+ }
+ else
+ {
+ return std::erf(r)/r;
+ }
+}
+
+/*! \brief Derivative of the direct-space PME correction to 1/r
+ *
+ * \param r argument
+ * \return Derivative of the PME correction function.
+ */
+double
+pmeCorrDerivative(double r)
+{
+ if (r == 0)
+ {
+ return 0;
+ }
+ else
+ {
+ return (2.0*std::exp(-r*r)/std::sqrt(3.14159265358979323846)*r-erf(r))/(r*r);
+ }
+}
+
+/*! \brief Typed-test list. We test QuadraticSplineTable and CubicSplineTable
+ */
+typedef ::testing::Types<QuadraticSplineTable, CubicSplineTable> SplineTableTypes;
+TYPED_TEST_CASE(SplineTableTest, SplineTableTypes);
+
+
+TYPED_TEST(SplineTableTest, HandlesIncorrectInput)
+{
+ // negative range
+ EXPECT_THROW_GMX(TypeParam( {{"LJ12", lj12Function, lj12Derivative}}, {-1.0, 0.0}), gmx::InvalidInputError);
+
+ // Too small range
+ EXPECT_THROW_GMX(TypeParam( {{"LJ12", lj12Function, lj12Derivative}}, {1.0, 1.00001}), gmx::InvalidInputError);
+
+ // bad tolerance
+ EXPECT_THROW_GMX(TypeParam( {{"LJ12", lj12Function, lj12Derivative}}, {1.0, 2.0}, 1e-20), gmx::ToleranceError);
+
+ // Range is so close to 0.0 that table would require >1e6 points
+ EXPECT_THROW_GMX(TypeParam( {{"LJ12", lj12Function, lj12Derivative}}, {1e-4, 2.0}), gmx::ToleranceError);
+
+ // mismatching function/derivative
+ EXPECT_THROW_GMX(TypeParam( { {"BadLJ12", lj12Derivative, lj12Function}}, {1.0, 2.0}), gmx::InconsistentInputError);
+}
+
+
+#ifndef NDEBUG
+TYPED_TEST(SplineTableTest, CatchesOutOfRangeValues)
+{
+ TypeParam table( {{"LJ12", lj12Function, lj12Derivative}}, {0.2, 1.0});
+ real x, func, der;
+
+ x = -GMX_REAL_EPS;
+ EXPECT_THROW_GMX(table.evaluateFunctionAndDerivative(x, &func, &der), gmx::RangeError);
+
+ x = 1.0;
+ EXPECT_THROW_GMX(table.evaluateFunctionAndDerivative(x, &func, &der), gmx::RangeError);
+}
+#endif
+
+
+TYPED_TEST(SplineTableTest, Sinc)
+{
+ std::pair<real, real> range(0.1, 10);
+
+ TypeParam sincTable( {{"Sinc", sincFunction, sincDerivative}}, range);
+
+ TestFixture::testSplineTableAgainstFunctions("Sinc", sincFunction, sincDerivative, sincTable, range);
+}
+
+
+TYPED_TEST(SplineTableTest, LJ12)
+{
+ std::pair<real, real> range(0.2, 2.0);
+
+ TypeParam lj12Table( {{"LJ12", lj12Function, lj12Derivative}}, range);
+
+ TestFixture::testSplineTableAgainstFunctions("LJ12", lj12Function, lj12Derivative, lj12Table, range);
+}
+
+
+TYPED_TEST(SplineTableTest, PmeCorrection)
+{
+ std::pair<real, real> range(0.0, 4.0);
+ real tolerance = 1e-5;
+
+ TypeParam pmeCorrTable( {{"PMECorr", pmeCorrFunction, pmeCorrDerivative}}, range, tolerance);
+
+ TestFixture::setTolerance(tolerance);
+ TestFixture::testSplineTableAgainstFunctions("PMECorr", pmeCorrFunction, pmeCorrDerivative, pmeCorrTable, range);
+}
+
+
+
+TYPED_TEST(SplineTableTest, HandlesIncorrectNumericalInput)
+{
+ // Lengths do not match
+ std::vector<double> functionValues(10);
+ std::vector<double> derivativeValues(20);
+ EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.001}},
+ {1.0, 2.0}), gmx::InconsistentInputError);
+
+ // Upper range is 2.0, spacing 0.1. This requires at least 21 points. Make sure we get an error for 20.
+ functionValues.resize(20);
+ derivativeValues.resize(20);
+ EXPECT_THROW_GMX(TypeParam( {{"EmptyVectors", functionValues, derivativeValues, 0.1}},
+ {1.0, 2.0}), gmx::InconsistentInputError);
+
+ // Create some test data
+ functionValues.clear();
+ derivativeValues.clear();
+
+ std::vector<double> badDerivativeValues;
+ double spacing = 1e-3;
+
+ for (std::size_t i = 0; i < 1001; i++)
+ {
+ double x = i * spacing;
+ double func = (x >= 0.1) ? lj12Function(x) : 0.0;
+ double der = (x >= 0.1) ? lj12Derivative(x) : 0.0;
+
+ functionValues.push_back(func);
+ derivativeValues.push_back(der);
+ badDerivativeValues.push_back(-der);
+ }
+
+ // Derivatives not consistent with function
+ EXPECT_THROW_GMX(TypeParam( {{"NumericalBadLJ12", functionValues, badDerivativeValues, spacing}},
+ {0.2, 1.0}), gmx::InconsistentInputError);
+
+ // Spacing 1e-3 is not sufficient for r^-12 in range [0.1,1.0]
+ // Make sure we get a tolerance error
+ EXPECT_THROW_GMX(TypeParam( {{"NumericalLJ12", functionValues, derivativeValues, spacing}},
+ {0.2, 1.0}), gmx::ToleranceError);
+}
+
+
+TYPED_TEST(SplineTableTest, NumericalInputPmeCorr)
+{
+ std::pair<real, real> range(0.0, 4.0);
+ std::vector<double> functionValues;
+ std::vector<double> derivativeValues;
+
+ double inputSpacing = 1e-3;
+ real tolerance = 1e-5;
+
+ // We only need data up to the argument 4.0, but add 1% margin
+ for (std::size_t i = 0; i < range.second*1.01/inputSpacing; i++)
+ {
+ double x = i * inputSpacing;
+
+ functionValues.push_back(pmeCorrFunction(x));
+ derivativeValues.push_back(pmeCorrDerivative(x));
+ }
+
+ TypeParam pmeCorrTable( {{"NumericalPMECorr", functionValues, derivativeValues, inputSpacing}},
+ range, tolerance);
+
+ TestFixture::setTolerance(tolerance);
+ TestFixture::testSplineTableAgainstFunctions("NumericalPMECorr", pmeCorrFunction, pmeCorrDerivative, pmeCorrTable, range);
+}
+
+TYPED_TEST(SplineTableTest, TwoFunctions)
+{
+ std::pair<real, real> range(0.2, 2.0);
+
+ TypeParam table( {{"LJ6", lj6Function, lj6Derivative}, {"LJ12", lj12Function, lj12Derivative}}, range);
+
+ // Test entire range for each function. This will use the method that interpolates a single function
+ TestFixture::template testSplineTableAgainstFunctions<2, 0>("LJ6", lj6Function, lj6Derivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<2, 1>("LJ12", lj12Function, lj12Derivative, table, range);
+
+ // Test the methods that evaluated both functions for one value
+ real x = 0.5 * (range.first + range.second);
+ real refFunc0 = lj6Function(x);
+ real refDer0 = lj6Derivative(x);
+ real refFunc1 = lj12Function(x);
+ real refDer1 = lj12Derivative(x);
+
+ real tstFunc0, tstDer0, tstFunc1, tstDer1;
+ real tmpFunc0, tmpFunc1, tmpDer0, tmpDer1;
+
+ // test that we reproduce the reference functions
+ table.evaluateFunctionAndDerivative(x, &tstFunc0, &tstDer0, &tstFunc1, &tstDer1);
+
+ real funcErr0 = std::abs(tstFunc0-refFunc0) / std::abs(refFunc0);
+ real funcErr1 = std::abs(tstFunc1-refFunc1) / std::abs(refFunc1);
+ real derErr0 = std::abs(tstDer0-refDer0) / std::abs(refDer0);
+ real derErr1 = std::abs(tstDer1-refDer1) / std::abs(refDer1);
+
+ // Use asserts, since the following ones compare to these values.
+ ASSERT_LT(funcErr0, TypeParam::defaultTolerance);
+ ASSERT_LT(derErr0, TypeParam::defaultTolerance);
+ ASSERT_LT(funcErr1, TypeParam::defaultTolerance);
+ ASSERT_LT(derErr1, TypeParam::defaultTolerance);
+
+ // Test that function/derivative-only interpolation methods work
+ table.evaluateFunction(x, &tmpFunc0, &tmpFunc1);
+ table.evaluateDerivative(x, &tmpDer0, &tmpDer1);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstDer0, tmpDer0);
+
+ // Test that scrambled order interpolation methods work
+ table.template evaluateFunctionAndDerivative<2, 1, 0>(x, &tstFunc1, &tstDer1, &tstFunc0, &tstDer0);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstDer0, tmpDer0);
+ EXPECT_EQ(tstDer1, tmpDer1);
+
+ // Test scrambled order for function/derivative-only methods
+ table.template evaluateFunction<2, 1, 0>(x, &tmpFunc1, &tmpFunc0);
+ table.template evaluateDerivative<2, 1, 0>(x, &tmpDer1, &tmpDer0);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstDer0, tmpDer0);
+ EXPECT_EQ(tstDer1, tmpDer1);
+}
+
+TYPED_TEST(SplineTableTest, ThreeFunctions)
+{
+ std::pair<real, real> range(0.2, 2.0);
+
+ TypeParam table( {{"Coulomb", coulombFunction, coulombDerivative}, {"LJ6", lj6Function, lj6Derivative}, {"LJ12", lj12Function, lj12Derivative}}, range);
+
+ // Test entire range for each function
+ TestFixture::template testSplineTableAgainstFunctions<3, 0>("Coulomb", coulombFunction, coulombDerivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<3, 1>("LJ6", lj6Function, lj6Derivative, table, range);
+ TestFixture::template testSplineTableAgainstFunctions<3, 2>("LJ12", lj12Function, lj12Derivative, table, range);
+
+ // Test the methods that evaluated both functions for one value
+ real x = 0.5 * (range.first + range.second);
+ real refFunc0 = coulombFunction(x);
+ real refDer0 = coulombDerivative(x);
+ real refFunc1 = lj6Function(x);
+ real refDer1 = lj6Derivative(x);
+ real refFunc2 = lj12Function(x);
+ real refDer2 = lj12Derivative(x);
+
+ real tstFunc0, tstDer0, tstFunc1, tstDer1, tstFunc2, tstDer2;
+ real tmpFunc0, tmpFunc1, tmpFunc2, tmpDer0, tmpDer1, tmpDer2;
+
+ // test that we reproduce the reference functions
+ table.evaluateFunctionAndDerivative(x, &tstFunc0, &tstDer0, &tstFunc1, &tstDer1, &tstFunc2, &tstDer2);
+
+ real funcErr0 = std::abs(tstFunc0-refFunc0) / std::abs(refFunc0);
+ real derErr0 = std::abs(tstDer0-refDer0) / std::abs(refDer0);
+ real funcErr1 = std::abs(tstFunc1-refFunc1) / std::abs(refFunc1);
+ real derErr1 = std::abs(tstDer1-refDer1) / std::abs(refDer1);
+ real funcErr2 = std::abs(tstFunc2-refFunc2) / std::abs(refFunc2);
+ real derErr2 = std::abs(tstDer2-refDer2) / std::abs(refDer2);
+
+ // Use asserts, since the following ones compare to these values.
+ ASSERT_LT(funcErr0, TypeParam::defaultTolerance);
+ ASSERT_LT(derErr0, TypeParam::defaultTolerance);
+ ASSERT_LT(funcErr1, TypeParam::defaultTolerance);
+ ASSERT_LT(derErr1, TypeParam::defaultTolerance);
+ ASSERT_LT(funcErr2, TypeParam::defaultTolerance);
+ ASSERT_LT(derErr2, TypeParam::defaultTolerance);
+
+ // Test that function/derivative-only interpolation methods work
+ table.evaluateFunction(x, &tmpFunc0, &tmpFunc1, &tmpFunc2);
+ table.evaluateDerivative(x, &tmpDer0, &tmpDer1, &tmpDer2);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstFunc2, tmpFunc2);
+ EXPECT_EQ(tstDer0, tmpDer0);
+ EXPECT_EQ(tstDer1, tmpDer1);
+ EXPECT_EQ(tstDer2, tmpDer2);
+
+ // Test two functions out of three
+ table.template evaluateFunctionAndDerivative<3, 0, 1>(x, &tmpFunc0, &tmpDer0, &tmpFunc1, &tmpDer1);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstDer0, tmpDer0);
+ EXPECT_EQ(tstDer1, tmpDer1);
+
+ // two out of three, function/derivative-only
+ table.template evaluateFunction<3, 0, 1>(x, &tmpFunc0, &tmpFunc1);
+ table.template evaluateDerivative<3, 0, 1>(x, &tmpDer0, &tmpDer1);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstDer0, tmpDer0);
+ EXPECT_EQ(tstDer1, tmpDer1);
+
+ // Test that scrambled order interpolation methods work
+ table.template evaluateFunctionAndDerivative<3, 2, 1, 0>(x, &tstFunc2, &tstDer2, &tstFunc1, &tstDer1, &tstFunc0, &tstDer0);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstFunc2, tmpFunc2);
+ EXPECT_EQ(tstDer0, tmpDer0);
+ EXPECT_EQ(tstDer1, tmpDer1);
+ EXPECT_EQ(tstDer2, tmpDer2);
+
+ // Test scrambled order for function/derivative-only methods
+ table.template evaluateFunction<3, 2, 1, 0>(x, &tmpFunc2, &tmpFunc1, &tmpFunc0);
+ table.template evaluateDerivative<3, 2, 1, 0>(x, &tmpDer2, &tmpDer1, &tmpDer0);
+ EXPECT_EQ(tstFunc0, tmpFunc0);
+ EXPECT_EQ(tstFunc1, tmpFunc1);
+ EXPECT_EQ(tstFunc2, tmpFunc2);
+ EXPECT_EQ(tstDer0, tmpDer0);
+ EXPECT_EQ(tstDer1, tmpDer1);
+ EXPECT_EQ(tstDer2, tmpDer2);
+}
+
+#if GMX_SIMD_HAVE_REAL
+TYPED_TEST(SplineTableTest, Simd)
+{
+ std::pair<real, real> range(0.2, 1.0);
+ TypeParam table( {{"LJ12", lj12Function, lj12Derivative}}, range);
+
+ // We already test that the SIMD operations handle the different elements
+ // correctly in the SIMD module, so here we only test that interpolation
+ // works for a single value in the middle of the interval
+
+ real x = 0.5 * (range.first + range.second);
+ real refFunc = lj12Function(x);
+ real refDer = lj12Derivative(x);
+ SimdReal tstFunc, tstDer;
+ real funcErr, derErr;
+ GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH) alignedMem[GMX_SIMD_REAL_WIDTH];
+
+ table.evaluateFunctionAndDerivative(SimdReal(x), &tstFunc, &tstDer);
+
+ store(alignedMem, tstFunc);
+ funcErr = std::abs(alignedMem[0]-refFunc) / std::abs(refFunc);
+
+ store(alignedMem, tstDer);
+ derErr = std::abs(alignedMem[0]-refDer ) / std::abs(refDer );
+
+ EXPECT_LT(funcErr, TypeParam::defaultTolerance);
+ EXPECT_LT(derErr, TypeParam::defaultTolerance);
+}
+
+TYPED_TEST(SplineTableTest, SimdTwoFunctions)
+{
+ std::pair<real, real> range(0.2, 2.0);
+
+ TypeParam table( {{"LJ6", lj6Function, lj6Derivative}, {"LJ12", lj12Function, lj12Derivative}}, range);
+
+ // We already test that the SIMD operations handle the different elements
+ // correctly in the SIMD module, so here we only test that interpolation
+ // works for a single value in the middle of the interval
+
+ real x = 0.5 * (range.first + range.second);
+ real refFunc0 = lj6Function(x);
+ real refDer0 = lj6Derivative(x);
+ real refFunc1 = lj12Function(x);
+ real refDer1 = lj12Derivative(x);
+ SimdReal tstFunc0, tstDer0;
+ SimdReal tstFunc1, tstDer1;
+ real funcErr0, derErr0;
+ real funcErr1, derErr1;
+ GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH) alignedMem[GMX_SIMD_REAL_WIDTH];
+
+ table.evaluateFunctionAndDerivative(SimdReal(x), &tstFunc0, &tstDer0, &tstFunc1, &tstDer1);
+
+ store(alignedMem, tstFunc0);
+ funcErr0 = std::abs(alignedMem[0]-refFunc0) / std::abs(refFunc0);
+
+ store(alignedMem, tstDer0);
+ derErr0 = std::abs(alignedMem[0]-refDer0 ) / std::abs(refDer0 );
+
+ store(alignedMem, tstFunc1);
+ funcErr1 = std::abs(alignedMem[0]-refFunc1) / std::abs(refFunc1);
+
+ store(alignedMem, tstDer1);
+ derErr1 = std::abs(alignedMem[0]-refDer1 ) / std::abs(refDer1 );
+
+ EXPECT_LT(funcErr0, TypeParam::defaultTolerance);
+ EXPECT_LT(derErr0, TypeParam::defaultTolerance);
+ EXPECT_LT(funcErr1, TypeParam::defaultTolerance);
+ EXPECT_LT(derErr1, TypeParam::defaultTolerance);
+}
+#endif
+
+#if GMX_SIMD_HAVE_REAL && !defined NDEBUG
+TYPED_TEST(SplineTableTest, CatchesOutOfRangeValuesSimd)
+{
+ std::pair<real, real> range(0.2, 1.0);
+ TypeParam table( {{"LJ12", lj12Function, lj12Derivative}}, range);
+ SimdReal x, func, der;
+
+ AlignedArray<real, GMX_SIMD_REAL_WIDTH> alignedMem;
+
+ alignedMem.fill(range.first);
+ // Make position 1 incorrect if width>=2, otherwise position 0
+ // range.first-GMX_REAL_EPS is not invalid. See comment in table.
+ alignedMem[ (GMX_SIMD_REAL_WIDTH >= 2) ? 1 : 0] = -GMX_REAL_EPS;
+ x = load(alignedMem);
+
+ EXPECT_THROW_GMX(table.evaluateFunctionAndDerivative(x, &func, &der), gmx::RangeError);
+
+ // Make position 1 incorrect if width>=2, otherwise position 0
+ alignedMem[ (GMX_SIMD_REAL_WIDTH >= 2) ? 1 : 0] = range.second;
+ x = load(alignedMem);
+
+ EXPECT_THROW_GMX(table.evaluateFunctionAndDerivative(x, &func, &der), gmx::RangeError);
+}
+
+TYPED_TEST(SplineTableTest, AcceptsInRangeValuesSimd)
+{
+ std::pair<real, real> range(0.2, 1.0);
+ TypeParam table( {{"LJ12", lj12Function, lj12Derivative}}, range);
+ SimdReal x, func, der;
+
+ GMX_ALIGNED(real, GMX_SIMD_REAL_WIDTH) alignedMem[GMX_SIMD_REAL_WIDTH];
+
+ // Test all values between 0 and range.second
+ for (std::size_t i = 0; i < GMX_SIMD_REAL_WIDTH; i++)
+ {
+ alignedMem[i] = range.second*(1.0-GMX_REAL_EPS)*i/(GMX_SIMD_REAL_WIDTH-1);
+ }
+ x = load(alignedMem);
+
+ EXPECT_NO_THROW_GMX(table.evaluateFunctionAndDerivative(x, &func, &der));
+}
+
+#endif
+
+} // namespace
+
+} // namespace test
+
+} // namespace gmx
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2006 David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*
* We call gettimeofday an extra time at the start to avoid cache misses.
*/
- gettimeofday(&t1, NULL);
- gettimeofday(&t1, NULL);
+ gettimeofday(&t1, nullptr);
+ gettimeofday(&t1, nullptr);
c1 = gmx_cycles_read();
do
d = d/(1.0+static_cast<double>(i));
}
/* Read the time again */
- gettimeofday(&t2, NULL);
+ gettimeofday(&t2, nullptr);
c2 = gmx_cycles_read();
timediff = static_cast<double>(t2.tv_sec-t1.tv_sec)+(t2.tv_usec-t1.tv_usec)*1e-6;
}
* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2006 David van der Spoel, Erik Lindahl, Berk Hess, University of Groningen.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define GMX_TIMING_CYCLECOUNTER_H
/*
- * define HAVE_RDTSCP to use the serializing rdtscp instruction instead of rdtsc.
+ * Define HAVE_RDTSCP=1 to use the serializing rdtscp instruction instead of rdtsc.
* This is only supported on newer Intel/AMD hardware, but provides better accuracy.
*/
#include "config.h"
gmx_cycles_t cycle;
unsigned low, high;
-#ifdef HAVE_RDTSCP
+#if HAVE_RDTSCP
__asm__ __volatile__("rdtscp" : "=a" (low), "=d" (high) :: "ecx" );
#else
__asm__ __volatile__("rdtsc" : "=a" (low), "=d" (high));
return __rdpmccntr64();
#else
/* x86 */
-# ifdef HAVE_RDTSCP
+# if HAVE_RDTSCP
unsigned int ui;
return __rdtscp(&ui);
# else
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/*! \internal \brief GPU timings for kernels and H2d/D2H transfers. */
struct gmx_wallclock_gpu_t
{
- struct gmx_nbnxn_kernel_timing_data_t ktime[2][2]; /**< table containing the timings of the four
- versions of the nonbonded kernels: force-only,
- force+energy, force+pruning, and force+energy+pruning */
- double nb_h2d_t; /**< host to device transfer time in nb calculation */
- double nb_d2h_t; /**< device to host transfer time in nb calculation */
- int nb_c; /**< total call count of the nonbonded gpu operations */
- double pl_h2d_t; /**< pair search step host to device transfer time */
- int pl_h2d_c; /**< pair search step host to device transfer call count */
+ gmx_nbnxn_kernel_timing_data_t ktime[2][2]; /**< table containing the timings of the four
+ versions of the nonbonded kernels: force-only,
+ force+energy, force+pruning, and force+energy+pruning */
+ gmx_nbnxn_kernel_timing_data_t pruneTime; /**< table containing the timings of the 1st pass prune-only kernels */
+ gmx_nbnxn_kernel_timing_data_t dynamicPruneTime; /**< table containing the timings of dynamic prune-only kernels */
+ double nb_h2d_t; /**< host to device transfer time in nb calculation */
+ double nb_d2h_t; /**< device to host transfer time in nb calculation */
+ int nb_c; /**< total call count of the nonbonded gpu operations */
+ double pl_h2d_t; /**< pair search step host to device transfer time */
+ int pl_h2d_c; /**< pair search step host to device transfer call count */
};
#ifdef __cplusplus
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <array>
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/timing/cyclecounter.h"
#include "gromacs/timing/gpu_timing.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
"Run", "Step", "PP during PME", "Domain decomp.", "DD comm. load",
"DD comm. bounds", "Vsite constr.", "Send X to PME", "Neighbor search", "Launch GPU ops.",
"Comm. coord.", "Born radii", "Force", "Wait + Comm. F", "PME mesh",
- "PME redist. X/F", "PME spread/gather", "PME 3D-FFT", "PME 3D-FFT Comm.", "PME solve LJ", "PME solve Elec",
+ "PME redist. X/F", "PME spread", "PME gather", "PME 3D-FFT", "PME 3D-FFT Comm.", "PME solve LJ", "PME solve Elec",
"PME wait for PP", "Wait + Recv. PME F", "Wait GPU nonlocal", "Wait GPU local", "NB X/F buffer ops.",
"Vsite spread", "COM pull force",
"Write traj.", "Update", "Constraints", "Comm. energies",
"Bonded-FEP F",
"Restraints F",
"Listed buffer ops.",
+ "Nonbonded pruning",
"Nonbonded F",
"Ewald F correction",
"NB X buffer ops.",
if (!wallcycle_have_counter())
{
- return NULL;
+ return nullptr;
}
snew(wc, 1);
wc->haveInvalidCount = FALSE;
wc->wc_barrier = FALSE;
- wc->wcc_all = NULL;
+ wc->wcc_all = nullptr;
wc->wc_depth = 0;
wc->ewc_prev = -1;
wc->reset_counters = resetstep;
#if GMX_MPI
- if (PAR(cr) && getenv("GMX_CYCLE_BARRIER") != NULL)
+ if (PAR(cr) && getenv("GMX_CYCLE_BARRIER") != nullptr)
{
if (fplog)
{
#endif
snew(wc->wcc, ewcNR);
- if (getenv("GMX_CYCLE_ALL") != NULL)
+ if (getenv("GMX_CYCLE_ALL") != nullptr)
{
if (fplog)
{
return wc;
}
-void wallcycle_destroy(gmx_wallcycle_t wc)
-{
- if (wc == NULL)
+/* TODO: Should be called from finish_run() or runner()
+ void wallcycle_destroy(gmx_wallcycle_t wc)
+ {
+ if (wc == nullptr)
{
return;
}
- if (wc->wcc != NULL)
+ if (wc->wcc != nullptr)
{
sfree(wc->wcc);
}
- if (wc->wcc_all != NULL)
+ if (wc->wcc_all != nullptr)
{
sfree(wc->wcc_all);
}
- if (wc->wcsc != NULL)
+ if (wc->wcsc != nullptr)
{
sfree(wc->wcsc);
}
sfree(wc);
-}
+ }
+ */
static void wallcycle_all_start(gmx_wallcycle_t wc, int ewc, gmx_cycles_t cycle)
{
{
gmx_cycles_t cycle;
- if (wc == NULL)
+ if (wc == nullptr)
{
return;
}
cycle = gmx_cycles_read();
wc->wcc[ewc].start = cycle;
- if (wc->wcc_all != NULL)
+ if (wc->wcc_all != nullptr)
{
wc->wc_depth++;
if (ewc == ewcRUN)
void wallcycle_start_nocount(gmx_wallcycle_t wc, int ewc)
{
- if (wc == NULL)
+ if (wc == nullptr)
{
return;
}
{
gmx_cycles_t cycle, last;
- if (wc == NULL)
+ if (wc == nullptr)
{
return 0;
}
{
int i;
- if (wc == NULL)
+ if (wc == nullptr)
{
return;
}
void wallcycle_scale_by_num_threads(gmx_wallcycle_t wc, bool isPmeRank, int nthreads_pp, int nthreads_pme)
{
- if (wc == NULL)
+ if (wc == nullptr)
{
return;
}
int i;
int nsum;
- if (wc == NULL)
+ if (wc == nullptr)
{
/* Default construction of std::array of non-class T can leave
the values indeterminate, just like a C array, and icc
MPI_Allreduce(cycles, cycles_sum.data(), nsum, MPI_DOUBLE, MPI_SUM,
cr->mpi_comm_mysim);
- if (wc->wcc_all != NULL)
+ if (wc->wcc_all != nullptr)
{
double *buf_all, *cyc_all;
int nnodes, int nthreads,
int ncalls, double c_sum, double tot)
{
- char nnodes_str[6];
- char nthreads_str[6];
- char ncalls_str[11];
+ char nnodes_str[STRLEN];
+ char nthreads_str[STRLEN];
+ char ncalls_str[STRLEN];
double wallt;
double percentage = (tot > 0.) ? (100. * c_sum / tot) : 0.;
}
-void wallcycle_print(FILE *fplog, int nnodes, int npme,
+void wallcycle_print(FILE *fplog, const gmx::MDLogger &mdlog, int nnodes, int npme,
int nth_pp, int nth_pme, double realtime,
gmx_wallcycle_t wc, const WallcycleCounts &cyc_sum,
struct gmx_wallclock_gpu_t *gpu_t)
char buf[STRLEN];
const char *hline = "-----------------------------------------------------------------------------";
- if (wc == NULL)
+ if (wc == nullptr)
{
return;
}
timing data might still be sensible for some non-Jenkins
run, than is lost from diagnosing Jenkins FP exceptions on
runs about whose execution time we don't care. */
- md_print_warn(NULL, fplog, "WARNING: A total of %f CPU cycles was recorded, so mdrun cannot print a time accounting\n", tot);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "WARNING: A total of %f CPU cycles was recorded, so mdrun cannot print a time accounting",
+ tot);
return;
}
if (wc->haveInvalidCount)
{
- md_print_warn(NULL, fplog, "%s\n",
- "NOTE: Detected invalid cycle counts, probably because threads moved between CPU cores that do not have synchronized cycle counters. Will not print the cycle accounting.");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("NOTE: Detected invalid cycle counts, probably because threads moved between CPU cores that do not have synchronized cycle counters. Will not print the cycle accounting.");
return;
}
tot_for_pp += cyc_sum[i];
}
}
- if (wc->wcc_all != NULL)
+ if (wc->wcc_all != nullptr)
{
for (i = 0; i < ewcNR; i++)
{
tot_k += gpu_t->ktime[i][j].t;
}
}
- tot_gpu += tot_k;
+ tot_gpu += tot_k + gpu_t->pruneTime.t;
tot_cpu_overlap = wc->wcc[ewcFORCE].c;
if (wc->wcc[ewcPMEMESH].n > 0)
}
}
}
-
+ if (gpu_t->pruneTime.c)
+ {
+ print_gputimes(fplog, "Pruning kernel", gpu_t->pruneTime.c, gpu_t->pruneTime.t, tot_gpu);
+ }
print_gputimes(fplog, "F D2H", gpu_t->nb_c, gpu_t->nb_d2h_t, tot_gpu);
fprintf(fplog, "%s\n", hline);
print_gputimes(fplog, "Total ", gpu_t->nb_c, tot_gpu, tot_gpu);
fprintf(fplog, "%s\n", hline);
+ if (gpu_t->dynamicPruneTime.c)
+ {
+ /* We print the dynamic pruning kernel timings after a separator
+ * and avoid adding it to tot_gpu as this is not in the force
+ * overlap. We print the fraction as relative to the rest.
+ */
+ print_gputimes(fplog, "*Dynamic pruning", gpu_t->dynamicPruneTime.c, gpu_t->dynamicPruneTime.t, tot_gpu);
+ fprintf(fplog, "%s\n", hline);
+ }
gpu_cpu_ratio = tot_gpu/tot_cpu_overlap;
if (gpu_t->nb_c > 0 && wc->wcc[ewcFORCE].n > 0)
/* The user could have used -notunepme,
* but we currently can't check that here.
*/
- md_print_warn(NULL, fplog,
- "\nNOTE: The GPU has >25%% less load than the CPU. This imbalance causes\n"
- " performance loss. Maybe the domain decomposition limits the PME tuning.\n"
- " In that case, try setting the DD grid manually (-dd) or lowering -dds.");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: The GPU has >25% less load than the CPU. This imbalance causes\n"
+ " performance loss. Maybe the domain decomposition limits the PME tuning.\n"
+ " In that case, try setting the DD grid manually (-dd) or lowering -dds.");
}
else
{
/* We should not end up here, unless the box is
* too small for increasing the cut-off for PME tuning.
*/
- md_print_warn(NULL, fplog,
- "\nNOTE: The GPU has >25%% less load than the CPU. This imbalance causes\n"
- " performance loss.");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: The GPU has >25% less load than the CPU. This imbalance causes\n"
+ " performance loss.");
}
}
if (gpu_cpu_ratio > 1.2)
{
- md_print_warn(NULL, fplog,
- "\nNOTE: The GPU has >20%% more load than the CPU. This imbalance causes\n"
- " performance loss, consider using a shorter cut-off and a finer PME grid.");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: The GPU has >20% more load than the CPU. This imbalance causes\n"
+ " performance loss, consider using a shorter cut-off and a finer PME grid.");
}
}
}
if (wc->wc_barrier)
{
- md_print_warn(NULL, fplog,
- "MPI_Barrier was called before each cycle start/stop\n"
- "call, so timings are not those of real runs.\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "MPI_Barrier was called before each cycle start/stop\n"
+ "call, so timings are not those of real runs.");
}
if (wc->wcc[ewcNB_XF_BUF_OPS].n > 0 &&
/* Only the sim master calls this function, so always print to stderr */
if (wc->wcc[ewcDOMDEC].n == 0)
{
- md_print_warn(NULL, fplog,
- "NOTE: %d %% of the run time was spent in pair search,\n"
- " you might want to increase nstlist (this has no effect on accuracy)\n",
- (int)(100*cyc_sum[ewcNS]/tot+0.5));
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: %d %% of the run time was spent in pair search,\n"
+ " you might want to increase nstlist (this has no effect on accuracy)\n",
+ (int)(100*cyc_sum[ewcNS]/tot+0.5));
}
else
{
- md_print_warn(NULL, fplog,
- "NOTE: %d %% of the run time was spent in domain decomposition,\n"
- " %d %% of the run time was spent in pair search,\n"
- " you might want to increase nstlist (this has no effect on accuracy)\n",
- (int)(100*cyc_sum[ewcDOMDEC]/tot+0.5),
- (int)(100*cyc_sum[ewcNS]/tot+0.5));
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: %d %% of the run time was spent in domain decomposition,\n"
+ " %d %% of the run time was spent in pair search,\n"
+ " you might want to increase nstlist (this has no effect on accuracy)\n",
+ (int)(100*cyc_sum[ewcDOMDEC]/tot+0.5),
+ (int)(100*cyc_sum[ewcNS]/tot+0.5));
}
}
if (cyc_sum[ewcMoveE] > tot*0.05)
{
- /* Only the sim master calls this function, so always print to stderr */
- md_print_warn(NULL, fplog,
- "NOTE: %d %% of the run time was spent communicating energies,\n"
- " you might want to use the -gcom option of mdrun\n",
- (int)(100*cyc_sum[ewcMoveE]/tot+0.5));
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "NOTE: %d %% of the run time was spent communicating energies,\n"
+ " you might want to use the -gcom option of mdrun\n",
+ (int)(100*cyc_sum[ewcMoveE]/tot+0.5));
}
}
extern gmx_int64_t wcycle_get_reset_counters(gmx_wallcycle_t wc)
{
- if (wc == NULL)
+ if (wc == nullptr)
{
return -1;
}
extern void wcycle_set_reset_counters(gmx_wallcycle_t wc, gmx_int64_t reset_counters)
{
- if (wc == NULL)
+ if (wc == nullptr)
{
return;
}
void wallcycle_sub_start(gmx_wallcycle_t wc, int ewcs)
{
- if (useCycleSubcounters && wc != NULL)
+ if (useCycleSubcounters && wc != nullptr)
{
wc->wcsc[ewcs].start = gmx_cycles_read();
}
void wallcycle_sub_start_nocount(gmx_wallcycle_t wc, int ewcs)
{
- if (useCycleSubcounters && wc != NULL)
+ if (useCycleSubcounters && wc != nullptr)
{
wallcycle_sub_start(wc, ewcs);
wc->wcsc[ewcs].n--;
void wallcycle_sub_stop(gmx_wallcycle_t wc, int ewcs)
{
- if (useCycleSubcounters && wc != NULL)
+ if (useCycleSubcounters && wc != nullptr)
{
wc->wcsc[ewcs].c += gmx_cycles_read() - wc->wcsc[ewcs].start;
wc->wcsc[ewcs].n++;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
ewcRUN, ewcSTEP, ewcPPDURINGPME, ewcDOMDEC, ewcDDCOMMLOAD,
ewcDDCOMMBOUND, ewcVSITECONSTR, ewcPP_PMESENDX, ewcNS, ewcLAUNCH_GPU_NB,
ewcMOVEX, ewcGB, ewcFORCE, ewcMOVEF, ewcPMEMESH,
- ewcPME_REDISTXF, ewcPME_SPREADGATHER, ewcPME_FFT, ewcPME_FFTCOMM, ewcLJPME, ewcPME_SOLVE,
+ ewcPME_REDISTXF, ewcPME_SPREAD, ewcPME_GATHER, ewcPME_FFT, ewcPME_FFTCOMM, ewcLJPME, ewcPME_SOLVE,
ewcPMEWAITCOMM, ewcPP_PMEWAITRECVF, ewcWAIT_GPU_NB_NL, ewcWAIT_GPU_NB_L, ewcNB_XF_BUF_OPS,
ewcVSITESPREAD, ewcPULLPOT,
ewcTRAJ, ewcUPDATE, ewcCONSTR, ewcMoveE, ewcROT, ewcROTadd, ewcSWAP, ewcIMD,
ewcsLISTED_FEP,
ewcsRESTRAINTS,
ewcsLISTED_BUF_OPS,
+ ewcsNONBONDED_PRUNING,
ewcsNONBONDED,
ewcsEWALD_CORRECTION,
ewcsNB_X_BUF_OPS,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
+struct t_commrec;
+
+namespace gmx
+{
+class MDLogger;
+}
+
typedef struct gmx_wallcycle *gmx_wallcycle_t;
typedef struct gmx_wallclock_gpu_t gmx_wallclock_gpu_t;
-struct t_commrec;
typedef std::array<double, ewcNR+ewcsNR> WallcycleCounts;
/* Convenience typedef */
/* Return a vector of the sum of cycle counts over the nodes in
cr->mpi_comm_mysim. */
-void wallcycle_print(FILE *fplog, int nnodes, int npme,
+void wallcycle_print(FILE *fplog, const gmx::MDLogger &mdlog, int nnodes, int npme,
int nth_pp, int nth_pme, double realtime,
gmx_wallcycle_t wc, const WallcycleCounts &cyc_sum,
struct gmx_wallclock_gpu_t *gpu_t);
headers claim sufficient support for POSIX (ie not Mac and
Windows), and it isn't BG/Q (whose compute node kernel only
supports gettimeofday, and bgclang doesn't provide a fully
- functional implementation clock_gettime, unlike xlc). */
+ functional implementation clock_gettime). */
#if HAVE_CLOCK_GETTIME && defined(_POSIX_TIMERS) && _POSIX_TIMERS > 0 && !(defined __bgq__ && defined __clang__)
struct timespec t;
double seconds;
headers claim sufficient support for POSIX (ie not Mac and
Windows), and it isn't BG/Q (whose compute node kernel only
supports gettimeofday, and bgclang doesn't provide a fully
- functional implementation clock_gettime, unlike xlc). */
+ functional implementation clock_gettime). */
#if HAVE_CLOCK_GETTIME && defined(_POSIX_THREAD_CPUTIME) && _POSIX_THREAD_CPUTIME > 0 && !(defined __bgq__ && defined __clang__)
struct timespec t;
double seconds;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "check.h"
+
#include <cmath>
#include <cstdio>
#include <cstring>
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdrunutility/mdmodules.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/tools/compare.h"
#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/block.h"
#include "gromacs/topology/ifunc.h"
float bBox;
} t_fr_time;
+static void comp_tpx(const char *fn1, const char *fn2,
+ gmx_bool bRMSD, real ftol, real abstol)
+{
+ const char *ff[2];
+ t_inputrec *ir[2];
+ t_state state[2];
+ gmx_mtop_t mtop[2];
+ t_topology top[2];
+ int i;
+
+ ff[0] = fn1;
+ ff[1] = fn2;
+ for (i = 0; i < (fn2 ? 2 : 1); i++)
+ {
+ ir[i] = new t_inputrec();
+ read_tpx_state(ff[i], ir[i], &state[i], &(mtop[i]));
+ gmx::MDModules().adjustInputrecBasedOnModules(ir[i]);
+ }
+ if (fn2)
+ {
+ cmp_inputrec(stdout, ir[0], ir[1], ftol, abstol);
+ /* Convert gmx_mtop_t to t_topology.
+ * We should implement direct mtop comparison,
+ * but it might be useful to keep t_topology comparison as an option.
+ */
+ top[0] = gmx_mtop_t_to_t_topology(&mtop[0], false);
+ top[1] = gmx_mtop_t_to_t_topology(&mtop[1], false);
+ cmp_top(stdout, &top[0], &top[1], ftol, abstol);
+ cmp_groups(stdout, &mtop[0].groups, &mtop[1].groups,
+ mtop[0].natoms, mtop[1].natoms);
+ comp_state(&state[0], &state[1], bRMSD, ftol, abstol);
+ }
+ else
+ {
+ if (ir[0]->efep == efepNO)
+ {
+ fprintf(stdout, "inputrec->efep = %s\n", efep_names[ir[0]->efep]);
+ }
+ else
+ {
+ if (ir[0]->bPull)
+ {
+ comp_pull_AB(stdout, ir[0]->pull, ftol, abstol);
+ }
+ /* Convert gmx_mtop_t to t_topology.
+ * We should implement direct mtop comparison,
+ * but it might be useful to keep t_topology comparison as an option.
+ */
+ top[0] = gmx_mtop_t_to_t_topology(&mtop[0], true);
+ cmp_top(stdout, &top[0], nullptr, ftol, abstol);
+ }
+ }
+}
+
+static void comp_trx(const gmx_output_env_t *oenv, const char *fn1, const char *fn2,
+ gmx_bool bRMSD, real ftol, real abstol)
+{
+ int i;
+ const char *fn[2];
+ t_trxframe fr[2];
+ t_trxstatus *status[2];
+ gmx_bool b[2];
+
+ fn[0] = fn1;
+ fn[1] = fn2;
+ fprintf(stderr, "Comparing trajectory files %s and %s\n", fn1, fn2);
+ for (i = 0; i < 2; i++)
+ {
+ b[i] = read_first_frame(oenv, &status[i], fn[i], &fr[i], TRX_READ_X|TRX_READ_V|TRX_READ_F);
+ }
+
+ if (b[0] && b[1])
+ {
+ do
+ {
+ comp_frame(stdout, &(fr[0]), &(fr[1]), bRMSD, ftol, abstol);
+
+ for (i = 0; i < 2; i++)
+ {
+ b[i] = read_next_frame(oenv, status[i], &fr[i]);
+ }
+ }
+ while (b[0] && b[1]);
+
+ for (i = 0; i < 2; i++)
+ {
+ if (b[i] && !b[1-i])
+ {
+ fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn[1-i], fn[i]);
+ }
+ close_trx(status[i]);
+ }
+ }
+ if (!b[0] && !b[1])
+ {
+ fprintf(stdout, "\nBoth files read correctly\n");
+ }
+}
+
static void tpx2system(FILE *fp, const gmx_mtop_t *mtop)
{
int nmol, nvsite = 0;
gmx_mtop_atomloop_block_t aloop;
- t_atom *atom;
+ const t_atom *atom;
fprintf(fp, "\\subsection{Simulation system}\n");
aloop = gmx_mtop_atomloop_block_init(mtop);
static void tpx2methods(const char *tpx, const char *tex)
{
- FILE *fp;
- t_inputrec ir;
- t_state state;
- gmx_mtop_t mtop;
+ FILE *fp;
+ t_state state;
+ gmx_mtop_t mtop;
+ t_inputrec ir;
read_tpx_state(tpx, &ir, &state, &mtop);
fp = gmx_fio_fopen(tex, "w");
fprintf(fp, "\\section{Methods}\n");
}
}
-void chk_trj(const gmx_output_env_t *oenv, const char *fn, const char *tpr, real tol)
+static void chk_trj(const gmx_output_env_t *oenv, const char *fn, const char *tpr, real tol)
{
t_trxframe fr;
t_count count;
gmx_bool bShowTimestep = TRUE, newline = FALSE;
t_trxstatus *status;
gmx_mtop_t mtop;
- gmx_localtop_t *top = NULL;
+ gmx_localtop_t *top = nullptr;
t_state state;
t_inputrec ir;
fprintf(stderr, "\n");
- close_trj(status);
+ close_trx(status);
fprintf(stderr, "\nItem #frames");
if (bShowTimestep)
PRINTITEM ( "Box", bBox );
}
-void chk_tps(const char *fn, real vdw_fac, real bon_lo, real bon_hi)
+static void chk_tps(const char *fn, real vdw_fac, real bon_lo, real bon_hi)
{
int natom, i, j, k;
t_topology top;
}
}
-void chk_ndx(const char *fn)
+static void chk_ndx(const char *fn)
{
t_blocka *grps;
char **grpname;
done_blocka(grps);
}
-void chk_enx(const char *fn)
+static void chk_enx(const char *fn)
{
int nre, fnr;
ener_file_t in;
- gmx_enxnm_t *enm = NULL;
+ gmx_enxnm_t *enm = nullptr;
t_enxframe *fr;
gmx_bool bShowTStep;
gmx_bool timeSet;
"consisting of a rough outline for a methods section for a paper."
};
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffOPTRD },
- { efTRX, "-f2", NULL, ffOPTRD },
+ { efTRX, "-f", nullptr, ffOPTRD },
+ { efTRX, "-f2", nullptr, ffOPTRD },
{ efTPR, "-s1", "top1", ffOPTRD },
{ efTPR, "-s2", "top2", ffOPTRD },
- { efTPS, "-c", NULL, ffOPTRD },
- { efEDR, "-e", NULL, ffOPTRD },
+ { efTPS, "-c", nullptr, ffOPTRD },
+ { efEDR, "-e", nullptr, ffOPTRD },
{ efEDR, "-e2", "ener2", ffOPTRD },
- { efNDX, "-n", NULL, ffOPTRD },
- { efTEX, "-m", NULL, ffOPTWR }
+ { efNDX, "-n", nullptr, ffOPTRD },
+ { efTEX, "-m", nullptr, ffOPTWR }
};
#define NFILE asize(fnm)
- const char *fn1 = NULL, *fn2 = NULL, *tex = NULL;
+ const char *fn1 = nullptr, *fn2 = nullptr, *tex = nullptr;
gmx_output_env_t *oenv;
static real vdw_fac = 0.8;
static real ftol = 0.001;
static real abstol = 0.001;
static gmx_bool bCompAB = FALSE;
- static char *lastener = NULL;
+ static char *lastener = nullptr;
static t_pargs pa[] = {
{ "-vdwfac", FALSE, etREAL, {&vdw_fac},
"Fraction of sum of VdW radii used as warning cutoff" },
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
{
if (bCompAB)
{
- if (fn1 == NULL)
+ if (fn1 == nullptr)
{
gmx_fatal(FARGS, "With -ab you need to set the -s1 option");
}
- fn2 = NULL;
+ fn2 = nullptr;
}
comp_tpx(fn1, fn2, bRMSD, ftol, abstol);
}
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/* This file is completely threadsafe - keep it that way! */
-
-#include "gmxpre.h"
-
-#include <cmath>
-#include <cstdio>
-#include <cstring>
-
-#include <algorithm>
-
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/mdtypes/inputrec.h"
-#include "gromacs/mdtypes/md_enums.h"
-#include "gromacs/mdtypes/pull-params.h"
-#include "gromacs/topology/ifunc.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/topology/topology.h"
-#include "gromacs/trajectory/trajectoryframe.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/stringutil.h"
-
-static void cmp_int(FILE *fp, const char *s, int index, int i1, int i2)
-{
- if (i1 != i2)
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%d] (%d - %d)\n", s, index, i1, i2);
- }
- else
- {
- fprintf(fp, "%s (%d - %d)\n", s, i1, i2);
- }
- }
-}
-
-static void cmp_int64(FILE *fp, const char *s, gmx_int64_t i1, gmx_int64_t i2)
-{
- if (i1 != i2)
- {
- fprintf(fp, "%s (", s);
- fprintf(fp, "%" GMX_PRId64, i1);
- fprintf(fp, " - ");
- fprintf(fp, "%" GMX_PRId64, i2);
- fprintf(fp, ")\n");
- }
-}
-
-static void cmp_us(FILE *fp, const char *s, int index, unsigned short i1, unsigned short i2)
-{
- if (i1 != i2)
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%d] (%hu - %hu)\n", s, index, i1, i2);
- }
- else
- {
- fprintf(fp, "%s (%hu - %hu)\n", s, i1, i2);
- }
- }
-}
-
-static void cmp_uc(FILE *fp, const char *s, int index, unsigned char i1, unsigned char i2)
-{
- if (i1 != i2)
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%d] (%d - %d)\n", s, index, i1, i2);
- }
- else
- {
- fprintf(fp, "%s (%d - %d)\n", s, i1, i2);
- }
- }
-}
-
-static gmx_bool cmp_bool(FILE *fp, const char *s, int index, gmx_bool b1, gmx_bool b2)
-{
- if (b1)
- {
- b1 = 1;
- }
- else
- {
- b1 = 0;
- }
- if (b2)
- {
- b2 = 1;
- }
- else
- {
- b2 = 0;
- }
- if (b1 != b2)
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%d] (%s - %s)\n", s, index,
- gmx::boolToString(b1), gmx::boolToString(b2));
- }
- else
- {
- fprintf(fp, "%s (%s - %s)\n", s,
- gmx::boolToString(b1), gmx::boolToString(b2));
- }
- }
- return b1 && b2;
-}
-
-static void cmp_str(FILE *fp, const char *s, int index,
- const char *s1, const char *s2)
-{
- if (std::strcmp(s1, s2) != 0)
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%d] (%s - %s)\n", s, index, s1, s2);
- }
- else
- {
- fprintf(fp, "%s (%s - %s)\n", s, s1, s2);
- }
- }
-}
-
-static gmx_bool equal_real(real i1, real i2, real ftol, real abstol)
-{
- return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol );
-}
-
-static gmx_bool equal_float(float i1, float i2, float ftol, float abstol)
-{
- return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol );
-}
-
-static gmx_bool equal_double(double i1, double i2, real ftol, real abstol)
-{
- return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol );
-}
-
-static void
-cmp_real(FILE *fp, const char *s, int index, real i1, real i2, real ftol, real abstol)
-{
- if (!equal_real(i1, i2, ftol, abstol))
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%2d] (%e - %e)\n", s, index, i1, i2);
- }
- else
- {
- fprintf(fp, "%s (%e - %e)\n", s, i1, i2);
- }
- }
-}
-
-static void
-cmp_float(FILE *fp, const char *s, int index, float i1, float i2, float ftol, float abstol)
-{
- if (!equal_float(i1, i2, ftol, abstol))
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%2d] (%e - %e)\n", s, index, i1, i2);
- }
- else
- {
- fprintf(fp, "%s (%e - %e)\n", s, i1, i2);
- }
- }
-}
-
-
-
-static void
-cmp_double(FILE *fp, const char *s, int index, double i1, double i2, double ftol, double abstol)
-{
- if (!equal_double(i1, i2, ftol, abstol))
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%2d] (%16.9e - %16.9e)\n", s, index, i1, i2);
- }
- else
- {
- fprintf(fp, "%s (%16.9e - %16.9e)\n", s, i1, i2);
- }
- }
-}
-
-static void cmp_rvec(FILE *fp, const char *s, int index, const rvec i1, const rvec i2, real ftol, real abstol)
-{
- if (!equal_real(i1[XX], i2[XX], ftol, abstol) ||
- !equal_real(i1[YY], i2[YY], ftol, abstol) ||
- !equal_real(i1[ZZ], i2[ZZ], ftol, abstol))
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%5d] (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
- s, index, i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
- }
- else
- {
- fprintf(fp, "%s (%12.5e %12.5e %12.5e) - (%12.5e %12.5e %12.5e)\n",
- s, i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
- }
- }
-}
-
-static void cmp_ivec(FILE *fp, const char *s, int index, const ivec i1, const ivec i2)
-{
- if ((i1[XX] != i2[XX]) || (i1[YY] != i2[YY]) || (i1[ZZ] != i2[ZZ]))
- {
- if (index != -1)
- {
- fprintf(fp, "%s[%5d] (%8d,%8d,%8d - %8d,%8d,%8d)\n", s, index,
- i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
- }
- else
- {
- fprintf(fp, "%s (%8d,%8d,%8d - %8d,%8d,%8d)\n", s,
- i1[XX], i1[YY], i1[ZZ], i2[XX], i2[YY], i2[ZZ]);
- }
- }
-}
-
-static void cmp_ilist(FILE *fp, int ftype, const t_ilist *il1, const t_ilist *il2)
-{
- int i;
- char buf[256];
-
- fprintf(fp, "comparing ilist %s\n", interaction_function[ftype].name);
- sprintf(buf, "%s->nr", interaction_function[ftype].name);
- cmp_int(fp, buf, -1, il1->nr, il2->nr);
- sprintf(buf, "%s->iatoms", interaction_function[ftype].name);
- if (((il1->nr > 0) && (!il1->iatoms)) ||
- ((il2->nr > 0) && (!il2->iatoms)) ||
- ((il1->nr != il2->nr)))
- {
- fprintf(fp, "Comparing radically different topologies - %s is different\n",
- buf);
- }
- else
- {
- for (i = 0; (i < il1->nr); i++)
- {
- cmp_int(fp, buf, i, il1->iatoms[i], il2->iatoms[i]);
- }
- }
-}
-
-void cmp_iparm(FILE *fp, const char *s, t_functype ft,
- const t_iparams &ip1, const t_iparams &ip2, real ftol, real abstol)
-{
- int i;
- gmx_bool bDiff;
-
- bDiff = FALSE;
- for (i = 0; i < MAXFORCEPARAM && !bDiff; i++)
- {
- bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], ftol, abstol);
- }
- if (bDiff)
- {
- fprintf(fp, "%s1: ", s);
- pr_iparams(fp, ft, &ip1);
- fprintf(fp, "%s2: ", s);
- pr_iparams(fp, ft, &ip2);
- }
-}
-
-void cmp_iparm_AB(FILE *fp, const char *s, t_functype ft, const t_iparams &ip1, real ftol, real abstol)
-{
- int nrfpA, nrfpB, p0, i;
- gmx_bool bDiff;
-
- /* Normally the first parameter is perturbable */
- p0 = 0;
- nrfpA = interaction_function[ft].nrfpA;
- nrfpB = interaction_function[ft].nrfpB;
- if (ft == F_PDIHS)
- {
- nrfpB = 2;
- }
- else if (interaction_function[ft].flags & IF_TABULATED)
- {
- /* For tabulated interactions only the second parameter is perturbable */
- p0 = 1;
- nrfpB = 1;
- }
- bDiff = FALSE;
- for (i = 0; i < nrfpB && !bDiff; i++)
- {
- bDiff = !equal_real(ip1.generic.buf[p0+i], ip1.generic.buf[nrfpA+i], ftol, abstol);
- }
- if (bDiff)
- {
- fprintf(fp, "%s: ", s);
- pr_iparams(fp, ft, &ip1);
- }
-}
-
-static void cmp_cmap(FILE *fp, const gmx_cmap_t *cmap1, const gmx_cmap_t *cmap2, real ftol, real abstol)
-{
- cmp_int(fp, "cmap ngrid", -1, cmap1->ngrid, cmap2->ngrid);
- cmp_int(fp, "cmap grid_spacing", -1, cmap1->grid_spacing, cmap2->grid_spacing);
- if (cmap1->ngrid == cmap2->ngrid &&
- cmap1->grid_spacing == cmap2->grid_spacing)
- {
- int g;
-
- for (g = 0; g < cmap1->ngrid; g++)
- {
- int i;
-
- fprintf(fp, "comparing cmap %d\n", g);
-
- for (i = 0; i < 4*cmap1->grid_spacing*cmap1->grid_spacing; i++)
- {
- cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], ftol, abstol);
- }
- }
- }
-}
-
-static void cmp_idef(FILE *fp, const t_idef *id1, const t_idef *id2, real ftol, real abstol)
-{
- int i;
- char buf1[64], buf2[64];
-
- fprintf(fp, "comparing idef\n");
- if (id2)
- {
- cmp_int(fp, "idef->ntypes", -1, id1->ntypes, id2->ntypes);
- cmp_int(fp, "idef->atnr", -1, id1->atnr, id2->atnr);
- for (i = 0; (i < std::min(id1->ntypes, id2->ntypes)); i++)
- {
- sprintf(buf1, "idef->functype[%d]", i);
- sprintf(buf2, "idef->iparam[%d]", i);
- cmp_int(fp, buf1, i, (int)id1->functype[i], (int)id2->functype[i]);
- cmp_iparm(fp, buf2, id1->functype[i],
- id1->iparams[i], id2->iparams[i], ftol, abstol);
- }
- cmp_real(fp, "fudgeQQ", -1, id1->fudgeQQ, id2->fudgeQQ, ftol, abstol);
- cmp_cmap(fp, &id1->cmap_grid, &id2->cmap_grid, ftol, abstol);
- for (i = 0; (i < F_NRE); i++)
- {
- cmp_ilist(fp, i, &(id1->il[i]), &(id2->il[i]));
- }
- }
- else
- {
- for (i = 0; (i < id1->ntypes); i++)
- {
- cmp_iparm_AB(fp, "idef->iparam", id1->functype[i], id1->iparams[i], ftol, abstol);
- }
- }
-}
-
-static void cmp_block(FILE *fp, const t_block *b1, const t_block *b2, const char *s)
-{
- char buf[32];
-
- fprintf(fp, "comparing block %s\n", s);
- sprintf(buf, "%s.nr", s);
- cmp_int(fp, buf, -1, b1->nr, b2->nr);
-}
-
-static void cmp_blocka(FILE *fp, const t_blocka *b1, const t_blocka *b2, const char *s)
-{
- char buf[32];
-
- fprintf(fp, "comparing blocka %s\n", s);
- sprintf(buf, "%s.nr", s);
- cmp_int(fp, buf, -1, b1->nr, b2->nr);
- sprintf(buf, "%s.nra", s);
- cmp_int(fp, buf, -1, b1->nra, b2->nra);
-}
-
-static void cmp_atom(FILE *fp, int index, const t_atom *a1, const t_atom *a2, real ftol, real abstol)
-{
- if (a2)
- {
- cmp_us(fp, "atom.type", index, a1->type, a2->type);
- cmp_us(fp, "atom.ptype", index, a1->ptype, a2->ptype);
- cmp_int(fp, "atom.resind", index, a1->resind, a2->resind);
- cmp_int(fp, "atom.atomnumber", index, a1->atomnumber, a2->atomnumber);
- cmp_real(fp, "atom.m", index, a1->m, a2->m, ftol, abstol);
- cmp_real(fp, "atom.q", index, a1->q, a2->q, ftol, abstol);
- cmp_us(fp, "atom.typeB", index, a1->typeB, a2->typeB);
- cmp_real(fp, "atom.mB", index, a1->mB, a2->mB, ftol, abstol);
- cmp_real(fp, "atom.qB", index, a1->qB, a2->qB, ftol, abstol);
- }
- else
- {
- cmp_us(fp, "atom.type", index, a1->type, a1->typeB);
- cmp_real(fp, "atom.m", index, a1->m, a1->mB, ftol, abstol);
- cmp_real(fp, "atom.q", index, a1->q, a1->qB, ftol, abstol);
- }
-}
-
-static void cmp_atoms(FILE *fp, const t_atoms *a1, const t_atoms *a2, real ftol, real abstol)
-{
- int i;
-
- fprintf(fp, "comparing atoms\n");
-
- if (a2)
- {
- cmp_int(fp, "atoms->nr", -1, a1->nr, a2->nr);
- for (i = 0; (i < a1->nr); i++)
- {
- cmp_atom(fp, i, &(a1->atom[i]), &(a2->atom[i]), ftol, abstol);
- }
- }
- else
- {
- for (i = 0; (i < a1->nr); i++)
- {
- cmp_atom(fp, i, &(a1->atom[i]), NULL, ftol, abstol);
- }
- }
-}
-
-static void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol)
-{
- fprintf(fp, "comparing top\n");
- if (t2)
- {
- cmp_idef(fp, &(t1->idef), &(t2->idef), ftol, abstol);
- cmp_atoms(fp, &(t1->atoms), &(t2->atoms), ftol, abstol);
- cmp_block(fp, &t1->cgs, &t2->cgs, "cgs");
- cmp_block(fp, &t1->mols, &t2->mols, "mols");
- cmp_bool(fp, "bIntermolecularInteractions", -1, t1->bIntermolecularInteractions, t2->bIntermolecularInteractions);
- cmp_blocka(fp, &t1->excls, &t2->excls, "excls");
- }
- else
- {
- cmp_idef(fp, &(t1->idef), NULL, ftol, abstol);
- cmp_atoms(fp, &(t1->atoms), NULL, ftol, abstol);
- }
-}
-
-static void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
- int natoms0, int natoms1)
-{
- int i, j;
- char buf[32];
-
- fprintf(fp, "comparing groups\n");
-
- for (i = 0; i < egcNR; i++)
- {
- sprintf(buf, "grps[%d].nr", i);
- cmp_int(fp, buf, -1, g0->grps[i].nr, g1->grps[i].nr);
- if (g0->grps[i].nr == g1->grps[i].nr)
- {
- for (j = 0; j < g0->grps[i].nr; j++)
- {
- sprintf(buf, "grps[%d].name[%d]", i, j);
- cmp_str(fp, buf, -1,
- *g0->grpname[g0->grps[i].nm_ind[j]],
- *g1->grpname[g1->grps[i].nm_ind[j]]);
- }
- }
- cmp_int(fp, "ngrpnr", i, g0->ngrpnr[i], g1->ngrpnr[i]);
- if (g0->ngrpnr[i] == g1->ngrpnr[i] && natoms0 == natoms1 &&
- (g0->grpnr[i] != NULL || g1->grpnr[i] != NULL))
- {
- for (j = 0; j < natoms0; j++)
- {
- cmp_int(fp, gtypes[i], j, ggrpnr(g0, i, j), ggrpnr(g1, i, j));
- }
- }
- }
- /* We have compared the names in the groups lists,
- * so we can skip the grpname list comparison.
- */
-}
-
-static void cmp_rvecs_rmstol(FILE *fp, const char *title, int n, const rvec x1[], const rvec x2[],
- real ftol, real abstol)
-{
- int i, m;
- double rms;
-
- /* For a vector you are usally not interested in a relative difference
- * on a component that is very small compared to the other components.
- * Therefore we do the relative comparision relative to the RMS component.
- */
- rms = 0.0;
- for (i = 0; (i < n); i++)
- {
- for (m = 0; m < DIM; m++)
- {
- rms += x1[i][m]*x1[i][m] + x2[i][m]*x2[i][m];
- }
- }
- rms = sqrt(rms/(2*n*DIM));
-
- /* Convert the relative tolerance into an absolute tolerance */
- if (ftol*rms < abstol)
- {
- abstol = ftol*rms;
- }
-
- /* And now do the actual comparision */
- for (i = 0; (i < n); i++)
- {
- cmp_rvec(fp, title, i, x1[i], x2[i], 0.0, abstol);
- }
-}
-
-static void cmp_rvecs(FILE *fp, const char *title, int n, const rvec x1[], const rvec x2[],
- gmx_bool bRMSD, real ftol, real abstol)
-{
- int i, m;
- double d, ssd;
-
- if (bRMSD)
- {
- ssd = 0;
- for (i = 0; (i < n); i++)
- {
- for (m = 0; m < DIM; m++)
- {
- d = x1[i][m] - x2[i][m];
- ssd += d*d;
- }
- }
- fprintf(fp, "%s RMSD %g\n", title, std::sqrt(ssd/n));
- }
- else
- {
- cmp_rvecs_rmstol(fp, title, n, x1, x2, ftol, abstol);
- }
-}
-
-static void cmp_grpopts(FILE *fp, const t_grpopts *opt1, const t_grpopts *opt2, real ftol, real abstol)
-{
- int i, j;
- char buf1[256], buf2[256];
-
- cmp_int(fp, "inputrec->grpopts.ngtc", -1, opt1->ngtc, opt2->ngtc);
- cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc);
- cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz);
- cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener);
- for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++)
- {
- cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol);
- cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol);
- cmp_real(fp, "inputrec->grpopts.tau_t", i, opt1->tau_t[i], opt2->tau_t[i], ftol, abstol);
- cmp_int(fp, "inputrec->grpopts.annealing", i, opt1->annealing[i], opt2->annealing[i]);
- cmp_int(fp, "inputrec->grpopts.anneal_npoints", i,
- opt1->anneal_npoints[i], opt2->anneal_npoints[i]);
- if (opt1->anneal_npoints[i] == opt2->anneal_npoints[i])
- {
- sprintf(buf1, "inputrec->grpopts.anneal_time[%d]", i);
- sprintf(buf2, "inputrec->grpopts.anneal_temp[%d]", i);
- for (j = 0; j < opt1->anneal_npoints[i]; j++)
- {
- cmp_real(fp, buf1, j, opt1->anneal_time[i][j], opt2->anneal_time[i][j], ftol, abstol);
- cmp_real(fp, buf2, j, opt1->anneal_temp[i][j], opt2->anneal_temp[i][j], ftol, abstol);
- }
- }
- }
- if (opt1->ngener == opt2->ngener)
- {
- for (i = 0; i < opt1->ngener; i++)
- {
- for (j = i; j < opt1->ngener; j++)
- {
- sprintf(buf1, "inputrec->grpopts.egp_flags[%d]", i);
- cmp_int(fp, buf1, j,
- opt1->egp_flags[opt1->ngener*i+j],
- opt2->egp_flags[opt1->ngener*i+j]);
- }
- }
- }
- for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++)
- {
- cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol);
- }
- for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++)
- {
- cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]);
- }
-}
-
-static void cmp_cosines(FILE *fp, const char *s, const t_cosines c1[DIM], const t_cosines c2[DIM], real ftol, real abstol)
-{
- int i, m;
- char buf[256];
-
- for (m = 0; (m < DIM); m++)
- {
- sprintf(buf, "inputrec->%s[%d]", s, m);
- cmp_int(fp, buf, 0, c1->n, c2->n);
- for (i = 0; (i < std::min(c1->n, c2->n)); i++)
- {
- cmp_real(fp, buf, i, c1->a[i], c2->a[i], ftol, abstol);
- cmp_real(fp, buf, i, c1->phi[i], c2->phi[i], ftol, abstol);
- }
- }
-}
-static void cmp_pull(FILE *fp)
-{
- fprintf(fp, "WARNING: Both files use COM pulling, but comparing of the pull struct is not implemented (yet). The pull parameters could be the same or different.\n");
-}
-
-static void cmp_simtempvals(FILE *fp, const t_simtemp *simtemp1, const t_simtemp *simtemp2, int n_lambda, real ftol, real abstol)
-{
- int i;
- cmp_int(fp, "inputrec->simtempvals->eSimTempScale", -1, simtemp1->eSimTempScale, simtemp2->eSimTempScale);
- cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high, simtemp2->simtemp_high, ftol, abstol);
- cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low, simtemp2->simtemp_low, ftol, abstol);
- for (i = 0; i < n_lambda; i++)
- {
- cmp_real(fp, "inputrec->simtempvals->temperatures", -1, simtemp1->temperatures[i], simtemp2->temperatures[i], ftol, abstol);
- }
-}
-
-static void cmp_expandedvals(FILE *fp, const t_expanded *expand1, const t_expanded *expand2, int n_lambda, real ftol, real abstol)
-{
- int i;
-
- cmp_bool(fp, "inputrec->fepvals->bInit_weights", -1, expand1->bInit_weights, expand2->bInit_weights);
- cmp_bool(fp, "inputrec->fepvals->bWLoneovert", -1, expand1->bWLoneovert, expand2->bWLoneovert);
-
- for (i = 0; i < n_lambda; i++)
- {
- cmp_real(fp, "inputrec->expandedvals->init_lambda_weights", -1,
- expand1->init_lambda_weights[i], expand2->init_lambda_weights[i], ftol, abstol);
- }
-
- cmp_int(fp, "inputrec->expandedvals->lambda-stats", -1, expand1->elamstats, expand2->elamstats);
- cmp_int(fp, "inputrec->expandedvals->lambda-mc-move", -1, expand1->elmcmove, expand2->elmcmove);
- cmp_int(fp, "inputrec->expandedvals->lmc-repeats", -1, expand1->lmc_repeats, expand2->lmc_repeats);
- cmp_int(fp, "inputrec->expandedvals->lmc-gibbsdelta", -1, expand1->gibbsdeltalam, expand2->gibbsdeltalam);
- cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart, expand2->lmc_forced_nstart);
- cmp_int(fp, "inputrec->expandedvals->lambda-weights-equil", -1, expand1->elmceq, expand2->elmceq);
- cmp_int(fp, "inputrec->expandedvals->,weight-equil-number-all-lambda", -1, expand1->equil_n_at_lam, expand2->equil_n_at_lam);
- cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples, expand2->equil_samples);
- cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps, expand2->equil_steps);
- cmp_real(fp, "inputrec->expandedvals->weight-equil-wl-delta", -1, expand1->equil_wl_delta, expand2->equil_wl_delta, ftol, abstol);
- cmp_real(fp, "inputrec->expandedvals->weight-equil-count-ratio", -1, expand1->equil_ratio, expand2->equil_ratio, ftol, abstol);
- cmp_bool(fp, "inputrec->expandedvals->symmetrized-transition-matrix", -1, expand1->bSymmetrizedTMatrix, expand2->bSymmetrizedTMatrix);
- cmp_int(fp, "inputrec->expandedvals->nstTij", -1, expand1->nstTij, expand2->nstTij);
- cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin, expand2->minvarmin); /*default is reasonable */
- cmp_int(fp, "inputrec->expandedvals->weight-c-range", -1, expand1->c_range, expand2->c_range); /* default is just C=0 */
- cmp_real(fp, "inputrec->expandedvals->wl-scale", -1, expand1->wl_scale, expand2->wl_scale, ftol, abstol);
- cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta, expand2->init_wl_delta, ftol, abstol);
- cmp_real(fp, "inputrec->expandedvals->wl-ratio", -1, expand1->wl_ratio, expand2->wl_ratio, ftol, abstol);
- cmp_int(fp, "inputrec->expandedvals->nstexpanded", -1, expand1->nstexpanded, expand2->nstexpanded);
- cmp_int(fp, "inputrec->expandedvals->lmc-seed", -1, expand1->lmc_seed, expand2->lmc_seed);
- cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp, ftol, abstol);
-}
-
-static void cmp_fepvals(FILE *fp, const t_lambda *fep1, const t_lambda *fep2, real ftol, real abstol)
-{
- int i, j;
- cmp_int(fp, "inputrec->nstdhdl", -1, fep1->nstdhdl, fep2->nstdhdl);
- cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state, fep2->init_fep_state, ftol, abstol);
- cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda, ftol, abstol);
- cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda);
- for (i = 0; i < efptNR; i++)
- {
- for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++)
- {
- cmp_double(fp, "inputrec->fepvals->all_lambda", -1, fep1->all_lambda[i][j], fep2->all_lambda[i][j], ftol, abstol);
- }
- }
- cmp_int(fp, "inputrec->fepvals->lambda_neighbors", 1, fep1->lambda_neighbors,
- fep2->lambda_neighbors);
- cmp_real(fp, "inputrec->fepvals->sc_alpha", -1, fep1->sc_alpha, fep2->sc_alpha, ftol, abstol);
- cmp_int(fp, "inputrec->fepvals->sc_power", -1, fep1->sc_power, fep2->sc_power);
- cmp_real(fp, "inputrec->fepvals->sc_r_power", -1, fep1->sc_r_power, fep2->sc_r_power, ftol, abstol);
- cmp_real(fp, "inputrec->fepvals->sc_sigma", -1, fep1->sc_sigma, fep2->sc_sigma, ftol, abstol);
- cmp_int(fp, "inputrec->fepvals->edHdLPrintEnergy", -1, fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy);
- cmp_bool(fp, "inputrec->fepvals->bScCoul", -1, fep1->bScCoul, fep1->bScCoul);
- cmp_int(fp, "inputrec->separate_dhdl_file", -1, fep1->separate_dhdl_file, fep2->separate_dhdl_file);
- cmp_int(fp, "inputrec->dhdl_derivatives", -1, fep1->dhdl_derivatives, fep2->dhdl_derivatives);
- cmp_int(fp, "inputrec->dh_hist_size", -1, fep1->dh_hist_size, fep2->dh_hist_size);
- cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing, ftol, abstol);
-}
-
-static void cmp_inputrec(FILE *fp, const t_inputrec *ir1, const t_inputrec *ir2, real ftol, real abstol)
-{
- fprintf(fp, "comparing inputrec\n");
-
- /* gcc 2.96 doesnt like these defines at all, but issues a huge list
- * of warnings. Maybe it will change in future versions, but for the
- * moment I've spelled them out instead. /EL 000820
- * #define CIB(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
- * #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
- * #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol)
- */
- cmp_int(fp, "inputrec->eI", -1, ir1->eI, ir2->eI);
- cmp_int64(fp, "inputrec->nsteps", ir1->nsteps, ir2->nsteps);
- cmp_int64(fp, "inputrec->init_step", ir1->init_step, ir2->init_step);
- cmp_int(fp, "inputrec->simulation_part", -1, ir1->simulation_part, ir2->simulation_part);
- cmp_int(fp, "inputrec->ePBC", -1, ir1->ePBC, ir2->ePBC);
- cmp_int(fp, "inputrec->bPeriodicMols", -1, ir1->bPeriodicMols, ir2->bPeriodicMols);
- cmp_int(fp, "inputrec->cutoff_scheme", -1, ir1->cutoff_scheme, ir2->cutoff_scheme);
- cmp_int(fp, "inputrec->ns_type", -1, ir1->ns_type, ir2->ns_type);
- cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist);
- cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm);
- cmp_int(fp, "inputrec->comm_mode", -1, ir1->comm_mode, ir2->comm_mode);
- cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog);
- cmp_int(fp, "inputrec->nstxout", -1, ir1->nstxout, ir2->nstxout);
- cmp_int(fp, "inputrec->nstvout", -1, ir1->nstvout, ir2->nstvout);
- cmp_int(fp, "inputrec->nstfout", -1, ir1->nstfout, ir2->nstfout);
- cmp_int(fp, "inputrec->nstcalcenergy", -1, ir1->nstcalcenergy, ir2->nstcalcenergy);
- cmp_int(fp, "inputrec->nstenergy", -1, ir1->nstenergy, ir2->nstenergy);
- cmp_int(fp, "inputrec->nstxout_compressed", -1, ir1->nstxout_compressed, ir2->nstxout_compressed);
- cmp_double(fp, "inputrec->init_t", -1, ir1->init_t, ir2->init_t, ftol, abstol);
- cmp_double(fp, "inputrec->delta_t", -1, ir1->delta_t, ir2->delta_t, ftol, abstol);
- cmp_real(fp, "inputrec->x_compression_precision", -1, ir1->x_compression_precision, ir2->x_compression_precision, ftol, abstol);
- cmp_real(fp, "inputrec->fourierspacing", -1, ir1->fourier_spacing, ir2->fourier_spacing, ftol, abstol);
- cmp_int(fp, "inputrec->nkx", -1, ir1->nkx, ir2->nkx);
- cmp_int(fp, "inputrec->nky", -1, ir1->nky, ir2->nky);
- cmp_int(fp, "inputrec->nkz", -1, ir1->nkz, ir2->nkz);
- cmp_int(fp, "inputrec->pme_order", -1, ir1->pme_order, ir2->pme_order);
- cmp_real(fp, "inputrec->ewald_rtol", -1, ir1->ewald_rtol, ir2->ewald_rtol, ftol, abstol);
- cmp_int(fp, "inputrec->ewald_geometry", -1, ir1->ewald_geometry, ir2->ewald_geometry);
- cmp_real(fp, "inputrec->epsilon_surface", -1, ir1->epsilon_surface, ir2->epsilon_surface, ftol, abstol);
- cmp_int(fp, "inputrec->bContinuation", -1, ir1->bContinuation, ir2->bContinuation);
- cmp_int(fp, "inputrec->bShakeSOR", -1, ir1->bShakeSOR, ir2->bShakeSOR);
- cmp_int(fp, "inputrec->etc", -1, ir1->etc, ir2->etc);
- cmp_int(fp, "inputrec->bPrintNHChains", -1, ir1->bPrintNHChains, ir2->bPrintNHChains);
- cmp_int(fp, "inputrec->epc", -1, ir1->epc, ir2->epc);
- cmp_int(fp, "inputrec->epct", -1, ir1->epct, ir2->epct);
- cmp_real(fp, "inputrec->tau_p", -1, ir1->tau_p, ir2->tau_p, ftol, abstol);
- cmp_rvec(fp, "inputrec->ref_p(x)", -1, ir1->ref_p[XX], ir2->ref_p[XX], ftol, abstol);
- cmp_rvec(fp, "inputrec->ref_p(y)", -1, ir1->ref_p[YY], ir2->ref_p[YY], ftol, abstol);
- cmp_rvec(fp, "inputrec->ref_p(z)", -1, ir1->ref_p[ZZ], ir2->ref_p[ZZ], ftol, abstol);
- cmp_rvec(fp, "inputrec->compress(x)", -1, ir1->compress[XX], ir2->compress[XX], ftol, abstol);
- cmp_rvec(fp, "inputrec->compress(y)", -1, ir1->compress[YY], ir2->compress[YY], ftol, abstol);
- cmp_rvec(fp, "inputrec->compress(z)", -1, ir1->compress[ZZ], ir2->compress[ZZ], ftol, abstol);
- cmp_int(fp, "refcoord_scaling", -1, ir1->refcoord_scaling, ir2->refcoord_scaling);
- cmp_rvec(fp, "inputrec->posres_com", -1, ir1->posres_com, ir2->posres_com, ftol, abstol);
- cmp_rvec(fp, "inputrec->posres_comB", -1, ir1->posres_comB, ir2->posres_comB, ftol, abstol);
- cmp_real(fp, "inputrec->verletbuf_tol", -1, ir1->verletbuf_tol, ir2->verletbuf_tol, ftol, abstol);
- cmp_real(fp, "inputrec->rlist", -1, ir1->rlist, ir2->rlist, ftol, abstol);
- cmp_real(fp, "inputrec->rtpi", -1, ir1->rtpi, ir2->rtpi, ftol, abstol);
- cmp_int(fp, "inputrec->coulombtype", -1, ir1->coulombtype, ir2->coulombtype);
- cmp_int(fp, "inputrec->coulomb_modifier", -1, ir1->coulomb_modifier, ir2->coulomb_modifier);
- cmp_real(fp, "inputrec->rcoulomb_switch", -1, ir1->rcoulomb_switch, ir2->rcoulomb_switch, ftol, abstol);
- cmp_real(fp, "inputrec->rcoulomb", -1, ir1->rcoulomb, ir2->rcoulomb, ftol, abstol);
- cmp_int(fp, "inputrec->vdwtype", -1, ir1->vdwtype, ir2->vdwtype);
- cmp_int(fp, "inputrec->vdw_modifier", -1, ir1->vdw_modifier, ir2->vdw_modifier); cmp_real(fp, "inputrec->rvdw_switch", -1, ir1->rvdw_switch, ir2->rvdw_switch, ftol, abstol);
- cmp_real(fp, "inputrec->rvdw", -1, ir1->rvdw, ir2->rvdw, ftol, abstol);
- cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol);
- cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol);
- cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol);
- cmp_int(fp, "inputrec->implicit_solvent", -1, ir1->implicit_solvent, ir2->implicit_solvent);
- cmp_int(fp, "inputrec->gb_algorithm", -1, ir1->gb_algorithm, ir2->gb_algorithm);
- cmp_int(fp, "inputrec->nstgbradii", -1, ir1->nstgbradii, ir2->nstgbradii);
- cmp_real(fp, "inputrec->rgbradii", -1, ir1->rgbradii, ir2->rgbradii, ftol, abstol);
- cmp_real(fp, "inputrec->gb_saltconc", -1, ir1->gb_saltconc, ir2->gb_saltconc, ftol, abstol);
- cmp_real(fp, "inputrec->gb_epsilon_solvent", -1, ir1->gb_epsilon_solvent, ir2->gb_epsilon_solvent, ftol, abstol);
- cmp_real(fp, "inputrec->gb_obc_alpha", -1, ir1->gb_obc_alpha, ir2->gb_obc_alpha, ftol, abstol);
- cmp_real(fp, "inputrec->gb_obc_beta", -1, ir1->gb_obc_beta, ir2->gb_obc_beta, ftol, abstol);
- cmp_real(fp, "inputrec->gb_obc_gamma", -1, ir1->gb_obc_gamma, ir2->gb_obc_gamma, ftol, abstol);
- cmp_real(fp, "inputrec->gb_dielectric_offset", -1, ir1->gb_dielectric_offset, ir2->gb_dielectric_offset, ftol, abstol);
- cmp_int(fp, "inputrec->sa_algorithm", -1, ir1->sa_algorithm, ir2->sa_algorithm);
- cmp_real(fp, "inputrec->sa_surface_tension", -1, ir1->sa_surface_tension, ir2->sa_surface_tension, ftol, abstol);
-
- cmp_int(fp, "inputrec->eDispCorr", -1, ir1->eDispCorr, ir2->eDispCorr);
- cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol);
- cmp_int(fp, "inputrec->efep", -1, ir1->efep, ir2->efep);
- cmp_fepvals(fp, ir1->fepvals, ir2->fepvals, ftol, abstol);
- cmp_int(fp, "inputrec->bSimTemp", -1, ir1->bSimTemp, ir2->bSimTemp);
- if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp))
- {
- cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
- }
- cmp_int(fp, "inputrec->bExpanded", -1, ir1->bExpanded, ir2->bExpanded);
- if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded))
- {
- cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
- }
- cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall);
- cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type);
- cmp_int(fp, "inputrec->wall_atomtype[0]", -1, ir1->wall_atomtype[0], ir2->wall_atomtype[0]);
- cmp_int(fp, "inputrec->wall_atomtype[1]", -1, ir1->wall_atomtype[1], ir2->wall_atomtype[1]);
- cmp_real(fp, "inputrec->wall_density[0]", -1, ir1->wall_density[0], ir2->wall_density[0], ftol, abstol);
- cmp_real(fp, "inputrec->wall_density[1]", -1, ir1->wall_density[1], ir2->wall_density[1], ftol, abstol);
- cmp_real(fp, "inputrec->wall_ewald_zfac", -1, ir1->wall_ewald_zfac, ir2->wall_ewald_zfac, ftol, abstol);
-
- cmp_bool(fp, "inputrec->bPull", -1, ir1->bPull, ir2->bPull);
- if (ir1->bPull && ir2->bPull)
- {
- cmp_pull(fp);
- }
-
- cmp_int(fp, "inputrec->eDisre", -1, ir1->eDisre, ir2->eDisre);
- cmp_real(fp, "inputrec->dr_fc", -1, ir1->dr_fc, ir2->dr_fc, ftol, abstol);
- cmp_int(fp, "inputrec->eDisreWeighting", -1, ir1->eDisreWeighting, ir2->eDisreWeighting);
- cmp_int(fp, "inputrec->bDisreMixed", -1, ir1->bDisreMixed, ir2->bDisreMixed);
- cmp_int(fp, "inputrec->nstdisreout", -1, ir1->nstdisreout, ir2->nstdisreout);
- cmp_real(fp, "inputrec->dr_tau", -1, ir1->dr_tau, ir2->dr_tau, ftol, abstol);
- cmp_real(fp, "inputrec->orires_fc", -1, ir1->orires_fc, ir2->orires_fc, ftol, abstol);
- cmp_real(fp, "inputrec->orires_tau", -1, ir1->orires_tau, ir2->orires_tau, ftol, abstol);
- cmp_int(fp, "inputrec->nstorireout", -1, ir1->nstorireout, ir2->nstorireout);
- cmp_real(fp, "inputrec->em_stepsize", -1, ir1->em_stepsize, ir2->em_stepsize, ftol, abstol);
- cmp_real(fp, "inputrec->em_tol", -1, ir1->em_tol, ir2->em_tol, ftol, abstol);
- cmp_int(fp, "inputrec->niter", -1, ir1->niter, ir2->niter);
- cmp_real(fp, "inputrec->fc_stepsize", -1, ir1->fc_stepsize, ir2->fc_stepsize, ftol, abstol);
- cmp_int(fp, "inputrec->nstcgsteep", -1, ir1->nstcgsteep, ir2->nstcgsteep);
- cmp_int(fp, "inputrec->nbfgscorr", 0, ir1->nbfgscorr, ir2->nbfgscorr);
- cmp_int(fp, "inputrec->eConstrAlg", -1, ir1->eConstrAlg, ir2->eConstrAlg);
- cmp_int(fp, "inputrec->nProjOrder", -1, ir1->nProjOrder, ir2->nProjOrder);
- cmp_real(fp, "inputrec->LincsWarnAngle", -1, ir1->LincsWarnAngle, ir2->LincsWarnAngle, ftol, abstol);
- cmp_int(fp, "inputrec->nLincsIter", -1, ir1->nLincsIter, ir2->nLincsIter);
- cmp_real(fp, "inputrec->bd_fric", -1, ir1->bd_fric, ir2->bd_fric, ftol, abstol);
- cmp_int64(fp, "inputrec->ld_seed", ir1->ld_seed, ir2->ld_seed);
- cmp_real(fp, "inputrec->cos_accel", -1, ir1->cos_accel, ir2->cos_accel, ftol, abstol);
- cmp_rvec(fp, "inputrec->deform(a)", -1, ir1->deform[XX], ir2->deform[XX], ftol, abstol);
- cmp_rvec(fp, "inputrec->deform(b)", -1, ir1->deform[YY], ir2->deform[YY], ftol, abstol);
- cmp_rvec(fp, "inputrec->deform(c)", -1, ir1->deform[ZZ], ir2->deform[ZZ], ftol, abstol);
-
-
- cmp_int(fp, "inputrec->userint1", -1, ir1->userint1, ir2->userint1);
- cmp_int(fp, "inputrec->userint2", -1, ir1->userint2, ir2->userint2);
- cmp_int(fp, "inputrec->userint3", -1, ir1->userint3, ir2->userint3);
- cmp_int(fp, "inputrec->userint4", -1, ir1->userint4, ir2->userint4);
- cmp_real(fp, "inputrec->userreal1", -1, ir1->userreal1, ir2->userreal1, ftol, abstol);
- cmp_real(fp, "inputrec->userreal2", -1, ir1->userreal2, ir2->userreal2, ftol, abstol);
- cmp_real(fp, "inputrec->userreal3", -1, ir1->userreal3, ir2->userreal3, ftol, abstol);
- cmp_real(fp, "inputrec->userreal4", -1, ir1->userreal4, ir2->userreal4, ftol, abstol);
- cmp_grpopts(fp, &(ir1->opts), &(ir2->opts), ftol, abstol);
- cmp_cosines(fp, "ex", ir1->ex, ir2->ex, ftol, abstol);
- cmp_cosines(fp, "et", ir1->et, ir2->et, ftol, abstol);
-}
-
-static void comp_pull_AB(FILE *fp, pull_params_t *pull, real ftol, real abstol)
-{
- int i;
-
- for (i = 0; i < pull->ncoord; i++)
- {
- fprintf(fp, "comparing pull coord %d\n", i);
- cmp_real(fp, "pull-coord->k", -1, pull->coord[i].k, pull->coord[i].kB, ftol, abstol);
- }
-}
-
-static void comp_state(const t_state *st1, const t_state *st2,
- gmx_bool bRMSD, real ftol, real abstol)
-{
- int i, j, nc;
-
- fprintf(stdout, "comparing flags\n");
- cmp_int(stdout, "flags", -1, st1->flags, st2->flags);
- fprintf(stdout, "comparing box\n");
- cmp_rvecs(stdout, "box", DIM, st1->box, st2->box, FALSE, ftol, abstol);
- fprintf(stdout, "comparing box_rel\n");
- cmp_rvecs(stdout, "box_rel", DIM, st1->box_rel, st2->box_rel, FALSE, ftol, abstol);
- fprintf(stdout, "comparing boxv\n");
- cmp_rvecs(stdout, "boxv", DIM, st1->boxv, st2->boxv, FALSE, ftol, abstol);
- if (st1->flags & (1<<estSVIR_PREV))
- {
- fprintf(stdout, "comparing shake vir_prev\n");
- cmp_rvecs(stdout, "svir_prev", DIM, st1->svir_prev, st2->svir_prev, FALSE, ftol, abstol);
- }
- if (st1->flags & (1<<estFVIR_PREV))
- {
- fprintf(stdout, "comparing force vir_prev\n");
- cmp_rvecs(stdout, "fvir_prev", DIM, st1->fvir_prev, st2->fvir_prev, FALSE, ftol, abstol);
- }
- if (st1->flags & (1<<estPRES_PREV))
- {
- fprintf(stdout, "comparing prev_pres\n");
- cmp_rvecs(stdout, "pres_prev", DIM, st1->pres_prev, st2->pres_prev, FALSE, ftol, abstol);
- }
- cmp_int(stdout, "ngtc", -1, st1->ngtc, st2->ngtc);
- cmp_int(stdout, "nhchainlength", -1, st1->nhchainlength, st2->nhchainlength);
- if (st1->ngtc == st2->ngtc && st1->nhchainlength == st2->nhchainlength)
- {
- for (i = 0; i < st1->ngtc; i++)
- {
- nc = i*st1->nhchainlength;
- for (j = 0; j < nc; j++)
- {
- cmp_real(stdout, "nosehoover_xi",
- i, st1->nosehoover_xi[nc+j], st2->nosehoover_xi[nc+j], ftol, abstol);
- }
- }
- }
- cmp_int(stdout, "nnhpres", -1, st1->nnhpres, st2->nnhpres);
- if (st1->nnhpres == st2->nnhpres && st1->nhchainlength == st2->nhchainlength)
- {
- for (i = 0; i < st1->nnhpres; i++)
- {
- nc = i*st1->nhchainlength;
- for (j = 0; j < nc; j++)
- {
- cmp_real(stdout, "nosehoover_xi",
- i, st1->nhpres_xi[nc+j], st2->nhpres_xi[nc+j], ftol, abstol);
- }
- }
- }
-
- cmp_int(stdout, "natoms", -1, st1->natoms, st2->natoms);
- if (st1->natoms == st2->natoms)
- {
- if ((st1->flags & (1<<estX)) && (st2->flags & (1<<estX)))
- {
- fprintf(stdout, "comparing x\n");
- cmp_rvecs(stdout, "x", st1->natoms, st1->x, st2->x, bRMSD, ftol, abstol);
- }
- if ((st1->flags & (1<<estV)) && (st2->flags & (1<<estV)))
- {
- fprintf(stdout, "comparing v\n");
- cmp_rvecs(stdout, "v", st1->natoms, st1->v, st2->v, bRMSD, ftol, abstol);
- }
- }
-}
-
-void comp_tpx(const char *fn1, const char *fn2,
- gmx_bool bRMSD, real ftol, real abstol)
-{
- const char *ff[2];
- t_inputrec ir[2];
- t_state state[2];
- gmx_mtop_t mtop[2];
- t_topology top[2];
- int i;
-
- ff[0] = fn1;
- ff[1] = fn2;
- for (i = 0; i < (fn2 ? 2 : 1); i++)
- {
- read_tpx_state(ff[i], &(ir[i]), &state[i], &(mtop[i]));
- }
- if (fn2)
- {
- cmp_inputrec(stdout, &ir[0], &ir[1], ftol, abstol);
- /* Convert gmx_mtop_t to t_topology.
- * We should implement direct mtop comparison,
- * but it might be useful to keep t_topology comparison as an option.
- */
- top[0] = gmx_mtop_t_to_t_topology(&mtop[0]);
- top[1] = gmx_mtop_t_to_t_topology(&mtop[1]);
- cmp_top(stdout, &top[0], &top[1], ftol, abstol);
- cmp_groups(stdout, &mtop[0].groups, &mtop[1].groups,
- mtop[0].natoms, mtop[1].natoms);
- comp_state(&state[0], &state[1], bRMSD, ftol, abstol);
- }
- else
- {
- if (ir[0].efep == efepNO)
- {
- fprintf(stdout, "inputrec->efep = %s\n", efep_names[ir[0].efep]);
- }
- else
- {
- if (ir[0].bPull)
- {
- comp_pull_AB(stdout, ir->pull, ftol, abstol);
- }
- /* Convert gmx_mtop_t to t_topology.
- * We should implement direct mtop comparison,
- * but it might be useful to keep t_topology comparison as an option.
- */
- top[0] = gmx_mtop_t_to_t_topology(&mtop[0]);
- cmp_top(stdout, &top[0], NULL, ftol, abstol);
- }
- }
-}
-
-void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
- gmx_bool bRMSD, real ftol, real abstol)
-{
- fprintf(fp, "\n");
- cmp_int(fp, "not_ok", -1, fr1->not_ok, fr2->not_ok);
- cmp_int(fp, "natoms", -1, fr1->natoms, fr2->natoms);
- if (cmp_bool(fp, "bTitle", -1, fr1->bTitle, fr2->bTitle))
- {
- cmp_str(fp, "title", -1, fr1->title, fr2->title);
- }
- if (cmp_bool(fp, "bStep", -1, fr1->bStep, fr2->bStep))
- {
- cmp_int(fp, "step", -1, fr1->step, fr2->step);
- }
- cmp_int(fp, "step", -1, fr1->step, fr2->step);
- if (cmp_bool(fp, "bTime", -1, fr1->bTime, fr2->bTime))
- {
- cmp_real(fp, "time", -1, fr1->time, fr2->time, ftol, abstol);
- }
- if (cmp_bool(fp, "bLambda", -1, fr1->bLambda, fr2->bLambda))
- {
- cmp_real(fp, "lambda", -1, fr1->lambda, fr2->lambda, ftol, abstol);
- }
- if (cmp_bool(fp, "bAtoms", -1, fr1->bAtoms, fr2->bAtoms))
- {
- cmp_atoms(fp, fr1->atoms, fr2->atoms, ftol, abstol);
- }
- if (cmp_bool(fp, "bPrec", -1, fr1->bPrec, fr2->bPrec))
- {
- cmp_real(fp, "prec", -1, fr1->prec, fr2->prec, ftol, abstol);
- }
- if (cmp_bool(fp, "bX", -1, fr1->bX, fr2->bX))
- {
- cmp_rvecs(fp, "x", std::min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol);
- }
- if (cmp_bool(fp, "bV", -1, fr1->bV, fr2->bV))
- {
- cmp_rvecs(fp, "v", std::min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol);
- }
- if (cmp_bool(fp, "bF", -1, fr1->bF, fr2->bF))
- {
- cmp_rvecs(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol);
- }
- if (cmp_bool(fp, "bBox", -1, fr1->bBox, fr2->bBox))
- {
- cmp_rvecs(fp, "box", 3, fr1->box, fr2->box, FALSE, ftol, abstol);
- }
-}
-
-void comp_trx(const gmx_output_env_t *oenv, const char *fn1, const char *fn2,
- gmx_bool bRMSD, real ftol, real abstol)
-{
- int i;
- const char *fn[2];
- t_trxframe fr[2];
- t_trxstatus *status[2];
- gmx_bool b[2];
-
- fn[0] = fn1;
- fn[1] = fn2;
- fprintf(stderr, "Comparing trajectory files %s and %s\n", fn1, fn2);
- for (i = 0; i < 2; i++)
- {
- b[i] = read_first_frame(oenv, &status[i], fn[i], &fr[i], TRX_READ_X|TRX_READ_V|TRX_READ_F);
- }
-
- if (b[0] && b[1])
- {
- do
- {
- comp_frame(stdout, &(fr[0]), &(fr[1]), bRMSD, ftol, abstol);
-
- for (i = 0; i < 2; i++)
- {
- b[i] = read_next_frame(oenv, status[i], &fr[i]);
- }
- }
- while (b[0] && b[1]);
-
- for (i = 0; i < 2; i++)
- {
- if (b[i] && !b[1-i])
- {
- fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn[1-i], fn[i]);
- }
- close_trj(status[i]);
- }
- }
- if (!b[0] && !b[1])
- {
- fprintf(stdout, "\nBoth files read correctly\n");
- }
-}
-
-static real ener_tensor_diag(int n, int *ind1, int *ind2,
- gmx_enxnm_t *enm1,
- int *tensi, int i,
- t_energy e1[], t_energy e2[])
-{
- int d1, d2;
- int j;
- real prod1, prod2;
- int nfound;
- size_t len;
-
- d1 = tensi[i]/DIM;
- d2 = tensi[i] - d1*DIM;
-
- /* Find the diagonal elements d1 and d2 */
- len = std::strlen(enm1[ind1[i]].name);
- prod1 = 1;
- prod2 = 1;
- nfound = 0;
- for (j = 0; j < n; j++)
- {
- if (tensi[j] >= 0 &&
- std::strlen(enm1[ind1[j]].name) == len &&
- std::strncmp(enm1[ind1[i]].name, enm1[ind1[j]].name, len-2) == 0 &&
- (tensi[j] == d1*DIM+d1 || tensi[j] == d2*DIM+d2))
- {
- prod1 *= fabs(e1[ind1[j]].e);
- prod2 *= fabs(e2[ind2[j]].e);
- nfound++;
- }
- }
-
- if (nfound == 2)
- {
- return 0.5*(std::sqrt(prod1) + std::sqrt(prod2));
- }
- else
- {
- return 0;
- }
-}
-
-static gmx_bool enernm_equal(const char *nm1, const char *nm2)
-{
- int len1, len2;
-
- len1 = std::strlen(nm1);
- len2 = std::strlen(nm2);
-
- /* Remove " (bar)" at the end of a name */
- if (len1 > 6 && std::strcmp(nm1+len1-6, " (bar)") == 0)
- {
- len1 -= 6;
- }
- if (len2 > 6 && std::strcmp(nm2+len2-6, " (bar)") == 0)
- {
- len2 -= 6;
- }
-
- return (len1 == len2 && gmx_strncasecmp(nm1, nm2, len1) == 0);
-}
-
-static void cmp_energies(FILE *fp, int step1, int step2,
- t_energy e1[], t_energy e2[],
- gmx_enxnm_t *enm1,
- real ftol, real abstol,
- int nre, int *ind1, int *ind2, int maxener)
-{
- int i, ii;
- int *tensi, len, d1, d2;
- real ftol_i, abstol_i;
-
- snew(tensi, maxener);
- /* Check for tensor elements ending on "-XX", "-XY", ... , "-ZZ" */
- for (i = 0; (i < maxener); i++)
- {
- ii = ind1[i];
- tensi[i] = -1;
- len = std::strlen(enm1[ii].name);
- if (len > 3 && enm1[ii].name[len-3] == '-')
- {
- d1 = enm1[ii].name[len-2] - 'X';
- d2 = enm1[ii].name[len-1] - 'X';
- if (d1 >= 0 && d1 < DIM &&
- d2 >= 0 && d2 < DIM)
- {
- tensi[i] = d1*DIM + d2;
- }
- }
- }
-
- for (i = 0; (i < maxener); i++)
- {
- /* Check if this is an off-diagonal tensor element */
- if (tensi[i] >= 0 && tensi[i] != 0 && tensi[i] != 4 && tensi[i] != 8)
- {
- /* Turn on the relative tolerance check (4 is maximum relative diff.) */
- ftol_i = 5;
- /* Do the relative tolerance through an absolute tolerance times
- * the size of diagonal components of the tensor.
- */
- abstol_i = ftol*ener_tensor_diag(nre, ind1, ind2, enm1, tensi, i, e1, e2);
- if (debug)
- {
- fprintf(debug, "tensor '%s' val %f diag %f\n",
- enm1[i].name, e1[i].e, abstol_i/ftol);
- }
- if (abstol_i > 0)
- {
- /* We found a diagonal, we need to check with the minimum tolerance */
- abstol_i = std::min(abstol_i, abstol);
- }
- else
- {
- /* We did not find a diagonal, ignore the relative tolerance check */
- abstol_i = abstol;
- }
- }
- else
- {
- ftol_i = ftol;
- abstol_i = abstol;
- }
- if (!equal_real(e1[ind1[i]].e, e2[ind2[i]].e, ftol_i, abstol_i))
- {
- fprintf(fp, "%-15s step %3d: %12g, step %3d: %12g\n",
- enm1[ind1[i]].name,
- step1, e1[ind1[i]].e,
- step2, e2[ind2[i]].e);
- }
- }
-
- sfree(tensi);
-}
-
-#if 0
-static void cmp_disres(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol)
-{
- int i;
- char bav[64], bt[64], bs[22];
-
- cmp_int(stdout, "ndisre", -1, fr1->ndisre, fr2->ndisre);
- if ((fr1->ndisre == fr2->ndisre) && (fr1->ndisre > 0))
- {
- sprintf(bav, "step %s: disre rav", gmx_step_str(fr1->step, bs));
- sprintf(bt, "step %s: disre rt", gmx_step_str(fr1->step, bs));
- for (i = 0; (i < fr1->ndisre); i++)
- {
- cmp_real(stdout, bav, i, fr1->disre_rm3tav[i], fr2->disre_rm3tav[i], ftol, abstol);
- cmp_real(stdout, bt, i, fr1->disre_rt[i], fr2->disre_rt[i], ftol, abstol);
- }
- }
-}
-#endif
-
-static void cmp_eblocks(t_enxframe *fr1, t_enxframe *fr2, real ftol, real abstol)
-{
- int i, j, k;
- char buf[64], bs[22];
-
- cmp_int(stdout, "nblock", -1, fr1->nblock, fr2->nblock);
- if ((fr1->nblock == fr2->nblock) && (fr1->nblock > 0))
- {
- for (j = 0; (j < fr1->nblock); j++)
- {
- t_enxblock *b1, *b2; /* convenience vars */
-
- b1 = &(fr1->block[j]);
- b2 = &(fr2->block[j]);
-
- sprintf(buf, "step %s: block[%d]", gmx_step_str(fr1->step, bs), j);
- cmp_int(stdout, buf, -1, b1->nsub, b2->nsub);
- cmp_int(stdout, buf, -1, b1->id, b2->id);
-
- if ( (b1->nsub == b2->nsub) && (b1->id == b2->id) )
- {
- for (i = 0; i < b1->nsub; i++)
- {
- t_enxsubblock *s1, *s2;
-
- s1 = &(b1->sub[i]);
- s2 = &(b2->sub[i]);
-
- cmp_int(stdout, buf, -1, (int)s1->type, (int)s2->type);
- cmp_int64(stdout, buf, s1->nr, s2->nr);
-
- if ((s1->type == s2->type) && (s1->nr == s2->nr))
- {
- switch (s1->type)
- {
- case xdr_datatype_float:
- for (k = 0; k < s1->nr; k++)
- {
- cmp_float(stdout, buf, i,
- s1->fval[k], s2->fval[k],
- ftol, abstol);
- }
- break;
- case xdr_datatype_double:
- for (k = 0; k < s1->nr; k++)
- {
- cmp_double(stdout, buf, i,
- s1->dval[k], s2->dval[k],
- ftol, abstol);
- }
- break;
- case xdr_datatype_int:
- for (k = 0; k < s1->nr; k++)
- {
- cmp_int(stdout, buf, i,
- s1->ival[k], s2->ival[k]);
- }
- break;
- case xdr_datatype_int64:
- for (k = 0; k < s1->nr; k++)
- {
- cmp_int64(stdout, buf,
- s1->lval[k], s2->lval[k]);
- }
- break;
- case xdr_datatype_char:
- for (k = 0; k < s1->nr; k++)
- {
- cmp_uc(stdout, buf, i,
- s1->cval[k], s2->cval[k]);
- }
- break;
- case xdr_datatype_string:
- for (k = 0; k < s1->nr; k++)
- {
- cmp_str(stdout, buf, i,
- s1->sval[k], s2->sval[k]);
- }
- break;
- default:
- gmx_incons("Unknown data type!!");
- }
- }
- }
- }
- }
- }
-}
-
-void comp_enx(const char *fn1, const char *fn2, real ftol, real abstol, const char *lastener)
-{
- int nre, nre1, nre2;
- ener_file_t in1, in2;
- int i, j, maxener, *ind1, *ind2, *have;
- gmx_enxnm_t *enm1 = NULL, *enm2 = NULL;
- t_enxframe *fr1, *fr2;
- gmx_bool b1, b2;
-
- fprintf(stdout, "comparing energy file %s and %s\n\n", fn1, fn2);
-
- in1 = open_enx(fn1, "r");
- in2 = open_enx(fn2, "r");
- do_enxnms(in1, &nre1, &enm1);
- do_enxnms(in2, &nre2, &enm2);
- if (nre1 != nre2)
- {
- fprintf(stdout, "There are %d and %d terms in the energy files\n\n",
- nre1, nre2);
- }
- else
- {
- fprintf(stdout, "There are %d terms in the energy files\n\n", nre1);
- }
-
- snew(ind1, nre1);
- snew(ind2, nre2);
- snew(have, nre2);
- nre = 0;
- for (i = 0; i < nre1; i++)
- {
- for (j = 0; j < nre2; j++)
- {
- if (enernm_equal(enm1[i].name, enm2[j].name))
- {
- ind1[nre] = i;
- ind2[nre] = j;
- have[j] = 1;
- nre++;
- break;
- }
- }
- if (nre == 0 || ind1[nre-1] != i)
- {
- cmp_str(stdout, "enm", i, enm1[i].name, "-");
- }
- }
- for (i = 0; i < nre2; i++)
- {
- if (have[i] == 0)
- {
- cmp_str(stdout, "enm", i, "-", enm2[i].name);
- }
- }
-
- maxener = nre;
- for (i = 0; i < nre; i++)
- {
- if ((lastener != NULL) && (std::strstr(enm1[i].name, lastener) != NULL))
- {
- maxener = i+1;
- break;
- }
- }
-
- fprintf(stdout, "There are %d terms to compare in the energy files\n\n",
- maxener);
-
- for (i = 0; i < maxener; i++)
- {
- cmp_str(stdout, "unit", i, enm1[ind1[i]].unit, enm2[ind2[i]].unit);
- }
-
- snew(fr1, 1);
- snew(fr2, 1);
- do
- {
- b1 = do_enx(in1, fr1);
- b2 = do_enx(in2, fr2);
- if (b1 && !b2)
- {
- fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn2, fn1);
- }
- else if (!b1 && b2)
- {
- fprintf(stdout, "\nEnd of file on %s but not on %s\n", fn1, fn2);
- }
- else if (!b1 && !b2)
- {
- fprintf(stdout, "\nFiles read successfully\n");
- }
- else
- {
- cmp_real(stdout, "t", -1, fr1->t, fr2->t, ftol, abstol);
- cmp_int(stdout, "step", -1, fr1->step, fr2->step);
- /* We don't want to print the nre mismatch for every frame */
- /* cmp_int(stdout,"nre",-1,fr1->nre,fr2->nre); */
- if ((fr1->nre >= nre) && (fr2->nre >= nre))
- {
- cmp_energies(stdout, fr1->step, fr1->step, fr1->ener, fr2->ener,
- enm1, ftol, abstol, nre, ind1, ind2, maxener);
- }
- /*cmp_disres(fr1,fr2,ftol,abstol);*/
- cmp_eblocks(fr1, fr2, ftol, abstol);
- }
- }
- while (b1 && b2);
-
- close_enx(in1);
- close_enx(in2);
-
- free_enxframe(fr2);
- sfree(fr2);
- free_enxframe(fr1);
- sfree(fr1);
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "convert_tpr.h"
+
#include <cmath>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/enxio.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trrio.h"
-#include "gromacs/gmxpreprocess/readir.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
int *invindex;
int i;
- top = gmx_mtop_t_to_t_topology(mtop);
+ top = gmx_mtop_t_to_t_topology(mtop, false);
bKeep = bKeepIt(gnx, top.atoms.nr, index);
invindex = invind(gnx, top.atoms.nr, index);
int gmx_convert_tpr(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] can edit run input files in four ways.[PAR]",
+ "[THISMODULE] can edit run input files in three ways.[PAR]",
"[BB]1.[bb] by modifying the number of steps in a run input file",
"with options [TT]-extend[tt], [TT]-until[tt] or [TT]-nsteps[tt]",
"(nsteps=-1 means unlimited number of steps)[PAR]",
- "[BB]2.[bb] (OBSOLETE) by creating a run input file",
- "for a continuation run when your simulation has crashed due to e.g.",
- "a full disk, or by making a continuation run input file.",
- "This option is obsolete, since mdrun now writes and reads",
- "checkpoint files.",
- "[BB]Note[bb] that a frame with coordinates and velocities is needed.",
- "When pressure and/or Nose-Hoover temperature coupling is used",
- "an energy file can be supplied to get an exact continuation",
- "of the original run.[PAR]",
- "[BB]3.[bb] by creating a [REF].tpx[ref] file for a subset of your original",
+ "[BB]2.[bb] by creating a [REF].tpx[ref] file for a subset of your original",
"tpx file, which is useful when you want to remove the solvent from",
"your [REF].tpx[ref] file, or when you want to make e.g. a pure C[GRK]alpha[grk] [REF].tpx[ref] file.",
"Note that you may need to use [TT]-nsteps -1[tt] (or similar) to get",
"this to work.",
"[BB]WARNING: this [REF].tpx[ref] file is not fully functional[bb].[PAR]",
- "[BB]4.[bb] by setting the charges of a specified group",
+ "[BB]3.[bb] by setting the charges of a specified group",
"to zero. This is useful when doing free energy estimates",
"using the LIE (Linear Interaction Energy) method."
};
- const char *top_fn, *frame_fn;
- struct t_fileio *fp;
- ener_file_t fp_ener = NULL;
- gmx_trr_header_t head;
+ const char *top_fn;
int i;
- gmx_int64_t nsteps_req, run_step, frame;
+ gmx_int64_t nsteps_req, run_step;
double run_t, state_t;
- gmx_bool bOK, bNsteps, bExtend, bUntil, bTime, bTraj;
- gmx_bool bFrame, bUse, bSel, bNeedEner, bReadEner, bScanEner, bFepState;
+ gmx_bool bSel;
+ gmx_bool bNsteps, bExtend, bUntil;
gmx_mtop_t mtop;
t_atoms atoms;
- t_inputrec *ir;
t_state state;
- rvec *newx = NULL, *newv = NULL, *tmpx, *tmpv;
- matrix newbox;
int gnx;
char *grpname;
- int *index = NULL;
- int nre;
- gmx_enxnm_t *enm = NULL;
- t_enxframe *fr_ener = NULL;
+ int *index = nullptr;
char buf[200], buf2[200];
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efTRN, "-f", NULL, ffOPTRD },
- { efEDR, "-e", NULL, ffOPTRD },
- { efNDX, NULL, NULL, ffOPTRD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
{ efTPR, "-o", "tprout", ffWRITE }
};
#define NFILE asize(fnm)
/* Command line options */
static int nsteps_req_int = 0;
- static real start_t = -1.0, extend_t = 0.0, until_t = 0.0;
- static int init_fep_state = 0;
- static gmx_bool bContinuation = TRUE, bZeroQ = FALSE, bVel = TRUE;
+ static real extend_t = 0.0, until_t = 0.0;
+ static gmx_bool bZeroQ = FALSE;
static t_pargs pa[] = {
{ "-extend", FALSE, etREAL, {&extend_t},
"Extend runtime by this amount (ps)" },
"Extend runtime until this ending time (ps)" },
{ "-nsteps", FALSE, etINT, {&nsteps_req_int},
"Change the number of steps" },
- { "-time", FALSE, etREAL, {&start_t},
- "Continue from frame at this time (ps) instead of the last frame" },
{ "-zeroq", FALSE, etBOOL, {&bZeroQ},
- "Set the charges of a group (from the index) to zero" },
- { "-vel", FALSE, etBOOL, {&bVel},
- "Require velocities from trajectory" },
- { "-cont", FALSE, etBOOL, {&bContinuation},
- "For exact continuation, the constraints should not be applied before the first step" },
- { "-init_fep_state", FALSE, etINT, {&init_fep_state},
- "fep state to initialize from" },
+ "Set the charges of a group (from the index) to zero" }
};
/* Parse the command line */
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
bNsteps = opt2parg_bSet("-nsteps", asize(pa), pa);
bExtend = opt2parg_bSet("-extend", asize(pa), pa);
bUntil = opt2parg_bSet("-until", asize(pa), pa);
- bFepState = opt2parg_bSet("-init_fep_state", asize(pa), pa);
- bTime = opt2parg_bSet("-time", asize(pa), pa);
- bTraj = (opt2bSet("-f", NFILE, fnm) || bTime);
top_fn = ftp2fn(efTPR, NFILE, fnm);
fprintf(stderr, "Reading toplogy and stuff from %s\n", top_fn);
- snew(ir, 1);
+ t_inputrec irInstance;
+ t_inputrec *ir = &irInstance;
read_tpx_state(top_fn, ir, &state, &mtop);
run_step = ir->init_step;
run_t = ir->init_step*ir->delta_t + ir->init_t;
- if (!EI_STATE_VELOCITY(ir->eI))
- {
- bVel = FALSE;
- }
-
- if (bTraj)
- {
- fprintf(stderr, "\n"
- "NOTE: Reading the state from trajectory is an obsolete feature of gmx convert-tpr.\n"
- " Continuation should be done by loading a checkpoint file with mdrun -cpi\n"
- " This guarantees that all state variables are transferred.\n"
- " gmx convert-tpr is now only useful for increasing nsteps,\n"
- " but even that can often be avoided by using mdrun -maxh\n"
- "\n");
-
- if (ir->bContinuation != bContinuation)
- {
- fprintf(stderr, "Modifying ir->bContinuation to %s\n",
- gmx::boolToString(bContinuation));
- }
- ir->bContinuation = bContinuation;
-
-
- bNeedEner = (ir->epc == epcPARRINELLORAHMAN || ir->etc == etcNOSEHOOVER);
- bReadEner = (bNeedEner && ftp2bSet(efEDR, NFILE, fnm));
- bScanEner = (bReadEner && !bTime);
-
- if (ir->epc != epcNO || EI_SD(ir->eI) || ir->eI == eiBD)
- {
- fprintf(stderr, "NOTE: The simulation uses pressure coupling and/or stochastic dynamics.\n"
- "gmx convert-tpr can not provide binary identical continuation.\n"
- "If you want that, supply a checkpoint file to mdrun\n\n");
- }
-
- if (EI_SD(ir->eI) || ir->eI == eiBD)
- {
- fprintf(stderr, "\nChanging ld-seed from %" GMX_PRId64 " ", ir->ld_seed);
- ir->ld_seed = static_cast<int>(gmx::makeRandomSeed());
- fprintf(stderr, "to %" GMX_PRId64 "\n\n", ir->ld_seed);
- }
-
- frame_fn = ftp2fn(efTRN, NFILE, fnm);
-
- if (fn2ftp(frame_fn) == efCPT)
- {
- int sim_part;
-
- fprintf(stderr,
- "\nREADING STATE FROM CHECKPOINT %s...\n\n",
- frame_fn);
-
- read_checkpoint_state(frame_fn, &sim_part,
- &run_step, &run_t, &state);
- }
- else
- {
- fprintf(stderr,
- "\nREADING COORDS, VELS AND BOX FROM TRAJECTORY %s...\n\n",
- frame_fn);
-
- fp = gmx_trr_open(frame_fn, "r");
- if (bScanEner)
- {
- fp_ener = open_enx(ftp2fn(efEDR, NFILE, fnm), "r");
- do_enxnms(fp_ener, &nre, &enm);
- snew(fr_ener, 1);
- fr_ener->t = -1e-12;
- }
-
- /* Now scan until the last set of x and v (step == 0)
- * or the ones at step step.
- */
- bFrame = TRUE;
- frame = 0;
- while (bFrame)
- {
- bFrame = gmx_trr_read_frame_header(fp, &head, &bOK);
- if (bOK && frame == 0)
- {
- if (mtop.natoms != head.natoms)
- {
- gmx_fatal(FARGS, "Number of atoms in Topology (%d) "
- "is not the same as in Trajectory (%d)\n",
- mtop.natoms, head.natoms);
- }
- snew(newx, head.natoms);
- snew(newv, head.natoms);
- }
- bFrame = bFrame && bOK;
- if (bFrame)
- {
- bOK = gmx_trr_read_frame_data(fp, &head, newbox, newx, newv, NULL);
- }
- bFrame = bFrame && bOK;
- bUse = FALSE;
- if (bFrame &&
- (head.x_size) && (head.v_size || !bVel))
- {
- bUse = TRUE;
- if (bScanEner)
- {
- /* Read until the energy time is >= the trajectory time */
- while (fr_ener->t < head.t && do_enx(fp_ener, fr_ener))
- {
- ;
- }
- bUse = (fr_ener->t == head.t);
- }
- if (bUse)
- {
- tmpx = newx;
- newx = state.x;
- state.x = tmpx;
- tmpv = newv;
- newv = state.v;
- state.v = tmpv;
- run_t = head.t;
- run_step = head.step;
- state.fep_state = head.fep_state;
- state.lambda[efptFEP] = head.lambda;
- copy_mat(newbox, state.box);
- }
- }
- if (bFrame || !bOK)
- {
- sprintf(buf, "\r%s %s frame %s%s: step %s%s time %s",
- "%s", "%s", "%6", GMX_PRId64, "%6", GMX_PRId64, " %8.3f");
- fprintf(stderr, buf,
- bUse ? "Read " : "Skipped", ftp2ext(fn2ftp(frame_fn)),
- frame, head.step, head.t);
- fflush(stderr);
- frame++;
- if (bTime && (head.t >= start_t))
- {
- bFrame = FALSE;
- }
- }
- }
- if (bScanEner)
- {
- close_enx(fp_ener);
- free_enxframe(fr_ener);
- free_enxnms(nre, enm);
- }
- gmx_trr_close(fp);
- fprintf(stderr, "\n");
-
- if (!bOK)
- {
- fprintf(stderr, "%s frame %s (step %s, time %g) is incomplete\n",
- ftp2ext(fn2ftp(frame_fn)), gmx_step_str(frame-1, buf2),
- gmx_step_str(head.step, buf), head.t);
- }
- fprintf(stderr, "\nUsing frame of step %s time %g\n",
- gmx_step_str(run_step, buf), run_t);
-
- if (bNeedEner)
- {
- if (bReadEner)
- {
- get_enx_state(ftp2fn(efEDR, NFILE, fnm), run_t, &mtop.groups, ir, &state);
- }
- else
- {
- fprintf(stderr, "\nWARNING: The simulation uses %s temperature and/or %s pressure coupling,\n"
- " the continuation will only be exact when an energy file is supplied\n\n",
- ETCOUPLTYPE(etcNOSEHOOVER),
- EPCOUPLTYPE(epcPARRINELLORAHMAN));
- }
- }
- if (bFepState)
- {
- ir->fepvals->init_fep_state = init_fep_state;
- }
- }
- }
-
if (bNsteps)
{
fprintf(stderr, "Setting nsteps to %s\n", gmx_step_str(nsteps_req, buf));
ir->init_step = run_step;
if (ftp2bSet(efNDX, NFILE, fnm) ||
- !(bNsteps || bExtend || bUntil || bTraj))
+ !(bNsteps || bExtend || bUntil))
{
atoms = gmx_mtop_global_atoms(&mtop);
get_index(&atoms, ftp2fn_null(efNDX, NFILE, fnm), 1,
{
fprintf(stderr, "Will write subset %s of original tpx containing %d "
"atoms\n", grpname, gnx);
- reduce_topology_x(gnx, index, &mtop, state.x, state.v);
+ reduce_topology_x(gnx, index, &mtop, as_rvec_array(state.x.data()), as_rvec_array(state.v.data()));
state.natoms = gnx;
}
else if (bZeroQ)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "dump.h"
+
#include "config.h"
#include <cassert>
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/mtxio.h"
#include "gromacs/fileio/tngio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trrio.h"
#include "gromacs/fileio/xtcio.h"
#include "gromacs/gmxpreprocess/gmxcpp.h"
#include "gromacs/linearalgebra/sparsematrix.h"
#include "gromacs/math/vecdump.h"
+#include "gromacs/mdrunutility/mdmodules.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/txtdump.h"
-static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
- gmx_bool bSysTop)
+static void list_tpx(const char *fn,
+ gmx_bool bShowNumbers,
+ gmx_bool bShowParameters,
+ const char *mdpfn,
+ gmx_bool bSysTop,
+ gmx_bool bOriginalInputrec)
{
FILE *gp;
int indent, i, j, **gcount, atot;
t_state state;
- t_inputrec ir;
t_tpxheader tpx;
gmx_mtop_t mtop;
gmx_groups_t *groups;
t_topology top;
read_tpxheader(fn, &tpx, TRUE);
-
+ t_inputrec ir;
read_tpx_state(fn,
- tpx.bIr ? &ir : NULL,
+ tpx.bIr ? &ir : nullptr,
&state,
- tpx.bTop ? &mtop : NULL);
+ tpx.bTop ? &mtop : nullptr);
+ if (tpx.bIr && !bOriginalInputrec)
+ {
+ gmx::MDModules().adjustInputrecBasedOnModules(&ir);
+ }
if (mdpfn && tpx.bIr)
{
gp = gmx_fio_fopen(mdpfn, "w");
- pr_inputrec(gp, 0, NULL, &(ir), TRUE);
+ pr_inputrec(gp, 0, nullptr, &ir, TRUE);
gmx_fio_fclose(gp);
}
{
if (bSysTop)
{
- top = gmx_mtop_t_to_t_topology(&mtop);
+ top = gmx_mtop_t_to_t_topology(&mtop, false);
}
if (available(stdout, &tpx, 0, fn))
{
indent = 0;
pr_title(stdout, indent, fn);
- pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &(ir) : NULL, FALSE);
+ pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &ir : nullptr, FALSE);
pr_tpxheader(stdout, indent, "header", &(tpx));
if (!bSysTop)
{
- pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers);
+ pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers, bShowParameters);
}
else
{
- pr_top(stdout, indent, "topology", &(top), bShowNumbers);
+ pr_top(stdout, indent, "topology", &(top), bShowNumbers, bShowParameters);
}
- pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : NULL, DIM);
- pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : NULL, DIM);
- pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : NULL, DIM);
- pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : NULL, DIM);
- pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : NULL, DIM);
- pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : NULL, DIM);
+ pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : nullptr, DIM);
+ pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : nullptr, DIM);
+ pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : nullptr, DIM);
+ pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : nullptr, DIM);
+ pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : nullptr, DIM);
+ pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : nullptr, DIM);
/* leave nosehoover_xi in for now to match the tpr version */
- pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi, state.ngtc);
+ pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi.data(), state.ngtc);
/*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
/*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
- pr_rvecs(stdout, indent, "x", tpx.bX ? state.x : NULL, state.natoms);
- pr_rvecs(stdout, indent, "v", tpx.bV ? state.v : NULL, state.natoms);
+ pr_rvecs(stdout, indent, "x", tpx.bX ? as_rvec_array(state.x.data()) : nullptr, state.natoms);
+ pr_rvecs(stdout, indent, "v", tpx.bV ? as_rvec_array(state.v.data()) : nullptr, state.natoms);
}
groups = &mtop.groups;
}
sfree(gcount);
}
- done_state(&state);
}
static void list_top(const char *fn)
#define BUFLEN 256
char buf[BUFLEN];
gmx_cpp_t handle;
- char *cppopts[] = { NULL };
+ char *cppopts[] = { nullptr };
status = cpp_open_file(fn, &handle, cppopts);
if (status != 0)
snew(v, trrheader.natoms);
snew(f, trrheader.natoms);
if (gmx_trr_read_frame_data(fpread, &trrheader,
- trrheader.box_size ? box : NULL,
- trrheader.x_size ? x : NULL,
- trrheader.v_size ? v : NULL,
- trrheader.f_size ? f : NULL))
+ trrheader.box_size ? box : nullptr,
+ trrheader.x_size ? x : nullptr,
+ trrheader.v_size ? v : nullptr,
+ trrheader.f_size ? f : nullptr))
{
sprintf(buf, "%s frame %d", fn, nframe);
indent = 0;
gmx_trr_close(fpread);
}
-void list_xtc(const char *fn)
+static void list_xtc(const char *fn)
{
t_fileio *xd;
int indent;
#ifdef GMX_USE_TNG
tng_trajectory_t tng;
gmx_int64_t nframe = 0;
- gmx_int64_t i, *block_ids = NULL, step, ndatablocks;
+ gmx_int64_t i, *block_ids = nullptr, step, ndatablocks;
gmx_bool bOK;
- real *values = NULL;
+ real *values = nullptr;
gmx_tng_open(fn, 'r', &tng);
gmx_print_tng_molecule_system(tng, stdout);
bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1,
0,
- NULL,
+ nullptr,
&step, &ndatablocks,
&block_ids);
do
}
while (gmx_get_tng_data_block_types_of_next_frame(tng, step,
0,
- NULL,
+ nullptr,
&step,
&ndatablocks,
&block_ids));
#endif
}
-void list_trx(const char *fn)
+static void list_trx(const char *fn)
{
switch (fn2ftp(fn))
{
}
}
-void list_ene(const char *fn)
+static void list_ene(const char *fn)
{
ener_file_t in;
gmx_bool bCont;
- gmx_enxnm_t *enm = NULL;
+ gmx_enxnm_t *enm = nullptr;
t_enxframe *fr;
int i, j, nre, b;
char buf[22];
static void list_mtx(const char *fn)
{
int nrow, ncol, i, j, k;
- real *full = NULL, value;
- gmx_sparsematrix_t * sparse = NULL;
+ real *full = nullptr, value;
+ gmx_sparsematrix_t * sparse = nullptr;
gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
- if (full == NULL)
+ if (full == nullptr)
{
snew(full, nrow*ncol);
for (i = 0; i < nrow*ncol; i++)
"Position restraint output from -sys -s is broken"
};
t_filenm fnm[] = {
- { efTPR, "-s", NULL, ffOPTRD },
- { efTRX, "-f", NULL, ffOPTRD },
- { efEDR, "-e", NULL, ffOPTRD },
- { efCPT, NULL, NULL, ffOPTRD },
- { efTOP, "-p", NULL, ffOPTRD },
+ { efTPR, "-s", nullptr, ffOPTRD },
+ { efTRX, "-f", nullptr, ffOPTRD },
+ { efEDR, "-e", nullptr, ffOPTRD },
+ { efCPT, nullptr, nullptr, ffOPTRD },
+ { efTOP, "-p", nullptr, ffOPTRD },
{ efMTX, "-mtx", "hessian", ffOPTRD },
- { efMDP, "-om", NULL, ffOPTWR }
+ { efMDP, "-om", nullptr, ffOPTWR }
};
#define NFILE asize(fnm)
gmx_output_env_t *oenv;
/* Command line options */
- static gmx_bool bShowNumbers = TRUE;
- static gmx_bool bSysTop = FALSE;
- t_pargs pa[] = {
+ gmx_bool bShowNumbers = TRUE;
+ gmx_bool bShowParams = FALSE;
+ gmx_bool bSysTop = FALSE;
+ gmx_bool bOriginalInputrec = FALSE;
+ t_pargs pa[] = {
{ "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
- { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" }
+ { "-param", FALSE, etBOOL, {&bShowParams}, "Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)" },
+ { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" },
+ { "-orgir", FALSE, etBOOL, {&bOriginalInputrec}, "Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them" }
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
if (ftp2bSet(efTPR, NFILE, fnm))
{
- list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers,
- ftp2fn_null(efMDP, NFILE, fnm), bSysTop);
+ list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers, bShowParams,
+ ftp2fn_null(efMDP, NFILE, fnm), bSysTop, bOriginalInputrec);
}
else if (ftp2bSet(efTRX, NFILE, fnm))
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
srenew(ap->bAvail, ap->maxprop);
for (i = ap->nprop; (i < ap->maxprop); i++)
{
- ap->atomnm[i] = NULL;
- ap->resnm[i] = NULL;
+ ap->atomnm[i] = nullptr;
+ ap->resnm[i] = nullptr;
ap->value[i] = 0;
ap->bAvail[i] = FALSE;
}
gmx_atomprop *ap = (gmx_atomprop*) aps;
int p;
- if (aps == NULL)
+ if (aps == nullptr)
{
printf("\nWARNING: gmx_atomprop_destroy called with a NULL pointer\n\n");
return;
static void vdw_warning(FILE *fp)
{
- if (NULL != fp)
+ if (nullptr != fp)
{
fprintf(fp, "NOTE: From version 5.0 %s uses the Van der Waals radii\n",
gmx::getProgramContext().displayName());
return ap->prop[epropElement].atomnm[i];
}
}
- return NULL;
+ return nullptr;
}
int gmx_atomprop_atomnumber(gmx_atomprop_t aps, const char *elem)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
+#include "gromacs/topology/atomprop.h"
#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/compare.h"
+#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/txtdump.h"
const char *ptype_str[eptNR+1] = {
- "Atom", "Nucleus", "Shell", "Bond", "VSite", NULL
+ "Atom", "Nucleus", "Shell", "Bond", "VSite", nullptr
};
void init_atom(t_atoms *at)
{
- at->nr = 0;
- at->nres = 0;
- at->atom = NULL;
- at->resinfo = NULL;
- at->atomname = NULL;
- at->atomtype = NULL;
- at->atomtypeB = NULL;
- at->pdbinfo = NULL;
+ at->nr = 0;
+ at->nres = 0;
+ at->atom = nullptr;
+ at->resinfo = nullptr;
+ at->atomname = nullptr;
+ at->atomtype = nullptr;
+ at->atomtypeB = nullptr;
+ at->pdbinfo = nullptr;
+ at->haveMass = FALSE;
+ at->haveCharge = FALSE;
+ at->haveType = FALSE;
+ at->haveBState = FALSE;
+ at->havePdbInfo = FALSE;
}
void init_atomtypes(t_atomtypes *at)
{
at->nr = 0;
- at->radius = NULL;
- at->vol = NULL;
- at->atomnumber = NULL;
- at->gb_radius = NULL;
- at->S_hct = NULL;
+ at->radius = nullptr;
+ at->vol = nullptr;
+ at->atomnumber = nullptr;
+ at->gb_radius = nullptr;
+ at->S_hct = nullptr;
}
void done_atom(t_atoms *at)
{
srenew(atoms->atomname, atoms->nr+natom_extra);
srenew(atoms->atom, atoms->nr+natom_extra);
- if (NULL != atoms->pdbinfo)
+ if (nullptr != atoms->pdbinfo)
{
srenew(atoms->pdbinfo, atoms->nr+natom_extra);
}
- if (NULL != atoms->atomtype)
+ if (nullptr != atoms->atomtype)
{
srenew(atoms->atomtype, atoms->nr+natom_extra);
}
- if (NULL != atoms->atomtypeB)
+ if (nullptr != atoms->atomtypeB)
{
srenew(atoms->atomtypeB, atoms->nr+natom_extra);
}
for (i = atoms->nr; (i < atoms->nr+natom_extra); i++)
{
- atoms->atomname[i] = NULL;
+ atoms->atomname[i] = nullptr;
memset(&atoms->atom[i], 0, sizeof(atoms->atom[i]));
- if (NULL != atoms->pdbinfo)
+ if (nullptr != atoms->pdbinfo)
{
std::memset(&atoms->pdbinfo[i], 0, sizeof(atoms->pdbinfo[i]));
}
- if (NULL != atoms->atomtype)
+ if (nullptr != atoms->atomtype)
{
- atoms->atomtype[i] = NULL;
+ atoms->atomtype[i] = nullptr;
}
- if (NULL != atoms->atomtypeB)
+ if (nullptr != atoms->atomtypeB)
{
- atoms->atomtypeB[i] = NULL;
+ atoms->atomtypeB[i] = nullptr;
}
}
atoms->nr += natom_extra;
atoms->nr = natoms;
atoms->nres = 0;
snew(atoms->atomname, natoms);
- atoms->atomtype = NULL;
- atoms->atomtypeB = NULL;
+ atoms->atomtype = nullptr;
+ atoms->atomtypeB = nullptr;
snew(atoms->resinfo, natoms);
snew(atoms->atom, natoms);
- if (bPdbinfo)
+ atoms->haveMass = FALSE;
+ atoms->haveCharge = FALSE;
+ atoms->haveType = FALSE;
+ atoms->haveBState = FALSE;
+ atoms->havePdbInfo = bPdbinfo;
+ if (atoms->havePdbInfo)
{
snew(atoms->pdbinfo, natoms);
}
else
{
- atoms->pdbinfo = NULL;
+ atoms->pdbinfo = nullptr;
}
}
int i;
snew(dst, 1);
- init_t_atoms(dst, src->nr, (NULL != src->pdbinfo));
+ init_t_atoms(dst, src->nr, (nullptr != src->pdbinfo));
dst->nr = src->nr;
- if (NULL != src->atomname)
+ if (nullptr != src->atomname)
{
snew(dst->atomname, src->nr);
}
- if (NULL != src->atomtype)
+ if (nullptr != src->atomtype)
{
snew(dst->atomtype, src->nr);
}
- if (NULL != src->atomtypeB)
+ if (nullptr != src->atomtypeB)
{
snew(dst->atomtypeB, src->nr);
}
for (i = 0; (i < src->nr); i++)
{
dst->atom[i] = src->atom[i];
- if (NULL != src->pdbinfo)
+ if (nullptr != src->pdbinfo)
{
dst->pdbinfo[i] = src->pdbinfo[i];
}
- if (NULL != src->atomname)
+ if (nullptr != src->atomname)
{
dst->atomname[i] = src->atomname[i];
}
- if (NULL != src->atomtype)
+ if (nullptr != src->atomtype)
{
dst->atomtype[i] = src->atomtype[i];
}
- if (NULL != src->atomtypeB)
+ if (nullptr != src->atomtypeB)
{
dst->atomtypeB[i] = src->atomtypeB[i];
}
ri = &atoms->resinfo[atoms->atom[atom_ind].resind];
ri->name = put_symtab(symtab, resname);
- ri->rtp = NULL;
+ ri->rtp = nullptr;
ri->nr = resnr;
ri->ic = ic;
ri->chainnum = chainnum;
}
}
}
+
+static void cmp_atom(FILE *fp, int index, const t_atom *a1, const t_atom *a2, real ftol, real abstol)
+{
+ if (a2)
+ {
+ cmp_us(fp, "atom.type", index, a1->type, a2->type);
+ cmp_us(fp, "atom.ptype", index, a1->ptype, a2->ptype);
+ cmp_int(fp, "atom.resind", index, a1->resind, a2->resind);
+ cmp_int(fp, "atom.atomnumber", index, a1->atomnumber, a2->atomnumber);
+ cmp_real(fp, "atom.m", index, a1->m, a2->m, ftol, abstol);
+ cmp_real(fp, "atom.q", index, a1->q, a2->q, ftol, abstol);
+ cmp_us(fp, "atom.typeB", index, a1->typeB, a2->typeB);
+ cmp_real(fp, "atom.mB", index, a1->mB, a2->mB, ftol, abstol);
+ cmp_real(fp, "atom.qB", index, a1->qB, a2->qB, ftol, abstol);
+ }
+ else
+ {
+ cmp_us(fp, "atom.type", index, a1->type, a1->typeB);
+ cmp_real(fp, "atom.m", index, a1->m, a1->mB, ftol, abstol);
+ cmp_real(fp, "atom.q", index, a1->q, a1->qB, ftol, abstol);
+ }
+}
+
+void cmp_atoms(FILE *fp, const t_atoms *a1, const t_atoms *a2, real ftol, real abstol)
+{
+ int i;
+
+ fprintf(fp, "comparing atoms\n");
+
+ if (a2)
+ {
+ cmp_int(fp, "atoms->nr", -1, a1->nr, a2->nr);
+ for (i = 0; (i < a1->nr); i++)
+ {
+ cmp_atom(fp, i, &(a1->atom[i]), &(a2->atom[i]), ftol, abstol);
+ }
+ }
+ else
+ {
+ for (i = 0; (i < a1->nr); i++)
+ {
+ cmp_atom(fp, i, &(a1->atom[i]), nullptr, ftol, abstol);
+ }
+ }
+}
+
+void atomsSetMassesBasedOnNames(t_atoms *atoms, gmx_bool printMissingMasses)
+{
+ if (atoms->haveMass)
+ {
+ /* We could decide to anyhow assign then or generate a fatal error,
+ * but it's probably most useful to keep the masses we have.
+ */
+ return;
+ }
+
+ int maxWarn = (printMissingMasses ? 10 : 0);
+ int numWarn = 0;
+
+ gmx_atomprop_t aps = gmx_atomprop_init();
+
+ gmx_bool haveMass = TRUE;
+ for (int i = 0; i < atoms->nr; i++)
+ {
+ if (!gmx_atomprop_query(aps, epropMass,
+ *atoms->resinfo[atoms->atom[i].resind].name,
+ *atoms->atomname[i],
+ &atoms->atom[i].m))
+ {
+ haveMass = FALSE;
+
+ if (numWarn < maxWarn)
+ {
+ fprintf(stderr, "Can not find mass in database for atom %s in residue %d %s\n",
+ *atoms->atomname[i],
+ atoms->resinfo[atoms->atom[i].resind].nr,
+ *atoms->resinfo[atoms->atom[i].resind].name);
+ numWarn++;
+ }
+ else
+ {
+ break;
+ }
+ }
+ }
+ atoms->haveMass = haveMass;
+
+ gmx_atomprop_destroy(aps);
+}
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
struct t_symtab;
/* The particle type */
typedef struct t_atoms
{
- int nr; /* Nr of atoms */
- t_atom *atom; /* Array of atoms (dim: nr) */
+ int nr; /* Nr of atoms */
+ t_atom *atom; /* Array of atoms (dim: nr) */
/* The following entries will not */
/* always be used (nres==0) */
- char ***atomname; /* Array of pointers to atom name */
+ char ***atomname; /* Array of pointers to atom name */
/* use: (*(atomname[i])) */
- char ***atomtype; /* Array of pointers to atom types */
+ char ***atomtype; /* Array of pointers to atom types */
/* use: (*(atomtype[i])) */
- char ***atomtypeB; /* Array of pointers to B atom types */
+ char ***atomtypeB; /* Array of pointers to B atom types */
/* use: (*(atomtypeB[i])) */
- int nres; /* The number of resinfo entries */
- t_resinfo *resinfo; /* Array of residue names and numbers */
- t_pdbinfo *pdbinfo; /* PDB Information, such as aniso. Bfac */
+ int nres; /* The number of resinfo entries */
+ t_resinfo *resinfo; /* Array of residue names and numbers */
+ t_pdbinfo *pdbinfo; /* PDB Information, such as aniso. Bfac */
+
+ /* Flags that tell if properties are set for all nr atoms.
+ * For B-state parameters, both haveBState and the mass/charge/type
+ * flag should be TRUE.
+ */
+ gmx_bool haveMass; /* Mass available */
+ gmx_bool haveCharge; /* Charge available */
+ gmx_bool haveType; /* Atom type available */
+ gmx_bool haveBState; /* B-state parameters available */
+ gmx_bool havePdbInfo; /* pdbinfo available */
} t_atoms;
typedef struct t_atomtypes
void pr_atomtypes(FILE *fp, int indent, const char *title,
const t_atomtypes *atomtypes, gmx_bool bShowNumbers);
-#ifdef __cplusplus
-}
-#endif
+void cmp_atoms(FILE *fp, const t_atoms *a1, const t_atoms *a2, real ftol, real abstol);
+
+/*! \brief Set mass for each atom using the atom and residue names using a database
+ *
+ * If atoms->haveMass = TRUE does nothing.
+ * If printMissingMasss = TRUE, prints details for first 10 missing masses
+ * to stderr.
+ */
+void atomsSetMassesBasedOnNames(t_atoms *atoms, gmx_bool printMissingMasses);
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
char **AtomsBuilder::symtabString(char **source)
{
- if (symtab_ != NULL)
+ if (symtab_ != nullptr)
{
return put_symtab(symtab_, *source);
}
void AtomsRemover::removeMarkedAtoms(t_atoms *atoms) const
{
const int originalAtomCount = atoms->nr;
- AtomsBuilder builder(atoms, NULL);
+ AtomsBuilder builder(atoms, nullptr);
if (atoms->nr > 0)
{
builder.setNextResidueNumber(atoms->resinfo[0].nr);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(block->index, block->nalloc_index);
block->index[0] = 0;
block->nalloc_a = 0;
- block->a = NULL;
+ block->a = nullptr;
}
t_blocka *new_blocka(void)
block->nra = 0;
sfree(block->index);
sfree(block->a);
- block->index = NULL;
- block->a = NULL;
+ block->index = nullptr;
+ block->a = nullptr;
block->nalloc_index = 0;
block->nalloc_a = 0;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
void pr_ilist(FILE *fp, int indent, const char *title,
- const t_functype *functype, const t_ilist *ilist, gmx_bool bShowNumbers)
+ const t_functype *functype, const t_ilist *ilist,
+ gmx_bool bShowNumbers,
+ gmx_bool bShowParameters, const t_iparams *iparams)
{
int i, j, k, type, ftype;
t_iatom *iatoms;
iatoms = ilist->iatoms;
for (i = j = 0; i < ilist->nr; )
{
-#ifndef DEBUG
pr_indent(fp, indent+INDENT);
type = *(iatoms++);
ftype = functype[type];
- fprintf(fp, "%d type=%d (%s)",
- bShowNumbers ? j : -1, bShowNumbers ? type : -1,
- interaction_function[ftype].name);
+ if (bShowNumbers)
+ {
+ fprintf(fp, "%d type=%d ", j, type);
+ }
j++;
+ printf("(%s)", interaction_function[ftype].name);
for (k = 0; k < interaction_function[ftype].nratoms; k++)
{
- fprintf(fp, " %d", *(iatoms++));
+ fprintf(fp, " %3d", *(iatoms++));
+ }
+ if (bShowParameters)
+ {
+ fprintf(fp, " ");
+ pr_iparams(fp, ftype, &iparams[type]);
}
fprintf(fp, "\n");
i += 1+interaction_function[ftype].nratoms;
-#else
- fprintf(fp, "%5d%5d\n", i, iatoms[i]);
- i++;
-#endif
}
}
}
pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
}
-void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, gmx_bool bShowNumbers)
+void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
+ gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
int i, j;
for (j = 0; (j < F_NRE); j++)
{
pr_ilist(fp, indent, interaction_function[j].longname,
- idef->functype, &idef->il[j], bShowNumbers);
+ idef->functype, &idef->il[j], bShowNumbers,
+ bShowParameters, idef->iparams);
}
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void pr_iparams(FILE *fp, t_functype ftype, const t_iparams *iparams);
void pr_ilist(FILE *fp, int indent, const char *title,
- const t_functype *functype, const t_ilist *ilist, gmx_bool bShowNumbers);
+ const t_functype *functype, const t_ilist *ilist,
+ gmx_bool bShowNumbers,
+ gmx_bool bShowParameters, const t_iparams *iparams);
void pr_ffparams(FILE *fp, int indent, const char *title,
const gmx_ffparams_t *ffparams, gmx_bool bShowNumbers);
-void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef, gmx_bool bShowNumbers);
+void pr_idef(FILE *fp, int indent, const char *title, const t_idef *idef,
+ gmx_bool bShowNumbers, gmx_bool bShowParameters);
#ifdef __cplusplus
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* fprintf(out,"%5d %5d\n",b->nr,b->nra); */
for (i = 0; (i < b->nr); i++)
{
- fprintf(out, "[ %s ]\n", gnames[i]);
+ fprintf(out, "[ %s ]", gnames[i]);
for (k = 0, j = b->index[i]; j < b->index[i+1]; j++, k++)
{
- fprintf(out, "%4d ", b->a[j]+1);
- if ((k % 15) == 14)
- {
- fprintf(out, "\n");
- }
+ const char sep = (k % 15 == 0 ? '\n' : ' ');
+ fprintf(out, "%c%4d", sep, b->a[j]+1);
}
fprintf(out, "\n");
}
fprintf(stderr, "Duplicating the whole system with an atom offset of %d atoms.\n", natoms);
for (i = 0; (i < b->nr); i++)
{
- fprintf(out, "[ %s_copy ]\n", gnames[i]);
+ fprintf(out, "[ %s_copy ]", gnames[i]);
for (k = 0, j = b->index[i]; j < b->index[i+1]; j++, k++)
{
- fprintf(out, "%4d ", b->a[j]+1 + natoms );
- if ((k % 15) == 14)
- {
- fprintf(out, "\n");
- }
+ const char sep = (k % 15 == 0 ? '\n' : ' ');
+ fprintf(out, "%c%4d", sep, b->a[j]+1 + natoms);
}
fprintf(out, "\n");
}
static void analyse_other(const char ** restype, const t_atoms *atoms,
t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
{
- restp_t *restp = NULL;
- char **attp = NULL;
+ restp_t *restp = nullptr;
+ char **attp = nullptr;
char *rname, *aname;
int *aid, *aaid;
int i, j, k, l, resind, naid, naaid, natp, nrestp = 0;
}
}
sfree(attp);
- attp = NULL;
+ attp = nullptr;
}
}
sfree(aid);
};
static const t_gmx_help_make_index_group constructing_data[] =
- {{ NULL, 0, "Protein", TRUE, -1, -1},
+ {{ nullptr, 0, "Protein", TRUE, -1, -1},
{ pnoh, asize(pnoh), "Protein-H", TRUE, 0, -1},
{ calpha, asize(calpha), "C-alpha", FALSE, -1, -1},
{ bb, asize(bb), "Backbone", FALSE, -1, -1},
void analyse(const t_atoms *atoms, t_blocka *gb, char ***gn, gmx_bool bASK, gmx_bool bVerb)
{
- gmx_residuetype_t*rt = NULL;
+ gmx_residuetype_t*rt = nullptr;
char *resnm;
int *aid;
const char ** restype;
snew(restype, atoms->nres);
ntypes = 0;
- p_typename = NULL;
+ p_typename = nullptr;
if (atoms->nres > 0)
{
int i = 0;
in = gmx_ffopen(gfile, "r");
snew(b, 1);
b->nr = 0;
- b->index = NULL;
+ b->index = nullptr;
b->nra = 0;
- b->a = NULL;
- *grpname = NULL;
+ b->a = nullptr;
+ *grpname = nullptr;
maxentries = 0;
while (get_a_line(in, line, STRLEN))
{
srenew(b->a, maxentries);
}
assert(b->a != NULL); // for clang analyzer
- b->a[i] = strtol(str, NULL, 10)-1;
+ b->a[i] = strtol(str, nullptr, 10)-1;
b->index[b->nr]++;
(b->nra)++;
pt = strstr(pt, str)+strlen(str);
n = strlen(s);
aa = -1;
/* first look for whole name match */
- if (aa == -1)
{
for (i = 0; i < ngrps; i++)
{
strcpy(string, grpname[i]);
upstring(string);
minstring(string);
- if (strstr(string, key) != NULL)
+ if (strstr(string, key) != nullptr)
{
if (aa != -1)
{
}
grps = init_index(statfile, &gnames);
rd_groups(grps, gnames, grpnames, ngrps, isize, index, grpnr);
-}
-
-void rd_index_nrs(char *statfile, int ngrps, int isize[],
- int *index[], char *grpnames[], int grpnr[])
-{
- char **gnames;
- t_blocka *grps;
-
- if (!statfile)
+ for (int i = 0; i < grps->nr; i++)
{
- gmx_fatal(FARGS, "No index file specified");
+ sfree(gnames[i]);
}
- grps = init_index(statfile, &gnames);
-
- rd_groups(grps, gnames, grpnames, ngrps, isize, index, grpnr);
+ sfree(gnames);
+ sfree(grpnr);
+ done_blocka(grps);
+ sfree(grps);
}
void get_index(const t_atoms *atoms, const char *fnm, int ngrps,
int isize[], int *index[], char *grpnames[])
{
char ***gnames;
- t_blocka *grps = NULL;
+ t_blocka *grps = nullptr;
int *grpnr;
snew(grpnr, ngrps);
snew(gnames, 1);
- if (fnm != NULL)
+ if (fnm != nullptr)
{
grps = init_index(fnm, gnames);
}
}
rd_groups(grps, *gnames, grpnames, ngrps, isize, index, grpnr);
+ for (int i = 0; i < grps->nr; ++i)
+ {
+ sfree((*gnames)[i]);
+ }
+ sfree(*gnames);
+ sfree(gnames);
+ sfree(grpnr);
+ done_blocka(grps);
+ sfree(grps);
}
t_cluster_ndx *cluster_index(FILE *fplog, const char *ndx)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* the dimension of the isize and grpnames arrays are ngrps.
*/
-void rd_index_nrs(char *statfile, int ngrps, int isize[],
- int *index[], char *grpnames[], int grpnr[]);
-/* the same but also reads the number of the selected group*/
-
void get_index(const t_atoms *atoms, const char *fnm, int ngrps,
int isize[], int *index[], char *grpnames[]);
/* Does the same as rd_index, but if the fnm pointer is NULL it
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ *
+ * \brief This file contains inline functions to look up atom information
+ * using the global atom index.
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \inlibraryapi
+ * \ingroup module_mtop
+ */
+
+#ifndef GMX_TOPOLOGY_MTOP_LOOKUP_H
+#define GMX_TOPOLOGY_MTOP_LOOKUP_H
+
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
+
+struct t_atom;
+
+/*! \brief Look up the molecule block and other indices of a global atom index
+ *
+ * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
+ * The input value of moleculeBlock should be in range. Use 0 as starting value.
+ * For subsequent calls to this function, e.g. in a loop, pass in the previously
+ * returned value for best performance. Atoms in a group tend to be in the same
+ * molecule(block), so this minimizes the search time.
+ *
+ * \param[in] mtop The molecule topology
+ * \param[in] globalAtomIndex The global atom index to look up
+ * \param[in,out] moleculeBlock The molecule block index in \p mtop
+ * \param[out] moleculeIndex The index of the molecule in the block, can be NULL
+ * \param[out] atomIndexInMolecule The atom index in the molecule, can be NULL
+ */
+static inline void
+mtopGetMolblockIndex(const gmx_mtop_t *mtop,
+ int globalAtomIndex,
+ int *moleculeBlock,
+ int *moleculeIndex,
+ int *atomIndexInMolecule)
+{
+ GMX_ASSERT(globalAtomIndex >= 0 && globalAtomIndex < mtop->natoms, "The atom index to look up should be within range");
+ GMX_ASSERT(moleculeBlock != nullptr, "molBlock can not be NULL");
+ GMX_ASSERT(*moleculeBlock >= 0 && *moleculeBlock < mtop->nmolblock, "The starting molecule block index for the search should be within range");
+
+ /* Search the molecue block index using bisection */
+ int molBlock0 = -1;
+ int molBlock1 = mtop->nmolblock;
+
+ int globalAtomStart;
+ while (TRUE)
+ {
+ globalAtomStart = mtop->molblock[*moleculeBlock].globalAtomStart;
+ if (globalAtomIndex < globalAtomStart)
+ {
+ molBlock1 = *moleculeBlock;
+ }
+ else if (globalAtomIndex >= mtop->molblock[*moleculeBlock].globalAtomEnd)
+ {
+ molBlock0 = *moleculeBlock;
+ }
+ else
+ {
+ break;
+ }
+ *moleculeBlock = ((molBlock0 + molBlock1 + 1) >> 1);
+ }
+
+ int molIndex = (globalAtomIndex - globalAtomStart) / mtop->molblock[*moleculeBlock].natoms_mol;
+ if (moleculeIndex != nullptr)
+ {
+ *moleculeIndex = molIndex;
+ }
+ if (atomIndexInMolecule != nullptr)
+ {
+ *atomIndexInMolecule = globalAtomIndex - globalAtomStart - molIndex*mtop->molblock[*moleculeBlock].natoms_mol;
+ }
+}
+
+/*! \brief Returns the atom data for an atom based on global atom index
+ *
+ * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
+ * The input value of moleculeBlock should be in range. Use 0 as starting value.
+ * For subsequent calls to this function, e.g. in a loop, pass in the previously
+ * returned value for best performance. Atoms in a group tend to be in the same
+ * molecule(block), so this minimizes the search time.
+ *
+ * \param[in] mtop The molecule topology
+ * \param[in] globalAtomIndex The global atom index to look up
+ * \param[in,out] moleculeBlock The molecule block index in \p mtop
+ */
+static inline const t_atom &
+mtopGetAtomParameters(const gmx_mtop_t *mtop,
+ int globalAtomIndex,
+ int *moleculeBlock)
+{
+ int atomIndexInMolecule;
+ mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
+ nullptr, &atomIndexInMolecule);
+ const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
+ return moltype.atoms.atom[atomIndexInMolecule];
+}
+
+/*! \brief Returns the mass of an atom based on global atom index
+ *
+ * Returns that A-state mass of the atom with global index \p globalAtomIndex.
+ * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
+ * The input value of moleculeBlock should be in range. Use 0 as starting value.
+ * For subsequent calls to this function, e.g. in a loop, pass in the previously
+ * returned value for best performance. Atoms in a group tend to be in the same
+ * molecule(block), so this minimizes the search time.
+ *
+ * \param[in] mtop The molecule topology
+ * \param[in] globalAtomIndex The global atom index to look up
+ * \param[in,out] moleculeBlock The molecule block index in \p mtop
+ */
+static inline real
+mtopGetAtomMass(const gmx_mtop_t *mtop,
+ int globalAtomIndex,
+ int *moleculeBlock)
+{
+ const t_atom &atom = mtopGetAtomParameters(mtop, globalAtomIndex, moleculeBlock);
+ return atom.m;
+}
+
+/*! \brief Look up the atom and residue name and residue number and index of a global atom index
+ *
+ * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
+ * The input value of moleculeBlock should be in range. Use 0 as starting value.
+ * For subsequent calls to this function, e.g. in a loop, pass in the previously
+ * returned value for best performance. Atoms in a group tend to be in the same
+ * molecule(block), so this minimizes the search time.
+ * Note that this function does a (somewhat expensive) lookup. If you want
+ * to look up data sequentially for all atoms in a molecule or the system,
+ * use one of the mtop loop functionalities.
+ *
+ * \param[in] mtop The molecule topology
+ * \param[in] globalAtomIndex The global atom index to look up
+ * \param[in,out] moleculeBlock The molecule block index in \p mtop
+ * \param[out] atomName The atom name, input can be NULL
+ * \param[out] residueNumber The residue number, input can be NULL
+ * \param[out] residueName The residue name, input can be NULL
+ * \param[out] globalResidueIndex The gobal residue index, input can be NULL
+ */
+static inline void
+mtopGetAtomAndResidueName(const gmx_mtop_t *mtop,
+ int globalAtomIndex,
+ int *moleculeBlock,
+ const char **atomName,
+ int *residueNumber,
+ const char **residueName,
+ int *globalResidueIndex)
+{
+ int moleculeIndex;
+ int atomIndexInMolecule;
+ mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
+ &moleculeIndex, &atomIndexInMolecule);
+
+ const gmx_molblock_t &molb = mtop->molblock[*moleculeBlock];
+ const t_atoms &atoms = mtop->moltype[molb.type].atoms;
+ if (atomName != nullptr)
+ {
+ *atomName = *(atoms.atomname[atomIndexInMolecule]);
+ }
+ if (residueNumber != nullptr)
+ {
+ if (atoms.nres > mtop->maxres_renum)
+ {
+ *residueNumber = atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].nr;
+ }
+ else
+ {
+ /* Single residue molecule, keep counting */
+ *residueNumber = molb.residueNumberStart + moleculeIndex*atoms.nres + atoms.atom[atomIndexInMolecule].resind;
+ }
+ }
+ if (residueName != nullptr)
+ {
+ *residueName = *(atoms.resinfo[atoms.atom[atomIndexInMolecule].resind].name);
+ }
+ if (globalResidueIndex != nullptr)
+ {
+ *globalResidueIndex = molb.globalResidueStart + moleculeIndex*atoms.nres + atoms.atom[atomIndexInMolecule].resind;
+ }
+}
+
+/*! \brief Returns residue information for an atom based on global atom index
+ *
+ * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
+ * The input value of moleculeBlock should be in range. Use 0 as starting value.
+ * For subsequent calls to this function, e.g. in a loop, pass in the previously
+ * returned value for best performance. Atoms in a group tend to be in the same
+ * molecule(block), so this minimizes the search time.
+ *
+ * \param[in] mtop The molecule topology
+ * \param[in] globalAtomIndex The global atom index to look up
+ * \param[in,out] moleculeBlock The molecule block index in \p mtop
+ */
+static inline const t_resinfo &
+mtopGetResidueInfo(const gmx_mtop_t *mtop,
+ int globalAtomIndex,
+ int *moleculeBlock)
+{
+ int atomIndexInMolecule;
+ mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
+ nullptr, &atomIndexInMolecule);
+ const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
+ const int resind = moltype.atoms.atom[atomIndexInMolecule].resind;
+ return moltype.atoms.resinfo[resind];
+}
+
+/*! \brief Returns PDB information for an atom based on global atom index
+ *
+ * The atom index has to be in range: 0 <= \p globalAtomIndex < \p mtop->natoms.
+ * The input value of moleculeBlock should be in range. Use 0 as starting value.
+ * For subsequent calls to this function, e.g. in a loop, pass in the previously
+ * returned value for best performance. Atoms in a group tend to be in the same
+ * molecule(block), so this minimizes the search time.
+ *
+ * \param[in] mtop The molecule topology
+ * \param[in] globalAtomIndex The global atom index to look up
+ * \param[in,out] moleculeBlock The molecule block index in \p mtop
+ */
+static inline const t_pdbinfo &
+mtopGetAtomPdbInfo(const gmx_mtop_t *mtop,
+ int globalAtomIndex,
+ int *moleculeBlock)
+{
+ int atomIndexInMolecule;
+ mtopGetMolblockIndex(mtop, globalAtomIndex, moleculeBlock,
+ nullptr, &atomIndexInMolecule);
+ const gmx_moltype_t &moltype = mtop->moltype[mtop->molblock[*moleculeBlock].type];
+ GMX_ASSERT(moltype.atoms.havePdbInfo, "PDB information not present when requested");
+ return moltype.atoms.pdbinfo[atomIndexInMolecule];
+}
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2008,2009,2010,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return maxresnr;
}
+static void finalizeMolblocks(gmx_mtop_t *mtop)
+{
+ int atomIndex = 0;
+ int residueIndex = 0;
+ int residueNumberStart = mtop->maxresnr + 1;
+ for (int mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ gmx_molblock_t *molb = &mtop->molblock[mb];
+ int numResPerMol = mtop->moltype[molb->type].atoms.nres;
+ molb->globalAtomStart = atomIndex;
+ molb->globalResidueStart = residueIndex;
+ atomIndex += molb->nmol*molb->natoms_mol;
+ residueIndex += molb->nmol*numResPerMol;
+ molb->globalAtomEnd = atomIndex;
+ molb->residueNumberStart = residueNumberStart;
+ if (numResPerMol <= mtop->maxres_renum)
+ {
+ residueNumberStart += molb->nmol*numResPerMol;
+ }
+ }
+}
+
void gmx_mtop_finalize(gmx_mtop_t *mtop)
{
char *env;
- mtop->maxres_renum = 1;
+ if (mtop->nmolblock == 1 && mtop->molblock[0].nmol == 1)
+ {
+ /* We have a single molecule only, no renumbering needed.
+ * This case also covers an mtop converted from pdb/gro/... input,
+ * so we retain the original residue numbering.
+ */
+ mtop->maxres_renum = 0;
+ }
+ else
+ {
+ /* We only renumber single residue molecules. Their intra-molecular
+ * residue numbering is anyhow irrelevant.
+ */
+ mtop->maxres_renum = 1;
+ }
env = getenv("GMX_MAXRESRENUM");
- if (env != NULL)
+ if (env != nullptr)
{
sscanf(env, "%d", &mtop->maxres_renum);
}
}
mtop->maxresnr = gmx_mtop_maxresnr(mtop, mtop->maxres_renum);
+
+ finalizeMolblocks(mtop);
}
void gmx_mtop_count_atomtypes(const gmx_mtop_t *mtop, int state, int typecount[])
return ncg;
}
+int gmx_mtop_nres(const gmx_mtop_t *mtop)
+{
+ int nres = 0;
+ for (int mb = 0; mb < mtop->nmolblock; ++mb)
+ {
+ nres +=
+ mtop->molblock[mb].nmol*
+ mtop->moltype[mtop->molblock[mb].type].atoms.nres;
+ }
+ return nres;
+}
+
void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop)
{
int mt;
}
}
-
-typedef struct
-{
- int a_start;
- int a_end;
- int na_mol;
-} mb_at_t;
-
-typedef struct gmx_mtop_atomlookup
-{
- const gmx_mtop_t *mtop;
- int nmb;
- int mb_start;
- mb_at_t *mba;
-} t_gmx_mtop_atomlookup;
-
-
-gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop)
-{
- t_gmx_mtop_atomlookup *alook;
- int mb;
- int a_start, a_end, na, na_start = -1;
-
- snew(alook, 1);
-
- alook->mtop = mtop;
- alook->nmb = mtop->nmolblock;
- alook->mb_start = 0;
- snew(alook->mba, alook->nmb);
-
- a_start = 0;
- for (mb = 0; mb < mtop->nmolblock; mb++)
- {
- na = mtop->molblock[mb].nmol*mtop->molblock[mb].natoms_mol;
- a_end = a_start + na;
-
- alook->mba[mb].a_start = a_start;
- alook->mba[mb].a_end = a_end;
- alook->mba[mb].na_mol = mtop->molblock[mb].natoms_mol;
-
- /* We start the binary search with the largest block */
- if (mb == 0 || na > na_start)
- {
- alook->mb_start = mb;
- na_start = na;
- }
-
- a_start = a_end;
- }
-
- return alook;
-}
-
-gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop)
-{
- t_gmx_mtop_atomlookup *alook;
- int mb;
- int na, na_start = -1;
-
- alook = gmx_mtop_atomlookup_init(mtop);
-
- /* Check if the starting molblock has settle */
- if (mtop->moltype[mtop->molblock[alook->mb_start].type].ilist[F_SETTLE].nr == 0)
- {
- /* Search the largest molblock with settle */
- alook->mb_start = -1;
- for (mb = 0; mb < mtop->nmolblock; mb++)
- {
- if (mtop->moltype[mtop->molblock[mb].type].ilist[F_SETTLE].nr > 0)
- {
- na = alook->mba[mb].a_end - alook->mba[mb].a_start;
- if (alook->mb_start == -1 || na > na_start)
- {
- alook->mb_start = mb;
- na_start = na;
- }
- }
- }
-
- if (alook->mb_start == -1)
- {
- gmx_incons("gmx_mtop_atomlookup_settle_init called without settles");
- }
- }
-
- return alook;
-}
-
-void
-gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook)
-{
- sfree(alook->mba);
- sfree(alook);
-}
-
-void gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
- int atnr_global,
- t_atom **atom)
-{
- int mb0, mb1, mb;
- int a_start, atnr_mol;
-
-#ifdef DEBUG_MTOP
- if (atnr_global < 0 || atnr_global >= mtop->natoms)
- {
- gmx_fatal(FARGS, "gmx_mtop_atomnr_to_moltype was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
- atnr_global, 0, mtop->natoms-1);
- }
-#endif
-
- mb0 = -1;
- mb1 = alook->nmb;
- mb = alook->mb_start;
-
- while (TRUE)
- {
- a_start = alook->mba[mb].a_start;
- if (atnr_global < a_start)
- {
- mb1 = mb;
- }
- else if (atnr_global >= alook->mba[mb].a_end)
- {
- mb0 = mb;
- }
- else
- {
- break;
- }
- mb = ((mb0 + mb1 + 1)>>1);
- }
-
- atnr_mol = (atnr_global - a_start) % alook->mba[mb].na_mol;
-
- *atom = &alook->mtop->moltype[alook->mtop->molblock[mb].type].atoms.atom[atnr_mol];
-}
-
-void gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
- int atnr_global,
- t_ilist **ilist_mol, int *atnr_offset)
-{
- int mb0, mb1, mb;
- int a_start, atnr_local;
-
-#ifdef DEBUG_MTOP
- if (atnr_global < 0 || atnr_global >= mtop->natoms)
- {
- gmx_fatal(FARGS, "gmx_mtop_atomnr_to_moltype was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
- atnr_global, 0, mtop->natoms-1);
- }
-#endif
-
- mb0 = -1;
- mb1 = alook->nmb;
- mb = alook->mb_start;
-
- while (TRUE)
- {
- a_start = alook->mba[mb].a_start;
- if (atnr_global < a_start)
- {
- mb1 = mb;
- }
- else if (atnr_global >= alook->mba[mb].a_end)
- {
- mb0 = mb;
- }
- else
- {
- break;
- }
- mb = ((mb0 + mb1 + 1)>>1);
- }
-
- *ilist_mol = alook->mtop->moltype[alook->mtop->molblock[mb].type].ilist;
-
- atnr_local = (atnr_global - a_start) % alook->mba[mb].na_mol;
-
- *atnr_offset = atnr_global - atnr_local;
-}
-
-void gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
- int atnr_global,
- int *molb, int *molnr, int *atnr_mol)
-{
- int mb0, mb1, mb;
- int a_start;
-
-#ifdef DEBUG_MTOP
- if (atnr_global < 0 || atnr_global >= mtop->natoms)
- {
- gmx_fatal(FARGS, "gmx_mtop_atomnr_to_moltype was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
- atnr_global, 0, mtop->natoms-1);
- }
-#endif
-
- mb0 = -1;
- mb1 = alook->nmb;
- mb = alook->mb_start;
-
- while (TRUE)
- {
- a_start = alook->mba[mb].a_start;
- if (atnr_global < a_start)
- {
- mb1 = mb;
- }
- else if (atnr_global >= alook->mba[mb].a_end)
- {
- mb0 = mb;
- }
- else
- {
- break;
- }
- mb = ((mb0 + mb1 + 1)>>1);
- }
-
- *molb = mb;
- *molnr = (atnr_global - a_start) / alook->mba[mb].na_mol;
- *atnr_mol = atnr_global - a_start - (*molnr)*alook->mba[mb].na_mol;
-}
-
-void gmx_mtop_atominfo_global(const gmx_mtop_t *mtop, int atnr_global,
- char **atomname, int *resnr, char **resname)
-{
- int mb, a_start, a_end, maxresnr, at_loc;
- t_atoms *atoms = NULL;
-
- if (atnr_global < 0 || atnr_global >= mtop->natoms)
- {
- gmx_fatal(FARGS, "gmx_mtop_atominfo_global was called with atnr_global=%d which is not in the atom range of this system (%d-%d)",
- atnr_global, 0, mtop->natoms-1);
- }
-
- mb = -1;
- a_end = 0;
- maxresnr = mtop->maxresnr;
- do
- {
- if (mb >= 0)
- {
- /* cppcheck-suppress nullPointer #6330 will be fixed in cppcheck 1.73 */
- if (atoms->nres <= mtop->maxres_renum)
- {
- /* Single residue molecule, keep counting */
- /* cppcheck-suppress nullPointer #6330 will be fixed in cppcheck 1.73 */
- maxresnr += mtop->molblock[mb].nmol*atoms->nres;
- }
- }
- mb++;
- atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
- a_start = a_end;
- a_end = a_start + mtop->molblock[mb].nmol*atoms->nr;
- }
- while (atnr_global >= a_end);
-
- at_loc = (atnr_global - a_start) % atoms->nr;
- *atomname = *(atoms->atomname[at_loc]);
- if (atoms->nres > mtop->maxres_renum)
- {
- *resnr = atoms->resinfo[atoms->atom[at_loc].resind].nr;
- }
- else
- {
- /* Single residue molecule, keep counting */
- *resnr = maxresnr + 1 + (atnr_global - a_start)/atoms->nr*atoms->nres + atoms->atom[at_loc].resind;
- }
- *resname = *(atoms->resinfo[atoms->atom[at_loc].resind].name);
-}
-
typedef struct gmx_mtop_atomloop_all
{
const gmx_mtop_t *mtop;
}
gmx_bool gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
- int *at_global, t_atom **atom)
+ int *at_global, const t_atom **atom)
{
- if (aloop == NULL)
+ if (aloop == nullptr)
{
gmx_incons("gmx_mtop_atomloop_all_next called without calling gmx_mtop_atomloop_all_init");
}
}
gmx_bool gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
- t_atom **atom, int *nmol)
+ const t_atom **atom, int *nmol)
{
- if (aloop == NULL)
+ if (aloop == nullptr)
{
gmx_incons("gmx_mtop_atomloop_all_next called without calling gmx_mtop_atomloop_all_init");
}
gmx_bool gmx_mtop_ilistloop_next(gmx_mtop_ilistloop_t iloop,
t_ilist **ilist_mol, int *nmol)
{
- if (iloop == NULL)
+ if (iloop == nullptr)
{
gmx_incons("gmx_mtop_ilistloop_next called without calling gmx_mtop_ilistloop_init");
}
t_ilist **ilist_mol, int *atnr_offset)
{
- if (iloop == NULL)
+ if (iloop == nullptr)
{
gmx_incons("gmx_mtop_ilistloop_all_next called without calling gmx_mtop_ilistloop_all_init");
}
int srcnr = src->nr;
int destnr = dest->nr;
+ if (dest->nr == 0)
+ {
+ dest->haveMass = src->haveMass;
+ dest->haveType = src->haveType;
+ dest->haveCharge = src->haveCharge;
+ dest->haveBState = src->haveBState;
+ dest->havePdbInfo = src->havePdbInfo;
+ }
+ else
+ {
+ dest->haveMass = dest->haveMass && src->haveMass;
+ dest->haveType = dest->haveType && src->haveType;
+ dest->haveCharge = dest->haveCharge && src->haveCharge;
+ dest->haveBState = dest->haveBState && src->haveBState;
+ dest->havePdbInfo = dest->havePdbInfo && src->havePdbInfo;
+ }
+
if (srcnr)
{
size = destnr+copies*srcnr;
srenew(dest->atom, size);
srenew(dest->atomname, size);
- srenew(dest->atomtype, size);
- srenew(dest->atomtypeB, size);
+ if (dest->haveType)
+ {
+ srenew(dest->atomtype, size);
+ if (dest->haveBState)
+ {
+ srenew(dest->atomtypeB, size);
+ }
+ }
+ if (dest->havePdbInfo)
+ {
+ srenew(dest->pdbinfo, size);
+ }
}
if (src->nres)
{
for (l = destnr, j = 0; (j < copies); j++, l += srcnr)
{
- memcpy((char *) &(dest->atomname[l]), (char *) &(src->atomname[0]),
- (size_t)(srcnr*sizeof(src->atomname[0])));
- memcpy((char *) &(dest->atomtype[l]), (char *) &(src->atomtype[0]),
- (size_t)(srcnr*sizeof(src->atomtype[0])));
- memcpy((char *) &(dest->atomtypeB[l]), (char *) &(src->atomtypeB[0]),
- (size_t)(srcnr*sizeof(src->atomtypeB[0])));
memcpy((char *) &(dest->atom[l]), (char *) &(src->atom[0]),
(size_t)(srcnr*sizeof(src->atom[0])));
+ memcpy((char *) &(dest->atomname[l]), (char *) &(src->atomname[0]),
+ (size_t)(srcnr*sizeof(src->atomname[0])));
+ if (dest->haveType)
+ {
+ memcpy((char *) &(dest->atomtype[l]), (char *) &(src->atomtype[0]),
+ (size_t)(srcnr*sizeof(src->atomtype[0])));
+ if (dest->haveBState)
+ {
+ memcpy((char *) &(dest->atomtypeB[l]), (char *) &(src->atomtypeB[0]),
+ (size_t)(srcnr*sizeof(src->atomtypeB[0])));
+ }
+ }
+ if (dest->havePdbInfo)
+ {
+ memcpy((char *) &(dest->pdbinfo[l]), (char *) &(src->pdbinfo[0]),
+ (size_t)(srcnr*sizeof(src->pdbinfo[0])));
+ }
}
/* Increment residue indices */
real *qA, *qB;
gmx_mtop_atomloop_all_t aloop;
int ag;
- t_atom *atom;
top->atomtypes = mtop->atomtypes;
idef->atnr = ffp->atnr;
idef->functype = ffp->functype;
idef->iparams = ffp->iparams;
- idef->iparams_posres = NULL;
+ idef->iparams_posres = nullptr;
idef->iparams_posres_nalloc = 0;
- idef->iparams_fbposres = NULL;
+ idef->iparams_fbposres = nullptr;
idef->iparams_fbposres_nalloc = 0;
idef->fudgeQQ = ffp->fudgeQQ;
idef->cmap_grid = ffp->cmap_grid;
{
idef->il[ftype].nr = 0;
idef->il[ftype].nalloc = 0;
- idef->il[ftype].iatoms = NULL;
+ idef->il[ftype].iatoms = nullptr;
}
natoms = 0;
snew(qA, mtop->natoms);
snew(qB, mtop->natoms);
aloop = gmx_mtop_atomloop_all_init(mtop);
+ const t_atom *atom;
while (gmx_mtop_atomloop_all_next(aloop, &ag, &atom))
{
qA[ag] = atom->q;
return top;
}
-t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop)
+t_topology gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bool freeMTop)
{
int mt, mb;
gmx_localtop_t ltop;
top.bIntermolecularInteractions = mtop->bIntermolecularInteractions;
top.symtab = mtop->symtab;
- /* We only need to free the moltype and molblock data,
- * all other pointers have been copied to top.
- *
- * Well, except for the group data, but we can't free those, because they
- * are used somewhere even after a call to this function.
- */
- for (mt = 0; mt < mtop->nmoltype; mt++)
+ if (freeMTop)
{
- done_moltype(&mtop->moltype[mt]);
- }
- sfree(mtop->moltype);
+ // Free pointers that have not been copied to top.
+ for (mt = 0; mt < mtop->nmoltype; mt++)
+ {
+ done_moltype(&mtop->moltype[mt]);
+ }
+ sfree(mtop->moltype);
- for (mb = 0; mb < mtop->nmolblock; mb++)
- {
- done_molblock(&mtop->molblock[mb]);
+ for (mb = 0; mb < mtop->nmolblock; mb++)
+ {
+ done_molblock(&mtop->molblock[mb]);
+ }
+ sfree(mtop->molblock);
+
+ done_gmx_groups_t(&mtop->groups);
}
- sfree(mtop->molblock);
return top;
}
std::vector<size_t> atom_index;
gmx_mtop_atomloop_block_t aloopb = gmx_mtop_atomloop_block_init(mtop);
- t_atom *atom;
+ const t_atom *atom;
int nmol, j = 0;
while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
{
}
return atom_index;
}
+
+void convertAtomsToMtop(t_symtab *symtab,
+ char **name,
+ t_atoms *atoms,
+ gmx_mtop_t *mtop)
+{
+ mtop->symtab = *symtab;
+
+ mtop->name = name;
+
+ mtop->nmoltype = 1;
+ // This snew clears all entries, we should replace it by an initializer
+ snew(mtop->moltype, mtop->nmoltype);
+ mtop->moltype[0].atoms = *atoms;
+ init_block(&mtop->moltype[0].cgs);
+ init_blocka(&mtop->moltype[0].excls);
+
+ mtop->nmolblock = 1;
+ // This snew clears all entries, we should replace it by an initializer
+ snew(mtop->molblock, mtop->nmolblock);
+ mtop->molblock[0].type = 0;
+ mtop->molblock[0].nmol = 1;
+ mtop->molblock[0].natoms_mol = atoms->nr;
+
+ mtop->bIntermolecularInteractions = FALSE;
+
+ mtop->natoms = atoms->nr;
+
+ gmx_mtop_finalize(mtop);
+}
#include <vector>
+#include "gromacs/topology/topology.h"
#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/gmxassert.h"
struct gmx_localtop_t;
-struct gmx_moltype_t;
-struct gmx_mtop_t;
struct t_atom;
struct t_atoms;
struct t_block;
struct t_ilist;
-struct t_topology;
+struct t_symtab;
/* Should be called after generating or reading mtop,
* to set some compute intesive variables to avoid
int
ncg_mtop(const gmx_mtop_t *mtop);
+/* Returns the total number of residues in mtop. */
+int gmx_mtop_nres(const gmx_mtop_t *mtop);
+
/* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
-
-/* Abstract data type for looking up atoms by global atom number */
-typedef struct gmx_mtop_atomlookup *gmx_mtop_atomlookup_t;
-
-/* Initialize atom lookup by global atom number */
-gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop);
-
-/* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
-gmx_mtop_atomlookup_t
-gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop);
-
-/* Destroy a gmx_mtop_atomlookup_t data structure */
-void
-gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook);
-
-
-/* Returns a pointer to the t_atom struct belonging to atnr_global.
- * This can be an expensive operation, so if possible use
- * one of the atom loop constructs below.
- */
-void
-gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
- int atnr_global,
- t_atom **atom);
-
-
-/* Returns a pointer to the molecule interaction array ilist_mol[F_NRE]
- * and the local atom number in the molecule belonging to atnr_global.
- */
-void
-gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
- int atnr_global,
- t_ilist **ilist_mol, int *atnr_offset);
-
-
-/* Returns the molecule block index
- * and the molecule number in the block
- * and the atom number offset for the atom indices in moltype
- * belonging to atnr_global.
- */
-void
-gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
- int atnr_global,
- int *molb, int *molnr, int *atnr_mol);
-
-
-/* Returns atom name, global resnr and residue name of atom atnr_global */
-void
-gmx_mtop_atominfo_global(const gmx_mtop_t *mtop, int atnr_global,
- char **atomname, int *resnr, char **resname);
-
-
/* Abstract type for atom loop over all atoms */
typedef struct gmx_mtop_atomloop_all *gmx_mtop_atomloop_all_t;
*/
gmx_bool
gmx_mtop_atomloop_all_next(gmx_mtop_atomloop_all_t aloop,
- int *at_global, t_atom **atom);
+ int *at_global, const t_atom **atom);
/* Return the atomname, the residue number and residue name
* of the current atom in the loop.
*/
gmx_bool
gmx_mtop_atomloop_block_next(gmx_mtop_atomloop_block_t aloop,
- t_atom **atom, int *nmol);
+ const t_atom **atom, int *nmol);
/* Abstract type for ilist loop over all ilists */
/* Generate a 'local' topology for the whole system.
- * When feeEnergyInteractionsAtEnd == true, the free energy interactions will
+ * When freeEnergyInteractionsAtEnd == true, the free energy interactions will
* be sorted to the end.
*/
gmx_localtop_t *
/* Converts a gmx_mtop_t struct to t_topology.
- * All memory relating only to mtop will be freed.
+ *
+ * If freeMTop == true, memory related to mtop will be freed so that done_top()
+ * on the result value will free all memory.
+ * If freeMTop == false, mtop and the return value will share some of their
+ * memory, and there is currently no way to consistently free all the memory.
*/
t_topology
-gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop);
+gmx_mtop_t_to_t_topology(gmx_mtop_t *mtop, bool freeMTop);
/*! \brief Get vector of atoms indices from topology
*
*/
std::vector<size_t> get_atom_index(const gmx_mtop_t *mtop);
+/*! \brief Converts a t_atoms struct to an mtop struct
+ *
+ * All pointers contained in \p atoms will be copied into \p mtop.
+ * Note that this will produce one moleculetype encompassing the whole system.
+ *
+ * \param[in] symtab The symbol table
+ * \param[in] name Pointer to the name for the topology
+ * \param[in] atoms The atoms to convert
+ * \param[out] mtop The molecular topology output containing atoms.
+ */
+void
+convertAtomsToMtop(t_symtab *symtab,
+ char **name,
+ t_atoms *atoms,
+ gmx_mtop_t *mtop);
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*prt = rt;
rt->n = 0;
- rt->resname = NULL;
- rt->restype = NULL;
+ rt->resname = nullptr;
+ rt->restype = nullptr;
db = libopen("residuetypes.dat");
int * ntypes)
{
int n = 0;
- const char **my_typename = NULL;
+ const char **my_typename = nullptr;
if (rt->n > 0)
{
}
else
{
- return NULL;
+ return nullptr;
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Returns a pointer to a static area which contains a copy
* of s without leading or trailing spaces. Strings are
* truncated to BUFSIZE positions.
+ *
+ * TODO This partially duplicates code in trim(), but perhaps
+ * replacing symtab with a std::map is a better fix.
*/
{
int len, i;
s, strlen(s), maxlen-1);
}
- for (; (*s) && ((*s) == ' '); s++)
+ for (; (*s) == ' '; s++)
{
;
}
base = 0;
symbuf = symtab->symbuf;
- while (symbuf != NULL)
+ while (symbuf != nullptr)
{
const int index = name-symbuf->buf;
if ( ( index >= 0 ) && ( index < symbuf->bufsize ) )
t_symbuf *symbuf;
symbuf = symtab->symbuf;
- while (symbuf != NULL)
+ while (symbuf != nullptr)
{
if (name < symbuf->bufsize)
{
}
}
gmx_fatal(FARGS, "symtab get_symtab_handle %d not found", name);
- return NULL;
+ return nullptr;
}
static t_symbuf *new_symbuf(void)
snew(symbuf, 1);
symbuf->bufsize = TABLESIZE;
snew(symbuf->buf, symbuf->bufsize);
- symbuf->next = NULL;
+ symbuf->next = nullptr;
return symbuf;
}
t_symbuf *symbuf;
gmx_bool bCont;
- if (symtab->symbuf == NULL)
+ if (symtab->symbuf == nullptr)
{
symtab->symbuf = new_symbuf();
}
{
for (i = 0; (i < symbuf->bufsize); i++)
{
- if (symbuf->buf[i] == NULL)
+ if (symbuf->buf[i] == nullptr)
{
symtab->nr++;
symbuf->buf[i] = gmx_strdup(name);
return &(symbuf->buf[i]);
}
}
- if (symbuf->next != NULL)
+ if (symbuf->next != nullptr)
{
symbuf = symbuf->next;
bCont = TRUE;
void open_symtab(t_symtab *symtab)
{
symtab->nr = 0;
- symtab->symbuf = NULL;
+ symtab->symbuf = nullptr;
}
void close_symtab(t_symtab gmx_unused *symtab)
close_symtab(symtab);
symbuf = symtab->symbuf;
- while (symbuf != NULL)
+ while (symbuf != nullptr)
{
for (i = 0; (i < symbuf->bufsize) && (i < symtab->nr); i++)
{
symbuf = symbuf->next;
sfree(freeptr);
}
- symtab->symbuf = NULL;
+ symtab->symbuf = nullptr;
if (symtab->nr != 0)
{
gmx_incons("Freeing symbol table (symtab) structure");
close_symtab(symtab);
symbuf = symtab->symbuf;
- while (symbuf != NULL)
+ while (symbuf != nullptr)
{
symtab->nr -= std::min(symbuf->bufsize, symtab->nr);
freeptr = symbuf;
symbuf = symbuf->next;
sfree(freeptr);
}
- symtab->symbuf = NULL;
+ symtab->symbuf = nullptr;
if (symtab->nr != 0)
{
gmx_incons("Freeing symbol table (symtab) structure");
i = 0;
nr = symtab->nr;
symbuf = symtab->symbuf;
- while (symbuf != NULL)
+ while (symbuf != nullptr)
{
for (j = 0; (j < symbuf->bufsize) && (j < nr); j++)
{
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/* Undoes the effect of open_symtab(), after invoking this function,
* no value can be added to the symbol table, only values can be
* retrieved using get_symtab().
+ *
+ * Note that this does no work.
*/
void free_symtab(t_symtab *symtab);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
#include "gromacs/math/vecdump.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/topology/idef.h"
#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/symtab.h"
+#include "gromacs/utility/compare.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/txtdump.h"
const char *gtypes[egcNR+1] = {
"T-Coupling", "Energy Mon.", "Acceleration", "Freeze",
- "User1", "User2", "VCM", "Compressed X", "Or. Res. Fit", "QMMM", NULL
+ "User1", "User2", "VCM", "Compressed X", "Or. Res. Fit", "QMMM", nullptr
};
static void init_groups(gmx_groups_t *groups)
{
groups->ngrpname = 0;
- groups->grpname = NULL;
+ groups->grpname = nullptr;
for (int g = 0; g < egcNR; g++)
{
- groups->grps[g].nm_ind = NULL;
+ groups->grps[g].nm_ind = nullptr;
groups->ngrpnr[g] = 0;
- groups->grpnr[g] = NULL;
+ groups->grpnr[g] = nullptr;
}
}
void init_mtop(gmx_mtop_t *mtop)
{
- mtop->name = NULL;
+ mtop->name = nullptr;
mtop->nmoltype = 0;
- mtop->moltype = NULL;
+ mtop->moltype = nullptr;
mtop->nmolblock = 0;
- mtop->molblock = NULL;
+ mtop->molblock = nullptr;
mtop->maxres_renum = 0;
mtop->maxresnr = -1;
init_groups(&mtop->groups);
void init_top(t_topology *top)
{
- top->name = NULL;
+ top->name = nullptr;
init_atom(&(top->atoms));
init_atomtypes(&(top->atomtypes));
init_block(&top->cgs);
}
}
-void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab)
+void done_gmx_groups_t(gmx_groups_t *g)
{
- if (bDoneSymtab)
+ int i;
+
+ for (i = 0; (i < egcNR); i++)
{
- done_symtab(&mtop->symtab);
+ if (nullptr != g->grps[i].nm_ind)
+ {
+ sfree(g->grps[i].nm_ind);
+ g->grps[i].nm_ind = nullptr;
+ }
+ if (nullptr != g->grpnr[i])
+ {
+ sfree(g->grpnr[i]);
+ g->grpnr[i] = nullptr;
+ }
}
+ /* The contents of this array is in symtab, don't free it here */
+ sfree(g->grpname);
+}
+
+void done_mtop(gmx_mtop_t *mtop)
+{
+ done_symtab(&mtop->symtab);
sfree(mtop->ffparams.functype);
sfree(mtop->ffparams.iparams);
+ for (int i = 0; i < mtop->ffparams.cmap_grid.ngrid; i++)
+ {
+ sfree(mtop->ffparams.cmap_grid.cmapdata[i].cmap);
+ }
+ sfree(mtop->ffparams.cmap_grid.cmapdata);
for (int i = 0; i < mtop->nmoltype; i++)
{
done_molblock(&mtop->molblock[i]);
}
sfree(mtop->molblock);
+ done_atomtypes(&mtop->atomtypes);
+ done_gmx_groups_t(&mtop->groups);
done_block(&mtop->mols);
}
for (int f = 0; f < F_NRE; ++f)
{
sfree(top->idef.il[f].iatoms);
- top->idef.il[f].iatoms = NULL;
+ top->idef.il[f].iatoms = nullptr;
top->idef.il[f].nalloc = 0;
}
done_blocka(&(top->excls));
}
+void done_top_mtop(t_topology *top, gmx_mtop_t *mtop)
+{
+ if (mtop != nullptr)
+ {
+ if (top != nullptr)
+ {
+ for (int f = 0; f < F_NRE; ++f)
+ {
+ sfree(top->idef.il[f].iatoms);
+ top->idef.il[f].iatoms = nullptr;
+ top->idef.il[f].nalloc = 0;
+ }
+ done_atom(&top->atoms);
+ done_block(&top->cgs);
+ done_blocka(&top->excls);
+ done_symtab(&top->symtab);
+ open_symtab(&mtop->symtab);
+ }
+ done_mtop(mtop);
+ }
+}
+
+bool gmx_mtop_has_masses(const gmx_mtop_t *mtop)
+{
+ if (mtop == nullptr)
+ {
+ return false;
+ }
+ return mtop->nmoltype == 0 || mtop->moltype[0].atoms.haveMass;
+}
+
+bool gmx_mtop_has_charges(const gmx_mtop_t *mtop)
+{
+ if (mtop == nullptr)
+ {
+ return false;
+ }
+ return mtop->nmoltype == 0 || mtop->moltype[0].atoms.haveCharge;
+}
+
+bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop)
+{
+ if (mtop == nullptr)
+ {
+ return false;
+ }
+ return mtop->nmoltype == 0 || mtop->moltype[0].atoms.haveType;
+}
+
+bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop)
+{
+ if (mtop == nullptr)
+ {
+ return false;
+ }
+ return mtop->nmoltype == 0 || mtop->moltype[0].atoms.havePdbInfo;
+}
+
static void pr_grps(FILE *fp, const char *title, const t_grps grps[], char **grpname[])
{
int i, j;
static void pr_moltype(FILE *fp, int indent, const char *title,
const gmx_moltype_t *molt, int n,
const gmx_ffparams_t *ffparams,
- gmx_bool bShowNumbers)
+ gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
int j;
for (j = 0; (j < F_NRE); j++)
{
pr_ilist(fp, indent, interaction_function[j].longname,
- ffparams->functype, &molt->ilist[j], bShowNumbers);
+ ffparams->functype, &molt->ilist[j],
+ bShowNumbers, bShowParameters, ffparams->iparams);
}
}
}
void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
- gmx_bool bShowNumbers)
+ gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
int mt, mb, j;
{
pr_ilist(fp, indent, interaction_function[j].longname,
mtop->ffparams.functype,
- &mtop->intermolecular_ilist[j], bShowNumbers);
+ &mtop->intermolecular_ilist[j],
+ bShowNumbers, bShowParameters, mtop->ffparams.iparams);
}
}
pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
- &mtop->ffparams, bShowNumbers);
+ &mtop->ffparams, bShowNumbers, bShowParameters);
}
pr_groups(fp, indent, &mtop->groups, bShowNumbers);
}
}
-void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers)
+void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
+ gmx_bool bShowNumbers, gmx_bool bShowParameters)
{
if (available(fp, top, indent, title))
{
pr_str(fp, indent, "bIntermolecularInteractions",
gmx::boolToString(top->bIntermolecularInteractions));
pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
- pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
+ pr_idef(fp, indent, "idef", &top->idef, bShowNumbers, bShowParameters);
+ }
+}
+
+static void cmp_ilist(FILE *fp, int ftype, const t_ilist *il1, const t_ilist *il2)
+{
+ int i;
+ char buf[256];
+
+ fprintf(fp, "comparing ilist %s\n", interaction_function[ftype].name);
+ sprintf(buf, "%s->nr", interaction_function[ftype].name);
+ cmp_int(fp, buf, -1, il1->nr, il2->nr);
+ sprintf(buf, "%s->iatoms", interaction_function[ftype].name);
+ if (((il1->nr > 0) && (!il1->iatoms)) ||
+ ((il2->nr > 0) && (!il2->iatoms)) ||
+ ((il1->nr != il2->nr)))
+ {
+ fprintf(fp, "Comparing radically different topologies - %s is different\n",
+ buf);
+ }
+ else
+ {
+ for (i = 0; (i < il1->nr); i++)
+ {
+ cmp_int(fp, buf, i, il1->iatoms[i], il2->iatoms[i]);
+ }
+ }
+}
+
+static void cmp_iparm(FILE *fp, const char *s, t_functype ft,
+ const t_iparams &ip1, const t_iparams &ip2, real ftol, real abstol)
+{
+ int i;
+ gmx_bool bDiff;
+
+ bDiff = FALSE;
+ for (i = 0; i < MAXFORCEPARAM && !bDiff; i++)
+ {
+ bDiff = !equal_real(ip1.generic.buf[i], ip2.generic.buf[i], ftol, abstol);
+ }
+ if (bDiff)
+ {
+ fprintf(fp, "%s1: ", s);
+ pr_iparams(fp, ft, &ip1);
+ fprintf(fp, "%s2: ", s);
+ pr_iparams(fp, ft, &ip2);
+ }
+}
+
+static void cmp_iparm_AB(FILE *fp, const char *s, t_functype ft,
+ const t_iparams &ip1, real ftol, real abstol)
+{
+ int nrfpA, nrfpB, p0, i;
+ gmx_bool bDiff;
+
+ /* Normally the first parameter is perturbable */
+ p0 = 0;
+ nrfpA = interaction_function[ft].nrfpA;
+ nrfpB = interaction_function[ft].nrfpB;
+ if (ft == F_PDIHS)
+ {
+ nrfpB = 2;
+ }
+ else if (interaction_function[ft].flags & IF_TABULATED)
+ {
+ /* For tabulated interactions only the second parameter is perturbable */
+ p0 = 1;
+ nrfpB = 1;
+ }
+ bDiff = FALSE;
+ for (i = 0; i < nrfpB && !bDiff; i++)
+ {
+ bDiff = !equal_real(ip1.generic.buf[p0+i], ip1.generic.buf[nrfpA+i], ftol, abstol);
+ }
+ if (bDiff)
+ {
+ fprintf(fp, "%s: ", s);
+ pr_iparams(fp, ft, &ip1);
+ }
+}
+
+static void cmp_cmap(FILE *fp, const gmx_cmap_t *cmap1, const gmx_cmap_t *cmap2, real ftol, real abstol)
+{
+ cmp_int(fp, "cmap ngrid", -1, cmap1->ngrid, cmap2->ngrid);
+ cmp_int(fp, "cmap grid_spacing", -1, cmap1->grid_spacing, cmap2->grid_spacing);
+ if (cmap1->ngrid == cmap2->ngrid &&
+ cmap1->grid_spacing == cmap2->grid_spacing)
+ {
+ int g;
+
+ for (g = 0; g < cmap1->ngrid; g++)
+ {
+ int i;
+
+ fprintf(fp, "comparing cmap %d\n", g);
+
+ for (i = 0; i < 4*cmap1->grid_spacing*cmap1->grid_spacing; i++)
+ {
+ cmp_real(fp, "", i, cmap1->cmapdata[g].cmap[i], cmap2->cmapdata[g].cmap[i], ftol, abstol);
+ }
+ }
+ }
+}
+
+static void cmp_idef(FILE *fp, const t_idef *id1, const t_idef *id2, real ftol, real abstol)
+{
+ int i;
+ char buf1[64], buf2[64];
+
+ fprintf(fp, "comparing idef\n");
+ if (id2)
+ {
+ cmp_int(fp, "idef->ntypes", -1, id1->ntypes, id2->ntypes);
+ cmp_int(fp, "idef->atnr", -1, id1->atnr, id2->atnr);
+ for (i = 0; (i < std::min(id1->ntypes, id2->ntypes)); i++)
+ {
+ sprintf(buf1, "idef->functype[%d]", i);
+ sprintf(buf2, "idef->iparam[%d]", i);
+ cmp_int(fp, buf1, i, (int)id1->functype[i], (int)id2->functype[i]);
+ cmp_iparm(fp, buf2, id1->functype[i],
+ id1->iparams[i], id2->iparams[i], ftol, abstol);
+ }
+ cmp_real(fp, "fudgeQQ", -1, id1->fudgeQQ, id2->fudgeQQ, ftol, abstol);
+ cmp_cmap(fp, &id1->cmap_grid, &id2->cmap_grid, ftol, abstol);
+ for (i = 0; (i < F_NRE); i++)
+ {
+ cmp_ilist(fp, i, &(id1->il[i]), &(id2->il[i]));
+ }
+ }
+ else
+ {
+ for (i = 0; (i < id1->ntypes); i++)
+ {
+ cmp_iparm_AB(fp, "idef->iparam", id1->functype[i], id1->iparams[i], ftol, abstol);
+ }
+ }
+}
+
+static void cmp_block(FILE *fp, const t_block *b1, const t_block *b2, const char *s)
+{
+ char buf[32];
+
+ fprintf(fp, "comparing block %s\n", s);
+ sprintf(buf, "%s.nr", s);
+ cmp_int(fp, buf, -1, b1->nr, b2->nr);
+}
+
+static void cmp_blocka(FILE *fp, const t_blocka *b1, const t_blocka *b2, const char *s)
+{
+ char buf[32];
+
+ fprintf(fp, "comparing blocka %s\n", s);
+ sprintf(buf, "%s.nr", s);
+ cmp_int(fp, buf, -1, b1->nr, b2->nr);
+ sprintf(buf, "%s.nra", s);
+ cmp_int(fp, buf, -1, b1->nra, b2->nra);
+}
+
+void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol)
+{
+ fprintf(fp, "comparing top\n");
+ if (t2)
+ {
+ cmp_idef(fp, &(t1->idef), &(t2->idef), ftol, abstol);
+ cmp_atoms(fp, &(t1->atoms), &(t2->atoms), ftol, abstol);
+ cmp_block(fp, &t1->cgs, &t2->cgs, "cgs");
+ cmp_block(fp, &t1->mols, &t2->mols, "mols");
+ cmp_bool(fp, "bIntermolecularInteractions", -1, t1->bIntermolecularInteractions, t2->bIntermolecularInteractions);
+ cmp_blocka(fp, &t1->excls, &t2->excls, "excls");
+ }
+ else
+ {
+ cmp_idef(fp, &(t1->idef), nullptr, ftol, abstol);
+ cmp_atoms(fp, &(t1->atoms), nullptr, ftol, abstol);
+ }
+}
+
+void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
+ int natoms0, int natoms1)
+{
+ int i, j;
+ char buf[32];
+
+ fprintf(fp, "comparing groups\n");
+
+ for (i = 0; i < egcNR; i++)
+ {
+ sprintf(buf, "grps[%d].nr", i);
+ cmp_int(fp, buf, -1, g0->grps[i].nr, g1->grps[i].nr);
+ if (g0->grps[i].nr == g1->grps[i].nr)
+ {
+ for (j = 0; j < g0->grps[i].nr; j++)
+ {
+ sprintf(buf, "grps[%d].name[%d]", i, j);
+ cmp_str(fp, buf, -1,
+ *g0->grpname[g0->grps[i].nm_ind[j]],
+ *g1->grpname[g1->grps[i].nm_ind[j]]);
+ }
+ }
+ cmp_int(fp, "ngrpnr", i, g0->ngrpnr[i], g1->ngrpnr[i]);
+ if (g0->ngrpnr[i] == g1->ngrpnr[i] && natoms0 == natoms1 &&
+ (g0->grpnr[i] != nullptr || g1->grpnr[i] != nullptr))
+ {
+ for (j = 0; j < natoms0; j++)
+ {
+ cmp_int(fp, gtypes[i], j, ggrpnr(g0, i, j), ggrpnr(g1, i, j));
+ }
+ }
}
+ /* We have compared the names in the groups lists,
+ * so we can skip the grpname list comparison.
+ */
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/topology/idef.h"
#include "gromacs/topology/symtab.h"
-#ifdef __cplusplus
-extern "C" {
-#endif
-
enum {
egcTC, egcENER, egcACC, egcFREEZE,
egcUser1, egcUser2, egcVCM, egcCompressedX,
t_blocka excls; /* The exclusions */
} gmx_moltype_t;
+/*! \brief Block of molecules of the same type, used in gmx_mtop_t */
typedef struct gmx_molblock_t
{
- int type; /* The molcule type index in mtop.moltype */
- int nmol; /* The number of molecules in this block */
- int natoms_mol; /* The number of atoms in one molecule */
- int nposres_xA; /* The number of posres coords for top A */
- rvec *posres_xA; /* The posres coords for top A */
- int nposres_xB; /* The number of posres coords for top B */
- rvec *posres_xB; /* The posres coords for top B */
+ int type; /**< The molecule type index in mtop.moltype */
+ int nmol; /**< The number of molecules in this block */
+ int nposres_xA; /**< The number of posres coords for top A */
+ rvec *posres_xA; /**< Position restraint coordinates for top A */
+ int nposres_xB; /**< The number of posres coords for top B */
+ rvec *posres_xB; /**< Position restraint coordinates for top B */
+
+ /* Convenience information, derived from other gmx_mtop_t contents */
+ int natoms_mol; /**< The number of atoms in one molecule */
+ int globalAtomStart; /**< Global atom index of the first atom in the block */
+ int globalAtomEnd; /**< Global atom index + 1 of the last atom in the block */
+ int globalResidueStart; /**< Global residue index of the first residue in the block */
+ int residueNumberStart; /**< Residue numbers start from this value if the number of residues per molecule is <= maxres_renum */
} gmx_molblock_t;
typedef struct gmx_groups_t
void init_top(t_topology *top);
void done_moltype(gmx_moltype_t *molt);
void done_molblock(gmx_molblock_t *molb);
-void done_mtop(gmx_mtop_t *mtop, gmx_bool bDoneSymtab);
+void done_gmx_groups_t(gmx_groups_t *g);
+void done_mtop(gmx_mtop_t *mtop);
void done_top(t_topology *top);
+// Frees both t_topology and gmx_mtop_t when the former has been created from
+// the latter.
+void done_top_mtop(t_topology *top, gmx_mtop_t *mtop);
-t_atoms *mtop2atoms(gmx_mtop_t *mtop);
-/* generate a t_atoms struct for the system from gmx_mtop_t */
+bool gmx_mtop_has_masses(const gmx_mtop_t *mtop);
+bool gmx_mtop_has_charges(const gmx_mtop_t *mtop);
+bool gmx_mtop_has_atomtypes(const gmx_mtop_t *mtop);
+bool gmx_mtop_has_pdbinfo(const gmx_mtop_t *mtop);
void pr_mtop(FILE *fp, int indent, const char *title, const gmx_mtop_t *mtop,
- gmx_bool bShowNumbers);
-void pr_top(FILE *fp, int indent, const char *title, const t_topology *top, gmx_bool bShowNumbers);
+ gmx_bool bShowNumbers, gmx_bool bShowParameters);
+void pr_top(FILE *fp, int indent, const char *title, const t_topology *top,
+ gmx_bool bShowNumbers, gmx_bool bShowParameters);
-#ifdef __cplusplus
-}
-#endif
+void cmp_top(FILE *fp, const t_topology *t1, const t_topology *t2, real ftol, real abstol);
+void cmp_groups(FILE *fp, const gmx_groups_t *g0, const gmx_groups_t *g1,
+ int natoms0, int natoms1);
#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2008, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
t_iatom *iabuf;
int iabuf_nalloc;
- if (qB == NULL)
+ if (qB == nullptr)
{
qB = qA;
}
iabuf_nalloc = 0;
- iabuf = NULL;
+ iabuf = nullptr;
iparams = idef->iparams;
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2015, by the GROMACS development team, led by
+# Copyright (c) 2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+gmx_add_libgromacs_sources(
+ trajectoryframe.cpp
+ )
+
gmx_install_headers(
energy.h
trajectoryframe.h
)
-
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "trajectoryframe.h"
+
+#include <cstdio>
+
+#include <algorithm>
+
+#include "gromacs/math/veccompare.h"
+#include "gromacs/topology/atoms.h"
+#include "gromacs/utility/compare.h"
+#include "gromacs/utility/smalloc.h"
+
+void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
+ gmx_bool bRMSD, real ftol, real abstol)
+{
+ fprintf(fp, "\n");
+ cmp_int(fp, "not_ok", -1, fr1->not_ok, fr2->not_ok);
+ cmp_int(fp, "natoms", -1, fr1->natoms, fr2->natoms);
+ if (cmp_bool(fp, "bStep", -1, fr1->bStep, fr2->bStep))
+ {
+ cmp_int(fp, "step", -1, fr1->step, fr2->step);
+ }
+ cmp_int(fp, "step", -1, fr1->step, fr2->step);
+ if (cmp_bool(fp, "bTime", -1, fr1->bTime, fr2->bTime))
+ {
+ cmp_real(fp, "time", -1, fr1->time, fr2->time, ftol, abstol);
+ }
+ if (cmp_bool(fp, "bLambda", -1, fr1->bLambda, fr2->bLambda))
+ {
+ cmp_real(fp, "lambda", -1, fr1->lambda, fr2->lambda, ftol, abstol);
+ }
+ if (cmp_bool(fp, "bAtoms", -1, fr1->bAtoms, fr2->bAtoms))
+ {
+ cmp_atoms(fp, fr1->atoms, fr2->atoms, ftol, abstol);
+ }
+ if (cmp_bool(fp, "bPrec", -1, fr1->bPrec, fr2->bPrec))
+ {
+ cmp_real(fp, "prec", -1, fr1->prec, fr2->prec, ftol, abstol);
+ }
+ if (cmp_bool(fp, "bX", -1, fr1->bX, fr2->bX))
+ {
+ cmp_rvecs(fp, "x", std::min(fr1->natoms, fr2->natoms), fr1->x, fr2->x, bRMSD, ftol, abstol);
+ }
+ if (cmp_bool(fp, "bV", -1, fr1->bV, fr2->bV))
+ {
+ cmp_rvecs(fp, "v", std::min(fr1->natoms, fr2->natoms), fr1->v, fr2->v, bRMSD, ftol, abstol);
+ }
+ if (cmp_bool(fp, "bF", -1, fr1->bF, fr2->bF))
+ {
+ cmp_rvecs(fp, "f", std::min(fr1->natoms, fr2->natoms), fr1->f, fr2->f, bRMSD, ftol, abstol);
+ }
+ if (cmp_bool(fp, "bBox", -1, fr1->bBox, fr2->bBox))
+ {
+ cmp_rvecs(fp, "box", 3, fr1->box, fr2->box, FALSE, ftol, abstol);
+ }
+}
+
+void done_frame(t_trxframe *frame)
+{
+ if (frame->atoms)
+ {
+ done_atom(frame->atoms);
+ sfree(frame->atoms);
+ }
+ sfree(frame->x);
+ sfree(frame->v);
+ sfree(frame->f);
+}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* Do not try to use a pointer when its gmx_bool is FALSE, as memory might
* not be allocated.
*/
-
#ifndef GMX_TRAJECTORY_TRX_H
#define GMX_TRAJECTORY_TRX_H
+#include <cstdio>
+
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
int not_ok; /* integrity flags */
gmx_bool bDouble; /* Double precision? */
int natoms; /* number of atoms (atoms, x, v, f, index) */
- gmx_bool bTitle;
- const char *title; /* title of the frame */
gmx_bool bStep;
gmx_int64_t step; /* MD step number */
gmx_bool bTime;
int *index; /* atom indices of contained coordinates */
} t_trxframe;
+void comp_frame(FILE *fp, t_trxframe *fr1, t_trxframe *fr2,
+ gmx_bool bRMSD, real ftol, real abstol);
+
+void done_frame(t_trxframe *frame);
+
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void TrajectoryAnalysisModule::registerBasicDataset(AbstractAnalysisData *data,
const char *name)
{
- GMX_RELEASE_ASSERT(data != NULL, "Attempting to register NULL data");
+ GMX_RELEASE_ASSERT(data != nullptr, "Attempting to register NULL data");
// TODO: Strong exception safety should be possible to implement.
GMX_RELEASE_ASSERT(impl_->datasets_.find(name) == impl_->datasets_.end(),
"Duplicate data set name registered");
impl_->datasets_[name] = data;
- impl_->datasetNames_.push_back(name);
+ impl_->datasetNames_.emplace_back(name);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/vec.h"
+#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
*/
TopologyInformation::TopologyInformation()
- : top_(NULL), bTop_(false), xtop_(NULL), ePBC_(-1)
+ : mtop_(nullptr), top_(nullptr), bTop_(false), xtop_(nullptr), ePBC_(-1)
{
clear_mat(boxtop_);
}
TopologyInformation::~TopologyInformation()
{
- if (top_)
+ done_top_mtop(top_, mtop_);
+ sfree(mtop_);
+ sfree(top_);
+ sfree(xtop_);
+}
+
+
+t_topology *TopologyInformation::topology() const
+{
+ if (top_ == nullptr && mtop_ != nullptr)
{
- done_top(top_);
- sfree(top_);
+ snew(top_, 1);
+ *top_ = gmx_mtop_t_to_t_topology(mtop_, false);
}
- sfree(xtop_);
+ return top_;
}
{
if (!xtop_)
{
- *x = NULL;
+ *x = nullptr;
GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
}
*x = xtop_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/timeunitmanager.h"
#include "gromacs/utility/classhelpers.h"
+struct gmx_mtop_t;
struct t_topology;
namespace gmx
{
public:
//! Returns true if a topology file was loaded.
- bool hasTopology() const { return top_ != NULL; }
+ bool hasTopology() const { return mtop_ != nullptr; }
//! Returns true if a full topology file was loaded.
bool hasFullTopology() const { return bTop_; }
//! Returns the loaded topology, or NULL if not loaded.
- t_topology *topology() const { return top_; }
+ const gmx_mtop_t *mtop() const { return mtop_; }
+ //! Returns the loaded topology, or NULL if not loaded.
+ t_topology *topology() const;
//! Returns the ePBC field from the topology.
int ePBC() const { return ePBC_; }
/*! \brief
TopologyInformation();
~TopologyInformation();
+ gmx_mtop_t *mtop_;
//! The topology structure, or NULL if no topology loaded.
- t_topology *top_;
+ // TODO: Replace fully with mtop.
+ mutable t_topology *top_;
//! true if full tpx file was loaded, false otherwise.
bool bTop_;
//! Coordinates from the topology (can be NULL).
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
module_->initAfterFirstFrame(settings_, common_.frame());
t_pbc pbc;
- t_pbc *ppbc = settings_.hasPBC() ? &pbc : NULL;
+ t_pbc *ppbc = settings_.hasPBC() ? &pbc : nullptr;
int nframes = 0;
AnalysisDataParallelOptions dataOptions;
{
common_.initFrame();
t_trxframe &frame = common_.frame();
- if (ppbc != NULL)
+ if (ppbc != nullptr)
{
set_pbc(ppbc, topology.ePBC(), frame.box);
}
}
while (common_.readNextFrame());
module_->finishFrames(pdata.get());
- if (pdata.get() != NULL)
+ if (pdata.get() != nullptr)
{
pdata->finish();
}
{
return createModule(factory());
};
- return ICommandLineOptionsModule::runAsMain(argc, argv, NULL, NULL, runnerFactory);
+ return ICommandLineOptionsModule::runAsMain(argc, argv, nullptr, nullptr, runnerFactory);
}
// static
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "modules/rdf.h"
#include "modules/sasa.h"
#include "modules/select.h"
+#include "modules/trajectory.h"
namespace gmx
{
registerModule<RdfInfo>(manager, group);
registerModule<SasaInfo>(manager, group);
registerModule<SelectInfo>(manager, group);
+ registerModule<TrajectoryInfo>(manager, group);
}
//! \endcond
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
Angle::Angle()
- : sel1info_(NULL), sel2info_(NULL),
+ : sel1info_(nullptr), sel2info_(nullptr),
g1type_(Group1Type_Angle), g2type_(Group2Type_None),
binWidth_(1.0), natoms1_(0), natoms2_(0)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const SelectionPosition &p1 = sel[g].position(i);
const SelectionPosition &p2 = sel[g].position(i+1);
rvec dx;
- if (pbc != NULL)
+ if (pbc != nullptr)
{
pbc_dx(pbc, p2.x(), p1.x(), dx);
}
real dist = norm(dx);
bool bPresent = p1.selected() && p2.selected();
distHandle.setPoint(n, dist, bPresent);
- xyzHandle.setPoints(n*3, 3, dx);
+ xyzHandle.setPoints(n*3, 3, dx, bPresent);
}
}
distHandle.finishFrame();
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const Selection &sel = pdata->parallelSelection(sel_);
gmx::UniformRealDistribution<real> dist;
- GMX_RELEASE_ASSERT(NULL != pbc, "You have no periodic boundary conditions");
+ GMX_RELEASE_ASSERT(nullptr != pbc, "You have no periodic boundary conditions");
// Analysis framework magic
dh.startFrame(frnr, fr.time);
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
//! Helper function to initialize the grouping for a selection.
-int initSelectionGroups(Selection *sel, t_topology *top, int type)
+int initSelectionGroups(Selection *sel, const gmx_mtop_t *top, int type)
{
e_index_t indexType = INDEX_UNKNOWN;
switch (type)
PairDistance::initAnalysis(const TrajectoryAnalysisSettings &settings,
const TopologyInformation &top)
{
- refGroupCount_ = initSelectionGroups(&refSel_, top.topology(), refGroupType_);
+ refGroupCount_ = initSelectionGroups(&refSel_, top.mtop(), refGroupType_);
maxGroupCount_ = 0;
distances_.setDataSetCount(sel_.size());
for (size_t i = 0; i < sel_.size(); ++i)
{
const int selGroupCount
- = initSelectionGroups(&sel_[i], top.topology(), selGroupType_);
+ = initSelectionGroups(&sel_[i], top.mtop(), selGroupType_);
const int columnCount = refGroupCount_ * selGroupCount;
maxGroupCount_ = std::max(maxGroupCount_, columnCount);
distances_.setColumnCount(i, columnCount);
GMX_THROW(InconsistentInputError("-surf only works with -ref that consists of atoms"));
}
const e_index_t type = (surface_ == SurfaceType_Molecule ? INDEX_MOL : INDEX_RES);
- surfaceGroupCount_ = refSel_.initOriginalIdsToGroup(top.topology(), type);
+ surfaceGroupCount_ = refSel_.initOriginalIdsToGroup(top.mtop(), type);
}
if (bExclusions_)
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2006, The GROMACS development team.
- * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/pleasecite.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/unique_cptr.h"
#include "surfacearea.h"
srenew(atoms->resinfo, r0+1);
atoms->atom[i0].resind = r0;
t_atoms_set_resinfo(atoms, i0, symtab, resnm, r0+1, ' ', 0, ' ');
- if (atoms->pdbinfo != NULL)
+ if (atoms->pdbinfo != nullptr)
{
srenew(atoms->pdbinfo, atoms->nr+ndots);
}
xnew[ii0][XX] = dots[k++];
xnew[ii0][YY] = dots[k++];
xnew[ii0][ZZ] = dots[k++];
- if (atoms->pdbinfo != NULL)
+ if (atoms->pdbinfo != nullptr)
{
atoms->pdbinfo[ii0].type = epdbATOM;
atoms->pdbinfo[ii0].atomnr = ii0;
}
atoms->nr = i0+ndots;
atoms->nres = r0+1;
- write_sto_conf(fn, title, atoms, xnew, NULL, ePBC, const_cast<rvec *>(box));
+ write_sto_conf(fn, title, atoms, xnew, nullptr, ePBC, const_cast<rvec *>(box));
atoms->nres = r0;
atoms->nr = i0;
}
aaa.pdbinfo[ii0].occup = 0.0;
}
aaa.nr = ndots;
- write_sto_conf(fn, title, &aaa, xnew, NULL, ePBC, const_cast<rvec *>(box));
+ write_sto_conf(fn, title, &aaa, xnew, nullptr, ePBC, const_cast<rvec *>(box));
do_conect(fn, ndots, xnew);
done_atom(&aaa);
}
};
Sasa::Sasa()
- : solsize_(0.14), ndots_(24), dgsDefault_(0), bIncludeSolute_(true), top_(NULL)
+ : solsize_(0.14), ndots_(24), dgsDefault_(0), bIncludeSolute_(true), top_(nullptr)
{
//minarea_ = 0.5;
registerAnalysisDataset(&area_, "area");
dgsFactor_.reserve(surfaceSel_.posCount());
}
- const int resCount = surfaceSel_.initOriginalIdsToGroup(top_, INDEX_RES);
+ const int resCount = surfaceSel_.initOriginalIdsToGroup(top.mtop(), INDEX_RES);
// TODO: Not exception-safe, but nice solution would be to have a C++
// atom properties class...
// surfacedots contains nsurfacedots entries, and contains the actual
// points.
real totarea, totvolume;
- real *area = NULL, *surfacedots = NULL;
+ real *area = nullptr, *surfacedots = nullptr;
int nsurfacedots;
calculator_.calculate(surfaceSel.coordinates().data(), pbc,
frameData.index_.size(), frameData.index_.data(), flag,
&surfacedots, &nsurfacedots);
// Unpack the atomwise areas into the frameData.atomAreas_ array for easier
// indexing in the case of dynamic surfaceSel.
- if (area != NULL)
+ if (area != nullptr)
{
if (surfaceSel.isDynamic())
{
}
sfree(area);
}
- scoped_guard_sfree dotsGuard(surfacedots);
+ const sfree_guard dotsGuard(surfacedots);
if (bConnolly)
{
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2009,2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/unique_cptr.h"
namespace gmx
{
*/
IndexFileWriterModule::IndexFileWriterModule()
- : fp_(NULL), currentGroup_(-1), currentSize_(0), bAnyWritten_(false)
+ : fp_(nullptr), currentGroup_(-1), currentSize_(0), bAnyWritten_(false)
{
}
void IndexFileWriterModule::closeFile()
{
- if (fp_ != NULL)
+ if (fp_ != nullptr)
{
gmx_fio_fclose(fp_);
- fp_ = NULL;
+ fp_ = nullptr;
}
}
{
std::string newName(name);
std::replace(newName.begin(), newName.end(), ' ', '_');
- groups_.push_back(GroupInfo(newName, bDynamic));
+ groups_.emplace_back(newName, bDynamic);
}
void
IndexFileWriterModule::pointsAdded(const AnalysisDataPointSetRef &points)
{
- if (fp_ == NULL)
+ if (fp_ == nullptr)
{
return;
}
void IndexFileWriterModule::dataFinished()
{
- if (fp_ != NULL)
+ if (fp_ != nullptr)
{
std::fprintf(fp_, "\n");
}
private:
SelectionList sel_;
- SelectionOptionInfo *selOpt_;
std::string fnSize_;
std::string fnFrac_;
};
Select::Select()
- : selOpt_(NULL), bTotNorm_(false), bFracNorm_(false), bResInd_(false),
+ : bTotNorm_(false), bFracNorm_(false), bResInd_(false),
bCumulativeLifetimes_(true), resNumberType_(ResidueNumbering_ByNumber),
- pdbAtoms_(PdbAtomsSelection_All), top_(NULL),
+ pdbAtoms_(PdbAtomsSelection_All), top_(nullptr),
occupancyModule_(new AnalysisDataAverageModule()),
lifetimeModule_(new AnalysisDataLifetimeModule())
{
"be combined with output from other programs and/or external",
"analysis programs to calculate more complex things.",
"For detailed help on the selection syntax, please use",
- "[TT]gmx help selections[tt].[PAR]",
+ "[TT]gmx help selections[tt].",
+ "",
"Any combination of the output options is possible, but note",
"that [TT]-om[tt] only operates on the first selection.",
"Also note that if you provide no output options, no output is",
- "produced.[PAR]",
+ "produced.",
+ "",
"With [TT]-os[tt], calculates the number of positions in each",
"selection for each frame. With [TT]-norm[tt], the output is",
"between 0 and 1 and describes the fraction from the maximum",
"RA residues). With [TT]-cfnorm[tt], the output is divided",
"by the fraction covered by the selection.",
"[TT]-norm[tt] and [TT]-cfnorm[tt] can be specified independently",
- "of one another.[PAR]",
+ "of one another.",
+ "",
"With [TT]-oc[tt], the fraction covered by each selection is",
- "written out as a function of time.[PAR]",
+ "written out as a function of time.",
+ "",
"With [TT]-oi[tt], the selected atoms/residues/molecules are",
"written out as a function of time. In the output, the first",
"column contains the frame time, the second contains the number",
"of positions, followed by the atom/residue/molecule numbers.",
"If more than one selection is specified, the size of the second",
"group immediately follows the last number of the first group",
- "and so on.[PAR]",
+ "and so on.",
+ "",
"With [TT]-on[tt], the selected atoms are written as a index file",
"compatible with [TT]make_ndx[tt] and the analyzing tools. Each selection",
"is written as a selection group and for dynamic selections a",
- "group is written for each frame.[PAR]",
+ "group is written for each frame.",
+ "",
"For residue numbers, the output of [TT]-oi[tt] can be controlled",
"with [TT]-resnr[tt]: [TT]number[tt] (default) prints the residue",
"numbers as they appear in the input file, while [TT]index[tt] prints",
"unique numbers assigned to the residues in the order they appear",
"in the input file, starting with 1. The former is more intuitive,",
"but if the input contains multiple residues with the same number,",
- "the output can be less useful.[PAR]",
+ "the output can be less useful.",
+ "",
"With [TT]-om[tt], a mask is printed for the first selection",
"as a function of time. Each line in the output corresponds to",
"one frame, and contains either 0/1 for each atom/residue/molecule",
"possibly selected. 1 stands for the atom/residue/molecule being",
- "selected for the current frame, 0 for not selected.[PAR]",
+ "selected for the current frame, 0 for not selected.",
+ "",
"With [TT]-of[tt], the occupancy fraction of each position (i.e.,",
"the fraction of frames where the position is selected) is",
- "printed.[PAR]",
+ "printed.",
+ "",
"With [TT]-ofpdb[tt], a PDB file is written out where the occupancy",
"column is filled with the occupancy fraction of each atom in the",
"selection. The coordinates in the PDB file will be those from the",
"appear in the output PDB file: with [TT]all[tt] all atoms are",
"present, with [TT]maxsel[tt] all atoms possibly selected by the",
"selection are present, and with [TT]selected[tt] only atoms that are",
- "selected at least in one frame are present.[PAR]",
+ "selected at least in one frame are present.",
+ "",
"With [TT]-olt[tt], a histogram is produced that shows the number of",
"selected positions as a function of the time the position was",
"continuously selected. [TT]-cumlt[tt] can be used to control whether",
"subintervals of longer intervals are included in the histogram.[PAR]",
"[TT]-om[tt], [TT]-of[tt], and [TT]-olt[tt] only make sense with",
- "dynamic selections."
+ "dynamic selections.",
+ "",
+ "To plot coordinates for selections, use [gmx-trajectory]."
};
settings->setHelpText(desc);
.store(&fnLifetime_).defaultBasename("lifetime")
.description("Lifetime histogram"));
- selOpt_ = options->addOption(SelectionOption("select").storeVector(&sel_)
- .required().multiValue()
- .description("Selections to analyze"));
+ options->addOption(SelectionOption("select").storeVector(&sel_)
+ .required().multiValue()
+ .description("Selections to analyze"));
options->addOption(BooleanOption("norm").store(&bTotNorm_)
.description("Normalize by total number of positions with -os"));
atoms = top_->topology()->atoms;
t_pdbinfo *pdbinfo;
snew(pdbinfo, atoms.nr);
- scoped_guard_sfree pdbinfoGuard(pdbinfo);
- if (atoms.pdbinfo != NULL)
+ const sfree_guard pdbinfoGuard(pdbinfo);
+ if (atoms.havePdbInfo)
{
std::memcpy(pdbinfo, atoms.pdbinfo, atoms.nr*sizeof(*pdbinfo));
}
+ else
+ {
+ atoms.havePdbInfo = TRUE;
+ }
atoms.pdbinfo = pdbinfo;
for (int i = 0; i < atoms.nr; ++i)
{
case PdbAtomsSelection_All:
{
t_trxstatus *status = open_trx(fnPDB_.c_str(), "w");
- write_trxframe(status, &fr, NULL);
+ write_trxframe(status, &fr, nullptr);
close_trx(status);
break;
}
atomIndicesSet.end());
t_trxstatus *status = open_trx(fnPDB_.c_str(), "w");
write_trxframe_indexed(status, &fr, allAtomIndices.size(),
- allAtomIndices.data(), NULL);
+ allAtomIndices.data(), nullptr);
close_trx(status);
break;
}
}
}
t_trxstatus *status = open_trx(fnPDB_.c_str(), "w");
- write_trxframe_indexed(status, &fr, indices.size(), indices.data(), NULL);
+ write_trxframe_indexed(status, &fr, indices.size(), indices.data(), nullptr);
close_trx(status);
break;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2007, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return;
}
real area = 0.0, vol = 0.0;
- real *dots = NULL, *atom_area = NULL;
+ real *dots = nullptr, *atom_area = nullptr;
int lfnr = 0, maxdots = 0;
if (mode & FLAG_VOLUME)
{
{
flags |= impl_->flags_;
*area = 0;
- if (volume == NULL)
+ if (volume == nullptr)
{
flags &= ~FLAG_VOLUME;
}
{
*volume = 0;
}
- if (at_area == NULL)
+ if (at_area == nullptr)
{
flags &= ~FLAG_ATOM_AREA;
}
else
{
- *at_area = NULL;
+ *at_area = nullptr;
}
- if (lidots == NULL)
+ if (lidots == nullptr)
{
flags &= ~FLAG_DOTS;
}
else
{
- *lidots = NULL;
+ *lidots = nullptr;
}
- if (n_dots == NULL)
+ if (n_dots == nullptr)
{
flags &= ~FLAG_DOTS;
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::analysismodules::Trajectory.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "trajectory.h"
+
+#include <algorithm>
+
+#include "gromacs/analysisdata/analysisdata.h"
+#include "gromacs/analysisdata/modules/plot.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/filenameoption.h"
+#include "gromacs/options/ioptionscontainer.h"
+#include "gromacs/selection/selection.h"
+#include "gromacs/selection/selectionoption.h"
+#include "gromacs/trajectory/trajectoryframe.h"
+#include "gromacs/trajectoryanalysis/analysissettings.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+namespace
+{
+
+/********************************************************************
+ * Trajectory
+ */
+
+class Trajectory : public TrajectoryAnalysisModule
+{
+ public:
+ Trajectory();
+
+ virtual void initOptions(IOptionsContainer *options,
+ TrajectoryAnalysisSettings *settings);
+ virtual void optionsFinished(TrajectoryAnalysisSettings *settings);
+ virtual void initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation &top);
+
+ virtual void analyzeFrame(int frnr, const t_trxframe &fr, t_pbc *pbc,
+ TrajectoryAnalysisModuleData *pdata);
+
+ virtual void finishAnalysis(int nframes);
+ virtual void writeOutput();
+
+ private:
+ SelectionList sel_;
+
+ std::string fnX_;
+ std::string fnV_;
+ std::string fnF_;
+ bool dimMask_[4];
+ bool maskSet_[4];
+
+ AnalysisData xdata_;
+ AnalysisData vdata_;
+ AnalysisData fdata_;
+};
+
+Trajectory::Trajectory()
+{
+ std::fill(std::begin(dimMask_), std::end(dimMask_), true);
+ dimMask_[DIM] = false;
+ std::fill(std::begin(maskSet_), std::end(maskSet_), false);
+ registerAnalysisDataset(&xdata_, "x");
+ registerAnalysisDataset(&vdata_, "v");
+ registerAnalysisDataset(&fdata_, "f");
+}
+
+
+void
+Trajectory::initOptions(IOptionsContainer *options, TrajectoryAnalysisSettings *settings)
+{
+ static const char *const desc[] = {
+ "[THISMODULE] plots coordinates, velocities, and/or forces for",
+ "provided selections. By default, the X, Y, and Z components for",
+ "the requested vectors are plotted, but specifying one or more of",
+ "[TT]-len[tt], [TT]-x[tt], [TT]-y[tt], and [TT]-z[tt] overrides this.",
+ "",
+ "For dynamic selections, currently the values are written out for",
+ "all positions that the selection could select."
+ };
+
+ settings->setHelpText(desc);
+
+ options->addOption(FileNameOption("ox").filetype(eftPlot).outputFile()
+ .store(&fnX_).defaultBasename("coord")
+ .description("Coordinates for each position as a function of time"));
+ options->addOption(FileNameOption("ov").filetype(eftPlot).outputFile()
+ .store(&fnV_).defaultBasename("veloc")
+ .description("Velocities for each position as a function of time"));
+ options->addOption(FileNameOption("of").filetype(eftPlot).outputFile()
+ .store(&fnF_).defaultBasename("force")
+ .description("Forces for each position as a function of time"));
+
+ options->addOption(SelectionOption("select").storeVector(&sel_)
+ .required().dynamicMask().multiValue()
+ .description("Selections to analyze"));
+
+ options->addOption(BooleanOption("x").store(&dimMask_[XX])
+ .storeIsSet(&maskSet_[XX])
+ .description("Plot X component"));
+ options->addOption(BooleanOption("y").store(&dimMask_[YY])
+ .storeIsSet(&maskSet_[YY])
+ .description("Plot Y component"));
+ options->addOption(BooleanOption("z").store(&dimMask_[ZZ])
+ .storeIsSet(&maskSet_[ZZ])
+ .description("Plot Z component"));
+ options->addOption(BooleanOption("len").store(&dimMask_[DIM])
+ .storeIsSet(&maskSet_[DIM])
+ .description("Plot vector length"));
+}
+
+
+void
+Trajectory::optionsFinished(TrajectoryAnalysisSettings *settings)
+{
+ int frameFlags = TRX_NEED_X;
+ if (!fnV_.empty())
+ {
+ frameFlags |= TRX_READ_V;
+ }
+ if (!fnF_.empty())
+ {
+ frameFlags |= TRX_READ_F;
+ }
+ settings->setFrameFlags(frameFlags);
+ if (std::count(std::begin(maskSet_), std::end(maskSet_), true) > 0)
+ {
+ for (int i = 0; i <= DIM; ++i)
+ {
+ if (!maskSet_[i])
+ {
+ dimMask_[i] = false;
+ }
+ }
+ }
+}
+
+
+void
+Trajectory::initAnalysis(const TrajectoryAnalysisSettings &settings,
+ const TopologyInformation & /*top*/)
+{
+ if (!fnX_.empty())
+ {
+ xdata_.setDataSetCount(sel_.size());
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ xdata_.setColumnCount(g, 3*sel_[g].posCount());
+ }
+ AnalysisDataVectorPlotModulePointer plot(
+ new AnalysisDataVectorPlotModule(settings.plotSettings()));
+ plot->setWriteMask(dimMask_);
+ plot->setFileName(fnX_);
+ plot->setTitle("Coordinates");
+ plot->setXAxisIsTime();
+ plot->setYLabel("Value [nm]");
+ xdata_.addModule(plot);
+ }
+ if (!fnV_.empty())
+ {
+ vdata_.setDataSetCount(sel_.size());
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ sel_[g].setEvaluateVelocities(true);
+ vdata_.setColumnCount(g, 3*sel_[g].posCount());
+ }
+ AnalysisDataVectorPlotModulePointer plot(
+ new AnalysisDataVectorPlotModule(settings.plotSettings()));
+ plot->setWriteMask(dimMask_);
+ plot->setFileName(fnV_);
+ plot->setTitle("Velocities");
+ plot->setXAxisIsTime();
+ plot->setYLabel("Value [nm/ps]");
+ vdata_.addModule(plot);
+ }
+ if (!fnF_.empty())
+ {
+ fdata_.setDataSetCount(sel_.size());
+ for (size_t g = 0; g < sel_.size(); ++g)
+ {
+ sel_[g].setEvaluateForces(true);
+ fdata_.setColumnCount(g, 3*sel_[g].posCount());
+ }
+ AnalysisDataVectorPlotModulePointer plot(
+ new AnalysisDataVectorPlotModule(settings.plotSettings()));
+ plot->setWriteMask(dimMask_);
+ plot->setFileName(fnF_);
+ plot->setTitle("Forces");
+ plot->setXAxisIsTime();
+ plot->setYLabel("Value [kJ mol\\S-1\\N nm\\S-1\\N]");
+ fdata_.addModule(plot);
+ }
+}
+
+
+void
+Trajectory::analyzeFrame(int frnr, const t_trxframe &fr, t_pbc * /* pbc */,
+ TrajectoryAnalysisModuleData *pdata)
+{
+ const SelectionList &sel = pdata->parallelSelections(sel_);
+
+ // There is some duplication here, but cppcheck cannot handle function
+ // types that return rvec references, and MSVC also apparently segfaults
+ // when using std::function with a member function here...
+ {
+ AnalysisDataHandle dh = pdata->dataHandle(xdata_);
+ if (dh.isValid())
+ {
+ dh.startFrame(frnr, fr.time);
+ for (size_t g = 0; g < sel.size(); ++g)
+ {
+ dh.selectDataSet(g);
+ for (int i = 0; i < sel[g].posCount(); ++i)
+ {
+ const SelectionPosition &pos = sel[g].position(i);
+ dh.setPoints(i*3, 3, pos.x(), pos.selected());
+ }
+ }
+ dh.finishFrame();
+ }
+ }
+ if (fr.bV)
+ {
+ AnalysisDataHandle dh = pdata->dataHandle(xdata_);
+ if (dh.isValid())
+ {
+ dh.startFrame(frnr, fr.time);
+ for (size_t g = 0; g < sel.size(); ++g)
+ {
+ dh.selectDataSet(g);
+ for (int i = 0; i < sel[g].posCount(); ++i)
+ {
+ const SelectionPosition &pos = sel[g].position(i);
+ dh.setPoints(i*3, 3, pos.v(), pos.selected());
+ }
+ }
+ dh.finishFrame();
+ }
+ }
+ if (fr.bF)
+ {
+ AnalysisDataHandle dh = pdata->dataHandle(xdata_);
+ if (dh.isValid())
+ {
+ dh.startFrame(frnr, fr.time);
+ for (size_t g = 0; g < sel.size(); ++g)
+ {
+ dh.selectDataSet(g);
+ for (int i = 0; i < sel[g].posCount(); ++i)
+ {
+ const SelectionPosition &pos = sel[g].position(i);
+ dh.setPoints(i*3, 3, pos.f(), pos.selected());
+ }
+ }
+ dh.finishFrame();
+ }
+ }
+}
+
+
+void
+Trajectory::finishAnalysis(int /*nframes*/)
+{
+}
+
+
+void
+Trajectory::writeOutput()
+{
+}
+
+} // namespace
+
+const char TrajectoryInfo::name[] = "trajectory";
+const char TrajectoryInfo::shortDescription[] =
+ "Print coordinates, velocities, and/or forces for selections";
+
+TrajectoryAnalysisModulePointer TrajectoryInfo::create()
+{
+ return TrajectoryAnalysisModulePointer(new Trajectory);
+}
+
+} // namespace analysismodules
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Declares trajectory analysis module for basic trajectory information.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_MODULES_TRAJECTORY_H
+#define GMX_TRAJECTORYANALYSIS_MODULES_TRAJECTORY_H
+
+#include "gromacs/trajectoryanalysis/analysismodule.h"
+
+namespace gmx
+{
+
+namespace analysismodules
+{
+
+class TrajectoryInfo
+{
+ public:
+ static const char name[];
+ static const char shortDescription[];
+ static TrajectoryAnalysisModulePointer create();
+};
+
+} // namespace analysismodules
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Implements gmx::UnionFinder and gmx::MappedUnionFinder.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#ifndef GMX_TRAJECTORYANALYSIS_UNIONFIND_H
+#define GMX_TRAJECTORYANALYSIS_UNIONFIND_H
+
+#include <algorithm>
+#include <numeric>
+#include <vector>
+
+#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+/*! \libinternal \brief
+ * Union-find data structure for keeping track of disjoint sets.
+ *
+ * Union-find keeps track of a number of items, represented here by continuous
+ * integer indices starting at zero, and supports the following operations:
+ * - Initialization puts each item into a set of its own.
+ * - Given two items, merge the sets that contain these items.
+ * - Given an item, find a representative item that is in the same set, such
+ * that queries for items in the same set yield the same value.
+ * Merging and querying is supported in amortized constant time.
+ *
+ * Note that in order to achieve the amortized behavior, querying the structure
+ * modifies the internal state, but does not alter the externally visible
+ * behavior.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+class UnionFinder
+{
+ public:
+ /*! \brief
+ * Initializes `count` items, putting each in its own set.
+ */
+ void init(int count)
+ {
+ parent_.clear();
+ rank_.clear();
+ parent_.reserve(count);
+ rank_.reserve(count);
+ parent_.resize(count);
+ rank_.resize(count, 0);
+ std::iota(parent_.begin(), parent_.end(), 0);
+ }
+ /*! \brief
+ * Merges sets that contain two given items.
+ *
+ * If the items are already in the same set, nothing happens.
+ */
+ void merge(int item1, int item2)
+ {
+ GMX_ASSERT(item1 >= 0 && item1 < count(), "Input index out of range");
+ GMX_ASSERT(item2 >= 0 && item2 < count(), "Input index out of range");
+ const int root1 = findRootAndCompressPath(item1);
+ const int root2 = findRootAndCompressPath(item2);
+ if (root1 != root2)
+ {
+ mergeRoots(root1, root2);
+ }
+ }
+ /*! \brief
+ * Returns a representative item from the set containing `item`.
+ */
+ int representativeItem(int item)
+ {
+ GMX_ASSERT(item >= 0 && item < count(), "Input index out of range");
+ return findRootAndCompressPath(item);
+ }
+ /*! \brief
+ * Returns the sizes of all sets (in arbitrary order).
+ */
+ std::vector<int> allSizes()
+ {
+ const int count = parent_.size();
+ std::vector<int> result(count, 0);
+ for (int i = 0; i < count; ++i)
+ {
+ ++result[findRootAndCompressPath(i)];
+ }
+ result.erase(std::remove(result.begin(), result.end(), 0),
+ result.end());
+ return result;
+ }
+
+ private:
+ //! Number of items.
+ int count() const { return parent_.size(); }
+ int findRootAndCompressPath(int i)
+ {
+ while (parent_[i] != i)
+ {
+ const int prev = i;
+ i = parent_[i];
+ parent_[prev] = parent_[i];
+ }
+ return i;
+ }
+ void mergeRoots(int root1, int root2)
+ {
+ if (rank_[root1] > rank_[root2])
+ {
+ parent_[root2] = root1;
+ }
+ else if (rank_[root2] > rank_[root1])
+ {
+ parent_[root1] = root2;
+ }
+ else
+ {
+ parent_[root1] = root2;
+ ++rank_[root1];
+ }
+ }
+
+ /*! \brief
+ * Parent item for each item in the tree representing the set.
+ *
+ * Root items are parents of themselves, and are the reprensentative
+ * items of their sets.
+ */
+ std::vector<int> parent_;
+ //! Worst-case height for each root (as if no compression was done).
+ std::vector<int> rank_;
+};
+
+/*! \libinternal \brief
+ * Extension of UnionFind that supports non-consecutive integer indices as
+ * items.
+ *
+ * Sometimes, it is more convenient to operate on a set of integers that do not
+ * start at zero and are not consecutive as UnionFind expects. This class
+ * implements a mapping on top of UnionFind such that this is possible.
+ *
+ * The current implementation assumes that the indices are bounded between zero
+ * and some reasonably small integer, i.e., the memory usage depends on the
+ * largest index number, not just on the number of items.
+ *
+ * \ingroup module_trajectoryanalysis
+ */
+class MappedUnionFinder
+{
+ public:
+ /*! \brief
+ * Initializes the finder with indices.
+ *
+ * The size of `indices` sets the number of input items, and each
+ * unique value in `indices` maps to a single internal item.
+ * If multiple indices are the same, then these items are considered
+ * equivalent.
+ */
+ void initWithGroupIndices(ConstArrayRef<int> indices)
+ {
+ mapping_.clear();
+ int groupCount = 0;
+ if (!indices.empty())
+ {
+ const int maxIndex = *std::max_element(indices.begin(),
+ indices.end());
+ mapping_.resize(maxIndex + 1, -1);
+ for (int item : indices)
+ {
+ GMX_ASSERT(item >= 0, "Negative group numbers not supported");
+ if (mapping_[item] == -1)
+ {
+ mapping_[item] = groupCount;
+ ++groupCount;
+ }
+ }
+ }
+ finder_.init(groupCount);
+ }
+ /*! \brief
+ * Returns a reprensetative value for an item that is unique for each
+ * set.
+ *
+ * `group` should be one of the values that were passed in as an index
+ * to initWithGroupIndices().
+ * The return value is an internal index that has no simple relation to
+ * the input indices.
+ */
+ int representativeValue(int group)
+ {
+ GMX_ASSERT(group >= 0 && group < maxGroupNumber(),
+ "Input value out of range");
+ GMX_ASSERT(mapping_[group] != -1,
+ "Input value not in initialization set");
+ return finder_.representativeItem(mapping_[group]);
+ }
+ /*! \brief
+ * Merges sets that contain two given items.
+ *
+ * If the items are already in the same set, nothing happens.
+ * Each input value should be one of the values that were passed in as
+ * an index to initWithGroupIndices().
+ */
+ void mergeGroups(int group1, int group2)
+ {
+ GMX_ASSERT(group1 >= 0 && group1 < maxGroupNumber(),
+ "Input value out of range");
+ GMX_ASSERT(group2 >= 0 && group2 < maxGroupNumber(),
+ "Input value out of range");
+ GMX_ASSERT(mapping_[group1] != -1,
+ "Input value not in initialization set");
+ GMX_ASSERT(mapping_[group2] != -1,
+ "Input value not in initialization set");
+ finder_.merge(mapping_[group1], mapping_[group2]);
+ }
+ /*! \brief
+ * Returns the sizes of all sets (in arbitrary order).
+ *
+ * If there were multiple identical indices passed to
+ * initWithGroupIndices(), these are only counted as one when
+ * computing the sizes.
+ */
+ std::vector<int> allSizes()
+ {
+ return finder_.allSizes();
+ }
+
+ private:
+ int maxGroupNumber() const { return mapping_.size(); }
+
+ UnionFinder finder_;
+ //! Mapping from input indices to zero-based indices used by finder_.
+ std::vector<int> mapping_;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void finishTrajectory();
// From ITopologyProvider
- virtual t_topology *getTopology(bool required)
+ virtual gmx_mtop_t *getTopology(bool required)
{
initTopology(required);
- return topInfo_.topology();
+ return topInfo_.mtop_;
}
virtual int getAtomCount()
{
: settings_(*settings),
startTime_(0.0), endTime_(0.0), deltaTime_(0.0),
bStartTimeSet_(false), bEndTimeSet_(false), bDeltaTimeSet_(false),
- bTrajOpen_(false), fr(NULL), gpbc_(NULL), status_(NULL), oenv_(NULL)
+ bTrajOpen_(false), fr(nullptr), gpbc_(nullptr), status_(nullptr), oenv_(nullptr)
{
}
// Load the topology if requested.
if (!topfile_.empty())
{
- snew(topInfo_.top_, 1);
- topInfo_.bTop_ = read_tps_conf(topfile_.c_str(), topInfo_.top_, &topInfo_.ePBC_,
- &topInfo_.xtop_, NULL, topInfo_.boxtop_, TRUE);
+ snew(topInfo_.mtop_, 1);
+ readConfAndTopology(topfile_.c_str(), &topInfo_.bTop_, topInfo_.mtop_,
+ &topInfo_.ePBC_, &topInfo_.xtop_, nullptr,
+ topInfo_.boxtop_);
+ // TODO: Only load this here if the tool actually needs it; selections
+ // take care of themselves.
+ for (int i = 0; i < topInfo_.mtop_->nmoltype; ++i)
+ {
+ gmx_moltype_t &moltype = topInfo_.mtop_->moltype[i];
+ if (!moltype.atoms.haveMass)
+ {
+ // Try to read masses from database, be silent about missing masses
+ atomsSetMassesBasedOnNames(&moltype.atoms, FALSE);
+ }
+ }
if (hasTrajectory()
&& !settings_.hasFlag(TrajectoryAnalysisSettings::efUseTopX))
{
sfree(topInfo_.xtop_);
- topInfo_.xtop_ = NULL;
+ topInfo_.xtop_ = nullptr;
}
}
}
TrajectoryAnalysisRunnerCommon::Impl::initFirstFrame()
{
// Return if we have already initialized the trajectory.
- if (fr != NULL)
+ if (fr != nullptr)
{
return;
}
close_trx(status_);
bTrajOpen_ = false;
}
- if (gpbc_ != NULL)
+ if (gpbc_ != nullptr)
{
gmx_rmpbc_done(gpbc_);
- gpbc_ = NULL;
+ gpbc_ = nullptr;
}
}
void
TrajectoryAnalysisRunnerCommon::initFrame()
{
- if (impl_->gpbc_ != NULL)
+ if (impl_->gpbc_ != nullptr)
{
gmx_rmpbc_trxfr(impl_->gpbc_, impl_->fr);
}
t_trxframe &
TrajectoryAnalysisRunnerCommon::frame() const
{
- GMX_RELEASE_ASSERT(impl_->fr != NULL, "Frame not available when accessed");
+ GMX_RELEASE_ASSERT(impl_->fr != nullptr, "Frame not available when accessed");
return *impl_->fr;
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2010,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
gmx_add_unit_test(TrajectoryAnalysisUnitTests trajectoryanalysis-test
moduletest.cpp
+ clustsize.cpp
cmdlinerunner.cpp
angle.cpp
distance.cpp
sasa.cpp
select.cpp
surfacearea.cpp
+ trajectory.cpp
+ unionfind.cpp
$<TARGET_OBJECTS:analysisdata-test-shared>)
add_executable(test_selection ${UNITTEST_TARGET_OPTIONS} test_selection.cpp)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx clustsize
+ *
+ * \todo These will be superseded by tests of the new style analysis
+ * modules.
+ *
+ * \author David van der Spoel <david.vanderspoel@icm.uu.se>
+ * \ingroup module_trajectoryanalysis
+ */
+
+#include "gmxpre.h"
+
+#include <cstring>
+
+#include <string>
+
+#include "gromacs/gmxana/gmx_ana.h"
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+#include "testutils/textblockmatchers.h"
+#include "testutils/xvgtest.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+namespace
+{
+
+class ClustsizeTest : public CommandLineTestBase
+{
+ public:
+ ClustsizeTest()
+ {
+ double tolerance = 1e-4;
+ test::XvgMatch xvg;
+ test::XvgMatch &toler = xvg.tolerance(gmx::test::relativeToleranceAsFloatingPoint(1, tolerance));
+
+ setOutputFile("-mc", ".xvg", toler);
+ setOutputFile("-nc", ".xvg", toler);
+ setOutputFile("-ac", ".xvg", toler);
+ setOutputFile("-hc", ".xvg", toler);
+ setInputFile("-f", "clustsize.pdb");
+ }
+
+ void runTest(const CommandLine &args)
+ {
+ CommandLine &cmdline = commandLine();
+ cmdline.merge(args);
+
+ gmx::test::TestReferenceChecker rootChecker(this->rootChecker());
+ rootChecker.checkString(args.toString(), "CommandLine");
+
+ ASSERT_EQ(0, gmx_clustsize(cmdline.argc(), cmdline.argv()));
+
+ checkOutputFiles();
+ }
+};
+
+TEST_F(ClustsizeTest, NoMolDefaultCutoff)
+{
+ const char *const command[] = { "clustsize" };
+ CommandLine args = CommandLine(command);
+
+ setInputFile("-n", "clustsize.ndx");
+
+ runTest(args);
+}
+
+TEST_F(ClustsizeTest, NoMolShortCutoff)
+{
+ const char *const command[] = { "clustsize", "-cut", "0.3" };
+ CommandLine args = CommandLine(command);
+
+ setInputFile("-n", "clustsize.ndx");
+
+ runTest(args);
+}
+
+TEST_F(ClustsizeTest, MolDefaultCutoff)
+{
+ const char *const command[] = { "clustsize", "-mol" };
+ CommandLine args = CommandLine(command);
+
+ setInputFile("-s", "clustsize.tpr");
+
+ runTest(args);
+}
+
+TEST_F(ClustsizeTest, MolShortCutoff)
+{
+ const char *const command[] = { "clustsize", "-mol", "-cut", "0.3" };
+ CommandLine args = CommandLine(command);
+
+ setInputFile("-s", "clustsize.tpr");
+
+ runTest(args);
+}
+
+TEST_F(ClustsizeTest, MolCSize)
+{
+ const char *const command[] = { "clustsize", "-mol", "-nlevels", "6" };
+ CommandLine args = CommandLine(command);
+
+ setOutputFile("-o", ".xpm", ExactTextMatch());
+ setOutputFile("-ow", ".xpm", ExactTextMatch());
+
+ setInputFile("-s", "clustsize.tpr");
+
+ runTest(args);
+}
+
+} // namespace
+
+} // namespace
+
+} // namespace
--- /dev/null
+[ SOL ]
+ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
+ 16 17 18 19 20 21 22 23 24
--- /dev/null
+TITLE 216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984
+REMARK THIS IS A SIMULATION BOX
+CRYST1 18.621 18.621 18.621 90.00 90.00 90.00 P 1 1
+MODEL 1
+ATOM 1 OW SOL 1 2.300 6.280 1.130 1.00 0.00
+ATOM 2 HW1 SOL 1 1.370 6.260 1.500 1.00 0.00
+ATOM 3 HW2 SOL 1 2.310 5.890 0.210 1.00 0.00
+ATOM 70 OW SOL 24 2.220 6.430 4.630 1.00 0.00
+ATOM 71 HW1 SOL 24 0.770 5.550 4.800 1.00 0.00
+ATOM 72 HW2 SOL 24 1.210 6.970 6.470 1.00 0.00
+ATOM 73 OW SOL 25 -0.200 -0.950 3.590 1.00 0.00
+ATOM 74 HW1 SOL 25 0.340 -1.240 4.390 1.00 0.00
+ATOM 75 HW2 SOL 25 0.100 -0.050 3.300 1.00 0.00
+ATOM 76 OW SOL 26 0.270 -2.660 1.170 1.00 0.00
+ATOM 77 HW1 SOL 26 0.080 -3.620 1.380 1.00 0.00
+ATOM 78 HW2 SOL 26 -0.060 -2.080 1.920 1.00 0.00
+ATOM 637 OW SOL 213 -5.620 4.530 6.910 1.00 0.00
+ATOM 638 HW1 SOL 213 -6.210 5.330 6.950 1.00 0.00
+ATOM 639 HW2 SOL 213 -5.470 4.180 7.840 1.00 0.00
+ATOM 640 OW SOL 214 -2.690 2.210 8.820 1.00 0.00
+ATOM 641 HW1 SOL 214 -3.530 2.200 9.360 1.00 0.00
+ATOM 642 HW2 SOL 214 -2.670 3.040 8.260 1.00 0.00
+ATOM 643 OW SOL 215 0.390 -7.850 3.000 1.00 0.00
+ATOM 644 HW1 SOL 215 1.380 -7.960 2.910 1.00 0.00
+ATOM 645 HW2 SOL 215 -0.010 -8.710 3.320 1.00 0.00
+ATOM 646 OW SOL 216 8.750 -2.160 3.370 1.00 0.00
+ATOM 647 HW1 SOL 216 7.980 -2.510 2.830 1.00 0.00
+ATOM 648 HW2 SOL 216 8.430 -1.450 3.990 1.00 0.00
+TER
+ENDMDL
+MODEL 2
+ATOM 1 OW SOL 1 2.300 6.280 1.130 1.00 0.00
+ATOM 2 HW1 SOL 1 1.370 6.260 1.500 1.00 0.00
+ATOM 3 HW2 SOL 1 2.310 5.890 0.210 1.00 0.00
+ATOM 70 OW SOL 24 1.220 6.430 5.630 1.00 0.00
+ATOM 71 HW1 SOL 24 0.770 5.550 5.800 1.00 0.00
+ATOM 72 HW2 SOL 24 1.210 6.970 6.470 1.00 0.00
+ATOM 73 OW SOL 25 -0.200 -0.950 3.590 1.00 0.00
+ATOM 74 HW1 SOL 25 0.340 -1.240 4.390 1.00 0.00
+ATOM 75 HW2 SOL 25 0.100 -0.050 3.300 1.00 0.00
+ATOM 76 OW SOL 26 0.270 -2.660 1.170 1.00 0.00
+ATOM 77 HW1 SOL 26 0.080 -3.620 1.380 1.00 0.00
+ATOM 78 HW2 SOL 26 -0.060 -2.080 1.920 1.00 0.00
+ATOM 637 OW SOL 213 -5.620 4.530 6.910 1.00 0.00
+ATOM 638 HW1 SOL 213 -6.210 5.330 6.950 1.00 0.00
+ATOM 639 HW2 SOL 213 -5.470 4.180 7.840 1.00 0.00
+ATOM 640 OW SOL 214 -2.690 2.210 8.820 1.00 0.00
+ATOM 641 HW1 SOL 214 -3.530 2.200 9.360 1.00 0.00
+ATOM 642 HW2 SOL 214 -2.670 3.040 8.260 1.00 0.00
+ATOM 643 OW SOL 215 0.390 -7.850 3.000 1.00 0.00
+ATOM 644 HW1 SOL 215 1.380 -7.960 2.910 1.00 0.00
+ATOM 645 HW2 SOL 215 -0.010 -8.710 3.320 1.00 0.00
+ATOM 646 OW SOL 216 8.750 -2.160 3.370 1.00 0.00
+ATOM 647 HW1 SOL 216 7.980 -2.510 2.830 1.00 0.00
+ATOM 648 HW2 SOL 216 8.430 -1.450 3.990 1.00 0.00
+TER
+ENDMDL
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void
AbstractTrajectoryAnalysisModuleTestFixture::Impl::ensureModuleCreated()
{
- if (module_.get() == NULL)
+ if (module_.get() == nullptr)
{
module_ = parent_.createModule();
const std::vector<std::string> &datasetNames(module_->datasetNames());
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">clustsize -mol -nlevels 6</String>
+ <OutputFiles Name="Files">
+ <File Name="-mc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Max cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>2</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>2</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-nc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Number of clusters"
+xaxis label "Time (ps)"
+yaxis label "N"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>5</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>6</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-ac">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Average cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>2.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>2.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-hc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Cluster size distribution"
+xaxis label "Cluster size"
+yaxis label "()"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>0</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>1</Real>
+ <Real>3.000</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>2</Real>
+ <Real>2.500</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-o">
+ <String Name="Contents"><![CDATA[
+/* XPM */
+/* This file can be converted to EPS by the GROMACS program xpm2ps */
+/* title: "Cluster size distribution" */
+/* legend: "# clusters" */
+/* x-label: "Time (ps)" */
+/* y-label: "Size" */
+/* type: "Continuous" */
+static char *gromacs_xpm[] = {
+"2 2 6 1",
+"A c #FFFFFF " /* "0" */,
+"B c #FFFF00 " /* "1" */,
+"C c #BFBF40 " /* "1.75" */,
+"D c #808080 " /* "2.5" */,
+"E c #4040BF " /* "3.25" */,
+"F c #0000FF " /* "4" */,
+/* x-axis: 1 2 */
+/* y-axis: 1 2 */
+"EC",
+"CF"
+]]></String>
+ </File>
+ <File Name="-ow">
+ <String Name="Contents"><![CDATA[
+/* XPM */
+/* This file can be converted to EPS by the GROMACS program xpm2ps */
+/* title: "Weighted cluster size distribution" */
+/* legend: "Fraction" */
+/* x-label: "Time (ps)" */
+/* y-label: "Size" */
+/* type: "Continuous" */
+static char *gromacs_xpm[] = {
+"2 2 6 1",
+"A c #FFFFFF " /* "0" */,
+"B c #FFFF00 " /* "2" */,
+"C c #BFBF40 " /* "3" */,
+"D c #808080 " /* "4" */,
+"E c #4040BF " /* "5" */,
+"F c #0000FF " /* "6" */,
+/* x-axis: 1 2 */
+/* y-axis: 1 2 */
+"FD",
+"BD"
+]]></String>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">clustsize -mol</String>
+ <OutputFiles Name="Files">
+ <File Name="-mc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Max cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>2</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>2</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-nc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Number of clusters"
+xaxis label "Time (ps)"
+yaxis label "N"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>5</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>6</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-ac">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Average cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>2.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>2.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-hc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Cluster size distribution"
+xaxis label "Cluster size"
+yaxis label "()"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>0</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>1</Real>
+ <Real>3.000</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>2</Real>
+ <Real>2.500</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">clustsize -mol -cut 0.3</String>
+ <OutputFiles Name="Files">
+ <File Name="-mc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Max cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>2</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>2</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-nc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Number of clusters"
+xaxis label "Time (ps)"
+yaxis label "N"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>7</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>7</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-ac">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Average cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>2.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>2.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-hc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Cluster size distribution"
+xaxis label "Cluster size"
+yaxis label "()"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>0</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>1</Real>
+ <Real>6.000</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>2</Real>
+ <Real>1.000</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">clustsize</String>
+ <OutputFiles Name="Files">
+ <File Name="-mc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Max cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>6</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>6</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-nc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Number of clusters"
+xaxis label "Time (ps)"
+yaxis label "N"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>5</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>6</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-ac">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Average cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>4.800</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>4.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-hc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Cluster size distribution"
+xaxis label "Cluster size"
+yaxis label "()"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>0</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>1</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>2</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>3.000</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">2</Int>
+ <Real>4</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">2</Int>
+ <Real>5</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">2</Int>
+ <Real>6</Real>
+ <Real>2.500</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">2</Int>
+ <Real>7</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">clustsize -cut 0.3</String>
+ <OutputFiles Name="Files">
+ <File Name="-mc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Max cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>6</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>6</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-nc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Number of clusters"
+xaxis label "Time (ps)"
+yaxis label "N"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>7</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>7</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-ac">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Average cluster size"
+xaxis label "Time (ps)"
+yaxis label "#molecules"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>1.000000e+00</Real>
+ <Real>3.429</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>2.000000e+00</Real>
+ <Real>3.429</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ <File Name="-hc">
+ <XvgLegend Name="Legend">
+ <String Name="XvgLegend"><![CDATA[
+title "Cluster size distribution"
+xaxis label "Cluster size"
+yaxis label "()"
+TYPE xy
+]]></String>
+ </XvgLegend>
+ <XvgData Name="Data">
+ <Sequence Name="Row0">
+ <Int Name="Length">2</Int>
+ <Real>0</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row1">
+ <Int Name="Length">2</Int>
+ <Real>1</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row2">
+ <Int Name="Length">2</Int>
+ <Real>2</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row3">
+ <Int Name="Length">2</Int>
+ <Real>3</Real>
+ <Real>6.000</Real>
+ </Sequence>
+ <Sequence Name="Row4">
+ <Int Name="Length">2</Int>
+ <Real>4</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row5">
+ <Int Name="Length">2</Int>
+ <Real>5</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ <Sequence Name="Row6">
+ <Int Name="Length">2</Int>
+ <Real>6</Real>
+ <Real>1.000</Real>
+ </Sequence>
+ <Sequence Name="Row7">
+ <Int Name="Length">2</Int>
+ <Real>7</Real>
+ <Real>0.000</Real>
+ </Sequence>
+ </XvgData>
+ </File>
+ </OutputFiles>
+</ReferenceData>
</DataValue>
<DataValue>
<Real Name="Value">0</Real>
+ <Bool Name="Present">false</Bool>
</DataValue>
<DataValue>
<Real Name="Value">1</Real>
+ <Bool Name="Present">false</Bool>
</DataValue>
<DataValue>
<Real Name="Value">0</Real>
+ <Bool Name="Present">false</Bool>
</DataValue>
<DataValue>
<Real Name="Value">0</Real>
+ <Bool Name="Present">false</Bool>
</DataValue>
<DataValue>
<Real Name="Value">1</Real>
+ <Bool Name="Present">false</Bool>
</DataValue>
<DataValue>
<Real Name="Value">0</Real>
+ <Bool Name="Present">false</Bool>
</DataValue>
</DataValues>
</DataFrame>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">trajectory -select 'resnr 1' 'resnr 3'</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="x">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">0</Int>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">1</Int>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame1">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">0</Int>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">1</Int>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ </OutputData>
+ <OutputFiles Name="Files">
+ <File Name="-ox"></File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">trajectory -select 'resnr 1' 'resnr 3'</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="f"></AnalysisData>
+ </OutputData>
+ <OutputFiles Name="Files">
+ <File Name="-of"></File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">trajectory -select 'resnr 1' 'resnr 3'</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="v"></AnalysisData>
+ </OutputData>
+ <OutputFiles Name="Files">
+ <File Name="-ov"></File>
+ </OutputFiles>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="CommandLine">trajectory -select 'resnr 1' 'resnr 3' -x</String>
+ <OutputData Name="Data">
+ <AnalysisData Name="x">
+ <DataFrame Name="Frame0">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">0</Int>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">1</Int>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ <DataFrame Name="Frame1">
+ <Real Name="X">0</Real>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">0</Int>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ <DataValues>
+ <Int Name="Count">9</Int>
+ <Int Name="DataSet">1</Int>
+ <DataValue>
+ <Real Name="Value">1</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">3</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">2</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">4</Real>
+ </DataValue>
+ <DataValue>
+ <Real Name="Value">0</Real>
+ </DataValue>
+ </DataValues>
+ </DataFrame>
+ </AnalysisData>
+ </OutputData>
+ <OutputFiles Name="Files">
+ <File Name="-ox"></File>
+ </OutputFiles>
+</ReferenceData>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
public:
SurfaceAreaTest()
: rng_(12345), area_(0.0), volume_(0.0),
- atomArea_(NULL), dotCount_(0), dots_(NULL)
+ atomArea_(nullptr), dotCount_(0), dots_(nullptr)
{
clear_mat(box_);
}
{
index_.push_back(x_.size());
}
- x_.push_back(gmx::RVec(x, y, z));
+ x_.emplace_back(x, y, z);
radius_.push_back(radius);
}
{
volume_ = 0.0;
sfree(atomArea_);
- atomArea_ = NULL;
+ atomArea_ = nullptr;
dotCount_ = 0;
sfree(dots_);
- dots_ = NULL;
+ dots_ = nullptr;
t_pbc pbc;
if (bPBC)
{
gmx::SurfaceAreaCalculator calculator;
calculator.setDotCount(ndots);
calculator.setRadii(radius_);
- calculator.calculate(as_rvec_array(x_.data()), bPBC ? &pbc : NULL,
+ calculator.calculate(as_rvec_array(x_.data()), bPBC ? &pbc : nullptr,
index_.size(), index_.data(), flags,
&area_, &volume_, &atomArea_,
&dots_, &dotCount_);
{
compound.checkReal(volume_, "Volume");
}
- if (atomArea_ != NULL)
+ if (atomArea_ != nullptr)
{
compound.checkSequenceArray(index_.size(), atomArea_, "AtomArea");
}
- if (dots_ != NULL)
+ if (dots_ != nullptr)
{
if (checkDotCoordinates)
{
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for functionality of the "trajectory" trajectory analysis module.
+ *
+ * Line coverage for the module code is good, but due to missing input data
+ * with velocities or forces, the output of these quantities is not really
+ * tested. But the values are only computed in the selection engine, and
+ * at least the low-level computation is tested there.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/modules/trajectory.h"
+
+#include <gtest/gtest.h>
+
+#include "testutils/cmdlinetest.h"
+#include "testutils/textblockmatchers.h"
+
+#include "moduletest.h"
+
+namespace
+{
+
+using gmx::test::CommandLine;
+using gmx::test::NoTextMatch;
+
+/********************************************************************
+ * Tests for gmx::analysismodules::Trajectory.
+ */
+
+//! Test fixture for the select analysis module.
+typedef gmx::test::TrajectoryAnalysisModuleTestFixture<gmx::analysismodules::TrajectoryInfo>
+ TrajectoryModuleTest;
+
+TEST_F(TrajectoryModuleTest, BasicTest)
+{
+ const char *const cmdline[] = {
+ "trajectory",
+ "-select", "resnr 1", "resnr 3"
+ };
+ setTopology("simple.gro");
+ setTrajectory("simple.gro");
+ setOutputFile("-ox", "coord.xvg", NoTextMatch());
+ includeDataset("x");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(TrajectoryModuleTest, PlotsXOnly)
+{
+ const char *const cmdline[] = {
+ "trajectory",
+ "-select", "resnr 1", "resnr 3",
+ "-x"
+ };
+ setTopology("simple.gro");
+ setTrajectory("simple.gro");
+ setOutputFile("-ox", "coord.xvg", NoTextMatch());
+ includeDataset("x");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(TrajectoryModuleTest, HandlesNoVelocities)
+{
+ const char *const cmdline[] = {
+ "trajectory",
+ "-select", "resnr 1", "resnr 3",
+ };
+ setTopology("simple.gro");
+ setTrajectory("simple.gro");
+ setOutputFile("-ov", "vel.xvg", NoTextMatch());
+ includeDataset("v");
+ runTest(CommandLine(cmdline));
+}
+
+TEST_F(TrajectoryModuleTest, HandlesNoForces)
+{
+ const char *const cmdline[] = {
+ "trajectory",
+ "-select", "resnr 1", "resnr 3",
+ };
+ setTopology("simple.gro");
+ setTrajectory("simple.gro");
+ setOutputFile("-of", "force.xvg", NoTextMatch());
+ includeDataset("f");
+ runTest(CommandLine(cmdline));
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for the union-find implementation in unionfind.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_trajectoryanalysis
+ */
+#include "gmxpre.h"
+
+#include "gromacs/trajectoryanalysis/modules/unionfind.h"
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+namespace
+{
+
+/********************************************************************
+ * Tests for UnionFinder
+ */
+
+TEST(UnionFinderTest, WorksEmpty)
+{
+ using ::testing::IsEmpty;
+ gmx::UnionFinder finder;
+ finder.init(0);
+ EXPECT_THAT(finder.allSizes(), IsEmpty());
+}
+
+TEST(UnionFinderTest, BasicMerges)
+{
+ using ::testing::Each;
+ using ::testing::UnorderedElementsAre;
+ gmx::UnionFinder finder;
+ finder.init(7);
+ EXPECT_EQ(7U, finder.allSizes().size());
+ EXPECT_THAT(finder.allSizes(), Each(1));
+ finder.merge(0, 1);
+ finder.merge(2, 3);
+ finder.merge(0, 4);
+ finder.merge(3, 5);
+ EXPECT_THAT(finder.allSizes(), UnorderedElementsAre(3, 3, 1));
+}
+
+TEST(UnionFinderTest, LargerMerges)
+{
+ using ::testing::UnorderedElementsAre;
+ gmx::UnionFinder finder;
+ finder.init(7);
+ finder.merge(0, 1);
+ finder.merge(2, 3);
+ finder.merge(4, 5);
+ finder.merge(3, 5);
+ finder.merge(1, 5);
+ EXPECT_THAT(finder.allSizes(), UnorderedElementsAre(6, 1));
+}
+
+TEST(UnionFinderTest, LongRightMerge)
+{
+ using ::testing::ElementsAre;
+ gmx::UnionFinder finder;
+ finder.init(7);
+ finder.merge(0, 1);
+ finder.merge(1, 2);
+ finder.merge(2, 3);
+ finder.merge(3, 4);
+ finder.merge(4, 5);
+ finder.merge(5, 6);
+ EXPECT_THAT(finder.allSizes(), ElementsAre(7));
+}
+
+TEST(UnionFinderTest, LongLeftMerge)
+{
+ using ::testing::ElementsAre;
+ gmx::UnionFinder finder;
+ finder.init(7);
+ finder.merge(5, 6);
+ finder.merge(4, 5);
+ finder.merge(3, 4);
+ finder.merge(2, 3);
+ finder.merge(1, 2);
+ finder.merge(0, 1);
+ EXPECT_THAT(finder.allSizes(), ElementsAre(7));
+}
+
+/********************************************************************
+ * Tests for MappedUnionFinder
+ */
+
+TEST(MappedUnionFinderTest, BasicMerges)
+{
+ using ::testing::Each;
+ const int mapping[] = {1, 1, 2, 2, 4, 6};
+ gmx::MappedUnionFinder finder;
+ finder.initWithGroupIndices(mapping);
+ EXPECT_EQ(4U, finder.allSizes().size());
+ EXPECT_THAT(finder.allSizes(), Each(1));
+ finder.mergeGroups(1, 4);
+ finder.mergeGroups(2, 6);
+ EXPECT_EQ(2U, finder.allSizes().size());
+ EXPECT_THAT(finder.allSizes(), Each(2));
+}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* managing directories and files.
* The fate of this header depends on what is decided in Redmine issue #950.
*
+ * <H3>Logging</H3>
+ *
+ * The headers logger.h and loggerbuilder.h provide interfaces and classes for
+ * writing log files (or logging to other targets). See \ref page_logging for
+ * an overview.
+ *
* \endif
*
* <H3>Implementation helpers</H3>
*
* \if libapi
*
+ * The header strconvert.h declares string parsing routines.
+ *
* The header gmxmpi.h abstracts away the mechanism of including either MPI or
* thread-MPI headers depending on compilation options.
* Similarly, gmxomp.h removes the need to use conditional compilation for code
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* gmx::alignedMalloc(). Just like system-provided routines, it provides
* memory that is aligned - but not padded.
*/
-static void *
+gmx_unused static void *
alignedMallocGeneric(std::size_t bytes, std::size_t alignment)
{
// The amount of extra memory (beyound what the user asked for) we need is:
* \note This is an internal routine that should only be called from
* gmx::alignedFree().
*/
-static void
+gmx_unused static void
alignedFreeGeneric(void *p)
{
if (p)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* \throws std::bad_alloc if the allocation fails.
*/
pointer
- allocate(std::size_t n, typename std::allocator<void>::const_pointer gmx_unused hint = 0)
+ allocate(std::size_t n, typename std::allocator<void>::const_pointer gmx_unused hint = nullptr)
{
void *p = internal::alignedMalloc(n*sizeof(T));
*/
template<class T2>
bool
- operator==(const AlignedAllocator<T2> &gmx_unused rhs) const { return std::is_same<T, T2>::value; }
+ operator==(const AlignedAllocator<T2> &gmx_unused rhs) const { return std::is_same<T, T2>::value; GMX_UNUSED_VALUE(rhs); }
/*! \brief Return true if two allocators are different
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstddef>
+#include <array>
#include <iterator>
#include <stdexcept>
#include <utility>
*/
struct EmptyArrayRef {};
-/*! \brief
- * STL-like container for an interface to a C array (or part of a std::vector).
+/*! \brief STL-like container for an interface to a C array of T (or part
+ * of a std::vector<T> or std::array<T>).
*
* \tparam T Value type of elements.
*
* following main differences:
* - This class does not have its own storage. Instead, it references an
* existing array of values (either a C-style array or part of an existing
- * std::vector<T>).
+ * std::vector<T> or std::array<T>).
* - It is only possible to modify the values themselves through ArrayRef;
* it is not possible to add or remove values.
* - Copying objects of this type is cheap, and the copies behave identically
* to the original object: the copy references the same set of values.
*
- * This class is useful for writing wrappers that expose a different view of
- * the internal data stored as a single vector/array.
+ * This class is useful for writing wrappers that expose a view of the
+ * internal data stored as a single vector/array, which can be a whole
+ * or part of the underlying storage.
*
* Methods in this class do not throw, except where indicated.
*
fromVector(typename std::vector<value_type>::iterator begin,
typename std::vector<value_type>::iterator end)
{
- value_type *p_begin = (begin != end) ? &*begin : NULL;
+ value_type *p_begin = (begin != end) ? &*begin : nullptr;
value_type *p_end = p_begin + (end-begin);
return ArrayRef<value_type>(p_begin, p_end);
}
* used to initialize any ArrayRef, without specifying the template
* type. It is not explicit to enable that usage.
*/
- ArrayRef(const EmptyArrayRef &) : begin_(NULL), end_(NULL) {}
+ ArrayRef(const EmptyArrayRef &) : begin_(nullptr), end_(nullptr) {}
/*! \brief
* Constructs a reference to a particular range.
*
GMX_ASSERT(end >= begin, "Invalid range");
}
/*! \brief
- * Constructs a reference to a whole vector.
+ * Constructs a reference to a whole std::vector<T>.
*
* \param[in] v Vector to reference.
*
* lifetime of this object.
*
* This constructor is not explicit to allow directly passing
- * std::vector to a method that takes ArrayRef.
+ * std::vector<T> to a method that takes ArrayRef.
*/
ArrayRef(std::vector<T> &v)
- : begin_((!v.empty()) ? &v[0] : NULL),
- end_((!v.empty()) ? &v[0] + v.size() : NULL)
+ : begin_((!v.empty()) ? &v[0] : nullptr),
+ end_((!v.empty()) ? &v[0] + v.size() : nullptr)
+ {
+ }
+ /*! \brief
+ * Constructs a reference to a whole std::array<T>.
+ *
+ * \param[in] a Array to reference.
+ *
+ * Passed array must remain valid for the lifetime of this
+ * object.
+ *
+ * This constructor is not explicit to allow directly passing
+ * std::array<T> to a method that takes ArrayRef.
+ */
+ template <size_t count>
+ ArrayRef(std::array<T, count> &a)
+ : begin_((!a.empty()) ? &a[0] : NULL),
+ end_((!a.empty()) ? &a[0] + a.size() : NULL)
{
}
//! \cond
*
* This constructor is not explicit to allow directly passing
* a C array to a function that takes an ArrayRef parameter.
- *
- * xlc on BG/Q compiles wrong code if the C array is a struct
- * field, unless value_type is char or unsigned char. There's
- * no good way to assert on this before C++11 (which that
- * compiler will never support).
*/
template <size_t count>
ArrayRef(value_type (&array)[count])
-/*! \brief
- * STL-like container for non-mutable interface to a C array (or part of a
- * std::vector).
+/*! \brief STL-like container for non-mutable interface to a C array of T
+ * (or part of a std::vector<T> or std::array<T>).
*
* \tparam T Value type of elements.
*
* following main differences:
* - This class does not have its own storage. Instead, it references an
* existing array of values (either a C-style array or part of an existing
- * std::vector<T>).
+ * std::vector<T> or std::array<T>).
* - Only const methods are provided to access the stored values.
* It is not possible to alter the referenced array.
* - Copying objects of this type is cheap, and the copies behave identically
* to the original object: the copy references the same set of values.
*
- * This class is useful for writing wrappers that expose a different view of
- * the internal data stored as a single vector/array.
+ * This class is useful for writing wrappers that expose a view of the
+ * internal data stored as a single vector/array, which can be a whole
+ * or part of the underlying storage.
*
* Methods in this class do not throw, except where indicated.
*
fromVector(typename std::vector<value_type>::const_iterator begin,
typename std::vector<value_type>::const_iterator end)
{
- const value_type *p_begin = (begin != end) ? &*begin : NULL;
+ const value_type *p_begin = (begin != end) ? &*begin : nullptr;
const value_type *p_end = p_begin + (end-begin);
return ConstArrayRef<value_type>(p_begin, p_end);
}
/*! \brief
* Constructs an empty reference.
*/
- ConstArrayRef() : begin_(NULL), end_(NULL) {}
+ ConstArrayRef() : begin_(nullptr), end_(nullptr) {}
/*! \brief
* Constructs an empty reference.
*
* used to initialize any Const ArrayRef, without specifying the
* template type. It is not explicit to enable that usage.
*/
- ConstArrayRef(const EmptyArrayRef &) : begin_(NULL), end_(NULL) {}
+ ConstArrayRef(const EmptyArrayRef &) : begin_(nullptr), end_(nullptr) {}
+ /*! \brief
+ * Constructs a const reference from a non-const reference.
+ */
+ ConstArrayRef(const ArrayRef<T> &other) : begin_(other.begin()), end_(other.end()) {}
/*! \brief
* Constructs a reference to a particular range.
*
GMX_ASSERT(end >= begin, "Invalid range");
}
/*! \brief
- * Constructs a reference to a whole vector.
+ * Constructs a reference to a whole std::vector<T>.
*
* \param[in] v Vector to reference.
*
* lifetime of this object.
*
* This constructor is not explicit to allow directly passing
- * std::vector to a method that takes ConstArrayRef.
+ * std::vector<T> to a method that takes ConstArrayRef.
*/
ConstArrayRef(const std::vector<T> &v)
- : begin_((!v.empty()) ? &v[0] : NULL),
- end_((!v.empty()) ? &v[0] + v.size() : NULL)
+ : begin_((!v.empty()) ? &v[0] : nullptr),
+ end_((!v.empty()) ? &v[0] + v.size() : nullptr)
+ {
+ }
+ /*! \brief
+ * Constructs a reference to a whole std::array<T>.
+ *
+ * \param[in] a Array to reference.
+ *
+ * Passed array must remain valid for the lifetime of this
+ * object.
+ *
+ * This constructor is not explicit to allow directly passing
+ * std::array<T> to a method that takes ConstArrayRef.
+ */
+ template <size_t count>
+ ConstArrayRef(const std::array<T, count> &a)
+ : begin_((!a.empty()) ? &a[0] : NULL),
+ end_((!a.empty()) ? &a[0] + a.size() : NULL)
{
}
//! \cond
*
* This constructor is not explicit to allow directly passing
* a C array to a function that takes a ConstArrayRef parameter.
- *
- * xlc on BG/Q compiles wrong code if the C array is a struct
- * field, unless value_type is char or unsigned char. There's
- * no good way to assert on this before C++11 (which that
- * compiler will never support).
*/
template <size_t count>
ConstArrayRef(const value_type (&array)[count])
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#endif
#endif
-/*! \def gmx_constexpr
- * \brief C++11 constexpr everywhere except MSVC 2013, where it is empty.
- *
- * Support for constexpr was not added until MSVC 2015, and it still
- * seems to be unreliable. Since interacting with parts of libc++ and
- * libstdc++ depend on it (for instance the min/max calls in our
- * random engines), we need to specify it for other compilers.
- */
-#ifndef gmx_constexpr
-#if !defined(_MSC_VER)
-# define gmx_constexpr constexpr
-#else
-# define gmx_constexpr
-#endif
-#endif
-
/*! \def GMX_ALIGNED(type, alignment)
* \brief
* Declare variable with data alignment
\endcode
*/
-#if (defined(__GNUC__) && !defined(__clang__)) || defined(__ibmxl__) || defined(__xlC__) || defined(__PATHCC__)
-// Gcc-4.6.4 does not support alignas, but both gcc, pathscale and xlc
-// support the standard GNU alignment attributes. PGI also sets __GNUC__ now,
-// and mostly supports it. clang 3.2 does not support the GCC alignment attribute.
-# define GMX_ALIGNED(type, alignment) __attribute__ ((aligned(alignment*sizeof(type)))) type
-#else
-// If nothing else works we rely on C++11. This will for instance work for MSVC2015 and later.
+// We rely on C++11. This will for instance work for MSVC2015 and later.
// If you get an error here, find out what attribute to use to get your compiler to align
// data properly and add it as a case.
-# define GMX_ALIGNED(type, alignment) alignas(alignment*alignof(type)) type
-#endif
-
+#define GMX_ALIGNED(type, alignment) alignas(alignment*sizeof(type)) type
/*! \brief
* Macro to explicitly ignore an unused value.
#include <cstring>
#include <algorithm>
+#include <string>
/* This file is completely threadsafe - keep it that way! */
#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
#include "cuda_version_information.h"
namespace
{
+using gmx::formatString;
+
//! \cond Doxygen does not need to care about most of this stuff, and the macro usage is painful to document
int centeringOffset(int width, int length)
return std::max(width - length, 0) / 2;
}
-void printCentered(FILE *fp, int width, const char *text)
+std::string formatCentered(int width, const char *text)
{
const int offset = centeringOffset(width, std::strlen(text));
- fprintf(fp, "%*s%s", offset, "", text);
+ return formatString("%*s%s", offset, "", text);
}
-void printCopyright(FILE *fp)
+void printCopyright(gmx::TextWriter *writer)
{
static const char * const Contributors[] = {
"Emile Apol",
#define NLICENSE (int)asize(LicenseText)
#endif
- printCentered(fp, 78, "GROMACS is written by:");
- fprintf(fp, "\n");
+ // TODO a centering behaviour of TextWriter could be useful here
+ writer->writeLine(formatCentered(78, "GROMACS is written by:"));
for (int i = 0; i < NCONTRIBUTORS; )
{
for (int j = 0; j < 4 && i < NCONTRIBUTORS; ++j, ++i)
"Formatting buffer is not long enough");
std::fill(buf, buf+width, ' ');
std::strcpy(buf+offset, Contributors[i]);
- fprintf(fp, " %-*s", width, buf);
+ writer->writeString(formatString(" %-*s", width, buf));
}
- fprintf(fp, "\n");
+ writer->ensureLineBreak();
}
- printCentered(fp, 78, "and the project leaders:");
- fprintf(fp, "\n");
- printCentered(fp, 78, "Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel");
- fprintf(fp, "\n\n");
+ writer->writeLine(formatCentered(78, "and the project leaders:"));
+ writer->writeLine(formatCentered(78, "Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel"));
+ writer->ensureEmptyLine();
for (int i = 0; i < NCR; ++i)
{
- fprintf(fp, "%s\n", CopyrightText[i]);
+ writer->writeLine(CopyrightText[i]);
}
- fprintf(fp, "\n");
+ writer->ensureEmptyLine();
for (int i = 0; i < NLICENSE; ++i)
{
- fprintf(fp, "%s\n", LicenseText[i]);
+ writer->writeLine(LicenseText[i]);
}
}
#endif
};
-void gmx_print_version_info(FILE *fp)
+void gmx_print_version_info(gmx::TextWriter *writer)
{
- fprintf(fp, "GROMACS version: %s\n", gmx_version());
+ writer->writeLine(formatString("GROMACS version: %s", gmx_version()));
const char *const git_hash = gmx_version_git_full_hash();
if (git_hash[0] != '\0')
{
- fprintf(fp, "GIT SHA1 hash: %s\n", git_hash);
+ writer->writeLine(formatString("GIT SHA1 hash: %s", git_hash));
}
const char *const base_hash = gmx_version_git_central_base_hash();
if (base_hash[0] != '\0')
{
- fprintf(fp, "Branched from: %s\n", base_hash);
+ writer->writeLine(formatString("Branched from: %s", base_hash));
}
#if GMX_DOUBLE
- fprintf(fp, "Precision: double\n");
+ writer->writeLine("Precision: double");
#else
- fprintf(fp, "Precision: single\n");
+ writer->writeLine("Precision: single");
#endif
- fprintf(fp, "Memory model: %u bit\n", (unsigned)(8*sizeof(void *)));
+ writer->writeLine(formatString("Memory model: %u bit", (unsigned)(8*sizeof(void *))));
#if GMX_THREAD_MPI
- fprintf(fp, "MPI library: thread_mpi\n");
+ writer->writeLine("MPI library: thread_mpi");
#elif GMX_MPI
- fprintf(fp, "MPI library: MPI\n");
+ writer->writeLine("MPI library: MPI");
#else
- fprintf(fp, "MPI library: none\n");
+ writer->writeLine("MPI library: none");
#endif
#if GMX_OPENMP
- fprintf(fp, "OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = %d)\n", GMX_OPENMP_MAX_THREADS);
-#else
- fprintf(fp, "OpenMP support: disabled\n");
-#endif
- fprintf(fp, "GPU support: %s\n", getGpuImplementationString());
- fprintf(fp, "SIMD instructions: %s\n", GMX_SIMD_STRING);
- fprintf(fp, "FFT library: %s\n", getFftDescriptionString());
-#ifdef HAVE_RDTSCP
- fprintf(fp, "RDTSCP usage: enabled\n");
+ writer->writeLine(formatString("OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = %d)", GMX_OPENMP_MAX_THREADS));
#else
- fprintf(fp, "RDTSCP usage: disabled\n");
+ writer->writeLine("OpenMP support: disabled");
#endif
+ writer->writeLine(formatString("GPU support: %s", getGpuImplementationString()));
+ writer->writeLine(formatString("SIMD instructions: %s", GMX_SIMD_STRING));
+ writer->writeLine(formatString("FFT library: %s", getFftDescriptionString()));
+ writer->writeLine(formatString("RDTSCP usage: %s", HAVE_RDTSCP ? "enabled" : "disabled"));
#ifdef GMX_USE_TNG
- fprintf(fp, "TNG support: enabled\n");
+ writer->writeLine("TNG support: enabled");
#else
- fprintf(fp, "TNG support: disabled\n");
+ writer->writeLine("TNG support: disabled");
#endif
#if GMX_HWLOC
- fprintf(fp, "Hwloc support: hwloc-%d.%d.%d\n",
- HWLOC_API_VERSION>>16,
- (HWLOC_API_VERSION>>8) & 0xFF,
- HWLOC_API_VERSION & 0xFF);
+ writer->writeLine(formatString("Hwloc support: hwloc-%d.%d.%d",
+ HWLOC_API_VERSION>>16,
+ (HWLOC_API_VERSION>>8) & 0xFF,
+ HWLOC_API_VERSION & 0xFF));
#else
- fprintf(fp, "Hwloc support: disabled\n");
+ writer->writeLine("Hwloc support: disabled");
#endif
#if HAVE_EXTRAE
unsigned major, minor, revision;
Extrae_get_version(&major, &minor, &revision);
- fprintf(fp, "Tracing support: enabled. Using Extrae-%d.%d.%d\n", major, minor, revision);
+ writer->writeLine(formatString("Tracing support: enabled. Using Extrae-%d.%d.%d", major, minor, revision));
#else
- fprintf(fp, "Tracing support: disabled\n");
+ writer->writeLine("Tracing support: disabled");
#endif
- fprintf(fp, "Built on: %s\n", BUILD_TIME);
- fprintf(fp, "Built by: %s\n", BUILD_USER);
- fprintf(fp, "Build OS/arch: %s\n", BUILD_HOST);
- fprintf(fp, "Build CPU vendor: %s\n", BUILD_CPU_VENDOR);
- fprintf(fp, "Build CPU brand: %s\n", BUILD_CPU_BRAND);
- fprintf(fp, "Build CPU family: %d Model: %d Stepping: %d\n",
- BUILD_CPU_FAMILY, BUILD_CPU_MODEL, BUILD_CPU_STEPPING);
+ writer->writeLine(formatString("Built on: %s", BUILD_TIME));
+ writer->writeLine(formatString("Built by: %s", BUILD_USER));
+ writer->writeLine(formatString("Build OS/arch: %s", BUILD_HOST));
+ writer->writeLine(formatString("Build CPU vendor: %s", BUILD_CPU_VENDOR));
+ writer->writeLine(formatString("Build CPU brand: %s", BUILD_CPU_BRAND));
+ writer->writeLine(formatString("Build CPU family: %d Model: %d Stepping: %d",
+ BUILD_CPU_FAMILY, BUILD_CPU_MODEL, BUILD_CPU_STEPPING));
/* TODO: The below strings can be quite long, so it would be nice to wrap
* them. Can wait for later, as the master branch has ready code to do all
* that. */
- fprintf(fp, "Build CPU features: %s\n", BUILD_CPU_FEATURES);
- fprintf(fp, "C compiler: %s\n", BUILD_C_COMPILER);
- fprintf(fp, "C compiler flags: %s\n", BUILD_CFLAGS);
- fprintf(fp, "C++ compiler: %s\n", BUILD_CXX_COMPILER);
- fprintf(fp, "C++ compiler flags: %s\n", BUILD_CXXFLAGS);
+ writer->writeLine(formatString("Build CPU features: %s", BUILD_CPU_FEATURES));
+ writer->writeLine(formatString("C compiler: %s", BUILD_C_COMPILER));
+ writer->writeLine(formatString("C compiler flags: %s", BUILD_CFLAGS));
+ writer->writeLine(formatString("C++ compiler: %s", BUILD_CXX_COMPILER));
+ writer->writeLine(formatString("C++ compiler flags: %s", BUILD_CXXFLAGS));
#ifdef HAVE_LIBMKL
/* MKL might be used for LAPACK/BLAS even if FFTs use FFTW, so keep it separate */
- fprintf(fp, "Linked with Intel MKL version %d.%d.%d.\n",
- __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__);
+ writer->writeLine(formatString("Linked with Intel MKL version %d.%d.%d.",
+ __INTEL_MKL__, __INTEL_MKL_MINOR__, __INTEL_MKL_UPDATE__));
#endif
#if GMX_GPU == GMX_GPU_OPENCL
- fprintf(fp, "OpenCL include dir: %s\n", OPENCL_INCLUDE_DIR);
- fprintf(fp, "OpenCL library: %s\n", OPENCL_LIBRARY);
- fprintf(fp, "OpenCL version: %s\n", OPENCL_VERSION_STRING);
+ writer->writeLine(formatString("OpenCL include dir: %s", OPENCL_INCLUDE_DIR));
+ writer->writeLine(formatString("OpenCL library: %s", OPENCL_LIBRARY));
+ writer->writeLine(formatString("OpenCL version: %s", OPENCL_VERSION_STRING));
#endif
#if GMX_GPU == GMX_GPU_CUDA
- gmx_print_version_info_cuda_gpu(fp);
+ writer->writeLine(formatString("CUDA compiler: %s\n", CUDA_NVCC_COMPILER_INFO));
+ writer->writeLine(formatString("CUDA compiler flags:%s\n", CUDA_NVCC_COMPILER_FLAGS));
+ auto driverVersion = gmx::getCudaDriverVersion();
+ writer->writeLine(formatString("CUDA driver: %d.%d\n", driverVersion.first, driverVersion.second));
+ auto runtimeVersion = gmx::getCudaRuntimeVersion();
+ writer->writeLine(formatString("CUDA runtime: %d.%d\n", runtimeVersion.first, runtimeVersion.second));
#endif
}
void printBinaryInformation(FILE *fp,
const IProgramContext &programContext)
{
- printBinaryInformation(fp, programContext, BinaryInformationSettings());
+ TextWriter writer(fp);
+ printBinaryInformation(&writer, programContext, BinaryInformationSettings());
}
void printBinaryInformation(FILE *fp,
const IProgramContext &programContext,
const BinaryInformationSettings &settings)
{
+ try
+ {
+ TextWriter writer(fp);
+ printBinaryInformation(&writer, programContext, settings);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+}
+
+void printBinaryInformation(TextWriter *writer,
+ const IProgramContext &programContext,
+ const BinaryInformationSettings &settings)
+{
+ // TODO Perhaps the writer could be configured with the prefix and
+ // suffix strings from the settings?
const char *prefix = settings.prefix_;
const char *suffix = settings.suffix_;
const char *precisionString = "";
const char *const name = programContext.displayName();
if (settings.bGeneratedByHeader_)
{
- fprintf(fp, "%sCreated by:%s\n", prefix, suffix);
+ writer->writeLine(formatString("%sCreated by:%s", prefix, suffix));
}
// TODO: It would be nice to know here whether we are really running a
// Gromacs binary or some other binary that is calling Gromacs; we
= formatString(":-) GROMACS - %s, %s%s (-:", name, gmx_version(), precisionString);
const int indent
= centeringOffset(78 - std::strlen(prefix) - std::strlen(suffix), title.length()) + 1;
- fprintf(fp, "%s%*c%s%s\n", prefix, indent, ' ', title.c_str(), suffix);
- fprintf(fp, "%s%s\n", prefix, suffix);
+ writer->writeLine(formatString("%s%*c%s%s", prefix, indent, ' ', title.c_str(), suffix));
+ writer->writeLine(formatString("%s%s", prefix, suffix));
if (settings.bCopyright_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with copyright");
- printCopyright(fp);
- fprintf(fp, "\n");
+ printCopyright(writer);
+ writer->ensureEmptyLine();
// This line is printed again after the copyright notice to make it
// appear together with all the other information, so that it is not
// necessary to read stuff above the copyright notice.
// The line above the copyright notice puts the copyright notice is
// context, though.
- fprintf(fp, "%sGROMACS: %s, version %s%s%s\n", prefix, name,
- gmx_version(), precisionString, suffix);
+ writer->writeLine(formatString("%sGROMACS: %s, version %s%s%s", prefix, name,
+ gmx_version(), precisionString, suffix));
}
const char *const binaryPath = programContext.fullBinaryPath();
if (!gmx::isNullOrEmpty(binaryPath))
{
- fprintf(fp, "%sExecutable: %s%s\n", prefix, binaryPath, suffix);
+ writer->writeLine(formatString("%sExecutable: %s%s", prefix, binaryPath, suffix));
}
const gmx::InstallationPrefixInfo installPrefix = programContext.installationPrefix();
if (!gmx::isNullOrEmpty(installPrefix.path))
{
- fprintf(fp, "%sData prefix: %s%s%s\n", prefix, installPrefix.path,
- installPrefix.bSourceLayout ? " (source tree)" : "", suffix);
+ writer->writeLine(formatString("%sData prefix: %s%s%s", prefix, installPrefix.path,
+ installPrefix.bSourceLayout ? " (source tree)" : "", suffix));
}
const std::string workingDir = Path::getWorkingDirectory();
if (!workingDir.empty())
{
- fprintf(fp, "%sWorking dir: %s%s\n", prefix, workingDir.c_str(), suffix);
+ writer->writeLine(formatString("%sWorking dir: %s%s", prefix, workingDir.c_str(), suffix));
}
const char *const commandLine = programContext.commandLine();
if (!gmx::isNullOrEmpty(commandLine))
{
- fprintf(fp, "%sCommand line:%s\n%s %s%s\n",
- prefix, suffix, prefix, commandLine, suffix);
+ writer->writeLine(formatString("%sCommand line:%s\n%s %s%s",
+ prefix, suffix, prefix, commandLine, suffix));
}
if (settings.bExtendedInfo_)
{
GMX_RELEASE_ASSERT(prefix[0] == '\0' && suffix[0] == '\0',
"Prefix/suffix not supported with extended info");
- fprintf(fp, "\n");
- gmx_print_version_info(fp);
+ writer->ensureEmptyLine();
+ gmx_print_version_info(writer);
}
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
class IProgramContext;
+class TextWriter;
/*! \libinternal \brief
* Settings for printBinaryInformation().
//! Needed to read the members without otherwise unnecessary accessors.
friend void printBinaryInformation(
- FILE *fp, const IProgramContext &programContext,
+ TextWriter *writer,
+ const IProgramContext &programContext,
const BinaryInformationSettings &settings);
};
const IProgramContext &programContext,
const BinaryInformationSettings &settings);
+/*! \brief
+ * Print basic information about the executable with custom settings.
+ *
+ * \param[out] writer Where to print the information.
+ * \param[in] programContext Program information object to use.
+ * \param[in] settings Specifies what to print.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * \see BinaryInformationSettings
+ */
+void printBinaryInformation(TextWriter *writer,
+ const IProgramContext &programContext,
+ const BinaryInformationSettings &settings);
+
} // namespace gmx
#endif
namespace gmx
{
+#ifdef DOXYGEN
/*! \brief
* Macro to declare a class non-copyable and non-assignable.
*
*
* \ingroup module_utility
*/
+#define GMX_DISALLOW_COPY_AND_ASSIGN(ClassName)
+#else
#define GMX_DISALLOW_COPY_AND_ASSIGN(ClassName) \
ClassName &operator=(const ClassName &) = delete; \
ClassName(const ClassName &) = delete
+#endif
/*! \brief
* Macro to declare a class non-assignable.
*
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/* This file is completely threadsafe - keep it that way! */
+
+#include "gmxpre.h"
+
+#include "compare.h"
+
+#include <cmath>
+#include <cstdio>
+#include <cstring>
+
+#include "gromacs/utility/strconvert.h"
+
+void cmp_int(FILE *fp, const char *s, int index, int i1, int i2)
+{
+ if (i1 != i2)
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%d] (%d - %d)\n", s, index, i1, i2);
+ }
+ else
+ {
+ fprintf(fp, "%s (%d - %d)\n", s, i1, i2);
+ }
+ }
+}
+
+void cmp_int64(FILE *fp, const char *s, gmx_int64_t i1, gmx_int64_t i2)
+{
+ if (i1 != i2)
+ {
+ fprintf(fp, "%s (", s);
+ fprintf(fp, "%" GMX_PRId64, i1);
+ fprintf(fp, " - ");
+ fprintf(fp, "%" GMX_PRId64, i2);
+ fprintf(fp, ")\n");
+ }
+}
+
+void cmp_us(FILE *fp, const char *s, int index, unsigned short i1, unsigned short i2)
+{
+ if (i1 != i2)
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%d] (%hu - %hu)\n", s, index, i1, i2);
+ }
+ else
+ {
+ fprintf(fp, "%s (%hu - %hu)\n", s, i1, i2);
+ }
+ }
+}
+
+void cmp_uc(FILE *fp, const char *s, int index, unsigned char i1, unsigned char i2)
+{
+ if (i1 != i2)
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%d] (%d - %d)\n", s, index, i1, i2);
+ }
+ else
+ {
+ fprintf(fp, "%s (%d - %d)\n", s, i1, i2);
+ }
+ }
+}
+
+gmx_bool cmp_bool(FILE *fp, const char *s, int index, gmx_bool b1, gmx_bool b2)
+{
+ if (b1)
+ {
+ b1 = 1;
+ }
+ else
+ {
+ b1 = 0;
+ }
+ if (b2)
+ {
+ b2 = 1;
+ }
+ else
+ {
+ b2 = 0;
+ }
+ if (b1 != b2)
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%d] (%s - %s)\n", s, index,
+ gmx::boolToString(b1), gmx::boolToString(b2));
+ }
+ else
+ {
+ fprintf(fp, "%s (%s - %s)\n", s,
+ gmx::boolToString(b1), gmx::boolToString(b2));
+ }
+ }
+ return b1 && b2;
+}
+
+void cmp_str(FILE *fp, const char *s, int index, const char *s1, const char *s2)
+{
+ if (std::strcmp(s1, s2) != 0)
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%d] (%s - %s)\n", s, index, s1, s2);
+ }
+ else
+ {
+ fprintf(fp, "%s (%s - %s)\n", s, s1, s2);
+ }
+ }
+}
+
+gmx_bool equal_real(real i1, real i2, real ftol, real abstol)
+{
+ return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol );
+}
+
+gmx_bool equal_float(float i1, float i2, float ftol, float abstol)
+{
+ return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol );
+}
+
+gmx_bool equal_double(double i1, double i2, real ftol, real abstol)
+{
+ return ( ( 2*fabs(i1 - i2) <= (fabs(i1) + fabs(i2))*ftol ) || fabs(i1-i2) <= abstol );
+}
+
+void
+cmp_real(FILE *fp, const char *s, int index, real i1, real i2, real ftol, real abstol)
+{
+ if (!equal_real(i1, i2, ftol, abstol))
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%2d] (%e - %e)\n", s, index, i1, i2);
+ }
+ else
+ {
+ fprintf(fp, "%s (%e - %e)\n", s, i1, i2);
+ }
+ }
+}
+
+void
+cmp_float(FILE *fp, const char *s, int index, float i1, float i2, float ftol, float abstol)
+{
+ if (!equal_float(i1, i2, ftol, abstol))
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%2d] (%e - %e)\n", s, index, i1, i2);
+ }
+ else
+ {
+ fprintf(fp, "%s (%e - %e)\n", s, i1, i2);
+ }
+ }
+}
+
+void
+cmp_double(FILE *fp, const char *s, int index, double i1, double i2, double ftol, double abstol)
+{
+ if (!equal_double(i1, i2, ftol, abstol))
+ {
+ if (index != -1)
+ {
+ fprintf(fp, "%s[%2d] (%16.9e - %16.9e)\n", s, index, i1, i2);
+ }
+ else
+ {
+ fprintf(fp, "%s (%16.9e - %16.9e)\n", s, i1, i2);
+ }
+ }
+}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Utilities for comparing data structures (for gmx check).
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_COMPARE_H
+#define GMX_UTILITY_COMPARE_H
+
+#include <cstdio>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/real.h"
+
+//! Compares two real values for equality.
+gmx_bool equal_real(real i1, real i2, real ftol, real abstol);
+//! Compares two float values for equality.
+gmx_bool equal_float(float i1, float i2, float ftol, float abstol);
+//! Compares two double values for equality.
+gmx_bool equal_double(double i1, double i2, real ftol, real abstol);
+
+//! Compares two integers and prints differences.
+void cmp_int(FILE *fp, const char *s, int index, int i1, int i2);
+
+//! Compares two 64-bit integers and prints differences.
+void cmp_int64(FILE *fp, const char *s, gmx_int64_t i1, gmx_int64_t i2);
+
+//! Compares two unsigned short values and prints differences.
+void cmp_us(FILE *fp, const char *s, int index, unsigned short i1, unsigned short i2);
+
+//! Compares two unsigned char values and prints differences.
+void cmp_uc(FILE *fp, const char *s, int index, unsigned char i1, unsigned char i2);
+
+//! Compares two boolean values and prints differences, and returns whether both are true.
+gmx_bool cmp_bool(FILE *fp, const char *s, int index, gmx_bool b1, gmx_bool b2);
+
+//! Compares two strings and prints differences.
+void cmp_str(FILE *fp, const char *s, int index, const char *s1, const char *s2);
+
+//! Compares two reals and prints differences.
+void cmp_real(FILE *fp, const char *s, int index, real i1, real i2, real ftol, real abstol);
+
+//! Compares two floats and prints differences.
+void cmp_float(FILE *fp, const char *s, int index, float i1, float i2, float ftol, float abstol);
+
+//! Compares two doubles and prints differences.
+void cmp_double(FILE *fp, const char *s, int index, double i1, double i2, double ftol, double abstol);
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* a mutex for locking the variable...
*/
#if GMX_COOL_QUOTES
- return (getenv("GMX_NO_QUOTES") == NULL);
+ return (getenv("GMX_NO_QUOTES") == nullptr);
#else
/*be uncool*/
return false;
{ "I was told I'd never make it to VP rank because I was too outspoken. Maybe so, but I think men will always find an excuse for keeping women in their 'place.' So, let's make that place the executive suite and start more of our own companies.", "Jean Bartik, ENIAC developer" },
{ "If it's a good idea, go ahead and do it. It's much easier to apologize than it is to get permission.", "Grace Hopper, developer of COBOL" },
{ "This isn't right. This isn't even wrong.", "Wolfgang Pauli" },
- { "Louis Pasteur's theory of germs is ridicolous fiction.", "Pierre Pachet, Professor of Physiology at Toulouse, 1872" },
+ { "Louis Pasteur's theory of germs is ridiculous fiction.", "Pierre Pachet, Professor of Physiology at Toulouse, 1872" },
{ "Research ! A mere excuse for idleness; it has never achieved, and will never achieve any results of the slightest value.", "Benjamin Jowett, British theologian, 1817-93" },
{ "Problems worthy of attack prove their worth by hitting back.", "Piet Hein" },
{ "You should never bet against anything in science at odds of more than about 10^12 to 1.", "Ernest Rutherford" },
{ "Sir, spare your threats: The bug which you would fright me with I seek.", "Hermione, Act III, scene II of Shakespeare's Winter's Tale" },
{ "Erwin with his psi can do / Calculations quite a few. / But one thing has not been seen / Just what psi really mean.", "Felix Bloch" },
{ "Only entropy comes easy.", "Anton Chekov" },
- { "The lovliest theories are being overthrown by these damned experiments; it is no fun being a chemist any more.", "Justus von Liebig, letter to J.J. Berzelius 1834" },
+ { "The loveliest theories are being overthrown by these damned experiments; it is no fun being a chemist any more.", "Justus von Liebig, letter to J.J. Berzelius 1834" },
{ "If all else fails, immortality can always be assured by spectacular error.", "John Kenneth Galbraith" },
{ "Always code as if the person who ends up maintaining your code is a violent psychopath who knows where you live.", "Martin Golding" },
{ "If I have not seen as far as others, it is because giants were standing on my shoulders.", "Hal Abelson" },
{ "They don't have half hours in the north", "Carl Caleman" },
{ "Safety lights are for dudes", "Ghostbusters 2016" },
{ "It's 2040 now. Our President is a plant.", "Ghostbusters 2016" },
+ { "It's just B I O L O G Y, can't you see?" "Joe Jackson" },
+ { "Input, output, electricity", "Joni Mitchell" },
+ { "Your daddy ain't your daddy but your daddy don't know", "Dalahan" },
+ { "Why is the Earth moving 'round the sun? Floating in the vacuum with no purpose, not a one", "Fleet Foxes" },
+ { "Everybody has a plan until they get punched in the mouth", "Mike Tyson" },
+ { "Sacrifices must be made", "Otto Lilienthal, dying after having crashed with his glider in 1896" },
+ { "The secret to getting ahead is getting started", "Mark Twain" },
+ { "Water is just water", "Berk Hess" },
+ { "GROMACS First : Making MD Great Again", "Vedran Miletic" },
+ { "You still have to climb to the shoulders of the giants", "Vedran Miletic" },
+ { "The road to openness is paved with git commits", "Vedran Miletic" },
+ { "Performance and power are great targets for tuning, but really you want to tune for money!", "Erik Lindahl" },
+ { "Here are all the 'gmx' tools... but no gmx writethesis", "Christian Blau" },
+ { "The best part of winter in Stockholm is going to Australia", "Mark Abraham" },
+ { "If you don't know what you're doing, use a (M)BAR-based method", "Erik Lindahl" },
+ { "All models are wrong, but some are useful.", "George Box" },
+ { "If your experiment needs a statistician, you need a better experiment.", "Ernest Rutherford" },
+ { "Facts are stubborn things, but statistics are more pliable.", "Laurence Peter" },
+ { "In ancient times they had no statistics so they had to fall back on lies.", "Stephen Leacock" },
+ { "If at first you don't succeed, try two more times so that your failure is statistically significant.", "Dallas Warren" },
+ { "Your theory is crazy, but it's not crazy enough to be true.", "Niels Bohr" },
+ { "Science may never come up with a better office communication system than the coffee break.", "Earl Wilson" },
+ { "A scientific truth does not triumph by convincing its opponents and making them see the light, but rather because its opponents eventually die and a new generation grows up that is familiar with it.", "Max Planck" },
+ { "Computer science is no more about computers than astronomy is about telescopes", "Edsger Dijkstra" },
+ { "If we knew what it was we were doing, it would not be called research, would it?", "Albert Einstein" },
+ { "I have not failed. I've just found 10,000 ways that won't work", "Thomas Alva Edison" },
+ { "The public have an insatiable curiosity to know everything, except what is worth knowing.", "Oscar Wilde" },
+ { "Philosophy of science is about as useful to scientists as ornithology is to birds.", "Richard Feynman" },
+ { "I had trouble with physics in college. When I signed up I thought it said psychics.", "Greg Tamblyn" },
+ { "There’s an old saying among scientific guys: “You can’t make an omelet without breaking eggs, ideally by dropping a cement truck on them from a crane.", "Dave Barry" },
+ { "Occams Razor is the scientific principle that, all things being equal, the simplest explanation is always the dog ate my homework.", "Greg Tamblyn" },
+ { "When you get right down to it, almost every explanation Man came up with for anything until about 1926 was stupid.", "Dave Barry" },
+ { "We all understand the twinge of discomfort at the thought that we share a common ancestor with the apes. No one can embarrass you like a relative.", "Neal DeGrasse Tyson" },
+ { "In physics, you don't have to go around making trouble for yourself. Nature does it for you.", "Frank Wilczek" },
+ { "Every revolutionary idea seems to evoke three stages of reaction. They may be summed up by the phrases: (1) It's completely impossible. (2) It's possible, but not worth doing. (3) I said it was a good idea all along.", "Arthur C. Clarke" },
+ { "Computers are like humans - they do everything except think.", "John von Neumann" },
+ { "With four parameters I can fit an elephant, and with five I can make him wiggle his trunk.", "John von Neumann" },
+ { "Christianity may be OK between consenting adults in private but should not be taught to young children.", "Francis Crick" },
+ { "All approaches at a higher level are suspect until confirmed at the molecular level.", "Francis Crick" },
+ { "We haven’t the money, so we’ve got to think.", "Ernest Rutherford" },
+ { "Furious activity is no substitute for understanding.", "H.H. Williams" },
+ { "Discovery: A couple of months in the laboratory can frequently save a couple of hours in the library.", "Anonymous" },
+ { "Never replicate a successful experiment.", "Fett's law." },
+ { "Raw data is like raw sewage, it requires some processing before it can be spread around. The opposite is true of theories.", "Jim Carr" },
+ { "A university faculty is 500 egotists with a common parking problem.", "Keith Sullivan" },
+ { "Studying expands knowledge. Knowledge is power. Power corrupts. Corruption is a crime. Crime doesn't pay.", "Anonymous" },
+ { "A professor is one who talks in someone else's sleep.", "W.H. Auden" },
+ { "A tidy laboratory means a lazy chemist.", "J.J. Berzelius" },
+ { "Microbiology Lab - Staph Only.", "Anonymous" },
+ { "I can’t go to a restaurant and order food because I keep looking at the fonts on the menu. Five minutes later I realize that it’s also talking about food.", "Donald Knuth" },
+ { "Physics is like sex: sure, it may give some practical results, but that’s not why we do it", "Richard P. Feynman" },
+ { "Statistics: The only science that enables different experts using the same figures to draw different conclusions.", "Evan Esar" },
+ { "If I could remember the names of all these particles, I’d be a botanist.", "Albert Einstein" },
+ { "Science... never solves a problem without creating ten more.", "George Bernard Shaw" },
+ { "A mathematician is a blind man in a dark room looking for a black cat which isn't there.", "Charles Darwin" },
+ { "Nothing shocks me. I'm a scientist.", "Harrison Ford as Indiana Jones" },
+ { "There is an infinite set A that is not too big.", "John von Neumann" },
+ { "If it's all right with Dirac, it's all right with me.", "Enrico Fermi, on being told that there was experimental evidence He-3 nuclei obey Fermi-Dirac statistics." },
+ { "I cannot think of a single one, not even intelligence.", "Enrico Fermi, when asked what characteristics physics Nobel laureates had in common." },
+ { "Heavier-than-air flying machines are impossible.", "Lord Kelvin, President of Royal Society, 1895." },
+ { "All that glitters may not be gold, but at least it contains free electrons.", "John Desmond Baernal" },
+ { "It is disconcerting to reflect on the number of students we have flunked in chemistry for not knowing what we later found to be untrue.", "Robert L. Weber" },
+ { "People are DNA's way of making more DNA.", "Edward O. Wilson" },
+ { "The best model of a cat is another cat..., specially the same cat.", "Arturo Rosenblueth" },
+ { "Computer dating is fine, if you are a computer.", "Rita May Brown" },
+ { "The most likely way for the world to be destroyed, most experts agree, is by accident. That’s where we come in; we’re computer professionals. We cause accidents.", "Nathaniel Borenstein" },
+ { "An intellectual is someone who has found something more interesting than sex.", "Edgar Wallace" },
+ { "Base eight is just like base ten really, if you’re missing two fingers.", "Tom Lehrer" },
+ { "If 10 years from now, when you are doing something quick and dirty, you suddenly visualize that I am looking over your shoulders and say to yourself: ‘Dijkstra would not have liked this’, well that would be enough immortality for me.", "Edsger Dijkstra" },
+ { "Memory is like an orgasm. It’s a lot better of you don’t have to fake it.", "Seymour Cray, on virtual memory" },
+ { "A computer once beat me at chess, but it was no match for me at kick boxing.", "Emo Philips" },
+ { "Home computers are being called upon to perform many new functions, including the consumption of homework formerly eaten by the dog.", "Doug Larson" }
};
if (beCool())
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cctype>
#include <cstring>
-#include <sstream>
#include <string>
#include <vector>
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/sysinfo.h"
+
+//! Comment sign to use.
+#define COMMENTSIGN ';'
int continuing(char *s)
{
char *fgets2(char *line, int n, FILE *stream)
{
char *c;
- if (fgets(line, n, stream) == NULL)
+ if (fgets(line, n, stream) == nullptr)
{
- return NULL;
+ return nullptr;
}
- if ((c = strchr(line, '\n')) != NULL)
+ if ((c = strchr(line, '\n')) != nullptr)
{
*c = '\0';
}
gmx_fatal(FARGS, "An input file contains a line longer than %d characters, while the buffer passed to fgets2 has size %d. The line starts with: '%20.20s'", n, n, line);
}
}
- if ((c = strchr(line, '\r')) != NULL)
+ if ((c = strchr(line, '\r')) != nullptr)
{
*c = '\0';
}
}
/* search for a comment mark and replace it by a zero */
- if ((c = strchr(line, COMMENTSIGN)) != NULL)
+ if ((c = strchr(line, COMMENTSIGN)) != nullptr)
{
(*c) = 0;
}
{
int i, c;
- if (NULL == str)
+ if (nullptr == str)
{
return;
}
{
int nul;
- if (NULL == str)
+ if (nullptr == str)
{
return;
}
rtrim (str);
}
-void nice_header(FILE *out, const char *fn)
-{
- int uid;
- char userbuf[256];
- char hostbuf[256];
- char timebuf[STRLEN];
-
- /* Print a nice header above the file */
- fprintf(out, "%c\n", COMMENTSIGN);
- fprintf(out, "%c\tFile '%s' was generated\n", COMMENTSIGN, fn ? fn : "unknown");
-
- uid = gmx_getuid();
- gmx_getusername(userbuf, 256);
- gmx_gethostname(hostbuf, 256);
- gmx_format_current_time(timebuf, STRLEN);
-
- fprintf(out, "%c\tBy user: %s (%d)\n", COMMENTSIGN, userbuf, uid);
- fprintf(out, "%c\tOn host: %s\n", COMMENTSIGN, hostbuf);
- fprintf(out, "%c\tAt date: %s\n", COMMENTSIGN, timebuf);
- fprintf(out, "%c\n", COMMENTSIGN);
-}
-
int gmx_strcasecmp_min(const char *str1, const char *str2)
{
char ch1, ch2;
* the current line (where it also won't fit, but looks better)
*/
- b2 = NULL;
+ b2 = nullptr;
b2len = strlen(buf)+1+indent;
snew(b2, b2len);
i0 = i2 = 0;
sprintf(buf, "%" GMX_PRId64, i);
return buf;
}
-
-void parse_digits_from_string(const char *digitstring, int *ndigits, int **digitlist)
-{
- /* TODO use std::string, once gmx_gpu_opt_t is ready for it */
- if (NULL == digitstring)
- {
- *ndigits = 0;
- *digitlist = NULL;
- return;
- }
-
- if (strstr(digitstring, ",") != NULL)
- {
- parse_digits_from_csv_string(digitstring, ndigits, digitlist);
- }
- else
- {
- parse_digits_from_plain_string(digitstring, ndigits, digitlist);
- }
-}
-
-void parse_digits_from_plain_string(const char *digitstring, int *ndigits, int **digitlist)
-{
- int i;
-
- if (NULL == digitstring)
- {
- *ndigits = 0;
- *digitlist = NULL;
- return;
- }
-
- *ndigits = strlen(digitstring);
-
- snew(*digitlist, *ndigits);
-
- for (i = 0; i < *ndigits; i++)
- {
- if (digitstring[i] < '0' || digitstring[i] > '9')
- {
- gmx_fatal(FARGS, "Invalid character in digit-only string: '%c'\n",
- digitstring[i]);
- }
- (*digitlist)[i] = digitstring[i] - '0';
- }
-}
-
-void parse_digits_from_csv_string(const char *digitstring, int *ndigits, int **digitlist)
-{
- if (NULL == digitstring)
- {
- *ndigits = 0;
- *digitlist = NULL;
- return;
- }
-
- std::vector<int> digits;
- std::istringstream ss(digitstring);
- std::string token;
- while (std::getline(ss, token, ','))
- {
- if (token.find_first_not_of("0123456789") != std::string::npos)
- {
- gmx_fatal(FARGS, "Invalid token in digit-only string: \"%s\"\n",
- token.c_str());
- }
- int number = static_cast<int>(str_to_int64_t(token.c_str(), NULL));
- digits.push_back(number);
- }
-
- *ndigits = digits.size();
- snew(*digitlist, *ndigits);
- for (size_t i = 0; i < digits.size(); i++)
- {
- (*digitlist)[i] = digits[i];
- }
-}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
/** Continuation character. */
#define CONTINUE '\\'
-/** Comment sign to use. */
-#define COMMENTSIGN ';'
/** Standard size for char* string buffers. */
#define STRLEN 4096
*/
char *fgets2(char *s, int n, FILE *stream);
-/** Remove portion of a line after a ::COMMENTSIGN. */
+/** Remove portion of a line after a ';' comment sign. */
void strip_comment(char *line);
/** Make a string uppercase. */
/** Remove leading and trailing whitespace from a string. */
void trim(char *str);
-/** Prints creation time stamp and user information into a file as comments. */
-void nice_header(FILE *out, const char *fn);
-
/** Version of gmx_strcasecmp() that also ignores '-' and '_'. */
int gmx_strcasecmp_min(const char *str1, const char *str2);
/** Version of gmx_strncasecmp() that also ignores '-' and '_'. */
*/
char *gmx_step_str(gmx_int64_t i, char *buf);
-/*! \brief Construct an array of digits found in the input string
- *
- * \param[in] digitstring String that must contain only digits
- * \param[out] ndigits Size of return array with the values of the digits
- * \param[out] digitlist Array of digits found in
- * digitstring. Allocated by this function
- * with size *ndigits. Calling code is
- * responsible for deallocation.
- *
- * If digitstring is NULL, then ndigits is set to zero and digitlist
- * to NULL. If digitstring contains a non-digit character, a fatal
- * error results.
- */
-void parse_digits_from_plain_string(const char *digitstring, int *ndigits, int **digitlist);
-
-/*! \brief Construct an array of digits from a comma separated input string
- *
- * \param[in] digitstring String that must contain only digits and commas
- * \param[out] ndigits Size of return array with the values of the digits
- * \param[out] digitlist Array of digits found in
- * digitstring. Allocated by this function
- * with size *ndigits. Calling code is
- * responsible for deallocation.
- *
- * If digitstring is NULL, then ndigits is set to zero and digitlist
- * to NULL. If digitstring contains a non digit-or-comma character, a fatal
- * error results.
- */
-void parse_digits_from_csv_string(const char *digitstring, int *ndigits, int **digitlist);
-
-/*! \brief Construct an array of digits an input string
- *
- *
- * \param[in] digitstring String that must contain only digits, or only
- * digits and commas
- * \param[out] ndigits Size of return array with the values of the digits
- * \param[out] digitlist Array of digits found in
- * digitstring. Allocated by this function
- * with size *ndigits. Calling code is
- * responsible for deallocation.
- * If digitstring is NULL, then ndigits is set to zero and digitlist
- * to NULL. If digitstring contains a non digit-or-comma character, a fatal
- * error results.
- */
-void parse_digits_from_string(const char *digitstring, int *ndigits, int **digitlist);
-
#ifdef __cplusplus
}
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "cuda_version_information.h"
-#include <cstdio>
+#include <utility>
-#include "buildinfo.h"
+namespace gmx
+{
-void gmx_print_version_info_cuda_gpu(FILE *fp)
+std::pair<int, int> getCudaDriverVersion()
{
- int cuda_driver, cuda_runtime;
- fprintf(fp, "CUDA compiler: %s\n", CUDA_NVCC_COMPILER_INFO);
- fprintf(fp, "CUDA compiler flags:%s\n", CUDA_NVCC_COMPILER_FLAGS);
- cuda_driver = 0;
+ int cuda_driver;
cudaDriverGetVersion(&cuda_driver);
- cuda_runtime = 0;
+ return std::pair<int, int>(cuda_driver/1000, cuda_driver%100);
+}
+
+std::pair<int, int> getCudaRuntimeVersion()
+{
+ int cuda_runtime;
cudaRuntimeGetVersion(&cuda_runtime);
- fprintf(fp, "CUDA driver: %d.%d\n", cuda_driver/1000, cuda_driver%100);
- fprintf(fp, "CUDA runtime: %d.%d\n", cuda_runtime/1000, cuda_runtime%100);
+ return std::pair<int, int>(cuda_runtime/1000, cuda_runtime%100);
}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_GMXLIB_CUDA_TOOLS_CUDA_VERSION_INFORMATION_H
-#define GMX_GMXLIB_CUDA_TOOLS_CUDA_VERSION_INFORMATION_H
+#ifndef GMX_UTILITY_CUDA_VERSION_INFORMATION_H
+#define GMX_UTILITY_CUDA_VERSION_INFORMATION_H
-#include <cstdio>
+#include <utility>
-void gmx_print_version_info_cuda_gpu(FILE *fp);
+namespace gmx
+{
+
+//! Returns a (major, minor) tuple of the CUDA driver version.
+std::pair<int, int> getCudaDriverVersion();
+
+//! Returns a (major, minor) tuple of the CUDA runtime version.
+std::pair<int, int> getCudaRuntimeVersion();
+
+} // namespace
#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
public:
static std::string getDefaultPath();
- Impl() : envName_(NULL), bEnvIsSet_(false) {}
+ Impl() : envName_(nullptr), bEnvIsSet_(false) {}
const char *envName_;
bool bEnvIsSet_;
std::string filename = findFile(options);
if (filename.empty())
{
- return NULL;
+ return nullptr;
}
#if 0
if (debug)
message.append(defaultPath);
message.append(" (default)");
}
- if (!bEnvIsSet && envName != NULL)
+ if (!bEnvIsSet && envName != nullptr)
{
message.append(
formatString("\nYou can set additional directories to search "
".", options.filename_, false);
for (i = files.begin(); i != files.end(); ++i)
{
- result.push_back(DataFileInfo(".", *i, false));
+ result.emplace_back(".", *i, false);
}
}
if (impl_ != nullptr)
j->c_str(), options.filename_, false);
for (i = files.begin(); i != files.end(); ++i)
{
- result.push_back(DataFileInfo(*j, *i, false));
+ result.emplace_back(*j, *i, false);
}
}
}
defaultPath.c_str(), options.filename_, false);
for (i = files.begin(); i != files.end(); ++i)
{
- result.push_back(DataFileInfo(defaultPath, *i, true));
+ result.emplace_back(defaultPath, *i, true);
}
}
if (result.empty() && options.bThrow_)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
errno = 0;
DIR *handle = opendir(dirname);
- if (handle == NULL)
+ if (handle == nullptr)
{
if (bThrow)
{
dirname);
GMX_THROW_WITH_ERRNO(FileIOError(message), "opendir", code);
}
- return NULL;
+ return nullptr;
}
return new Impl(handle);
}
{
errno = 0;
dirent *p = readdir(dirent_handle);
- if (p == NULL)
+ if (p == nullptr)
{
if (errno == 0)
{
DirectoryEnumerator::DirectoryEnumerator(const char *dirname, bool bThrow)
: impl_(nullptr)
{
- GMX_RELEASE_ASSERT(dirname != NULL && dirname[0] != '\0',
+ GMX_RELEASE_ASSERT(dirname != nullptr && dirname[0] != '\0',
"Attempted to open empty/null directory path");
impl_.reset(Impl::init(dirname, bThrow));
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"System I/O error",
"Error in user input",
"Inconsistency in user input",
+ "Requested tolerance cannot be achieved",
"Simulation instability detected",
"Feature not implemented",
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
eeInvalidInput,
//! Invalid user input (conflicting or unsupported settings).
eeInconsistentInput,
+ //! Requested tolerance cannot be achieved.
+ eeTolerance,
//! Simulation instability detected.
eeInstability,
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::fprintf(fp, "\n-------------------------------------------------------\n");
std::fprintf(fp, "Program: %s, version %s\n", programName, gmx_version());
- if (file != NULL)
+ if (file != nullptr)
{
std::fprintf(fp, "Source file: %s (line %d)\n",
Path::stripSourcePrefix(file), line);
}
- if (func != NULL)
+ if (func != nullptr)
{
std::fprintf(fp, "Function: %s\n", func);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char *GromacsException::what() const noexcept
{
const ErrorMessage *msg = getInfo<ExceptionInfoMessage>();
- if (msg == NULL)
+ if (msg == nullptr)
{
return "No reason provided";
}
void GromacsException::prependContext(const std::string &context)
{
const ErrorMessage *msg = getInfo<ExceptionInfoMessage>();
- GMX_RELEASE_ASSERT(msg != NULL, "Message should always be set");
+ GMX_RELEASE_ASSERT(msg != nullptr, "Message should always be set");
setInfo(ExceptionInfoMessage(msg->prependContext(context)));
}
return eeInconsistentInput;
}
+int ToleranceError::errorCode() const
+{
+ return eeTolerance;
+}
+
int SimulationInstabilityError::errorCode() const
{
return eeInstability;
return eeAPIError;
}
+int RangeError::errorCode() const
+{
+ return eeRange;
+}
+
int NotImplementedError::errorCode() const
{
return eeNotImplemented;
{
std::fprintf(fp_, "%*sReason: %s\n", indent, "",
std::strerror(errorNumber));
- if (funcName != NULL)
+ if (funcName != nullptr)
{
std::fprintf(fp_, "%*s(call to %s() returned error code %d)\n",
indent, "", funcName, errorNumber);
{
writer_->wrapperSettings().setIndent(indent);
writer_->writeLine(formatString("Reason: %s", std::strerror(errorNumber)));
- if (funcName != NULL)
+ if (funcName != nullptr)
{
writer_->writeLine(
formatString("(call to %s() returned error code %d)",
{
writeLine(formatString("Reason: %s", std::strerror(errorNumber)).c_str(),
indent);
- if (funcName != NULL)
+ if (funcName != nullptr)
{
writeLine(formatString("(call to %s() returned error code %d)",
funcName, errorNumber).c_str(),
const std::exception &ex, int indent)
{
const GromacsException *gmxEx = dynamic_cast<const GromacsException *>(&ex);
- if (gmxEx != NULL)
+ if (gmxEx != nullptr)
{
// TODO: Add an option to print location information for the tests
bool bAnythingWritten = false;
// TODO: Remove duplicate context if present in multiple nested exceptions.
const ErrorMessage *msg = gmxEx->getInfo<ExceptionInfoMessage>();
- if (msg != NULL)
+ if (msg != nullptr)
{
- while (msg != NULL && msg->isContext())
+ while (msg != nullptr && msg->isContext())
{
writer->writeLine(msg->text().c_str(), indent*2);
++indent;
msg = &msg->child();
}
- if (msg != NULL && !msg->text().empty())
+ if (msg != nullptr && !msg->text().empty())
{
writer->writeLine(msg->text().c_str(), indent*2);
bAnythingWritten = true;
}
const int *errorNumber = gmxEx->getInfo<ExceptionInfoErrno>();
- if (errorNumber != NULL && *errorNumber != 0)
+ if (errorNumber != nullptr && *errorNumber != 0)
{
const char * const *funcName
= gmxEx->getInfo<ExceptionInfoApiFunction>();
writer->writeErrNoInfo(*errorNumber,
- funcName != NULL ? *funcName : NULL,
+ funcName != nullptr ? *funcName : nullptr,
(indent+1)*2);
bAnythingWritten = true;
}
const internal::NestedExceptionList *nested
= gmxEx->getInfo<ExceptionInfoNestedExceptions>();
- if (nested != NULL)
+ if (nested != nullptr)
{
internal::NestedExceptionList::const_iterator ni;
for (ni = nested->begin(); ni != nested->end(); ++ni)
bool bPrintType = false;
const GromacsException *gmxEx = dynamic_cast<const GromacsException *>(&ex);
// TODO: Treat more of the standard exceptions
- if (gmxEx != NULL)
+ if (gmxEx != nullptr)
{
title = getErrorCodeString(gmxEx->errorCode());
}
- else if (dynamic_cast<const tMPI::system_error *>(&ex) != NULL)
+ else if (dynamic_cast<const tMPI::system_error *>(&ex) != nullptr)
{
title = "System error in thread synchronization";
}
- else if (dynamic_cast<const std::bad_alloc *>(&ex) != NULL)
+ else if (dynamic_cast<const std::bad_alloc *>(&ex) != nullptr)
{
title = "Memory allocation failed";
}
- else if (dynamic_cast<const std::logic_error *>(&ex) != NULL)
+ else if (dynamic_cast<const std::logic_error *>(&ex) != nullptr)
{
title = "Standard library logic error (bug)";
bPrintType = true;
}
- else if (dynamic_cast<const std::runtime_error *>(&ex) != NULL)
+ else if (dynamic_cast<const std::runtime_error *>(&ex) != nullptr)
{
title = "Standard library runtime error (possible bug)";
bPrintType = true;
virtual int errorCode() const;
};
+/*! \brief
+ * Exception class when a specified tolerance cannot be achieved.
+ *
+ * \inpublicapi
+ */
+class ToleranceError : public GromacsException
+{
+ public:
+ /*! \brief
+ * Creates an exception object with the provided initializer/reason.
+ *
+ * \param[in] details Initializer for the exception.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * It is possible to call this constructor either with an explicit
+ * ExceptionInitializer object (useful for more complex cases), or
+ * a simple string if only a reason string needs to be provided.
+ */
+ explicit ToleranceError(const ExceptionInitializer &details)
+ : GromacsException(details) {}
+
+ virtual int errorCode() const;
+};
+
/*! \brief
* Exception class for simulation instabilities.
*
virtual int errorCode() const;
};
+/*! \brief
+ * Exception class for out-of-range values or indices
+ *
+ * \inpublicapi
+ */
+class RangeError : public GromacsException
+{
+ public:
+ //! \copydoc FileIOError::FileIOError()
+ explicit RangeError(const ExceptionInitializer &details)
+ : GromacsException(details) {}
+
+ virtual int errorCode() const;
+};
+
/*! \brief
* Exception class for use of an unimplemented feature.
*
virtual int errorCode() const;
};
-
/*! \brief
* Macro for throwing an exception.
*
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <exception>
-#include "thread_mpi/threads.h"
-
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/errorcodes.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/mutex.h"
#include "gromacs/utility/programcontext.h"
#if GMX_MPI
#include "errorformat.h"
-static bool bDebug = false;
-static tMPI_Thread_mutex_t where_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+static bool bDebug = false;
+static gmx::Mutex where_mutex;
+
+FILE *debug = nullptr;
+gmx_bool gmx_debug_at = FALSE;
-FILE *debug = NULL;
-gmx_bool gmx_debug_at = FALSE;
+static FILE *log_file = nullptr;
+static gmx::Mutex error_mutex;
-static FILE *log_file = NULL;
-static tMPI_Thread_mutex_t error_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+using Lock = gmx::lock_guard<gmx::Mutex>;
void gmx_init_debug(const int dbglevel, const char *dbgfile)
{
if (bFirst)
{
- tMPI_Thread_mutex_lock(&where_mutex);
+ Lock lock(where_mutex);
if (bFirst) /* we repeat the check in the locked section because things
might have changed */
{
- if ((temp = getenv("GMX_PRINT_DEBUG_LINES")) != NULL)
+ if ((temp = getenv("GMX_PRINT_DEBUG_LINES")) != nullptr)
{
- nskip = strtol(temp, NULL, 10);
+ nskip = strtol(temp, nullptr, 10);
}
bFirst = FALSE;
}
- tMPI_Thread_mutex_unlock(&where_mutex);
}
+ // TODO None of this is thread safe, and presumably it was only
+ // meant to run when debugging. But it runs many times every MD
+ // step. Nice. See Redmine #2122.
if (nskip >= 0)
{
/* Skip the first n occasions, this allows to see where it goes wrong */
{
if (log_file)
{
- gmx::internal::printFatalErrorHeader(log_file, title, NULL, file, line);
+ gmx::internal::printFatalErrorHeader(log_file, title, nullptr, file, line);
gmx::internal::printFatalErrorMessageLine(log_file, msg, 0);
gmx::internal::printFatalErrorFooter(log_file);
}
- gmx::internal::printFatalErrorHeader(stderr, title, NULL, file, line);
+ gmx::internal::printFatalErrorHeader(stderr, title, nullptr, file, line);
gmx::internal::printFatalErrorMessageLine(stderr, msg, 0);
gmx::internal::printFatalErrorFooter(stderr);
}
void gmx_set_error_handler(gmx_error_handler_t func)
{
- tMPI_Thread_mutex_lock(&error_mutex);
+ Lock lock(error_mutex);
gmx_error_handler = func;
- tMPI_Thread_mutex_unlock(&error_mutex);
}
static const char *gmx_strerror(const char *key)
{ "range", "Range checking error" }
};
- if (key == NULL)
+ if (key == nullptr)
{
return "NULL error type (should not occur)";
}
static void call_error_handler(const char *key, const char *file, int line, const char *msg)
{
- if (msg == NULL)
+ if (msg == nullptr)
{
msg = "Empty gmx_fatal message (bug).";
}
- tMPI_Thread_mutex_lock(&error_mutex);
+ Lock lock(error_mutex);
gmx_error_handler(gmx_strerror(key), msg, file, line);
- tMPI_Thread_mutex_unlock(&error_mutex);
}
void gmx_exit_on_fatal_error(ExitType exitType, int returnValue)
if ((n < n_min) || (n >= n_max))
{
- if (warn_str != NULL)
+ if (warn_str != nullptr)
{
strcpy(buf, warn_str);
strcat(buf, "\n");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::string result;
char buf[bufsize];
buf[0] = '\0';
- while (std::fgets(buf, bufsize, fp) != NULL)
+ while (std::fgets(buf, bufsize, fp) != nullptr)
{
const size_t length = std::strlen(buf);
result.append(buf, length);
{
}
FileStreamImpl(const char *filename, const char *mode)
- : fp_(NULL), bClose_(true)
+ : fp_(nullptr), bClose_(true)
{
fp_ = std::fopen(filename, mode);
- if (fp_ == NULL)
+ if (fp_ == nullptr)
{
GMX_THROW_WITH_ERRNO(
FileIOError(formatString("Could not open file '%s'", filename)),
}
~FileStreamImpl()
{
- if (fp_ != NULL && bClose_)
+ if (fp_ != nullptr && bClose_)
{
if (std::fclose(fp_) != 0)
{
FILE *handle()
{
- GMX_RELEASE_ASSERT(fp_ != NULL,
+ GMX_RELEASE_ASSERT(fp_ != nullptr,
"Attempted to access a file object that is not open");
return fp_;
}
void close()
{
- GMX_RELEASE_ASSERT(fp_ != NULL,
+ GMX_RELEASE_ASSERT(fp_ != nullptr,
"Attempted to close a file object that is not open");
GMX_RELEASE_ASSERT(bClose_,
"Attempted to close a file object that should not be");
const bool bOk = (std::fclose(fp_) == 0);
- fp_ = NULL;
+ fp_ = nullptr;
if (!bOk)
{
GMX_THROW_WITH_ERRNO(
FILE *TextInputFile::openRawHandle(const char *filename)
{
FILE *fp = fopen(filename, "r");
- if (fp == NULL)
+ if (fp == nullptr)
{
GMX_THROW_WITH_ERRNO(
FileIOError(formatString("Could not open file '%s'", filename)),
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <windows.h>
#endif
-#include "thread_mpi/threads.h"
-
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/datafilefinder.h"
#include "gromacs/utility/dir_separator.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/mutex.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
struct t_pstack *prev;
} t_pstack;
-static t_pstack *pstack = NULL;
+static t_pstack *pstack = nullptr;
static bool bUnbuffered = false;
static int s_maxBackupCount = 0;
/* this linked list is an intrinsically globally shared object, so we have
to protect it with mutexes */
-static tMPI_Thread_mutex_t pstack_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
+static gmx::Mutex pstack_mutex;
+
+using Lock = gmx::lock_guard<gmx::Mutex>;
namespace gmx
{
const DataFileFinder &getLibraryFileFinder()
{
- if (g_libFileFinder != NULL)
+ if (g_libFileFinder != nullptr)
{
return *g_libFileFinder;
}
if (count < 0)
{
const char *env = getenv("GMX_MAXBACKUP");
- if (env != NULL)
+ if (env != nullptr)
{
// TODO: Check that the value is converted properly.
- count = strtol(env, NULL, 10);
+ count = strtol(env, nullptr, 10);
if (count < 0)
{
count = 0;
s_maxBackupCount = count;
}
-void push_ps(FILE *fp)
+static void push_ps(FILE *fp)
{
t_pstack *ps;
- tMPI_Thread_mutex_lock(&pstack_mutex);
+ Lock pstackLock(pstack_mutex);
snew(ps, 1);
ps->fp = fp;
ps->prev = pstack;
pstack = ps;
-
- tMPI_Thread_mutex_unlock(&pstack_mutex);
}
#ifdef GMX_FAHCORE
t_pstack *ps, *tmp;
int ret = 0;
- tMPI_Thread_mutex_lock(&pstack_mutex);
+ Lock pstackLock(pstack_mutex);
ps = pstack;
- if (ps == NULL)
+ if (ps == nullptr)
{
- if (fp != NULL)
+ if (fp != nullptr)
{
ret = fclose(fp);
}
}
else if (ps->fp == fp)
{
- if (fp != NULL)
+ if (fp != nullptr)
{
ret = pclose(fp);
}
}
else
{
- while ((ps->prev != NULL) && (ps->prev->fp != fp))
+ while ((ps->prev != nullptr) && (ps->prev->fp != fp))
{
ps = ps->prev;
}
- if ((ps->prev != NULL) && ps->prev->fp == fp)
+ if ((ps->prev != nullptr) && ps->prev->fp == fp)
{
- if (ps->prev->fp != NULL)
+ if (ps->prev->fp != nullptr)
{
ret = pclose(ps->prev->fp);
}
}
else
{
- if (fp != NULL)
+ if (fp != nullptr)
{
ret = fclose(fp);
}
}
}
- tMPI_Thread_mutex_unlock(&pstack_mutex);
return ret;
#endif
}
void frewind(FILE *fp)
{
- tMPI_Thread_mutex_lock(&pstack_mutex);
+ Lock pstackLock(pstack_mutex);
t_pstack *ps = pstack;
- while (ps != NULL)
+ while (ps != nullptr)
{
if (ps->fp == fp)
{
fprintf(stderr, "Cannot rewind compressed file!\n");
- tMPI_Thread_mutex_unlock(&pstack_mutex);
return;
}
ps = ps->prev;
}
rewind(fp);
- tMPI_Thread_mutex_unlock(&pstack_mutex);
}
int gmx_fseek(FILE *stream, gmx_off_t offset, int whence)
sprintf(buf, "uncompress -c < %s", fn);
fprintf(stderr, "Going to execute '%s'\n", buf);
- if ((fp = popen(buf, mode)) == NULL)
+ if ((fp = popen(buf, mode)) == nullptr)
{
gmx_open(fn);
}
sprintf(buf, "gunzip -c < %s", fn);
fprintf(stderr, "Going to execute '%s'\n", buf);
- if ((fp = popen(buf, mode)) == NULL)
+ if ((fp = popen(buf, mode)) == nullptr)
{
gmx_open(fn);
}
{
FILE *test;
- if (fname == NULL)
+ if (fname == nullptr)
{
return FALSE;
}
test = fopen(fname, "r");
- if (test == NULL)
+ if (test == nullptr)
{
/*Windows doesn't allow fopen of directory - so we need to check this seperately */
#if GMX_NATIVE_WINDOWS
#ifdef SKIP_FFOPS
return fopen(file, mode);
#else
- FILE *ff = NULL;
- char buf[256], *bufsize = 0, *ptr;
+ FILE *ff = nullptr;
+ char buf[256], *bufsize = nullptr, *ptr;
gmx_bool bRead;
int bs;
- if (file == NULL)
+ if (file == nullptr)
{
- return NULL;
+ return nullptr;
}
if (mode[0] == 'w')
strcpy(buf, file);
if (!bRead || gmx_fexist(buf))
{
- if ((ff = fopen(buf, mode)) == NULL)
+ if ((ff = fopen(buf, mode)) == nullptr)
{
gmx_file(buf);
}
/* Check whether we should be using buffering (default) or not
* (for debugging)
*/
- if (bUnbuffered || ((bufsize = getenv("GMX_LOG_BUFFER")) != NULL))
+ if (bUnbuffered || ((bufsize = getenv("GMX_LOG_BUFFER")) != nullptr))
{
/* Check whether to use completely unbuffered */
if (bUnbuffered)
}
else
{
- bs = strtol(bufsize, NULL, 10);
+ bs = strtol(bufsize, nullptr, 10);
}
if (bs <= 0)
{
- setbuf(ff, NULL);
+ setbuf(ff, nullptr);
}
else
{
}
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- return NULL;
+ return nullptr;
}
FILE *low_libopen(const char *file, gmx_bool bFatal)
return fp;
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
- return NULL;
+ return nullptr;
}
char *gmxlibfn(const char *file)
FILE *gmx_fopen_temporary(char *buf)
{
int i, len;
- FILE *fpout = NULL;
+ FILE *fpout = nullptr;
if ((len = strlen(buf)) < 7)
{
gmx_fatal(FARGS, "Error creating temporary file %s: %s", buf,
strerror(errno));
}
- if ((fpout = fdopen(fd, "w")) == NULL)
+ if ((fpout = fdopen(fd, "w")) == nullptr)
{
gmx_fatal(FARGS, "Cannot open temporary file %s", buf);
}
{
/* the full copy buffer size: */
#define FILECOPY_BUFSIZE (1<<16)
- FILE *in = NULL;
- FILE *out = NULL;
+ FILE *in = nullptr;
+ FILE *out = nullptr;
char *buf;
snew(buf, FILECOPY_BUFSIZE);
#else
char *pdum = getcwd(buffer, size);
#endif
- if (pdum == NULL)
+ if (pdum == nullptr)
{
gmx_fatal(FARGS, "Cannot get working directory. Reason: %s",
strerror(errno));
*/
/*! \libinternal \file
* \brief
- * Wraps <mpi.h> usage in Gromacs.
+ * Wraps mpi.h usage in Gromacs.
*
* This header wraps the MPI header <mpi.h>, and should be included instead of
* that one. It abstracts away the case that depending on compilation
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
bool shouldSetAffinity = true;
- *message = NULL;
+ *message = nullptr;
#if GMX_OPENMP
/* We assume that the affinity setting is available on all platforms
* gcc supports. Even if this is not the case (e.g. Mac OS) the user
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
const char *const gomp_env = getenv("GOMP_CPU_AFFINITY");
- const bool bGompCpuAffinitySet = (gomp_env != NULL);
+ const bool bGompCpuAffinitySet = (gomp_env != nullptr);
/* turn off internal pinning if GOMP_CPU_AFFINITY is set & non-empty */
if (bGompCpuAffinitySet && *gomp_env != '\0')
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
bool match(const char *value) const
{
- int rc = regexec(®ex_, value, 0, NULL, 0);
+ int rc = regexec(®ex_, value, 0, nullptr, 0);
if (rc != 0 && rc != REG_NOMATCH)
{
// TODO: Handle errors.
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "ikeyvaluetreeerror.h"
+
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+class DefaultKeyValueTreeErrorHandler : public IKeyValueTreeErrorHandler
+{
+ public:
+ virtual bool onError(UserInputError *ex, const KeyValueTreePath &context)
+ {
+ std::string message
+ = formatString("While processing '%s':", context.toString().c_str());
+ ex->prependContext(message);
+ return false;
+ }
+};
+
+} // namespace
+
+IKeyValueTreeErrorHandler::~IKeyValueTreeErrorHandler()
+{
+}
+
+//! \cond libapi
+IKeyValueTreeErrorHandler *defaultKeyValueTreeErrorHandler()
+{
+ static DefaultKeyValueTreeErrorHandler instance;
+ return &instance;
+}
+//! \endcond
+
+} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifndef GMX_GMXLIB_MD_LOGGING_H
-#define GMX_GMXLIB_MD_LOGGING_H
+/*! \libinternal \file
+ * \brief
+ * Declares an error handling interface for key-value tree operations.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_KEYVALUETREEERROR_H
+#define GMX_UTILITY_KEYVALUETREEERROR_H
-#include <cstdio>
+namespace gmx
+{
-struct t_commrec;
+class KeyValueTreePath;
+class UserInputError;
-void md_print_info(const t_commrec *cr, FILE *fplog,
- const char *fmt, ...);
-/* Print an general information message to stderr on the master node
- * and to fplog if fplog!=NULL.
- * fmt is a standard printf formatting string which should end in \n,
- * the arguments after that contain the values to be printed, as in printf.
- */
+class IKeyValueTreeErrorHandler
+{
+ public:
+ virtual bool onError(UserInputError *ex, const KeyValueTreePath &context) = 0;
-void md_print_warn(const t_commrec *cr, FILE *fplog,
- const char *fmt, ...);
-/* As md_print_info above, but for important notices or warnings.
- * The only difference with md_print_info is that a newline is printed
- * before and after the message such that it stands out.
+ protected:
+ ~IKeyValueTreeErrorHandler();
+};
+
+//! \cond libapi
+/*! \brief
+ * Returns a default IKeyValueTreeErrorHandler that throws on first exception.
+ *
+ * \ingroup module_utility
*/
+IKeyValueTreeErrorHandler *defaultKeyValueTreeErrorHandler();
+//! \endcond
+
+} // namespace gmx
#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "inmemoryserializer.h"
+
+#include <algorithm>
+#include <vector>
+
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+template <typename T>
+class CharBuffer
+{
+ public:
+ static const size_t ValueSize = sizeof(T);
+
+ explicit CharBuffer(T value)
+ {
+ u.v = value;
+ }
+ explicit CharBuffer(const char buffer[])
+ {
+ std::copy(buffer, buffer + ValueSize, u.c);
+ }
+
+ T value() const { return u.v; }
+
+ void appendTo(std::vector<char> *buffer)
+ {
+ buffer->insert(buffer->end(), u.c, u.c + ValueSize);
+ }
+
+ private:
+ union {
+ char c[ValueSize];
+ T v;
+ } u;
+};
+
+} // namespace
+
+/********************************************************************
+ * InMemorySerializer
+ */
+
+class InMemorySerializer::Impl
+{
+ public:
+ template <typename T>
+ void doValue(T value)
+ {
+ CharBuffer<T>(value).appendTo(&buffer_);
+ }
+ void doString(const std::string &value)
+ {
+ doValue<size_t>(value.size());
+ buffer_.insert(buffer_.end(), value.begin(), value.end());
+ }
+
+ std::vector<char> buffer_;
+};
+
+InMemorySerializer::InMemorySerializer()
+ : impl_(new Impl)
+{
+}
+
+InMemorySerializer::~InMemorySerializer()
+{
+}
+
+std::vector<char> InMemorySerializer::finishAndGetBuffer()
+{
+ return std::move(impl_->buffer_);
+}
+
+void InMemorySerializer::doBool(bool *value)
+{
+ impl_->doValue(*value);
+}
+
+void InMemorySerializer::doUChar(unsigned char *value)
+{
+ impl_->doValue(*value);
+}
+
+void InMemorySerializer::doInt(int *value)
+{
+ impl_->doValue(*value);
+}
+
+void InMemorySerializer::doInt64(gmx_int64_t *value)
+{
+ impl_->doValue(*value);
+}
+
+void InMemorySerializer::doFloat(float *value)
+{
+ impl_->doValue(*value);
+}
+
+void InMemorySerializer::doDouble(double *value)
+{
+ impl_->doValue(*value);
+}
+
+void InMemorySerializer::doString(std::string *value)
+{
+ impl_->doString(*value);
+}
+
+/********************************************************************
+ * InMemoryDeserializer
+ */
+
+class InMemoryDeserializer::Impl
+{
+ public:
+ explicit Impl(const std::vector<char> &buffer)
+ : buffer_(buffer), pos_(0)
+ {
+ }
+
+ template <typename T>
+ void doValue(T *value)
+ {
+ *value = CharBuffer<T>(&buffer_[pos_]).value();
+ pos_ += CharBuffer<T>::ValueSize;
+ }
+ void doString(std::string *value)
+ {
+ size_t size;
+ doValue<size_t>(&size);
+ *value = std::string(&buffer_[pos_], size);
+ pos_ += size;
+ }
+
+ const std::vector<char> &buffer_;
+ size_t pos_;
+};
+
+InMemoryDeserializer::InMemoryDeserializer(const std::vector<char> &buffer)
+ : impl_(new Impl(buffer))
+{
+}
+
+InMemoryDeserializer::~InMemoryDeserializer()
+{
+}
+
+void InMemoryDeserializer::doBool(bool *value)
+{
+ impl_->doValue(value);
+}
+
+void InMemoryDeserializer::doUChar(unsigned char *value)
+{
+ impl_->doValue(value);
+}
+
+void InMemoryDeserializer::doInt(int *value)
+{
+ impl_->doValue(value);
+}
+
+void InMemoryDeserializer::doInt64(gmx_int64_t *value)
+{
+ impl_->doValue(value);
+}
+
+void InMemoryDeserializer::doFloat(float *value)
+{
+ impl_->doValue(value);
+}
+
+void InMemoryDeserializer::doDouble(double *value)
+{
+ impl_->doValue(value);
+}
+
+void InMemoryDeserializer::doString(std::string *value)
+{
+ impl_->doString(value);
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::ISerializer implementation for in-memory serialization.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_INMEMORYSERIALIZER_H
+#define GMX_UTILITY_INMEMORYSERIALIZER_H
+
+#include <vector>
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/iserializer.h"
+
+namespace gmx
+{
+
+class InMemorySerializer : public ISerializer
+{
+ public:
+ InMemorySerializer();
+ virtual ~InMemorySerializer();
+
+ std::vector<char> finishAndGetBuffer();
+
+ // From ISerializer
+ virtual bool reading() const { return false; }
+ virtual void doBool(bool *value);
+ virtual void doUChar(unsigned char *value);
+ virtual void doInt(int *value);
+ virtual void doInt64(gmx_int64_t *value);
+ virtual void doFloat(float *value);
+ virtual void doDouble(double *value);
+ virtual void doString(std::string *value);
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+class InMemoryDeserializer : public ISerializer
+{
+ public:
+ explicit InMemoryDeserializer(const std::vector<char> &buffer);
+ virtual ~InMemoryDeserializer();
+
+ // From ISerializer
+ virtual bool reading() const { return true; }
+ virtual void doBool(bool *value);
+ virtual void doUChar(unsigned char *value);
+ virtual void doInt(int *value);
+ virtual void doInt64(gmx_int64_t *value);
+ virtual void doFloat(float *value);
+ virtual void doDouble(double *value);
+ virtual void doString(std::string *value);
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
i = static_cast<int>(step);
- if (warn != NULL && (static_cast<gmx_int64_t>(i) != step))
+ if (warn != nullptr && (static_cast<gmx_int64_t>(i) != step))
{
fprintf(stderr, "\nWARNING during %s:\n", warn);
fprintf(stderr, "int64 value ");
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares a generic serialization interface that supports both directions.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_ISERIALIZER_H
+#define GMX_UTILITY_ISERIALIZER_H
+
+#include <string>
+
+#include "gromacs/utility/basedefinitions.h"
+
+namespace gmx
+{
+
+/*! \libinternal
+ * \brief Interface for types that convert standard data types into a
+ * form suitable for storage or transfer.
+ *
+ * Different implementations could suit MPI, file I/O, or in-memory
+ * conversion. */
+class ISerializer
+{
+ public:
+ //! Destructor.
+ virtual ~ISerializer() {}
+ /*! \brief Returns whether the serializer is reading or
+ * writing, because details like memory management vary
+ * accordingly. */
+ virtual bool reading() const = 0;
+ //! \brief Serialize values of different types.
+ ///@{
+ virtual void doBool(bool *value) = 0;
+ virtual void doUChar(unsigned char *value) = 0;
+ virtual void doInt(int *value) = 0;
+ virtual void doInt64(gmx_int64_t *value) = 0;
+ virtual void doFloat(float *value) = 0;
+ virtual void doDouble(double *value) = 0;
+ virtual void doString(std::string *value) = 0;
+ ///@}
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "keyvaluetree.h"
+
+#include <string>
+#include <vector>
+
+#include "gromacs/utility/compare.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+//! Helper function to split a KeyValueTreePath to its components
+std::vector<std::string> splitPathElements(const std::string &path)
+{
+ GMX_ASSERT(!path.empty() && path[0] == '/',
+ "Paths to KeyValueTree should start with '/'");
+ return splitDelimitedString(path.substr(1), '/');
+}
+
+} // namespace
+
+/********************************************************************
+ * KeyValueTreePath
+ */
+
+KeyValueTreePath::KeyValueTreePath(const char *path)
+ : path_(splitPathElements(path))
+{
+}
+
+KeyValueTreePath::KeyValueTreePath(const std::string &path)
+ : path_(splitPathElements(path))
+{
+}
+
+std::string KeyValueTreePath::toString() const
+{
+ return "/" + joinStrings(path_, "/");
+}
+
+/********************************************************************
+ * KeyValueTreeObject
+ */
+
+bool KeyValueTreeObject::hasDistinctProperties(const KeyValueTreeObject &obj) const
+{
+ for (const auto &prop : obj.values_)
+ {
+ if (keyExists(prop.key()))
+ {
+ GMX_RELEASE_ASSERT(!prop.value().isArray(),
+ "Comparison of arrays not implemented");
+ if (prop.value().isObject() && valueMap_.at(prop.key()).isObject())
+ {
+ return valueMap_.at(prop.key()).asObject().hasDistinctProperties(prop.value().asObject());
+ }
+ return false;
+ }
+ }
+ return true;
+}
+
+/********************************************************************
+ * Key value tree dump
+ */
+
+//! \cond libapi
+void dumpKeyValueTree(TextWriter *writer, const KeyValueTreeObject &tree)
+{
+ for (const auto &prop : tree.properties())
+ {
+ const auto &value = prop.value();
+ if (value.isObject())
+ {
+ writer->writeString(prop.key());
+ writer->writeLine(":");
+ int oldIndent = writer->wrapperSettings().indent();
+ writer->wrapperSettings().setIndent(oldIndent + 2);
+ dumpKeyValueTree(writer, value.asObject());
+ writer->wrapperSettings().setIndent(oldIndent);
+ }
+ else
+ {
+ int indent = writer->wrapperSettings().indent();
+ writer->writeString(formatString("%*s", -(33-indent), prop.key().c_str()));
+ writer->writeString(" = ");
+ if (value.isArray())
+ {
+ writer->writeString("[");
+ for (const auto &elem : value.asArray().values())
+ {
+ GMX_RELEASE_ASSERT(!elem.isObject() && !elem.isArray(),
+ "Arrays of objects not currently implemented");
+ writer->writeString(" ");
+ writer->writeString(simpleValueToString(elem));
+ }
+ writer->writeString(" ]");
+ }
+ else
+ {
+ writer->writeString(simpleValueToString(value));
+ }
+ writer->writeLine();
+ }
+ }
+}
+//! \endcond
+
+/********************************************************************
+ * Key value tree comparison
+ */
+
+namespace
+{
+
+class CompareHelper
+{
+ public:
+ CompareHelper(TextWriter *writer, real ftol, real abstol)
+ : writer_(writer), ftol_(ftol), abstol_(abstol)
+ {
+ }
+
+ void compareObjects(const KeyValueTreeObject &obj1,
+ const KeyValueTreeObject &obj2)
+ {
+ for (const auto &prop1 : obj1.properties())
+ {
+ currentPath_.append(prop1.key());
+ if (obj2.keyExists(prop1.key()))
+ {
+ compareValues(prop1.value(), obj2[prop1.key()]);
+ }
+ else
+ {
+ handleMissingKeyInSecondObject(prop1.value());
+ }
+ currentPath_.pop_back();
+ }
+ for (const auto &prop2 : obj2.properties())
+ {
+ currentPath_.append(prop2.key());
+ if (!obj1.keyExists(prop2.key()))
+ {
+ handleMissingKeyInFirstObject(prop2.value());
+ }
+ currentPath_.pop_back();
+ }
+ }
+
+ private:
+ void compareValues(const KeyValueTreeValue &value1,
+ const KeyValueTreeValue &value2)
+ {
+ if (value1.type() == value2.type())
+ {
+ if (value1.isObject())
+ {
+ compareObjects(value1.asObject(), value2.asObject());
+ }
+ else if (value1.isArray())
+ {
+ GMX_RELEASE_ASSERT(false, "Array comparison not implemented");
+ }
+ else if (!areSimpleValuesOfSameTypeEqual(value1, value2))
+ {
+ writer_->writeString(currentPath_.toString());
+ writer_->writeLine(formatString(" (%s - %s)", simpleValueToString(value1).c_str(), simpleValueToString(value2).c_str()));
+ }
+ }
+ else if ((value1.isType<double>() && value2.isType<float>())
+ || (value1.isType<float>() && value2.isType<double>()))
+ {
+ const bool firstIsDouble
+ = value1.isType<double>();
+ const float v1 = firstIsDouble ? value1.cast<double>() : value1.cast<float>();
+ const float v2 = firstIsDouble ? value2.cast<float>() : value2.cast<double>();
+ if (!equal_float(v1, v2, ftol_, abstol_))
+ {
+ writer_->writeString(currentPath_.toString());
+ writer_->writeLine(formatString(" (%e - %e)", v1, v2));
+ }
+ }
+ else
+ {
+ handleMismatchingTypes(value1, value2);
+ }
+ }
+
+ bool areSimpleValuesOfSameTypeEqual(
+ const KeyValueTreeValue &value1,
+ const KeyValueTreeValue &value2)
+ {
+ GMX_ASSERT(value1.type() == value2.type(),
+ "Caller should ensure that types are equal");
+ if (value1.isType<bool>())
+ {
+ return value1.cast<bool>() == value2.cast<bool>();
+ }
+ else if (value1.isType<int>())
+ {
+ return value1.cast<int>() == value2.cast<int>();
+ }
+ else if (value1.isType<gmx_int64_t>())
+ {
+ return value1.cast<gmx_int64_t>() == value2.cast<gmx_int64_t>();
+ }
+ else if (value1.isType<double>())
+ {
+ return equal_double(value1.cast<double>(), value2.cast<double>(), ftol_, abstol_);
+ }
+ else if (value1.isType<float>())
+ {
+ return equal_float(value1.cast<float>(), value2.cast<float>(), ftol_, abstol_);
+ }
+ else if (value1.isType<std::string>())
+ {
+ return value1.cast<std::string>() == value2.cast<std::string>();
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(false, "Unknown value type");
+ return false;
+ }
+ }
+
+ void handleMismatchingTypes(const KeyValueTreeValue & /* value1 */,
+ const KeyValueTreeValue & /* value2 */)
+ {
+ writer_->writeString(currentPath_.toString());
+ writer_->writeString(" type mismatch");
+ }
+
+ void handleMissingKeyInFirstObject(const KeyValueTreeValue &value)
+ {
+ const std::string message = formatString(
+ "%s (missing - %s)", currentPath_.toString().c_str(),
+ formatValueForMissingMessage(value).c_str());
+ writer_->writeLine(message);
+ }
+ void handleMissingKeyInSecondObject(const KeyValueTreeValue &value)
+ {
+ const std::string message = formatString(
+ "%s (%s - missing)", currentPath_.toString().c_str(),
+ formatValueForMissingMessage(value).c_str());
+ writer_->writeLine(message);
+ }
+
+ std::string formatValueForMissingMessage(const KeyValueTreeValue &value)
+ {
+ if (value.isObject() || value.isArray())
+ {
+ return "present";
+ }
+ return simpleValueToString(value);
+ }
+
+ KeyValueTreePath currentPath_;
+ TextWriter *writer_;
+ real ftol_;
+ real abstol_;
+};
+
+} // namespace
+
+//! \cond libapi
+void compareKeyValueTrees(TextWriter *writer,
+ const KeyValueTreeObject &tree1,
+ const KeyValueTreeObject &tree2,
+ real ftol,
+ real abstol)
+{
+ CompareHelper helper(writer, ftol, abstol);
+ helper.compareObjects(tree1, tree2);
+}
+//! \endcond
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares a data structure for JSON-like structured key-value mapping.
+ *
+ * A tree is composed of nodes that can have different types:
+ * - _Value_ (gmx::KeyValueTreeValue) is a generic node that can
+ * represent either a scalar value of arbitrary type, or an object or
+ * an array.
+ * - _Array_ (gmx::KeyValueTreeArray) is a collection of any number of values
+ * (including zero). The values can be of any type and different types
+ * can be mixed in the same array.
+ * - _Object_ (gmx::KeyValueTreeObject) is a collection of properties.
+ * Each property must have a unique key. Order of properties is preserved,
+ * i.e., they can be iterated in the order they were added.
+ * - _Property_ (gmx::KeyValueTreeProperty) is an arbitrary type of value
+ * associated with a string key.
+ * The root object of a tree is typically an object, but could also be an
+ * array. The data structure itself does not enforce any other constraints,
+ * but the context in which it is used can limit the allowed scalar types or,
+ * e.g., require arrays to have values of uniform type. Also, several
+ * operations defined for the structure (string output, comparison,
+ * serialization, etc.) only work on a limited set of scalar types, or have
+ * limitations with the types of trees they work on (in particular, arrays are
+ * currently poorly supported).
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_KEYVALUETREE_H
+#define GMX_UTILITY_KEYVALUETREE_H
+
+#include <algorithm>
+#include <functional>
+#include <map>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include "gromacs/utility/real.h"
+#include "gromacs/utility/variant.h"
+
+namespace gmx
+{
+
+class KeyValueTreeArray;
+class KeyValueTreeObject;
+class TextWriter;
+
+/*! \libinternal \brief
+ * Identifies an entry in a key-value tree.
+ *
+ * This class is mainly an internal utility within the key-value tree
+ * implementation, but it is exposed on the API level where string-based
+ * specification of a location in the tree is necessary. Constructors are not
+ * explicit to allow passing a simple string in contexts where a
+ * KeyValueTreePath is expected.
+ *
+ * The string specifying a location should start with a `/`, followed by the
+ * names of the properties separated by `/`. For example, `/a/b/c` specifies
+ * property `c` in an object that is the value of `b` in an object that is the
+ * value of `a` at the root of the tree.
+ * Currently, there is no support for specifying paths to values within arrays
+ * (since none of the places where this is used implement array handling,
+ * either).
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class KeyValueTreePath
+{
+ public:
+ //! Creates an empty path (corresponds to the root object).
+ KeyValueTreePath() = default;
+ //! Creates a path from given string representation.
+ KeyValueTreePath(const char *path);
+ //! Creates a path from given string representation.
+ KeyValueTreePath(const std::string &path);
+
+ //! Adds another element to the path, making it a child of the old path.
+ void append(const std::string &key) { path_.push_back(key); }
+ //! Adds elements from another path to the path.
+ void append(const KeyValueTreePath &other)
+ {
+ auto elements = other.elements();
+ path_.insert(path_.end(), elements.begin(), elements.end());
+ }
+ //! Removes the last element in the path, making it the parent path.
+ void pop_back() { return path_.pop_back(); }
+ //! Removes and returns the last element in the path.
+ std::string pop_last()
+ {
+ std::string result = std::move(path_.back());
+ path_.pop_back();
+ return result;
+ }
+
+ //! Whether the path is empty (pointing to the root object).
+ bool empty() const { return path_.empty(); }
+ //! Returns the number of elements (=nesting level) in the path.
+ size_t size() const { return path_.size(); }
+ //! Returns the i'th path element.
+ const std::string &operator[](int i) const { return path_[i]; }
+ //! Returns all the path elements.
+ const std::vector<std::string> &elements() const { return path_; }
+
+ //! Formats the path as a string for display.
+ std::string toString() const;
+
+ private:
+ std::vector<std::string> path_;
+};
+
+//! \cond libapi
+
+//! Combines two paths as with KeyValueTreePath::append().
+inline KeyValueTreePath operator+(const KeyValueTreePath &a, const KeyValueTreePath &b)
+{
+ KeyValueTreePath result(a);
+ result.append(b);
+ return result;
+}
+
+//! Combines an element to a path as with KeyValueTreePath::append().
+inline KeyValueTreePath operator+(const KeyValueTreePath &a, const std::string &b)
+{
+ KeyValueTreePath result(a);
+ result.append(b);
+ return result;
+}
+//! \endcond
+
+class KeyValueTreeValue
+{
+ public:
+ //! Returns whether the value is an array (KeyValueTreeArray).
+ bool isArray() const;
+ //! Returns whether the value is an object (KeyValueTreeObject).
+ bool isObject() const;
+ //! Returns whether the value is of a given type.
+ template <typename T>
+ bool isType() const { return value_.isType<T>(); }
+ //! Returns the type of the value.
+ std::type_index type() const { return value_.type(); }
+
+ KeyValueTreeArray &asArray();
+ KeyValueTreeObject &asObject();
+ const KeyValueTreeArray &asArray() const;
+ const KeyValueTreeObject &asObject() const;
+ template <typename T>
+ const T &cast() const { return value_.cast<T>(); }
+
+ //! Returns the raw Variant value (always possible).
+ const Variant &asVariant() const { return value_; }
+
+ private:
+ explicit KeyValueTreeValue(Variant &&value) : value_(std::move(value)) {}
+
+ Variant value_;
+
+ friend class KeyValueTreeBuilder;
+ friend class KeyValueTreeObjectBuilder;
+ friend class KeyValueTreeValueBuilder;
+};
+
+class KeyValueTreeArray
+{
+ public:
+ //! Whether all elements of the array are objects.
+ bool isObjectArray() const
+ {
+ return std::all_of(values_.begin(), values_.end(),
+ std::mem_fn(&KeyValueTreeValue::isObject));
+ }
+
+ //! Returns the values in the array.
+ const std::vector<KeyValueTreeValue> &values() const { return values_; }
+
+ private:
+ std::vector<KeyValueTreeValue> values_;
+
+ friend class KeyValueTreeArrayBuilderBase;
+};
+
+class KeyValueTreeProperty
+{
+ public:
+ const std::string &key() const { return value_->first; }
+ const KeyValueTreeValue &value() const { return value_->second; }
+
+ private:
+ typedef std::map<std::string, KeyValueTreeValue>::const_iterator
+ IteratorType;
+
+ explicit KeyValueTreeProperty(IteratorType value) : value_(value) {}
+
+ IteratorType value_;
+
+ friend class KeyValueTreeObject;
+ friend class KeyValueTreeObjectBuilder;
+};
+
+class KeyValueTreeObject
+{
+ public:
+ KeyValueTreeObject() = default;
+ //! Creates a deep copy of an object.
+ KeyValueTreeObject(const KeyValueTreeObject &other)
+ {
+ for (const auto &value : other.values_)
+ {
+ auto iter = valueMap_.insert(std::make_pair(value.key(), value.value())).first;
+ values_.push_back(KeyValueTreeProperty(iter));
+ }
+ }
+ //! Assigns a deep copy of an object.
+ KeyValueTreeObject &operator=(KeyValueTreeObject &other)
+ {
+ KeyValueTreeObject tmp(other);
+ std::swap(tmp.valueMap_, valueMap_);
+ std::swap(tmp.values_, values_);
+ return *this;
+ }
+ //! Default move constructor.
+ KeyValueTreeObject(KeyValueTreeObject &&) = default;
+ //! Default move assignment.
+ KeyValueTreeObject &operator=(KeyValueTreeObject &&) = default;
+
+ /*! \brief
+ * Returns all properties in the object.
+ *
+ * The properties are in the order they were added to the object.
+ */
+ const std::vector<KeyValueTreeProperty> &properties() const { return values_; }
+
+ //! Whether a property with given key exists.
+ bool keyExists(const std::string &key) const
+ {
+ return valueMap_.find(key) != valueMap_.end();
+ }
+ //! Returns value for a given key.
+ const KeyValueTreeValue &operator[](const std::string &key) const
+ {
+ GMX_ASSERT(keyExists(key), "Accessing non-existent value");
+ return valueMap_.at(key);
+ }
+
+ /*! \brief
+ * Returns whether the given object shares any keys with `this`.
+ */
+ bool hasDistinctProperties(const KeyValueTreeObject &obj) const;
+
+ private:
+ //! Keeps the properties by key.
+ std::map<std::string, KeyValueTreeValue> valueMap_;
+ //! Keeps the insertion order of properties.
+ std::vector<KeyValueTreeProperty> values_;
+
+ friend class KeyValueTreeObjectBuilder;
+};
+
+/********************************************************************
+ * Inline functions that could not be declared within the classes
+ */
+
+inline bool KeyValueTreeValue::isArray() const
+{
+ return value_.isType<KeyValueTreeArray>();
+}
+inline bool KeyValueTreeValue::isObject() const
+{
+ return value_.isType<KeyValueTreeObject>();
+}
+inline const KeyValueTreeArray &KeyValueTreeValue::asArray() const
+{
+ return value_.cast<KeyValueTreeArray>();
+}
+inline const KeyValueTreeObject &KeyValueTreeValue::asObject() const
+{
+ return value_.cast<KeyValueTreeObject>();
+}
+inline KeyValueTreeArray &KeyValueTreeValue::asArray()
+{
+ return value_.castRef<KeyValueTreeArray>();
+}
+inline KeyValueTreeObject &KeyValueTreeValue::asObject()
+{
+ return value_.castRef<KeyValueTreeObject>();
+}
+
+//! \cond libapi
+/*! \brief
+ * Writes a human-readable representation of the tree with given writer.
+ *
+ * The output format is designed to be readable by humans; if some
+ * particular machine-readable format is needed, that should be
+ * implemented outside the generic key-value tree code.
+ *
+ * \ingroup module_utility
+ */
+void dumpKeyValueTree(TextWriter *writer, const KeyValueTreeObject &tree);
+
+/*! \brief
+ * Compares two KeyValueTrees and prints any differences.
+ *
+ * \ingroup module_utility
+ */
+void compareKeyValueTrees(TextWriter *writer,
+ const KeyValueTreeObject &tree1,
+ const KeyValueTreeObject &tree2,
+ real ftol,
+ real abstol);
+
+//! Helper function to format a simple KeyValueTreeValue.
+static inline std::string
+simpleValueToString(const KeyValueTreeValue &value)
+{
+ return simpleValueToString(value.asVariant());
+}
+
+//! \endcond
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares classes for building the data structures in keyvaluetree.h.
+ *
+ * These are separate from the data structures to enforce clear separation of
+ * the APIs, and to make the data structure immutable after construction.
+ *
+ * For the main use case described in \ref page_mdmodules, they are mainly
+ * used internally, but currently gmx::KeyValueTreeObjectBuilder (and
+ * everything it references) is exposed for more complex transforms through
+ * gmx::IKeyValueTreeTransformRules.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_KEYVALUETREEBUILDER_H
+#define GMX_UTILITY_KEYVALUETREEBUILDER_H
+
+#include <initializer_list>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/variant.h"
+
+namespace gmx
+{
+
+class KeyValueTreeArrayBuilder;
+class KeyValueTreeObjectBuilder;
+
+/*! \libinternal \brief
+ * Root builder for creating trees that have an object at the root.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class KeyValueTreeBuilder
+{
+ public:
+ //! Returns a builder for the root object.
+ KeyValueTreeObjectBuilder rootObject();
+
+ /*! \brief
+ * Builds the final object.
+ *
+ * The builder should not be accessed after this call.
+ */
+ KeyValueTreeObject build() { return std::move(root_); }
+
+ private:
+ /*! \brief
+ * Helper function for other builders to create values of certain type.
+ */
+ template <typename T>
+ static KeyValueTreeValue createValue(const T &value)
+ {
+ return KeyValueTreeValue(Variant::create<T>(value));
+ }
+ /*! \brief
+ * Helper function for other builders to create default-constructed
+ * values.
+ */
+ template <typename T>
+ static KeyValueTreeValue createValue()
+ {
+ return KeyValueTreeValue(Variant::create<T>(T()));
+ }
+
+ KeyValueTreeObject root_;
+
+ //! For access to createValue() methods.
+ friend class KeyValueTreeObjectArrayBuilder;
+ //! For access to createValue() methods.
+ friend class KeyValueTreeObjectBuilder;
+ //! For access to createValue() methods.
+ template <typename T>
+ friend class KeyValueTreeUniformArrayBuilder;
+};
+
+/*! \libinternal \brief
+ * Builder for KeyValueTreeValue objects.
+ *
+ * This builder can be constructed directly and can create self-standing
+ * KeyValueTreeValue objects.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class KeyValueTreeValueBuilder
+{
+ public:
+ //! Assigns a scalar value of certain type.
+ template <typename T>
+ void setValue(const T &value)
+ {
+ value_ = Variant::create<T>(value);
+ }
+ //! Assigns a Variant value to the built value.
+ void setVariantValue(Variant &&value)
+ {
+ value_ = std::move(value);
+ }
+ /*! \brief
+ * Returns an object builder for building an object into this value.
+ *
+ * Any method call in this value builder invalidates the returned
+ * builder.
+ */
+ KeyValueTreeObjectBuilder createObject();
+ /*! \brief
+ * Returns an array builder for building an array into this value.
+ *
+ * Any method call in this value builder invalidates the returned
+ * builder.
+ */
+ KeyValueTreeArrayBuilder createArray();
+
+ /*! \brief
+ * Builds the final value.
+ *
+ * The builder should not be accessed after this call.
+ */
+ KeyValueTreeValue build() { return KeyValueTreeValue(std::move(value_)); }
+
+ private:
+ Variant value_;
+};
+
+class KeyValueTreeArrayBuilderBase
+{
+ protected:
+ //! Creates an array builder for populating given array object.
+ explicit KeyValueTreeArrayBuilderBase(KeyValueTreeArray *array)
+ : array_(array)
+ {
+ }
+
+ //! Appends a raw Variant value to the array.
+ KeyValueTreeValue &addRawValue(Variant &&value)
+ {
+ KeyValueTreeValueBuilder builder;
+ builder.setVariantValue(std::move(value));
+ array_->values_.push_back(builder.build());
+ return array_->values_.back();
+ }
+ //! Appends a raw KeyValueTreeValue to the array.
+ KeyValueTreeValue &addRawValue(KeyValueTreeValue &&value)
+ {
+ array_->values_.push_back(std::move(value));
+ return array_->values_.back();
+ }
+
+ private:
+ KeyValueTreeArray *array_;
+};
+
+class KeyValueTreeArrayBuilder : public KeyValueTreeArrayBuilderBase
+{
+ public:
+ using KeyValueTreeArrayBuilderBase::addRawValue;
+
+ private:
+ explicit KeyValueTreeArrayBuilder(KeyValueTreeArray *array)
+ : KeyValueTreeArrayBuilderBase(array)
+ {
+ }
+
+ friend class KeyValueTreeObjectBuilder;
+ friend class KeyValueTreeValueBuilder;
+};
+
+/*! \libinternal \brief
+ * Builder for KeyValueTreeArray objects where all elements are of type `T`.
+ *
+ * The builder does not own the array being constructed, but instead holds a
+ * reference to an object within a tree rooted in KeyValueTreeBuilder or
+ * KeyValueTreeValueBuilder.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+template <typename T>
+class KeyValueTreeUniformArrayBuilder : public KeyValueTreeArrayBuilderBase
+{
+ public:
+ //! Appends a value to the array.
+ void addValue(const T &value)
+ {
+ addRawValue(KeyValueTreeBuilder::createValue<T>(value));
+ }
+
+ private:
+ explicit KeyValueTreeUniformArrayBuilder(KeyValueTreeArray *array)
+ : KeyValueTreeArrayBuilderBase(array)
+ {
+ }
+
+ friend class KeyValueTreeObjectBuilder;
+};
+
+/*! \libinternal \brief
+ * Builder for KeyValueTreeArray objects where all elements are
+ * KeyValueTreeObject objects.
+ *
+ * The builder does not own the array being constructed, but instead holds a
+ * reference to an object within a tree rooted in KeyValueTreeBuilder or
+ * KeyValueTreeValueBuilder.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class KeyValueTreeObjectArrayBuilder : public KeyValueTreeArrayBuilderBase
+{
+ public:
+ /*! \brief
+ * Appends an object to the array.
+ *
+ * The object is created empty and can be built using the returned
+ * builder.
+ */
+ KeyValueTreeObjectBuilder addObject();
+
+ private:
+ explicit KeyValueTreeObjectArrayBuilder(KeyValueTreeArray *array)
+ : KeyValueTreeArrayBuilderBase(array)
+ {
+ }
+
+ friend class KeyValueTreeObjectBuilder;
+};
+
+/*! \libinternal \brief
+ * Builder for KeyValueTreeObject objects.
+ *
+ * The builder does not own the object being constructed, but instead holds a
+ * reference to an object within a tree rooted in KeyValueTreeBuilder or
+ * KeyValueTreeValueBuilder.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class KeyValueTreeObjectBuilder
+{
+ public:
+ //! Adds a property with given key from a KeyValueTreeValue.
+ void addRawValue(const std::string &key, KeyValueTreeValue &&value)
+ {
+ addProperty(key, std::move(value));
+ }
+ //! Adds a property with given key from a Variant value.
+ void addRawValue(const std::string &key, Variant &&value)
+ {
+ addProperty(key, KeyValueTreeValue(std::move(value)));
+ }
+ //! Adds a scalar property with given key, type, and value.
+ template <typename T>
+ void addValue(const std::string &key, const T &value)
+ {
+ addRawValue(key, KeyValueTreeBuilder::createValue<T>(value));
+ }
+ /*! \brief
+ * Adds an object-valued property with given key.
+ *
+ * The object is created empty and can be built using the returned
+ * builder.
+ */
+ KeyValueTreeObjectBuilder addObject(const std::string &key)
+ {
+ auto iter = addProperty(key, KeyValueTreeBuilder::createValue<KeyValueTreeObject>());
+ return KeyValueTreeObjectBuilder(&iter->second);
+ }
+ /*! \brief
+ * Adds a generic array-valued property with given key.
+ *
+ * The array is created empty and can be built using the returned
+ * builder.
+ */
+ KeyValueTreeArrayBuilder addArray(const std::string &key)
+ {
+ auto iter = addProperty(key, KeyValueTreeBuilder::createValue<KeyValueTreeArray>());
+ return KeyValueTreeArrayBuilder(&iter->second.asArray());
+ }
+ /*! \brief
+ * Adds an array-valued property with uniform value types with given
+ * key.
+ *
+ * \tparam T Type for all values in the array.
+ *
+ * The array is created empty and can be built using the returned
+ * builder.
+ */
+ template <typename T>
+ KeyValueTreeUniformArrayBuilder<T> addUniformArray(const std::string &key)
+ {
+ auto iter = addProperty(key, KeyValueTreeBuilder::createValue<KeyValueTreeArray>());
+ return KeyValueTreeUniformArrayBuilder<T>(&iter->second.asArray());
+ }
+ /*! \brief
+ * Adds an array-valued property with uniform value types with given
+ * key and values.
+ *
+ * \tparam T Type for all values in the array.
+ *
+ * The array is created to contain the values from `values`.
+ */
+ template <typename T>
+ void addUniformArray(const std::string &key, std::initializer_list<T> values)
+ {
+ auto builder = addUniformArray<T>(key);
+ for (const auto &value : values)
+ {
+ builder.addValue(value);
+ }
+ }
+ /*! \brief
+ * Adds an array-valued property with objects in the array with given
+ * key.
+ *
+ * The array is created empty and can be built using the returned
+ * builder.
+ */
+ KeyValueTreeObjectArrayBuilder addObjectArray(const std::string &key)
+ {
+ auto iter = addProperty(key, KeyValueTreeBuilder::createValue<KeyValueTreeArray>());
+ return KeyValueTreeObjectArrayBuilder(&iter->second.asArray());
+ }
+
+ //! Whether a property with given key exists.
+ bool keyExists(const std::string &key) const { return object_->keyExists(key); }
+ //! Returns value for a given key.
+ const KeyValueTreeValue &operator[](const std::string &key) const
+ {
+ return (*object_)[key];
+ }
+ //! Returns an object builder for an existing object.
+ KeyValueTreeObjectBuilder getObjectBuilder(const std::string &key)
+ {
+ GMX_ASSERT(keyExists(key), "Requested non-existent value");
+ GMX_ASSERT((*this)[key].isObject(), "Accessing non-object value as object");
+ return KeyValueTreeObjectBuilder(&object_->valueMap_.at(key).asObject());
+ }
+
+ /*! \brief
+ * Returns whether the given object shares any keys with \p this.
+ */
+ bool objectHasDistinctProperties(const KeyValueTreeObject &obj) const
+ {
+ return object_->hasDistinctProperties(obj);
+ }
+ /*! \brief
+ * Merges properties from a given object to `this`.
+ *
+ * The objects should not share any keys, i.e.,
+ * objectHasDistinctProperties() should return `true`.
+ */
+ void mergeObject(KeyValueTreeObject &&obj)
+ {
+ GMX_ASSERT(objectHasDistinctProperties(obj),
+ "Trying to merge overlapping object");
+ for (auto &prop : obj.valueMap_)
+ {
+ addRawValue(prop.first, std::move(prop.second));
+ }
+ }
+
+ private:
+ explicit KeyValueTreeObjectBuilder(KeyValueTreeObject *object)
+ : object_(object)
+ {
+ }
+ explicit KeyValueTreeObjectBuilder(KeyValueTreeValue *value)
+ : object_(&value->asObject())
+ {
+ }
+
+ std::map<std::string, KeyValueTreeValue>::iterator
+ addProperty(const std::string &key, KeyValueTreeValue &&value)
+ {
+ GMX_RELEASE_ASSERT(!keyExists(key), "Duplicate key value");
+ object_->values_.reserve(object_->values_.size() + 1);
+ auto iter = object_->valueMap_.insert(std::make_pair(key, std::move(value))).first;
+ object_->values_.push_back(KeyValueTreeProperty(iter));
+ return iter;
+ }
+
+ KeyValueTreeObject *object_;
+
+ friend class KeyValueTreeBuilder;
+ friend class KeyValueTreeValueBuilder;
+ friend class KeyValueTreeObjectArrayBuilder;
+};
+
+/********************************************************************
+ * Inline functions that could not be declared within the classes
+ */
+
+inline KeyValueTreeObjectBuilder KeyValueTreeBuilder::rootObject()
+{
+ return KeyValueTreeObjectBuilder(&root_);
+}
+
+inline KeyValueTreeObjectBuilder KeyValueTreeValueBuilder::createObject()
+{
+ value_ = Variant::create<KeyValueTreeObject>(KeyValueTreeObject());
+ return KeyValueTreeObjectBuilder(&value_.castRef<KeyValueTreeObject>());
+}
+
+inline KeyValueTreeArrayBuilder KeyValueTreeValueBuilder::createArray()
+{
+ value_ = Variant::create<KeyValueTreeArray>(KeyValueTreeArray());
+ return KeyValueTreeArrayBuilder(&value_.castRef<KeyValueTreeArray>());
+}
+
+inline KeyValueTreeObjectBuilder KeyValueTreeObjectArrayBuilder::addObject()
+{
+ auto &value = addRawValue(KeyValueTreeBuilder::createValue<KeyValueTreeObject>());
+ return KeyValueTreeObjectBuilder(&value);
+}
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "keyvaluetreeserializer.h"
+
+#include "gromacs/utility/iserializer.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/mutex.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+class ValueSerializer
+{
+ public:
+ static void initSerializers();
+
+ static void serialize(const KeyValueTreeValue &value, ISerializer *serializer);
+ static KeyValueTreeValue deserialize(ISerializer *serializer);
+
+ private:
+ ValueSerializer();
+
+ typedef void (*SerializerFunction)(const KeyValueTreeValue &value, ISerializer *serializer);
+ typedef void (*DeserializerFunction)(KeyValueTreeValueBuilder *builder, ISerializer *serializer);
+
+ struct Serializer
+ {
+ unsigned char typeTag;
+ SerializerFunction serialize;
+ DeserializerFunction deserialize;
+ };
+
+ static Mutex s_initMutex;
+ static std::map<std::type_index, Serializer> s_serializers;
+ static std::map<unsigned char, DeserializerFunction> s_deserializers;
+};
+
+Mutex ValueSerializer::s_initMutex;
+std::map<std::type_index, ValueSerializer::Serializer> ValueSerializer::s_serializers;
+std::map<unsigned char, ValueSerializer::DeserializerFunction> ValueSerializer::s_deserializers;
+
+template <typename T>
+struct SerializationTraits
+{
+};
+
+template <>
+struct SerializationTraits<KeyValueTreeObject>
+{
+ static void serialize(const KeyValueTreeObject &value, ISerializer *serializer)
+ {
+ int count = value.properties().size();
+ serializer->doInt(&count);
+ for (const auto &prop : value.properties())
+ {
+ serializer->doString(const_cast<std::string *>(&prop.key()));
+ ValueSerializer::serialize(prop.value(), serializer);
+ }
+ }
+ static void deserialize(KeyValueTreeValueBuilder *value, ISerializer *serializer)
+ {
+ KeyValueTreeObjectBuilder builder(value->createObject());
+ deserializeObject(&builder, serializer);
+ }
+ static void deserializeObject(KeyValueTreeObjectBuilder *builder, ISerializer *serializer)
+ {
+ int count;
+ std::string key;
+ serializer->doInt(&count);
+ for (int i = 0; i < count; ++i)
+ {
+ serializer->doString(&key);
+ builder->addRawValue(key, ValueSerializer::deserialize(serializer));
+ }
+ }
+};
+
+template <>
+struct SerializationTraits<KeyValueTreeArray>
+{
+ static void serialize(const KeyValueTreeArray &array, ISerializer *serializer)
+ {
+ int count = array.values().size();
+ serializer->doInt(&count);
+ for (const auto &value : array.values())
+ {
+ ValueSerializer::serialize(value, serializer);
+ }
+ }
+ static void deserialize(KeyValueTreeValueBuilder *value, ISerializer *serializer)
+ {
+ KeyValueTreeArrayBuilder builder(value->createArray());
+ int count;
+ serializer->doInt(&count);
+ for (int i = 0; i < count; ++i)
+ {
+ builder.addRawValue(ValueSerializer::deserialize(serializer));
+ }
+ }
+};
+
+template <>
+struct SerializationTraits<std::string>
+{
+ static void serialize(const std::string &value, ISerializer *serializer)
+ {
+ serializer->doString(const_cast<std::string *>(&value));
+ }
+ static void deserialize(KeyValueTreeValueBuilder *builder, ISerializer *serializer)
+ {
+ std::string value;
+ serializer->doString(&value);
+ builder->setValue<std::string>(value);
+ }
+};
+
+template <>
+struct SerializationTraits<bool>
+{
+ static void serialize(bool value, ISerializer *serializer)
+ {
+ serializer->doBool(&value);
+ }
+ static void deserialize(KeyValueTreeValueBuilder *builder, ISerializer *serializer)
+ {
+ bool value;
+ serializer->doBool(&value);
+ builder->setValue<bool>(value);
+ }
+};
+
+template <>
+struct SerializationTraits<int>
+{
+ static void serialize(int value, ISerializer *serializer)
+ {
+ serializer->doInt(&value);
+ }
+ static void deserialize(KeyValueTreeValueBuilder *builder, ISerializer *serializer)
+ {
+ int value;
+ serializer->doInt(&value);
+ builder->setValue<int>(value);
+ }
+};
+
+template <>
+struct SerializationTraits<gmx_int64_t>
+{
+ static void serialize(gmx_int64_t value, ISerializer *serializer)
+ {
+ serializer->doInt64(&value);
+ }
+ static void deserialize(KeyValueTreeValueBuilder *builder, ISerializer *serializer)
+ {
+ gmx_int64_t value;
+ serializer->doInt64(&value);
+ builder->setValue<gmx_int64_t>(value);
+ }
+};
+
+template <>
+struct SerializationTraits<float>
+{
+ static void serialize(float value, ISerializer *serializer)
+ {
+ serializer->doFloat(&value);
+ }
+ static void deserialize(KeyValueTreeValueBuilder *builder, ISerializer *serializer)
+ {
+ float value;
+ serializer->doFloat(&value);
+ builder->setValue<float>(value);
+ }
+};
+
+template <>
+struct SerializationTraits<double>
+{
+ static void serialize(double value, ISerializer *serializer)
+ {
+ serializer->doDouble(&value);
+ }
+ static void deserialize(KeyValueTreeValueBuilder *builder, ISerializer *serializer)
+ {
+ double value;
+ serializer->doDouble(&value);
+ builder->setValue<double>(value);
+ }
+};
+
+//! Helper function for serializing values of a certain type.
+template <typename T>
+void serializeValueType(const KeyValueTreeValue &value, ISerializer *serializer)
+{
+ SerializationTraits<T>::serialize(value.cast<T>(), serializer);
+}
+
+#define SERIALIZER(tag, type) \
+ { std::type_index(typeid(type)), \
+ { tag, &serializeValueType<type>, &SerializationTraits<type>::deserialize } \
+ }
+
+// static
+void ValueSerializer::initSerializers()
+{
+ lock_guard<Mutex> lock(s_initMutex);
+ if (!s_serializers.empty())
+ {
+ return;
+ }
+ s_serializers = {
+ SERIALIZER('O', KeyValueTreeObject),
+ SERIALIZER('A', KeyValueTreeArray),
+ SERIALIZER('s', std::string),
+ SERIALIZER('b', bool),
+ SERIALIZER('i', int),
+ SERIALIZER('l', gmx_int64_t),
+ SERIALIZER('f', float),
+ SERIALIZER('d', double),
+ };
+ for (const auto item : s_serializers)
+ {
+ s_deserializers[item.second.typeTag] = item.second.deserialize;
+ }
+}
+
+void ValueSerializer::serialize(const KeyValueTreeValue &value, ISerializer *serializer)
+{
+ auto iter = s_serializers.find(value.type());
+ GMX_RELEASE_ASSERT(iter != s_serializers.end(),
+ "Unknown value type for serializization");
+ unsigned char typeTag = iter->second.typeTag;
+ serializer->doUChar(&typeTag);
+ iter->second.serialize(value, serializer);
+}
+
+KeyValueTreeValue ValueSerializer::deserialize(ISerializer *serializer)
+{
+ unsigned char typeTag;
+ serializer->doUChar(&typeTag);
+ auto iter = s_deserializers.find(typeTag);
+ GMX_RELEASE_ASSERT(iter != s_deserializers.end(),
+ "Unknown type tag for deserializization");
+ KeyValueTreeValueBuilder builder;
+ iter->second(&builder, serializer);
+ return builder.build();
+}
+
+} // namespace
+
+//! \cond libapi
+void serializeKeyValueTree(const KeyValueTreeObject &root, ISerializer *serializer)
+{
+ GMX_RELEASE_ASSERT(!serializer->reading(),
+ "Incorrect serializer direction");
+ ValueSerializer::initSerializers();
+ SerializationTraits<KeyValueTreeObject>::serialize(root, serializer);
+}
+
+KeyValueTreeObject deserializeKeyValueTree(ISerializer *serializer)
+{
+ GMX_RELEASE_ASSERT(serializer->reading(),
+ "Incorrect serializer direction");
+ ValueSerializer::initSerializers();
+ KeyValueTreeBuilder builder;
+ KeyValueTreeObjectBuilder obj(builder.rootObject());
+ SerializationTraits<KeyValueTreeObject>::deserializeObject(&obj, serializer);
+ return builder.build();
+}
+//! \endcond
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares serialization routines for KeyValueTree objects.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_KEYVALUETREESERIALIZER_H
+#define GMX_UTILITY_KEYVALUETREESERIALIZER_H
+
+namespace gmx
+{
+
+class KeyValueTreeObject;
+class ISerializer;
+
+//! \cond libapi
+/*! \brief
+ * Serializes a KeyValueTreeObject with given serializer.
+ *
+ * \ingroup module_utility
+ */
+void serializeKeyValueTree(const KeyValueTreeObject &root, ISerializer *serializer);
+/*! \brief
+ * Deserializes a KeyValueTreeObject from a given serializer.
+ *
+ * \ingroup module_utility
+ */
+KeyValueTreeObject deserializeKeyValueTree(ISerializer *serializer);
+//! \endcond
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "keyvaluetreetransform.h"
+
+#include <functional>
+#include <map>
+#include <memory>
+#include <typeindex>
+#include <vector>
+
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/ikeyvaluetreeerror.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/stringcompare.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+/********************************************************************
+ * IKeyValueTreeTransformRules
+ */
+
+IKeyValueTreeTransformRules::~IKeyValueTreeTransformRules()
+{
+}
+
+/********************************************************************
+ * KeyValueTreeTransformRulesScoped::Impl
+ */
+
+class KeyValueTreeTransformRulesScoped::Impl : public IKeyValueTreeTransformRules
+{
+ public:
+ Impl(internal::KeyValueTreeTransformerImpl *impl, const KeyValueTreePath &prefix)
+ : impl_(impl), prefix_(prefix)
+ {
+ }
+
+ KeyValueTreeTransformRuleBuilder addRule() override
+ {
+ return KeyValueTreeTransformRuleBuilder(impl_, prefix_);
+ }
+
+ KeyValueTreeTransformRulesScoped
+ scopedTransform(const KeyValueTreePath &scope) override
+ {
+ return KeyValueTreeTransformRulesScoped(impl_, prefix_ + scope);
+ }
+
+ private:
+ internal::KeyValueTreeTransformerImpl *impl_;
+ KeyValueTreePath prefix_;
+};
+
+/********************************************************************
+ * KeyValueTreeTransformRulesScoped
+ */
+
+KeyValueTreeTransformRulesScoped::KeyValueTreeTransformRulesScoped(
+ internal::KeyValueTreeTransformerImpl *impl, const KeyValueTreePath &prefix)
+ : impl_(new Impl(impl, prefix))
+{
+}
+
+KeyValueTreeTransformRulesScoped::KeyValueTreeTransformRulesScoped(
+ KeyValueTreeTransformRulesScoped &&) = default;
+
+KeyValueTreeTransformRulesScoped &
+KeyValueTreeTransformRulesScoped::operator=(
+ KeyValueTreeTransformRulesScoped &&) = default;
+
+KeyValueTreeTransformRulesScoped::~KeyValueTreeTransformRulesScoped()
+{
+}
+
+IKeyValueTreeTransformRules *KeyValueTreeTransformRulesScoped::rules()
+{
+ return impl_.get();
+}
+
+/********************************************************************
+ * IKeyValueTreeBackMapping
+ */
+
+IKeyValueTreeBackMapping::~IKeyValueTreeBackMapping()
+{
+}
+
+namespace
+{
+
+class KeyValueTreeBackMapping : public IKeyValueTreeBackMapping
+{
+ public:
+ class Entry
+ {
+ public:
+ Entry() = default;
+ explicit Entry(const KeyValueTreePath &path) : sourcePath_(path) {}
+
+ Entry *getOrCreateChildEntry(const std::string &key)
+ {
+ auto iter = childEntries_.find(key);
+ if (iter == childEntries_.end())
+ {
+ iter = childEntries_.insert(std::make_pair(key, Entry())).first;
+ }
+ return &iter->second;
+ }
+ void setMapping(const KeyValueTreePath &path,
+ const KeyValueTreeValue &value)
+ {
+ GMX_RELEASE_ASSERT(sourcePath_.empty(),
+ "Multiple entries map to same path");
+ if (value.isObject())
+ {
+ const KeyValueTreeObject &object = value.asObject();
+ for (const auto &prop : object.properties())
+ {
+ GMX_RELEASE_ASSERT(!prop.value().isObject(),
+ "Nested objects not implemented");
+ childEntries_[prop.key()] = Entry(path);
+ }
+ }
+ else
+ {
+ sourcePath_ = path;
+ }
+ }
+
+ KeyValueTreePath sourcePath_;
+ std::map<std::string, Entry> childEntries_;
+ };
+
+ virtual KeyValueTreePath
+ originalPath(const KeyValueTreePath &path) const
+ {
+ const Entry *entry = &rootEntry_;
+ for (const auto &element : path.elements())
+ {
+ auto iter = entry->childEntries_.find(element);
+ if (iter == entry->childEntries_.end())
+ {
+ break;
+ }
+ entry = &iter->second;
+ }
+ GMX_RELEASE_ASSERT(entry->childEntries_.empty()
+ && !entry->sourcePath_.empty(),
+ "Requested path not uniquely mapped");
+ return entry->sourcePath_;
+ }
+
+ Entry *rootEntry() { return &rootEntry_; }
+
+ private:
+ Entry rootEntry_;
+};
+
+} // namespace
+
+namespace internal
+{
+
+/********************************************************************
+ * KeyValueTreeTransformerImpl
+ */
+
+class KeyValueTreeTransformerImpl
+{
+ public:
+ class Rule
+ {
+ public:
+ typedef std::function<void(KeyValueTreeValueBuilder *, const KeyValueTreeValue &)>
+ TransformFunction;
+ typedef std::map<std::string, Rule, StringCompare> ChildRuleMap;
+
+ explicit Rule(StringCompareType keyMatchType)
+ : expectedType_(typeid(void)), childRules_(keyMatchType)
+ {
+ }
+
+ const Rule *findMatchingChildRule(const std::string &key) const
+ {
+ auto iter = childRules_.find(key);
+ if (iter == childRules_.end())
+ {
+ return nullptr;
+ }
+ return &iter->second;
+ }
+ Rule *getOrCreateChildRule(const std::string &key)
+ {
+ auto iter = childRules_.find(key);
+ if (iter == childRules_.end())
+ {
+ return createChildRule(key, StringCompareType::Exact);
+ }
+ return &iter->second;
+ }
+ Rule *createChildRule(const std::string &key,
+ StringCompareType keyMatchType)
+ {
+ auto result = childRules_.insert(std::make_pair(key, Rule(keyMatchType)));
+ GMX_RELEASE_ASSERT(result.second,
+ "Cannot specify key match type after child rules");
+ return &result.first->second;
+ }
+
+ void collectMappedPaths(const KeyValueTreePath &prefix,
+ std::vector<KeyValueTreePath> *result) const
+ {
+ for (const auto &value : childRules_)
+ {
+ KeyValueTreePath path = prefix;
+ path.append(value.first);
+ const Rule &rule = value.second;
+ if (rule.transform_)
+ {
+ result->push_back(path);
+ }
+ else
+ {
+ rule.collectMappedPaths(path, result);
+ }
+ }
+ }
+
+ KeyValueTreePath targetPath_;
+ std::string targetKey_;
+ std::type_index expectedType_;
+ TransformFunction transform_;
+ ChildRuleMap childRules_;
+ };
+
+ class Transformer
+ {
+ public:
+ explicit Transformer(IKeyValueTreeErrorHandler *errorHandler)
+ : errorHandler_(errorHandler),
+ backMapping_(new KeyValueTreeBackMapping)
+ {
+ if (errorHandler_ == nullptr)
+ {
+ errorHandler_ = defaultKeyValueTreeErrorHandler();
+ }
+ }
+
+ void transform(const Rule *rootRule, const KeyValueTreeObject &tree)
+ {
+ if (rootRule != nullptr)
+ {
+ doChildTransforms(rootRule, tree);
+ }
+ }
+
+ KeyValueTreeTransformResult result()
+ {
+ return KeyValueTreeTransformResult(builder_.build(),
+ std::move(backMapping_));
+ }
+
+ private:
+ void doTransform(const Rule *rule, const KeyValueTreeValue &value);
+ void doChildTransforms(const Rule *rule, const KeyValueTreeObject &object);
+ void applyTransformedValue(const Rule *rule, KeyValueTreeValue &&value);
+
+ IKeyValueTreeErrorHandler *errorHandler_;
+ KeyValueTreeBuilder builder_;
+ std::unique_ptr<KeyValueTreeBackMapping> backMapping_;
+ KeyValueTreePath context_;
+ };
+
+ KeyValueTreeTransformerImpl()
+ : rootScope_(this, KeyValueTreePath())
+ {
+ }
+
+ Rule *getOrCreateRootRule()
+ {
+ if (rootRule_ == nullptr)
+ {
+ createRootRule(StringCompareType::Exact);
+ }
+ return rootRule_.get();
+ }
+ void createRootRule(StringCompareType keyMatchType)
+ {
+ GMX_RELEASE_ASSERT(rootRule_ == nullptr,
+ "Cannot specify key match type after child rules");
+ rootRule_.reset(new Rule(keyMatchType));
+ }
+
+ std::unique_ptr<Rule> rootRule_;
+ KeyValueTreeTransformRulesScoped rootScope_;
+};
+
+/********************************************************************
+ * KeyValueTreeTransformerImpl::Transformer
+ */
+
+void KeyValueTreeTransformerImpl::Transformer::doTransform(
+ const Rule *rule, const KeyValueTreeValue &value)
+{
+ if (rule->transform_ != nullptr)
+ {
+ KeyValueTreeValueBuilder valueBuilder;
+ try
+ {
+ if (value.type() != rule->expectedType_)
+ {
+ // TODO: Better error message.
+ GMX_THROW(InvalidInputError("Unexpected type of value"));
+ }
+ rule->transform_(&valueBuilder, value);
+ }
+ catch (UserInputError &ex)
+ {
+ if (!errorHandler_->onError(&ex, context_))
+ {
+ throw;
+ }
+ return;
+ }
+ applyTransformedValue(rule, valueBuilder.build());
+ return;
+ }
+ if (!rule->childRules_.empty())
+ {
+ doChildTransforms(rule, value.asObject());
+ }
+}
+
+void KeyValueTreeTransformerImpl::Transformer::doChildTransforms(
+ const Rule *rule, const KeyValueTreeObject &object)
+{
+ for (const auto &prop : object.properties())
+ {
+ const Rule *childRule = rule->findMatchingChildRule(prop.key());
+ if (childRule != nullptr)
+ {
+ context_.append(prop.key());
+ doTransform(childRule, prop.value());
+ context_.pop_back();
+ }
+ }
+}
+
+void KeyValueTreeTransformerImpl::Transformer::applyTransformedValue(
+ const Rule *rule, KeyValueTreeValue &&value)
+{
+ KeyValueTreeObjectBuilder objBuilder = builder_.rootObject();
+ KeyValueTreeBackMapping::Entry *mapEntry = backMapping_->rootEntry();
+ for (const std::string &key : rule->targetPath_.elements())
+ {
+ if (objBuilder.keyExists(key))
+ {
+ GMX_RELEASE_ASSERT(objBuilder[key].isObject(),
+ "Inconsistent transform (different items map to same path)");
+ objBuilder = objBuilder.getObjectBuilder(key);
+ }
+ else
+ {
+ objBuilder = objBuilder.addObject(key);
+ }
+ mapEntry = mapEntry->getOrCreateChildEntry(key);
+ }
+ mapEntry = mapEntry->getOrCreateChildEntry(rule->targetKey_);
+ mapEntry->setMapping(context_, value);
+ if (objBuilder.keyExists(rule->targetKey_))
+ {
+ GMX_RELEASE_ASSERT(value.isObject(),
+ "Inconsistent transform (different items map to same path)");
+ GMX_RELEASE_ASSERT(objBuilder[rule->targetKey_].isObject(),
+ "Inconsistent transform (different items map to same path)");
+ objBuilder = objBuilder.getObjectBuilder(rule->targetKey_);
+ GMX_RELEASE_ASSERT(objBuilder.objectHasDistinctProperties(value.asObject()),
+ "Inconsistent transform (different items map to same path)");
+ objBuilder.mergeObject(std::move(value.asObject()));
+ }
+ else
+ {
+ objBuilder.addRawValue(rule->targetKey_, std::move(value));
+ }
+}
+
+} // namespace internal
+
+/********************************************************************
+ * KeyValueTreeTransformer
+ */
+
+KeyValueTreeTransformer::KeyValueTreeTransformer()
+ : impl_(new internal::KeyValueTreeTransformerImpl)
+{
+}
+
+KeyValueTreeTransformer::~KeyValueTreeTransformer()
+{
+}
+
+IKeyValueTreeTransformRules *KeyValueTreeTransformer::rules()
+{
+ return impl_->rootScope_.rules();
+}
+
+std::vector<KeyValueTreePath> KeyValueTreeTransformer::mappedPaths() const
+{
+ std::vector<KeyValueTreePath> result;
+ if (impl_->rootRule_)
+ {
+ impl_->rootRule_->collectMappedPaths(KeyValueTreePath(), &result);
+ }
+ return result;
+}
+
+KeyValueTreeTransformResult
+KeyValueTreeTransformer::transform(const KeyValueTreeObject &tree,
+ IKeyValueTreeErrorHandler *errorHandler) const
+{
+ internal::KeyValueTreeTransformerImpl::Transformer transformer(errorHandler);
+ transformer.transform(impl_->rootRule_.get(), tree);
+ return transformer.result();
+}
+
+/********************************************************************
+ * KeyValueTreeTransformRuleBuilder::Data
+ */
+
+class KeyValueTreeTransformRuleBuilder::Data
+{
+ public:
+ typedef internal::KeyValueTreeTransformerImpl::Rule Rule;
+
+ explicit Data(const KeyValueTreePath &prefix)
+ : prefixPath_(prefix), expectedType_(typeid(void)),
+ keyMatchType_(StringCompareType::Exact), keyMatchRule_(false)
+ {
+ }
+
+ void createRule(internal::KeyValueTreeTransformerImpl *impl)
+ {
+ if (keyMatchRule_)
+ {
+ createRuleWithKeyMatchType(impl);
+ return;
+ }
+ GMX_RELEASE_ASSERT(transform_ != nullptr,
+ "Transform has not been specified");
+ Rule *rule = impl->getOrCreateRootRule();
+ for (const std::string &key : fromPath_.elements())
+ {
+ GMX_RELEASE_ASSERT(rule->targetKey_.empty(),
+ "Cannot specify multiple rules from a single path");
+ rule = rule->getOrCreateChildRule(key);
+ }
+ GMX_RELEASE_ASSERT(rule->targetKey_.empty(),
+ "Cannot specify multiple rules from a single path");
+ rule->targetKey_ = toPath_.pop_last();
+ rule->targetPath_ = std::move(toPath_);
+ rule->expectedType_ = expectedType_;
+ rule->transform_ = transform_;
+ }
+
+ void createRuleWithKeyMatchType(internal::KeyValueTreeTransformerImpl *impl)
+ {
+ if (fromPath_.empty())
+ {
+ impl->createRootRule(keyMatchType_);
+ }
+ else
+ {
+ std::string lastKey = fromPath_.pop_last();
+ Rule *rule = impl->getOrCreateRootRule();
+ for (const std::string &key : fromPath_.elements())
+ {
+ rule = rule->getOrCreateChildRule(key);
+ }
+ rule->createChildRule(lastKey, keyMatchType_);
+ }
+ }
+
+ const KeyValueTreePath prefixPath_;
+ KeyValueTreePath fromPath_;
+ KeyValueTreePath toPath_;
+ std::type_index expectedType_;
+ Rule::TransformFunction transform_;
+ StringCompareType keyMatchType_;
+ bool keyMatchRule_;
+};
+
+/********************************************************************
+ * KeyValueTreeTransformRuleBuilder
+ */
+
+KeyValueTreeTransformRuleBuilder::KeyValueTreeTransformRuleBuilder(
+ internal::KeyValueTreeTransformerImpl *impl, const KeyValueTreePath &prefix)
+ : impl_(impl), data_(new Data(prefix))
+{
+}
+
+KeyValueTreeTransformRuleBuilder::~KeyValueTreeTransformRuleBuilder()
+{
+ if (!std::uncaught_exception())
+ {
+ data_->createRule(impl_);
+ }
+}
+
+void KeyValueTreeTransformRuleBuilder::setFromPath(const KeyValueTreePath &path)
+{
+ data_->fromPath_ = path;
+}
+
+void KeyValueTreeTransformRuleBuilder::setExpectedType(const std::type_index &type)
+{
+ data_->expectedType_ = type;
+}
+
+void KeyValueTreeTransformRuleBuilder::setToPath(const KeyValueTreePath &path)
+{
+ data_->toPath_ = data_->prefixPath_ + path;
+}
+
+void KeyValueTreeTransformRuleBuilder::setKeyMatchType(StringCompareType keyMatchType)
+{
+ data_->keyMatchType_ = keyMatchType;
+ data_->keyMatchRule_ = true;
+}
+
+void KeyValueTreeTransformRuleBuilder::addTransformToVariant(
+ std::function<Variant(const Variant &)> transform)
+{
+ data_->transform_ =
+ [transform] (KeyValueTreeValueBuilder *builder, const KeyValueTreeValue &value)
+ {
+ builder->setVariantValue(transform(value.asVariant()));
+ };
+}
+
+void KeyValueTreeTransformRuleBuilder::addTransformToObject(
+ std::function<void(KeyValueTreeObjectBuilder *, const Variant &)> transform)
+{
+ data_->transform_ =
+ [transform] (KeyValueTreeValueBuilder *builder, const KeyValueTreeValue &value)
+ {
+ KeyValueTreeObjectBuilder obj = builder->createObject();
+ transform(&obj, value.asVariant());
+ };
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares utilities for transforming key-value trees.
+ *
+ * See \ref page_mdmodules for the main use case that these support.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_KEYVALUETREETRANSFORM_H
+#define GMX_UTILITY_KEYVALUETREETRANSFORM_H
+
+#include <functional>
+#include <string>
+#include <typeindex>
+#include <vector>
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/variant.h"
+
+namespace gmx
+{
+
+class IKeyValueTreeErrorHandler;
+class KeyValueTreeObjectBuilder;
+
+enum class StringCompareType;
+
+class KeyValueTreeTransformResult;
+class KeyValueTreeTransformRuleBuilder;
+class KeyValueTreeTransformRulesScoped;
+
+namespace internal
+{
+class KeyValueTreeTransformerImpl;
+}
+
+/*! \libinternal \brief
+ * Interface to declare rules for transforming key-value trees.
+ *
+ * This interface is used to add transformation rules for key-value trees.
+ * A transformation is a set of rules that is used to map an input key-value
+ * tree to an output key-value tree, with possible conversion steps performed
+ * in the process. Currently, each rule maps one item from the source tree to
+ * one item in the target tree (it is possible to expand a single value into an
+ * object with multiple properties). See KeyValueTreeTransformRuleBuilder for
+ * the kinds of rules currently supported.
+ *
+ * The main use currently is in converting flat-format mdp files to a
+ * structured internal representation.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class IKeyValueTreeTransformRules
+{
+ public:
+ /*! \brief
+ * Creates a new rule.
+ *
+ * Properties of the new rule must be specified using the returned
+ * builder.
+ */
+ virtual KeyValueTreeTransformRuleBuilder addRule() = 0;
+ /*! \brief
+ * Creates a scoped set of rules, where all rules use a target sub-tree.
+ *
+ * \param[in] scope Prefix defining the scope in the target tree
+ *
+ * Any rules added to the returned scope will have `scope` prefixed to
+ * their target paths, i.e., it is not possible to produce elements
+ * outside the specified subtree.
+ */
+ virtual KeyValueTreeTransformRulesScoped
+ scopedTransform(const KeyValueTreePath &scope) = 0;
+
+ protected:
+ ~IKeyValueTreeTransformRules();
+};
+
+/*! \libinternal \brief
+ * Helper object returned from IKeyValueTreeTransformRules::scopedTransform().
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class KeyValueTreeTransformRulesScoped
+{
+ public:
+ //! Internal constructor for creating the scope.
+ KeyValueTreeTransformRulesScoped(
+ internal::KeyValueTreeTransformerImpl *impl,
+ const KeyValueTreePath &prefix);
+ //! Supports returning the object from IKeyValueTreeTransformRules::scopedTransform().
+ KeyValueTreeTransformRulesScoped(KeyValueTreeTransformRulesScoped &&other);
+ //! Supports returning the object from IKeyValueTreeTransformRules::scopedTransform().
+ KeyValueTreeTransformRulesScoped &operator=(KeyValueTreeTransformRulesScoped &&other);
+ ~KeyValueTreeTransformRulesScoped();
+
+ //! Returns the interface for adding rules to this scope.
+ IKeyValueTreeTransformRules *rules();
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+/*! \libinternal \brief
+ * Provides methods to specify one transformation rule.
+ *
+ * \if internal
+ * The builder is implemented as a set of nested objects, each of which is
+ * provides methods for setting a particular property of the rule. Setting a
+ * property returns another object that has relevant methods for the context.
+ * This provides some structure to the methods, and catches at least some types
+ * of incorrect rules already at compile time.
+ * Additionally, if you use an IDE with completion facilities, it can nicely
+ * guide you through which values you need to specify.
+ * All values are stored within the main builder object, and the rule is
+ * created at the end of the statement.
+ * \endif
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class KeyValueTreeTransformRuleBuilder
+{
+ public:
+ /*! \internal \brief
+ * Base class used for implementing parameter provider objects.
+ */
+ class Base
+ {
+ protected:
+ //! Creates a parameter provider object within given builder.
+ explicit Base(KeyValueTreeTransformRuleBuilder *builder)
+ : builder_(builder)
+ {
+ }
+
+ //! The parent builder.
+ KeyValueTreeTransformRuleBuilder *builder_;
+ };
+
+ /*! \libinternal \brief
+ * Properties that can be specified after from().to().
+ *
+ * \tparam FromType Type specified for from() to map from.
+ * \tparam ToType Type specified for to() to map to.
+ */
+ template <typename FromType, typename ToType>
+ class ToValue : public Base
+ {
+ public:
+ //! Creates a parameter provider object within given builder.
+ explicit ToValue(KeyValueTreeTransformRuleBuilder *builder)
+ : Base(builder)
+ {
+ }
+
+ /*! \brief
+ * Specifies the transformation function to convert the value
+ * from FromType to ToType.
+ */
+ void transformWith(std::function<ToType(const FromType &)> transform)
+ {
+ builder_->addTransformToVariant(
+ [transform] (const Variant &value)
+ {
+ return Variant::create<ToType>(transform(value.cast<FromType>()));
+ });
+ }
+ };
+
+ /*! \libinternal \brief
+ * Properties that can be specified after from().toObject().
+ *
+ * \tparam FromType Type specified for from() to map from.
+ */
+ template <typename FromType>
+ class ToObject : public Base
+ {
+ public:
+ //! Creates a parameter provider object within given builder.
+ explicit ToObject(KeyValueTreeTransformRuleBuilder *builder)
+ : Base(builder)
+ {
+ }
+
+ /*! \brief
+ * Specifies the transformation function to build the output
+ * object.
+ *
+ * The transform should build the output object with the
+ * provided builder.
+ */
+ void transformWith(std::function<void(KeyValueTreeObjectBuilder *, const FromType &)> transform)
+ {
+ builder_->addTransformToObject(
+ [transform] (KeyValueTreeObjectBuilder *builder, const Variant &value)
+ {
+ transform(builder, value.cast<FromType>());
+ });
+ }
+ };
+
+ /*! \libinternal \brief
+ * Properties that can be specified after from().
+ *
+ * \tparam FromType Type specified for from() to map from.
+ */
+ template <typename FromType>
+ class AfterFrom : public Base
+ {
+ public:
+ //! Creates a parameter provider object within given builder.
+ explicit AfterFrom(KeyValueTreeTransformRuleBuilder *builder)
+ : Base(builder)
+ {
+ }
+
+ /*! \brief
+ * Specifies a rule that maps to a value at given path.
+ *
+ * \tparam ToType Type to map to.
+ * \param[in] path Path to map to.
+ *
+ * It is an error if multiple rules map to the same path, or to
+ * a parent path of the target of an existing rule.
+ * Note that it is possible to have a to() rule map to a child
+ * of a toObject() rule, provided that the path is not created
+ * by the object rule.
+ */
+ template <typename ToType>
+ ToValue<FromType, ToType> to(const KeyValueTreePath &path)
+ {
+ builder_->setToPath(path);
+ return ToValue<FromType, ToType>(builder_);
+ }
+
+ /*! \brief
+ * Specifies a rule that maps to an object (collection of named
+ * values) at given path.
+ *
+ * \param[in] path Path to map to.
+ *
+ * It is an error if multiple rules map to the same path, or to
+ * a parent path of the target of an existing rule.
+ * However, it is allowed to have two toObject() rules map to
+ * the same path, provided that the properties they produce are
+ * distinct.
+ */
+ ToObject<FromType> toObject(const KeyValueTreePath &path)
+ {
+ builder_->setToPath(path);
+ return ToObject<FromType>(builder_);
+ }
+ };
+
+ //! Internal constructor for creating a builder.
+ KeyValueTreeTransformRuleBuilder(internal::KeyValueTreeTransformerImpl *impl,
+ const KeyValueTreePath &prefix);
+ //! Supports returning the builder from IKeyValueTreeTransformRules::addRule().
+ KeyValueTreeTransformRuleBuilder(KeyValueTreeTransformRuleBuilder &&) = default;
+ //! Supports returning the builder from IKeyValueTreeTransformRules::addRule().
+ KeyValueTreeTransformRuleBuilder &operator=(KeyValueTreeTransformRuleBuilder &&) = default;
+ ~KeyValueTreeTransformRuleBuilder();
+
+ /*! \brief
+ * Specifies a rule that maps a value at given path.
+ *
+ * \tparam FromType Type of value expected at `path`.
+ * \param[in] path Path to map in this rule.
+ *
+ * If the input tree has `path`, but it is not of type `FromType`,
+ * the transform will produce an error.
+ *
+ * It is an error to use the same path in two from() rules. Similarly,
+ * it is an error to use a child path of a path used in a different
+ * from() rule.
+ */
+ template <typename FromType>
+ AfterFrom<FromType> from(const KeyValueTreePath &path)
+ {
+ setFromPath(path);
+ setExpectedType(typeid(FromType));
+ return AfterFrom<FromType>(this);
+ }
+ /*! \brief
+ * Specifies how strings are matched when matching rules against a path.
+ *
+ * For properties of the object at `path`, `keyMatchType` is used for
+ * string comparison.
+ *
+ * This rule must be specified first for a path, before any other
+ * from() rule specifies the path or a subpath.
+ * The rule only applies to immediate properties at the given path, not
+ * recursively.
+ * It is an error to specify the match type multiple times for a path.
+ */
+ void keyMatchType(const KeyValueTreePath &path, StringCompareType keyMatchType)
+ {
+ setFromPath(path);
+ setKeyMatchType(keyMatchType);
+ }
+
+ private:
+ void setFromPath(const KeyValueTreePath &path);
+ void setExpectedType(const std::type_index &type);
+ void setToPath(const KeyValueTreePath &path);
+ void setKeyMatchType(StringCompareType keyMatchType);
+ void addTransformToVariant(std::function<Variant(const Variant &)> transform);
+ void addTransformToObject(std::function<void(KeyValueTreeObjectBuilder *, const Variant &)> transform);
+
+ class Data;
+
+ internal::KeyValueTreeTransformerImpl *impl_;
+ std::unique_ptr<Data> data_;
+};
+
+class KeyValueTreeTransformer
+{
+ public:
+ KeyValueTreeTransformer();
+ ~KeyValueTreeTransformer();
+
+ IKeyValueTreeTransformRules *rules();
+
+ std::vector<KeyValueTreePath> mappedPaths() const;
+
+ KeyValueTreeTransformResult
+ transform(const KeyValueTreeObject &tree,
+ IKeyValueTreeErrorHandler *errorHandler) const;
+
+ private:
+ PrivateImplPointer<internal::KeyValueTreeTransformerImpl> impl_;
+};
+
+class IKeyValueTreeBackMapping
+{
+ public:
+ virtual ~IKeyValueTreeBackMapping();
+
+ virtual KeyValueTreePath
+ originalPath(const KeyValueTreePath &path) const = 0;
+};
+
+class KeyValueTreeTransformResult
+{
+ public:
+ KeyValueTreeObject object() { return std::move(object_); }
+ const IKeyValueTreeBackMapping &backMapping() const { return *mapping_; }
+
+ private:
+ typedef std::unique_ptr<IKeyValueTreeBackMapping> MappingPointer;
+
+ KeyValueTreeTransformResult(KeyValueTreeObject &&object,
+ MappingPointer &&mapping)
+ : object_(std::move(object)), mapping_(std::move(mapping))
+ {
+ }
+
+ KeyValueTreeObject object_;
+ MappingPointer mapping_;
+
+ friend class internal::KeyValueTreeTransformerImpl;
+};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "logger.h"
+
+#include <cstdarg>
+
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+namespace
+{
+
+//! Helper method for reading logging targets from an array.
+ILogTarget *getTarget(ILogTarget *targets[MDLogger::LogLevelCount],
+ MDLogger::LogLevel level)
+{
+ return targets[static_cast<int>(level)];
+}
+
+} // namespace
+
+ILogTarget::~ILogTarget()
+{
+}
+
+
+LogEntryWriter &LogEntryWriter::appendTextFormatted(const char *fmt, ...)
+{
+ va_list ap;
+
+ va_start(ap, fmt);
+ entry_.text.append(formatStringV(fmt, ap));
+ va_end(ap);
+ return *this;
+}
+
+MDLogger::MDLogger()
+ : warning(nullptr), info(nullptr)
+{
+}
+
+MDLogger::MDLogger(ILogTarget *targets[LogLevelCount])
+ : warning(getTarget(targets, LogLevel::Warning)),
+ info(getTarget(targets, LogLevel::Info))
+{
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares functionality for logging.
+ *
+ * See \ref page_logging for an overview of the functionality.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_LOGGER_H
+#define GMX_UTILITY_LOGGER_H
+
+#include <string>
+
+namespace gmx
+{
+
+struct LogEntry
+{
+ LogEntry() : asParagraph(false) {}
+
+ std::string text;
+ bool asParagraph;
+};
+
+/*! \libinternal \brief
+ * Target where log output can be written.
+ *
+ * \ingroup module_utility
+ */
+class ILogTarget
+{
+ public:
+ virtual ~ILogTarget();
+
+ //! Writes a log entry to this target.
+ virtual void writeEntry(const LogEntry &entry) = 0;
+};
+
+/*! \libinternal \brief
+ * Helper class for creating log entries with ::GMX_LOG.
+ *
+ * \ingroup module_utility
+ */
+class LogEntryWriter
+{
+ public:
+ //! Appends given text to the log entry.
+ LogEntryWriter &appendText(const char *text)
+ {
+ entry_.text.append(text);
+ return *this;
+ }
+ //! Appends given text to the log entry.
+ LogEntryWriter &appendText(const std::string &text)
+ {
+ entry_.text.append(text);
+ return *this;
+ }
+ //! Appends given text to the log entry, with printf-style formatting.
+ LogEntryWriter &appendTextFormatted(const char *fmt, ...);
+ //! Writes the log entry with empty lines before and after.
+ LogEntryWriter &asParagraph()
+ {
+ entry_.asParagraph = true;
+ return *this;
+ }
+
+ private:
+ LogEntry entry_;
+
+ friend class LogWriteHelper;
+};
+
+/*! \internal \brief
+ * Helper class for implementing ::GMX_LOG.
+ *
+ * \ingroup module_utility
+ */
+class LogWriteHelper
+{
+ public:
+ //! Initializes a helper for writing to the given target.
+ explicit LogWriteHelper(ILogTarget *target) : target_(target) {}
+
+ // Should be explicit, once that works in CUDA.
+ /*! \brief
+ * Returns whether anything needs to be written.
+ *
+ * Note that the return value is unintuitively `false` when the target
+ * is active, to allow implementing ::GMX_LOG like it is now.
+ */
+ operator bool() const { return target_ == nullptr; }
+
+ /*! \brief
+ * Writes the entry from the given writer to the log target.
+ *
+ * This is implemented as an assignment operator to get proper
+ * precedence for operations for the ::GMX_LOG macro; this is a common
+ * technique for implementing macros that allow streming information to
+ * them (see, e.g., Google Test).
+ */
+ void operator=(const LogEntryWriter &entryWriter)
+ {
+ target_->writeEntry(entryWriter.entry_);
+ }
+
+ private:
+ ILogTarget *target_;
+};
+
+/*! \libinternal \brief
+ * Represents a single logging level.
+ *
+ * Typically this type is not used directly, but instances in MDLogger are
+ * simply accessed through ::GMX_LOG in code that writes to the log.
+ *
+ * \ingroup module_utility
+ */
+class LogLevelHelper
+{
+ public:
+ //! Initializes a helper for writing to the given target.
+ explicit LogLevelHelper(ILogTarget *target) : target_(target) {}
+
+ // Both of the below should be explicit, once that works in CUDA.
+ //! Returns whether the output for this log level goes anywhere.
+ operator bool() const { return target_ != nullptr; }
+
+ //! Creates a helper for ::GMX_LOG.
+ operator LogWriteHelper() const { return LogWriteHelper(target_); }
+
+ private:
+ ILogTarget *target_;
+};
+
+/*! \libinternal \brief
+ * Declares a logging interface.
+ *
+ * Typically, this object is not created directly, but instead through
+ * LoggerBuilder.
+ *
+ * For now, this is named MDLogger, since it is used only there, and it is not
+ * clear whether the logging levels can be the same throughout the code. It
+ * should be relatively straightforward to split this into multiple classes
+ * with different supported logging levels without changing calling code, or to
+ * rename it to Logger if we do not need any specialization.
+ *
+ * \ingroup module_utility
+ */
+class MDLogger
+{
+ public:
+ //! Supported logging levels.
+ enum LogLevel
+ {
+ Warning,
+ Info
+ };
+ //! Number of logging levels.
+ static const int LogLevelCount = static_cast<int>(Info) + 1;
+
+ MDLogger();
+ //! Creates a logger with the given targets.
+ explicit MDLogger(ILogTarget *targets[LogLevelCount]);
+
+ //! For writing at LogLevel::Warning level.
+ LogLevelHelper warning;
+ //! For writing at LogLevel::Info level.
+ LogLevelHelper info;
+};
+
+/*! \brief
+ * Helper to log information using gmx::MDLogger.
+ *
+ * \param logger LogLevelHelper instance to use for logging.
+ *
+ * Used as
+ * \code
+ GMX_LOG(logger.warning).appendText(...);
+ \endcode
+ * and ensures that the code to format the output is only executed when the
+ * output goes somewhere.
+ *
+ * See LogEntryWriter for functions that can be used with the macro (such as
+ * the appendText() in the example).
+ *
+ * \ingroup module_utility
+ */
+#define GMX_LOG(logger) \
+ if (::gmx::LogWriteHelper helper = ::gmx::LogWriteHelper(logger)) { } else \
+ helper = ::gmx::LogEntryWriter()
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "loggerbuilder.h"
+
+#include <memory>
+#include <vector>
+
+#include "gromacs/utility/filestream.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/textwriter.h"
+
+namespace gmx
+{
+
+class LogTargetCollection : public ILogTarget
+{
+ public:
+ void addTarget(ILogTarget *target)
+ {
+ targets_.push_back(target);
+ }
+
+ virtual void writeEntry(const LogEntry &entry)
+ {
+ for (ILogTarget *target : targets_)
+ {
+ target->writeEntry(entry);
+ }
+ }
+
+ private:
+ std::vector<ILogTarget *> targets_;
+};
+
+class LogTargetFormatter : public ILogTarget
+{
+ public:
+ explicit LogTargetFormatter(TextOutputStream *stream) : writer_(stream) {}
+
+ virtual void writeEntry(const LogEntry &entry);
+
+ private:
+ TextWriter writer_;
+};
+
+
+void LogTargetFormatter::writeEntry(const LogEntry &entry)
+{
+ if (entry.asParagraph)
+ {
+ writer_.ensureEmptyLine();
+ }
+ writer_.writeLine(entry.text);
+ if (entry.asParagraph)
+ {
+ writer_.ensureEmptyLine();
+ }
+}
+
+/********************************************************************
+ * LoggerOwner::Impl
+ */
+
+class LoggerOwner::Impl
+{
+ public:
+ explicit Impl(ILogTarget *loggerTargets[MDLogger::LogLevelCount])
+ : logger_(loggerTargets)
+ {
+ }
+
+ MDLogger logger_;
+ std::vector<std::unique_ptr<TextOutputStream> > streams_;
+ std::vector<std::unique_ptr<ILogTarget> > targets_;
+};
+
+/********************************************************************
+ * LoggerOwner
+ */
+
+LoggerOwner::LoggerOwner(std::unique_ptr<Impl> impl)
+ : impl_(impl.release()), logger_(&impl_->logger_)
+{
+}
+
+LoggerOwner::LoggerOwner(LoggerOwner &&other)
+ : impl_(std::move(other.impl_)), logger_(&impl_->logger_)
+{
+}
+
+LoggerOwner &LoggerOwner::operator=(LoggerOwner &&other)
+{
+ impl_ = std::move(other.impl_);
+ logger_ = &impl_->logger_;
+ return *this;
+}
+
+LoggerOwner::~LoggerOwner()
+{
+}
+
+/********************************************************************
+ * LoggerBuilder::Impl
+ */
+
+class LoggerBuilder::Impl
+{
+ public:
+ std::vector<std::unique_ptr<TextOutputStream> > streams_;
+ std::vector<std::unique_ptr<ILogTarget> > targets_;
+ std::vector<ILogTarget *> loggerTargets_[MDLogger::LogLevelCount];
+};
+
+/********************************************************************
+ * LoggerBuilder
+ */
+
+LoggerBuilder::LoggerBuilder()
+ : impl_(new Impl)
+{
+}
+
+LoggerBuilder::~LoggerBuilder()
+{
+}
+
+void LoggerBuilder::addTargetStream(MDLogger::LogLevel level, TextOutputStream *stream)
+{
+ impl_->targets_.push_back(std::unique_ptr<ILogTarget>(new LogTargetFormatter(stream)));
+ ILogTarget *target = impl_->targets_.back().get();
+ for (int i = 0; i <= static_cast<int>(level); ++i)
+ {
+ impl_->loggerTargets_[i].push_back(target);
+ }
+}
+
+void LoggerBuilder::addTargetFile(MDLogger::LogLevel level, FILE *fp)
+{
+ std::unique_ptr<TextOutputStream> stream(new TextOutputFile(fp));
+ addTargetStream(level, stream.get());
+ impl_->streams_.push_back(std::move(stream));
+}
+
+LoggerOwner LoggerBuilder::build()
+{
+ ILogTarget *loggerTargets[MDLogger::LogLevelCount];
+ for (int i = 0; i < MDLogger::LogLevelCount; ++i)
+ {
+ auto &levelTargets = impl_->loggerTargets_[i];
+ loggerTargets[i] = nullptr;
+ if (!levelTargets.empty())
+ {
+ if (levelTargets.size() == 1)
+ {
+ loggerTargets[i] = levelTargets[0];
+ }
+ else
+ {
+ std::unique_ptr<LogTargetCollection> collection(new LogTargetCollection);
+ for (auto &target : levelTargets)
+ {
+ collection->addTarget(target);
+ }
+ loggerTargets[i] = collection.get();
+ impl_->targets_.push_back(std::move(collection));
+ }
+ }
+ levelTargets.clear();
+ }
+ std::unique_ptr<LoggerOwner::Impl> data(new LoggerOwner::Impl(loggerTargets));
+ data->targets_ = std::move(impl_->targets_);
+ data->streams_ = std::move(impl_->streams_);
+ return LoggerOwner(std::move(data));
+}
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares functionality for initializing logging.
+ *
+ * See \ref page_logging for an overview of the functionality.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_LOGGERBUILDER_H
+#define GMX_UTILITY_LOGGERBUILDER_H
+
+#include <memory>
+#include <string>
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/logger.h"
+
+namespace gmx
+{
+
+class TextOutputStream;
+
+class LoggerFormatterBuilder;
+class LoggerOwner;
+
+/*! \libinternal \brief
+ * Initializes loggers.
+ *
+ * This class provides methods for specifying logging targets for a logger and
+ * building the logger after all targets have been specified. Having this
+ * separate from the logger allows using different internal data structures
+ * during initialization and operation, and simplifies the responsibilities of
+ * the involved classes.
+ *
+ * \ingroup module_utility
+ */
+class LoggerBuilder
+{
+ public:
+ LoggerBuilder();
+ ~LoggerBuilder();
+
+ /*! \brief
+ * Adds a stream to which log output is written.
+ *
+ * All output at level \p level or above it is written to \p stream.
+ * The caller is responsible of closing and freeing \p stream once the
+ * logger is discarded.
+ */
+ void addTargetStream(MDLogger::LogLevel level, TextOutputStream *stream);
+ /*! \brief
+ * Adds a file to which log output is written.
+ *
+ * All output at level \p level or above it is written to \p fp.
+ * The caller is responsible of closing \p fp once the logger is
+ * discarded.
+ */
+ void addTargetFile(MDLogger::LogLevel level, FILE *fp);
+
+ /*! \brief
+ * Builds the logger with the targets set for this builder.
+ *
+ * After this function has been called, the builder can (and should) be
+ * discarded.
+ */
+ LoggerOwner build();
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+/*! \libinternal \brief
+ * Manages memory for a logger built with LoggerBuilder.
+ *
+ * This class is responsible of managing all memory allocated by LoggerBuilder
+ * that is needed for operation of the actual logger. Also the actual logger
+ * instance is owned by this class. This allows keeing the actual logger simple
+ * and streamlined.
+ *
+ * This class supports move construction and assignment, which allows
+ * initializing it on the stack and assigning a new instance if the targets
+ * need to be changed.
+ *
+ * \ingroup module_utility
+ */
+class LoggerOwner
+{
+ public:
+ //! Move-constructs the owner.
+ LoggerOwner(LoggerOwner &&other);
+ ~LoggerOwner();
+
+ //! Move-assings the owner.
+ LoggerOwner &operator=(LoggerOwner &&other);
+
+ //! Returns the logger for writing the logs.
+ const MDLogger &logger() const { return *logger_; }
+
+ private:
+ class Impl;
+
+ LoggerOwner(std::unique_ptr<Impl> impl);
+
+ PrivateImplPointer<Impl> impl_;
+ const MDLogger *logger_;
+
+ friend class LoggerBuilder;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2014,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void MessageStringCollector::startContext(const char *name)
{
- impl_->contexts_.push_back(name);
+ impl_->contexts_.emplace_back(name);
}
void MessageStringCollector::append(const std::string &message)
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions from niceheader.h.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_utility
+ */
+#include "gmxpre.h"
+
+#include "niceheader.h"
+
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/sysinfo.h"
+#include "gromacs/utility/textwriter.h"
+
+namespace gmx
+{
+
+void niceHeader(TextWriter *writer, const char *fn, char commentChar)
+{
+ int uid;
+ char userbuf[256];
+ char hostbuf[256];
+ char timebuf[256];
+
+ /* Write a nice header for an output file */
+ writer->writeLine(formatString("%c", commentChar));
+ writer->writeLine(formatString("%c\tFile '%s' was generated", commentChar, fn ? fn : "unknown"));
+
+ uid = gmx_getuid();
+ gmx_getusername(userbuf, 256);
+ gmx_gethostname(hostbuf, 256);
+ gmx_format_current_time(timebuf, 256);
+
+ writer->writeLine(formatString("%c\tBy user: %s (%d)", commentChar, userbuf, uid));
+ writer->writeLine(formatString("%c\tOn host: %s", commentChar, hostbuf));
+ writer->writeLine(formatString("%c\tAt date: %s", commentChar, timebuf));
+ writer->writeLine(formatString("%c", commentChar));
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares function for printing a nice header for text output files.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_NICEHEADER_H
+#define GMX_UTILITY_NICEHEADER_H
+
+namespace gmx
+{
+
+class TextWriter;
+
+/*! \brief
+ * Prints creation time stamp and user information into a string as comments, and returns it.
+ *
+ * \param[out] writer Where to print the information.
+ * \param[in] fn Name of the file being written; if nullptr, described as "unknown".
+ * \param[in] commentChar Character to use as the starting delimiter for comments.
+ * \throws std::bad_alloc if out of memory. */
+void niceHeader(TextWriter *writer, const char *fn, char commentChar);
+
+} // namespace
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
result.push_back("");
#endif
const char *path = std::getenv("PATH");
- if (path != NULL)
+ if (path != nullptr)
{
splitPathEnvironment(path, &result);
}
// static
bool File::exists(const char *filename, NotFoundHandler onNotFound)
{
- if (filename == NULL)
+ if (filename == nullptr)
{
return false;
}
FILE *test = std::fopen(filename, "r");
- if (test == NULL)
+ if (test == nullptr)
{
const bool wasError = (errno != ENOENT && errno != ENOTDIR);
NotFoundInfo info(filename, "The file could not be opened.",
if (!S_ISREG(st_buf.st_mode))
{
NotFoundInfo info(filename, "The file is not a regular file.",
- NULL, true, 0);
+ nullptr, true, 0);
onNotFound(info);
return false;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers",
"SoftwareX",
1, 2015, "19-25" },
+ { "Ballenegger2009",
+ "V. Ballenegger, A. Arnold, J. J. Cerdà",
+ "Simulations of non-neutral slab systems with long-range electrostatic interactions in two-dimensional periodic boundary conditions",
+ "J. Chem. Phys",
+ 131, 2009, "094107" },
+ { "Hub2014a",
+ "J. S. Hub, B. L. de Groot, H. Grubmueller, G. Groenhof",
+ "Quantifying Artifacts in Ewald Simulations of Inhomogeneous Systems with a Net Charge",
+ "J. Chem. Theory Comput.",
+ 10, 2014, "381-393" },
};
#define NSTR (int)asize(citedb)
char *title;
#define LINE_WIDTH 79
- if (fp == NULL)
+ if (fp == nullptr)
{
return;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const IProgramContext &getProgramContext()
{
- if (g_programContext != NULL)
+ if (g_programContext != nullptr)
{
return *g_programContext;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2010,2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
cbase = (char *)base;
- swaptype = (size_t)(cbase - (char *)0) % sizeof(int) || size % sizeof(int) ? 2 : size == sizeof(int) ? 0 : 1;
+ swaptype = (size_t)(cbase - (char *)nullptr) % sizeof(int) || size % sizeof(int) ? 2 : size == sizeof(int) ? 0 : 1;
if (nmemb < 7)
{
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \libinternal \file
- * \brief
- * Declares gmx::scoped_cptr and gmx::scoped_guard_sfree.
- *
- * \author Teemu Murtola <teemu.murtola@gmail.com>
- * \inlibraryapi
- * \ingroup module_utility
- */
-#ifndef GMX_UTILITY_SCOPED_PTR_SFREE_H
-#define GMX_UTILITY_SCOPED_PTR_SFREE_H
-
-#include "gromacs/utility/classhelpers.h"
-#include "gromacs/utility/smalloc.h"
-
-namespace gmx
-{
-
-//! sfree wrapper to be used as scoped_cptr deleter
-template <class T>
-inline void sfree_wrapper(T *p)
-{
- sfree(p);
-}
-
-/*! \libinternal \brief
- * Stripped-down version of scoped_ptr that uses sfree() or custom deleter.
- *
- * Currently only implements some operations; other operations can be added
- * if they become necessary.
- * The presence of a release() method is not strictly according to `scoped_ptr`
- * design, but makes it easier to make existing C code exception-safe, and does
- * not really warrant a separate class for such a purpose.
- *
- * This class provides a basic guard/smart pointer for C pointers.
- *
- * Methods in this class do not throw.
- *
- * \inlibraryapi
- * \ingroup module_utility
- */
-template <class T, void D(T *) = sfree_wrapper>
-class scoped_cptr
-{
- public:
- /*! \brief
- * Initializes a scoped_cptr that frees \p ptr on scope exit.
- *
- * \param[in] ptr Pointer to use for initialization.
- */
- explicit scoped_cptr(T *ptr = NULL) : ptr_(ptr) {}
- //! Frees the pointer passed to the constructor.
- ~scoped_cptr() { D(ptr_); }
- //! Returns the stored pointer.
- T *get() const { return ptr_; }
- //! Check for non-null pointer in boolean context.
- explicit operator bool () const { return ptr_ != 0; }
- //! Sets the pointer and frees previous pointer if necessary.
- void reset(T *ptr) { D(ptr_); ptr_ = ptr; }
- //! Clears the pointer without freeing the memory, and returns the old value.
- T *release() { T *ptr = ptr_; ptr_ = NULL; return ptr; }
-
- private:
- T *ptr_;
-
- GMX_DISALLOW_COPY_AND_ASSIGN(scoped_cptr);
-};
-
-//! Simple guard which calls sfree. See scoped_cptr for details.
-typedef scoped_cptr<void> scoped_guard_sfree;
-
-} // namespace gmx
-
-#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
void *p;
- p = NULL;
+ p = nullptr;
if (size == 0)
{
- p = NULL;
+ p = nullptr;
}
else
{
- if ((p = malloc(size)) == NULL)
+ if ((p = malloc(size)) == nullptr)
{
gmx_fatal(errno, __FILE__, __LINE__,
"Not enough memory. Failed to malloc %" GMX_PRId64 " bytes for %s\n"
{
void *p;
- p = NULL;
+ p = nullptr;
if ((nelem == 0) || (elsize == 0))
{
- p = NULL;
+ p = nullptr;
}
else
{
}
memset(p, 0, (size_t) (nelem * elsize));
#else
- if ((p = calloc((size_t)nelem, (size_t)elsize)) == NULL)
+ if ((p = calloc((size_t)nelem, (size_t)elsize)) == nullptr)
{
gmx_fatal(errno, __FILE__, __LINE__,
"Not enough memory. Failed to calloc %" GMX_PRId64
void *p;
size_t size = nelem*elsize;
- p = NULL;
+ p = nullptr;
if (size == 0)
{
save_free(name, file, line, ptr);
size/1048576.0, name, file, line, rank);
}
#endif
- if (ptr == NULL)
+ if (ptr == nullptr)
{
p = malloc((size_t)size);
}
{
p = realloc(ptr, (size_t)size);
}
- if (p == NULL)
+ if (p == nullptr)
{
gmx_fatal(errno, __FILE__, __LINE__,
"Not enough memory. Failed to realloc %" GMX_PRId64 " bytes for %s, %s=%x\n"
#ifdef DEBUG
log_action(0, name, file, line, 0, 0, ptr);
#endif
- if (ptr != NULL)
+ if (ptr != nullptr)
{
free(ptr);
}
size_t nelem, size_t elsize, size_t alignment)
{
void *aligned = save_malloc_aligned(name, file, line, nelem, elsize, alignment);
- if (aligned != NULL)
+ if (aligned != nullptr)
{
memset(aligned, 0, (size_t)(nelem * elsize));
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions in strconvert.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_utility
+ */
+#include "gmxpre.h"
+
+#include "strconvert.h"
+
+#include <cerrno>
+#include <cstdlib>
+
+#include <limits>
+#include <string>
+
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
+
+namespace gmx
+{
+
+//! \cond libapi
+
+bool boolFromString(const char *value)
+{
+ if (gmx_strcasecmp(value, "1") == 0
+ || gmx_strcasecmp(value, "yes") == 0
+ || gmx_strcasecmp(value, "true") == 0)
+ {
+ return true;
+ }
+ if (gmx_strcasecmp(value, "0") == 0
+ || gmx_strcasecmp(value, "no") == 0
+ || gmx_strcasecmp(value, "false") == 0)
+ {
+ return false;
+ }
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(value) + "'; supported values are: 1, 0, yes, no, true, false"));
+}
+
+int intFromString(const char *str)
+{
+ errno = 0;
+ char *endptr;
+ const long int value = std::strtol(str, &endptr, 10);
+ if (errno == ERANGE
+ || value < std::numeric_limits<int>::min()
+ || value > std::numeric_limits<int>::max())
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; it causes an integer overflow"));
+ }
+ if (str[0] == '\0' || *endptr != '\0')
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; expected an integer"));
+ }
+ return value;
+}
+
+gmx_int64_t int64FromString(const char *str)
+{
+ errno = 0;
+ char *endptr;
+ const gmx_int64_t value = str_to_int64_t(str, &endptr);
+ if (errno == ERANGE)
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; it causes an integer overflow"));
+ }
+ if (str[0] == '\0' || *endptr != '\0')
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; expected an integer"));
+ }
+ return value;
+}
+
+float floatFromString(const char *str)
+{
+ errno = 0;
+ char *endptr;
+ const double value = std::strtod(str, &endptr);
+ if (errno == ERANGE
+ || value < -std::numeric_limits<float>::max()
+ || value > std::numeric_limits<float>::max())
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; it causes an overflow/underflow"));
+ }
+ if (str[0] == '\0' || *endptr != '\0')
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; expected a number"));
+ }
+ return value;
+}
+
+double doubleFromString(const char *str)
+{
+ errno = 0;
+ char *endptr;
+ const double value = std::strtod(str, &endptr);
+ if (errno == ERANGE)
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; it causes an overflow/underflow"));
+ }
+ if (str[0] == '\0' || *endptr != '\0')
+ {
+ GMX_THROW(InvalidInputError("Invalid value: '" + std::string(str)
+ + "'; expected a number"));
+ }
+ return value;
+}
+
+//! \endcond
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares common utility functions for conversions to and from strings.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_STRCONVERT_H
+#define GMX_UTILITY_STRCONVERT_H
+
+#include <string>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/stringutil.h"
+
+namespace gmx
+{
+
+//! \cond libapi
+//! \addtogroup module_utility
+//! \{
+
+/*! \brief
+ * Parses a boolean from a string.
+ *
+ * \throws InvalidInputError if `str` is not recognized as a boolean value.
+ */
+bool boolFromString(const char *str);
+/*! \brief
+ * Parses an integer from a string.
+ *
+ * \throws InvalidInputError if `str` is not a valid integer.
+ *
+ * Also checks for overflow.
+ */
+int intFromString(const char *str);
+/*! \brief
+ * Parses a 64-bit integer from a string.
+ *
+ * \throws InvalidInputError if `str` is not a valid integer.
+ *
+ * Also checks for overflow.
+ */
+gmx_int64_t int64FromString(const char *str);
+/*! \brief
+ * Parses a float value from a string.
+ *
+ * \throws InvalidInputError if `str` is not a valid number.
+ *
+ * Also checks for overflow.
+ */
+float floatFromString(const char *str);
+/*! \brief
+ * Parses a double value from a string.
+ *
+ * \throws InvalidInputError if `str` is not a valid number.
+ *
+ * Also checks for overflow.
+ */
+double doubleFromString(const char *str);
+
+/*! \brief
+ * Parses a value from a string to a given type.
+ *
+ * \tparam T Type of value to parse.
+ *
+ * `T` can only be one of the types that is explicity supported.
+ * The main use for this function is to write `fromString<real>(value)`,
+ * but it can also be used for other types for consistency.
+ */
+template <typename T> static inline T fromString(const char *str);
+//! \copydoc fromString(const char *)
+template <typename T> static inline T fromString(const std::string &str)
+{
+ return fromString<T>(str.c_str());
+}
+/*! \copydoc fromString(const char *)
+ *
+ * Provided for situations where overload resolution cannot easily resolve the
+ * desired std::string parameter.
+ */
+template <typename T> static inline T fromStdString(const std::string &str)
+{
+ return fromString<T>(str.c_str());
+}
+
+//! Implementation for boolean values.
+template <> inline
+bool fromString<bool>(const char *str) { return boolFromString(str); }
+//! Implementation for integer values.
+template <> inline
+int fromString<int>(const char *str) { return intFromString(str); }
+//! Implementation for 64-bit integer values.
+template <> inline
+gmx_int64_t fromString<gmx_int64_t>(const char *str) { return int64FromString(str); }
+//! Implementation for float values.
+template <> inline
+float fromString<float>(const char *str) { return floatFromString(str); }
+//! Implementation for double values.
+template <> inline
+double fromString<double>(const char *str) { return doubleFromString(str); }
+
+/*! \brief
+ * Converts a boolean to a "true"/"false" string.
+ *
+ * Does not throw.
+ */
+static inline const char *boolToString(bool value)
+{
+ return value ? "true" : "false";
+}
+/*! \brief
+ * Returns a string containing the value of \c t.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+static inline std::string intToString(int t)
+{
+ return formatString("%d", t);
+}
+//! \copydoc intToString(int)
+static inline std::string int64ToString(gmx_int64_t t)
+{
+ return formatString("%" GMX_PRId64, t);
+}
+//! \copydoc intToString(int)
+static inline std::string doubleToString(double t)
+{
+ return formatString("%g", t);
+}
+
+/*! \name
+ * Overloads for converting a value of a given type to a string.
+ *
+ * \throws std::bad_alloc if out of memory.
+ * \{
+ */
+static inline std::string toString(bool t) { return boolToString(t); }
+static inline std::string toString(int t) { return intToString(t); }
+static inline std::string toString(gmx_int64_t t) { return int64ToString(t); }
+static inline std::string toString(float t) { return doubleToString(t); }
+static inline std::string toString(double t) { return doubleToString(t); }
+static inline std::string toString(std::string t) { return t; }
+//! \}
+
+//! \}
+//! \endcond
+
+} // namespace gmx
+
+#endif
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
std::strcpy(temp, line);
dum = std::strchr(temp, '[');
- if (dum == NULL)
+ if (dum == nullptr)
{
return FALSE;
}
dum[0] = ' ';
dum = std::strchr(temp, ']');
- if (dum == NULL)
+ if (dum == nullptr)
{
gmx_fatal(FARGS, "header is not terminated on line:\n'%s'\n", line);
return FALSE;
char *pret;
pret = fgets(buf, STRLEN, in);
- if (pret == NULL || sscanf(buf, "%d", &nstr) != 1)
+ if (pret == nullptr || sscanf(buf, "%d", &nstr) != 1)
{
gmx_warning("File is empty");
gmx_ffclose(in);
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares utility functionst for string comparison.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_STRINGCOMPARE_H
+#define GMX_UTILITY_STRINGCOMPARE_H
+
+#include <string>
+
+#include "gromacs/utility/cstringutil.h"
+
+namespace gmx
+{
+
+//! \cond libapi
+/*! \brief
+ * Specifies how strings should be compared in various contexts.
+ *
+ * \ingroup module_utility
+ */
+enum class StringCompareType
+{
+ //! Only exact matches are accepted.
+ Exact,
+ //! Case-insensitive comparison.
+ CaseInsensitive,
+ //! Case-insensitive comparison that also ignores '-' and '_'.
+ CaseAndDashInsensitive
+};
+//! \endcond
+
+/*! \libinternal \brief
+ * Compare object for std::string STL containers and algorithms that supports
+ * run-time decision on how to compare.
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+class StringCompare
+{
+ public:
+ /*! \brief
+ * Creates a comparer with the given type
+ *
+ * This is not explicit, which allows passing \ref StringCompareType
+ * directly to, e.g., `std::map` constructors.
+ */
+ StringCompare(StringCompareType type = StringCompareType::Exact)
+ : type_(type) {}
+
+ //! The comparison operation.
+ bool operator()(const std::string &a, const std::string &b) const
+ {
+ switch (type_)
+ {
+ case StringCompareType::Exact:
+ return a < b;
+ case StringCompareType::CaseInsensitive:
+ return gmx_strcasecmp(a.c_str(), b.c_str()) < 0;
+ case StringCompareType::CaseAndDashInsensitive:
+ return gmx_strcasecmp_min(a.c_str(), b.c_str()) < 0;
+ }
+ return a < b;
+ }
+
+ private:
+ StringCompareType type_;
+};
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <sstream>
#include <string>
#include <vector>
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
namespace gmx
std::string stripSuffixIfPresent(const std::string &str, const char *suffix)
{
- if (suffix != NULL)
+ if (suffix != nullptr)
{
size_t suffixLength = std::strlen(suffix);
if (suffixLength > 0 && endsWith(str, suffix))
std::string formatString(const char *fmt, ...)
{
- va_list ap;
+ va_list ap;
+ va_start(ap, fmt);
+ std::string result = formatStringV(fmt, ap);
+ va_end(ap);
+ return result;
+}
+
+std::string formatStringV(const char *fmt, va_list ap)
+{
+ va_list ap_copy;
char staticBuf[1024];
int length = 1024;
std::vector<char> dynamicBuf;
// provides their own way of doing things...
while (1)
{
- va_start(ap, fmt);
- int n = vsnprintf(buf, length, fmt, ap);
- va_end(ap);
+ va_copy(ap_copy, ap);
+ int n = vsnprintf(buf, length, fmt, ap_copy);
+ va_end(ap_copy);
if (n > -1 && n < length)
{
std::string result(buf);
}
if (startPos != end)
{
- result.push_back(std::string(startPos, currPos));
+ result.emplace_back(startPos, currPos);
}
}
return result;
}
+std::vector<std::string> splitDelimitedString(const std::string &str, char delim)
+{
+ std::vector<std::string> result;
+ size_t currPos = 0;
+ const size_t len = str.length();
+ if (len > 0)
+ {
+ size_t nextDelim;
+ do
+ {
+ nextDelim = str.find(delim, currPos);
+ result.push_back(str.substr(currPos, nextDelim - currPos));
+ currPos = nextDelim < len ? nextDelim + 1 : len;
+ }
+ while (currPos < len || nextDelim < len);
+ }
+ return result;
+}
+
+std::vector<std::string> splitAndTrimDelimitedString(const std::string &str, char delim)
+{
+ std::vector<std::string> result;
+
+ result = splitDelimitedString(str, delim);
+ std::transform(result.begin(), result.end(), result.begin(), stripString);
+ return result;
+}
+
namespace
{
replaceInternal(const std::string &input, const char *from, const char *to,
bool bWholeWords)
{
- GMX_RELEASE_ASSERT(from != NULL && to != NULL,
+ GMX_RELEASE_ASSERT(from != nullptr && to != nullptr,
"Replacement strings must not be NULL");
size_t matchLength = std::strlen(from);
std::string result;
{
const char *nextBreakPtr = std::strpbrk(input + lineEnd, " \n");
size_t nextBreak
- = (nextBreakPtr != NULL ? nextBreakPtr - input : inputLength);
+ = (nextBreakPtr != nullptr ? nextBreakPtr - input : inputLength);
if (nextBreak > lastAllowedBreakPoint && lineEnd > lineStart)
{
break;
}
int indent = (bFirstLine ? settings_.firstLineIndent() : settings_.indent());
bool bContinuation = (lineEnd < inputLength && input[lineEnd - 1] != '\n');
- // Strip trailing whitespace.
- if (!settings_.bKeepFinalSpaces_ || lineEnd < inputLength || input[inputLength - 1] == '\n')
+ // Remove explicit line breaks in input
+ // (the returned line should not contain line breaks).
+ while (lineEnd > lineStart && input[lineEnd - 1] == '\n')
+ {
+ --lineEnd;
+ }
+ // Strip trailing whitespace, unless they are explicit in the input and it
+ // has been requested to keep them.
+ if (bContinuation || !settings_.bKeepFinalSpaces_)
{
while (lineEnd > lineStart && std::isspace(input[lineEnd - 1]))
{
return result;
}
+std::vector<int> parseDigitsFromString(const std::string &input)
+{
+ std::vector<int> digits;
+ std::istringstream ss(input);
+ std::string token;
+ digits.reserve(input.length());
+ token.reserve(input.length());
+ while (std::getline(ss, token, ','))
+ {
+ for (const auto &c : token)
+ {
+ if (std::isdigit(c) == 0)
+ {
+ GMX_THROW(InvalidInputError(formatString("Invalid character in digit-only string: \"%c\"\n", c)));
+ }
+ digits.push_back(c - '0');
+ }
+ }
+ return digits;
+}
+
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#ifndef GMX_UTILITY_STRINGUTIL_H
#define GMX_UTILITY_STRINGUTIL_H
+#include <cstdarg>
#include <cstring>
#include <string>
*/
static inline bool isNullOrEmpty(const char *str)
{
- return str == NULL || str[0] == '\0';
+ return str == nullptr || str[0] == '\0';
}
/*! \brief
* \throws std::bad_alloc if out of memory.
*/
std::string stripString(const std::string &str);
-
/*! \brief
* Formats a string (snprintf() wrapper).
*
* supported.
*/
std::string formatString(const char *fmt, ...);
+/*! \brief
+ * Formats a string (vsnprintf() wrapper).
+ *
+ * \throws std::bad_alloc if out of memory.
+ *
+ * This function works like vsprintf(), except that it returns an std::string
+ * instead of requiring a preallocated buffer. Arbitrary length output is
+ * supported.
+ */
+std::string formatStringV(const char *fmt, va_list ap);
/*! \brief Function object that wraps a call to formatString() that
* expects a single conversion argument, for use with algorithms. */
return joinStrings(array, array + count, separator);
}
-/*! \brief
- * Converts a boolean to a "true"/"false" string.
- *
- * Does not throw.
- */
-static inline const char *boolToString(bool value)
-{
- return value ? "true" : "false";
-}
-
/*! \brief
* Splits a string to whitespace separated tokens.
*
* separator.
*/
std::vector<std::string> splitString(const std::string &str);
+/*! \brief
+ * Splits a string to tokens separated by a given delimiter.
+ *
+ * \param[in] str String to process.
+ * \param[in] delim Delimiter to use for splitting.
+ * \returns \p str split into tokens at delimiter.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Unlike splitString(), consecutive delimiters will generate empty tokens, as
+ * will leading or trailing delimiters.
+ * Empty input will return an empty vector.
+ */
+std::vector<std::string> splitDelimitedString(const std::string &str, char delim);
+/*! \brief
+ * Splits \c str to tokens separated by delimiter \c delim. Removes
+ * leading and trailing whitespace from those strings with std::isspace.
+ *
+ * \param[in] str String to process.
+ * \param[in] delim Delimiter to use for splitting.
+ * \returns \p str split into tokens at delimiter, with whitespace stripped.
+ * \throws std::bad_alloc if out of memory.
+ *
+ * Unlike splitString(), consecutive delimiters will generate empty tokens, as
+ * will leading or trailing delimiters.
+ * Empty input will return an empty vector.
+ * Input with only whitespace will return a vector of size 1,
+ * that contains an empty token.
+ */
+std::vector<std::string> splitAndTrimDelimitedString(const std::string &str, char delim);
/*! \brief
* Replace all occurrences of a string with another string.
TextLineWrapperSettings settings_;
};
+/*! \brief Construct a vector of decimal digits parsed from an \c input string.
+ *
+ * \param[in] input String that must contain only decimal digits, or only
+ * decimal digits separated by comma delimiters.
+ *
+ * \returns Vector of any digits found in \c input.
+ *
+ * \throws std::bad_alloc if out of memory
+ * InvalidInputError if an invalid digit character is found.
+ */
+std::vector<int> parseDigitsFromString(const std::string &input);
+
//! \}
} // namespace gmx
void gmx_format_current_time(char *buf, size_t len)
{
- time_t clock = time(NULL);
+ time_t clock = time(nullptr);
gmx_ctime_r(&clock, buf, len);
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014, by the GROMACS development team, led by
+ * Copyright (c) 2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \libinternal \file
* \brief
- * Declares functions for obtaining information about the operating environment
- * and the current process.
+ * Declares functions that wrap platform-specific calls for obtaining
+ * information about the operating environment and the current
+ * process.
*
* \author Teemu Murtola <teemu.murtola@gmail.com>
* \inlibraryapi
#include <stddef.h>
#include <time.h>
-#ifdef __cplusplus
-extern "C" {
-#endif
-
/*! \addtogroup module_utility
* \{
*/
/*! \} */
-#ifdef __cplusplus
-}
-#endif
-
#endif
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
arrayref.cpp
basedefinitions.cpp
bitmask32.cpp bitmask64.cpp bitmask128.cpp
+ keyvaluetreeserializer.cpp
+ keyvaluetreetransform.cpp
+ logger.cpp
+ mutex.cpp
path.cpp
stringutil.cpp
+ textreader.cpp
textwriter.cpp
+ typetraits.cpp
)
#include "gromacs/utility/arrayref.h"
-#include "config.h"
-
#include <vector>
#include <gtest/gtest.h>
*
* There, we take a non-const struct-field array of static length and
* make an ArrayRef to it using the template constructor that is
- * supposed to infer the length from the static size. But on xlc on
- * BlueGene/Q, if the base type is not char (or unsigned char), the
- * generated code ends up with an ArrayRef of zero size, so everything
- * breaks. Presumably the default code path accidentally works for
- * char.
- *
- * Fortunately, all current uses of that constructor have a base type
- * of char, so there's no big problem. Using a pointer-based
- * constructor does work, if there's ever a problem (and that is
- * tested above). */
+ * supposed to infer the length from the static size. This has
+ * been a problem (for a compiler that we no longer support),
+ * so we test it.
+ */
TYPED_TEST(ArrayRefTest, ConstructFromStructFieldWithTemplateConstructorWorks)
{
h.a[i] = a[i];
}
typename TestFixture::ArrayRefType arrayRef(h.a);
-#if GMX_TARGET_BGQ && defined(__xlC__)
- if (sizeof(typename TestFixture::ValueType) == sizeof(char))
-#endif
- {
- this->runTests(h.a, h.size, h.a, arrayRef);
- }
+ this->runTests(h.a, h.size, h.a, arrayRef);
}
#else // GTEST_HAS_TYPED_TEST
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "gromacs/utility/keyvaluetreeserializer.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/inmemoryserializer.h"
+#include "gromacs/utility/iserializer.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+
+#include "testutils/refdata.h"
+
+namespace
+{
+
+class RefDataSerializer : public gmx::ISerializer
+{
+ public:
+ RefDataSerializer(gmx::test::TestReferenceChecker *parentChecker,
+ const char *id)
+ : checker_(parentChecker->checkCompound("SerializedData", id))
+ {
+ }
+
+ virtual bool reading() const { return false; }
+
+ virtual void doBool(bool *value)
+ {
+ checker_.checkBoolean(*value, nullptr);
+ }
+ virtual void doUChar(unsigned char *value)
+ {
+ checker_.checkUChar(*value, nullptr);
+ }
+ virtual void doInt(int *value)
+ {
+ checker_.checkInteger(*value, nullptr);
+ }
+ virtual void doInt64(gmx_int64_t *value)
+ {
+ checker_.checkInt64(*value, nullptr);
+ }
+ virtual void doFloat(float *value)
+ {
+ checker_.checkFloat(*value, nullptr);
+ }
+ virtual void doDouble(double *value)
+ {
+ checker_.checkDouble(*value, nullptr);
+ }
+ virtual void doString(std::string *value)
+ {
+ checker_.checkString(*value, nullptr);
+ }
+
+ private:
+ gmx::test::TestReferenceChecker checker_;
+};
+
+class KeyValueTreeSerializerTest : public ::testing::Test
+{
+ public:
+ void runTest()
+ {
+ gmx::KeyValueTreeObject input(builder_.build());
+ gmx::test::TestReferenceData data;
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ checker.checkKeyValueTreeObject(input, "Input");
+ {
+ RefDataSerializer serializer(&checker, "Stream");
+ gmx::serializeKeyValueTree(input, &serializer);
+ }
+ std::vector<char> buffer = serializeTree(input);
+ {
+ gmx::InMemoryDeserializer deserializer(buffer);
+ gmx::KeyValueTreeObject output
+ = gmx::deserializeKeyValueTree(&deserializer);
+ checker.checkKeyValueTreeObject(output, "Input");
+ }
+ }
+
+ gmx::KeyValueTreeBuilder builder_;
+
+ private:
+ std::vector<char> serializeTree(const gmx::KeyValueTreeObject &tree)
+ {
+ gmx::InMemorySerializer serializer;
+ gmx::serializeKeyValueTree(tree, &serializer);
+ return serializer.finishAndGetBuffer();
+ }
+};
+
+TEST_F(KeyValueTreeSerializerTest, EmptyTree)
+{
+ runTest();
+}
+
+TEST_F(KeyValueTreeSerializerTest, SimpleObject)
+{
+ builder_.rootObject().addValue<int>("foo", 1);
+ builder_.rootObject().addValue<std::string>("bar", "a");
+ builder_.rootObject().addValue<float>("f", 1.5);
+ builder_.rootObject().addValue<double>("d", 2.5);
+ runTest();
+}
+
+TEST_F(KeyValueTreeSerializerTest, ObjectWithArrays)
+{
+ auto arr1 = builder_.rootObject().addUniformArray<int>("a");
+ arr1.addValue(1);
+ arr1.addValue(2);
+ auto arr2 = builder_.rootObject().addUniformArray<std::string>("b");
+ arr2.addValue("foo");
+ arr2.addValue("bar");
+ runTest();
+}
+
+TEST_F(KeyValueTreeSerializerTest, ObjectWithObjects)
+{
+ auto obj1 = builder_.rootObject().addObject("obj");
+ obj1.addValue<int>("a", 1);
+ obj1.addValue<std::string>("b", "foo");
+ auto obj2 = builder_.rootObject().addObject("obj2");
+ obj2.addValue<int>("c", 2);
+ obj2.addValue<std::string>("d", "bar");
+ builder_.rootObject().addValue<int>("foo", 3);
+ runTest();
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "gromacs/utility/keyvaluetreetransform.h"
+
+#include <string>
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/strconvert.h"
+#include "gromacs/utility/stringcompare.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/testasserts.h"
+
+namespace
+{
+
+class TreeValueTransformTest : public ::testing::Test
+{
+ public:
+ void testTransform(const gmx::KeyValueTreeObject &input,
+ const gmx::KeyValueTreeTransformer &transform)
+ {
+ gmx::KeyValueTreeTransformResult result = transform.transform(input, nullptr);
+ gmx::KeyValueTreeObject object = result.object();
+
+ gmx::test::TestReferenceData data;
+ gmx::test::TestReferenceChecker checker(data.rootChecker());
+ checker.checkKeyValueTreeObject(input, "Input");
+ auto mappedPaths = transform.mappedPaths();
+ checker.checkSequence(mappedPaths.begin(), mappedPaths.end(), "MappedPaths",
+ &TreeValueTransformTest::checkMappedPath);
+ checker.checkKeyValueTreeObject(object, "Tree");
+ checkBackMapping(&checker, object, result.backMapping());
+ }
+
+ private:
+ static void checkMappedPath(gmx::test::TestReferenceChecker *checker,
+ const gmx::KeyValueTreePath &path)
+ {
+ checker->checkString(path.toString(), nullptr);
+ }
+ void checkBackMapping(gmx::test::TestReferenceChecker *checker,
+ const gmx::KeyValueTreeObject &object,
+ const gmx::IKeyValueTreeBackMapping &mapping)
+ {
+ auto compound(checker->checkCompound("BackMapping", "Mapping"));
+ checkBackMappingImpl(&compound, object, mapping, gmx::KeyValueTreePath());
+ }
+
+ void checkBackMappingImpl(gmx::test::TestReferenceChecker *checker,
+ const gmx::KeyValueTreeObject &object,
+ const gmx::IKeyValueTreeBackMapping &mapping,
+ const gmx::KeyValueTreePath &prefix)
+ {
+ for (const auto &prop : object.properties())
+ {
+ gmx::KeyValueTreePath path = prefix;
+ path.append(prop.key());
+ if (prop.value().isObject())
+ {
+ checkBackMappingImpl(checker, prop.value().asObject(), mapping, path);
+ }
+ else
+ {
+ gmx::KeyValueTreePath orgPath = mapping.originalPath(path);
+ checker->checkString(orgPath.toString(), path.toString().c_str());
+ }
+ }
+ }
+};
+
+TEST_F(TreeValueTransformTest, SimpleTransforms)
+{
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<std::string>("a", "1");
+ builder.rootObject().addValue<std::string>("b", "2");
+ gmx::KeyValueTreeObject input = builder.build();
+
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .from<std::string>("/a").to<int>("/i").transformWith(&gmx::fromStdString<int>);
+ transform.rules()->addRule()
+ .from<std::string>("/b").to<int>("/j").transformWith(&gmx::fromStdString<int>);
+
+ testTransform(input, transform);
+}
+
+TEST_F(TreeValueTransformTest, SimpleTransformsCaseAndDashInsensitive)
+{
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<std::string>("a-x", "1");
+ builder.rootObject().addValue<std::string>("by", "2");
+ gmx::KeyValueTreeObject input = builder.build();
+
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .keyMatchType("/", gmx::StringCompareType::CaseAndDashInsensitive);
+ transform.rules()->addRule()
+ .from<std::string>("/Ax").to<int>("/i").transformWith(&gmx::fromStdString<int>);
+ transform.rules()->addRule()
+ .from<std::string>("/B-Y").to<int>("/j").transformWith(&gmx::fromStdString<int>);
+
+ testTransform(input, transform);
+}
+
+TEST_F(TreeValueTransformTest, SimpleTransformsToObject)
+{
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<std::string>("a", "1");
+ builder.rootObject().addValue<std::string>("b", "2");
+ gmx::KeyValueTreeObject input = builder.build();
+
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .from<std::string>("/a").to<int>("/foo/i").transformWith(&gmx::fromStdString<int>);
+ transform.rules()->addRule()
+ .from<std::string>("/b").to<int>("/foo/j").transformWith(&gmx::fromStdString<int>);
+
+ testTransform(input, transform);
+}
+
+
+TEST_F(TreeValueTransformTest, ObjectFromString)
+{
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<std::string>("a", "1 2");
+ gmx::KeyValueTreeObject input = builder.build();
+
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .from<std::string>("/a").toObject("/foo").transformWith(
+ [] (gmx::KeyValueTreeObjectBuilder *builder, const std::string &value)
+ {
+ std::vector<std::string> values = gmx::splitString(value);
+ builder->addValue<int>("a", gmx::fromString<int>(values[0]));
+ builder->addValue<int>("b", gmx::fromString<int>(values[1]));
+ });
+
+ testTransform(input, transform);
+}
+
+TEST_F(TreeValueTransformTest, ObjectFromMultipleStrings)
+{
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<std::string>("a", "1");
+ builder.rootObject().addValue<std::string>("b", "2 3");
+ gmx::KeyValueTreeObject input = builder.build();
+
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .from<std::string>("/a").to<int>("/foo/a").transformWith(&gmx::fromStdString<int>);
+ transform.rules()->addRule()
+ .from<std::string>("/b").toObject("/foo").transformWith(
+ [] (gmx::KeyValueTreeObjectBuilder *builder, const std::string &value)
+ {
+ std::vector<std::string> values = gmx::splitString(value);
+ builder->addValue<int>("b", gmx::fromString<int>(values[0]));
+ builder->addValue<int>("c", gmx::fromString<int>(values[1]));
+ });
+
+ testTransform(input, transform);
+}
+
+TEST_F(TreeValueTransformTest, ScopedTransformRules)
+{
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<std::string>("a", "1");
+ builder.rootObject().addValue<std::string>("b", "2");
+ gmx::KeyValueTreeObject input = builder.build();
+
+ gmx::KeyValueTreeTransformer transform;
+ auto scope = transform.rules()->scopedTransform("/foo");
+ scope.rules()->addRule()
+ .from<std::string>("/a").to<int>("/i").transformWith(&gmx::fromStdString<int>);
+ scope.rules()->addRule()
+ .from<std::string>("/b").to<int>("/j").transformWith(&gmx::fromStdString<int>);
+
+ testTransform(input, transform);
+}
+
+/********************************************************************
+ * Tests for errors
+ */
+
+TEST(TreeValueTransformErrorTest, ConversionError)
+{
+ gmx::KeyValueTreeBuilder builder;
+ builder.rootObject().addValue<std::string>("a", "foo");
+ gmx::KeyValueTreeObject input = builder.build();
+
+ gmx::KeyValueTreeTransformer transform;
+ transform.rules()->addRule()
+ .from<std::string>("/a").to<int>("/i").transformWith(&gmx::fromStdString<int>);
+
+ EXPECT_THROW_GMX(transform.transform(input, nullptr), gmx::InvalidInputError);
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "gromacs/utility/logger.h"
+
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/loggerbuilder.h"
+#include "gromacs/utility/stringstream.h"
+
+#include "testutils/stringtest.h"
+#include "testutils/testfilemanager.h"
+
+namespace
+{
+
+//! Test fixture for logging tests.
+typedef gmx::test::StringTestBase LoggerTest;
+
+TEST_F(LoggerTest, EmptyLoggerWorks)
+{
+ gmx::MDLogger logger;
+ GMX_LOG(logger.info).appendText("foobar");
+ GMX_LOG(logger.warning).appendText("foobar").asParagraph();
+}
+
+TEST_F(LoggerTest, LogsToStream)
+{
+ gmx::StringOutputStream stream;
+ gmx::LoggerBuilder builder;
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Info, &stream);
+ gmx::LoggerOwner owner = builder.build();
+ const gmx::MDLogger &logger = owner.logger();
+ GMX_LOG(logger.info).appendText("line");
+ GMX_LOG(logger.warning).appendText("par").asParagraph();
+ GMX_LOG(logger.info).appendText("line2");
+ checkText(stream.toString(), "Output");
+}
+
+TEST_F(LoggerTest, LogsToFile)
+{
+ gmx::test::TestFileManager files;
+ std::string filename(files.getTemporaryFilePath("log.txt"));
+ FILE *fp = fopen(filename.c_str(), "w");
+ {
+ gmx::LoggerBuilder builder;
+ builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fp);
+ gmx::LoggerOwner owner = builder.build();
+ const gmx::MDLogger &logger = owner.logger();
+ GMX_LOG(logger.info).appendText("line");
+ GMX_LOG(logger.warning).appendText("par").asParagraph();
+ GMX_LOG(logger.info).appendText("line2");
+ }
+ fclose(fp);
+ checkFileContents(filename, "Output");
+}
+
+TEST_F(LoggerTest, LevelFilteringWorks)
+{
+ gmx::StringOutputStream stream;
+ gmx::LoggerBuilder builder;
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &stream);
+ gmx::LoggerOwner owner = builder.build();
+ const gmx::MDLogger &logger = owner.logger();
+ GMX_LOG(logger.info).appendText("line");
+ GMX_LOG(logger.warning).appendText("par").asParagraph();
+ GMX_LOG(logger.info).appendText("line2");
+ checkText(stream.toString(), "Output");
+}
+
+TEST_F(LoggerTest, LogsToMultipleStreams)
+{
+ gmx::StringOutputStream stream1;
+ gmx::StringOutputStream stream2;
+ gmx::LoggerBuilder builder;
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Info, &stream1);
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Warning, &stream2);
+ gmx::LoggerOwner owner = builder.build();
+ const gmx::MDLogger &logger = owner.logger();
+ GMX_LOG(logger.info).appendText("line");
+ GMX_LOG(logger.warning).appendText("par").asParagraph();
+ GMX_LOG(logger.info).appendText("line2");
+ checkText(stream1.toString(), "Output1");
+ checkText(stream2.toString(), "Output2");
+}
+
+} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Tests for gmx::Mutex
+ *
+ * These tests ensure that basic mutual-exclusion properties hold.
+ * Note that no testing can prove there isn't a bug, but if one
+ * exists, then these tests might expose one.
+ *
+ * In particular, try_lock can be implemented differently on different
+ * platforms, or with different default mutex types, so we should
+ * check that the behaviour continues to conform with the thread-MPI
+ * documentation.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_utility
+ */
+
+#include "gmxpre.h"
+
+#include "gromacs/utility/mutex.h"
+
+#include "config.h"
+
+#include <future>
+#include <gtest/gtest.h>
+
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Convenience definition.
+using Lock = gmx::lock_guard<Mutex>;
+
+TEST(MutexBasicTest, CanBeMade)
+{
+ Mutex m;
+}
+
+TEST(MutexBasicTest, CanBeLocked)
+{
+ Mutex m;
+ ASSERT_NO_THROW(m.lock());
+ m.unlock();
+}
+
+TEST(MutexBasicTest, CanBeTryLocked)
+{
+ Mutex m;
+ ASSERT_TRUE(m.try_lock());
+ m.unlock();
+}
+
+TEST(MutexBasicTest, CanBeUsedInLockGuard)
+{
+ Mutex m;
+ Lock g(m);
+}
+
+//! A shared value for a mutex to protect
+static int g_sharedValue;
+//! A mutex to protect a shared value
+static Mutex g_sharedValueMutex;
+
+//! Function type for asynchronous tasks.
+using TaskType = std::function<int(void)>;
+
+//! A task that just does work.
+int updateSharedValue()
+{
+ return ++g_sharedValue;
+}
+
+//! A task that does work after it gets the mutex.
+int updateSharedValueWithLock()
+{
+ Lock guard(g_sharedValueMutex);
+ return updateSharedValue();
+}
+
+//! A task that does work only if it can get the mutex immediately.
+int updateSharedValueWithTryLock()
+{
+ // Special return value to signal when work was not done because
+ // the lock was not acquired.
+ int result = -1;
+ if (g_sharedValueMutex.try_lock())
+ {
+ result = updateSharedValue();
+ g_sharedValueMutex.unlock();
+ }
+ return result;
+}
+
+/*! \brief Parameterized test fixture.
+ *
+ * Checks that different launch policies work. In further tests of
+ * mutual exclusion, we need to specify std::thread::async, to require
+ * that a thread actually launched. The default policy permits the
+ * std:: implementation to avoid launching a thread, and at least the
+ * behaviour of thread-MPI try_lock also varies with the threading
+ * implementation underlying it. */
+class DifferentTasksTest : public ::testing::TestWithParam<TaskType>
+{
+ public:
+ //! Constructor
+ DifferentTasksTest()
+ {
+ g_sharedValue = 0;
+ }
+ //! Check the results
+ void checkResults()
+ {
+ int result;
+ EXPECT_NO_THROW(result = futureResult_.get()) << "Future should not contain an exception";
+ EXPECT_EQ(1, result) << "Task should have run";
+ EXPECT_EQ(1, g_sharedValue) << "Shared value should be updated";
+ }
+ //! Contains the result the task returns.
+ std::future<int> futureResult_;
+};
+
+TEST_P(DifferentTasksTest, StdAsyncWorksWithDefaultPolicy)
+{
+ auto task = GetParam();
+ EXPECT_NO_THROW(futureResult_ = std::async(task)) << "Async should succeed";
+ checkResults();
+}
+
+TEST_P(DifferentTasksTest, StdAsyncWorksWithAsyncLaunchPolicy)
+{
+ auto task = GetParam();
+ EXPECT_NO_THROW(futureResult_ = std::async(std::launch::async, task)) << "Async should succeed";
+ checkResults();
+}
+
+TEST_P(DifferentTasksTest, StdAsyncWorksWithDeferredLaunchPolicy)
+{
+ auto task = GetParam();
+ EXPECT_NO_THROW(futureResult_ = std::async(std::launch::deferred, task)) << "Async should succeed";
+ checkResults();
+}
+
+// Test that the different launch policies work with the different tasks
+INSTANTIATE_TEST_CASE_P(WithAndWithoutMutex, DifferentTasksTest, ::testing::Values(updateSharedValue, updateSharedValueWithLock, updateSharedValueWithTryLock));
+
+TEST(MutexTaskTest, MutualExclusionWorksWithLock)
+{
+ g_sharedValue = 0;
+ std::future<int> result;
+ {
+ // Hold the mutex, launch a lock attempt on another
+ // thread, check that the shared value isn't changed, then
+ // release the mutex by leaving the scope, after which the
+ // other thread's lock can get the mutex.
+ Lock guard(g_sharedValueMutex);
+ result = std::async(std::launch::async, updateSharedValueWithLock);
+ EXPECT_EQ(0, g_sharedValue) << "Task should not have run yet";
+ }
+ EXPECT_EQ(1, result.get()) << "Task should have run";
+ EXPECT_EQ(1, g_sharedValue) << "Shared value should be updated";
+}
+
+TEST(MutexTaskTest, MutualExclusionWorksWithTryLockOnOtherThread)
+{
+ g_sharedValue = 0;
+ {
+ // Hold the mutex, launch a try_lock attempt on another
+ // thread, check that the shared value isn't changed, then
+ // make sure the try_lock attempt has returned, double check
+ // that the shared value isn't changed, and release the mutex
+ // by leaving the scope.
+ Lock guard(g_sharedValueMutex);
+ auto result = std::async(std::launch::async, updateSharedValueWithTryLock);
+ EXPECT_EQ(0, g_sharedValue) << "Data race detected";
+ EXPECT_EQ(-1, result.get()) << "The try_lock should fail";
+ EXPECT_EQ(0, g_sharedValue) << "Task should not have run";
+ }
+ EXPECT_EQ(0, g_sharedValue) << "Mutex release can't affect the protected value";
+}
+
+TEST(MutexTaskTest, MutualExclusionWorksWithTryLockOnSameThread)
+{
+ g_sharedValue = 0;
+ int finalSharedValue = GMX_NATIVE_WINDOWS ? 1 : 0;
+ {
+ // Hold the mutex and launch a try_lock attempt on this
+ // thread. Behaviour then varies with the implementation
+ // underlying thread-MPI.
+ Lock guard(g_sharedValueMutex);
+ int result = updateSharedValueWithTryLock();
+ if (GMX_NATIVE_WINDOWS)
+ {
+ EXPECT_EQ(1, result) << "The try_lock should succeed";
+ EXPECT_EQ(finalSharedValue, g_sharedValue) << "Task should have run";
+ }
+ else
+ {
+ EXPECT_EQ(-1, result) << "The try_lock should fail";
+ EXPECT_EQ(finalSharedValue, g_sharedValue) << "Task should not have run";
+ }
+ }
+ EXPECT_EQ(finalSharedValue, g_sharedValue) << "Mutex release can't affect the protected value";
+}
+
+} // namespace
+} // namespace
+} // namespace
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input"></Object>
+ <SerializedData Name="Stream">
+ <Int>0</Int>
+ </SerializedData>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <Sequence Name="a">
+ <Int Name="Length">2</Int>
+ <Int>1</Int>
+ <Int>2</Int>
+ </Sequence>
+ <Sequence Name="b">
+ <Int Name="Length">2</Int>
+ <String>foo</String>
+ <String>bar</String>
+ </Sequence>
+ </Object>
+ <SerializedData Name="Stream">
+ <Int>2</Int>
+ <String>a</String>
+ <UChar>65</UChar>
+ <Int>2</Int>
+ <UChar>105</UChar>
+ <Int>1</Int>
+ <UChar>105</UChar>
+ <Int>2</Int>
+ <String>b</String>
+ <UChar>65</UChar>
+ <Int>2</Int>
+ <UChar>115</UChar>
+ <String>foo</String>
+ <UChar>115</UChar>
+ <String>bar</String>
+ </SerializedData>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <Object Name="obj">
+ <Int Name="a">1</Int>
+ <String Name="b">foo</String>
+ </Object>
+ <Object Name="obj2">
+ <Int Name="c">2</Int>
+ <String Name="d">bar</String>
+ </Object>
+ <Int Name="foo">3</Int>
+ </Object>
+ <SerializedData Name="Stream">
+ <Int>3</Int>
+ <String>obj</String>
+ <UChar>79</UChar>
+ <Int>2</Int>
+ <String>a</String>
+ <UChar>105</UChar>
+ <Int>1</Int>
+ <String>b</String>
+ <UChar>115</UChar>
+ <String>foo</String>
+ <String>obj2</String>
+ <UChar>79</UChar>
+ <Int>2</Int>
+ <String>c</String>
+ <UChar>105</UChar>
+ <Int>2</Int>
+ <String>d</String>
+ <UChar>115</UChar>
+ <String>bar</String>
+ <String>foo</String>
+ <UChar>105</UChar>
+ <Int>3</Int>
+ </SerializedData>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <Int Name="foo">1</Int>
+ <String Name="bar">a</String>
+ <Real Name="f">1.5</Real>
+ <Real Name="d">2.5</Real>
+ </Object>
+ <SerializedData Name="Stream">
+ <Int>4</Int>
+ <String>foo</String>
+ <UChar>105</UChar>
+ <Int>1</Int>
+ <String>bar</String>
+ <UChar>115</UChar>
+ <String>a</String>
+ <String>f</String>
+ <UChar>102</UChar>
+ <Real>1.5</Real>
+ <String>d</String>
+ <UChar>100</UChar>
+ <Real>2.5</Real>
+ </SerializedData>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="Output"><![CDATA[
+par
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="Output"><![CDATA[
+line
+
+par
+
+line2
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="Output1"><![CDATA[
+line
+
+par
+
+line2
+]]></String>
+ <String Name="Output2"><![CDATA[
+par
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="Output"><![CDATA[
+line
+
+par
+
+line2
+]]></String>
+</ReferenceData>
A quick brown
fox jumps
over the lazy
+dog]]></String>
+ <String Name="WrappedAt14WithTrailingWhitespace"><![CDATA[
+ A quick brown
+fox jumps
+ over the lazy
dog]]></String>
</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <String Name="Output"><![CDATA[
+Line
+Line
+Line
+Line
+Line
+Line
+]]></String>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <String Name="a">1</String>
+ <String Name="b">2 3</String>
+ </Object>
+ <Sequence Name="MappedPaths">
+ <Int Name="Length">2</Int>
+ <String>/a</String>
+ <String>/b</String>
+ </Sequence>
+ <Object Name="Tree">
+ <Object Name="foo">
+ <Int Name="a">1</Int>
+ <Int Name="b">2</Int>
+ <Int Name="c">3</Int>
+ </Object>
+ </Object>
+ <BackMapping Name="Mapping">
+ <String Name="/foo/a">/a</String>
+ <String Name="/foo/b">/b</String>
+ <String Name="/foo/c">/b</String>
+ </BackMapping>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <String Name="a">1 2</String>
+ </Object>
+ <Sequence Name="MappedPaths">
+ <Int Name="Length">1</Int>
+ <String>/a</String>
+ </Sequence>
+ <Object Name="Tree">
+ <Object Name="foo">
+ <Int Name="a">1</Int>
+ <Int Name="b">2</Int>
+ </Object>
+ </Object>
+ <BackMapping Name="Mapping">
+ <String Name="/foo/a">/a</String>
+ <String Name="/foo/b">/a</String>
+ </BackMapping>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <String Name="a">1</String>
+ <String Name="b">2</String>
+ </Object>
+ <Sequence Name="MappedPaths">
+ <Int Name="Length">2</Int>
+ <String>/a</String>
+ <String>/b</String>
+ </Sequence>
+ <Object Name="Tree">
+ <Object Name="foo">
+ <Int Name="i">1</Int>
+ <Int Name="j">2</Int>
+ </Object>
+ </Object>
+ <BackMapping Name="Mapping">
+ <String Name="/foo/i">/a</String>
+ <String Name="/foo/j">/b</String>
+ </BackMapping>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <String Name="a">1</String>
+ <String Name="b">2</String>
+ </Object>
+ <Sequence Name="MappedPaths">
+ <Int Name="Length">2</Int>
+ <String>/a</String>
+ <String>/b</String>
+ </Sequence>
+ <Object Name="Tree">
+ <Int Name="i">1</Int>
+ <Int Name="j">2</Int>
+ </Object>
+ <BackMapping Name="Mapping">
+ <String Name="/i">/a</String>
+ <String Name="/j">/b</String>
+ </BackMapping>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <String Name="a-x">1</String>
+ <String Name="by">2</String>
+ </Object>
+ <Sequence Name="MappedPaths">
+ <Int Name="Length">2</Int>
+ <String>/Ax</String>
+ <String>/B-Y</String>
+ </Sequence>
+ <Object Name="Tree">
+ <Int Name="i">1</Int>
+ <Int Name="j">2</Int>
+ </Object>
+ <BackMapping Name="Mapping">
+ <String Name="/i">/a-x</String>
+ <String Name="/j">/by</String>
+ </BackMapping>
+</ReferenceData>
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Object Name="Input">
+ <String Name="a">1</String>
+ <String Name="b">2</String>
+ </Object>
+ <Sequence Name="MappedPaths">
+ <Int Name="Length">2</Int>
+ <String>/a</String>
+ <String>/b</String>
+ </Sequence>
+ <Object Name="Tree">
+ <Object Name="foo">
+ <Int Name="i">1</Int>
+ <Int Name="j">2</Int>
+ </Object>
+ </Object>
+ <BackMapping Name="Mapping">
+ <String Name="/foo/i">/a</String>
+ <String Name="/foo/j">/b</String>
+ </BackMapping>
+</ReferenceData>
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
#include "gromacs/utility/arrayref.h"
+#include "gromacs/utility/exceptions.h"
#include "testutils/refdata.h"
#include "testutils/stringtest.h"
+namespace gmx
+{
+namespace test
+{
namespace
{
TEST(StringUtilityTest, EndsWith)
{
EXPECT_TRUE(gmx::endsWith("foobar", "bar"));
- EXPECT_TRUE(gmx::endsWith("foobar", NULL));
+ EXPECT_TRUE(gmx::endsWith("foobar", nullptr));
EXPECT_TRUE(gmx::endsWith("foobar", ""));
EXPECT_TRUE(gmx::endsWith("", ""));
EXPECT_FALSE(gmx::endsWith("", "foobar"));
TEST(StringUtilityTest, StripSuffixIfPresent)
{
EXPECT_EQ("foo", gmx::stripSuffixIfPresent("foobar", "bar"));
- EXPECT_EQ("foobar", gmx::stripSuffixIfPresent("foobar", NULL));
+ EXPECT_EQ("foobar", gmx::stripSuffixIfPresent("foobar", nullptr));
EXPECT_EQ("foobar", gmx::stripSuffixIfPresent("foobar", ""));
EXPECT_EQ("foobar", gmx::stripSuffixIfPresent("foobar", "bbar"));
EXPECT_EQ("foobar", gmx::stripSuffixIfPresent("foobar", "barr"));
EXPECT_THAT(gmx::splitString(" "), IsEmpty());
}
+TEST(StringUtilityTest, SplitDelimitedString)
+{
+ using ::testing::ElementsAre;
+ using ::testing::IsEmpty;
+ EXPECT_THAT(gmx::splitDelimitedString("foo;bar", ';'), ElementsAre("foo", "bar"));
+ EXPECT_THAT(gmx::splitDelimitedString(";foo;bar;", ';'), ElementsAre("", "foo", "bar", ""));
+ EXPECT_THAT(gmx::splitDelimitedString("foo;;bar", ';'), ElementsAre("foo", "", "bar"));
+ EXPECT_THAT(gmx::splitDelimitedString("foo", ';'), ElementsAre("foo"));
+ EXPECT_THAT(gmx::splitDelimitedString(";", ';'), ElementsAre("", ""));
+ EXPECT_THAT(gmx::splitDelimitedString("", ';'), IsEmpty());
+}
+
+TEST(StringUtilityTest, SplitAndTrimDelimitedString)
+{
+ using ::testing::ElementsAre;
+ using ::testing::IsEmpty;
+ EXPECT_THAT(splitAndTrimDelimitedString("", ';'), IsEmpty());
+ EXPECT_THAT(splitAndTrimDelimitedString(" \t\n ", ';'), ElementsAre(""));
+ EXPECT_THAT(splitAndTrimDelimitedString("foo", ';'), ElementsAre("foo"));
+ EXPECT_THAT(splitAndTrimDelimitedString(" foo ", ';'), ElementsAre("foo"));
+ EXPECT_THAT(splitAndTrimDelimitedString("foo;bar", ';'), ElementsAre("foo", "bar"));
+ EXPECT_THAT(splitAndTrimDelimitedString(";foo;bar", ';'), ElementsAre("", "foo", "bar"));
+ EXPECT_THAT(splitAndTrimDelimitedString("foo;bar;", ';'), ElementsAre("foo", "bar", ""));
+ EXPECT_THAT(splitAndTrimDelimitedString(";foo;bar;", ';'), ElementsAre("", "foo", "bar", ""));
+ EXPECT_THAT(splitAndTrimDelimitedString("foo;;bar", ';'), ElementsAre("foo", "", "bar"));
+ EXPECT_THAT(splitAndTrimDelimitedString("foo ; bar ", ';'), ElementsAre("foo", "bar"));
+ EXPECT_THAT(splitAndTrimDelimitedString(" ; foo ; bar ", ';'), ElementsAre("", "foo", "bar"));
+ EXPECT_THAT(splitAndTrimDelimitedString(" foo ; bar ; ", ';'), ElementsAre("foo", "bar", ""));
+ EXPECT_THAT(splitAndTrimDelimitedString(" ; foo\n ; bar ; ", ';'), ElementsAre("", "foo", "bar", ""));
+ EXPECT_THAT(splitAndTrimDelimitedString(" foo ; ; \tbar", ';'), ElementsAre("foo", "", "bar"));
+}
+
/********************************************************************
* Tests for formatString()
*/
wrapper.settings().setKeepFinalSpaces(true);
EXPECT_EQ("line ", wrapper.wrapToString("line "));
- EXPECT_EQ("line\n", wrapper.wrapToString("line \n"));
+ EXPECT_EQ("line \n", wrapper.wrapToString("line \n"));
}
TEST_F(TextLineWrapperTest, HandlesTrailingNewlines)
checkText(wrapper.wrapToString(g_wrapTextWhitespace),
"WrappedAt14");
+
+ wrapper.settings().setKeepFinalSpaces(true);
+ checkText(wrapper.wrapToString(g_wrapTextWhitespace),
+ "WrappedAt14WithTrailingWhitespace");
}
+TEST(StringUtilityTest, ParseDigitsFromString)
+{
+ using ::testing::ElementsAre;
+ using ::testing::IsEmpty;
+ EXPECT_THAT(parseDigitsFromString("01"), ElementsAre(0, 1));
+ EXPECT_THAT(parseDigitsFromString("0,1"), ElementsAre(0, 1));
+ EXPECT_THAT(parseDigitsFromString(",0,1"), ElementsAre(0, 1));
+ EXPECT_THAT(parseDigitsFromString("0,1,"), ElementsAre(0, 1));
+ EXPECT_THAT(parseDigitsFromString(",0,1,"), ElementsAre(0, 1));
+ EXPECT_THAT(parseDigitsFromString(","), IsEmpty());
+ EXPECT_THAT(parseDigitsFromString(",,"), IsEmpty());
+ EXPECT_THAT(parseDigitsFromString(""), IsEmpty());
+ EXPECT_THROW(parseDigitsFromString("a"), InvalidInputError);
+ EXPECT_THROW(parseDigitsFromString("0a"), InvalidInputError);
+}
+
+} // namespace
+} // namespace
} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Tests for gmx::TextReader.
+ *
+ * \author Mark Abraham <mark.j.abraham@gmail.com>
+ * \ingroup module_utility
+ */
+#include "gmxpre.h"
+
+#include "gromacs/utility/textreader.h"
+
+#include <functional>
+#include <string>
+#include <vector>
+
+#include <gmock/gmock.h>
+#include <gtest/gtest.h>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/stringstream.h"
+#include "gromacs/utility/stringutil.h"
+
+#include "testutils/refdata.h"
+#include "testutils/stringtest.h"
+
+namespace gmx
+{
+namespace test
+{
+namespace
+{
+
+//! Convenience name.
+using Container = std::vector<std::string>;
+//! Convenience type for callbacks.
+using TestCallbackFunc = void(*)(TextReader &);
+
+//! Helper struct.
+struct TextReaderTestParams
+{
+ //! Input data.
+ const Container input;
+ //! Callback to configure the reader with the behaviour being tested.
+ TestCallbackFunc callback;
+ //! Output to expect from the configured reader acting on the \c input.
+ const Container expectedOutput;
+};
+
+//! Test fixture.
+class TextReaderTest : public ::testing::TestWithParam<TextReaderTestParams>
+{
+};
+
+TEST_P(TextReaderTest, UsingDifferentConfigurations)
+{
+ const auto ¶ms = GetParam();
+
+ // Prepare the reader with the input lines.
+ StringInputStream stream(params.input);
+ TextReader reader(&stream);
+ // Configure the intended reading behaviour.
+ params.callback(reader);
+ // Read the input and store what is read.
+ Container readLines;
+ std::string line;
+ while (reader.readLine(&line))
+ {
+ readLines.push_back(line);
+ }
+ // Check the results
+ EXPECT_THAT(readLines, ::testing::ElementsAreArray(params.expectedOutput));
+}
+
+//! Test input data. Some configurations will remove comments delimited by '#'.
+const Container g_inputs =
+{
+ "",
+ " \t ",
+ "expected text",
+ " expected text ",
+ "expected text \t",
+ " \t expected text",
+ " \t expected text \t",
+ "expected text#",
+ "expected text\t #",
+ "expected text# ",
+ "expected text # not expected ",
+ "#",
+ "\t #",
+ " # not expected ",
+};
+
+/*! \brief A case of expected output data that is produced from two
+ * different configurations.
+ *
+ * Note that the implementation of StringInputStream joins the input
+ * container with "\n", so the inputs are always changed before being
+ * read. The name of this variable reflects that TextReader does not
+ * change them during reading. */
+const Container g_unchangedOutputs =
+{
+ "\n",
+ " \t \n",
+ "expected text\n",
+ " expected text \n",
+ "expected text \t\n",
+ " \t expected text\n",
+ " \t expected text \t\n",
+ "expected text#\n",
+ "expected text\t #\n",
+ "expected text# \n",
+ "expected text # not expected \n",
+ "#\n",
+ "\t #\n",
+ " # not expected \n",
+};
+INSTANTIATE_TEST_CASE_P(ParsesLinesDifferently, TextReaderTest,
+ ::testing::Values(TextReaderTestParams {
+ g_inputs,
+ [](TextReader &r)
+ {
+ GMX_UNUSED_VALUE(r);
+ },
+ g_unchangedOutputs
+ },
+ TextReaderTestParams {
+ g_inputs,
+ [](TextReader &r)
+ {
+ r.setTrimLeadingWhiteSpace(true);
+ },
+ { "",
+ "",
+ "expected text\n",
+ "expected text \n",
+ "expected text \t\n",
+ "expected text\n",
+ "expected text \t\n",
+ "expected text#\n",
+ "expected text\t #\n",
+ "expected text# \n",
+ "expected text # not expected \n",
+ "#\n",
+ "#\n",
+ "# not expected \n", }
+ },
+ TextReaderTestParams {
+ g_inputs,
+ [](TextReader &r)
+ {
+ r.setTrimTrailingWhiteSpace(true);
+ },
+ { "",
+ "",
+ "expected text",
+ " expected text",
+ "expected text",
+ " \t expected text",
+ " \t expected text",
+ "expected text#",
+ "expected text\t #",
+ "expected text#",
+ "expected text # not expected",
+ "#",
+ "\t #",
+ " # not expected", }
+ },
+ TextReaderTestParams {
+ g_inputs,
+ [](TextReader &r)
+ {
+ r.setTrimTrailingWhiteSpace(true);
+ r.setTrimLeadingWhiteSpace(true);
+ },
+ { "",
+ "",
+ "expected text",
+ "expected text",
+ "expected text",
+ "expected text",
+ "expected text",
+ "expected text#",
+ "expected text\t #",
+ "expected text#",
+ "expected text # not expected",
+ "#",
+ "#",
+ "# not expected", }
+ },
+ TextReaderTestParams {
+ g_inputs,
+ [](TextReader &r)
+ {
+ r.setTrimTrailingComment(true, '#');
+ },
+ { "\n",
+ " \t \n",
+ "expected text\n",
+ " expected text \n",
+ "expected text \t\n",
+ " \t expected text\n",
+ " \t expected text \t\n",
+ "expected text",
+ "expected text\t ",
+ "expected text",
+ "expected text ",
+ "",
+ "\t ",
+ " ", }
+ },
+ TextReaderTestParams {
+ g_inputs,
+ [](TextReader &r)
+ {
+ r.setTrimTrailingComment(true, '#');
+ r.setTrimTrailingComment(false, 0);
+ },
+ g_unchangedOutputs
+ },
+ TextReaderTestParams {
+ g_inputs,
+ [](TextReader &r)
+ {
+ r.setTrimTrailingComment(true, '#');
+ r.setTrimTrailingWhiteSpace(true);
+ },
+ { "",
+ "",
+ "expected text",
+ " expected text",
+ "expected text",
+ " \t expected text",
+ " \t expected text",
+ "expected text",
+ "expected text",
+ "expected text",
+ "expected text",
+ "",
+ "",
+ "", }
+ }
+ ));
+
+} // namespace
+} // namespace
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
checkOutput();
}
+TEST_F(TextWriterTest, PreservesTrailingWhitespace)
+{
+ writer_.writeString("Line ");
+ writer_.writeLine();
+ writer_.writeString(std::string("Line "));
+ writer_.writeLine();
+ writer_.writeLine("Line ");
+ writer_.writeLine(std::string("Line "));
+ writer_.writeString("Line \n");
+ writer_.writeString(std::string("Line \n"));
+ checkOutput();
+}
+
} // namespace
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+#include "gmxpre.h"
+
+#include "gromacs/utility/typetraits.h"
+
+#include <gtest/gtest.h>
+
+namespace gmx
+{
+namespace test
+{
+TEST(TypeTraitsTest, IsIntegralConstant)
+{
+ EXPECT_FALSE(isIntegralConstant<int>::value);
+ EXPECT_TRUE((isIntegralConstant<std::integral_constant<int, 5> >::value));
+ EXPECT_FALSE((isIntegralConstant<std::integral_constant<short, 5>, long>::value));
+ EXPECT_TRUE((isIntegralConstant<std::integral_constant<long, 5>, long>::value));
+}
+}
+}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return readFileToString(filename.c_str());
}
+//! Implementation class
class TextReader::Impl
{
public:
+ //! Constructor.
explicit Impl(const TextInputStreamPointer &stream)
- : stream_(stream)
+ : stream_(stream), trimLeadingWhiteSpace_(false), trimTrailingWhiteSpace_(false),
+ trimTrailingComment_(false), commentChar_(0)
{
}
+ //! Stream used by this reader.
TextInputStreamPointer stream_;
+ //! Whether leading whitespace should be removed.
+ bool trimLeadingWhiteSpace_;
+ //! Whether trailing whitespace should be removed.
+ bool trimTrailingWhiteSpace_;
+ //! Whether a trailing comment should be removed.
+ bool trimTrailingComment_;
+ /*! \brief Character that denotes the start of a comment on a line.
+ *
+ * Zero until TextReader::setTrimTrailingComment is called to
+ * activate such trimming with a given character. */
+ char commentChar_;
};
TextReader::TextReader(const std::string &filename)
{
}
-bool TextReader::readLine(std::string *line)
+bool TextReader::readLine(std::string *linePtr)
{
- return impl_->stream_->readLine(line);
-}
-
-bool TextReader::readLineTrimmed(std::string *line)
-{
- if (!readLine(line))
+ if (!impl_->stream_->readLine(linePtr))
{
return false;
}
- const size_t endPos = line->find_last_not_of(" \t\r\n");
- if (endPos != std::string::npos)
+ auto &line = *linePtr;
+ const char whiteSpaceChars[] = " \t\r\n";
+ if (impl_->trimLeadingWhiteSpace_)
+ {
+ const size_t endPos = line.find_first_not_of(whiteSpaceChars);
+ if (endPos == std::string::npos)
+ {
+ line.resize(0);
+ }
+ else
+ {
+ line = line.substr(endPos, std::string::npos);
+ }
+ }
+ if (impl_->trimTrailingComment_)
{
- line->resize(endPos + 1);
+ auto commentPos = line.find(impl_->commentChar_);
+ if (commentPos != std::string::npos)
+ {
+ line.resize(commentPos);
+ }
+ }
+ if (impl_->trimTrailingWhiteSpace_)
+ {
+ const size_t endPos = line.find_last_not_of(whiteSpaceChars);
+ if (endPos == std::string::npos)
+ {
+ line.resize(0);
+ }
+ else
+ {
+ line.resize(endPos + 1);
+ }
}
return true;
}
+void TextReader::setTrimLeadingWhiteSpace(bool doTrimming)
+{
+ impl_->trimLeadingWhiteSpace_ = doTrimming;
+}
+
+void TextReader::setTrimTrailingWhiteSpace(bool doTrimming)
+{
+ impl_->trimTrailingWhiteSpace_ = doTrimming;
+}
+
+void TextReader::setTrimTrailingComment(bool doTrimming, char commentChar)
+{
+ impl_->trimTrailingComment_ = doTrimming;
+ if (impl_->trimTrailingComment_)
+ {
+ impl_->commentChar_ = commentChar;
+ }
+}
+
std::string TextReader::readAll()
{
std::string result;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
// ...
}
\endcode
+ *
+ * Behaviours such as trimming whitespace or comments can be
+ * configured by calling other methods before this one.
*/
bool readLine(std::string *line);
- /*! \brief
- * Reads a single line from the stream.
+ /*! \brief Sets whether the reader should trim leading whitespace
+ * from a line before returning it.
*
- * \param[out] line String to receive the line.
- * \returns false if nothing was read because the file ended.
+ * \param[in] doTrimming Whether trimming should be active.
+ */
+ void setTrimLeadingWhiteSpace(bool doTrimming);
+ /*! \brief Sets whether the reader should trim trailing whitespace
+ * from a line before returning it.
*
- * On error or when false is returned, \p line will be empty.
- * Works as readLine(), except that trailing whitespace will be removed
- * from \p line.
+ * Note that comment trimming will precede whitespace trimming
+ * when both are active.
*
- * \see readLine()
+ * \param[in] doTrimming Whether trimming should be active.
*/
- bool readLineTrimmed(std::string *line);
-
+ void setTrimTrailingWhiteSpace(bool doTrimming);
+ /*! \brief Sets whether the reader should trim at trailing
+ * comment from a line before returning it.
+ *
+ * Note that comment trimming will precede whitespace trimming
+ * when both are active.
+ *
+ * \param[in] commentChar The character that begins a comment.
+ *
+ * \param[in] doTrimming Whether trimming should be active.
+ */
+ void setTrimTrailingComment(bool doTrimming, char commentChar);
/*! \brief
* Reads all remaining lines from the stream as a single string.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void writeWrappedString(const std::string &str)
{
- writeRawString(wrapper_.wrapToString(str));
+ if (newLineCount_ > 0)
+ {
+ writeRawString(wrapper_.wrapToString(str));
+ }
+ else
+ {
+ writeRawString(str);
+ }
}
TextOutputStreamPointer stream_;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
fprintf(fp, "%s: not available\n", title);
}
- return (p != NULL);
+ return (p != nullptr);
}
int pr_title(FILE *fp, int indent, const char *title)
const char *flong = "%15.8e";
const char *format;
- if (getenv("GMX_PRINT_LONGFORMAT") != NULL)
+ if (getenv("GMX_PRINT_LONGFORMAT") != nullptr)
{
format = flong;
}
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares type traits
+ *
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+
+#ifndef GMX_UTILITY_TYPETRAITS_H
+#define GMX_UTILITY_TYPETRAITS_H
+
+#include <type_traits>
+
+namespace gmx
+{
+
+/*! \libinternal \brief
+ * Is true if type is a std::integral_constant
+ *
+ * If the optional integral type is given, than it is only true for a
+ * std::integral_constant of that integral type.
+ *
+ * \tparam T type to check
+ * \tparam Int optional integral type
+ */
+template<typename T, typename Int = void>
+struct isIntegralConstant : public std::false_type {};
+
+template<typename Int, Int N>
+struct isIntegralConstant<std::integral_constant<Int, N>, void> : public std::true_type {};
+
+template<typename Int, Int N>
+struct isIntegralConstant<std::integral_constant<Int, N>, Int> : public std::true_type {};
+
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2012,2014,2015,2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::unique_cptr and gmx::sfree_guard.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_UNIQUE_PTR_SFREE_H
+#define GMX_UTILITY_UNIQUE_PTR_SFREE_H
+
+#include <cstdlib>
+
+#include <memory>
+
+#include "gromacs/utility/smalloc.h"
+
+namespace gmx
+{
+
+/*! \brief Wrapper of standard library free(), to be used as
+ * unique_cptr deleter for memory allocated by malloc, e.g. by an
+ * external library such as TNG. */
+template <class T>
+inline void free_wrapper(T *p)
+{
+ free(p);
+}
+
+//! sfree wrapper to be used as unique_cptr deleter
+template <class T>
+inline void sfree_wrapper(T *p)
+{
+ sfree(p);
+}
+
+//! \internal \brief wrap function into functor to be used as deleter
+template<class T, void D(T *)>
+struct functor_wrapper {
+ //! call wrapped function
+ void operator()(T* t) { D(t); }
+};
+
+//! unique_ptr which takes function pointer (has to return void) as template argument
+template<typename T, void D(T *) = sfree_wrapper>
+using unique_cptr = std::unique_ptr<T, functor_wrapper<T, D> >;
+
+//! Simple guard which calls sfree. See unique_cptr for details.
+typedef unique_cptr<void> sfree_guard;
+
+
+//! Create unique_ptr with any deleter function or lambda
+template<typename T, typename D>
+std::unique_ptr<T, D> create_unique_with_deleter(T *t, D d) { return std::unique_ptr<T, D>(t, d); }
+
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \internal \file
+ * \brief
+ * Implements functionality from variant.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_utility
+ */
#include "gmxpre.h"
-#include "md_logging.h"
-
-#include <cstdarg>
-#include <cstdio>
+#include "variant.h"
-#include "gromacs/mdtypes/commrec.h"
+#include <string>
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/strconvert.h"
-void md_print_info(const t_commrec *cr, FILE *fplog,
- const char *fmt, ...)
+namespace gmx
{
- va_list ap;
- if (cr == NULL || SIMMASTER(cr))
+//! \cond libapi
+std::string simpleValueToString(const Variant &value)
+{
+ if (value.isType<bool>())
{
- va_start(ap, fmt);
-
- vfprintf(stderr, fmt, ap);
-
- va_end(ap);
+ // TODO: Consider if this would be better as yes/no instead of
+ // true/false.
+ return toString(value.cast<bool>());
}
- if (fplog != NULL)
+ else if (value.isType<float>())
{
- va_start(ap, fmt);
-
- vfprintf(fplog, fmt, ap);
-
- va_end(ap);
+ return toString(value.cast<float>());
}
-}
-
-void md_print_warn(const t_commrec *cr, FILE *fplog,
- const char *fmt, ...)
-{
- va_list ap;
-
- if (cr == NULL || SIMMASTER(cr))
+ else if (value.isType<double>())
{
- va_start(ap, fmt);
-
- fprintf(stderr, "\n");
- vfprintf(stderr, fmt, ap);
- fprintf(stderr, "\n");
-
- va_end(ap);
+ return toString(value.cast<double>());
}
- if (fplog != NULL)
+ else if (value.isType<int>())
{
- va_start(ap, fmt);
-
- fprintf(fplog, "\n");
- vfprintf(fplog, fmt, ap);
- fprintf(fplog, "\n");
-
- va_end(ap);
+ return toString(value.cast<int>());
}
+ else if (value.isType<gmx_int64_t>())
+ {
+ return toString(value.cast<gmx_int64_t>());
+ }
+ else if (value.isType<std::string>())
+ {
+ return value.cast<std::string>();
+ }
+ GMX_RELEASE_ASSERT(false, "Unknown value type");
+ return std::string();
}
+//! \endcond
+
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::Variant.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_utility
+ */
+#ifndef GMX_UTILITY_VARIANT_H
+#define GMX_UTILITY_VARIANT_H
+
+#include <memory>
+#include <string>
+#include <type_traits>
+#include <typeindex>
+#include <typeinfo>
+#include <utility>
+
+#include "gromacs/utility/gmxassert.h"
+
+namespace gmx
+{
+
+/*! \libinternal \brief
+ * Represents a dynamically typed value of an arbitrary type.
+ *
+ * To create a variant, either initialize it as empty, or with the create()
+ * method (or the equivalent constructor, if the type parameter can be deduced
+ * and is clear to the reader from the context).
+ *
+ * To query the type of the contents in the variant, use isEmpty(), type(), and
+ * isType().
+ *
+ * To access the value, you need to know the type as a compile-time constant
+ * (e.g., through branching based on isType()), and then use cast() or
+ * tryCast().
+ *
+ * Methods in this class do not throw unless otherwise indicated.
+ *
+ * This provides essentially the same functionality as boost::any.
+ *
+ * \ingroup module_utility
+ */
+class Variant
+{
+ public:
+ /*! \brief
+ * Creates a variant that holds the given value.
+ *
+ * \throws std::bad_alloc if out of memory.
+ *
+ * This method allows explicitly specifying the template argument,
+ * contrary to the templated constructor.
+ */
+ template <typename T>
+ static Variant create(const T &value) { return Variant(value); }
+ /*! \brief
+ * Creates a variant that holds the given value.
+ *
+ * \throws std::bad_alloc if out of memory.
+ *
+ * In addition to allowing specifying the template argument, this
+ * method avoids copying when move-construction is possible.
+ */
+ template <typename T>
+ static Variant create(T &&value) { return Variant(std::move(value)); }
+
+ //! Creates an empty variant value.
+ Variant() {}
+ /*! \brief
+ * Creates a variant that holds the given value.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ template <typename T>
+ explicit Variant(const T &value)
+ : content_(new Content<typename std::decay<T>::type>(value))
+ {
+ }
+ /*! \brief
+ * Creates a variant that holds the given value.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ template <typename T>
+ explicit Variant(T &&value)
+ : content_(new Content<typename std::decay<T>::type>(std::move(value)))
+ {
+ }
+ /*! \brief
+ * Creates a deep copy of a variant.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ Variant(const Variant &other) : content_(other.cloneContent()) {}
+ //! Move-constructs a variant.
+ Variant(Variant &&other) noexcept : content_(std::move(other.content_)) {}
+ /*! \brief
+ * Assigns the variant.
+ *
+ * \throws std::bad_alloc if out of memory.
+ */
+ Variant &operator=(const Variant &other)
+ {
+ content_.reset(other.cloneContent());
+ return *this;
+ }
+ //! Move-assigns the variant.
+ Variant &operator=(Variant &&other) noexcept
+ {
+ content_ = std::move(other.content_);
+ return *this;
+ }
+
+ //! Whether any value is stored.
+ bool isEmpty() const { return content_ == nullptr; }
+ //! Returns the dynamic type of the value that is currently stored.
+ std::type_index type() const
+ {
+ const std::type_info &info
+ = !isEmpty() ? content_->typeInfo() : typeid(void);
+ return std::type_index(info);
+ }
+ //! Returns whether the type stored matches the template parameter.
+ template <typename T>
+ bool isType() const
+ {
+ return !isEmpty() && content_->typeInfo() == typeid(T);
+ }
+
+ /*! \brief
+ * Tries to get the value as the given type.
+ *
+ * \tparam T Type to get.
+ * \returns Pointer to the value, or nullptr if the type does not match
+ * the stored value.
+ */
+ template <typename T>
+ const T *tryCast() const
+ {
+ return isType<T>() ? &static_cast<Content<T> *>(content_.get())->value_ : nullptr;
+ }
+ /*! \brief
+ * Gets the value when the type is known.
+ *
+ * \tparam T Type to get (which must match what the variant stores).
+ *
+ * Asserts if the variant is empty or does not contain the requested type.
+ */
+ template <typename T>
+ const T &cast() const
+ {
+ const T *value = tryCast<T>();
+ GMX_RELEASE_ASSERT(value != nullptr, "Cast to incorrect type");
+ return *value;
+ }
+ /*! \brief
+ * Tries to get the value as the given type as a non-const pointer.
+ *
+ * \tparam T Type to get.
+ * \returns Pointer to the value, or nullptr if the type does not match
+ * the stored value.
+ *
+ * This method allows modifying the value in-place, which is useful
+ * with more complicated data structures.
+ */
+ template <typename T>
+ T *tryCastRef()
+ {
+ return isType<T>() ? &static_cast<Content<T> *>(content_.get())->value_ : nullptr;
+ }
+ /*! \brief
+ * Gets the value when the type is known as a modifiable reference.
+ *
+ * \tparam T Type to get (which must match what the variant stores).
+ *
+ * Asserts if the variant is empty or does not contain the requested type.
+ */
+ template <typename T>
+ T &castRef()
+ {
+ T *value = tryCastRef<T>();
+ GMX_RELEASE_ASSERT(value != nullptr, "Cast to incorrect type");
+ return *value;
+ }
+
+ private:
+ class IContent
+ {
+ public:
+ virtual ~IContent() {}
+ virtual const std::type_info &typeInfo() const = 0;
+ virtual IContent *clone() const = 0;
+ };
+
+ template <typename T>
+ class Content : public IContent
+ {
+ public:
+ explicit Content(const T &value) : value_(value) {}
+ explicit Content(T &&value) : value_(std::move(value)) {}
+
+ virtual const std::type_info &typeInfo() const { return typeid(T); }
+ virtual IContent *clone() const { return new Content(value_); }
+
+ T value_;
+ };
+
+ //! Creates a deep copy of the content.
+ IContent *cloneContent() const
+ {
+ return content_ != nullptr ? content_->clone() : nullptr;
+ }
+
+ std::unique_ptr<IContent> content_;
+};
+
+//! \cond libapi
+/*! \brief
+ * Converts a Variant value to a string.
+ *
+ * As the name suggests, only some types of "simple" values (such as int) are
+ * supported. Asserts for unsupported types.
+ *
+ * \ingroup module_utility
+ */
+std::string simpleValueToString(const Variant &value);
+//! \endcond
+
+} // namespace gmx
+
+#endif
# may break some generators, according to CMake documentation. If
# so, we can consider adding some dummy file to make it work.
add_library(fahcore $<TARGET_OBJECTS:mdrun_objlib>)
+ target_link_libraries(fahcore PRIVATE ${GMX_COMMON_LIBRARIES})
elseif(GMX_BUILD_MDRUN_ONLY)
add_executable(mdrun $<TARGET_OBJECTS:mdrun_objlib> mdrun_main.cpp)
- target_link_libraries(mdrun libgromacs ${GMX_EXE_LINKER_FLAGS} ${GMX_STDLIB_LIBRARIES})
+ target_link_libraries(mdrun libgromacs
+ ${GMX_COMMON_LIBRARIES}
+ ${GMX_EXE_LINKER_FLAGS}
+ ${GMX_STDLIB_LIBRARIES})
set(BINARY_NAME "mdrun${GMX_BINARY_SUFFIX}")
set_target_properties(mdrun PROPERTIES
OUTPUT_NAME "${BINARY_NAME}"
${GMX_MAIN_SOURCES}
$<TARGET_OBJECTS:mdrun_objlib>
$<TARGET_OBJECTS:view_objlib>)
- target_link_libraries(gmx libgromacs ${GMX_EXE_LINKER_FLAGS} ${GMX_STDLIB_LIBRARIES})
+ target_link_libraries(gmx libgromacs
+ ${GMX_COMMON_LIBRARIES}
+ ${GMX_EXE_LINKER_FLAGS}
+ ${GMX_STDLIB_LIBRARIES})
if(GMX_X11)
target_link_libraries(gmx ${X11_LIBRARIES})
endif()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
virtual const char *shortDescription() const
{
- return NULL;
+ return nullptr;
}
virtual void init(gmx::CommandLineModuleSettings * /*settings*/)
#include <stdlib.h>
#include <algorithm>
+#include <memory>
#include "thread_mpi/threads.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
+#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/ewald/pme-load-balancing.h"
#include "gromacs/fileio/trxio.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
#include "gromacs/mdlib/ebin.h"
+#include "gromacs/mdlib/expanded.h"
#include "gromacs/mdlib/force.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdlib/mdebin.h"
#include "gromacs/mdlib/mdoutf.h"
#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/mdsetup.h"
#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
#include "gromacs/mdlib/ns.h"
#include "gromacs/mdtypes/interaction_const.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/smalloc.h"
}
}
-static void reset_all_counters(FILE *fplog, t_commrec *cr,
+static void reset_all_counters(FILE *fplog, const gmx::MDLogger &mdlog, t_commrec *cr,
gmx_int64_t step,
gmx_int64_t *step_rel, t_inputrec *ir,
gmx_wallcycle_t wcycle, t_nrnb *nrnb,
char sbuf[STEPSTRSIZE];
/* Reset all the counters related to performance over the run */
- md_print_warn(cr, fplog, "step %s: resetting all time and cycle counters\n",
- gmx_step_str(step, sbuf));
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "step %s: resetting all time and cycle counters",
+ gmx_step_str(step, sbuf));
if (use_GPU(nbv))
{
}
/*! \libinternal
- \copydoc integrator_t (FILE *fplog, t_commrec *cr,
+ \copydoc integrator_t (FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout,
+ gmx::IMDOutputProvider *outputProvider,
t_inputrec *inputrec,
gmx_mtop_t *top_global, t_fcdata *fcd,
t_state *state_global,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t ed,
t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
+ const ReplicaExchangeParameters &replExParams,
+ gmx_membed_t *membed,
gmx_walltime_accounting_t walltime_accounting)
*/
-double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
- const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
+double gmx::do_md(FILE *fplog, t_commrec *cr, const gmx::MDLogger &mdlog,
+ int nfile, const t_filenm fnm[],
+ const gmx_output_env_t *oenv,
+ const MdrunOptions &mdrunOptions,
gmx_vsite_t *vsite, gmx_constr_t constr,
- int stepout, t_inputrec *ir,
+ gmx::IMDOutputProvider *outputProvider,
+ t_inputrec *ir,
gmx_mtop_t *top_global,
t_fcdata *fcd,
t_state *state_global,
+ ObservablesHistory *observablesHistory,
t_mdatoms *mdatoms,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
- gmx_edsam_t ed, t_forcerec *fr,
- int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
+ t_forcerec *fr,
+ const ReplicaExchangeParameters &replExParams,
gmx_membed_t *membed,
- real cpt_period, real max_hours,
- int imdport,
- unsigned long Flags,
gmx_walltime_accounting_t walltime_accounting)
{
- gmx_mdoutf_t outf = NULL;
+ gmx_mdoutf_t outf = nullptr;
gmx_int64_t step, step_rel;
double elapsed_time;
double t, t0, lam0[efptNR];
gmx_bool bGStatEveryStep, bGStat, bCalcVir, bCalcEnerStep, bCalcEner;
- gmx_bool bNS, bNStList, bSimAnn, bStopCM, bRerunMD,
- bFirstStep, startingFromCheckpoint, bInitStep, bLastStep = FALSE,
+ gmx_bool bNS, bNStList, bSimAnn, bStopCM,
+ bFirstStep, bInitStep, bLastStep = FALSE,
bBornRadii, bUsingEnsembleRestraints;
gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
t_trxstatus *status;
rvec mu_tot;
t_vcm *vcm;
- matrix pcoupl_mu, M;
+ matrix parrinellorahmanMu, M;
t_trxframe rerun_fr;
- gmx_repl_ex_t repl_ex = NULL;
+ gmx_repl_ex_t repl_ex = nullptr;
int nchkpt = 1;
gmx_localtop_t *top;
- t_mdebin *mdebin = NULL;
- t_state *state = NULL;
+ t_mdebin *mdebin = nullptr;
gmx_enerdata_t *enerd;
- rvec *f = NULL;
+ PaddedRVecVector f {};
gmx_global_stat_t gstat;
- gmx_update_t *upd = NULL;
- t_graph *graph = NULL;
+ gmx_update_t *upd = nullptr;
+ t_graph *graph = nullptr;
gmx_groups_t *groups;
gmx_ekindata_t *ekind;
gmx_shellfc_t *shellfc;
gmx_bool bResetCountersHalfMaxH = FALSE;
gmx_bool bTemp, bPres, bTrotter;
real dvdl_constr;
- rvec *cbuf = NULL;
+ rvec *cbuf = nullptr;
int cbuf_nalloc = 0;
matrix lastbox;
int lamnew = 0;
/* PME load balancing data for GPU kernels */
- pme_load_balancing_t *pme_loadbal = NULL;
+ pme_load_balancing_t *pme_loadbal = nullptr;
gmx_bool bPMETune = FALSE;
gmx_bool bPMETunePrinting = FALSE;
// signals, and will use this object to achieve that.
SimulationSignaller nullSignaller(nullptr, nullptr, false, false);
- /* Check for special mdrun options */
- bRerunMD = (Flags & MD_RERUN);
- if (Flags & MD_RESETCOUNTERSHALFWAY)
+ if (mdrunOptions.timingOptions.resetHalfway)
{
if (ir->nsteps > 0)
{
wcycle_set_reset_counters(wcycle, ir->nsteps/2);
}
/* Signal to reset the counters halfway the simulation time. */
- bResetCountersHalfMaxH = (max_hours > 0);
+ bResetCountersHalfMaxH = (mdrunOptions.maximumHoursToRun > 0);
}
/* md-vv uses averaged full step velocities for T-control
md uses averaged half step kinetic energies to determine temperature unless defined otherwise by GMX_EKIN_AVE_VEL; */
bTrotter = (EI_VV(ir->eI) && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir) || inputrecNvtTrotter(ir)));
+ const gmx_bool bRerunMD = mdrunOptions.rerun;
+ int nstglobalcomm = mdrunOptions.globalCommunicationInterval;
+
if (bRerunMD)
{
/* Since we don't know if the frames read are related in any way,
nstglobalcomm = 1;
}
- nstglobalcomm = check_nstglobalcomm(fplog, cr, nstglobalcomm, ir);
+ nstglobalcomm = check_nstglobalcomm(mdlog, nstglobalcomm, ir);
bGStatEveryStep = (nstglobalcomm == 1);
if (bRerunMD)
}
groups = &top_global->groups;
+ gmx_edsam *ed = nullptr;
+ if (opt2bSet("-ei", nfile, fnm) || observablesHistory->edsamHistory != nullptr)
+ {
+ /* Initialize essential dynamics sampling */
+ ed = init_edsam(opt2fn_null("-ei", nfile, fnm), opt2fn("-eo", nfile, fnm),
+ top_global, ir, cr, constr,
+ as_rvec_array(state_global->x.data()),
+ state_global->box, observablesHistory,
+ oenv, mdrunOptions.continuationOptions.appendFiles);
+ }
+
if (ir->eSwapCoords != eswapNO)
{
/* Initialize ion swapping code */
- init_swapcoords(fplog, bVerbose, ir, opt2fn_master("-swap", nfile, fnm, cr),
- top_global, state_global->x, state_global->box, &state_global->swapstate, cr, oenv, Flags);
+ init_swapcoords(fplog, ir, opt2fn_master("-swap", nfile, fnm, cr),
+ top_global, as_rvec_array(state_global->x.data()), state_global->box, observablesHistory, cr, oenv, mdrunOptions);
}
/* Initial values */
- init_md(fplog, cr, ir, oenv, &t, &t0, state_global->lambda,
+ init_md(fplog, cr, outputProvider, ir, oenv, mdrunOptions,
+ &t, &t0, state_global->lambda,
&(state_global->fep_state), lam0,
nrnb, top_global, &upd,
nfile, fnm, &outf, &mdebin,
- force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, Flags, wcycle);
+ force_vir, shake_vir, mu_tot, &bSimAnn, &vcm, wcycle);
clear_mat(total_vir);
clear_mat(pres);
snew(enerd, 1);
init_enerdata(top_global->groups.grps[egcENER].nr, ir->fepvals->n_lambda,
enerd);
- if (DOMAINDECOMP(cr))
- {
- f = NULL;
- }
- else
- {
- snew(f, top_global->natoms);
- }
/* Kinetic energy data */
snew(ekind, 1);
}
}
+ // Local state only becomes valid now.
+ std::unique_ptr<t_state> stateInstance;
+ t_state * state;
+
if (DOMAINDECOMP(cr))
{
top = dd_init_local_top(top_global);
- snew(state, 1);
+ stateInstance = std::unique_ptr<t_state>(new t_state);
+ state = stateInstance.get();
dd_init_local_state(cr->dd, state_global, state);
}
else
{
- top = gmx_mtop_generate_local_top(top_global, ir->efep != efepNO);
-
- state = serial_init_local_state(state_global);
-
- atoms2md(top_global, ir, 0, NULL, top_global->natoms, mdatoms);
-
- if (vsite)
- {
- set_vsite_top(vsite, top, mdatoms, cr);
- }
-
- if (ir->ePBC != epbcNONE && !fr->bMolPBC)
- {
- graph = mk_graph(fplog, &(top->idef), 0, top_global->natoms, FALSE, FALSE);
- }
-
- if (shellfc)
- {
- make_local_shells(cr, mdatoms, shellfc);
- }
+ state_change_natoms(state_global, state_global->natoms);
+ /* We need to allocate one element extra, since we might use
+ * (unaligned) 4-wide SIMD loads to access rvec entries.
+ */
+ f.resize(state_global->natoms + 1);
+ /* Copy the pointer to the global state */
+ state = state_global;
- setup_bonded_threading(fr, &top->idef);
+ snew(top, 1);
+ mdAlgorithmsSetupAtomData(cr, ir, top_global, top, fr,
+ &graph, mdatoms, vsite, shellfc);
- update_realloc(upd, state->nalloc);
+ update_realloc(upd, state->natoms);
}
+ // TODO Global state should be destroyed now that we have local
+ // state. Nothing should need to use it. (Global topology should
+ // persist.)
/* Set up interactive MD (IMD) */
- init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, state_global->x,
- nfile, fnm, oenv, imdport, Flags);
+ init_IMD(ir, cr, top_global, fplog, ir->nstcalcenergy, as_rvec_array(state_global->x.data()),
+ nfile, fnm, oenv, mdrunOptions);
if (DOMAINDECOMP(cr))
{
state_global, top_global, ir,
state, &f, mdatoms, top, fr,
vsite, constr,
- nrnb, NULL, FALSE);
+ nrnb, nullptr, FALSE);
shouldCheckNumberOfBondedInteractions = true;
- update_realloc(upd, state->nalloc);
+ update_realloc(upd, state->natoms);
}
update_mdatoms(mdatoms, state->lambda[efptMASS]);
- startingFromCheckpoint = Flags & MD_STARTFROMCPT;
+ const ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
+ bool startingFromCheckpoint = continuationOptions.startedFromCheckpoint;
if (ir->bExpanded)
{
- init_expanded_ensemble(startingFromCheckpoint, ir, &state->dfhist);
+ init_expanded_ensemble(startingFromCheckpoint, ir, state->dfhist);
}
if (MASTER(cr))
if (startingFromCheckpoint)
{
/* Update mdebin with energy history if appending to output files */
- if (Flags & MD_APPENDFILES)
+ if (continuationOptions.appendFiles)
{
- restore_energyhistory_from_state(mdebin, state_global->enerhist);
+ restore_energyhistory_from_state(mdebin, observablesHistory->energyHistory.get());
}
- else
+ else if (observablesHistory->energyHistory.get() != nullptr)
{
- /* We might have read an energy history from checkpoint,
- * free the allocated memory and reset the counts.
+ /* We might have read an energy history from checkpoint.
+ * As we are not appending, we want to restart the statistics.
+ * Free the allocated memory and reset the counts.
*/
- done_energyhistory(state_global->enerhist);
- init_energyhistory(state_global->enerhist);
+ observablesHistory->energyHistory = {};
}
}
+ if (observablesHistory->energyHistory.get() == nullptr)
+ {
+ observablesHistory->energyHistory = std::unique_ptr<energyhistory_t>(new energyhistory_t {});
+ }
/* Set the initial energy history in state by updating once */
- update_energyhistory(state_global->enerhist, mdebin);
+ update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
}
/* Initialize constraints */
set_constraints(constr, top, ir, mdatoms, cr);
}
- if (repl_ex_nst > 0 && MASTER(cr))
+ const bool useReplicaExchange = (replExParams.exchangeInterval > 0);
+ if (useReplicaExchange && MASTER(cr))
{
repl_ex = init_replica_exchange(fplog, cr->ms, state_global, ir,
- repl_ex_nst, repl_ex_nex, repl_ex_seed);
+ replExParams);
}
/* PME tuning is only supported in the Verlet scheme, with PME for
* Coulomb. It is not supported with only LJ PME, or for
* reruns. */
- bPMETune = ((Flags & MD_TUNEPME) && EEL_PME(fr->eeltype) && !bRerunMD &&
- !(Flags & MD_REPRODUCIBLE) && ir->cutoff_scheme != ecutsGROUP);
+ bPMETune = (mdrunOptions.tunePme && EEL_PME(fr->eeltype) && !bRerunMD &&
+ !mdrunOptions.reproducible && ir->cutoff_scheme != ecutsGROUP);
if (bPMETune)
{
- pme_loadbal_init(&pme_loadbal, cr, fplog, ir, state->box,
- fr->ic, fr->pmedata, use_GPU(fr->nbv),
+ pme_loadbal_init(&pme_loadbal, cr, mdlog, ir, state->box,
+ fr->ic, fr->nbv->listParams.get(), fr->pmedata, use_GPU(fr->nbv),
&bPMETunePrinting);
}
if (!ir->bContinuation && !bRerunMD)
{
- if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
+ if (state->flags & (1 << estV))
{
- /* Set the velocities of frozen particles to zero */
+ /* Set the velocities of vsites, shells and frozen atoms to zero */
for (i = 0; i < mdatoms->homenr; i++)
{
- for (m = 0; m < DIM; m++)
+ if (mdatoms->ptype[i] == eptVSite ||
+ mdatoms->ptype[i] == eptShell)
+ {
+ clear_rvec(state->v[i]);
+ }
+ else if (mdatoms->cFREEZE)
{
- if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+ for (m = 0; m < DIM; m++)
{
- state->v[i][m] = 0;
+ if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
+ {
+ state->v[i][m] = 0;
+ }
}
}
}
if (vsite)
{
/* Construct the virtual sites for the initial configuration */
- construct_vsites(vsite, state->x, ir->delta_t, NULL,
+ construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, nullptr,
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, state->box);
}
{
nstfep = gmx_greatest_common_divisor(ir->expandedvals->nstexpanded, nstfep);
}
- if (repl_ex_nst > 0)
+ if (useReplicaExchange)
{
- nstfep = gmx_greatest_common_divisor(repl_ex_nst, nstfep);
+ nstfep = gmx_greatest_common_divisor(replExParams.exchangeInterval, nstfep);
}
}
*/
bStopCM = (ir->comm_mode != ecmNO && !ir->bContinuation);
- if (Flags & MD_READ_EKIN)
+ if (continuationOptions.haveReadEkin)
{
restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
}
| (bStopCM ? CGLO_STOPCM : 0)
| (EI_VV(ir->eI) ? CGLO_PRESSURE : 0)
| (EI_VV(ir->eI) ? CGLO_CONSTRAINT : 0)
- | ((Flags & MD_READ_EKIN) ? CGLO_READEKIN : 0));
+ | (continuationOptions.haveReadEkin ? CGLO_READEKIN : 0));
bSumEkinhOld = FALSE;
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld, cglo_flags
| (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0));
perhaps loses some logic?*/
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- NULL, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
+ nullptr, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
constr, &nullSignaller, state->box,
- NULL, &bSumEkinhOld,
+ nullptr, &bSumEkinhOld,
cglo_flags &~(CGLO_STOPCM | CGLO_PRESSURE));
}
/* Calculate the initial half step temperature, and save the ekinh_old */
- if (!(Flags & MD_STARTFROMCPT))
+ if (!continuationOptions.startedFromCheckpoint)
{
for (i = 0; (i < ir->opts.ngtc); i++)
{
fprintf(stderr, "starting md rerun '%s', reading coordinates from"
" input trajectory '%s'\n\n",
*(top_global->name), opt2fn("-rerun", nfile, fnm));
- if (bVerbose)
+ if (mdrunOptions.verbose)
{
fprintf(stderr, "Calculated time to finish depends on nsteps from "
"run input file,\nwhich may not correspond to the time "
}
}
- /* loop over MD steps or if rerunMD to end of input trajectory */
- bFirstStep = TRUE;
+ /* Loop over MD steps or if rerunMD to end of input trajectory,
+ * or, if max_hours>0, until max_hours is reached.
+ */
+ real max_hours = mdrunOptions.maximumHoursToRun;
+ bFirstStep = TRUE;
/* Skip the first Nose-Hoover integration when we get the state from tpx */
bInitStep = !startingFromCheckpoint || EI_VV(ir->eI);
bSumEkinhOld = FALSE;
// checkpoints and stop conditions to act on the same step, so
// the propagation of such signals must take place between
// simulations, not just within simulations.
- bool checkpointIsLocal = (repl_ex_nst <= 0) && !bUsingEnsembleRestraints;
- bool stopConditionIsLocal = (repl_ex_nst <= 0) && !bUsingEnsembleRestraints;
+ bool checkpointIsLocal = !useReplicaExchange && !bUsingEnsembleRestraints;
+ bool stopConditionIsLocal = !useReplicaExchange && !bUsingEnsembleRestraints;
bool resetCountersIsLocal = true;
signals[eglsCHKPT] = SimulationSignal(checkpointIsLocal);
signals[eglsSTOPCOND] = SimulationSignal(stopConditionIsLocal);
signals[eglsRESETCOUNTERS] = SimulationSignal(resetCountersIsLocal);
}
+ DdOpenBalanceRegionBeforeForceComputation ddOpenBalanceRegion = (DOMAINDECOMP(cr) ? DdOpenBalanceRegionBeforeForceComputation::yes : DdOpenBalanceRegionBeforeForceComputation::no);
+ DdCloseBalanceRegionAfterForceComputation ddCloseBalanceRegion = (DOMAINDECOMP(cr) ? DdCloseBalanceRegionAfterForceComputation::yes : DdCloseBalanceRegionAfterForceComputation::no);
+
step = ir->init_step;
step_rel = 0;
// TODO extract this to new multi-simulation module
- if (MASTER(cr) && MULTISIM(cr) && (repl_ex_nst <= 0 ))
+ if (MASTER(cr) && MULTISIM(cr) && !useReplicaExchange)
{
if (!multisim_int_all_are_equal(cr->ms, ir->nsteps))
{
- md_print_info(cr, fplog,
- "Note: The number of steps is not consistent across multi simulations,\n"
- "but we are proceeding anyway!\n");
+ GMX_LOG(mdlog.warning).appendText(
+ "Note: The number of steps is not consistent across multi simulations,\n"
+ "but we are proceeding anyway!");
}
if (!multisim_int_all_are_equal(cr->ms, ir->init_step))
{
- md_print_info(cr, fplog,
- "Note: The initial step is not consistent across multi simulations,\n"
- "but we are proceeding anyway!\n");
+ GMX_LOG(mdlog.warning).appendText(
+ "Note: The initial step is not consistent across multi simulations,\n"
+ "but we are proceeding anyway!");
}
}
{
/* PME grid + cut-off optimization with GPUs or PME nodes */
pme_loadbal_do(pme_loadbal, cr,
- (bVerbose && MASTER(cr)) ? stderr : NULL,
- fplog,
+ (mdrunOptions.verbose && MASTER(cr)) ? stderr : nullptr,
+ fplog, mdlog,
ir, fr, state,
wcycle,
step, step_rel,
&& (ir->bExpanded) && (step > 0) && (!startingFromCheckpoint));
}
- bDoReplEx = ((repl_ex_nst > 0) && (step > 0) && !bLastStep &&
- do_per_step(step, repl_ex_nst));
+ bDoReplEx = (useReplicaExchange && (step > 0) && !bLastStep &&
+ do_per_step(step, replExParams.exchangeInterval));
if (bSimAnn)
{
copy_mat(rerun_fr.box, state_global->box);
copy_mat(state_global->box, state->box);
- if (vsite && (Flags & MD_RERUN_VSITE))
+ if (vsite && mdrunOptions.rerunConstructVsites)
{
if (DOMAINDECOMP(cr))
{
/* Following is necessary because the graph may get out of sync
* with the coordinates if we only have every N'th coordinate set
*/
- mk_mshift(fplog, graph, fr->ePBC, state->box, state->x);
- shift_self(graph, state->box, state->x);
+ mk_mshift(fplog, graph, fr->ePBC, state->box, as_rvec_array(state->x.data()));
+ shift_self(graph, state->box, as_rvec_array(state->x.data()));
}
- construct_vsites(vsite, state->x, ir->delta_t, state->v,
+ construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, state->box);
if (graph)
{
- unshift_self(graph, state->box, state->x);
+ unshift_self(graph, state->box, as_rvec_array(state->x.data()));
}
}
}
* beyond the last step. But we don't consider that to be an issue.
*/
do_log = do_per_step(step, ir->nstlog) || (bFirstStep && !startingFromCheckpoint) || bLastStep || bRerunMD;
- do_verbose = bVerbose &&
- (step % stepout == 0 || bFirstStep || bLastStep || bRerunMD);
+ do_verbose = mdrunOptions.verbose &&
+ (step % mdrunOptions.verboseStepPrintInterval == 0 || bFirstStep || bLastStep || bRerunMD);
if (bNS && !(bFirstStep && ir->bContinuation && !bRerunMD))
{
nrnb, wcycle,
do_verbose && !bPMETunePrinting);
shouldCheckNumberOfBondedInteractions = true;
- update_realloc(upd, state->nalloc);
+ update_realloc(upd, state->natoms);
}
}
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
constr, &nullSignaller, state->box,
&totalNumberOfBondedInteractions, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE | CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS);
* but never at the first step or with rerun.
*/
bCPT = (((signals[eglsCHKPT].set && (bNS || ir->nstlist == 0)) ||
- (bLastStep && (Flags & MD_CONFOUT))) &&
+ (bLastStep && mdrunOptions.writeConfout)) &&
step > ir->init_step && !bRerunMD);
if (bCPT)
{
if (shellfc)
{
/* Now is the time to relax the shells */
- relax_shell_flexcon(fplog, cr, bVerbose, step,
+ relax_shell_flexcon(fplog, cr, mdrunOptions.verbose, step,
ir, bNS, force_flags, top,
constr, enerd, fcd,
- state, f, force_vir, mdatoms,
+ state, &f, force_vir, mdatoms,
nrnb, wcycle, graph, groups,
shellfc, fr, bBornRadii, t, mu_tot,
- vsite, mdoutf_get_fp_field(outf));
+ vsite,
+ ddOpenBalanceRegion, ddCloseBalanceRegion);
}
else
{
* Check comments in sim_util.c
*/
do_force(fplog, cr, ir, step, nrnb, wcycle, top, groups,
- state->box, state->x, &state->hist,
- f, force_vir, mdatoms, enerd, fcd,
+ state->box, &state->x, &state->hist,
+ &f, force_vir, mdatoms, enerd, fcd,
state->lambda, graph,
- fr, vsite, mu_tot, t, mdoutf_get_fp_field(outf), ed, bBornRadii,
- (bNS ? GMX_FORCE_NS : 0) | force_flags);
+ fr, vsite, mu_tot, t, ed, bBornRadii,
+ (bNS ? GMX_FORCE_NS : 0) | force_flags,
+ ddOpenBalanceRegion, ddCloseBalanceRegion);
}
if (EI_VV(ir->eI) && !startingFromCheckpoint && !bRerunMD)
/* ############### START FIRST UPDATE HALF-STEP FOR VV METHODS############### */
{
- rvec *vbuf = NULL;
+ rvec *vbuf = nullptr;
wallcycle_start(wcycle, ewcUPDATE);
if (ir->eI == eiVV && bInitStep)
* so that the input is actually the initial step.
*/
snew(vbuf, state->natoms);
- copy_rvecn(state->v, vbuf, 0, state->natoms); /* should make this better for parallelizing? */
+ copy_rvecn(as_rvec_array(state->v.data()), vbuf, 0, state->natoms); /* should make this better for parallelizing? */
}
else
{
trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ1);
}
- update_coords(fplog, step, ir, mdatoms, state, f, fcd,
+ update_coords(fplog, step, ir, mdatoms, state, &f, fcd,
ekind, M, upd, etrtVELOCITY1,
cr, constr);
if (!bRerunMD || rerun_fr.bV || bForceUpdate) /* Why is rerun_fr.bV here? Unclear. */
{
wallcycle_stop(wcycle, ewcUPDATE);
- update_constraints(fplog, step, NULL, ir, mdatoms,
- state, fr->bMolPBC, graph, f,
+ update_constraints(fplog, step, nullptr, ir, mdatoms,
+ state, fr->bMolPBC, graph, &f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
TRUE, bCalcVir);
{
/* Need to unshift here if a do_force has been
called in the previous step */
- unshift_self(graph, state->box, state->x);
+ unshift_self(graph, state->box, as_rvec_array(state->x.data()));
}
/* if VV, compute the pressure and constraints */
/* For VV2, we strictly only need this if using pressure
if (inputrecNvtTrotter(ir) && ir->eI == eiVV)
{
/* update temperature and kinetic energy now that step is over - this is the v(t+dt) point */
- enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, NULL, (ir->eI == eiVV), FALSE);
+ enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, nullptr, (ir->eI == eiVV), FALSE);
enerd->term[F_EKIN] = trace(ekind->ekin);
}
}
* the full step kinetic energy and possibly for T-coupling.*/
/* This may not be quite working correctly yet . . . . */
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
- wcycle, enerd, NULL, NULL, NULL, NULL, mu_tot,
+ wcycle, enerd, nullptr, nullptr, nullptr, nullptr, mu_tot,
constr, &nullSignaller, state->box,
- NULL, &bSumEkinhOld,
+ nullptr, &bSumEkinhOld,
CGLO_GSTAT | CGLO_TEMPERATURE);
wallcycle_start(wcycle, ewcUPDATE);
}
/* if it's the initial step, we performed this first step just to get the constraint virial */
if (ir->eI == eiVV && bInitStep)
{
- copy_rvecn(vbuf, state->v, 0, state->natoms);
+ copy_rvecn(vbuf, as_rvec_array(state->v.data()), 0, state->natoms);
sfree(vbuf);
}
wallcycle_stop(wcycle, ewcUPDATE);
/* compute the conserved quantity */
if (EI_VV(ir->eI))
{
- saved_conserved_quantity = compute_conserved_from_auxiliary(ir, state, &MassQ);
+ saved_conserved_quantity = NPT_energy(ir, state, &MassQ);
if (ir->eI == eiVV)
{
last_ekin = enerd->term[F_EKIN];
statistics, but if performing simulated tempering, we
do update the velocities and the tau_t. */
- lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, &state->dfhist, step, state->v, mdatoms);
+ lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, state->fep_state, state->dfhist, step, as_rvec_array(state->v.data()), mdatoms);
/* history is maintained in state->dfhist, but state_global is what is sent to trajectory and log output */
- copy_df_history(&state_global->dfhist, &state->dfhist);
+ copy_df_history(state_global->dfhist, state->dfhist);
}
/* Now we have the energies and forces corresponding to the
* the update.
*/
do_md_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
- ir, state, state_global, top_global, fr,
- outf, mdebin, ekind, f,
+ ir, state, state_global, observablesHistory,
+ top_global, fr,
+ outf, mdebin, ekind, &f,
&nchkpt,
- bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
+ bCPT, bRerunMD, bLastStep,
+ mdrunOptions.writeConfout,
bSumEkinhOld);
/* Check if IMD step and do IMD communication, if bIMD is TRUE. */
- bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, state->x, ir, t, wcycle);
+ bIMDstep = do_IMD(ir->bIMD, step, cr, bNS, state->box, as_rvec_array(state->x.data()), ir, t, wcycle);
/* kludge -- virial is lost with restart for MTTK NPT control. Must reload (saved earlier). */
if (startingFromCheckpoint && (inputrecNptTrotter(ir) || inputrecNphTrotter(ir)))
* where we do global communication,
* otherwise the other nodes don't know.
*/
+ const real cpt_period = mdrunOptions.checkpointOptions.period;
if (MASTER(cr) && ((bGStat || !PAR(cr)) &&
cpt_period >= 0 &&
(cpt_period == 0 ||
/* if we have constraints, we have to remove the kinetic energy parallel to the bonds */
if (constr && bIfRandomize)
{
- update_constraints(fplog, step, NULL, ir, mdatoms,
- state, fr->bMolPBC, graph, f,
+ update_constraints(fplog, step, nullptr, ir, mdatoms,
+ state, fr->bMolPBC, graph, &f,
&top->idef, tmp_vir,
cr, nrnb, wcycle, upd, constr,
TRUE, bCalcVir);
else
{
update_tcouple(step, ir, state, ekind, &MassQ, mdatoms);
- update_pcouple(fplog, step, ir, state, pcoupl_mu, M, bInitStep);
+ update_pcouple_before_coordinates(fplog, step, ir, state,
+ parrinellorahmanMu, M,
+ bInitStep);
}
if (EI_VV(ir->eI))
{
/* velocity half-step update */
- update_coords(fplog, step, ir, mdatoms, state, f, fcd,
+ update_coords(fplog, step, ir, mdatoms, state, &f, fcd,
ekind, M, upd, etrtVELOCITY2,
cr, constr);
}
cbuf_nalloc = state->natoms;
srenew(cbuf, cbuf_nalloc);
}
- copy_rvecn(state->x, cbuf, 0, state->natoms);
+ copy_rvecn(as_rvec_array(state->x.data()), cbuf, 0, state->natoms);
}
- update_coords(fplog, step, ir, mdatoms, state, f, fcd,
+ update_coords(fplog, step, ir, mdatoms, state, &f, fcd,
ekind, M, upd, etrtPOSITION, cr, constr);
wallcycle_stop(wcycle, ewcUPDATE);
update_constraints(fplog, step, &dvdl_constr, ir, mdatoms, state,
- fr->bMolPBC, graph, f,
+ fr->bMolPBC, graph, &f,
&top->idef, shake_vir,
cr, nrnb, wcycle, upd, constr,
FALSE, bCalcVir);
compute_globals(fplog, gstat, cr, ir, fr, ekind, state, mdatoms, nrnb, vcm,
wcycle, enerd, force_vir, shake_vir, total_vir, pres, mu_tot,
constr, &nullSignaller, lastbox,
- NULL, &bSumEkinhOld,
+ nullptr, &bSumEkinhOld,
(bGStat ? CGLO_GSTAT : 0) | CGLO_TEMPERATURE
);
wallcycle_start(wcycle, ewcUPDATE);
trotter_update(ir, step, ekind, enerd, state, total_vir, mdatoms, &MassQ, trotter_seq, ettTSEQ4);
/* now we know the scaling, we can compute the positions again again */
- copy_rvecn(cbuf, state->x, 0, state->natoms);
+ copy_rvecn(cbuf, as_rvec_array(state->x.data()), 0, state->natoms);
- update_coords(fplog, step, ir, mdatoms, state, f, fcd,
+ update_coords(fplog, step, ir, mdatoms, state, &f, fcd,
ekind, M, upd, etrtPOSITION, cr, constr);
wallcycle_stop(wcycle, ewcUPDATE);
- /* do we need an extra constraint here? just need to copy out of state->v to upd->xp? */
+ /* do we need an extra constraint here? just need to copy out of as_rvec_array(state->v.data()) to upd->xp? */
/* are the small terms in the shake_vir here due
* to numerical errors, or are they important
* physically? I'm thinking they are just errors, but not completely sure.
* For now, will call without actually constraining, constr=NULL*/
- update_constraints(fplog, step, NULL, ir, mdatoms,
- state, fr->bMolPBC, graph, f,
+ update_constraints(fplog, step, nullptr, ir, mdatoms,
+ state, fr->bMolPBC, graph, &f,
&top->idef, tmp_vir,
- cr, nrnb, wcycle, upd, NULL,
+ cr, nrnb, wcycle, upd, nullptr,
FALSE, bCalcVir);
}
if (EI_VV(ir->eI))
else if (graph)
{
/* Need to unshift here */
- unshift_self(graph, state->box, state->x);
+ unshift_self(graph, state->box, as_rvec_array(state->x.data()));
}
- if (vsite != NULL)
+ if (vsite != nullptr)
{
wallcycle_start(wcycle, ewcVSITECONSTR);
- if (graph != NULL)
+ if (graph != nullptr)
{
- shift_self(graph, state->box, state->x);
+ shift_self(graph, state->box, as_rvec_array(state->x.data()));
}
- construct_vsites(vsite, state->x, ir->delta_t, state->v,
+ construct_vsites(vsite, as_rvec_array(state->x.data()), ir->delta_t, as_rvec_array(state->v.data()),
top->idef.iparams, top->idef.il,
fr->ePBC, fr->bMolPBC, cr, state->box);
- if (graph != NULL)
+ if (graph != nullptr)
{
- unshift_self(graph, state->box, state->x);
+ unshift_self(graph, state->box, as_rvec_array(state->x.data()));
}
wallcycle_stop(wcycle, ewcVSITECONSTR);
}
Currently done every step so that dhdl is correct in the .edr */
sum_dhdl(enerd, state->lambda, ir->fepvals);
}
- update_box(fplog, step, ir, mdatoms, state, f,
- pcoupl_mu, nrnb, upd);
+
+ update_pcouple_after_coordinates(fplog, step, ir, mdatoms,
+ pres, force_vir, shake_vir,
+ parrinellorahmanMu,
+ state, nrnb, upd);
/* ################# END UPDATE STEP 2 ################# */
/* #### We now have r(t+dt) and v(t+dt/2) ############# */
bSumEkinhOld = TRUE;
}
- /* ######### BEGIN PREPARING EDR OUTPUT ########### */
-
- /* use the directly determined last velocity, not actually the averaged half steps */
- if (bTrotter && ir->eI == eiVV)
+ if (bCalcEner)
{
- enerd->term[F_EKIN] = last_ekin;
- }
- enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
+ /* ######### BEGIN PREPARING EDR OUTPUT ########### */
- if (EI_VV(ir->eI))
- {
- enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
- }
- else
- {
- enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + compute_conserved_from_auxiliary(ir, state, &MassQ);
+ /* use the directly determined last velocity, not actually the averaged half steps */
+ if (bTrotter && ir->eI == eiVV)
+ {
+ enerd->term[F_EKIN] = last_ekin;
+ }
+ enerd->term[F_ETOT] = enerd->term[F_EPOT] + enerd->term[F_EKIN];
+
+ if (integratorHasConservedEnergyQuantity(ir))
+ {
+ if (EI_VV(ir->eI))
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + saved_conserved_quantity;
+ }
+ else
+ {
+ enerd->term[F_ECONSERVED] = enerd->term[F_ETOT] + NPT_energy(ir, state, &MassQ);
+ }
+ }
+ /* ######### END PREPARING EDR OUTPUT ########### */
}
- /* ######### END PREPARING EDR OUTPUT ########### */
/* Output stuff */
if (MASTER(cr))
if (fplog && do_log && bDoExpanded)
{
/* only needed if doing expanded ensemble */
- PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : NULL,
- &state_global->dfhist, state->fep_state, ir->nstlog, step);
+ PrintFreeEnergyInfoToFile(fplog, ir->fepvals, ir->expandedvals, ir->bSimTemp ? ir->simtempvals : nullptr,
+ state_global->dfhist, state->fep_state, ir->nstlog, step);
}
if (bCalcEner)
{
gmx_bool do_dr = do_per_step(step, ir->nstdisreout);
gmx_bool do_or = do_per_step(step, ir->nstorireout);
- print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : NULL,
+ print_ebin(mdoutf_get_fp_ene(outf), do_ene, do_dr, do_or, do_log ? fplog : nullptr,
step, t,
eprNORMAL, mdebin, fcd, groups, &(ir->opts));
do_per_step(step, ir->swap->nstswap))
{
bNeedRepartition = do_swapcoords(cr, step, t, ir, wcycle,
- bRerunMD ? rerun_fr.x : state->x,
+ bRerunMD ? rerun_fr.x : as_rvec_array(state->x.data()),
bRerunMD ? rerun_fr.box : state->box,
- top_global, MASTER(cr) && bVerbose, bRerunMD);
+ MASTER(cr) && mdrunOptions.verbose,
+ bRerunMD);
if (bNeedRepartition && DOMAINDECOMP(cr))
{
vsite, constr,
nrnb, wcycle, FALSE);
shouldCheckNumberOfBondedInteractions = true;
- update_realloc(upd, state->nalloc);
+ update_realloc(upd, state->natoms);
}
bFirstStep = FALSE;
bInitStep = FALSE;
- startingFromCheckpoint = FALSE;
+ startingFromCheckpoint = false;
/* ####### SET VARIABLES FOR NEXT ITERATION IF THEY STILL NEED IT ###### */
/* With all integrators, except VV, we need to retain the pressure
/* ####### END SET VARIABLES FOR NEXT ITERATION ###### */
- if ( (membed != NULL) && (!bLastStep) )
+ if ( (membed != nullptr) && (!bLastStep) )
{
- rescale_membed(step_rel, membed, state_global->x);
+ rescale_membed(step_rel, membed, as_rvec_array(state_global->x.data()));
}
if (bRerunMD)
"resetting counters later in the run, e.g. with gmx "
"mdrun -resetstep.", step);
}
- reset_all_counters(fplog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
- use_GPU(fr->nbv) ? fr->nbv : NULL);
+ reset_all_counters(fplog, mdlog, cr, step, &step_rel, ir, wcycle, nrnb, walltime_accounting,
+ use_GPU(fr->nbv) ? fr->nbv : nullptr);
wcycle_set_reset_counters(wcycle, -1);
if (!(cr->duty & DUTY_PME))
{
if (bRerunMD && MASTER(cr))
{
- close_trj(status);
+ close_trx(status);
}
if (!(cr->duty & DUTY_PME))
if (bPMETune)
{
- pme_loadbal_done(pme_loadbal, cr, fplog, use_GPU(fr->nbv));
+ pme_loadbal_done(pme_loadbal, fplog, mdlog, use_GPU(fr->nbv));
}
done_shellfc(fplog, shellfc, step_rel);
- if (repl_ex_nst > 0 && MASTER(cr))
+ if (useReplicaExchange && MASTER(cr))
{
print_replica_exchange_statistics(fplog, repl_ex);
}
finish_swapcoords(ir->swap);
}
+ /* Do essential dynamics cleanup if needed. Close .edo file */
+ done_ed(&ed);
+
/* IMD cleanup, if bIMD is TRUE. */
IMD_finalize(ir->bIMD, ir->imd);
#include "config.h"
-#include <stdio.h>
-#include <string.h>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
#include "gromacs/commandline/filenm.h"
#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/readinp.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/mdlib/main.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/utility/arraysize.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#include "mdrun_main.h"
+#include "repl_ex.h"
#include "runner.h"
/*! \brief Return whether either of the command-line parameters that
//! Implements C-style main function for mdrun
int gmx_mdrun(int argc, char *argv[])
+{
+ gmx::Mdrunner runner;
+ return runner.mainFunction(argc, argv);
+}
+
+namespace gmx
+{
+
+int Mdrunner::mainFunction(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] is the main computational chemistry engine",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
- "be printed to stderr.",
+ "be printed to stderr. It will also terminate the run when non-finite",
+ "forces are present.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
};
- t_commrec *cr;
- t_filenm fnm[] = {
- { efTPR, NULL, NULL, ffREAD },
- { efTRN, "-o", NULL, ffWRITE },
- { efCOMPRESSED, "-x", NULL, ffOPTWR },
- { efCPT, "-cpi", NULL, ffOPTRD | ffALLOW_MISSING },
- { efCPT, "-cpo", NULL, ffOPTWR },
- { efSTO, "-c", "confout", ffWRITE },
- { efEDR, "-e", "ener", ffWRITE },
- { efLOG, "-g", "md", ffWRITE },
- { efXVG, "-dhdl", "dhdl", ffOPTWR },
- { efXVG, "-field", "field", ffOPTWR },
- { efXVG, "-table", "table", ffOPTRD },
- { efXVG, "-tablep", "tablep", ffOPTRD },
- { efXVG, "-tableb", "table", ffOPTRDMULT },
- { efTRX, "-rerun", "rerun", ffOPTRD },
- { efXVG, "-tpi", "tpi", ffOPTWR },
- { efXVG, "-tpid", "tpidist", ffOPTWR },
- { efEDI, "-ei", "sam", ffOPTRD },
- { efXVG, "-eo", "edsam", ffOPTWR },
- { efXVG, "-devout", "deviatie", ffOPTWR },
- { efXVG, "-runav", "runaver", ffOPTWR },
- { efXVG, "-px", "pullx", ffOPTWR },
- { efXVG, "-pf", "pullf", ffOPTWR },
- { efXVG, "-ro", "rotation", ffOPTWR },
- { efLOG, "-ra", "rotangles", ffOPTWR },
- { efLOG, "-rs", "rotslabs", ffOPTWR },
- { efLOG, "-rt", "rottorque", ffOPTWR },
- { efMTX, "-mtx", "nm", ffOPTWR },
- { efRND, "-multidir", NULL, ffOPTRDMULT},
- { efDAT, "-membed", "membed", ffOPTRD },
- { efTOP, "-mp", "membed", ffOPTRD },
- { efNDX, "-mn", "membed", ffOPTRD },
- { efXVG, "-if", "imdforces", ffOPTWR },
- { efXVG, "-swap", "swapions", ffOPTWR }
- };
- const int NFILE = asize(fnm);
-
- /* Command line options ! */
- gmx_bool bDDBondCheck = TRUE;
- gmx_bool bDDBondComm = TRUE;
- gmx_bool bTunePME = TRUE;
- gmx_bool bVerbose = FALSE;
- gmx_bool bRerunVSite = FALSE;
- gmx_bool bConfout = TRUE;
- gmx_bool bReproducible = FALSE;
- gmx_bool bIMDwait = FALSE;
- gmx_bool bIMDterm = FALSE;
- gmx_bool bIMDpull = FALSE;
-
- int npme = -1;
- int nstlist = 0;
- int nmultisim = 0;
- int nstglobalcomm = -1;
- int repl_ex_nst = 0;
- int repl_ex_seed = -1;
- int repl_ex_nex = 0;
- int nstepout = 100;
- int resetstep = -1;
- gmx_int64_t nsteps = -2; /* the value -2 means that the mdp option will be used */
- int imdport = 8888; /* can be almost anything, 8888 is easy to remember */
-
- rvec realddxyz = {0, 0, 0};
- const char *ddrank_opt[ddrankorderNR+1] =
- { NULL, "interleave", "pp_pme", "cartesian", NULL };
- const char *dddlb_opt[] =
- { NULL, "auto", "no", "yes", NULL };
- const char *thread_aff_opt[threadaffNR+1] =
- { NULL, "auto", "on", "off", NULL };
- const char *nbpu_opt[] =
- { NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
- real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
- char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
- real cpt_period = 15.0, max_hours = -1;
+
+ /* Command line options */
+ rvec realddxyz = {0, 0, 0};
+ const char *ddrank_opt_choices[static_cast<int>(DdRankOrder::nr)+1] =
+ { nullptr, "interleave", "pp_pme", "cartesian", nullptr };
+ const char *dddlb_opt_choices[static_cast<int>(DlbOption::nr)+1] =
+ { nullptr, "auto", "no", "yes", nullptr };
+ const char *thread_aff_opt_choices[threadaffNR+1] =
+ { nullptr, "auto", "on", "off", nullptr };
+ const char *nbpu_opt_choices[] =
+ { nullptr, "auto", "cpu", "gpu", "gpu_cpu", nullptr };
gmx_bool bTryToAppendFiles = TRUE;
- gmx_bool bKeepAndNumCPT = FALSE;
- gmx_bool bResetCountersHalfWay = FALSE;
- gmx_output_env_t *oenv = NULL;
+ const char *gpuIdTaskAssignment = "";
- /* Non transparent initialization of a complex gmx_hw_opt_t struct.
- * But unfortunately we are not allowed to call a function here,
- * since declarations follow below.
- */
- gmx_hw_opt_t hw_opt = {
- 0, 0, 0, 0, threadaffSEL, 0, 0,
- { NULL, FALSE, 0, NULL }
- };
+ ImdOptions &imdOptions = mdrunOptions.imdOptions;
- t_pargs pa[] = {
+ t_pargs pa[] = {
{ "-dd", FALSE, etRVEC, {&realddxyz},
"Domain decomposition grid, 0 is optimize" },
- { "-ddorder", FALSE, etENUM, {ddrank_opt},
+ { "-ddorder", FALSE, etENUM, {ddrank_opt_choices},
"DD rank order" },
- { "-npme", FALSE, etINT, {&npme},
+ { "-npme", FALSE, etINT, {&domdecOptions.numPmeRanks},
"Number of separate ranks to be used for PME, -1 is guess" },
{ "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
"Total number of threads to start (0 is guess)" },
"Number of OpenMP threads per MPI rank to start (0 is guess)" },
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
- { "-pin", FALSE, etENUM, {thread_aff_opt},
+ { "-pin", FALSE, etENUM, {thread_aff_opt_choices},
"Whether mdrun should try to set thread affinities" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
"The lowest logical core number to which mdrun should pin the first thread" },
{ "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
"Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
- { "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
+ { "-gpu_id", FALSE, etSTR, {&gpuIdTaskAssignment},
"List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
- { "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
+ { "-ddcheck", FALSE, etBOOL, {&domdecOptions.checkBondedInteractions},
"Check for all bonded interactions with DD" },
- { "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
+ { "-ddbondcomm", FALSE, etBOOL, {&domdecOptions.useBondedCommunication},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
- { "-rdd", FALSE, etREAL, {&rdd},
+ { "-rdd", FALSE, etREAL, {&domdecOptions.minimumCommunicationRange},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
- { "-rcon", FALSE, etREAL, {&rconstr},
+ { "-rcon", FALSE, etREAL, {&domdecOptions.constraintCommunicationRange},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
- { "-dlb", FALSE, etENUM, {dddlb_opt},
+ { "-dlb", FALSE, etENUM, {dddlb_opt_choices},
"Dynamic load balancing (with DD)" },
- { "-dds", FALSE, etREAL, {&dlb_scale},
+ { "-dds", FALSE, etREAL, {&domdecOptions.dlbScaling},
"Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
"provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
- { "-ddcsx", FALSE, etSTR, {&ddcsx},
+ { "-ddcsx", FALSE, etSTR, {&domdecOptions.cellSizeX},
"HIDDENA string containing a vector of the relative sizes in the x "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
- { "-ddcsy", FALSE, etSTR, {&ddcsy},
+ { "-ddcsy", FALSE, etSTR, {&domdecOptions.cellSizeY},
"HIDDENA string containing a vector of the relative sizes in the y "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
- { "-ddcsz", FALSE, etSTR, {&ddcsz},
+ { "-ddcsz", FALSE, etSTR, {&domdecOptions.cellSizeZ},
"HIDDENA string containing a vector of the relative sizes in the z "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
- { "-gcom", FALSE, etINT, {&nstglobalcomm},
+ { "-gcom", FALSE, etINT, {&mdrunOptions.globalCommunicationInterval},
"Global communication frequency" },
- { "-nb", FALSE, etENUM, {&nbpu_opt},
+ { "-nb", FALSE, etENUM, {nbpu_opt_choices},
"Calculate non-bonded interactions on" },
- { "-nstlist", FALSE, etINT, {&nstlist},
+ { "-nstlist", FALSE, etINT, {&nstlist_cmdline},
"Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
- { "-tunepme", FALSE, etBOOL, {&bTunePME},
+ { "-tunepme", FALSE, etBOOL, {&mdrunOptions.tunePme},
"Optimize PME load between PP/PME ranks or GPU/CPU (only with the Verlet cut-off scheme)" },
- { "-v", FALSE, etBOOL, {&bVerbose},
+ { "-v", FALSE, etBOOL, {&mdrunOptions.verbose},
"Be loud and noisy" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
- { "-reprod", FALSE, etBOOL, {&bReproducible},
+ { "-reprod", FALSE, etBOOL, {&mdrunOptions.reproducible},
"Try to avoid optimizations that affect binary reproducibility" },
- { "-cpt", FALSE, etREAL, {&cpt_period},
+ { "-cpt", FALSE, etREAL, {&mdrunOptions.checkpointOptions.period},
"Checkpoint interval (minutes)" },
- { "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
+ { "-cpnum", FALSE, etBOOL, {&mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bTryToAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
- { "-nsteps", FALSE, etINT64, {&nsteps},
+ { "-nsteps", FALSE, etINT64, {&mdrunOptions.numStepsCommandline},
"Run this number of steps, overrides .mdp file option (-1 means infinite, -2 means use mdp option, smaller is invalid)" },
- { "-maxh", FALSE, etREAL, {&max_hours},
+ { "-maxh", FALSE, etREAL, {&mdrunOptions.maximumHoursToRun},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
- { "-replex", FALSE, etINT, {&repl_ex_nst},
+ { "-replex", FALSE, etINT, {&replExParams.exchangeInterval},
"Attempt replica exchange periodically with this period (steps)" },
- { "-nex", FALSE, etINT, {&repl_ex_nex},
+ { "-nex", FALSE, etINT, {&replExParams.numExchanges},
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
- { "-reseed", FALSE, etINT, {&repl_ex_seed},
+ { "-reseed", FALSE, etINT, {&replExParams.randomSeed},
"Seed for replica exchange, -1 is generate a seed" },
- { "-imdport", FALSE, etINT, {&imdport},
+ { "-imdport", FALSE, etINT, {&imdOptions.port},
"HIDDENIMD listening port" },
- { "-imdwait", FALSE, etBOOL, {&bIMDwait},
+ { "-imdwait", FALSE, etBOOL, {&imdOptions.wait},
"HIDDENPause the simulation while no IMD client is connected" },
- { "-imdterm", FALSE, etBOOL, {&bIMDterm},
+ { "-imdterm", FALSE, etBOOL, {&imdOptions.terminatable},
"HIDDENAllow termination of the simulation from IMD client" },
- { "-imdpull", FALSE, etBOOL, {&bIMDpull},
+ { "-imdpull", FALSE, etBOOL, {&imdOptions.pull},
"HIDDENAllow pulling in the simulation from IMD client" },
- { "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
+ { "-rerunvsite", FALSE, etBOOL, {&mdrunOptions.rerunConstructVsites},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
- { "-confout", FALSE, etBOOL, {&bConfout},
+ { "-confout", FALSE, etBOOL, {&mdrunOptions.writeConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
- { "-stepout", FALSE, etINT, {&nstepout},
+ { "-stepout", FALSE, etINT, {&mdrunOptions.verboseStepPrintInterval},
"HIDDENFrequency of writing the remaining wall clock time for the run" },
- { "-resetstep", FALSE, etINT, {&resetstep},
+ { "-resetstep", FALSE, etINT, {&mdrunOptions.timingOptions.resetStep},
"HIDDENReset cycle counters after these many time steps" },
- { "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
+ { "-resethway", FALSE, etBOOL, {&mdrunOptions.timingOptions.resetHalfway},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
- unsigned long Flags;
- ivec ddxyz;
- int dd_rank_order;
- gmx_bool bDoAppendFiles, bStartFromCpt;
- FILE *fplog;
- int rc;
- char **multidir = NULL;
+ int rc;
+ char **multidir = nullptr;
cr = init_commrec();
}
*/
- if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
- asize(desc), desc, 0, NULL, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_Flags, nfile, fnm, asize(pa), pa,
+ asize(desc), desc, 0, nullptr, &oenv))
{
+ sfree(cr);
return 0;
}
+ // Handle the option that permits the user to select a GPU task
+ // assignment, which could be in an environment variable (so that
+ // there is a way to customize it, when using MPI in heterogeneous
+ // contexts).
+ {
+ // TODO Argument parsing can't handle std::string. We should
+ // fix that by changing the parsing, once more of the roles of
+ // handling, validating and implementing defaults for user
+ // command-line options have been seperated.
+ hw_opt.gpuIdTaskAssignment = gpuIdTaskAssignment;
+ const char *env = getenv("GMX_GPU_ID");
+ if (env != nullptr)
+ {
+ if (!hw_opt.gpuIdTaskAssignment.empty())
+ {
+ gmx_fatal(FARGS, "GMX_GPU_ID and -gpu_id can not be used at the same time");
+ }
+ hw_opt.gpuIdTaskAssignment = env;
+ }
+ }
- dd_rank_order = nenum(ddrank_opt);
-
- hw_opt.thread_affinity = nenum(thread_aff_opt);
+ hw_opt.thread_affinity = nenum(thread_aff_opt_choices);
/* now check the -multi and -multidir option */
- if (opt2bSet("-multidir", NFILE, fnm))
+ if (opt2bSet("-multidir", nfile, fnm))
{
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
- nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
+ nmultisim = opt2fns(&multidir, "-multidir", nfile, fnm);
}
- if (repl_ex_nst != 0 && nmultisim < 2)
+ if (replExParams.exchangeInterval != 0 && nmultisim < 2)
{
gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
}
- if (repl_ex_nex < 0)
+ if (replExParams.numExchanges < 0)
{
gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
}
if (nmultisim >= 1)
{
#if !GMX_THREAD_MPI
- init_multisystem(cr, nmultisim, multidir, NFILE, fnm);
+ init_multisystem(cr, nmultisim, multidir, nfile, fnm);
#else
gmx_fatal(FARGS, "mdrun -multi or -multidir are not supported with the thread-MPI library. "
"Please compile GROMACS with a proper external MPI library.");
#endif
}
- if (!opt2bSet("-cpi", NFILE, fnm))
+ if (!opt2bSet("-cpi", nfile, fnm))
{
// If we are not starting from a checkpoint we never allow files to be appended
// to, since that has caused a ton of strange behaviour and bugs in the past.
}
}
- handleRestart(cr, bTryToAppendFiles, NFILE, fnm, &bDoAppendFiles, &bStartFromCpt);
-
- Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
- Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
- Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
- Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
- Flags = Flags | (bConfout ? MD_CONFOUT : 0);
- Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
- Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
- Flags = Flags | (bDoAppendFiles ? MD_APPENDFILES : 0);
- Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
- Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
- Flags = Flags | (bStartFromCpt ? MD_STARTFROMCPT : 0);
- Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
- Flags = Flags | (opt2parg_bSet("-ntomp", asize(pa), pa) ? MD_NTOMPSET : 0);
- Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
- Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
- Flags = Flags | (bIMDpull ? MD_IMDPULL : 0);
+ ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
+
+ continuationOptions.appendFilesOptionSet = opt2parg_bSet("-append", asize(pa), pa);
+
+ handleRestart(cr, bTryToAppendFiles, nfile, fnm, &continuationOptions.appendFiles, &continuationOptions.startedFromCheckpoint);
+
+ mdrunOptions.rerun = opt2bSet("-rerun", nfile, fnm);
+ mdrunOptions.ntompOptionIsSet = opt2parg_bSet("-ntomp", asize(pa), pa);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
- if (MASTER(cr) && !bDoAppendFiles)
+ if (MASTER(cr) && !continuationOptions.appendFiles)
{
- gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
- Flags & MD_APPENDFILES, &fplog);
+ gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
+ continuationOptions.appendFiles, &fplog);
}
else
{
- fplog = NULL;
+ fplog = nullptr;
}
- ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
- ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
- ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
+ domdecOptions.rankOrder = static_cast<DdRankOrder>(nenum(ddrank_opt_choices));
+ domdecOptions.dlbOption = static_cast<DlbOption>(nenum(dddlb_opt_choices));
+ domdecOptions.numCells[XX] = (int)(realddxyz[XX] + 0.5);
+ domdecOptions.numCells[YY] = (int)(realddxyz[YY] + 0.5);
+ domdecOptions.numCells[ZZ] = (int)(realddxyz[ZZ] + 0.5);
- rc = gmx::mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose,
- nstglobalcomm, ddxyz, dd_rank_order, npme, rdd, rconstr,
- dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
- nbpu_opt[0], nstlist,
- nsteps, nstepout, resetstep,
- nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
- pforce, cpt_period, max_hours, imdport, Flags);
+ nbpu_opt = nbpu_opt_choices[0];
+ rc = mdrunner();
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
- if (MASTER(cr) && !bDoAppendFiles)
+ if (MASTER(cr) && !continuationOptions.appendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <stdlib.h>
#include "gromacs/commandline/filenm.h"
-#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/fileio/readinp.h"
+#include "gromacs/fileio/warninp.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/index.h"
+#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topology.h"
#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/filestream.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
int mol_id = 0;
int i;
int atnr_mol;
- gmx_mtop_atomlookup_t alook;
- alook = gmx_mtop_atomlookup_settle_init(mtop);
- gmx_mtop_atomnr_to_molblock_ind(alook, at, block, &mol_id, &atnr_mol);
+ *block = 0;
+ mtopGetMolblockIndex(mtop, at, block, &mol_id, &atnr_mol);
for (i = 0; i < *block; i++)
{
mol_id += mtop->molblock[i].nmol;
}
*type = mtop->molblock[*block].type;
- gmx_mtop_atomlookup_destroy(alook);
-
return mol_id;
}
wi = init_warning(TRUE, 0);
- inp = read_inpfile(membed_input, &ninp, wi);
+ {
+ gmx::TextInputFile stream(membed_input);
+ inp = read_inpfile(&stream, membed_input, &ninp, wi);
+ stream.close();
+ }
ITYPE ("nxy", *it_xy, 1000);
ITYPE ("nz", *it_z, 0);
RTYPE ("xyinit", *xy_fac, 0.5);
ITYPE ("maxwarn", *maxwarn, 0);
ITYPE ("pieces", *pieces, 1);
EETYPE("asymmetry", *bALLOW_ASYMMETRY, yesno_names);
+
check_warning_error(wi, FARGS);
- write_inpfile(membed_input, ninp, inp, FALSE, wi);
+ {
+ gmx::TextOutputFile stream(membed_input);
+ write_inpfile(&stream, membed_input, ninp, inp, FALSE, WriteMdpHeader::yes, wi);
+ stream.close();
+ }
done_warning(wi, FARGS);
}
mtop->mols.index = new_mols;
mtop->natoms -= n;
state->natoms -= n;
- state->nalloc = state->natoms;
- snew(x_tmp, state->nalloc);
- snew(v_tmp, state->nalloc);
+ snew(x_tmp, state->natoms);
+ snew(v_tmp, state->natoms);
for (i = 0; i < egcNR; i++)
{
- if (groups->grpnr[i] != NULL)
+ if (groups->grpnr[i] != nullptr)
{
groups->ngrpnr[i] = state->natoms;
snew(new_egrp[i], state->natoms);
{
for (j = 0; j < egcNR; j++)
{
- if (groups->grpnr[j] != NULL)
+ if (groups->grpnr[j] != nullptr)
{
new_egrp[j][i-rm] = groups->grpnr[j][i];
}
}
}
}
- sfree(state->x);
- state->x = x_tmp;
- sfree(state->v);
- state->v = v_tmp;
+ for (int i = 0; i < state->natoms; i++)
+ {
+ copy_rvec(x_tmp[i], state->x[i]);
+ }
+ sfree(x_tmp);
+ for (int i = 0; i < state->natoms; i++)
+ {
+ copy_rvec(v_tmp[i], state->v[i]);
+ }
+ sfree(v_tmp);
for (i = 0; i < egcNR; i++)
{
- if (groups->grpnr[i] != NULL)
+ if (groups->grpnr[i] != nullptr)
{
sfree(groups->grpnr[i]);
groups->grpnr[i] = new_egrp[i];
}
/* remove al bonded interactions from mtop for the molecule to be embedded */
-int rm_bonded(t_block *ins_at, gmx_mtop_t *mtop)
+static int rm_bonded(t_block *ins_at, gmx_mtop_t *mtop)
{
int i, j, m;
int type, natom, nmol, at, atom1 = 0, rm_at = 0;
if (buf[0] != ';')
{
strcpy(buf2, buf);
- if ((temp = strchr(buf2, '\n')) != NULL)
+ if ((temp = strchr(buf2, '\n')) != nullptr)
{
temp[0] = '\0';
}
if (buf2[0] == '[')
{
buf2[0] = ' ';
- if ((temp = strchr(buf2, '\n')) != NULL)
+ if ((temp = strchr(buf2, '\n')) != nullptr)
{
temp[0] = '\0';
}
int i, rm_bonded_at, fr_id, fr_i = 0, tmp_id, warn = 0;
int ng, j, max_lip_rm, ins_grp_id, ntype, lip_rm;
real prot_area;
- rvec *r_ins = NULL;
+ rvec *r_ins = nullptr;
t_block *ins_at, *rest_at;
pos_ins_t *pos_ins;
mem_t *mem_p;
gmx_bool bExcl = FALSE;
t_atoms atoms;
t_pbc *pbc;
- char **piecename = NULL;
- gmx_membed_t *membed = NULL;
+ char **piecename = nullptr;
+ gmx_membed_t *membed = nullptr;
/* input variables */
- const char *membed_input;
real xy_fac = 0.5;
real xy_max = 1.0;
real z_fac = 1.0;
if (MASTER(cr))
{
/* get input data out membed file */
- membed_input = opt2fn("-membed", nfile, fnm);
- get_input(membed_input, &xy_fac, &xy_max, &z_fac, &z_max, &it_xy, &it_z, &probe_rad, &low_up_rm,
- &maxwarn, &pieces, &bALLOW_ASYMMETRY);
+ try
+ {
+ get_input(opt2fn("-membed", nfile, fnm),
+ &xy_fac, &xy_max, &z_fac, &z_max, &it_xy, &it_z, &probe_rad, &low_up_rm,
+ &maxwarn, &pieces, &bALLOW_ASYMMETRY);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
if (!EI_DYNAMICS(inputrec->eI) )
{
/* Check that moleculetypes in insertion group are not part of the rest of the system */
check_types(ins_at, rest_at, mtop);
- init_mem_at(mem_p, mtop, state->x, state->box, pos_ins);
+ init_mem_at(mem_p, mtop, as_rvec_array(state->x.data()), state->box, pos_ins);
- prot_area = est_prot_area(pos_ins, state->x, ins_at, mem_p);
+ prot_area = est_prot_area(pos_ins, as_rvec_array(state->x.data()), ins_at, mem_p);
if ( (prot_area > prot_vs_box) && ( (state->box[XX][XX]*state->box[YY][YY]-state->box[XX][YY]*state->box[YY][XX]) < box_vs_prot) )
{
warn++;
/* resize the protein by xy and by z if necessary*/
snew(r_ins, ins_at->nr);
- init_resize(ins_at, r_ins, pos_ins, mem_p, state->x, bALLOW_ASYMMETRY);
+ init_resize(ins_at, r_ins, pos_ins, mem_p, as_rvec_array(state->x.data()), bALLOW_ASYMMETRY);
membed->fac[0] = membed->fac[1] = xy_fac;
membed->fac[2] = z_fac;
membed->xy_step = (xy_max-xy_fac)/(double)(it_xy);
membed->z_step = (z_max-z_fac)/(double)(it_z-1);
- resize(r_ins, state->x, pos_ins, membed->fac);
+ resize(r_ins, as_rvec_array(state->x.data()), pos_ins, membed->fac);
/* remove overlapping lipids and water from the membrane box*/
/*mark molecules to be removed*/
set_pbc(pbc, inputrec->ePBC, state->box);
snew(rm_p, 1);
- lip_rm = gen_rm_list(rm_p, ins_at, rest_at, pbc, mtop, state->x, mem_p, pos_ins,
+ lip_rm = gen_rm_list(rm_p, ins_at, rest_at, pbc, mtop, as_rvec_array(state->x.data()), mem_p, pos_ins,
probe_rad, low_up_rm, bALLOW_ASYMMETRY);
lip_rm -= low_up_rm;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct t_commrec;
struct t_filenm;
struct t_inputrec;
-struct t_state;
+class t_state;
/* initialisation of membed code */
gmx_membed_t *init_membed(FILE *fplog, int nfile, const t_filenm fnm[], gmx_mtop_t *mtop,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/state.h"
#include "gromacs/random/threefry.h"
#include "gromacs/random/uniformintdistribution.h"
#include "gromacs/random/uniformrealdistribution.h"
return bDiff;
}
-gmx_repl_ex_t init_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- const t_state *state,
- const t_inputrec *ir,
- int nst, int nex, int init_seed)
+gmx_repl_ex_t
+init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ const ReplicaExchangeParameters &replExParams)
{
real pres;
int i, j, k;
fprintf(fplog, "\nInitializing Replica Exchange\n");
- if (ms == NULL || ms->nsim == 1)
+ if (ms == nullptr || ms->nsim == 1)
{
gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
}
check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
check_multi_int64(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
+ const int nst = replExParams.exchangeInterval;
check_multi_int64(fplog, ms, (ir->init_step+nst-1)/nst,
"first exchange step: init_step/-replex", FALSE);
check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
}
}
re->nst = nst;
- if (init_seed == -1)
+ if (replExParams.randomSeed == -1)
{
if (MASTERSIM(ms))
{
}
else
{
- re->seed = init_seed;
+ re->seed = replExParams.randomSeed;
}
fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
{
snew(re->de[i], re->nrepl);
}
- re->nex = nex;
+ re->nex = replExParams.numExchanges;
return re;
}
exchange_rvecs(ms, b, state->svir_prev, DIM);
exchange_rvecs(ms, b, state->fvir_prev, DIM);
exchange_rvecs(ms, b, state->pres_prev, DIM);
- exchange_doubles(ms, b, state->nosehoover_xi, ngtc);
- exchange_doubles(ms, b, state->nosehoover_vxi, ngtc);
- exchange_doubles(ms, b, state->nhpres_xi, nnhpres);
- exchange_doubles(ms, b, state->nhpres_vxi, nnhpres);
- exchange_doubles(ms, b, state->therm_integral, state->ngtc);
- exchange_rvecs(ms, b, state->x, state->natoms);
- exchange_rvecs(ms, b, state->v, state->natoms);
+ exchange_doubles(ms, b, state->nosehoover_xi.data(), ngtc);
+ exchange_doubles(ms, b, state->nosehoover_vxi.data(), ngtc);
+ exchange_doubles(ms, b, state->nhpres_xi.data(), nnhpres);
+ exchange_doubles(ms, b, state->nhpres_vxi.data(), nnhpres);
+ exchange_doubles(ms, b, state->therm_integral.data(), state->ngtc);
+ exchange_doubles(ms, b, &state->baros_integral, 1);
+ exchange_rvecs(ms, b, as_rvec_array(state->x.data()), state->natoms);
+ exchange_rvecs(ms, b, as_rvec_array(state->v.data()), state->natoms);
}
-static void copy_rvecs(rvec *s, rvec *d, int n)
+static void copy_state_serial(const t_state *src, t_state *dest)
{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- copy_rvec(s[i], d[i]);
- }
- }
-}
-
-static void copy_doubles(const double *s, double *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-static void copy_reals(const real *s, real *d, int n)
-{
- int i;
-
- if (d != NULL)
+ if (dest != src)
{
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
- }
-}
-
-static void copy_ints(const int *s, int *d, int n)
-{
- int i;
-
- if (d != NULL)
- {
- for (i = 0; i < n; i++)
- {
- d[i] = s[i];
- }
+ /* Currently the local state is always a pointer to the global
+ * in serial, so we should never end up here.
+ * TODO: Implement a (trivial) t_state copy once converted to C++.
+ */
+ GMX_RELEASE_ASSERT(false, "State copying is currently not implemented in replica exchange");
}
}
-#define scopy_rvecs(v, n) copy_rvecs(state->v, state_local->v, n);
-#define scopy_doubles(v, n) copy_doubles(state->v, state_local->v, n);
-#define scopy_reals(v, n) copy_reals(state->v, state_local->v, n);
-#define scopy_ints(v, n) copy_ints(state->v, state_local->v, n);
-
-static void copy_state_nonatomdata(t_state *state, t_state *state_local)
-{
- /* When t_state changes, this code should be updated. */
- int ngtc, nnhpres;
- ngtc = state->ngtc * state->nhchainlength;
- nnhpres = state->nnhpres* state->nhchainlength;
- scopy_rvecs(box, DIM);
- scopy_rvecs(box_rel, DIM);
- scopy_rvecs(boxv, DIM);
- state_local->veta = state->veta;
- state_local->vol0 = state->vol0;
- scopy_rvecs(svir_prev, DIM);
- scopy_rvecs(fvir_prev, DIM);
- scopy_rvecs(pres_prev, DIM);
- scopy_doubles(nosehoover_xi, ngtc);
- scopy_doubles(nosehoover_vxi, ngtc);
- scopy_doubles(nhpres_xi, nnhpres);
- scopy_doubles(nhpres_vxi, nnhpres);
- scopy_doubles(therm_integral, state->ngtc);
- scopy_rvecs(x, state->natoms);
- scopy_rvecs(v, state->natoms);
- copy_ints(&(state->fep_state), &(state_local->fep_state), 1);
- scopy_reals(lambda, efptNR);
-}
-
static void scale_velocities(t_state *state, real fac)
{
int i;
- if (state->v)
+ if (as_rvec_array(state->v.data()))
{
for (i = 0; i < state->natoms; i++)
{
fprintf(fplog, "Repl %2s %2d", leg, ind[0]);
for (i = 1; i < n; i++)
{
- fprintf(fplog, " %c %2d", (bEx != 0 && bEx[i]) ? 'x' : ' ', ind[i]);
+ fprintf(fplog, " %c %2d", (bEx != nullptr && bEx[i]) ? 'x' : ' ', ind[i]);
}
fprintf(fplog, "\n");
}
}
else
{
- copy_state_nonatomdata(state_local, state);
+ copy_state_serial(state_local, state);
}
if (MASTER(cr))
if (!DOMAINDECOMP(cr))
{
/* Copy the global state to the local state data structure */
- copy_state_nonatomdata(state, state_local);
+ copy_state_serial(state, state_local);
}
}
re->prob[i] = re->prob_sum[i]/re->nattempt[i%2];
}
}
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_ind(fplog, "", re->nrepl, re->ind, nullptr);
print_prob(fplog, "", re->nrepl, re->prob);
fprintf(fplog, "Repl number of exchanges:\n");
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_ind(fplog, "", re->nrepl, re->ind, nullptr);
print_count(fplog, "", re->nrepl, re->nexchange);
fprintf(fplog, "Repl average number of exchanges:\n");
re->prob[i] = ((real)re->nexchange[i])/re->nattempt[i%2];
}
}
- print_ind(fplog, "", re->nrepl, re->ind, NULL);
+ print_ind(fplog, "", re->nrepl, re->ind, nullptr);
print_prob(fplog, "", re->nrepl, re->prob);
fprintf(fplog, "\n");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
struct gmx_multisim_t;
struct t_commrec;
struct t_inputrec;
-struct t_state;
+class t_state;
+
+/* The parameters for the replica exchange algorithm */
+struct ReplicaExchangeParameters
+{
+ ReplicaExchangeParameters() :
+ exchangeInterval(0),
+ numExchanges(0),
+ randomSeed(-1)
+ {
+ };
+
+ int exchangeInterval; /* Interval in steps at which to attempt exchanges, 0 means no replica exchange */
+ int numExchanges; /* The number of exchanges to attempt at an exchange step */
+ int randomSeed; /* The random seed, -1 means generate a seed */
+};
/* Abstract type for replica exchange */
typedef struct gmx_repl_ex *gmx_repl_ex_t;
-gmx_repl_ex_t init_replica_exchange(FILE *fplog,
- const gmx_multisim_t *ms,
- const t_state *state,
- const t_inputrec *ir,
- int nst, int nmultiex, int init_seed);
-/* Should only be called on the master nodes */
+gmx_repl_ex_t
+init_replica_exchange(FILE *fplog,
+ const gmx_multisim_t *ms,
+ const t_state *state,
+ const t_inputrec *ir,
+ const ReplicaExchangeParameters &replExParams);
+/* Should only be called on the master ranks */
gmx_bool replica_exchange(FILE *fplog,
const t_commrec *cr,
t_state *state, gmx_enerdata_t *enerd,
t_state *state_local,
gmx_int64_t step, real time);
-/* Attempts replica exchange, should be called on all nodes.
+/* Attempts replica exchange, should be called on all ranks.
* Returns TRUE if this state has been exchanged.
* When running each replica in parallel,
- * this routine collects the state on the master node before exchange.
+ * this routine collects the state on the master rank before exchange.
* With domain decomposition, the global state after exchange is stored
- * in state and still needs to be redistributed over the nodes.
+ * in state and still needs to be redistributed over the ranks.
*/
void print_replica_exchange_statistics(FILE *fplog, gmx_repl_ex_t re);
-/* Should only be called on the master nodes */
+/* Should only be called on the master ranks */
#endif /* _repl_ex_h */
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <algorithm>
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/hardware/cpuinfo.h"
#include "gromacs/hardware/detecthardware.h"
-#include "gromacs/hardware/gpu_hw_info.h"
+#include "gromacs/hardware/hardwareassign.h"
#include "gromacs/hardware/hardwaretopology.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/topology/topology.h"
+#include "gromacs/utility/baseversion.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/logger.h"
#include "gromacs/utility/stringutil.h"
* and after a switch point doesn't change too much.
*/
+//! Constant used to help minimize preprocessed code
static const bool bHasOmpSupport = GMX_OPENMP;
#if GMX_THREAD_MPI
const int nthreads_omp_faster_default = 8;
const int nthreads_omp_faster_Nehalem = 12;
const int nthreads_omp_faster_Intel_AVX = 16;
+const int nthreads_omp_faster_AMD_Ryzen = 16;
/* For CPU only runs the fastest options are usually MPI or OpenMP only.
* With one GPU, using MPI only is almost never optimal, so we need to
* compare running pure OpenMP with combined MPI+OpenMP. This means higher
// Intel Nehalem
nth = nthreads_omp_faster_Nehalem;
}
+ else if (cpuInfo.vendor() == gmx::CpuInfo::Vendor::Amd && cpuInfo.family() >= 23)
+ {
+ // AMD Ryzen
+ nth = nthreads_omp_faster_AMD_Ryzen;
+ }
else
{
nth = nthreads_omp_faster_default;
}
/* Returns that maximum OpenMP thread count that passes the efficiency check */
-static int nthreads_omp_efficient_max(int gmx_unused nrank,
- const gmx::CpuInfo &cpuInfo,
- gmx_bool bUseGPU)
+gmx_unused static int nthreads_omp_efficient_max(int gmx_unused nrank,
+ const gmx::CpuInfo &cpuInfo,
+ gmx_bool bUseGPU)
{
#if GMX_OPENMP && GMX_MPI
if (nrank > 1)
/* Return the number of thread-MPI ranks to use.
* This is chosen such that we can always obey our own efficiency checks.
*/
-static int get_tmpi_omp_thread_division(const gmx_hw_info_t *hwinfo,
- const gmx_hw_opt_t *hw_opt,
- int nthreads_tot,
- int ngpu)
+gmx_unused static int get_tmpi_omp_thread_division(const gmx_hw_info_t *hwinfo,
+ const gmx_hw_opt_t &hw_opt,
+ int nthreads_tot,
+ int ngpu)
{
int nrank;
const gmx::CpuInfo &cpuInfo = *hwinfo->cpuInfo;
* If the user does not set the number of OpenMP threads, nthreads_omp==0 and
* this code has no effect.
*/
- GMX_RELEASE_ASSERT(hw_opt->nthreads_omp >= 0, "nthreads_omp is negative, but previous checks should have prevented this");
- while (nrank*hw_opt->nthreads_omp > hwinfo->nthreads_hw_avail && nrank > 1)
+ GMX_RELEASE_ASSERT(hw_opt.nthreads_omp >= 0, "nthreads_omp is negative, but previous checks should have prevented this");
+ while (nrank*hw_opt.nthreads_omp > hwinfo->nthreads_hw_avail && nrank > 1)
{
nrank--;
}
/* #thread < #gpu is very unlikely, but if so: waste gpu(s) */
nrank = nthreads_tot;
}
- else if (gmx_gpu_sharing_supported() &&
- (nthreads_tot > nthreads_omp_faster(cpuInfo, ngpu > 0) ||
- (ngpu > 1 && nthreads_tot/ngpu > nthreads_omp_mpi_target_max)))
+ else if (nthreads_tot > nthreads_omp_faster(cpuInfo, ngpu > 0) ||
+ (ngpu > 1 && nthreads_tot/ngpu > nthreads_omp_mpi_target_max))
{
/* The high OpenMP thread count will likely result in sub-optimal
* performance. Increase the rank count to reduce the thread count
(nthreads_tot/(ngpu*(nshare + 1)) >= nthreads_omp_mpi_ok_min_gpu && nthreads_tot % nrank != 0));
}
}
- else if (hw_opt->nthreads_omp > 0)
+ else if (hw_opt.nthreads_omp > 0)
{
/* Here we could oversubscribe, when we do, we issue a warning later */
- nrank = std::max(1, nthreads_tot/hw_opt->nthreads_omp);
+ nrank = std::max(1, nthreads_tot/hw_opt.nthreads_omp);
}
else
{
}
-static int getMaxGpuUsable(FILE *fplog, const t_commrec *cr, const gmx_hw_info_t *hwinfo,
- int cutoff_scheme, gmx_bool bUseGpu)
-{
- /* This code relies on the fact that GPU are not detected when GPU
- * acceleration was disabled at run time by the user.
- */
- if (cutoff_scheme == ecutsVERLET &&
- bUseGpu &&
- hwinfo->gpu_info.n_dev_compatible > 0)
- {
- if (gmx_multiple_gpu_per_node_supported())
- {
- return hwinfo->gpu_info.n_dev_compatible;
- }
- else
- {
- if (hwinfo->gpu_info.n_dev_compatible > 1)
- {
- md_print_warn(cr, fplog, "More than one compatible GPU is available, but GROMACS can only use one of them. Using a single thread-MPI rank.\n");
- }
- return 1;
- }
- }
- else
- {
- return 0;
- }
-}
-
-
#if GMX_THREAD_MPI
static bool
* Thus all options should be internally consistent and consistent
* with the hardware, except that ntmpi could be larger than #GPU.
*/
-int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
- gmx_hw_opt_t *hw_opt,
- const t_inputrec *inputrec,
- const gmx_mtop_t *mtop,
- const t_commrec *cr,
- FILE *fplog,
- gmx_bool bUseGpu,
- bool doMembed)
+int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
+ gmx_hw_opt_t *hw_opt,
+ int numPmeRanks,
+ bool nonbondedOnGpu,
+ const t_inputrec *inputrec,
+ const gmx_mtop_t *mtop,
+ const gmx::MDLogger &mdlog,
+ bool doMembed)
{
int nthreads_hw, nthreads_tot_max, nrank, ngpu;
int min_atoms_per_mpi_rank;
const gmx::CpuInfo &cpuInfo = *hwinfo->cpuInfo;
const gmx::HardwareTopology &hwTop = *hwinfo->hardwareTopology;
+ /* If the user made a GPU task assignment, that sets the number of thread-MPI ranks. */
+ auto userGpuTaskAssignment = gmx::parseGpuTaskAssignment(hw_opt->gpuIdTaskAssignment);
+ int numGpuIdsSupplied = static_cast<int>(userGpuTaskAssignment.size());
+
+ /* TODO Here we handle the case where the user set GPU IDs, and
+ further below we handle the case where the algorithm does not
+ support multiple ranks. We need also to handle the case where
+ the user set multiple GPU IDs for an algorithm that cannot
+ handle multiple ranks. */
+ if (hw_opt->nthreads_tmpi < 1 && numGpuIdsSupplied > 0)
+ {
+ /* If the user chose both mdrun -nt -gpu_id, is that consistent? */
+ if (numPmeRanks <= 0)
+ {
+ if (hw_opt->nthreads_tot > 0 &&
+ (hw_opt->nthreads_tot % numGpuIdsSupplied) != 0)
+ {
+ gmx_fatal(FARGS, "Cannot run %d total threads with %d GPU ranks. Choose the total number of threads to be a multiple of the number of GPU ranks.", hw_opt->nthreads_tot, numGpuIdsSupplied);
+ }
+ return numGpuIdsSupplied;
+ }
+ else
+ {
+ gmx_fatal(FARGS, "The combination of choosing a number of PME ranks, and specific GPU IDs "
+ "is not supported. Use also -ntmpi and/or -ntomp and -ntomp_pme to specify what "
+ "distribution of threads to ranks you require.");
+ }
+ }
+
{
/* Check if an algorithm does not support parallel simulation. */
// TODO This might work better if e.g. implemented algorithms
{
gmx_fatal(FARGS, "%s However, you asked for more than 1 thread-MPI rank, so mdrun cannot continue. Choose a single rank, or a different algorithm.", message.c_str());
}
- md_print_warn(cr, fplog, "%s Choosing to use only a single thread-MPI rank.", message.c_str());
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted("%s Choosing to use only a single thread-MPI rank.", message.c_str());
+
+ if (numGpuIdsSupplied > 1)
+ {
+ gmx_fatal(FARGS, "You supplied %d GPU IDs but only 1 rank can be used "
+ "by this simulation. Supply only one GPU ID.", numGpuIdsSupplied);
+ }
return 1;
}
}
if (hw_opt->nthreads_tmpi > 0)
{
- /* Trivial, return right away */
+ if (numPmeRanks <= 0)
+ {
+ int numPpRanks = hw_opt->nthreads_tmpi;
+ if ((numGpuIdsSupplied > 0) &&
+ (numGpuIdsSupplied != numPpRanks))
+ {
+ gmx_fatal(FARGS, "Cannot run %d thread-MPI total ranks with %d "
+ "GPU IDs supplied. The number of particle-particle (PP) ranks and the "
+ "number of GPU IDs must match.", hw_opt->nthreads_tmpi, numGpuIdsSupplied);
+ }
+ }
+ else
+ {
+ int numPpRanks = hw_opt->nthreads_tmpi - numPmeRanks;
+ if ((numGpuIdsSupplied > 0) &&
+ (numGpuIdsSupplied != numPpRanks))
+ {
+ gmx_fatal(FARGS, "Cannot run %d thread-MPI total ranks with %d PME ranks and %d "
+ "GPU IDs supplied. The number of particle-particle ranks and the "
+ "number of GPU IDs must match.", hw_opt->nthreads_tmpi, numPmeRanks, numGpuIdsSupplied);
+ }
+ }
+ /* Trivial, return the user's choice right away */
return hw_opt->nthreads_tmpi;
}
+ GMX_RELEASE_ASSERT(numGpuIdsSupplied == 0,
+ "If mdrun -gpu_id had information, the number of ranks should have already been chosen");
+ // Now implement automatic selection of number of thread-MPI ranks
nthreads_hw = hwinfo->nthreads_hw_avail;
if (nthreads_hw <= 0)
nthreads_tot_max = nthreads_hw;
}
- ngpu = getMaxGpuUsable(fplog, cr, hwinfo, inputrec->cutoff_scheme, bUseGpu);
+ /* nonbondedOnGpu might be false e.g. because this simulation uses
+ * the group scheme, or is a rerun with energy groups. */
+ ngpu = (nonbondedOnGpu ? hwinfo->gpu_info.n_dev_compatible : 0);
if (inputrec->cutoff_scheme == ecutsGROUP)
{
}
nrank =
- get_tmpi_omp_thread_division(hwinfo, hw_opt, nthreads_tot_max, ngpu);
+ get_tmpi_omp_thread_division(hwinfo, *hw_opt, nthreads_tot_max, ngpu);
if (inputrec->eI == eiNM || EI_TPI(inputrec->eI))
{
void check_resource_division_efficiency(const gmx_hw_info_t *hwinfo,
- const gmx_hw_opt_t *hw_opt,
+ int numTotalThreads,
+ bool willUsePhysicalGpu,
gmx_bool bNtOmpOptionSet,
t_commrec *cr,
- FILE *fplog)
+ const gmx::MDLogger &mdlog)
{
#if GMX_OPENMP && GMX_MPI
- int nth_omp_min, nth_omp_max, ngpu;
+ int nth_omp_min, nth_omp_max;
char buf[1000];
#if GMX_THREAD_MPI
const char *mpi_option = " (option -ntmpi)";
*/
#if GMX_THREAD_MPI
GMX_RELEASE_ASSERT(nthreads_omp_faster_default >= nthreads_omp_mpi_ok_max, "Inconsistent OpenMP thread count default values");
- GMX_RELEASE_ASSERT(hw_opt->nthreads_tmpi >= 1, "Must have at least one thread-MPI rank");
#endif
GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(emntDefault) >= 1, "Must have at least one OpenMP thread");
nth_omp_min = gmx_omp_nthreads_get(emntDefault);
nth_omp_max = gmx_omp_nthreads_get(emntDefault);
- ngpu = hw_opt->gpu_opt.n_dev_use;
+ bool anyRankIsUsingGpus = willUsePhysicalGpu;
/* Thread-MPI seems to have a bug with reduce on 1 node, so use a cond. */
if (cr->nnodes + cr->npmenodes > 1)
{
count[0] = -nth_omp_min;
count[1] = nth_omp_max;
- count[2] = ngpu;
+ count[2] = willUsePhysicalGpu;
MPI_Allreduce(count, count_max, 3, MPI_INT, MPI_MAX, cr->mpi_comm_mysim);
/* In case of an inhomogeneous run setup we use the maximum counts */
- nth_omp_min = -count_max[0];
- nth_omp_max = count_max[1];
- ngpu = count_max[2];
+ nth_omp_min = -count_max[0];
+ nth_omp_max = count_max[1];
+ anyRankIsUsingGpus = count_max[2] > 0;
}
int nthreads_omp_mpi_ok_min;
- if (ngpu == 0)
+ if (!anyRankIsUsingGpus)
{
nthreads_omp_mpi_ok_min = nthreads_omp_mpi_ok_min_cpu;
}
if (DOMAINDECOMP(cr) && cr->nnodes > 1)
{
if (nth_omp_max < nthreads_omp_mpi_ok_min ||
- (!(ngpu > 0 && !gmx_gpu_sharing_supported()) &&
- nth_omp_max > nthreads_omp_mpi_ok_max))
+ nth_omp_max > nthreads_omp_mpi_ok_max)
{
/* Note that we print target_max here, not ok_max */
sprintf(buf, "Your choice of number of MPI ranks and amount of resources results in using %d OpenMP threads per rank, which is most likely inefficient. The optimum is usually between %d and %d threads per rank.",
if (bNtOmpOptionSet)
{
- md_print_warn(cr, fplog, "NOTE: %s\n", buf);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted("NOTE: %s", buf);
}
else
{
const gmx::CpuInfo &cpuInfo = *hwinfo->cpuInfo;
/* No domain decomposition (or only one domain) */
- if (!(ngpu > 0 && !gmx_gpu_sharing_supported()) &&
- nth_omp_max > nthreads_omp_faster(cpuInfo, ngpu > 0))
+ if (nth_omp_max > nthreads_omp_faster(cpuInfo, anyRankIsUsingGpus))
{
/* To arrive here, the user/system set #ranks and/or #OMPthreads */
gmx_bool bEnvSet;
char buf2[256];
- bEnvSet = (getenv("OMP_NUM_THREADS") != NULL);
+ bEnvSet = (getenv("OMP_NUM_THREADS") != nullptr);
if (bNtOmpOptionSet || bEnvSet)
{
sprintf(buf2, "Your choice of %d MPI rank%s and the use of %d total threads %sleads to the use of %d OpenMP threads",
cr->nnodes + cr->npmenodes,
cr->nnodes + cr->npmenodes == 1 ? "" : "s",
- hw_opt->nthreads_tot > 0 ? hw_opt->nthreads_tot : hwinfo->nthreads_hw_avail,
+ numTotalThreads > 0 ? numTotalThreads : hwinfo->nthreads_hw_avail,
hwinfo->nphysicalnode > 1 ? "on a node " : "",
nth_omp_max);
}
*/
if (bNtOmpOptionSet || (bEnvSet && nth_omp_min != nth_omp_max))
{
- md_print_warn(cr, fplog, "NOTE: %s\n", buf);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted("NOTE: %s", buf);
}
else
{
}
#else /* GMX_OPENMP && GMX_MPI */
/* No OpenMP and/or MPI: it doesn't make much sense to check */
- GMX_UNUSED_VALUE(hw_opt);
GMX_UNUSED_VALUE(bNtOmpOptionSet);
+ GMX_UNUSED_VALUE(numTotalThreads);
+ GMX_UNUSED_VALUE(willUsePhysicalGpu);
+ GMX_UNUSED_VALUE(cr);
/* Check if we have more than 1 physical core, if detected,
* or more than 1 hardware thread if physical cores were not detected.
*/
-#if !GMX_OPENMP && !GMX_MPI
- if (hwinfo->hardwareTopology->numberOfCores() > 1)
+ if (!GMX_OPENMP && !GMX_MPI && hwinfo->hardwareTopology->numberOfCores() > 1)
{
- md_print_warn(cr, fplog, "NOTE: GROMACS was compiled without OpenMP and (thread-)MPI support, can only use a single CPU core\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText("NOTE: GROMACS was compiled without OpenMP and (thread-)MPI support, can only use a single CPU core");
}
-#else
- GMX_UNUSED_VALUE(hwinfo);
- GMX_UNUSED_VALUE(cr);
- GMX_UNUSED_VALUE(fplog);
-#endif
-
#endif /* GMX_OPENMP && GMX_MPI */
}
hw_opt->nthreads_tmpi,
hw_opt->nthreads_omp,
hw_opt->nthreads_omp_pme,
- hw_opt->gpu_opt.gpu_id != NULL ? hw_opt->gpu_opt.gpu_id : "");
+ hw_opt->gpuIdTaskAssignment.c_str());
}
/* Checks we can do when we don't (yet) know the cut-off scheme */
}
}
- if (hw_opt->nthreads_tot == 1)
+ if (hw_opt->nthreads_tot > 0)
{
- hw_opt->nthreads_tmpi = 1;
-
- if (hw_opt->nthreads_omp > 1)
+ if (hw_opt->nthreads_omp > hw_opt->nthreads_tot)
{
- gmx_fatal(FARGS, "You requested %d OpenMP threads with %d total threads",
- hw_opt->nthreads_tmpi, hw_opt->nthreads_tot);
+ gmx_fatal(FARGS, "You requested %d OpenMP threads with %d total threads. Choose a total number of threads that is a multiple of the number of OpenMP threads.",
+ hw_opt->nthreads_omp, hw_opt->nthreads_tot);
}
- hw_opt->nthreads_omp = 1;
- hw_opt->nthreads_omp_pme = 1;
- }
- /* Parse GPU IDs, if provided.
- * We check consistency with the tMPI thread count later.
- */
- gmx_parse_gpu_ids(&hw_opt->gpu_opt);
-
-#if GMX_THREAD_MPI
- if (hw_opt->gpu_opt.n_dev_use > 0 && hw_opt->nthreads_tmpi == 0)
- {
- /* Set the number of MPI threads equal to the number of GPUs */
- hw_opt->nthreads_tmpi = hw_opt->gpu_opt.n_dev_use;
-
- if (hw_opt->nthreads_tot > 0 &&
- hw_opt->nthreads_tmpi > hw_opt->nthreads_tot)
+ if (hw_opt->nthreads_tmpi > hw_opt->nthreads_tot)
{
- /* We have more GPUs than total threads requested.
- * We choose to (later) generate a mismatch error,
- * instead of launching more threads than requested.
- */
- hw_opt->nthreads_tmpi = hw_opt->nthreads_tot;
+ gmx_fatal(FARGS, "You requested %d thread-MPI ranks with %d total threads. Choose a total number of threads that is a multiple of the number of thread-MPI ranks.",
+ hw_opt->nthreads_tmpi, hw_opt->nthreads_tot);
}
}
-#endif
if (debug)
{
}
/* Checks we can do when we know the thread-MPI rank count */
-void check_and_update_hw_opt_3(gmx_hw_opt_t gmx_unused *hw_opt)
+void check_and_update_hw_opt_3(gmx_hw_opt_t *hw_opt)
{
#if GMX_THREAD_MPI
GMX_RELEASE_ASSERT(hw_opt->nthreads_tmpi >= 1, "Must have at least one thread-MPI rank");
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstdio>
+#include <vector>
+
#include "gromacs/utility/basedefinitions.h"
struct gmx_hw_info_t;
struct t_commrec;
struct t_inputrec;
+namespace gmx
+{
+class MDLogger;
+}
+
/* Return the number of threads to use for thread-MPI based on how many
* were requested, which algorithms we're using,
* and how many particles there are.
* with the hardware, except that ntmpi could be larger than #GPU.
* If necessary, this function will modify hw_opt->nthreads_omp.
*/
-int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
- gmx_hw_opt_t *hw_opt,
- const t_inputrec *inputrec,
- const gmx_mtop_t *mtop,
- const t_commrec *cr,
- FILE *fplog,
- gmx_bool bUseGpu,
- bool doMembed);
+int get_nthreads_mpi(const gmx_hw_info_t *hwinfo,
+ gmx_hw_opt_t *hw_opt,
+ int numPmeRanks,
+ bool nonbondedOnGpu,
+ const t_inputrec *inputrec,
+ const gmx_mtop_t *mtop,
+ const gmx::MDLogger &mdlog,
+ bool doMembed);
/* Check if the number of OpenMP threads is within reasonable range
* considering the hardware used. This is a crude check, but mainly
* This function should be called after thread-MPI and OpenMP are set up.
*/
void check_resource_division_efficiency(const gmx_hw_info_t *hwinfo,
- const gmx_hw_opt_t *hw_opt,
+ int numTotalThreads,
+ bool willUsePhysicalGpu,
gmx_bool bNtOmpOptionSet,
- struct t_commrec *cr,
- FILE *fplog);
+ t_commrec *cr,
+ const gmx::MDLogger &mdlog);
/* Checks we can do when we don't (yet) know the cut-off scheme */
void check_and_update_hw_opt_1(gmx_hw_opt_t *hw_opt,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "config.h"
-#include <assert.h>
-#include <signal.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cassert>
+#include <csignal>
+#include <cstdlib>
+#include <cstring>
#include <algorithm>
#include "gromacs/commandline/filenm.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
-#include "gromacs/essentialdynamics/edsam.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/fileio/checkpoint.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/fileio/tpxio.h"
-#include "gromacs/gmxlib/md_logging.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/cpuinfo.h"
#include "gromacs/hardware/detecthardware.h"
+#include "gromacs/hardware/hardwareassign.h"
+#include "gromacs/hardware/printhardware.h"
#include "gromacs/listed-forces/disre.h"
#include "gromacs/listed-forces/orires.h"
#include "gromacs/math/calculate-ewald-splitting-coefficient.h"
#include "gromacs/mdlib/mdatoms.h"
#include "gromacs/mdlib/mdrun.h"
#include "gromacs/mdlib/minimize.h"
+#include "gromacs/mdlib/nb_verlet.h"
#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_tuning.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdlib/sighandler.h"
#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/tpi.h"
+#include "gromacs/mdrunutility/mdmodules.h"
#include "gromacs/mdrunutility/threadaffinity.h"
#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/edsamhistory.h"
+#include "gromacs/mdtypes/energyhistory.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/observableshistory.h"
#include "gromacs/mdtypes/state.h"
+#include "gromacs/mdtypes/swaphistory.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pulling/pull.h"
#include "gromacs/pulling/pull_rotation.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/filestream.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/logger.h"
+#include "gromacs/utility/loggerbuilder.h"
#include "gromacs/utility/pleasecite.h"
+#include "gromacs/utility/programcontext.h"
#include "gromacs/utility/smalloc.h"
#include "deform.h"
#define MIN_ATOMS_PER_MPI_THREAD 90
#define MIN_ATOMS_PER_GPU 900
-struct mdrunner_arglist
-{
- gmx_hw_opt_t hw_opt;
- FILE *fplog;
- t_commrec *cr;
- int nfile;
- const t_filenm *fnm;
- const gmx_output_env_t *oenv;
- gmx_bool bVerbose;
- int nstglobalcomm;
- ivec ddxyz;
- int dd_rank_order;
- int npme;
- real rdd;
- real rconstr;
- const char *dddlb_opt;
- real dlb_scale;
- const char *ddcsx;
- const char *ddcsy;
- const char *ddcsz;
- const char *nbpu_opt;
- int nstlist_cmdline;
- gmx_int64_t nsteps_cmdline;
- int nstepout;
- int resetstep;
- int nmultisim;
- int repl_ex_nst;
- int repl_ex_nex;
- int repl_ex_seed;
- real pforce;
- real cpt_period;
- real max_hours;
- int imdport;
- unsigned long Flags;
-};
-
-
-/* The function used for spawning threads. Extracts the mdrunner()
- arguments from its one argument and calls mdrunner(), after making
- a commrec. */
-static void mdrunner_start_fn(void *arg)
+namespace gmx
{
- try
- {
- struct mdrunner_arglist *mda = (struct mdrunner_arglist*)arg;
- struct mdrunner_arglist mc = *mda; /* copy the arg list to make sure
- that it's thread-local. This doesn't
- copy pointed-to items, of course,
- but those are all const. */
- t_commrec *cr; /* we need a local version of this */
- FILE *fplog = NULL;
- t_filenm *fnm;
- fnm = dup_tfn(mc.nfile, mc.fnm);
+void Mdrunner::reinitializeOnSpawnedThread()
+{
+ // TODO This duplication is formally necessary if any thread might
+ // modify any memory in fnm or the pointers it contains. If the
+ // contents are ever provably const, then we can remove this
+ // allocation (and memory leak).
+ // TODO This should probably become part of a copy constructor for
+ // Mdrunner.
+ fnm = dup_tfn(nfile, fnm);
- cr = reinitialize_commrec_for_this_thread(mc.cr);
+ cr = reinitialize_commrec_for_this_thread(cr);
- if (MASTER(cr))
- {
- fplog = mc.fplog;
- }
+ if (!MASTER(cr))
+ {
+ // Only the master rank writes to the log files
+ fplog = nullptr;
+ }
+}
- gmx::mdrunner(&mc.hw_opt, fplog, cr, mc.nfile, fnm, mc.oenv,
- mc.bVerbose, mc.nstglobalcomm,
- mc.ddxyz, mc.dd_rank_order, mc.npme, mc.rdd,
- mc.rconstr, mc.dddlb_opt, mc.dlb_scale,
- mc.ddcsx, mc.ddcsy, mc.ddcsz,
- mc.nbpu_opt, mc.nstlist_cmdline,
- mc.nsteps_cmdline, mc.nstepout, mc.resetstep,
- mc.nmultisim, mc.repl_ex_nst, mc.repl_ex_nex, mc.repl_ex_seed, mc.pforce,
- mc.cpt_period, mc.max_hours, mc.imdport, mc.Flags);
+/*! \brief The callback used for running on spawned threads.
+ *
+ * Obtains the pointer to the master mdrunner object from the one
+ * argument permitted to the thread-launch API call, copies it to make
+ * a new runner for this thread, reinitializes necessary data, and
+ * proceeds to the simulation. */
+static void mdrunner_start_fn(void *arg)
+{
+ try
+ {
+ auto masterMdrunner = reinterpret_cast<const gmx::Mdrunner *>(arg);
+ /* copy the arg list to make sure that it's thread-local. This
+ doesn't copy pointed-to items, of course, but those are all
+ const. */
+ gmx::Mdrunner mdrunner = *masterMdrunner;
+ mdrunner.reinitializeOnSpawnedThread();
+ mdrunner.mdrunner();
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
-/* called by mdrunner() to start a specific number of threads (including
- the main thread) for thread-parallel runs. This in turn calls mdrunner()
- for each thread.
- All options besides nthreads are the same as for mdrunner(). */
-static t_commrec *mdrunner_start_threads(gmx_hw_opt_t *hw_opt,
- FILE *fplog, t_commrec *cr, int nfile,
- const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
- ivec ddxyz, int dd_rank_order, int npme,
- real rdd, real rconstr,
- const char *dddlb_opt, real dlb_scale,
- const char *ddcsx, const char *ddcsy, const char *ddcsz,
- const char *nbpu_opt, int nstlist_cmdline,
- gmx_int64_t nsteps_cmdline,
- int nstepout, int resetstep,
- int nmultisim, int repl_ex_nst, int repl_ex_nex, int repl_ex_seed,
- real pforce, real cpt_period, real max_hours,
- unsigned long Flags)
+/*! \brief Start thread-MPI threads.
+ *
+ * Called by mdrunner() to start a specific number of threads
+ * (including the main thread) for thread-parallel runs. This in turn
+ * calls mdrunner() for each thread. All options are the same as for
+ * mdrunner(). */
+t_commrec *Mdrunner::spawnThreads(int numThreadsToLaunch)
{
- int ret;
- struct mdrunner_arglist *mda;
- t_commrec *crn; /* the new commrec */
- t_filenm *fnmn;
/* first check whether we even need to start tMPI */
- if (hw_opt->nthreads_tmpi < 2)
+ if (numThreadsToLaunch < 2)
{
return cr;
}
- /* a few small, one-time, almost unavoidable memory leaks: */
- snew(mda, 1);
- fnmn = dup_tfn(nfile, fnm);
-
- /* fill the data structure to pass as void pointer to thread start fn */
- /* hw_opt contains pointers, which should all be NULL at this stage */
- mda->hw_opt = *hw_opt;
- mda->fplog = fplog;
- mda->cr = cr;
- mda->nfile = nfile;
- mda->fnm = fnmn;
- mda->oenv = oenv;
- mda->bVerbose = bVerbose;
- mda->nstglobalcomm = nstglobalcomm;
- mda->ddxyz[XX] = ddxyz[XX];
- mda->ddxyz[YY] = ddxyz[YY];
- mda->ddxyz[ZZ] = ddxyz[ZZ];
- mda->dd_rank_order = dd_rank_order;
- mda->npme = npme;
- mda->rdd = rdd;
- mda->rconstr = rconstr;
- mda->dddlb_opt = dddlb_opt;
- mda->dlb_scale = dlb_scale;
- mda->ddcsx = ddcsx;
- mda->ddcsy = ddcsy;
- mda->ddcsz = ddcsz;
- mda->nbpu_opt = nbpu_opt;
- mda->nstlist_cmdline = nstlist_cmdline;
- mda->nsteps_cmdline = nsteps_cmdline;
- mda->nstepout = nstepout;
- mda->resetstep = resetstep;
- mda->nmultisim = nmultisim;
- mda->repl_ex_nst = repl_ex_nst;
- mda->repl_ex_nex = repl_ex_nex;
- mda->repl_ex_seed = repl_ex_seed;
- mda->pforce = pforce;
- mda->cpt_period = cpt_period;
- mda->max_hours = max_hours;
- mda->Flags = Flags;
+ gmx::Mdrunner spawnedMdrunner = *this;
+ // TODO This duplication is formally necessary if any thread might
+ // modify any memory in fnm or the pointers it contains. If the
+ // contents are ever provably const, then we can remove this
+ // allocation (and memory leak).
+ // TODO This should probably become part of a copy constructor for
+ // Mdrunner.
+ spawnedMdrunner.fnm = dup_tfn(this->nfile, fnm);
/* now spawn new threads that start mdrunner_start_fn(), while
the main thread returns, we set thread affinity later */
- ret = tMPI_Init_fn(TRUE, hw_opt->nthreads_tmpi, TMPI_AFFINITY_NONE,
- mdrunner_start_fn, (void*)(mda) );
- if (ret != TMPI_SUCCESS)
+ if (tMPI_Init_fn(TRUE, numThreadsToLaunch, TMPI_AFFINITY_NONE,
+ mdrunner_start_fn, static_cast<void*>(&spawnedMdrunner)) != TMPI_SUCCESS)
{
- return NULL;
+ GMX_THROW(gmx::InternalError("Failed to spawn thread-MPI threads"));
}
- crn = reinitialize_commrec_for_this_thread(cr);
- return crn;
+ return reinitialize_commrec_for_this_thread(cr);
}
-#endif /* GMX_THREAD_MPI */
-
-
-/*! \brief Cost of non-bonded kernels
- *
- * We determine the extra cost of the non-bonded kernels compared to
- * a reference nstlist value of 10 (which is the default in grompp).
- */
-static const int nbnxnReferenceNstlist = 10;
-//! The values to try when switching
-const int nstlist_try[] = { 20, 25, 40 };
-//! Number of elements in the neighborsearch list trials.
-#define NNSTL sizeof(nstlist_try)/sizeof(nstlist_try[0])
-/* Increase nstlist until the non-bonded cost increases more than listfac_ok,
- * but never more than listfac_max.
- * A standard (protein+)water system at 300K with PME ewald_rtol=1e-5
- * needs 1.28 at rcoulomb=0.9 and 1.24 at rcoulomb=1.0 to get to nstlist=40.
- * Note that both CPU and GPU factors are conservative. Performance should
- * not go down due to this tuning, except with a relatively slow GPU.
- * On the other hand, at medium/high parallelization or with fast GPUs
- * nstlist will not be increased enough to reach optimal performance.
- */
-/* CPU: pair-search is about a factor 1.5 slower than the non-bonded kernel */
-//! Max OK performance ratio beween force calc and neighbor searching
-static const float nbnxn_cpu_listfac_ok = 1.05;
-//! Too high performance ratio beween force calc and neighbor searching
-static const float nbnxn_cpu_listfac_max = 1.09;
-/* CPU: pair-search is about a factor 2-3 slower than the non-bonded kernel */
-//! Max OK performance ratio beween force calc and neighbor searching
-static const float nbnxn_knl_listfac_ok = 1.22;
-//! Too high performance ratio beween force calc and neighbor searching
-static const float nbnxn_knl_listfac_max = 1.3;
-/* GPU: pair-search is a factor 1.5-3 slower than the non-bonded kernel */
-//! Max OK performance ratio beween force calc and neighbor searching
-static const float nbnxn_gpu_listfac_ok = 1.20;
-//! Too high performance ratio beween force calc and neighbor searching
-static const float nbnxn_gpu_listfac_max = 1.30;
-
-/*! \brief Try to increase nstlist when using the Verlet cut-off scheme */
-static void increase_nstlist(FILE *fp, t_commrec *cr,
- t_inputrec *ir, int nstlist_cmdline,
- const gmx_mtop_t *mtop, matrix box,
- gmx_bool bGPU, const gmx::CpuInfo &cpuinfo)
-{
- float listfac_ok, listfac_max;
- int nstlist_orig, nstlist_prev;
- verletbuf_list_setup_t ls;
- real rlistWithReferenceNstlist, rlist_inc, rlist_ok, rlist_max;
- real rlist_new, rlist_prev;
- size_t nstlist_ind = 0;
- t_state state_tmp;
- gmx_bool bBox, bDD, bCont;
- const char *nstl_gpu = "\nFor optimal performance with a GPU nstlist (now %d) should be larger.\nThe optimum depends on your CPU and GPU resources.\nYou might want to try several nstlist values.\n";
- const char *nve_err = "Can not increase nstlist because an NVE ensemble is used";
- const char *vbd_err = "Can not increase nstlist because verlet-buffer-tolerance is not set or used";
- const char *box_err = "Can not increase nstlist because the box is too small";
- const char *dd_err = "Can not increase nstlist because of domain decomposition limitations";
- char buf[STRLEN];
-
- if (nstlist_cmdline <= 0)
- {
- if (ir->nstlist == 1)
- {
- /* The user probably set nstlist=1 for a reason,
- * don't mess with the settings.
- */
- return;
- }
-
- if (fp != NULL && bGPU && ir->nstlist < nstlist_try[0])
- {
- fprintf(fp, nstl_gpu, ir->nstlist);
- }
- nstlist_ind = 0;
- while (nstlist_ind < NNSTL && ir->nstlist >= nstlist_try[nstlist_ind])
- {
- nstlist_ind++;
- }
- if (nstlist_ind == NNSTL)
- {
- /* There are no larger nstlist value to try */
- return;
- }
- }
-
- if (EI_MD(ir->eI) && ir->etc == etcNO)
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "%s\n", nve_err);
- }
- if (fp != NULL)
- {
- fprintf(fp, "%s\n", nve_err);
- }
-
- return;
- }
-
- if (ir->verletbuf_tol == 0 && bGPU)
- {
- gmx_fatal(FARGS, "You are using an old tpr file with a GPU, please generate a new tpr file with an up to date version of grompp");
- }
-
- if (ir->verletbuf_tol < 0)
- {
- if (MASTER(cr))
- {
- fprintf(stderr, "%s\n", vbd_err);
- }
- if (fp != NULL)
- {
- fprintf(fp, "%s\n", vbd_err);
- }
-
- return;
- }
-
- if (bGPU)
- {
- listfac_ok = nbnxn_gpu_listfac_ok;
- listfac_max = nbnxn_gpu_listfac_max;
- }
- else if (cpuinfo.feature(gmx::CpuInfo::Feature::X86_Avx512ER))
- {
- listfac_ok = nbnxn_knl_listfac_ok;
- listfac_max = nbnxn_knl_listfac_max;
- }
- else
- {
- listfac_ok = nbnxn_cpu_listfac_ok;
- listfac_max = nbnxn_cpu_listfac_max;
- }
-
- nstlist_orig = ir->nstlist;
- if (nstlist_cmdline > 0)
- {
- if (fp)
- {
- sprintf(buf, "Getting nstlist=%d from command line option",
- nstlist_cmdline);
- }
- ir->nstlist = nstlist_cmdline;
- }
-
- verletbuf_get_list_setup(TRUE, bGPU, &ls);
+} // namespace
- /* Allow rlist to make the list a given factor larger than the list
- * would be with the reference value for nstlist (10).
- */
- nstlist_prev = ir->nstlist;
- ir->nstlist = nbnxnReferenceNstlist;
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL,
- &rlistWithReferenceNstlist);
- ir->nstlist = nstlist_prev;
-
- /* Determine the pair list size increase due to zero interactions */
- rlist_inc = nbnxn_get_rlist_effective_inc(ls.cluster_size_j,
- mtop->natoms/det(box));
- rlist_ok = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_ok) - rlist_inc;
- rlist_max = (rlistWithReferenceNstlist + rlist_inc)*std::cbrt(listfac_max) - rlist_inc;
- if (debug)
- {
- fprintf(debug, "nstlist tuning: rlist_inc %.3f rlist_ok %.3f rlist_max %.3f\n",
- rlist_inc, rlist_ok, rlist_max);
- }
-
- nstlist_prev = nstlist_orig;
- rlist_prev = ir->rlist;
- do
- {
- if (nstlist_cmdline <= 0)
- {
- ir->nstlist = nstlist_try[nstlist_ind];
- }
-
- /* Set the pair-list buffer size in ir */
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL, &rlist_new);
-
- /* Does rlist fit in the box? */
- bBox = (gmx::square(rlist_new) < max_cutoff2(ir->ePBC, box));
- bDD = TRUE;
- if (bBox && DOMAINDECOMP(cr))
- {
- /* Check if rlist fits in the domain decomposition */
- if (inputrec2nboundeddim(ir) < DIM)
- {
- gmx_incons("Changing nstlist with domain decomposition and unbounded dimensions is not implemented yet");
- }
- copy_mat(box, state_tmp.box);
- bDD = change_dd_cutoff(cr, &state_tmp, ir, rlist_new);
- }
-
- if (debug)
- {
- fprintf(debug, "nstlist %d rlist %.3f bBox %d bDD %d\n",
- ir->nstlist, rlist_new, bBox, bDD);
- }
-
- bCont = FALSE;
-
- if (nstlist_cmdline <= 0)
- {
- if (bBox && bDD && rlist_new <= rlist_max)
- {
- /* Increase nstlist */
- nstlist_prev = ir->nstlist;
- rlist_prev = rlist_new;
- bCont = (nstlist_ind+1 < NNSTL && rlist_new < rlist_ok);
- }
- else
- {
- /* Stick with the previous nstlist */
- ir->nstlist = nstlist_prev;
- rlist_new = rlist_prev;
- bBox = TRUE;
- bDD = TRUE;
- }
- }
-
- nstlist_ind++;
- }
- while (bCont);
-
- if (!bBox || !bDD)
- {
- gmx_warning(!bBox ? box_err : dd_err);
- if (fp != NULL)
- {
- fprintf(fp, "\n%s\n", bBox ? box_err : dd_err);
- }
- ir->nstlist = nstlist_orig;
- }
- else if (ir->nstlist != nstlist_orig || rlist_new != ir->rlist)
- {
- sprintf(buf, "Changing nstlist from %d to %d, rlist from %g to %g",
- nstlist_orig, ir->nstlist,
- ir->rlist, rlist_new);
- if (MASTER(cr))
- {
- fprintf(stderr, "%s\n\n", buf);
- }
- if (fp != NULL)
- {
- fprintf(fp, "%s\n\n", buf);
- }
- ir->rlist = rlist_new;
- }
-}
+#endif /* GMX_THREAD_MPI */
/*! \brief Initialize variables for Verlet scheme simulation */
static void prepare_verlet_scheme(FILE *fplog,
t_inputrec *ir,
int nstlist_cmdline,
const gmx_mtop_t *mtop,
- matrix box,
- gmx_bool bUseGPU,
+ const matrix box,
+ bool makeGpuPairList,
const gmx::CpuInfo &cpuinfo)
{
/* For NVE simulations, we will retain the initial list buffer */
* calc_verlet_buffer_size gives the same results for 4x8 and 4x4
* and 4x2 gives a larger buffer than 4x4, this is ok.
*/
- verletbuf_get_list_setup(TRUE, bUseGPU, &ls);
+ verletbuf_get_list_setup(true, makeGpuPairList, &ls);
- calc_verlet_buffer_size(mtop, det(box), ir, -1, &ls, NULL, &rlist_new);
+ calc_verlet_buffer_size(mtop, det(box), ir, ir->nstlist, ir->nstlist - 1, -1, &ls, nullptr, &rlist_new);
if (rlist_new != ir->rlist)
{
- if (fplog != NULL)
+ if (fplog != nullptr)
{
fprintf(fplog, "\nChanging rlist from %g to %g for non-bonded %dx%d atom kernels\n\n",
ir->rlist, rlist_new,
if (EI_DYNAMICS(ir->eI))
{
/* Set or try nstlist values */
- increase_nstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, bUseGPU, cpuinfo);
+ increaseNstlist(fplog, cr, ir, nstlist_cmdline, mtop, box, makeGpuPairList, cpuinfo);
}
}
*
* with value passed on the command line (if any)
*/
-static void override_nsteps_cmdline(FILE *fplog,
- gmx_int64_t nsteps_cmdline,
- t_inputrec *ir,
- const t_commrec *cr)
+static void override_nsteps_cmdline(const gmx::MDLogger &mdlog,
+ gmx_int64_t nsteps_cmdline,
+ t_inputrec *ir)
{
assert(ir);
- assert(cr);
/* override with anything else than the default -2 */
if (nsteps_cmdline > -2)
gmx_step_str(nsteps_cmdline, sbuf_steps));
}
- md_print_warn(cr, fplog, "%s\n", sbuf_msg);
+ GMX_LOG(mdlog.warning).asParagraph().appendText(sbuf_msg);
}
else if (nsteps_cmdline < -2)
{
namespace gmx
{
+//! Halt the run if there are inconsistences between user choices to run with GPUs and/or hardware detection.
+static void exitIfCannotForceGpuRun(bool requirePhysicalGpu,
+ EmulateGpuNonbonded emulateGpuNonbonded,
+ bool useVerletScheme,
+ bool compatibleGpusFound)
+{
+ /* Was GPU acceleration either explicitly (-nb gpu) or implicitly
+ * (gpu ID passed) requested? */
+ if (!requirePhysicalGpu)
+ {
+ return;
+ }
+
+ if (GMX_GPU == GMX_GPU_NONE)
+ {
+ gmx_fatal(FARGS, "GPU acceleration requested, but %s was compiled without GPU support!",
+ gmx::getProgramContext().displayName());
+ }
+
+ if (emulateGpuNonbonded == EmulateGpuNonbonded::Yes)
+ {
+ gmx_fatal(FARGS, "GPU emulation cannot be requested together with GPU acceleration!");
+ }
+
+ if (!useVerletScheme)
+ {
+ gmx_fatal(FARGS, "GPU acceleration requested, but can't be used without cutoff-scheme=Verlet");
+ }
+
+ if (!compatibleGpusFound)
+ {
+ gmx_fatal(FARGS, "GPU acceleration requested, but no compatible GPUs were detected.");
+ }
+}
+
+/*! \brief Return whether GPU acceleration is useful with the given settings.
+ *
+ * If not, logs a message about falling back to CPU code. */
+static bool gpuAccelerationIsUseful(const MDLogger &mdlog,
+ const t_inputrec *ir,
+ bool doRerun)
+{
+ if (doRerun && ir->opts.ngener > 1)
+ {
+ /* Rerun execution time is dominated by I/O and pair search,
+ * so GPUs are not very useful, plus they do not support more
+ * than one energy group. If the user requested GPUs
+ * explicitly, a fatal error is given later. With non-reruns,
+ * we fall back to a single whole-of system energy group
+ * (which runs much faster than a multiple-energy-groups
+ * implementation would), and issue a note in the .log
+ * file. Users can re-run if they want the information. */
+ GMX_LOG(mdlog.warning).asParagraph().appendText("Multiple energy groups is not implemented for GPUs, so is not useful for this rerun, so falling back to the CPU");
+ return false;
+ }
+
+ return true;
+}
+
//! \brief Return the correct integrator function.
static integrator_t *my_integrator(unsigned int ei)
{
}
}
-int mdrunner(gmx_hw_opt_t *hw_opt,
- FILE *fplog, t_commrec *cr, int nfile,
- const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm,
- ivec ddxyz, int dd_rank_order, int npme, real rdd, real rconstr,
- const char *dddlb_opt, real dlb_scale,
- const char *ddcsx, const char *ddcsy, const char *ddcsz,
- const char *nbpu_opt, int nstlist_cmdline,
- gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
- int gmx_unused nmultisim, int repl_ex_nst, int repl_ex_nex,
- int repl_ex_seed, real pforce, real cpt_period, real max_hours,
- int imdport, unsigned long Flags)
+//! Initializes the logger for mdrun.
+static gmx::LoggerOwner buildLogger(FILE *fplog, const t_commrec *cr)
+{
+ gmx::LoggerBuilder builder;
+ if (fplog != nullptr)
+ {
+ builder.addTargetFile(gmx::MDLogger::LogLevel::Info, fplog);
+ }
+ if (cr == nullptr || SIMMASTER(cr))
+ {
+ builder.addTargetStream(gmx::MDLogger::LogLevel::Warning,
+ &gmx::TextOutputFile::standardError());
+ }
+ return builder.build();
+}
+
+int Mdrunner::mdrunner()
{
- gmx_bool bForceUseGPU, bTryUseGPU, bRerunMD;
- t_inputrec *inputrec;
- t_state *state = NULL;
matrix box;
gmx_ddbox_t ddbox = {0};
int npme_major, npme_minor;
t_nrnb *nrnb;
- gmx_mtop_t *mtop = NULL;
- t_mdatoms *mdatoms = NULL;
- t_forcerec *fr = NULL;
- t_fcdata *fcd = NULL;
+ gmx_mtop_t *mtop = nullptr;
+ t_mdatoms *mdatoms = nullptr;
+ t_forcerec *fr = nullptr;
+ t_fcdata *fcd = nullptr;
real ewaldcoeff_q = 0;
real ewaldcoeff_lj = 0;
- struct gmx_pme_t **pmedata = NULL;
- gmx_vsite_t *vsite = NULL;
+ struct gmx_pme_t **pmedata = nullptr;
+ gmx_vsite_t *vsite = nullptr;
gmx_constr_t constr;
int nChargePerturbed = -1, nTypePerturbed = 0, status;
gmx_wallcycle_t wcycle;
- gmx_walltime_accounting_t walltime_accounting = NULL;
+ gmx_walltime_accounting_t walltime_accounting = nullptr;
int rc;
gmx_int64_t reset_counters;
- gmx_edsam_t ed = NULL;
int nthreads_pme = 1;
- gmx_membed_t * membed = NULL;
- gmx_hw_info_t *hwinfo = NULL;
- /* The master rank decides early on bUseGPU and broadcasts this later */
- gmx_bool bUseGPU = FALSE;
+ gmx_membed_t * membed = nullptr;
+ gmx_hw_info_t *hwinfo = nullptr;
/* CAUTION: threads may be started later on in this function, so
cr doesn't reflect the final parallel state right now */
- snew(inputrec, 1);
+ gmx::MDModules mdModules;
+ t_inputrec inputrecInstance;
+ t_inputrec *inputrec = &inputrecInstance;
snew(mtop, 1);
- if (Flags & MD_APPENDFILES)
+ if (mdrunOptions.continuationOptions.appendFiles)
{
- fplog = NULL;
+ fplog = nullptr;
}
bool doMembed = opt2bSet("-membed", nfile, fnm);
- bRerunMD = (Flags & MD_RERUN);
- bForceUseGPU = (strncmp(nbpu_opt, "gpu", 3) == 0);
- bTryUseGPU = (strncmp(nbpu_opt, "auto", 4) == 0) || bForceUseGPU;
+ bool doRerun = mdrunOptions.rerun;
+
+ /* Handle GPU-related user options. Later, we check consistency
+ * with things like whether support is compiled, or tMPI thread
+ * count. */
+ EmulateGpuNonbonded emulateGpuNonbonded = (getenv("GMX_EMULATE_GPU") != nullptr ?
+ EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
+ bool forceUseCpu = (strncmp(nbpu_opt, "cpu", 3) == 0);
+ if (!hw_opt.gpuIdTaskAssignment.empty() && forceUseCpu)
+ {
+ gmx_fatal(FARGS, "GPU IDs were specified, and short-ranged interactions were assigned to the CPU. Make no more than one of these choices.");
+ }
+ bool forceUsePhysicalGpu = (strncmp(nbpu_opt, "gpu", 3) == 0) || !hw_opt.gpuIdTaskAssignment.empty();
+ bool tryUsePhysicalGpu = (strncmp(nbpu_opt, "auto", 4) == 0) && hw_opt.gpuIdTaskAssignment.empty() && (emulateGpuNonbonded == EmulateGpuNonbonded::No);
+ GMX_RELEASE_ASSERT(!(forceUsePhysicalGpu && tryUsePhysicalGpu), "Must either force use of "
+ "GPUs for short-ranged interactions, or try to use them, not both.");
+
+ // Here we assume that SIMMASTER(cr) does not change even after the
+ // threads are started.
+ gmx::LoggerOwner logOwner(buildLogger(fplog, cr));
+ gmx::MDLogger mdlog(logOwner.logger());
- /* Detect hardware, gather information. This is an operation that is
- * global for this process (MPI rank). */
- hwinfo = gmx_detect_hardware(fplog, cr, bTryUseGPU);
+ hwinfo = gmx_detect_hardware(mdlog, cr);
- gmx_print_detected_hardware(fplog, cr, hwinfo);
+ gmx_print_detected_hardware(fplog, cr, mdlog, hwinfo);
- if (fplog != NULL)
+ if (fplog != nullptr)
{
/* Print references after all software/hardware printing */
please_cite(fplog, "Abraham2015");
please_cite(fplog, "Berendsen95a");
}
- snew(state, 1);
+ // TODO state should be nullptr on non-master ranks, and perhaps call it globalState
+ std::unique_ptr<t_state> stateInstance = std::unique_ptr<t_state>(new t_state);
+ t_state * state = stateInstance.get();
+
if (SIMMASTER(cr))
{
/* Read (nearly) all data required for the simulation */
read_tpx_state(ftp2fn(efTPR, nfile, fnm), inputrec, state, mtop);
+ exitIfCannotForceGpuRun(forceUsePhysicalGpu,
+ emulateGpuNonbonded,
+ inputrec->cutoff_scheme == ecutsVERLET,
+ compatibleGpusFound(hwinfo->gpu_info));
+
if (inputrec->cutoff_scheme == ecutsVERLET)
{
- /* Here the master rank decides if all ranks will use GPUs */
- bUseGPU = (hwinfo->gpu_info.n_dev_compatible > 0 ||
- getenv("GMX_EMULATE_GPU") != NULL);
-
- /* TODO add GPU kernels for this and replace this check by:
- * (bUseGPU && (ir->vdwtype == evdwPME &&
- * ir->ljpme_combination_rule == eljpmeLB))
- * update the message text and the content of nbnxn_acceleration_supported.
- */
- if (bUseGPU &&
- !nbnxn_gpu_acceleration_supported(fplog, cr, inputrec, bRerunMD))
+ /* TODO This logic could run later, e.g. before -npme -1
+ is handled. If inputrec has already been communicated,
+ then the resulting tryUsePhysicalGpu does not need to
+ be communicated. */
+ if ((tryUsePhysicalGpu || forceUsePhysicalGpu) &&
+ !gpuAccelerationIsUseful(mdlog, inputrec, doRerun))
{
/* Fallback message printed by nbnxn_acceleration_supported */
- if (bForceUseGPU)
+ if (forceUsePhysicalGpu)
{
gmx_fatal(FARGS, "GPU acceleration requested, but not supported with the given input settings");
}
- bUseGPU = FALSE;
+ tryUsePhysicalGpu = false;
}
-
- prepare_verlet_scheme(fplog, cr,
- inputrec, nstlist_cmdline, mtop, state->box,
- bUseGPU, *hwinfo->cpuInfo);
}
else
{
gmx_fatal(FARGS, "Can not set nstlist with the group cut-off scheme");
}
- if (hwinfo->gpu_info.n_dev_compatible > 0)
+ if (compatibleGpusFound(hwinfo->gpu_info))
{
- md_print_warn(cr, fplog,
- "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
- " To use a GPU, set the mdp option: cutoff-scheme = Verlet\n");
+ GMX_LOG(mdlog.warning).asParagraph().appendText(
+ "NOTE: GPU(s) found, but the current simulation can not use GPUs\n"
+ " To use a GPU, set the mdp option: cutoff-scheme = Verlet");
}
-
- if (bForceUseGPU)
- {
- gmx_fatal(FARGS, "GPU requested, but can't be used without cutoff-scheme=Verlet");
- }
-
-#if GMX_TARGET_BGQ
- md_print_warn(cr, fplog,
- "NOTE: There is no SIMD implementation of the group scheme kernels on\n"
- " BlueGene/Q. You will observe better performance from using the\n"
- " Verlet cut-off scheme.\n");
-#endif
+ tryUsePhysicalGpu = false;
}
}
+ bool nonbondedOnGpu = (tryUsePhysicalGpu || forceUsePhysicalGpu) && compatibleGpusFound(hwinfo->gpu_info);
/* Check and update the hardware options for internal consistency */
- check_and_update_hw_opt_1(hw_opt, cr, npme);
+ check_and_update_hw_opt_1(&hw_opt, cr, domdecOptions.numPmeRanks);
/* Early check for externally set process affinity. */
- gmx_check_thread_affinity_set(fplog, cr,
- hw_opt, hwinfo->nthreads_hw_avail, FALSE);
+ gmx_check_thread_affinity_set(mdlog, cr,
+ &hw_opt, hwinfo->nthreads_hw_avail, FALSE);
#if GMX_THREAD_MPI
if (SIMMASTER(cr))
{
- if (npme > 0 && hw_opt->nthreads_tmpi <= 0)
+ if (domdecOptions.numPmeRanks > 0 && hw_opt.nthreads_tmpi <= 0)
{
gmx_fatal(FARGS, "You need to explicitly specify the number of MPI threads (-ntmpi) when using separate PME ranks");
}
* This is done later for normal MPI and also once more with tMPI
* for all tMPI ranks.
*/
- check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
-
- /* NOW the threads will be started: */
- hw_opt->nthreads_tmpi = get_nthreads_mpi(hwinfo,
- hw_opt,
- inputrec, mtop,
- cr, fplog, bUseGPU,
- doMembed);
-
- if (hw_opt->nthreads_tmpi > 1)
- {
- t_commrec *cr_old = cr;
- /* now start the threads. */
- cr = mdrunner_start_threads(hw_opt, fplog, cr_old, nfile, fnm,
- oenv, bVerbose, nstglobalcomm,
- ddxyz, dd_rank_order, npme, rdd, rconstr,
- dddlb_opt, dlb_scale, ddcsx, ddcsy, ddcsz,
- nbpu_opt, nstlist_cmdline,
- nsteps_cmdline, nstepout, resetstep, nmultisim,
- repl_ex_nst, repl_ex_nex, repl_ex_seed, pforce,
- cpt_period, max_hours,
- Flags);
- /* the main thread continues here with a new cr. We don't deallocate
- the old cr because other threads may still be reading it. */
- if (cr == NULL)
- {
- gmx_comm("Failed to spawn threads");
- }
- }
+ check_and_update_hw_opt_2(&hw_opt, inputrec->cutoff_scheme);
+
+ /* Determine how many thread-MPI ranks to start.
+ *
+ * TODO Over-writing the user-supplied value here does
+ * prevent any possible subsequent checks from working
+ * correctly. */
+ hw_opt.nthreads_tmpi = get_nthreads_mpi(hwinfo,
+ &hw_opt,
+ domdecOptions.numPmeRanks,
+ nonbondedOnGpu,
+ inputrec, mtop,
+ mdlog,
+ doMembed);
+
+ // Now start the threads for thread MPI.
+ cr = spawnThreads(hw_opt.nthreads_tmpi);
+ /* The main thread continues here with a new cr. We don't deallocate
+ the old cr because other threads may still be reading it. */
+ // TODO Both master and spawned threads call dup_tfn and
+ // reinitialize_commrec_for_this_thread. Find a way to express
+ // this better.
}
#endif
/* END OF CAUTION: cr is now reliable */
/* now broadcast everything to the non-master nodes/threads: */
init_parallel(cr, inputrec, mtop);
- /* The master rank decided on the use of GPUs,
- * broadcast this information to all ranks.
- */
- gmx_bcast_sim(sizeof(bUseGPU), &bUseGPU, cr);
+ gmx_bcast_sim(sizeof(nonbondedOnGpu), &nonbondedOnGpu, cr);
}
+ // TODO: Error handling
+ mdModules.assignOptionsToModules(*inputrec->params, nullptr);
- if (fplog != NULL)
+ if (fplog != nullptr)
{
pr_inputrec(fplog, 0, "Input Parameters", inputrec, FALSE);
fprintf(fplog, "\n");
/* A parallel command line option consistency check that we can
only do after any threads have started. */
- if (!PAR(cr) &&
- (ddxyz[XX] > 1 || ddxyz[YY] > 1 || ddxyz[ZZ] > 1 || npme > 0))
+ if (!PAR(cr) && (domdecOptions.numCells[XX] > 1 ||
+ domdecOptions.numCells[YY] > 1 ||
+ domdecOptions.numCells[ZZ] > 1 ||
+ domdecOptions.numPmeRanks > 0))
{
gmx_fatal(FARGS,
"The -dd or -npme option request a parallel simulation, "
);
}
- if (bRerunMD &&
+ if (doRerun &&
(EI_ENERGY_MINIMIZATION(inputrec->eI) || eiNM == inputrec->eI))
{
gmx_fatal(FARGS, "The .mdp file specified an energy mininization or normal mode algorithm, and these are not compatible with mdrun -rerun");
if (!(EEL_PME(inputrec->coulombtype) || EVDW_PME(inputrec->vdwtype)))
{
- if (npme > 0)
+ if (domdecOptions.numPmeRanks > 0)
{
gmx_fatal_collective(FARGS, cr->mpi_comm_mysim, MASTER(cr),
"PME-only ranks are requested, but the system does not use PME for electrostatics or LJ");
}
- npme = 0;
+ domdecOptions.numPmeRanks = 0;
}
- if (bUseGPU && npme < 0)
+ if (nonbondedOnGpu && domdecOptions.numPmeRanks < 0)
{
/* With GPUs we don't automatically use PME-only ranks. PME ranks can
* improve performance with many threads per GPU, since our OpenMP
* scaling is bad, but it's difficult to automate the setup.
*/
- npme = 0;
+ domdecOptions.numPmeRanks = 0;
}
#ifdef GMX_FAHCORE
snew(fcd, 1);
/* This needs to be called before read_checkpoint to extend the state */
- init_disres(fplog, mtop, inputrec, cr, fcd, state, repl_ex_nst > 0);
+ init_disres(fplog, mtop, inputrec, cr, fcd, state, replExParams.exchangeInterval > 0);
- init_orires(fplog, mtop, state->x, inputrec, cr, &(fcd->orires),
+ init_orires(fplog, mtop, as_rvec_array(state->x.data()), inputrec, cr, &(fcd->orires),
state);
if (inputrecDeform(inputrec))
tMPI_Thread_mutex_unlock(&deform_init_box_mutex);
}
- if (Flags & MD_STARTFROMCPT)
+ ObservablesHistory observablesHistory = {};
+
+ ContinuationOptions &continuationOptions = mdrunOptions.continuationOptions;
+
+ if (continuationOptions.startedFromCheckpoint)
{
/* Check if checkpoint file exists before doing continuation.
* This way we can use identical input options for the first and subsequent runs...
gmx_bool bReadEkin;
load_checkpoint(opt2fn_master("-cpi", nfile, fnm, cr), &fplog,
- cr, ddxyz, &npme,
- inputrec, state, &bReadEkin,
- (Flags & MD_APPENDFILES),
- (Flags & MD_APPENDFILESSET),
- (Flags & MD_REPRODUCIBLE));
+ cr, domdecOptions.numCells,
+ inputrec, state, &bReadEkin, &observablesHistory,
+ continuationOptions.appendFiles,
+ continuationOptions.appendFilesOptionSet,
+ mdrunOptions.reproducible);
if (bReadEkin)
{
- Flags |= MD_READ_EKIN;
+ continuationOptions.haveReadEkin = true;
}
}
- if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ if (SIMMASTER(cr) && continuationOptions.appendFiles)
{
gmx_log_open(ftp2fn(efLOG, nfile, fnm), cr,
- Flags, &fplog);
+ continuationOptions.appendFiles, &fplog);
+ logOwner = buildLogger(fplog, nullptr);
+ mdlog = logOwner.logger();
}
- /* override nsteps with value from cmdline */
- override_nsteps_cmdline(fplog, nsteps_cmdline, inputrec, cr);
+ /* override nsteps with value set on the commamdline */
+ override_nsteps_cmdline(mdlog, mdrunOptions.numStepsCommandline, inputrec);
if (SIMMASTER(cr))
{
gmx_bcast(sizeof(box), box, cr);
}
- // TODO This should move to do_md(), because it only makes sense
- // with dynamical integrators, but there is no test coverage and
- // it interacts with constraints, somehow.
- /* Essential dynamics */
- if (opt2bSet("-ei", nfile, fnm))
+ /* Update rlist and nstlist. */
+ if (inputrec->cutoff_scheme == ecutsVERLET)
{
- /* Open input and output files, allocate space for ED data structure */
- ed = ed_open(mtop->natoms, &state->edsamstate, nfile, fnm, Flags, oenv, cr);
+ prepare_verlet_scheme(fplog, cr, inputrec, nstlist_cmdline, mtop, box,
+ nonbondedOnGpu || (emulateGpuNonbonded == EmulateGpuNonbonded::Yes), *hwinfo->cpuInfo);
}
if (PAR(cr) && !(EI_TPI(inputrec->eI) ||
inputrec->eI == eiNM))
{
- cr->dd = init_domain_decomposition(fplog, cr, Flags, ddxyz, npme,
- dd_rank_order,
- rdd, rconstr,
- dddlb_opt, dlb_scale,
- ddcsx, ddcsy, ddcsz,
+ cr->dd = init_domain_decomposition(fplog, cr, domdecOptions, mdrunOptions,
mtop, inputrec,
- box, state->x,
+ box, as_rvec_array(state->x.data()),
&ddbox, &npme_major, &npme_minor);
+ // Note that local state still does not exist yet.
}
else
{
#if GMX_MPI
if (MULTISIM(cr))
{
- md_print_info(cr, fplog,
- "This is simulation %d out of %d running as a composite GROMACS\n"
- "multi-simulation job. Setup for this simulation:\n\n",
- cr->ms->sim, cr->ms->nsim);
+ GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
+ "This is simulation %d out of %d running as a composite GROMACS\n"
+ "multi-simulation job. Setup for this simulation:\n",
+ cr->ms->sim, cr->ms->nsim);
}
- md_print_info(cr, fplog, "Using %d MPI %s\n",
- cr->nnodes,
+ GMX_LOG(mdlog.warning).appendTextFormatted(
+ "Using %d MPI %s\n",
+ cr->nnodes,
#if GMX_THREAD_MPI
- cr->nnodes == 1 ? "thread" : "threads"
+ cr->nnodes == 1 ? "thread" : "threads"
#else
- cr->nnodes == 1 ? "process" : "processes"
+ cr->nnodes == 1 ? "process" : "processes"
#endif
- );
+ );
fflush(stderr);
#endif
/* Check and update hw_opt for the cut-off scheme */
- check_and_update_hw_opt_2(hw_opt, inputrec->cutoff_scheme);
+ check_and_update_hw_opt_2(&hw_opt, inputrec->cutoff_scheme);
/* Check and update hw_opt for the number of MPI ranks */
- check_and_update_hw_opt_3(hw_opt);
+ check_and_update_hw_opt_3(&hw_opt);
- gmx_omp_nthreads_init(fplog, cr,
+ gmx_omp_nthreads_init(mdlog, cr,
hwinfo->nthreads_hw_avail,
- hw_opt->nthreads_omp,
- hw_opt->nthreads_omp_pme,
+ hw_opt.nthreads_omp,
+ hw_opt.nthreads_omp_pme,
(cr->duty & DUTY_PP) == 0,
inputrec->cutoff_scheme == ecutsVERLET);
}
#endif
- if (bUseGPU)
+ // Contains the ID of the GPU used by each PP rank on this node,
+ // indexed by that rank. Empty if no GPUs are selected for use on
+ // this node.
+ std::vector<int> gpuTaskAssignment;
+ if (nonbondedOnGpu)
{
- /* Select GPU id's to use */
- gmx_select_gpu_ids(fplog, cr, &hwinfo->gpu_info, bForceUseGPU,
- &hw_opt->gpu_opt);
+ /* Currently the DD code assigns duty to ranks that can
+ * include PP work that currently can be executed on a single
+ * GPU, if present and compatible. This has to be coordinated
+ * across PP ranks on a node, with possible multiple devices
+ * or sharing devices on a node, either from the user
+ * selection, or automatically. */
+ bool rankCanUseGpu = cr->duty & DUTY_PP;
+ gpuTaskAssignment = mapPpRanksToGpus(rankCanUseGpu, cr, hwinfo->gpu_info, hw_opt);
}
- else
+
+ reportGpuUsage(mdlog, hwinfo->gpu_info, !hw_opt.gpuIdTaskAssignment.empty(),
+ gpuTaskAssignment, cr->nrank_pp_intranode, cr->nnodes > 1);
+
+ if (!gpuTaskAssignment.empty())
{
- /* Ignore (potentially) manually selected GPUs */
- hw_opt->gpu_opt.n_dev_use = 0;
+ GMX_RELEASE_ASSERT(cr->nrank_pp_intranode == static_cast<int>(gpuTaskAssignment.size()),
+ "The number of PP ranks on each node must equal the number of GPU tasks used on each node");
}
- /* check consistency across ranks of things like SIMD
- * support and number of GPUs selected */
- gmx_check_hw_runconf_consistency(fplog, hwinfo, cr, hw_opt, bUseGPU);
+ /* Prevent other ranks from continuing after an issue was found
+ * and reported as a fatal error.
+ *
+ * TODO This function implements a barrier so that MPI runtimes
+ * can organize an orderly shutdown if one of the ranks has had to
+ * issue a fatal error in various code already run. When we have
+ * MPI-aware error handling and reporting, this should be
+ * improved. */
+#if GMX_MPI
+ if (PAR(cr))
+ {
+ MPI_Barrier(cr->mpi_comm_mysim);
+ }
+#endif
/* Now that we know the setup is consistent, check for efficiency */
- check_resource_division_efficiency(hwinfo, hw_opt, Flags & MD_NTOMPSET,
- cr, fplog);
+ check_resource_division_efficiency(hwinfo, hw_opt.nthreads_tot, !gpuTaskAssignment.empty(), mdrunOptions.ntompOptionIsSet,
+ cr, mdlog);
+
+ gmx_device_info_t *shortRangedDeviceInfo = nullptr;
+ int shortRangedDeviceId = -1;
+ if (cr->duty & DUTY_PP)
+ {
+ if (!gpuTaskAssignment.empty())
+ {
+ shortRangedDeviceId = gpuTaskAssignment[cr->rank_pp_intranode];
+ shortRangedDeviceInfo = getDeviceInfo(hwinfo->gpu_info, shortRangedDeviceId);
+ }
+ }
if (DOMAINDECOMP(cr))
{
/* When we share GPUs over ranks, we need to know this for the DLB */
- dd_setup_dlb_resource_sharing(cr, hwinfo, hw_opt);
+ dd_setup_dlb_resource_sharing(cr, shortRangedDeviceId);
}
/* getting number of PP/PME threads
*/
nthreads_pme = gmx_omp_nthreads_get(emntPME);
- wcycle = wallcycle_init(fplog, resetstep, cr);
+ wcycle = wallcycle_init(fplog, mdrunOptions.timingOptions.resetStep, cr);
if (PAR(cr))
{
/* Note that membed cannot work in parallel because mtop is
* changed here. Fix this if we ever want to make it run with
* multiple ranks. */
- membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &cpt_period);
+ membed = init_membed(fplog, nfile, fnm, mtop, inputrec, state, cr, &mdrunOptions.checkpointOptions.period);
}
snew(nrnb, 1);
bcast_state(cr, state);
/* Initiate forcerecord */
- fr = mk_forcerec();
- fr->hwinfo = hwinfo;
- fr->gpu_opt = &hw_opt->gpu_opt;
- init_forcerec(fplog, fr, fcd, inputrec, mtop, cr, box,
+ fr = mk_forcerec();
+ fr->forceProviders = mdModules.initForceProviders();
+ init_forcerec(fplog, mdlog, fr, fcd,
+ inputrec, mtop, cr, box,
opt2fn("-table", nfile, fnm),
opt2fn("-tablep", nfile, fnm),
getFilenm("-tableb", nfile, fnm),
nbpu_opt,
+ shortRangedDeviceInfo,
FALSE,
pforce);
/* Make molecules whole at start of run */
if (fr->ePBC != epbcNONE)
{
- do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, state->x);
+ do_pbc_first_mtop(fplog, inputrec->ePBC, box, mtop, as_rvec_array(state->x.data()));
}
if (vsite)
{
* for the initial distribution in the domain decomposition
* and for the initial shell prediction.
*/
- construct_vsites_mtop(vsite, mtop, state->x);
+ construct_vsites_mtop(vsite, mtop, as_rvec_array(state->x.data()));
}
}
}
else
{
- pmedata = NULL;
+ pmedata = nullptr;
}
}
else
/* This is a PME only node */
/* We don't need the state */
- done_state(state);
+ stateInstance.reset();
+ state = nullptr;
ewaldcoeff_q = calc_ewaldcoeff_q(inputrec->rcoulomb, inputrec->ewald_rtol);
ewaldcoeff_lj = calc_ewaldcoeff_lj(inputrec->rvdw, inputrec->ewald_rtol_lj);
snew(pmedata, 1);
}
- if (hw_opt->thread_affinity != threadaffOFF)
+ if (hw_opt.thread_affinity != threadaffOFF)
{
/* Before setting affinity, check whether the affinity has changed
* - which indicates that probably the OpenMP library has changed it
* since we first checked).
*/
- gmx_check_thread_affinity_set(fplog, cr,
- hw_opt, hwinfo->nthreads_hw_avail, TRUE);
+ gmx_check_thread_affinity_set(mdlog, cr,
+ &hw_opt, hwinfo->nthreads_hw_avail, TRUE);
+
+ int nthread_local;
+ /* threads on this MPI process or TMPI thread */
+ if (cr->duty & DUTY_PP)
+ {
+ nthread_local = gmx_omp_nthreads_get(emntNonbonded);
+ }
+ else
+ {
+ nthread_local = gmx_omp_nthreads_get(emntPME);
+ }
/* Set the CPU affinity */
- gmx_set_thread_affinity(fplog, cr, hw_opt, hwinfo);
+ gmx_set_thread_affinity(mdlog, cr, &hw_opt, *hwinfo->hardwareTopology,
+ nthread_local, nullptr);
}
/* Initiate PME if necessary,
if (cr->duty & DUTY_PME)
{
- status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
- mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
- (Flags & MD_REPRODUCIBLE), nthreads_pme);
+ try
+ {
+ status = gmx_pme_init(pmedata, cr, npme_major, npme_minor, inputrec,
+ mtop ? mtop->natoms : 0, nChargePerturbed, nTypePerturbed,
+ mdrunOptions.reproducible,
+ ewaldcoeff_q, ewaldcoeff_lj,
+ nthreads_pme);
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
if (status != 0)
{
gmx_fatal(FARGS, "Error %d initializing PME", status);
inputrec->pull_work =
init_pull(fplog, inputrec->pull, inputrec, nfile, fnm,
mtop, cr, oenv, inputrec->fepvals->init_lambda,
- EI_DYNAMICS(inputrec->eI) && MASTER(cr), Flags);
+ EI_DYNAMICS(inputrec->eI) && MASTER(cr),
+ continuationOptions);
}
if (inputrec->bRot)
{
/* Initialize enforced rotation code */
- init_rot(fplog, inputrec, nfile, fnm, cr, state->x, state->box, mtop, oenv,
- bVerbose, Flags);
+ init_rot(fplog, inputrec, nfile, fnm, cr, as_rvec_array(state->x.data()), state->box, mtop, oenv,
+ mdrunOptions);
}
- constr = init_constraints(fplog, mtop, inputrec, ed, state, cr);
+ /* Let init_constraints know whether we have essential dynamics constraints.
+ * TODO: inputrec should tell us whether we use an algorithm, not a file option or the checkpoint
+ */
+ bool doEdsam = (opt2fn_null("-ei", nfile, fnm) != nullptr || observablesHistory.edsamHistory);
+
+ constr = init_constraints(fplog, mtop, inputrec, doEdsam, cr);
if (DOMAINDECOMP(cr))
{
* because fr->cginfo_mb is set later.
*/
dd_init_bondeds(fplog, cr->dd, mtop, vsite, inputrec,
- Flags & MD_DDBONDCHECK, fr->cginfo_mb);
+ domdecOptions.checkBondedInteractions,
+ fr->cginfo_mb);
}
/* Now do whatever the user wants us to do (how flexible...) */
- my_integrator(inputrec->eI) (fplog, cr, nfile, fnm,
- oenv, bVerbose,
- nstglobalcomm,
+ my_integrator(inputrec->eI) (fplog, cr, mdlog, nfile, fnm,
+ oenv,
+ mdrunOptions,
vsite, constr,
- nstepout, inputrec, mtop,
- fcd, state,
- mdatoms, nrnb, wcycle, ed, fr,
- repl_ex_nst, repl_ex_nex, repl_ex_seed,
+ mdModules.outputProvider(),
+ inputrec, mtop,
+ fcd, state, &observablesHistory,
+ mdatoms, nrnb, wcycle, fr,
+ replExParams,
membed,
- cpt_period, max_hours,
- imdport,
- Flags,
walltime_accounting);
if (inputrec->bRot)
/* Finish up, write some stuff
* if rerunMD, don't write last frame again
*/
- finish_run(fplog, cr,
+ finish_run(fplog, mdlog, cr,
inputrec, nrnb, wcycle, walltime_accounting,
- fr ? fr->nbv : NULL,
+ fr ? fr->nbv : nullptr,
EI_DYNAMICS(inputrec->eI) && !MULTISIM(cr));
+ // Free PME data
+ if (pmedata)
+ {
+ gmx_pme_destroy(*pmedata); // TODO: pmedata is always a single element list, refactor
+ pmedata = nullptr;
+ }
/* Free GPU memory and context */
- free_gpu_resources(fr, cr, &hwinfo->gpu_info, fr ? fr->gpu_opt : NULL);
+ free_gpu_resources(fr, cr, shortRangedDeviceInfo);
if (doMembed)
{
walltime_accounting_destroy(walltime_accounting);
/* Close logfile already here if we were appending to it */
- if (MASTER(cr) && (Flags & MD_APPENDFILES))
+ if (MASTER(cr) && continuationOptions.appendFiles)
{
gmx_log_close(fplog);
}
rc = (int)gmx_get_stop_condition();
- done_ed(&ed);
-
#if GMX_THREAD_MPI
/* we need to join all threads. The sub-threads join when they
exit this function, but the master thread needs to be told to
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \internal \file
+/*! \libinternal \file
*
* \brief Declares the routine running the inetgrators.
*
#include <cstdio>
+#include <array>
+
+#include "gromacs/commandline/filenm.h"
+#include "gromacs/domdec/domdec.h"
#include "gromacs/hardware/hw_info.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
+#include "repl_ex.h"
+
struct gmx_output_env_t;
+struct ReplicaExchangeParameters;
struct t_commrec;
-struct t_filenm;
namespace gmx
{
-/*! \brief Driver routine, that calls the different methods
+/*! \libinternal \brief Runner object for supporting setup and execution of mdrun.
+ *
+ * This class has responsibility for the lifetime of data structures
+ * that exist for the life of the simulation, e.g. for logging and
+ * communication.
*
- * \param[in] hw_opt Hardware detection structure
- * \param[in] fplog File pointer for log file
- * \param[in] cr Communication data
- * \param[in] nfile Number of files
- * \param[in] fnm Array of filenames and file properties
- * \param[in] oenv Output variables for storing xvg files etc.
- * \param[in] bVerbose Verbose output or not
- * \param[in] nstglobalcomm Number of steps between global communication
- * \param[in] ddxyz Division of sub-boxes over processors for
- * use in domain decomposition parallellization
- * \param[in] dd_rank_order Ordering of the PP and PME ranks
- * \param[in] npme The number of separate PME ranks requested, -1 = auto
- * \param[in] rdd The maximum distance for bonded interactions with DD (nm)
- * \param[in] rconstr Maximum distance for P-LINCS (nm)
- * \param[in] dddlb_opt File name for debugging
- * \param[in] dlb_scale File name for debugging
- * \param[in] ddcsx File name for debugging
- * \param[in] ddcsy File name for debugging
- * \param[in] ddcsz File name for debugging
- * \param[in] nbpu_opt Type of nonbonded processing unit
- * \param[in] nstlist_cmdline Override neighbor search frequency
- * \param[in] nsteps_cmdline Override number of simulation steps
- * \param[in] nstepout How often to write to the console
- * \param[in] resetstep Reset the step counter
- * \param[in] nmultisim Number of parallel simulations to run
- * \param[in] repl_ex_nst Number steps between replica exchange attempts
- * \param[in] repl_ex_nex Number of replicas in REMD
- * \param[in] repl_ex_seed The seed for Monte Carlo swaps
- * \param[in] pforce Minimum force for printing (for debugging)
- * \param[in] cpt_period How often to checkpoint the simulation
- * \param[in] max_hours Maximume length of the simulation (wall time)
- * \param[in] imdport Interactive MD port (socket)
- * \param[in] Flags More command line options
+ * \todo Most of the attributes should be declared by specific modules
+ * as command-line options. Accordingly, they do not conform to the
+ * naming scheme, because that would make for a lot of noise in the
+ * diff, only to have it change again when the options move to their
+ * modules.
+ *
+ * \todo Preparing logging and MPI contexts could probably be a
+ * higher-level responsibility, so that an Mdrunner would get made
+ * without needing to re-initialize these components (as currently
+ * happens always for the master rank, and differently for the spawned
+ * ranks with thread-MPI).
*/
-int mdrunner(gmx_hw_opt_t *hw_opt,
- FILE *fplog, struct t_commrec *cr, int nfile,
- const t_filenm fnm[], const gmx_output_env_t *oenv, gmx_bool bVerbose,
- int nstglobalcomm, ivec ddxyz, int dd_rank_order, int npme,
- real rdd, real rconstr, const char *dddlb_opt, real dlb_scale,
- const char *ddcsx, const char *ddcsy, const char *ddcsz,
- const char *nbpu_opt, int nstlist_cmdline,
- gmx_int64_t nsteps_cmdline, int nstepout, int resetstep,
- int nmultisim, int repl_ex_nst, int repl_ex_nex,
- int repl_ex_seed, real pforce, real cpt_period, real max_hours,
- int imdport, unsigned long Flags);
+class Mdrunner
+{
+ private:
+ //! Parallelism-related user options.
+ gmx_hw_opt_t hw_opt;
+ //! Filenames and properties from command-line argument values.
+ std::array<t_filenm, 34> filenames =
+ {{{ efTPR, nullptr, nullptr, ffREAD },
+ { efTRN, "-o", nullptr, ffWRITE },
+ { efCOMPRESSED, "-x", nullptr, ffOPTWR },
+ { efCPT, "-cpi", nullptr, ffOPTRD | ffALLOW_MISSING },
+ { efCPT, "-cpo", nullptr, ffOPTWR },
+ { efSTO, "-c", "confout", ffWRITE },
+ { efEDR, "-e", "ener", ffWRITE },
+ { efLOG, "-g", "md", ffWRITE },
+ { efXVG, "-dhdl", "dhdl", ffOPTWR },
+ { efXVG, "-field", "field", ffOPTWR },
+ { efXVG, "-table", "table", ffOPTRD },
+ { efXVG, "-tablep", "tablep", ffOPTRD },
+ { efXVG, "-tableb", "table", ffOPTRDMULT },
+ { efTRX, "-rerun", "rerun", ffOPTRD },
+ { efXVG, "-tpi", "tpi", ffOPTWR },
+ { efXVG, "-tpid", "tpidist", ffOPTWR },
+ { efEDI, "-ei", "sam", ffOPTRD },
+ { efXVG, "-eo", "edsam", ffOPTWR },
+ { efXVG, "-devout", "deviatie", ffOPTWR },
+ { efXVG, "-runav", "runaver", ffOPTWR },
+ { efXVG, "-px", "pullx", ffOPTWR },
+ { efXVG, "-pf", "pullf", ffOPTWR },
+ { efXVG, "-ro", "rotation", ffOPTWR },
+ { efLOG, "-ra", "rotangles", ffOPTWR },
+ { efLOG, "-rs", "rotslabs", ffOPTWR },
+ { efLOG, "-rt", "rottorque", ffOPTWR },
+ { efMTX, "-mtx", "nm", ffOPTWR },
+ { efRND, "-multidir", nullptr, ffOPTRDMULT},
+ { efDAT, "-membed", "membed", ffOPTRD },
+ { efTOP, "-mp", "membed", ffOPTRD },
+ { efNDX, "-mn", "membed", ffOPTRD },
+ { efXVG, "-if", "imdforces", ffOPTWR },
+ { efXVG, "-swap", "swapions", ffOPTWR }}};
+ /*! \brief Filename arguments.
+ *
+ * Provided for compatibility with old C-style code accessing
+ * command-line arguments that are file names. */
+ t_filenm *fnm = filenames.data();
+ /*! \brief Number of filename argument values.
+ *
+ * Provided for compatibility with old C-style code accessing
+ * command-line arguments that are file names. */
+ int nfile = filenames.size();
+ //! Output context for writing text files
+ gmx_output_env_t *oenv = nullptr;
+ //! Ongoing collection of mdrun options
+ MdrunOptions mdrunOptions;
+ //! Options for the domain decomposition.
+ DomdecOptions domdecOptions;
+ //! Target short-range interations for "cpu", "gpu", "gpu_cpu", or "auto". Default is "auto".
+ const char *nbpu_opt = nullptr;
+ //! Command-line override for the duration of a neighbor list with the Verlet scheme.
+ int nstlist_cmdline = 0;
+ //! Number of simulations in multi-simulation set.
+ int nmultisim = 0;
+ //! Parameters for replica-exchange simulations.
+ ReplicaExchangeParameters replExParams;
+ //! Print a warning if any force is larger than this (in kJ/mol nm).
+ real pforce = -1;
+ //! Handle to file used for logging.
+ FILE *fplog;
+ //! Handle to communication data structure.
+ t_commrec *cr;
+ public:
+ /*! \brief Defaulted constructor.
+ *
+ * Note that when member variables are not present in the constructor
+ * member initialization list (which is true for the default constructor),
+ * then they are initialized with any default member initializer specified
+ * when they were declared, or default initialized. */
+ Mdrunner() = default;
+ //! Start running mdrun by calling its C-style main function.
+ int mainFunction(int argc, char *argv[]);
+ /*! \brief Driver routine, that calls the different simulation methods. */
+ int mdrunner();
+ //! Called when thread-MPI spawns threads.
+ t_commrec *spawnThreads(int numThreadsToLaunch);
+ /*! \brief Re-initializes the object after threads spawn.
+ *
+ * \todo Can this be refactored so that the Mdrunner on a spawned thread is
+ * constructed ready to use? */
+ void reinitializeOnSpawnedThread();
+};
} // namespace gmx
# pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
)
-gmx_register_integration_test(
- ${testname}
- ${exename}
- )
+gmx_register_gtest_test(${testname} ${exename} INTEGRATION_TEST)
set(testname "MdrunMpiTests")
set(exename "mdrun-mpi-test")
# pseudo-library for code for mdrun
$<TARGET_OBJECTS:mdrun_objlib>
)
-gmx_register_mpi_integration_test(
- ${testname}
- ${exename}
- 2
- )
+gmx_register_gtest_test(${testname} ${exename} MPI_RANKS 2 INTEGRATION_TEST)
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/enxio.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/testasserts.h"
}
//! Helper function to obtain resources
-t_enxframe *make_enxframe()
+static t_enxframe *make_enxframe()
{
t_enxframe *frame;
#include <vector>
#include "gromacs/fileio/enxio.h"
-#include "gromacs/utility/scoped_cptr.h"
+#include "gromacs/utility/unique_cptr.h"
#include "testutils/testasserts.h"
class EnergyFrame;
//! Convenience smart pointer typedef
-typedef scoped_cptr<ener_file, done_ener_file> ener_file_ptr;
+typedef unique_cptr<ener_file, done_ener_file> ener_file_ptr;
//! Helper function to free resources (NB free_enxframe only frees the contents, not the pointer itself)
void done_enxframe(t_enxframe *fr);
//! Convenience smart pointer typedef
-typedef scoped_cptr<t_enxframe, done_enxframe> enxframe_ptr;
+typedef unique_cptr<t_enxframe, done_enxframe> enxframe_ptr;
/*! \internal
* \brief Manages returning an EnergyFrame containing required energy
//! Convert energy field name to its index within a t_enxframe from this file.
std::map<std::string, int> indicesOfEnergyFields_;
//! Owning handle of an open energy file ready to read frames.
- ener_file_ptr energyFileGuard_;
+ const ener_file_ptr energyFileGuard_;
//! Owning handle of contents of .edr file frame after reading.
- enxframe_ptr enxframeGuard_;
+ const enxframe_ptr enxframeGuard_;
//! Whether the API has been used properly (ie. probe before reading).
bool haveProbedForNextFrame_;
//! Whether there has been a probe that found a next frame.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "programs/mdrun/mdrun_main.h"
#include "testutils/cmdlinetest.h"
-#include "testutils/integrationtests.h"
+#include "testutils/mpitest.h"
+#include "testutils/testfilemanager.h"
#include "testutils/testoptions.h"
namespace gmx
namespace
{
-#if GMX_THREAD_MPI || defined(DOXYGEN)
-//! Number of tMPI threads for child mdrun call.
-int g_numThreads = 1;
-#endif
#if GMX_OPENMP || defined(DOXYGEN)
//! Number of OpenMP threads for child mdrun call.
int g_numOpenMPThreads = 1;
GMX_TEST_OPTIONS(MdrunTestOptions, options)
{
GMX_UNUSED_VALUE(options);
-#if GMX_THREAD_MPI
- options->addOption(IntegerOption("nt").store(&g_numThreads)
- .description("Number of thread-MPI threads/ranks for child mdrun calls"));
-#endif
#if GMX_OPENMP
options->addOption(IntegerOption("nt_omp").store(&g_numOpenMPThreads)
.description("Number of OpenMP threads for child mdrun calls"));
}
-SimulationRunner::SimulationRunner(IntegrationTestFixture *fixture) :
- fixture_(fixture),
+SimulationRunner::SimulationRunner(TestFileManager *fileManager) :
topFileName_(),
groFileName_(),
fullPrecisionTrajectoryFileName_(),
ndxFileName_(),
- mdpInputFileName_(fixture_->fileManager_.getTemporaryFilePath("input.mdp")),
- mdpOutputFileName_(fixture_->fileManager_.getTemporaryFilePath("output.mdp")),
- tprFileName_(fixture_->fileManager_.getTemporaryFilePath(".tpr")),
- logFileName_(fixture_->fileManager_.getTemporaryFilePath(".log")),
- edrFileName_(fixture_->fileManager_.getTemporaryFilePath(".edr")),
- nsteps_(-2)
+ mdpInputFileName_(fileManager->getTemporaryFilePath("input.mdp")),
+ mdpOutputFileName_(fileManager->getTemporaryFilePath("output.mdp")),
+ tprFileName_(fileManager->getTemporaryFilePath(".tpr")),
+ logFileName_(fileManager->getTemporaryFilePath(".log")),
+ edrFileName_(fileManager->getTemporaryFilePath(".edr")),
+ nsteps_(-2),
+ fileManager_(*fileManager)
{
#if GMX_LIB_MPI
GMX_RELEASE_ASSERT(gmx_mpi_initialized(), "MPI system not initialized for mdrun tests");
// and verlet-buffer-tolerance = -1 gives a grompp error. If we keep
// things that way, this function should be renamed. For now,
// force the use of the group scheme.
+// TODO There is possible outstanding unexplained behaviour of mdp
+// input parsing e.g. Redmine 2074, so this particular set of mdp
+// contents is also tested with GetIrTest in gmxpreprocess-test.
void
SimulationRunner::useEmptyMdpFile()
{
void
SimulationRunner::useTopGroAndNdxFromDatabase(const char *name)
{
- topFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".top").c_str());
- groFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
- ndxFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".ndx").c_str());
+ topFileName_ = fileManager_.getInputFilePath((std::string(name) + ".top").c_str());
+ groFileName_ = fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
+ ndxFileName_ = fileManager_.getInputFilePath((std::string(name) + ".ndx").c_str());
}
void
SimulationRunner::useGroFromDatabase(const char *name)
{
- groFileName_ = fixture_->fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
+ groFileName_ = fileManager_.getInputFilePath((std::string(name) + ".gro").c_str());
}
int
caller.addOption("-n", ndxFileName_);
caller.addOption("-p", topFileName_);
caller.addOption("-c", groFileName_);
+ caller.addOption("-r", groFileName_);
caller.addOption("-po", mdpOutputFileName_);
caller.addOption("-o", tprFileName_);
caller.addOption("-o", fullPrecisionTrajectoryFileName_);
caller.addOption("-x", reducedPrecisionTrajectoryFileName_);
- caller.addOption("-deffnm", fixture_->fileManager_.getTemporaryFilePath("state"));
+ caller.addOption("-deffnm", fileManager_.getTemporaryFilePath("state"));
if (nsteps_ > -2)
{
caller.addOption("-nsteps", nsteps_);
}
-#if GMX_MPI
-# if GMX_GPU != GMX_GPU_NONE
-# if GMX_THREAD_MPI
- int numGpusNeeded = g_numThreads;
-# else /* Must be real MPI */
- int numGpusNeeded = gmx_node_num();
-# endif
- std::string gpuIdString(numGpusNeeded, '0');
- caller.addOption("-gpu_id", gpuIdString.c_str());
-# endif
-#endif
-
#if GMX_THREAD_MPI
- caller.addOption("-ntmpi", g_numThreads);
+ caller.addOption("-ntmpi", getNumberOfTestMpiRanks());
#endif
#if GMX_OPENMP
caller.addOption("-ntomp", g_numOpenMPThreads);
#endif
-#if GMX_GPU != GMX_GPU_NONE
- /* TODO Ideally, with real MPI, we could call
- * gmx_collect_hardware_mpi() here and find out how many nodes
- * mdrun will run on. For now, we assume that we're running on one
- * node regardless of the number of ranks, because that's true in
- * Jenkins and for most developers running the tests. */
- int numberOfNodes = 1;
-#if GMX_THREAD_MPI
- /* Can't use gmx_node_num() because it is only valid after spawn of thread-MPI threads */
- int numberOfRanks = g_numThreads;
-#elif GMX_LIB_MPI
- int numberOfRanks = gmx_node_num();
-#else
- int numberOfRanks = 1;
-#endif
- if (numberOfRanks > numberOfNodes && !gmx_multiple_gpu_per_node_supported())
- {
- if (gmx_node_rank() == 0)
- {
- fprintf(stderr, "GROMACS in this build configuration cannot run on more than one GPU per node,\n so with %d ranks and %d nodes, this test will disable GPU support", numberOfRanks, numberOfNodes);
- }
- caller.addOption("-nb", "cpu");
- }
-#endif
return gmx_mdrun(caller.argc(), caller.argv());
}
// ====
-MdrunTestFixture::MdrunTestFixture() : runner_(this)
+MdrunTestFixture::MdrunTestFixture() : runner_(&fileManager_)
{
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <gtest/gtest.h>
+#include "gromacs/utility/classhelpers.h"
+
#include "testutils/cmdlinetest.h"
-#include "testutils/integrationtests.h"
+#include "testutils/testfilemanager.h"
namespace gmx
{
-
namespace test
{
class SimulationRunner
{
public:
- /*! \brief Constructor, which establishes the fixture that
- * will own each object */
- explicit SimulationRunner(IntegrationTestFixture *fixture_);
+ //! Initializes a runner with given manager for temporary files.
+ explicit SimulationRunner(TestFileManager *fileManager);
//! Use an empty .mdp file as input to grompp
void useEmptyMdpFile();
* with default command line */
int callMdrun();
- private:
- //! Provides access to the test fixture, e.g. for the TestFileManager
- IntegrationTestFixture *fixture_;
- public:
//@{
/*! \name Names for frequently used grompp and mdrun output files
*
std::string swapFileName_;
int nsteps_;
//@}
+
+ private:
+ TestFileManager &fileManager_;
+
+ GMX_DISALLOW_COPY_AND_ASSIGN(SimulationRunner);
};
/*! \internal
*
* \ingroup module_mdrun_integration_tests
*/
-class MdrunTestFixtureBase : public IntegrationTestFixture
+class MdrunTestFixtureBase : public ::testing::Test
{
public:
MdrunTestFixtureBase();
*
* \ingroup module_mdrun_integration_tests
*/
-class MdrunTestFixture : public IntegrationTestFixture
+class MdrunTestFixture : public ::testing::Test
{
public:
MdrunTestFixture();
virtual ~MdrunTestFixture();
+ //! Manages temporary files during the test.
+ TestFileManager fileManager_;
//! Helper object to manage the preparation for and call of mdrun
SimulationRunner runner_;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* database. These all have two identical frames of two SPC water
* molecules, which were generated via trjconv from the .gro
* version. */
-const char *trajectoryFileNames[] = {
- "../../../gromacs/gmxana/legacytests/spc2-traj.trr",
-#if defined GMX_USE_TNG && HAVE_ZLIB
- "../../../gromacs/gmxana/legacytests/spc2-traj.tng",
+const char *const trajectoryFileNames[] = {
+ "../../../gromacs/gmxana/tests/spc2-traj.trr",
+#if GMX_USE_TNG
+ "../../../gromacs/gmxana/tests/spc2-traj.tng",
#endif
- "../../../gromacs/gmxana/legacytests/spc2-traj.xtc",
- "../../../gromacs/gmxana/legacytests/spc2-traj.gro",
- "../../../gromacs/gmxana/legacytests/spc2-traj.pdb",
- "../../../gromacs/gmxana/legacytests/spc2-traj.g96"
+ "../../../gromacs/gmxana/tests/spc2-traj.xtc",
+ "../../../gromacs/gmxana/tests/spc2-traj.gro",
+ "../../../gromacs/gmxana/tests/spc2-traj.pdb",
+ "../../../gromacs/gmxana/tests/spc2-traj.g96"
};
// TODO later. Find a better way to manage this file database and
// these string arrays that index it
INSTANTIATE_TEST_CASE_P(NoFatalErrorFrom,
MdrunRerun,
- ::testing::ValuesIn(gmx::ArrayRef<const char*>(trajectoryFileNames)));
+ ::testing::ValuesIn(trajectoryFileNames));
/*! \todo Add other tests for mdrun -rerun, e.g.
*
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
//! Build a simple .mdp file
-void organizeMdpFile(SimulationRunner *runner)
+static void organizeMdpFile(SimulationRunner *runner)
{
// Make sure -maxh has a chance to propagate
runner->useStringAsMdpFile("nsteps = 100\n"
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2016, by the GROMACS development team, led by
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/fileio/trxio.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/scoped_cptr.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/testasserts.h"
{
//! Helper function to obtain resources
-t_trxframe *make_trxframe()
+static t_trxframe *make_trxframe()
{
t_trxframe *frame;
#include "gromacs/fileio/oenv.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/trajectory/trajectoryframe.h"
-#include "gromacs/utility/scoped_cptr.h"
+#include "gromacs/utility/unique_cptr.h"
#include "testutils/testasserts.h"
class TrajectoryFrame;
//! Convenience smart pointer typedef
-typedef scoped_cptr<gmx_output_env_t, output_env_done> oenv_ptr;
+typedef unique_cptr<gmx_output_env_t, output_env_done> oenv_ptr;
//! Convenience smart pointer typedef
-typedef scoped_cptr<t_trxstatus, close_trx> trxstatus_file_ptr;
+typedef unique_cptr<t_trxstatus, close_trx> trxstatus_file_ptr;
//! Helper function to free all resources
void done_trxframe(t_trxframe *fr);
//! Convenience smart pointer typedef
-typedef scoped_cptr<t_trxframe, done_trxframe> trxframe_ptr;
+typedef unique_cptr<t_trxframe, done_trxframe> trxframe_ptr;
/*! \internal
* \brief Manages returning a t_trxframe whose contents were read from
//! Owning handle of an open trajectory file ready to read frames.
trxstatus_file_ptr trajectoryFileGuard_;
//! Owning handle of contents of trajectory file frame after reading.
- trxframe_ptr trxframeGuard_;
+ const trxframe_ptr trxframeGuard_;
//! Whether the first frame has been read
bool haveReadFirstFrame_;
//! Whether the API has been used properly (ie. probe before reading).
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
t_gmx *gmx;
- gmx = (t_gmx *)data;
+ gmx = static_cast<t_gmx *>(data);
if (dlg_mess == DLG_EXIT)
{
hide_mb(gmx);
char *set, void *data)
{
t_gmx *gmx;
- gmx = (t_gmx *)data;
+ gmx = static_cast<t_gmx *>(data);
hide_mb(gmx);
if (dlg_mess == DLG_EXIT)
t_gmx *gmx;
t_dlg *dlg;
- gmx = (t_gmx *)data;
+ gmx = static_cast<t_gmx *>(data);
dlg = gmx->dlgs[edExport];
switch (dlg_mess)
{
eg0, egTOPOL, egCONFIN, egPARAM, eg1, eg1PROC, eg32PROC
};
-static void Extract(t_dlg *dlg, int ID, char *buf)
-{
- char *et;
-
- et = EditText(dlg, ID);
- if (et)
- {
- std::strcpy(buf, et);
- }
-}
-
enum bond_set {
ebShowH = 11, ebDPlus, ebRMPBC, ebCue, ebSkip, ebWait
};
t_gmx *gmx;
char *endptr;
- gmx = (t_gmx *)data;
+ gmx = static_cast<t_gmx *>(data);
if (ebond == -1)
{
ebond = gmx->man->molw->bond_type;
esFUNCT = 1, esBSHOW, esINFIL, esINDEXFIL, esLSQ, esSHOW, esPLOTFIL
};
-static bool in_set(int i, int n, int set[])
-{
- int j;
- for (j = 0; (j < n); j++)
- {
- if (set[j] == i)
- {
- return true;
- }
- }
- return false;
-}
-
typedef t_dlg *t_mmb (t_x11 *x11, t_gmx *gmx);
typedef struct {
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"pixmap", "statictext", "edittext", "defbutton"
};
-void ReadDlgError(const char *infile, eDLGERR err, const char *s,
- const char *file, int line)
+static void ReadDlgError(const char *infile, eDLGERR err, const char *s,
+ const char *file, int line)
{
std::fprintf(stderr, "Error: ");
switch (err)
snew(fitem, 1);
fitem->nname = 0;
- fitem->name = NULL;
- fitem->set = NULL;
- fitem->get = NULL;
- fitem->def = NULL;
- fitem->help = NULL;
+ fitem->name = nullptr;
+ fitem->set = nullptr;
+ fitem->get = nullptr;
+ fitem->def = nullptr;
+ fitem->help = nullptr;
return fitem;
}
t_fgroup *fgroup;
snew(fgroup, 1);
- fgroup->name = NULL;
+ fgroup->name = nullptr;
fgroup->nfitem = 0;
- fgroup->fitem = NULL;
+ fgroup->fitem = nullptr;
return fgroup;
}
fgrid->w = 0;
fgrid->h = 0;
fgrid->nfgroup = 0;
- fgrid->fgroup = NULL;
+ fgrid->fgroup = nullptr;
fgrid->nfsimple = 0;
- fgrid->fsimple = NULL;
+ fgrid->fsimple = nullptr;
return fgrid;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
int g, i;
snew(f, 1);
- if (fn != NULL)
+ if (fn != nullptr)
{
f->grps = init_index(fn, &f->grpnames);
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
#define COFFS 70
static t_mess Mess[] = {
- { "GROMACS", 0, 20, NULL },
- { NULL, 16, 9, NULL },
- { "Copyright (c) 1991-2013", COFFS+ 2, 9, NULL },
- { "D.v.d.Spoel, E.Lindahl, B.Hess", COFFS+11, 9, NULL },
- { "& Groningen University ", COFFS+20, 9, NULL },
- { "click to dismiss", COFFS+31, 8, NULL }
+ { "GROMACS", 0, 20, nullptr },
+ { nullptr, 16, 9, nullptr },
+ { "Copyright (c) 1991-2013", COFFS+ 2, 9, nullptr },
+ { "D.v.d.Spoel, E.Lindahl, B.Hess", COFFS+11, 9, nullptr },
+ { "& Groningen University ", COFFS+20, 9, nullptr },
+ { "click to dismiss", COFFS+31, 8, nullptr }
};
#define NMESS asize(Mess)
int i;
logo->bQuitOnClick = bQuitOnClick;
InitWin(&logo->wd, 0, 0, 360, 270, 1, "GROMACS");
bg = LIGHTGREY;
- if ((newcol = std::getenv("GMX_LOGO_COLOR")) != NULL)
+ if ((newcol = std::getenv("GMX_LOGO_COLOR")) != nullptr)
{
GetNamedColor(x11, newcol, &bg);
}
logo->wd.x, logo->wd.y,
logo->wd.width, logo->wd.height,
logo->wd.bwidth, WHITE, bg);
- for (i = 0, logo->bigfont = NULL; (i < NBF); i++)
+ for (i = 0, logo->bigfont = nullptr; (i < NBF); i++)
{
- if ((logo->bigfont = XLoadQueryFont(x11->disp, bfname[i])) != NULL)
+ if ((logo->bigfont = XLoadQueryFont(x11->disp, bfname[i])) != nullptr)
{
break;
}
#ifdef DEBUG
std::fprintf(stderr, "Big Logofont: %s\n", bfname[i]);
#endif
- for (i = 0, logo->smallfont = NULL; (i < NSF); i++)
+ for (i = 0, logo->smallfont = nullptr; (i < NSF); i++)
{
- if ((logo->smallfont = XLoadQueryFont(x11->disp, sfname[i])) != NULL)
+ if ((logo->smallfont = XLoadQueryFont(x11->disp, sfname[i])) != nullptr)
{
break;
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
snew(man->szLab, sh.natoms);
snew(man->bHydro, sh.natoms);
snew(bB, sh.natoms);
- read_tpx_top(status, NULL, man->box, &man->natom, NULL, NULL, &man->top);
+ read_tpx_top(status, nullptr, man->box, &man->natom, nullptr, nullptr, &man->top);
man->gpbc = gmx_rmpbc_init(&man->top.idef, -1, man->natom);
man->natom =
{
t_windata *wd;
- wd = (t_windata *)data;
+ wd = static_cast<t_windata *>(data);
switch (event->type)
{
case Expose:
t_manager *man;
int width, height;
- man = (t_manager *)data;
+ man = static_cast<t_manager *>(data);
switch (event->type)
{
case ConfigureNotify:
t_manager *man;
snew(man, 1);
- man->status = NULL;
+ man->status = nullptr;
man->bPlus = true;
man->bSort = true;
man->oenv = oenv;
man->molw = init_mw(x11, man->wd.self, 0, 0, 1, 1, WHITE, BLUE, ePBC, box);
/* Title Window */
- InitWin(&(man->title), 0, 0, 1, 1, 0, NULL);
+ InitWin(&(man->title), 0, 0, 1, 1, 0, nullptr);
man->title.self = XCreateSimpleWindow(x11->disp, man->molw->wd.self,
man->title.x, man->title.y,
man->title.width, man->title.height,
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "molps.h"
+
#include <cstdlib>
#include "gromacs/fileio/writeps.h"
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
#define NAC asize(ac)
-int search_ac(const char *type)
+static int search_ac(const char *type)
{
unsigned int i, nb, mij, best, besti;
best = 0;
besti = 0;
- if (NULL != type)
+ if (nullptr != type)
{
for (i = 0; (i < NAC); i++)
{
return &(ac[i].rgb);
}
-void DrawLegend(t_x11 *x11, t_windata *Win)
+static void DrawLegend(t_x11 *x11, t_windata *Win)
{
#define NLAB 6
#define COLS 3
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
Window To;
XEvent letter;
- mw = (t_molwin *)data;
+ mw = static_cast<t_molwin *>(data);
To = mw->wd.Parent;
letter.type = ClientMessage;
letter.xclient.display = x11->disp;
return false;
}
-void set_def (t_molwin *mw, int ePBC, matrix box)
+static void set_def (t_molwin *mw, int ePBC, matrix box)
{
mw->bShowHydrogen = true;
mw->bond_type = eBFat;
int compare_obj(const void *a, const void *b)
{
- t_object *oa, *ob;
- real z;
+ const t_object *oa, *ob;
+ real z;
- oa = (t_object *)a;
- ob = (t_object *)b;
+ oa = static_cast<const t_object *>(a);
+ ob = static_cast<const t_object *>(b);
z = oa->z-ob->z;
return nvis;
}
-void draw_objects(Display *disp, Window w, GC gc, int nobj,
- t_object objs[], iv2 vec2[], rvec x[],
- unsigned long col[], int size[], bool bShowHydro, int bond_type,
- bool bPlus)
+static void draw_objects(Display *disp, Window w, GC gc, int nobj,
+ t_object objs[], iv2 vec2[], rvec x[],
+ unsigned long col[], int size[], bool bShowHydro, int bond_type,
+ bool bPlus)
{
bool bBalls;
int i;
{ 4, 5 }, { 5, 6 }, { 6, 7 }, { 7, 4 },
{ 0, 4 }, { 1, 5 }, { 2, 6 }, { 3, 7 }
};
- static int *edge = NULL;
+ static int *edge = nullptr;
int i, j, k, i0, i1;
rvec corner[NCUCEDGE], box_center;
vec4 x4;
if (boxtype == esbTrunc)
{
calc_compact_unitcell_vertices(view->ecenter, box, corner);
- if (edge == NULL)
+ if (edge == nullptr)
{
edge = compact_unitcell_edges();
}
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "x11.h"
#include "xutil.h"
-bool ChildCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
+static bool ChildCallBack(t_x11 *x11, XEvent *event, Window w, void *data)
{
t_child *child;
t_mentry *m;
return false;
}
-bool MenuCallBack(t_x11 *x11, XEvent *event, Window /*w*/, void *data)
+static bool MenuCallBack(t_x11 *x11, XEvent *event, Window /*w*/, void *data)
{
t_menu *m;
kid->m = &(ent[l]);
kid->Parent = Parent;
w = &(kid->wd);
- InitWin(w, j*mlen, k*mht, mlen-2, mht-2, 1, NULL);
+ InitWin(w, j*mlen, k*mht, mlen-2, mht-2, 1, nullptr);
w->self = XCreateSimpleWindow(x11->disp, m->wd.self,
w->x, w->y, w->width, w->height,
w->bwidth, bg, bg);
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
#include "gmxpre.h"
+#include "view.h"
+
#include "config.h"
#include <cstdio>
case IDDOEXPORT:
write_sto_conf(gmx->confout, *gmx->man->top.name,
&(gmx->man->top.atoms),
- gmx->man->x, NULL, gmx->man->molw->ePBC, gmx->man->box);
+ gmx->man->x, nullptr, gmx->man->molw->ePBC, gmx->man->box);
break;
case IDQUIT:
show_mb(gmx, emQuit);
snew(gmx->wd, 1);
ePBC = read_tpx_top(ftp2fn(efTPR, nfile, fnm),
- NULL, box, &natom, NULL, NULL, &top);
+ nullptr, box, &natom, nullptr, nullptr, &top);
read_first_frame(oenv, &status, ftp2fn(efTRX, nfile, fnm), &fr, TRX_DONT_SKIP);
close_trx(status);
hints.min_width = 2*EWIDTH+40;
hints.min_height = EHEIGHT+LDHEIGHT+LEGHEIGHT+40;
XSetStandardProperties(x11->disp, gmx->wd->self, gmx->wd->text, program,
- pm, NULL, 0, &hints);
+ pm, nullptr, 0, &hints);
x11->RegisterCallback(x11, gmx->wd->self, x11->root, MainCallBack, gmx);
x11->SetInputMask(x11, gmx->wd->self,
gmx_output_env_t *oenv;
t_filenm fnm[] = {
- { efTRX, "-f", NULL, ffREAD },
- { efTPR, NULL, NULL, ffREAD },
- { efNDX, NULL, NULL, ffOPTRD }
+ { efTRX, "-f", nullptr, ffREAD },
+ { efTPR, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD }
};
#define NFILE asize(fnm)
if (parse_common_args(&argc, argv, PCA_CAN_TIME, NFILE, fnm,
- 0, NULL, asize(desc), desc, asize(bugs), bugs, &oenv))
+ 0, nullptr, asize(desc), desc, asize(bugs), bugs, &oenv))
{
#if !GMX_X11
std::fprintf(stderr, "Compiled without X-Windows - can not run viewer.\n");
#else
t_x11 *x11;
- if ((x11 = GetX11(&argc, argv)) == NULL)
+ if ((x11 = GetX11(&argc, argv)) == nullptr)
{
std::fprintf(stderr, "Can't connect to X Server.\n"
"Check your DISPLAY environment variable\n");
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
if (name)
{
- bFont = ((font = XLQF(err, disp, name)) != NULL);
+ bFont = ((font = XLQF(err, disp, name)) != nullptr);
}
else
{
- font = NULL;
+ font = nullptr;
}
for (i = 0; (!bFont && (i < MAXNAMES)); i++)
{
- bFont = ((font = XLQF(err, disp, fontnames[i])) != NULL);
+ bFont = ((font = XLQF(err, disp, fontnames[i])) != nullptr);
}
if (!bFont)
fontlist = XListFonts(disp, "?", 1, &count);
if (count != 0)
{
- bFont = ((font = XLQF(err, disp, fontlist[0])) != NULL);
+ bFont = ((font = XLQF(err, disp, fontlist[0])) != nullptr);
}
}
if (!bFont)
/* Filter out expose events with non-zero count field */
if (event.xexpose.count != 0)
{
- curs = NULL;
+ curs = nullptr;
}
break;
case ConfigureNotify:
item->cb = cb;
item->mask = 0;
item->data = data;
- item->next = NULL;
+ item->next = nullptr;
if (x11->wlist)
{
char **ARGV;
char *display;
char *fontname;
- char *title, *FG = NULL, *BG = NULL;
+ char *title, *FG = nullptr, *BG = nullptr;
bool bVerbose = false;
int i;
argv[i] = ARGV[i];
}
*argc = ARGC;
- argv[ARGC] = NULL;
+ argv[ARGC] = nullptr;
snew(x11, 1);
x11->dispname = display;
x11->console = stderr;
}
else
- if ((x11->console = std::fopen("/dev/null", "w")) == NULL)
+ if ((x11->console = std::fopen("/dev/null", "w")) == nullptr)
{
x11->console = stderr;
}
- if ((x11->disp = XOpenDisplay(display)) == NULL)
+ if ((x11->disp = XOpenDisplay(display)) == nullptr)
{
if (bVerbose)
{
std::fprintf(x11->console, "Display %s invalid\n", display);
}
- return NULL;
+ return nullptr;
}
- if ((x11->font = GetFont(x11->console, x11->disp, fontname)) == NULL)
+ if ((x11->font = GetFont(x11->console, x11->disp, fontname)) == nullptr)
{
- return NULL;
+ return nullptr;
}
- if ((x11->gc = GetGC(x11->disp, x11->font)) == NULL)
+ if ((x11->gc = GetGC(x11->disp, x11->font)) == nullptr)
{
- return NULL;
+ return nullptr;
}
x11->root = DefaultRootWindow(x11->disp);
}
x11->title = gmx_strdup(title);
sfree(title);
- x11->wlist = NULL;
+ x11->wlist = nullptr;
x11->GetNamedColor = &GetNamedColor;
x11->MainLoop = &MainLoop;
x11->RegisterCallback = &RegisterCallback;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
return dlg->dlgitem[i];
}
}
- return NULL;
+ return nullptr;
}
t_dlgitem *FindWin(t_dlg *dlg, Window win)
return dlg->dlgitem[i];
}
}
- return NULL;
+ return nullptr;
}
/*****************************
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
*w = dlgitem->win.width;
*h = dlgitem->win.height;
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
*x0 = dlgitem->win.x;
*y0 = dlgitem->win.y;
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
return dlgitem->win.x;
}
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
return dlgitem->win.y;
}
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
return dlgitem->win.width;
}
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
return dlgitem->win.height;
}
int old_w, old_h;
#endif
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
#ifdef DEBUG
old_w = dlgitem->win.width;
t_dlgitem *dlgitem;
int old_x, old_y;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
old_x = dlgitem->win.x;
old_y = dlgitem->win.y;
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
if (dlgitem->type == edlgCB)
{
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
if (dlgitem->type == edlgET)
{
{
t_dlgitem *dlgitem;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
if (dlgitem->type == edlgET)
{
}
}
- return NULL;
+ return nullptr;
}
/*****************************
"No help for this item"
};
MessageBox(dlg->x11, dlg->wDad, "No Help", 2, lines,
- MB_OK | MB_ICONSTOP | MB_APPLMODAL, NULL, NULL);
+ MB_OK | MB_ICONSTOP | MB_APPLMODAL, nullptr, nullptr);
}
void HelpDlg(t_dlg *dlg)
"First press the OK button."
};
MessageBox(dlg->x11, dlg->win.self, "Help Dialogbox",
- 3, lines, MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, NULL, NULL);
+ 3, lines, MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, nullptr, nullptr);
}
void HelpNow(t_dlg *dlg, t_dlgitem *dlgitem)
char buf[80];
bool bCont = true;
int i, nlines = 0;
- char **lines = NULL;
+ char **lines = nullptr;
if (!dlgitem->help)
{
while (bCont);
MessageBox(dlg->x11, dlg->wDad, "Help",
nlines, lines,
- MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, NULL, NULL);
+ MB_OK | MB_ICONINFORMATION | MB_APPLMODAL, nullptr, nullptr);
for (i = 0; (i < nlines); i++)
{
sfree(lines[i]);
int i, nWndProc;
t_dlgitem *dlgitem;
- if ((dlgitem = FindWin(dlg, w)) != NULL)
+ if ((dlgitem = FindWin(dlg, w)) != nullptr)
{
nWndProc = (dlgitem->WndProc)(x11, dlgitem, event);
#ifdef DEBUG
* the item itself may not be freed until the dlg is done with
*
****************************/
-void DoCreateDlg(t_dlg *dlg)
+static void DoCreateDlg(t_dlg *dlg)
{
XSizeHints hints;
XSetWindowAttributes attr;
hints.y = dlg->win.y;
hints.flags = PPosition;
XSetStandardProperties(dlg->x11->disp, dlg->win.self, dlg->title,
- dlg->title, None, NULL, 0, &hints);
+ dlg->title, None, nullptr, 0, &hints);
}
void AddDlgItem(t_dlg *dlg, t_dlgitem *item)
t_dlgitem *dlgitem;
int i;
- if ((dlgitem = FindItem(dlg, id)) != NULL)
+ if ((dlgitem = FindItem(dlg, id)) != nullptr)
{
dlg->x11->UnRegisterCallback(dlg->x11, dlgitem->win.self);
if (dlgitem->win.self)
{
XDestroyWindow(dlg->x11->disp, dlg->win.self);
}
- dlg->dlgitem = NULL;
+ dlg->dlgitem = nullptr;
}
}
}
else
{
- dlg->title = NULL;
+ dlg->title = nullptr;
}
if (w == 0)
{
{
y = y0;
}
- InitWin(&(dlg->win), x, y, w, h, bw, NULL);
+ InitWin(&(dlg->win), x, y, w, h, bw, nullptr);
SetDlgSize(dlg, w, h, x0 || y0);
dlg->wDad = Parent;
dlg->fg = x11->fg;
dlg->bg = x11->bg;
dlg->nitem = 0;
- dlg->dlgitem = NULL;
+ dlg->dlgitem = nullptr;
DoCreateDlg(dlg);
return dlg;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
for (j = 0; (j < h); j++)
{
grid[i][j].nitem = 0;
- grid[i][j].list = NULL;
+ grid[i][j].list = nullptr;
}
}
return grid;
GroupID = (*ID)++;
item = &(grid[fgroup->x][fgroup->y]);
AddListItem(item, CreateGroupBox(x11, fgroup->name, GroupID,
- 0, NULL, 0, 0, 0, 0, 0));
+ 0, nullptr, 0, 0, 0, 0, 0));
x = 2*OFFS_X;
y = item->list[0]->win.y+item->list[0]->win.height;
w = 0;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
return DefWndProc(x11, dlgitem, event);
}
- XLookupString(&(event->xkey), c, BUFSIZE, &keysym, NULL);
+ XLookupString(&(event->xkey), c, BUFSIZE, &keysym, nullptr);
#ifdef DEBUG
std::printf("Keysym: %x\n", keysym);
#endif
t_dlgitem *dlgitem;
dlgitem = newitem();
- InitWin(&(dlgitem->win), x0, y0, w, h, bw, NULL);
+ InitWin(&(dlgitem->win), x0, y0, w, h, bw, nullptr);
dlgitem->ID = id;
dlgitem->type = edlgPM;
dlgitem->u.pixmap.pm = pm;
}
w += 2*OFFS_X;
}
- InitWin(&(dlgitem->win), x0, y0, w, h, bw, NULL);
+ InitWin(&(dlgitem->win), x0, y0, w, h, bw, nullptr);
dlgitem->ID = id;
dlgitem->GroupID = groupid;
dlgitem->type = edlgST;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#define ID_ICON -2
#define ID_TEXT -1
-static bmchar *icon_bits = NULL;
+static bmchar *icon_bits = nullptr;
static int icon_width = 0;
static int icon_height = 0;
static unsigned long icon_fg = 0;
static unsigned long icon_bg = 0;
-void SetIcon(unsigned char *bits, int w, int h, unsigned long fg, unsigned long bg)
+static void SetIcon(unsigned char *bits, int w, int h, unsigned long fg, unsigned long bg)
{
icon_bits = (bmchar *)bits;
icon_width = w;
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
const char *s, int x, int y, int width, int height,
eXPos eX, eYPos eY)
{
- SpecialTextInRect(x11, NULL, win, s, x, y, width, height, eX, eY);
+ SpecialTextInRect(x11, nullptr, win, s, x, y, width, height, eX, eY);
}
void TextInWin(t_x11 *x11, t_windata *win,
}
else
{
- win->text = NULL;
+ win->text = nullptr;
}
#ifdef DEBUG
std::printf("%s: %d x %d at %d, %d\n", text, w, h, x0, y0);
struct t_mpos *prev;
} t_mpos;
-static t_mpos *mpos = NULL;
+static t_mpos *mpos = nullptr;
void PushMouse(Display *disp, Window dest, int x, int y)
{
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+if (NOT GMX_BUILD_UNITTESTS)
+ gmx_add_missing_tests_notice("Unit tests have not been run. You need to set GMX_BUILD_UNITTESTS=ON if you want to build and run them.")
+ return()
+endif()
+
include_directories(BEFORE SYSTEM ${GMOCK_INCLUDE_DIRS})
set(TESTUTILS_SOURCES
cmdlinetest.cpp
conftest.cpp
- integrationtests.cpp
+ filematchers.cpp
interactivetest.cpp
+ loggertest.cpp
mpi-printer.cpp
+ mpitest.cpp
refdata.cpp
refdata-xml.cpp
+ stdiohelper.cpp
stringtest.cpp
testasserts.cpp
testfilemanager.cpp
set(TESTUTILS_LIBS testutils)
set_property(TARGET testutils APPEND PROPERTY COMPILE_DEFINITIONS "${GMOCK_COMPILE_DEFINITIONS}")
set_property(TARGET testutils APPEND PROPERTY COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
-target_link_libraries(testutils libgromacs ${GMOCK_LIBRARIES})
+target_link_libraries(testutils libgromacs ${GMX_COMMON_LIBRARIES} ${GMOCK_LIBRARIES})
if(HAVE_TINYXML2)
include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR})
include_directories(BEFORE SYSTEM "../external/tinyxml2")
endif()
+# TODO Use gmx_add_missing_tests_notice() instead of the messages below.
+set(GMX_CAN_RUN_MPI_TESTS 1)
+if (GMX_MPI)
+ set(_an_mpi_variable_had_content 0)
+ foreach(VARNAME MPIEXEC MPIEXEC_NUMPROC_FLAG MPIEXEC_PREFLAGS MPIEXEC_POSTFLAGS)
+ # These variables need a valid value for the test to run
+ # and pass, but conceivably any of them might be valid
+ # with arbitrary (including empty) content. They can't be
+ # valid if they've been populated with the CMake
+ # find_package magic suffix/value "NOTFOUND", though.
+ if (${VARNAME} MATCHES ".*NOTFOUND")
+ message(STATUS "CMake variable ${VARNAME} was not detected to be a valid value. To test GROMACS correctly, check the advice in the install guide.")
+ set(GMX_CAN_RUN_MPI_TESTS 0)
+ endif()
+ if (NOT VARNAME STREQUAL MPIEXEC AND ${VARNAME})
+ set(_an_mpi_variable_had_content 1)
+ endif()
+ endforeach()
+ if(_an_mpi_variable_had_content AND NOT MPIEXEC)
+ message(STATUS "CMake variable MPIEXEC must have a valid value if one of the other related MPIEXEC variables does. To test GROMACS correctly, check the advice in the install guide.")
+ set(GMX_CAN_RUN_MPI_TESTS 0)
+ endif()
+elseif (NOT GMX_THREAD_MPI)
+ set(GMX_CAN_RUN_MPI_TESTS 0)
+endif()
+
set(TESTUTILS_DIR ${CMAKE_CURRENT_SOURCE_DIR})
set(TESTUTILS_DIR ${TESTUTILS_DIR} PARENT_SCOPE)
set(TESTUTILS_LIBS ${TESTUTILS_LIBS} PARENT_SCOPE)
+set(GMX_CAN_RUN_MPI_TESTS ${GMX_CAN_RUN_MPI_TESTS} PARENT_SCOPE)
add_subdirectory(tests)
add_executable(${EXENAME} ${UNITTEST_TARGET_OPTIONS}
${_source_files} ${TESTUTILS_DIR}/unittest_main.cpp)
target_link_libraries(${EXENAME}
- ${TESTUTILS_LIBS} libgromacs ${GMOCK_LIBRARIES} ${GMX_EXE_LINKER_FLAGS} ${GMX_STDLIB_LIBRARIES})
+ ${TESTUTILS_LIBS} libgromacs ${GMOCK_LIBRARIES}
+ ${GMX_COMMON_LIBRARIES} ${GMX_EXE_LINKER_FLAGS} ${GMX_STDLIB_LIBRARIES})
set_property(TARGET ${EXENAME}
APPEND PROPERTY COMPILE_FLAGS "${GMOCK_COMPILE_FLAGS}")
set_property(TARGET ${EXENAME}
endif()
endfunction()
-function (gmx_register_unit_test NAME EXENAME)
- if (GMX_BUILD_UNITTESTS AND BUILD_TESTING)
- add_test(NAME ${NAME}
- COMMAND ${EXENAME} --gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Temporary/${NAME}.xml)
- set_tests_properties(${NAME} PROPERTIES LABELS "GTest;UnitTest")
- add_dependencies(tests ${EXENAME})
- endif()
-endfunction ()
-
-# Use this function to register a test binary as an integration test
-function (gmx_register_integration_test NAME EXENAME)
- if (GMX_BUILD_UNITTESTS AND BUILD_TESTING)
- add_test(NAME ${NAME}
- COMMAND ${EXENAME} --gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Temporary/${NAME}.xml)
- set_tests_properties(${testname} PROPERTIES LABELS "IntegrationTest")
- add_dependencies(tests ${EXENAME})
-
- # GMX_EXTRA_LIBRARIES might be needed for mdrun integration tests at
- # some point.
- # target_link_libraries(${EXENAME} ${GMX_EXTRA_LIBRARIES} ${GMX_STDLIB_LIBRARIES})
- endif()
-endfunction ()
-
-# Use this function to register a test binary as an integration test
-# that requires MPI. The intended number of MPI ranks is also passed
+# Use this function with MPI_RANKS <N> INTEGRATION_TEST to register a test
+# binary as an integration test that requires MPI. The intended number of MPI
+# ranks is also passed
#
-# TODO When a test case needs it, generalize the NUMPROC mechanism so
+# TODO When a test case needs it, generalize the MPI_RANKS mechanism so
# that ctest can run the test binary over a range of numbers of MPI
# ranks.
-function (gmx_register_mpi_integration_test NAME EXENAME NUMPROC)
+function (gmx_register_gtest_test NAME EXENAME)
if (GMX_BUILD_UNITTESTS AND BUILD_TESTING)
- if (GMX_MPI)
- foreach(VARNAME MPIEXEC MPIEXEC_NUMPROC_FLAG MPIEXEC_PREFLAGS MPIEXEC_POSTFLAGS)
- # These variables need a valid value for the test to run
- # and pass, but conceivably any of them might be valid
- # with arbitrary (including empty) content. They can't be
- # valid if they've been populated with the CMake
- # find_package magic suffix/value "NOTFOUND", though.
- if (${VARNAME} MATCHES ".*NOTFOUND")
- message(STATUS "CMake variable ${VARNAME} was not detected to be a valid value. To test GROMACS correctly, check the advice in the install guide.")
- set(_cannot_run_mpi_tests 1)
- endif()
- if (NOT VARNAME STREQUAL MPIEXEC AND ${VARNAME})
- set(_an_mpi_variable_had_content 1)
- endif()
- endforeach()
- if(_an_mpi_variable_had_content AND NOT MPIEXEC)
- message(STATUS "CMake variable MPIEXEC must have a valid value if one of the other related MPIEXEC variables does. To test GROMACS correctly, check the advice in the install guide.")
- set(_cannot_run_mpi_tests 1)
+ set(_options INTEGRATION_TEST)
+ set(_one_value_args MPI_RANKS)
+ cmake_parse_arguments(ARG "${_options}" "${_one_value_args}" "" ${ARGN})
+ set(_xml_path ${CMAKE_BINARY_DIR}/Testing/Temporary/${NAME}.xml)
+ set(_labels GTest)
+ set(_timeout 30)
+ if (ARG_INTEGRATION_TEST)
+ list(APPEND _labels IntegrationTest)
+ set(_timeout 120)
+ gmx_get_test_prefix_cmd(_prefix_cmd IGNORE_LEAKS)
+ else()
+ list(APPEND _labels UnitTest)
+ gmx_get_test_prefix_cmd(_prefix_cmd)
+ endif()
+ set(_cmd ${_prefix_cmd} $<TARGET_FILE:${EXENAME}>)
+ if (ARG_MPI_RANKS)
+ if (NOT GMX_CAN_RUN_MPI_TESTS)
+ return()
endif()
- if(NOT _cannot_run_mpi_tests)
- add_test(NAME ${NAME}
- COMMAND
- ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${NUMPROC}
- ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${EXENAME}> ${MPIEXEC_POSTFLAGS}
- --gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Temporary/${NAME}.xml
- )
- set_tests_properties(${testname} PROPERTIES LABELS "MpiIntegrationTest")
- add_dependencies(tests ${EXENAME})
+ list(APPEND _labels MpiTest)
+ if (GMX_MPI)
+ set(_cmd
+ ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${ARG_MPI_RANKS}
+ ${MPIEXEC_PREFLAGS} ${_cmd} ${MPIEXEC_POSTFLAGS})
+ elseif (GMX_THREAD_MPI)
+ list(APPEND _cmd -ntmpi ${ARG_MPI_RANKS})
endif()
-
- # GMX_EXTRA_LIBRARIES might be needed for mdrun integration tests at
- # some point.
- # target_link_libraries(${EXENAME} ${GMX_EXTRA_LIBRARIES} ${GMX_STDLIB_LIBRARIES})
- elseif(GMX_THREAD_MPI)
- add_test(NAME ${NAME}
- COMMAND
- $<TARGET_FILE:${EXENAME}> -nt ${NUMPROC}
- --gtest_output=xml:${CMAKE_BINARY_DIR}/Testing/Temporary/${NAME}.xml
- )
- set_tests_properties(${testname} PROPERTIES LABELS "MpiIntegrationTest")
- add_dependencies(tests ${EXENAME})
-
- # GMX_EXTRA_LIBRARIES might be needed for mdrun integration tests at
- # some point.
- # target_link_libraries(${EXENAME} ${GMX_EXTRA_LIBRARIES} ${GMX_STDLIB_LIBRARIES})
endif()
+ add_test(NAME ${NAME}
+ COMMAND ${_cmd} --gtest_output=xml:${_xml_path})
+ set_tests_properties(${NAME} PROPERTIES LABELS "${_labels}")
+ set_tests_properties(${NAME} PROPERTIES TIMEOUT ${_timeout})
+ add_dependencies(tests ${EXENAME})
endif()
endfunction ()
function (gmx_add_unit_test NAME EXENAME)
gmx_add_gtest_executable(${EXENAME} ${ARGN})
- gmx_register_unit_test(${NAME} ${EXENAME})
+ gmx_register_gtest_test(${NAME} ${EXENAME})
+endfunction()
+
+function (gmx_add_mpi_unit_test NAME EXENAME RANKS)
+ if (GMX_MPI OR (GMX_THREAD_MPI AND GTEST_IS_THREADSAFE))
+ gmx_add_gtest_executable(${EXENAME} MPI ${ARGN})
+ gmx_register_gtest_test(${NAME} ${EXENAME} MPI_RANKS ${RANKS})
+ endif()
endfunction()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/commandline/cmdlineoptionsmodule.h"
#include "gromacs/commandline/cmdlineprogramcontext.h"
#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/filestream.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringstream.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/textreader.h"
#include "gromacs/utility/textwriter.h"
+#include "testutils/filematchers.h"
#include "testutils/refdata.h"
#include "testutils/testfilemanager.h"
-#include "testutils/textblockmatchers.h"
namespace gmx
{
for (size_t i = 0; i < count; ++i)
{
char *arg = strdup(cmdline[i]);
- if (arg == NULL)
+ if (arg == nullptr)
{
throw std::bad_alloc();
}
args_.push_back(arg);
argv_.push_back(arg);
}
- argv_.push_back(NULL);
+ argv_.push_back(nullptr);
}
CommandLine::Impl::~Impl()
*/
CommandLine::CommandLine()
- : impl_(new Impl(NULL, 0))
+ : impl_(new Impl(nullptr, 0))
{
}
impl_->args_.reserve(newSize);
impl_->argv_.reserve(newSize + 1);
char *newArg = strdup(arg);
- if (newArg == NULL)
+ if (newArg == nullptr)
{
throw std::bad_alloc();
}
impl_->args_.push_back(newArg);
impl_->argv_.pop_back(); // Remove the trailing NULL.
impl_->argv_.push_back(newArg);
- impl_->argv_.push_back(NULL);
+ impl_->argv_.push_back(nullptr);
impl_->argc_ = static_cast<int>(newSize);
}
-namespace
+void CommandLine::addOption(const char *name)
{
-
-//! Helper function for converting values to strings
-template <typename T>
-std::string value2string(T value)
-{
- std::stringstream ss;
- ss << value;
- return ss.str();
+ append(name);
}
-} // namespace
-
void CommandLine::addOption(const char *name, const char *value)
{
append(name);
void CommandLine::addOption(const char *name, int value)
{
append(name);
- append(value2string(value));
+ append(gmx::toString(value));
}
void CommandLine::addOption(const char *name, double value)
{
append(name);
- append(value2string(value));
+ append(gmx::toString(value));
}
void CommandLine::merge(const CommandLine &args)
return CommandLineProgramContext(argc(), argv()).commandLine();
}
+bool CommandLine::contains(const char *name) const
+{
+ for (int i = 0; i < impl_->argc_; ++i)
+ {
+ if (std::strcmp(arg(i), name) == 0)
+ {
+ return true;
+ }
+ }
+ return false;
+}
+
/********************************************************************
* CommandLineTestHelper::Impl
*/
struct OutputFileInfo
{
OutputFileInfo(const char *option, const std::string &path,
- TextBlockMatcherPointer matcher)
+ FileMatcherPointer matcher)
: option(option), path(path), matcher(move(matcher))
{
}
- OutputFileInfo(OutputFileInfo &&other)
- : option(std::move(other.option)), path(std::move(other.path)),
- matcher(std::move(other.matcher))
- {
- }
-
- OutputFileInfo &operator=(OutputFileInfo &&other)
- {
- option = std::move(other.option);
- path = std::move(other.path);
- matcher = std::move(other.matcher);
- return *this;
- }
std::string option;
std::string path;
- TextBlockMatcherPointer matcher;
+ FileMatcherPointer matcher;
};
typedef std::vector<OutputFileInfo> OutputFileList;
{
// The name and description are not used in the tests, so they can be NULL.
const std::unique_ptr<ICommandLineModule> wrapperModule(
- ICommandLineOptionsModule::createModule(NULL, NULL, std::move(module)));
+ ICommandLineOptionsModule::createModule(nullptr, nullptr, std::move(module)));
return runModuleDirect(wrapperModule.get(), commandLine);
}
void CommandLineTestHelper::setOutputFile(
CommandLine *args, const char *option, const char *filename,
const ITextBlockMatcherSettings &matcher)
+{
+ setOutputFile(args, option, filename, TextFileMatch(matcher));
+}
+
+void CommandLineTestHelper::setOutputFile(
+ CommandLine *args, const char *option, const char *filename,
+ const IFileMatcherSettings &matcher)
{
std::string suffix(filename);
if (startsWith(filename, "."))
}
std::string fullFilename = impl_->fileManager_.getTemporaryFilePath(suffix);
args->addOption(option, fullFilename);
- impl_->outputFiles_.push_back(
- Impl::OutputFileInfo(option, fullFilename, matcher.createMatcher()));
+ impl_->outputFiles_.emplace_back(option, fullFilename, matcher.createFileMatcher());
}
void CommandLineTestHelper::checkOutputFiles(TestReferenceChecker checker) const
TestReferenceChecker outputChecker(
checker.checkCompound("OutputFiles", "Files"));
Impl::OutputFileList::const_iterator outfile;
- for (outfile = impl_->outputFiles_.begin();
- outfile != impl_->outputFiles_.end();
- ++outfile)
+ for (const auto &outfile : impl_->outputFiles_)
{
TestReferenceChecker fileChecker(
- outputChecker.checkCompound("File", outfile->option.c_str()));
- TextInputFile stream(outfile->path);
- outfile->matcher->checkStream(&stream, &fileChecker);
- stream.close();
+ outputChecker.checkCompound("File", outfile.option.c_str()));
+ outfile.matcher->checkFile(outfile.path, &fileChecker);
}
}
}
impl_->helper_.setOutputFile(&impl_->cmdline_, option, filename, matcher);
}
+void CommandLineTestBase::setOutputFile(
+ const char *option, const char *filename,
+ const IFileMatcherSettings &matcher)
+{
+ impl_->helper_.setOutputFile(&impl_->cmdline_, option, filename, matcher);
+}
+
CommandLine &CommandLineTestBase::commandLine()
{
return impl_->cmdline_;
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
namespace test
{
+class IFileMatcherSettings;
class ITextBlockMatcherSettings;
class TestFileManager;
class TestReferenceChecker;
void append(const char *arg);
//! Convenience overload taking a std::string.
void append(const std::string &arg) { append(arg.c_str()); }
+ /*! \brief
+ * Adds an option to the command line, typically a boolean.
+ *
+ * \param[in] name Name of the option to append, which
+ * should start with "-".
+ */
+ void addOption(const char *name);
/*! \brief
* Adds an option-value pair to the command line.
*
//! Returns the command line formatted as a single string.
std::string toString() const;
+ //! Whether the command line contains the given option.
+ bool contains(const char *name) const;
+
private:
class Impl;
*
* If the output file is needed to trigger some computation, or is
* unconditionally produced by the code under test, but the contents
- * are not interesting for the test, use NoTextMatch as the matcher.
+ * are not interesting for the test, use NoContentsMatch as the matcher.
+ * Note that the existence of the output file is still verified.
*/
void setOutputFile(CommandLine *args, const char *option,
const char *filename,
const ITextBlockMatcherSettings &matcher);
+ //! \copydoc setOutputFile(CommandLine *, const char *, const char *, const ITextBlockMatcherSettings &)
+ void setOutputFile(CommandLine *args, const char *option,
+ const char *filename,
+ const IFileMatcherSettings &matcher);
/*! \brief
* Checks output files added with setOutputFile() against reference
*/
void setOutputFile(const char *option, const char *filename,
const ITextBlockMatcherSettings &matcher);
+ /*! \brief
+ * Sets an output file parameter and adds it to the set of tested files.
+ *
+ * \see CommandLineTestHelper::setOutputFile()
+ */
+ void setOutputFile(const char *option, const char *filename,
+ const IFileMatcherSettings &matcher);
/*! \brief
* Returns the internal CommandLine object used to construct the
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements classes from filematchers.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "filematchers.h"
+
+#include "gromacs/utility/filestream.h"
+
+#include "testutils/textblockmatchers.h"
+
+namespace gmx
+{
+namespace test
+{
+
+namespace
+{
+
+class TextFileMatcher : public IFileMatcher
+{
+ public:
+ explicit TextFileMatcher(TextBlockMatcherPointer matcher)
+ : matcher_(std::move(matcher))
+ {
+ }
+
+ virtual void checkFile(const std::string &path,
+ TestReferenceChecker *checker)
+ {
+ TextInputFile stream(path);
+ matcher_->checkStream(&stream, checker);
+ stream.close();
+ }
+
+ private:
+ TextBlockMatcherPointer matcher_;
+};
+
+} // namespace
+
+IFileMatcher::~IFileMatcher()
+{
+}
+
+IFileMatcherSettings::~IFileMatcherSettings()
+{
+}
+
+FileMatcherPointer TextFileMatch::createFileMatcher() const
+{
+ return FileMatcherPointer(new TextFileMatcher(streamSettings_.createMatcher()));
+}
+
+FileMatcherPointer NoContentsMatch::createFileMatcher() const
+{
+ return TextFileMatch(NoTextMatch()).createFileMatcher();
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares utility classes for testing file contents.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+#ifndef GMX_TESTUTILS_FILEMATCHERS_H
+#define GMX_TESTUTILS_FILEMATCHERS_H
+
+#include <memory>
+#include <string>
+
+namespace gmx
+{
+namespace test
+{
+
+class ITextBlockMatcherSettings;
+class TestReferenceChecker;
+
+/*! \libinternal \brief
+ * Represents a file matcher, matching file contents against reference (or
+ * other) data.
+ *
+ * Typical pattern of declaring such matchers is to
+ * - Create a factory that implements IFileMatcherSettings,
+ * - Make that factory provide any necessary parameters that the matcher needs,
+ * using a "named parameter" idiom (see XvgMatch for an example), and
+ * - Make the factory create and return an instance of an internal
+ * implementation class that implements IFileMatcher and provides
+ * the actual matching logic.
+ *
+ * Any method that then wants to accept a matcher can accept a
+ * IFileMatcherSettings.
+ *
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class IFileMatcher
+{
+ public:
+ virtual ~IFileMatcher();
+
+ /*! \brief
+ * Matches contents of a file.
+ *
+ * \param path Path to the file to match.
+ * \param checker Checker to use for matching.
+ *
+ * The method can change the state of the provided checker (e.g., by
+ * changing the default tolerance).
+ * The caller is responsible of providing a checker where such state
+ * changes do not matter.
+ */
+ virtual void checkFile(const std::string &path,
+ TestReferenceChecker *checker) = 0;
+};
+
+//! Smart pointer for managing a IFileMatcher.
+typedef std::unique_ptr<IFileMatcher> FileMatcherPointer;
+
+/*! \libinternal \brief
+ * Represents a factory for creating a file matcher.
+ *
+ * See derived classes for available matchers. Each derived class represents
+ * one type of matcher (see IFileMatcher), and provides any methods
+ * necessary to pass parameters to such a matcher. Methods that accept a
+ * matcher can then take in this interface, and call createFileMatcher() to use
+ * the matcher that the caller of the method specifies.
+ *
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class IFileMatcherSettings
+{
+ public:
+ //! Factory method that constructs the matcher after parameters are set.
+ virtual FileMatcherPointer createFileMatcher() const = 0;
+
+ protected:
+ virtual ~IFileMatcherSettings();
+};
+
+/*! \libinternal \brief
+ * Use a ITextStreamMatcher for matching the contents.
+ *
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class TextFileMatch : public IFileMatcherSettings
+{
+ public:
+ //! Creates a matcher to match contents with given text matcher.
+ explicit TextFileMatch(const ITextBlockMatcherSettings &streamSettings)
+ : streamSettings_(streamSettings)
+ {
+ }
+
+ virtual FileMatcherPointer createFileMatcher() const;
+
+ private:
+ const ITextBlockMatcherSettings &streamSettings_;
+};
+
+/*! \libinternal \brief
+ * Do not check the contents of the file.
+ *
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class NoContentsMatch : public IFileMatcherSettings
+{
+ public:
+ virtual FileMatcherPointer createFileMatcher() const;
+};
+
+} // namespace test
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
void checkOutput()
{
- const std::string id = formatString("Output%d", static_cast<int>(currentLine_));
- if (checker_.checkPresent(bHasOutput_, id.c_str()))
+ if (bHasOutput_)
{
+ const std::string id = formatString("Output%d", static_cast<int>(currentLine_));
StringTestBase::checkText(&checker_, currentOutput_, id.c_str());
+ bHasOutput_ = false;
}
- bHasOutput_ = false;
currentOutput_.clear();
}
- void checkPendingInput()
- {
- const std::string id = formatString("Input%d", static_cast<int>(currentLine_+1));
- checker_.checkPresent(false, id.c_str());
- }
TestReferenceChecker checker_;
ConstArrayRef<const char *> inputLines_;
void InteractiveTestHelper::checkSession()
{
impl_->checkOutput();
- impl_->checkPendingInput();
+ impl_->checker_.checkUnusedEntries();
}
} // namespace test
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements gmx::test::LoggerTestHelper.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "loggertest.h"
+
+#include <gmock/gmock.h>
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/logger.h"
+
+namespace gmx
+{
+namespace test
+{
+
+using ::testing::NiceMock;
+
+namespace
+{
+class MockLogTarget : public ILogTarget
+{
+ public:
+ MOCK_METHOD1(writeEntry, void(const LogEntry &));
+};
+} // namespace
+
+/********************************************************************
+ * LoggerTestHelper::Impl
+ */
+
+class LoggerTestHelper::Impl
+{
+ public:
+ Impl()
+ {
+ // TODO: Add support for -stdout for echoing the log to stdout.
+ logger_.warning = LogLevelHelper(&getTarget(MDLogger::LogLevel::Warning));
+ logger_.info = LogLevelHelper(&getTarget(MDLogger::LogLevel::Info));
+ }
+
+ NiceMock<MockLogTarget> &getTarget(MDLogger::LogLevel level)
+ {
+ return targets_[static_cast<int>(level)];
+ }
+
+ NiceMock<MockLogTarget> targets_[MDLogger::LogLevelCount];
+ MDLogger logger_;
+};
+
+/********************************************************************
+ * LoggerTestHelper
+ */
+
+LoggerTestHelper::LoggerTestHelper()
+ : impl_(new Impl)
+{
+}
+
+LoggerTestHelper::~LoggerTestHelper()
+{
+}
+
+const MDLogger &LoggerTestHelper::logger()
+{
+ return impl_->logger_;
+}
+
+void LoggerTestHelper::expectEntryMatchingRegex(gmx::MDLogger::LogLevel level,
+ const char *re)
+{
+ using ::testing::ContainsRegex;
+ using ::testing::Field;
+ auto &target = impl_->getTarget(level);
+ EXPECT_CALL(target, writeEntry(Field(&LogEntry::text, ContainsRegex(re))));
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016,2017, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Declares gmx::test::LoggerTestHelper.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+#ifndef GMX_TESTUTILS_LOGGERTEST_H
+#define GMX_TESTUTILS_LOGGERTEST_H
+
+#include "gromacs/utility/classhelpers.h"
+#include "gromacs/utility/logger.h"
+
+namespace gmx
+{
+
+namespace test
+{
+
+/*! \libinternal \brief
+ * Helper class for tests to check output written to a logger.
+ *
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+class LoggerTestHelper
+{
+ public:
+ LoggerTestHelper();
+ ~LoggerTestHelper();
+
+ //! Returns the logger to pass to code under test.
+ const MDLogger &logger();
+
+ /*! \brief
+ * Expects a log entry at a given level matching a given regex.
+ *
+ * Currently, the order of the entries is not checked, and if this
+ * method is called once for a log level, then it needs to be called
+ * for all entries produced by the test.
+ *
+ * If not called for a log level, all entries for that level are
+ * accepted.
+ */
+ void expectEntryMatchingRegex(gmx::MDLogger::LogLevel level,
+ const char *re);
+
+ private:
+ class Impl;
+
+ PrivateImplPointer<Impl> impl_;
+};
+
+} // namespace test
+} // namespace gmx
+
+#endif
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief
+ * Implements functions in mpitest.h.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_testutils
+ */
+#include "gmxpre.h"
+
+#include "mpitest.h"
+
+#include "config.h"
+
+#include <gtest/gtest.h>
+
+#include "thread_mpi/tmpi.h"
+
+#include "gromacs/options/basicoptions.h"
+#include "gromacs/options/ioptionscontainer.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/exceptions.h"
+
+#include "testutils/testoptions.h"
+
+namespace gmx
+{
+namespace test
+{
+
+#if GMX_THREAD_MPI
+
+namespace
+{
+
+//! Number of tMPI threads.
+int g_numThreads = 1;
+//! \cond
+GMX_TEST_OPTIONS(ThreadMpiTestOptions, options)
+{
+ options->addOption(IntegerOption("ntmpi").store(&g_numThreads)
+ .description("Number of thread-MPI threads/ranks for the test"));
+}
+//! \endcond
+
+//! Thread entry function for other thread-MPI threads.
+void threadStartFunc(void *data)
+{
+ std::function<void()> &testBody = *reinterpret_cast<std::function<void()> *>(data);
+ try
+ {
+ testBody();
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+}
+
+//! Helper function for starting thread-MPI threads for a test.
+bool startThreads(std::function<void()> *testBody)
+{
+ int ret = tMPI_Init_fn(TRUE, g_numThreads, TMPI_AFFINITY_NONE,
+ threadStartFunc, testBody);
+ return ret == TMPI_SUCCESS;
+}
+
+class InTestGuard
+{
+ public:
+ explicit InTestGuard(bool *inTest) : inTest_(inTest) { *inTest = true; }
+ ~InTestGuard() { *inTest_ = false; }
+
+ private:
+ bool *inTest_;
+};
+
+} // namespace
+
+//! \cond internal
+bool threadMpiTestRunner(std::function<void()> testBody)
+{
+ static bool inTest = false;
+
+ if (inTest || g_numThreads <= 1)
+ {
+ return true;
+ }
+#if GMX_THREAD_MPI && !GTEST_IS_THREADSAFE
+ ADD_FAILURE()
+ << "Google Test is not thread safe on this platform. "
+ << "Cannot run multi-rank tests with thread-MPI.";
+#else
+ InTestGuard guard(&inTest);
+ if (!startThreads(&testBody))
+ {
+ return false;
+ }
+ try
+ {
+ testBody();
+ }
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ tMPI_Finalize();
+#endif
+ return false;
+}
+//! \endcond
+
+#endif
+
+int getNumberOfTestMpiRanks()
+{
+#if GMX_THREAD_MPI
+ return g_numThreads;
+#else
+ return gmx_node_num();
+#endif
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2016, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \libinternal \file
+ * \brief
+ * Helper functions for MPI tests to make thread-MPI look like real MPI.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \inlibraryapi
+ * \ingroup module_testutils
+ */
+#ifndef GMX_TESTUTILS_MPITEST_H
+#define GMX_TESTUTILS_MPITEST_H
+
+#include "config.h"
+
+#include <functional>
+#include <type_traits>
+
+#include "gromacs/utility/basenetwork.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/*! \brief
+ * Returns the number of MPI ranks to use for an MPI test.
+ *
+ * For thread-MPI builds, this will return the requested number of ranks
+ * even before the thread-MPI threads have been started.
+ *
+ * \ingroup module_testutils
+ */
+int getNumberOfTestMpiRanks();
+//! \cond internal
+/*! \brief
+ * Helper function for GMX_MPI_TEST().
+ *
+ * \ingroup module_testutils
+ */
+bool threadMpiTestRunner(std::function<void()> testBody);
+//! \endcond
+
+/*! \brief
+ * Declares that this test is an MPI-enabled unit test.
+ *
+ * \param[in] expectedRankCount Expected number of ranks for this test.
+ * The test will fail if run with unsupported number of ranks.
+ *
+ * To write unit tests that run under MPI, you need to do a few things:
+ * - Put GMX_MPI_TEST() as the first statement in your test body and
+ * specify the number of ranks this test expects.
+ * - Declare your unit test in CMake with gmx_add_mpi_unit_test().
+ * Note that all tests in the binary should fulfill the conditions above,
+ * and work with the same number of ranks.
+ * TODO: Figure out a mechanism for mixing tests with different rank counts in
+ * the same binary (possibly, also MPI and non-MPI tests).
+ *
+ * When you do the above, the following will happen:
+ * - The test will get compiled only if thread-MPI or real MPI is enabled.
+ * - The test will get executed on the number of ranks specified.
+ * If you are using real MPI, the whole test binary is run under MPI and
+ * test execution across the processes is synchronized (GMX_MPI_TEST()
+ * actually has no effect in this case, the synchronization is handled at a
+ * higher level).
+ * If you are using thread-MPI, GMX_MPI_TEST() is required and it
+ * initializes thread-MPI with the specified number of threads and runs the
+ * rest of the test on each of the threads.
+ *
+ * You need to be extra careful for variables in the test fixture, if you use
+ * one: when run under thread-MPI, these will be shared across all the ranks,
+ * while under real MPI, these are naturally different for each process.
+ * Local variables in the test body are private to each rank in both cases.
+ *
+ * Currently, it is not possible to specify the number of ranks as one, because
+ * that will lead to problems with (at least) thread-MPI, but such tests can be
+ * written as serial tests anyways.
+ *
+ * \ingroup module_testutils
+ */
+#if GMX_THREAD_MPI
+#define GMX_MPI_TEST(expectedRankCount) \
+ do { \
+ ASSERT_EQ(expectedRankCount, ::gmx::test::getNumberOfTestMpiRanks()); \
+ typedef std::remove_reference<decltype(*this)>::type MyTestClass; \
+ if (!::gmx::test::threadMpiTestRunner(std::bind(&MyTestClass::TestBody, this))) \
+ { \
+ return; \
+ } \
+ } while (0)
+#else
+#define GMX_MPI_TEST(expectedRankCount) \
+ ASSERT_EQ(expectedRankCount, ::gmx::test::getNumberOfTestMpiRanks())
+#endif
+
+} // namespace test
+} // namespace gmx
+
+#endif
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/strconvert.h"
#include "gromacs/utility/stringutil.h"
#include "testutils/refdata-impl.h"
std::string value_;
};
-//! Helper function to parse a floating-point value.
-// TODO: Move this into src/gromacs/utility/, and consolidate with similar code
-// elsewhere.
-double convertDouble(const std::string &value)
-{
- char *endptr;
- double convertedValue = std::strtod(value.c_str(), &endptr);
- // TODO: Check for overflow
- if (*endptr != '\0')
- {
- GMX_THROW(InvalidInputError("Invalid floating-point value: " + value));
- }
- return convertedValue;
-}
//! Helper function to parse a floating-point reference data value.
-double convertDoubleReferenceValue(const std::string &value)
+static inline double convertDoubleReferenceValue(const std::string &value)
{
try
{
- return convertDouble(value);
+ return fromString<double>(value);
}
catch (const InvalidInputError &ex)
{
virtual ::testing::AssertionResult
checkEntry(const ReferenceDataEntry &entry, const std::string &fullId) const
{
- FloatType value = static_cast<FloatType>(convertDouble(value_));
+ FloatType value = fromString<FloatType>(value_);
FloatType refValue = static_cast<FloatType>(convertDoubleReferenceValue(entry.value()));
FloatingPointDifference diff(refValue, value);
if (tolerance_.isWithin(diff))
FloatingPointTolerance tolerance_;
};
+template <typename ValueType>
+class ValueExtractor : public IReferenceDataEntryChecker
+{
+ public:
+ explicit ValueExtractor(ValueType *value)
+ : value_(value)
+ {
+ }
+
+ virtual void fillEntry(ReferenceDataEntry *) const
+ {
+ GMX_THROW(TestException("Extracting value from non-existent reference data entry"));
+ }
+ virtual ::testing::AssertionResult
+ checkEntry(const ReferenceDataEntry &entry, const std::string &) const
+ {
+ extractValue(entry.value());
+ return ::testing::AssertionSuccess();
+ }
+
+ void extractValue(const std::string &value) const
+ {
+ *value_ = fromString<ValueType>(value);
+ }
+
+ private:
+ ValueType *value_;
+};
+
+template <> inline void
+ValueExtractor<std::string>::extractValue(const std::string &value) const
+{
+ *value_ = value;
+}
+
} // namespace test
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
}
ReferenceDataEntry(const char *type, const char *id)
- : type_(type), id_(id != NULL ? id : ""), isTextBlock_(false),
- correspondingOutputEntry_(NULL)
+ : type_(type), id_(id != nullptr ? id : ""), isTextBlock_(false),
+ hasBeenChecked_(false), correspondingOutputEntry_(nullptr)
{
}
bool idMatches(const char *id) const
{
- return (id == NULL && id_.empty()) || (id != NULL && id_ == id);
+ return (id == nullptr && id_.empty()) || (id != nullptr && id_ == id);
}
ChildIterator findChild(const char *id, const ChildIterator &prev) const
bool wrappingSearch = true;
if (child != children_.end())
{
- if (id == NULL && (*child)->id().empty())
+ if (id == nullptr && (*child)->id().empty())
{
wrappingSearch = false;
++child;
return prev != children_.end();
}
+ bool hasBeenChecked() const { return hasBeenChecked_; }
+ void setChecked() { hasBeenChecked_ = true; }
+
+ void setCheckedIncludingChildren()
+ {
+ setChecked();
+ for (const auto &child : children_)
+ {
+ child->setCheckedIncludingChildren();
+ }
+ }
+
EntryPointer cloneToOutputEntry()
{
EntryPointer entry(new ReferenceDataEntry(type_.c_str(), id_.c_str()));
}
void setCorrespondingOutputEntry(ReferenceDataEntry *entry)
{
- GMX_RELEASE_ASSERT(correspondingOutputEntry_ == NULL,
+ GMX_RELEASE_ASSERT(correspondingOutputEntry_ == nullptr,
"Output entry already exists");
correspondingOutputEntry_ = entry;
}
std::string value_;
bool isTextBlock_;
ChildList children_;
+ bool hasBeenChecked_;
ReferenceDataEntry *correspondingOutputEntry_;
};
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/keyvaluetree.h"
#include "gromacs/utility/path.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/variant.h"
#include "testutils/refdata-checkers.h"
#include "testutils/refdata-impl.h"
}
};
+//! Formats a path to a reference data entry with a non-null id.
+std::string formatEntryPath(const std::string &prefix, const std::string &id)
+{
+ return prefix + "/" + id;
+}
+
+//! Formats a path to a reference data entry with a null id.
+std::string formatSequenceEntryPath(const std::string &prefix, int seqIndex)
+{
+ return formatString("%s/[%d]", prefix.c_str(), seqIndex+1);
+}
+
+//! Finds all entries that have not been checked under a given root.
+void gatherUnusedEntries(const ReferenceDataEntry &root,
+ const std::string &rootPath,
+ std::vector<std::string> *unusedPaths)
+{
+ if (!root.hasBeenChecked())
+ {
+ unusedPaths->push_back(rootPath);
+ return;
+ }
+ int seqIndex = 0;
+ for (const auto &child : root.children())
+ {
+ std::string path;
+ if (child->id().empty())
+ {
+ path = formatSequenceEntryPath(rootPath, seqIndex);
+ ++seqIndex;
+ }
+ else
+ {
+ path = formatEntryPath(rootPath, child->id());
+ }
+ gatherUnusedEntries(*child, path, unusedPaths);
+ }
+}
+
+//! Produces a GTest assertion of any entries under given root have not been checked.
+void checkUnusedEntries(const ReferenceDataEntry &root, const std::string &rootPath)
+{
+ std::vector<std::string> unusedPaths;
+ gatherUnusedEntries(root, rootPath, &unusedPaths);
+ if (!unusedPaths.empty())
+ {
+ std::string paths;
+ if (unusedPaths.size() > 5)
+ {
+ paths = joinStrings(unusedPaths.begin(), unusedPaths.begin() + 5, "\n ");
+ paths = " " + paths + "\n ...";
+ }
+ else
+ {
+ paths = joinStrings(unusedPaths.begin(), unusedPaths.end(), "\n ");
+ paths = " " + paths;
+ }
+ ADD_FAILURE() << "Reference data items not used in test:" << std::endl << paths;
+ }
+}
+
} // namespace
void initReferenceData(IOptionsContainer *options)
void TestReferenceDataImpl::onTestEnd(bool testPassed)
{
+ if (!bInUse_)
+ {
+ return;
+ }
// TODO: Only write the file with update-changed if there were actual changes.
- if (testPassed && bInUse_ && outputRootEntry_)
+ if (outputRootEntry_)
{
- std::string dirname = Path::getParentPath(fullFilename_);
- if (!Directory::exists(dirname))
+ if (testPassed)
{
- if (Directory::create(dirname) != 0)
+ std::string dirname = Path::getParentPath(fullFilename_);
+ if (!Directory::exists(dirname))
{
- GMX_THROW(TestException("Creation of reference data directory failed: " + dirname));
+ if (Directory::create(dirname) != 0)
+ {
+ GMX_THROW(TestException("Creation of reference data directory failed: " + dirname));
+ }
}
+ writeReferenceDataFile(fullFilename_, *outputRootEntry_);
}
- writeReferenceDataFile(fullFilename_, *outputRootEntry_);
+ }
+ else if (compareRootEntry_)
+ {
+ checkUnusedEntries(*compareRootEntry_, "");
}
}
static const char * const cBooleanNodeName;
//! String constant for naming XML elements for string values.
static const char * const cStringNodeName;
+ //! String constant for naming XML elements for unsigned char values.
+ static const char * const cUCharNodeName;
//! String constant for naming XML elements for integer values.
static const char * const cIntegerNodeName;
//! String constant for naming XML elements for int64 values.
static const char * const cIdAttrName;
//! String constant for naming compounds for vectors.
static const char * const cVectorType;
+ //! String constant for naming compounds for key-value tree objects.
+ static const char * const cObjectType;
//! String constant for naming compounds for sequences.
static const char * const cSequenceType;
//! String constant for value identifier for sequence length.
{
GMX_RELEASE_ASSERT(initialized(),
"Accessing uninitialized reference data checker.");
- return compareRootEntry_ == NULL;
+ return compareRootEntry_ == nullptr;
}
//! Whether initialized with other means than the default constructor.
/*! \brief
* Current number of unnamed elements in a sequence.
*
- * It is the index of the next added unnamed element.
+ * It is the index of the current unnamed element.
*/
int seqIndex_;
};
const char *const TestReferenceChecker::Impl::cBooleanNodeName = "Bool";
const char *const TestReferenceChecker::Impl::cStringNodeName = "String";
+const char *const TestReferenceChecker::Impl::cUCharNodeName = "UChar";
const char *const TestReferenceChecker::Impl::cIntegerNodeName = "Int";
const char *const TestReferenceChecker::Impl::cInt64NodeName = "Int64";
const char *const TestReferenceChecker::Impl::cUInt64NodeName = "UInt64";
const char *const TestReferenceChecker::Impl::cRealNodeName = "Real";
const char *const TestReferenceChecker::Impl::cIdAttrName = "Name";
const char *const TestReferenceChecker::Impl::cVectorType = "Vector";
+const char *const TestReferenceChecker::Impl::cObjectType = "Object";
const char *const TestReferenceChecker::Impl::cSequenceType = "Sequence";
const char *const TestReferenceChecker::Impl::cSequenceLengthName = "Length";
TestReferenceChecker::Impl::Impl(bool initialized)
: initialized_(initialized), defaultTolerance_(defaultRealTolerance()),
- compareRootEntry_(NULL), outputRootEntry_(NULL),
- updateMismatchingEntries_(false), bSelfTestMode_(false), seqIndex_(0)
+ compareRootEntry_(nullptr), outputRootEntry_(nullptr),
+ updateMismatchingEntries_(false), bSelfTestMode_(false), seqIndex_(-1)
{
}
ReferenceDataEntry *outputRootEntry,
bool updateMismatchingEntries, bool bSelfTestMode,
const FloatingPointTolerance &defaultTolerance)
- : initialized_(true), defaultTolerance_(defaultTolerance), path_(path + "/"),
+ : initialized_(true), defaultTolerance_(defaultTolerance), path_(path),
compareRootEntry_(compareRootEntry), outputRootEntry_(outputRootEntry),
lastFoundEntry_(compareRootEntry->children().end()),
updateMismatchingEntries_(updateMismatchingEntries),
- bSelfTestMode_(bSelfTestMode), seqIndex_(0)
+ bSelfTestMode_(bSelfTestMode), seqIndex_(-1)
{
}
std::string
TestReferenceChecker::Impl::appendPath(const char *id) const
{
- std::string printId = (id != NULL) ? id : formatString("[%d]", seqIndex_);
- return path_ + printId;
+ return id != nullptr
+ ? formatEntryPath(path_, id)
+ : formatSequenceEntryPath(path_, seqIndex_);
}
ReferenceDataEntry *TestReferenceChecker::Impl::findEntry(const char *id)
{
ReferenceDataEntry::ChildIterator entry = compareRootEntry_->findChild(id, lastFoundEntry_);
- seqIndex_ = (id == NULL) ? seqIndex_+1 : 0;
+ seqIndex_ = (id == nullptr) ? seqIndex_+1 : -1;
if (compareRootEntry_->isValidChild(entry))
{
lastFoundEntry_ = entry;
return entry->get();
}
- return NULL;
+ return nullptr;
}
ReferenceDataEntry *
const IReferenceDataEntryChecker &checker)
{
ReferenceDataEntry *entry = findEntry(id);
- if (entry == NULL && outputRootEntry_ != NULL)
+ if (entry == nullptr && outputRootEntry_ != nullptr)
{
lastFoundEntry_ = compareRootEntry_->addChild(createEntry(type, id, checker));
entry = lastFoundEntry_->get();
}
std::string fullId = appendPath(id);
ReferenceDataEntry *entry = findOrCreateEntry(type, id, checker);
- if (entry == NULL)
+ if (entry == nullptr)
{
return ::testing::AssertionFailure()
<< "Reference data item " << fullId << " not found";
}
+ entry->setChecked();
::testing::AssertionResult result(checkEntry(*entry, fullId, type, checker));
- if (outputRootEntry_ != NULL && entry->correspondingOutputEntry() == NULL)
+ if (outputRootEntry_ != nullptr && entry->correspondingOutputEntry() == nullptr)
{
if (!updateMismatchingEntries_ || result)
{
{
return TestReferenceChecker(new TestReferenceChecker::Impl(true));
}
+ impl_->compareRootEntry_->setChecked();
return TestReferenceChecker(
new TestReferenceChecker::Impl("", impl_->compareRootEntry_.get(),
impl_->outputRootEntry_.get(),
}
+void TestReferenceChecker::checkUnusedEntries()
+{
+ if (impl_->compareRootEntry_)
+ {
+ gmx::test::checkUnusedEntries(*impl_->compareRootEntry_, impl_->path_);
+ // Mark them checked so that they are reported only once.
+ impl_->compareRootEntry_->setCheckedIncludingChildren();
+ }
+}
+
+
bool TestReferenceChecker::checkPresent(bool bPresent, const char *id)
{
- if (impl_->shouldIgnore() || impl_->outputRootEntry_ != NULL)
+ if (impl_->shouldIgnore() || impl_->outputRootEntry_ != nullptr)
{
return bPresent;
}
std::string fullId = impl_->appendPath(id);
NullChecker checker;
ReferenceDataEntry *entry = impl_->findOrCreateEntry(type, id, checker);
- if (entry == NULL)
+ if (entry == nullptr)
{
ADD_FAILURE() << "Reference data item " << fullId << " not found";
return TestReferenceChecker(new Impl(true));
}
+ entry->setChecked();
if (impl_->updateMismatchingEntries_)
{
entry->makeCompound(type);
return TestReferenceChecker(new Impl(true));
}
}
- if (impl_->outputRootEntry_ != NULL && entry->correspondingOutputEntry() == NULL)
+ if (impl_->outputRootEntry_ != nullptr && entry->correspondingOutputEntry() == nullptr)
{
impl_->outputRootEntry_->addChild(entry->cloneToOutputEntry());
}
}
+void TestReferenceChecker::checkUChar(unsigned char value, const char *id)
+{
+ EXPECT_PLAIN(impl_->processItem(Impl::cUCharNodeName, id,
+ ExactStringChecker(formatString("%d", value))));
+}
+
void TestReferenceChecker::checkInteger(int value, const char *id)
{
EXPECT_PLAIN(impl_->processItem(Impl::cIntegerNodeName, id,
}
+void TestReferenceChecker::checkVariant(const Variant &variant, const char *id)
+{
+ if (variant.isType<bool>())
+ {
+ checkBoolean(variant.cast<bool>(), id);
+ }
+ else if (variant.isType<int>())
+ {
+ checkInteger(variant.cast<int>(), id);
+ }
+ else if (variant.isType<gmx_int64_t>())
+ {
+ checkInt64(variant.cast<gmx_int64_t>(), id);
+ }
+ else if (variant.isType<float>())
+ {
+ checkFloat(variant.cast<float>(), id);
+ }
+ else if (variant.isType<double>())
+ {
+ checkDouble(variant.cast<double>(), id);
+ }
+ else if (variant.isType<std::string>())
+ {
+ checkString(variant.cast<std::string>(), id);
+ }
+ else
+ {
+ GMX_THROW(TestException("Unsupported variant type"));
+ }
+}
+
+
+void TestReferenceChecker::checkKeyValueTreeObject(const KeyValueTreeObject &tree, const char *id)
+{
+ TestReferenceChecker compound(checkCompound(Impl::cObjectType, id));
+ for (const auto &prop : tree.properties())
+ {
+ compound.checkKeyValueTreeValue(prop.value(), prop.key().c_str());
+ }
+ compound.checkUnusedEntries();
+}
+
+
+void TestReferenceChecker::checkKeyValueTreeValue(const KeyValueTreeValue &value, const char *id)
+{
+ if (value.isObject())
+ {
+ checkKeyValueTreeObject(value.asObject(), id);
+ }
+ else if (value.isArray())
+ {
+ const auto &values = value.asArray().values();
+ checkSequence(values.begin(), values.end(), id);
+ }
+ else
+ {
+ checkVariant(value.asVariant(), id);
+ }
+}
+
+
TestReferenceChecker
TestReferenceChecker::checkSequenceCompound(const char *id, size_t length)
{
return compound;
}
+
+unsigned char TestReferenceChecker::readUChar(const char *id)
+{
+ if (impl_->shouldIgnore())
+ {
+ GMX_THROW(TestException("Trying to read from non-existent reference data value"));
+ }
+ int value = 0;
+ EXPECT_PLAIN(impl_->processItem(Impl::cUCharNodeName, id,
+ ValueExtractor<int>(&value)));
+ return value;
+}
+
+
+int TestReferenceChecker::readInteger(const char *id)
+{
+ if (impl_->shouldIgnore())
+ {
+ GMX_THROW(TestException("Trying to read from non-existent reference data value"));
+ }
+ int value = 0;
+ EXPECT_PLAIN(impl_->processItem(Impl::cIntegerNodeName, id,
+ ValueExtractor<int>(&value)));
+ return value;
+}
+
+
+gmx_int64_t TestReferenceChecker::readInt64(const char *id)
+{
+ if (impl_->shouldIgnore())
+ {
+ GMX_THROW(TestException("Trying to read from non-existent reference data value"));
+ }
+ gmx_int64_t value = 0;
+ EXPECT_PLAIN(impl_->processItem(Impl::cInt64NodeName, id,
+ ValueExtractor<gmx_int64_t>(&value)));
+ return value;
+}
+
+
+float TestReferenceChecker::readFloat(const char *id)
+{
+ if (impl_->shouldIgnore())
+ {
+ GMX_THROW(TestException("Trying to read from non-existent reference data value"));
+ }
+ float value = 0;
+ EXPECT_PLAIN(impl_->processItem(Impl::cRealNodeName, id,
+ ValueExtractor<float>(&value)));
+ return value;
+}
+
+
+double TestReferenceChecker::readDouble(const char *id)
+{
+ if (impl_->shouldIgnore())
+ {
+ GMX_THROW(TestException("Trying to read from non-existent reference data value"));
+ }
+ double value = 0;
+ EXPECT_PLAIN(impl_->processItem(Impl::cRealNodeName, id,
+ ValueExtractor<double>(&value)));
+ return value;
+}
+
+
+std::string TestReferenceChecker::readString(const char *id)
+{
+ if (impl_->shouldIgnore())
+ {
+ GMX_THROW(TestException("Trying to read from non-existent reference data value"));
+ }
+ std::string value;
+ EXPECT_PLAIN(impl_->processItem(Impl::cStringNodeName, id,
+ ValueExtractor<std::string>(&value)));
+ return value;
+}
+
} // namespace test
} // namespace gmx
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
class IOptionsContainer;
+class KeyValueTreeObject;
+class KeyValueTreeValue;
+class Variant;
namespace test
{
*/
void setDefaultTolerance(const FloatingPointTolerance &tolerance);
+ /*! \brief
+ * Checks that all reference values have been compared against.
+ *
+ * All values under the compound represented by this checker are
+ * checked, and a non-fatal Google Test assertion is produced if some
+ * values have not been used.
+ *
+ * If not called explicitly, the same check will be done for all
+ * reference data values when the test ends.
+ *
+ * This method also marks the values used, so that subsequent checks
+ * (including the check at the end of the test) will not produce
+ * another assertion about the same values.
+ */
+ void checkUnusedEntries();
+
/*! \brief
* Checks whether a data item is present.
*
* is easier to edit by hand to set the desired output formatting.
*/
void checkTextBlock(const std::string &value, const char *id);
+ //! Check a single unsigned char value.
+ void checkUChar(unsigned char value, const char *id);
//! Check a single integer value.
void checkInteger(int value, const char *id);
//! Check a single int64 value.
void checkVector(const double value[3], const char *id);
//! Check a single floating-point value from a string.
void checkRealFromString(const std::string &value, const char *id);
+ //! Checks a variant value that contains a supported simple type.
+ void checkVariant(const Variant &value, const char *id);
+ //! Checks a key-value tree rooted at a object.
+ void checkKeyValueTreeObject(const KeyValueTreeObject &tree, const char *id);
+ //! Checks a generic key-value tree value.
+ void checkKeyValueTreeValue(const KeyValueTreeValue &value, const char *id);
+
+ /*! \name Methods to read values from reference data
+ *
+ * These methods assume that a value with the given `id` has already
+ * been created in the test with `check*()` methods, and that it has
+ * the correct type.
+ *
+ * Currently, these methods do not work correctly if the reference data
+ * file does not exist, so a test using them may fail with exceptions
+ * before the reference data has been generated.
+ * \{
+ */
+ //! Reads an unsigned char value.
+ unsigned char readUChar(const char *id);
+ //! Reads an integer value.
+ int readInteger(const char *id);
+ //! Reads a 64-bit integer value.
+ gmx_int64_t readInt64(const char *id);
+ //! Reads a float value.
+ float readFloat(const char *id);
+ //! Reads a double value.
+ double readDouble(const char *id);
+ //! Reads a string value.
+ std::string readString(const char *id);
+ //! \}
/*! \name Overloaded versions of simple checker methods
*
{
checkVector(value, id);
}
+ //! Check a generic key-value tree value.
+ void checkValue(const KeyValueTreeValue &value, const char *id)
+ {
+ checkKeyValueTreeValue(value, id);
+ }
/*!\}*/
/*! \brief
TestReferenceChecker compound(checkSequenceCompound(id, length));
for (Iterator i = begin; i != end; ++i)
{
- compound.checkValue(*i, NULL);
+ compound.checkValue(*i, nullptr);
}
}
/*! \brief
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \internal \file
* \brief
- * Implements classes in integrationtests.h.
+ * Implements classes in stdiohelper.h.
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \ingroup module_testutils
*/
#include "gmxpre.h"
-#include "integrationtests.h"
+#include "stdiohelper.h"
-#include <stdio.h>
+#include <cerrno>
+#include <cstdio>
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/textwriter.h"
+#include "testutils/testfilemanager.h"
+
namespace gmx
{
namespace test
{
/********************************************************************
- * IntegrationTestFixture
+ * StdioTestHelper
*/
-IntegrationTestFixture::IntegrationTestFixture()
-{
-}
-
-IntegrationTestFixture::~IntegrationTestFixture()
-{
-}
-
void
-IntegrationTestFixture::redirectStringToStdin(const char* theString)
+StdioTestHelper::redirectStringToStdin(const char *theString)
{
- std::string fakeStdin("fake-stdin");
+ const std::string fakeStdin = fileManager_.getTemporaryFilePath(".stdin");
gmx::TextWriter::writeFileFromString(fakeStdin, theString);
- if (NULL == std::freopen(fakeStdin.c_str(), "r", stdin))
+ if (nullptr == std::freopen(fakeStdin.c_str(), "r", stdin))
{
GMX_THROW_WITH_ERRNO(FileIOError("Failed to redirect a string to stdin"),
"freopen",
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
*/
/*! \libinternal \file
* \brief
- * Declares test fixture for integration tests
+ * Declares gmx::test::StdioTestHelper.
*
* \author Mark Abraham <mark.j.abraham@gmail.com>
* \inlibraryapi
* \ingroup module_testutils
*/
-#ifndef GMX_INTEGRATION_TESTS_MODULETEST_H
-#define GMX_INTEGRATION_TESTS_MODULETEST_H
+#ifndef GMX_TESTUTILS_STDIOHELPER_H
+#define GMX_TESTUTILS_STDIOHELPER_H
-#include <gtest/gtest.h>
-
-#include "testutils/testfilemanager.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
-
namespace test
{
+class TestFileManager;
+
/*! \libinternal \brief
- * Test fixture for integration tests.
+ * Helper class for tests where code reads directly from `stdin`.
*
* Any method in this class may throw std::bad_alloc if out of memory.
*
* \inlibraryapi
* \ingroup module_testutils
*/
-class IntegrationTestFixture : public ::testing::Test
+class StdioTestHelper
{
- protected:
- IntegrationTestFixture();
- virtual ~IntegrationTestFixture();
+ public:
+ //! Creates a helper using the given file manager.
+ explicit StdioTestHelper(TestFileManager *fileManager)
+ : fileManager_(*fileManager)
+ {
+ }
/*! \brief Accepts a string as input, writes it to a temporary
* file and then reopens stdin to read the contents of that
*
* \throws FileIOError when the freopen() fails
*/
- void redirectStringToStdin(const char* theString);
+ void redirectStringToStdin(const char *theString);
- /*! \brief Discards stdout while running a test
- *
- * \todo Implement this when the output routines are
- * sufficiently modular to permit it to work. */
- void redirectStdoutToDevNull();
- /*! \brief Discards stderr while running a test
- *
- * \todo Implement this when the output routines are
- * sufficiently modular to permit it to work. */
- void redirectStderrToDevNull();
-
- /* TEST_F() constructs derived classes, and those classes and
- * their member objects might need to access implementation
- * details, so we cannot use the private access specifer
- * here. */
- public:
+ private:
+ TestFileManager &fileManager_;
- /*! \brief Object that manages finding input files, writing
- * temporary output files and cleaning up files.
- */
- ::gmx::test::TestFileManager fileManager_;
+ GMX_DISALLOW_COPY_AND_ASSIGN(StdioTestHelper);
};
} // namespace test
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* If this flag is not given, they check the strings using the XML reference
* framework (see TestReferenceData).
*
+ * Tests that need simple checking of a string, or container of
+ * strings, should consider the normal implementation in
+ * TestReferenceChecker.
+ *
* \inlibraryapi
* \ingroup module_testutils
*/
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* FloatingPointDifference
*/
-FloatingPointDifference::FloatingPointDifference(float value1, float value2)
+FloatingPointDifference::FloatingPointDifference(float ref, float value)
+ : termMagnitude_(std::abs(ref))
{
- initDifference(value1, value2,
+ initDifference(ref, value,
&absoluteDifference_, &ulpDifference_, &bSignDifference_);
bDouble_ = false;
}
-FloatingPointDifference::FloatingPointDifference(double value1, double value2)
+FloatingPointDifference::FloatingPointDifference(double ref, double value)
+ : termMagnitude_(std::abs(ref))
{
- initDifference(value1, value2,
+ initDifference(ref, value,
&absoluteDifference_, &ulpDifference_, &bSignDifference_);
bDouble_ = true;
}
std::string FloatingPointDifference::toString() const
{
- const double eps = isDouble() ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS;
- return formatString("%g (%" GMX_PRIu64 " %s-prec. ULPs, rel. %.3g)%s",
+ std::string relDiffStr;
+
+ if (termMagnitude_ > 0)
+ {
+ // If the reference value is finite we calculate the proper quotient
+ relDiffStr = formatString("%.3g", std::abs(absoluteDifference_/termMagnitude_));
+ }
+ else if (absoluteDifference_ == 0.0)
+ {
+ // If the numbers are identical the quotient is strictly NaN here, but
+ // there no reason to worry when we have a perfect match.
+ relDiffStr = formatString("%.3g", 0.0);
+ }
+ else
+ {
+ // If the reference value is zero and numbers are non-identical, relative difference is infinite.
+ relDiffStr = formatString("Inf");
+ }
+
+ return formatString("%g (%" GMX_PRIu64 " %s-prec. ULPs, rel. %s)%s",
absoluteDifference_, ulpDifference_,
isDouble() ? "double" : "single",
- ulpDifference_ * eps,
+ relDiffStr.c_str(),
bSignDifference_ ? ", signs differ" : "");
}
return true;
}
+ // By using smaller-than-or-equal below, we allow the test to pass if
+ // the numbers are identical, even if the term magnitude is 0, which seems
+ // a reasonable thing to do...
+ const double relativeTolerance
+ = difference.isDouble() ? doubleRelativeTolerance_ : singleRelativeTolerance_;
+
+ if (difference.asAbsolute() <= relativeTolerance * difference.termMagnitude())
+ {
+ return true;
+ }
+
const gmx_uint64_t ulpTolerance
= difference.isDouble() ? doubleUlpTolerance_ : singleUlpTolerance_;
if (ulpTolerance < GMX_UINT64_MAX && difference.asUlps() <= ulpTolerance)
{
return true;
}
+
return false;
}
std::string result;
const double absoluteTolerance
= difference.isDouble() ? doubleAbsoluteTolerance_ : singleAbsoluteTolerance_;
+ const double relativeTolerance
+ = difference.isDouble() ? doubleRelativeTolerance_ : singleRelativeTolerance_;
const gmx_uint64_t ulpTolerance
= difference.isDouble() ? doubleUlpTolerance_ : singleUlpTolerance_;
- const double eps
- = difference.isDouble() ? GMX_DOUBLE_EPS : GMX_FLOAT_EPS;
if (absoluteTolerance > 0.0)
{
result.append(formatString("abs. %g", absoluteTolerance));
}
+ if (relativeTolerance > 0.0)
+ {
+ if (!result.empty())
+ {
+ result.append(", ");
+ }
+ result.append(formatString("rel. %.3g", relativeTolerance));
+ }
if (ulpTolerance < GMX_UINT64_MAX)
{
if (!result.empty())
{
result.append(", ");
}
- result.append(formatString("%" GMX_PRIu64 " ULPs (rel. %.3g)", ulpTolerance, ulpTolerance * eps));
+ result.append(formatString("%" GMX_PRIu64 " ULPs", ulpTolerance));
}
if (bSignMustMatch_)
{
FloatingPointTolerance
relativeToleranceAsFloatingPoint(double magnitude, double tolerance)
{
- const double absoluteTolerance = magnitude * tolerance;
+ const double absoluteTolerance = std::abs(magnitude) * tolerance;
return FloatingPointTolerance(absoluteTolerance, absoluteTolerance,
- relativeToleranceToUlp<float>(tolerance),
- relativeToleranceToUlp<double>(tolerance),
+ tolerance, tolerance,
+ GMX_UINT64_MAX, GMX_UINT64_MAX,
false);
}
//! \endcond
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
class FloatingPointDifference
{
public:
- //! Initializes a single-precision difference.
- FloatingPointDifference(float value1, float value2);
- //! Initializes a double-precision difference.
- FloatingPointDifference(double value1, double value2);
+
+ /*! \brief Initializes a single-precision difference.
+ *
+ * \param ref First term in difference
+ * \param value Second term in difference
+ *
+ * For absolute and ULP differences the two parameters are equivalent,
+ * since the difference is symmetric. For relative differences
+ * the first term is interpreted as the reference value, from which
+ * we extract the magnitude to compare with.
+ */
+ FloatingPointDifference(float ref, float value);
+
+ /*! \brief Initializes a double-precision difference.
+ *
+ * \param ref First term in difference
+ * \param value Second term in difference
+ *
+ * For absolute and ULP differences the two parameters are equivalent,
+ * since the difference is symmetric. For relative differences
+ * the first term is interpreted as the reference value, from which
+ * we extract the magnitude to compare with.
+ */
+ FloatingPointDifference(double ref, double value);
/*! \brief
* Whether one or both of the compared values were NaN.
//! Formats the difference as a string for assertion failure messages.
std::string toString() const;
+ //! Returns the magnitude of the original second term of the difference.
+ double termMagnitude() const { return termMagnitude_; }
+
private:
+
+ //! Save the magnitude of the reference value for relative (i.e., not ULP) tolerance
+ double termMagnitude_;
//! Stores the absolute difference, or NaN if one or both values were NaN.
double absoluteDifference_;
gmx_uint64_t ulpDifference_;
* the given tolerance for the check to pass.
* Setting the absolute tolerance to zero disables the absolute tolerance
* check.
+ * - _relative tolerance_: the absolute difference between the numbers must
+ * be smaller than the tolerance multiplied by the first number. Setting
+ * the relative tolerance to zero disables this check.
* - _ULP tolerance_: ULP (units of least precision) difference between the
* values must be smaller than the given tolerance for the check to pass.
* Setting the ULP tolerance to zero requires exact match.
* check (note that this also applies to `0.0` and `-0.0`: a value with a
* different sign than the zero will fail the check).
*
- * Either an absolute or a ULP tolerance must always be specified.
- * If both are specified, then the check passes if either of the tolerances is
- * satisfied.
+ * Either an absolute, relative, or ULP tolerance must always be specified.
+ * If several of them are specified, then the check passes if either of the
+ * tolerances is satisfied.
*
- * Any combination of absolute and ULP tolerance can be combined with the sign
- * check. In this case, the sign check must succeed for the check to pass,
- * even if other tolerances are satisfied.
+ * Any combination of absolute, relative, and ULP tolerance can be combined with
+ * the sign check. In this case, the sign check must succeed for the check to
+ * pass, even if other tolerances are satisfied.
*
* The tolerances can be specified separately for single and double precision
* comparison. Different initialization functions have different semantics on
* Allowed absolute difference in a single-precision number.
* \param[in] doubleAbsoluteTolerance
* Allowed absolute difference in a double-precision number.
+ * \param[in] singleRelativeTolerance
+ * Allowed relative difference in a single-precision number.
+ * \param[in] doubleRelativeTolerance
+ * Allowed relative difference in a double-precision number.
* \param[in] singleUlpTolerance
* Allowed ULP difference in a single-precision number.
* \param[in] doubleUlpTolerance
*/
FloatingPointTolerance(float singleAbsoluteTolerance,
double doubleAbsoluteTolerance,
+ float singleRelativeTolerance,
+ double doubleRelativeTolerance,
gmx_uint64_t singleUlpTolerance,
gmx_uint64_t doubleUlpTolerance,
bool bSignMustMatch)
: singleAbsoluteTolerance_(singleAbsoluteTolerance),
doubleAbsoluteTolerance_(doubleAbsoluteTolerance),
+ singleRelativeTolerance_(singleRelativeTolerance),
+ doubleRelativeTolerance_(doubleRelativeTolerance),
singleUlpTolerance_(singleUlpTolerance),
doubleUlpTolerance_(doubleUlpTolerance),
bSignMustMatch_(bSignMustMatch)
private:
float singleAbsoluteTolerance_;
double doubleAbsoluteTolerance_;
+ float singleRelativeTolerance_;
+ double doubleRelativeTolerance_;
gmx_uint64_t singleUlpTolerance_;
gmx_uint64_t doubleUlpTolerance_;
bool bSignMustMatch_;
static inline FloatingPointTolerance
ulpTolerance(gmx_uint64_t ulpDiff)
{
- return FloatingPointTolerance(0.0, 0.0, ulpDiff, ulpDiff, false);
+ return FloatingPointTolerance(0.0, 0.0, 0.0, 0.0, ulpDiff, ulpDiff, false);
}
/*! \brief
* \param[in] magnitude Magnitude of the numbers the computation operates in.
* \param[in] tolerance Relative tolerance permitted (e.g. 1e-4).
*
- * In addition to setting an ULP tolerance equivalent to \p tolerance for both
+ * In addition to setting an relative tolerance for both
* precisions, this sets the absolute tolerance such that values close to zero
* (in general, smaller than \p magnitude) do not fail the check if they
* differ by less than \p tolerance evaluated at \p magnitude. This accounts
* accuracy of values much less than \p magnitude do not matter for
* correctness.
*
- * The ULP tolerance for different precisions will be different to make them
- * both match \p tolerance.
- *
* \related FloatingPointTolerance
*/
FloatingPointTolerance
{
return FloatingPointTolerance(magnitude*singleUlpDiff*GMX_FLOAT_EPS,
magnitude*doubleUlpDiff*GMX_DOUBLE_EPS,
+ 0.0, 0.0,
singleUlpDiff, doubleUlpDiff, false);
}
static inline FloatingPointTolerance
absoluteTolerance(double tolerance)
{
- return FloatingPointTolerance(tolerance, tolerance,
+ return FloatingPointTolerance(tolerance, tolerance, 0.0, 0.0,
GMX_UINT64_MAX, GMX_UINT64_MAX, false);
}
//! \}
-/*! \name Assertions for NULL comparison
- *
- * These macros should be used instead of `(EXPECT|ASSERT)_EQ(NULL, ...)`,
- * because Google Test doesn't support the NULL comparison with xlC++ 12.1 on
- * BG/Q.
- */
-//! \{
-
-/*! \brief
- * Asserts that a pointer is null.
- *
- * Works exactly like EXPECT_EQ comparing with a null pointer. */
-#define EXPECT_NULL(val) EXPECT_EQ((void *) NULL, val)
-/*! \brief
- * Asserts that a pointer is null.
- *
- * Works exactly like ASSERT_EQ comparing with a null pointer. */
-#define ASSERT_NULL(val) ASSERT_EQ((void *) NULL, val)
-
-//! \}
-
//! \cond internal
/*! \internal \brief
* Helper method for `(EXPECT|ASSERT)_PLAIN`.
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
};
std::string TestFileManager::Impl::s_inputDirectory;
-const char *TestFileManager::Impl::s_globalOutputTempDirectory = NULL;
+const char *TestFileManager::Impl::s_globalOutputTempDirectory = nullptr;
/** Controls whether TestFileManager should delete temporary files
after the test finishes. */
static bool g_bDeleteFilesAfterTest = true;
const char *TestFileManager::getGlobalOutputTempDirectory()
{
- GMX_RELEASE_ASSERT(Impl::s_globalOutputTempDirectory != NULL, "Global path for temporary output files from tests is not set");
+ GMX_RELEASE_ASSERT(Impl::s_globalOutputTempDirectory != nullptr, "Global path for temporary output files from tests is not set");
return Impl::s_globalOutputTempDirectory;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
{
if (existingFiles_.count(filename) == 0)
{
- File::NotFoundInfo info(filename, "File not present in test", NULL, false, 0);
+ File::NotFoundInfo info(filename, "File not present in test", nullptr, false, 0);
onNotFound(info);
return false;
}
if (!impl_->stdoutStream_)
{
impl_->stdoutStream_.reset(new StringOutputStream);
- impl_->fileList_.push_back(Impl::FileListEntry("<stdout>", impl_->stdoutStream_));
+ impl_->fileList_.emplace_back("<stdout>", impl_->stdoutStream_);
}
return *impl_->stdoutStream_;
}
TestFileOutputRedirector::openTextOutputFile(const char *filename)
{
Impl::StringStreamPointer stream(new StringOutputStream);
- impl_->fileList_.push_back(Impl::FileListEntry(filename, stream));
+ impl_->fileList_.emplace_back(filename, stream);
return stream;
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
"\nYou can use the following GROMACS-specific command-line flags\n"
"to control the behavior of the tests:\n\n");
TextWriter writer(&TextOutputFile::standardError());
- CommandLineHelpContext context(&writer, eHelpOutputFormat_Console, NULL, program);
+ CommandLineHelpContext context(&writer, eHelpOutputFormat_Console, nullptr, program);
context.setModuleDisplayName(program);
CommandLineHelpWriter(options).writeHelp(context);
}
{
if (!usesMpi && gmx_node_num() > 1)
{
+ // We cannot continue, since some tests might be using
+ // MPI_COMM_WORLD, which could deadlock if we would only
+ // continue with the master rank here.
if (gmx_node_rank() == 0)
{
fprintf(stderr, "NOTE: You are running %s on %d MPI ranks, "
"but it is does not contain MPI-enabled tests. "
- "Rank 0 will run the tests, other ranks will exit.",
+ "The test will now exit.\n",
context.programName(), gmx_node_num());
}
- else
- {
- finalizeForCommandLine();
- std::exit(0);
- }
+ finalizeForCommandLine();
+ std::exit(1);
}
g_testContext.reset(new TestProgramContext(context));
setProgramContext(g_testContext.get());
// Use the default finder that does not respect GMXLIB, since the tests
// generally can only get confused by a different set of data files.
- setLibraryFileFinder(NULL);
+ setLibraryFileFinder(nullptr);
::testing::InitGoogleMock(argc, *argv);
- if (dataPath != NULL)
+ if (dataPath != nullptr)
{
TestFileManager::setInputDataDirectory(
Path::join(CMAKE_SOURCE_DIR, dataPath));
}
- if (tempPath != NULL)
+ if (tempPath != nullptr)
{
TestFileManager::setGlobalOutputTempDirectory(tempPath);
}
bool bHelp = false;
std::string sourceRoot;
- Options options(NULL, NULL);
+ Options options;
// TODO: A single option that accepts multiple names would be nicer.
// Also, we recognize -help, but GTest doesn't, which leads to a bit
// unintuitive behavior.
void finalizeTestUtils()
{
- setProgramContext(NULL);
+ setProgramContext(nullptr);
g_testContext.reset();
finalizeForCommandLine();
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2011,2012,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2011,2012,2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
refdata_tests.cpp
testasserts_tests.cpp
xvgtest_tests.cpp)
+
+gmx_add_mpi_unit_test(TestUtilsMpiUnitTests testutils-mpi-test 2
+ mpitest.cpp)
void addOutput(const char *output)
{
- events_.push_back(Event(WriteOutput, output));
+ events_.emplace_back(WriteOutput, output);
}
void addInputLine(const char *inputLine)
{
}
void addReadInput()
{
- events_.push_back(Event(ReadInput, ""));
+ events_.emplace_back(ReadInput, "");
}
void addInput(const char *inputLine)
{
{
addInputLine(inputLine);
helper_.setLastNewline(false);
- events_.push_back(Event(ReadInputNoNewline, ""));
+ events_.emplace_back(ReadInputNoNewline, "");
}
void run()
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/* This file is completely threadsafe - keep it that way! */
+/*! \internal \file
+ * \brief
+ * Tests for infrastructure for running tests under MPI.
+ *
+ * \author Teemu Murtola <teemu.murtola@gmail.com>
+ * \ingroup module_testutils
+ */
#include "gmxpre.h"
-#include "energyhistory.h"
+#include "testutils/mpitest.h"
-#include <cstring>
+#include "config.h"
-#include <algorithm>
+#include <gtest/gtest.h>
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/basenetwork.h"
+#include "gromacs/utility/gmxmpi.h"
-static void done_delta_h_history(delta_h_history_t *dht)
+namespace
{
- int i;
-
- for (i = 0; i < dht->nndh; i++)
- {
- sfree(dht->dh[i]);
- }
- sfree(dht->dh);
- sfree(dht->ndh);
-}
-void init_energyhistory(energyhistory_t * enerhist)
+class MpiSelfTest : public ::testing::Test
{
- enerhist->nener = 0;
+ public:
+ MpiSelfTest() : reached {0, 0}
+ {}
- enerhist->ener_ave = NULL;
- enerhist->ener_sum = NULL;
- enerhist->ener_sum_sim = NULL;
- enerhist->dht = NULL;
+ int reached[2];
+};
- enerhist->nsteps = 0;
- enerhist->nsum = 0;
- enerhist->nsteps_sim = 0;
- enerhist->nsum_sim = 0;
-
- enerhist->dht = NULL;
-}
-
-void done_energyhistory(energyhistory_t * enerhist)
+TEST_F(MpiSelfTest, Runs)
{
- sfree(enerhist->ener_ave);
- sfree(enerhist->ener_sum);
- sfree(enerhist->ener_sum_sim);
-
- if (enerhist->dht != NULL)
+ GMX_MPI_TEST(2);
+#if GMX_THREAD_MPI
+ reached[gmx_node_rank()] = 1;
+ MPI_Barrier(MPI_COMM_WORLD);
+#else
+ int value = 1;
+ MPI_Gather(&value, 1, MPI_INT, reached, 1, MPI_INT, 0, MPI_COMM_WORLD);
+#endif
+ if (gmx_node_rank() == 0)
{
- done_delta_h_history(enerhist->dht);
- sfree(enerhist->dht);
+ EXPECT_EQ(1, reached[0]);
+ EXPECT_EQ(1, reached[1]);
}
}
+
+} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2011,2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "testutils/refdata.h"
+#include <string>
#include <vector>
#include <gtest/gtest.h>
#include <gtest/gtest-spi.h>
+#include "gromacs/utility/keyvaluetree.h"
+#include "gromacs/utility/keyvaluetreebuilder.h"
+#include "gromacs/utility/variant.h"
+
#include "testutils/testasserts.h"
#include "testutils/testexceptions.h"
//! Helper function for HandlesSequenceOfCustomData
void checkCustomVector(TestReferenceChecker *checker, const dvec &value)
{
- checker->checkVector(value, NULL);
+ checker->checkVector(value, nullptr);
}
TEST(ReferenceDataTest, HandlesSequenceOfCustomData)
TestReferenceChecker checker(data.rootChecker());
EXPECT_NONFATAL_FAILURE(checker.checkInteger(1, "missing"), "");
EXPECT_NONFATAL_FAILURE(checker.checkSequenceArray(5, seq, "missing"), "");
+ // Needed to not make the test fail because of unused "int" and "seq".
+ EXPECT_NONFATAL_FAILURE(checker.checkUnusedEntries(), "");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesUncheckedData)
+{
+ const int seq[5] = { -1, 3, 5, 2, 4 };
+
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkInteger(1, "int");
+ checker.checkSequenceArray(5, seq, "seq");
+ checker.checkUnusedEntries();
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkInteger(1, "int");
+ EXPECT_NONFATAL_FAILURE(checker.checkUnusedEntries(), "");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesUncheckedDataInSequence)
+{
+ const int seq[5] = { -1, 3, 5, 2, 4 };
+
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkInteger(1, "int");
+ checker.checkSequenceArray(5, seq, "seq");
+ checker.checkUnusedEntries();
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkInteger(1, "int");
+ EXPECT_NONFATAL_FAILURE(checker.checkSequenceArray(3, seq, "seq"), "");
+ // It might be nicer to not report the unused sequence entries also
+ // here, but both behaviors are quite OK.
+ EXPECT_NONFATAL_FAILURE(checker.checkUnusedEntries(), "");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesUncheckedDataInCompound)
+{
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ TestReferenceChecker compound(checker.checkCompound("Compound", "Compound"));
+ compound.checkInteger(1, "int1");
+ compound.checkInteger(2, "int2");
+ compound.checkUnusedEntries();
+ checker.checkInteger(1, "int");
+ checker.checkUnusedEntries();
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ TestReferenceChecker compound(checker.checkCompound("Compound", "Compound"));
+ compound.checkInteger(1, "int1");
+ EXPECT_NONFATAL_FAILURE(compound.checkUnusedEntries(), "");
+ checker.checkInteger(1, "int");
+ checker.checkUnusedEntries();
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesVariants)
+{
+ using gmx::Variant;
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkVariant(Variant::create<bool>(true), "bool");
+ checker.checkVariant(Variant::create<int>(1), "int");
+ checker.checkVariant(Variant::create<double>(3.5), "real");
+ checker.checkVariant(Variant::create<std::string>("foo"), "str");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkVariant(Variant::create<bool>(true), "bool");
+ checker.checkVariant(Variant::create<int>(1), "int");
+ checker.checkVariant(Variant::create<double>(3.5), "real");
+ checker.checkVariant(Variant::create<std::string>("foo"), "str");
+ }
+}
+
+//! Helper for building a KeyValueTree for testing.
+gmx::KeyValueTreeObject buildKeyValueTree(bool full)
+{
+ gmx::KeyValueTreeBuilder builder;
+ auto root = builder.rootObject();
+ auto obj = root.addObject("o");
+ obj.addValue<int>("i", 1);
+ if (full)
+ {
+ obj.addValue<std::string>("s", "x");
+ }
+ auto arr = root.addUniformArray<int>("a");
+ arr.addValue(2);
+ arr.addValue(3);
+ root.addValue<std::string>("s", "y");
+ return builder.build();
+}
+
+
+TEST(ReferenceDataTest, HandlesKeyValueTree)
+{
+ gmx::KeyValueTreeObject tree = buildKeyValueTree(true);
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkKeyValueTreeObject(tree, "tree");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkKeyValueTreeObject(tree, "tree");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesKeyValueTreeExtraKey)
+{
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkKeyValueTreeObject(buildKeyValueTree(false), "tree");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ EXPECT_NONFATAL_FAILURE(checker.checkKeyValueTreeObject(buildKeyValueTree(true), "tree"), "");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesKeyValueTreeMissingKey)
+{
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkKeyValueTreeObject(buildKeyValueTree(true), "tree");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ EXPECT_NONFATAL_FAILURE(checker.checkKeyValueTreeObject(buildKeyValueTree(false), "tree"), "");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesVariantsWithIncorrectValue)
+{
+ using gmx::Variant;
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkVariant(Variant::create<bool>(true), "bool");
+ checker.checkVariant(Variant::create<int>(1), "int");
+ checker.checkVariant(Variant::create<double>(3.5), "real");
+ checker.checkVariant(Variant::create<std::string>("foo"), "str");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ EXPECT_NONFATAL_FAILURE(checker.checkVariant(Variant::create<bool>(false), "bool"), "");
+ EXPECT_NONFATAL_FAILURE(checker.checkVariant(Variant::create<int>(2), "int"), "");
+ EXPECT_NONFATAL_FAILURE(checker.checkVariant(Variant::create<double>(2.5), "real"), "");
+ EXPECT_NONFATAL_FAILURE(checker.checkVariant(Variant::create<std::string>("bar"), "str"), "");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesVariantsWithIncorrectType)
+{
+ using gmx::Variant;
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkVariant(Variant::create<bool>(true), "bool");
+ checker.checkVariant(Variant::create<int>(1), "int");
+ checker.checkVariant(Variant::create<double>(3.5), "real");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ EXPECT_NONFATAL_FAILURE(checker.checkVariant(Variant::create<int>(1), "bool"), "");
+ EXPECT_NONFATAL_FAILURE(checker.checkVariant(Variant::create<bool>(true), "int"), "");
+ EXPECT_NONFATAL_FAILURE(checker.checkVariant(Variant::create<int>(2), "real"), "");
}
}
TestReferenceChecker checker(data.rootChecker());
for (const auto &s : strings)
{
- checker.checkString(s, NULL);
- checker.checkTextBlock(s, NULL);
+ checker.checkString(s, nullptr);
+ checker.checkTextBlock(s, nullptr);
}
}
{
TestReferenceChecker checker(data.rootChecker());
for (const auto &s : strings)
{
- checker.checkString(s, NULL);
- checker.checkTextBlock(s, NULL);
+ checker.checkString(s, nullptr);
+ checker.checkTextBlock(s, nullptr);
}
}
}
{
TestReferenceData data(gmx::test::erefdataUpdateAll);
TestReferenceChecker checker(data.rootChecker());
- checker.checkString("Test", NULL);
- checker.checkString("Test2", NULL);
+ checker.checkString("Test", nullptr);
+ checker.checkString("Test2", nullptr);
}
{
TestReferenceData data(gmx::test::erefdataCompare);
TestReferenceChecker checker(data.rootChecker());
- checker.checkString("Test", NULL);
- checker.checkString("Test2", NULL);
- EXPECT_NONFATAL_FAILURE(checker.checkString("Test", NULL), "");
+ checker.checkString("Test", nullptr);
+ checker.checkString("Test2", nullptr);
+ EXPECT_NONFATAL_FAILURE(checker.checkString("Test", nullptr), "");
}
}
TestReferenceData data(gmx::test::erefdataUpdateAll);
TestReferenceChecker checker(data.rootChecker());
checker.checkInteger(1, "int1");
- checker.checkString("Test", NULL);
- checker.checkString("Test2", NULL);
+ checker.checkString("Test", nullptr);
+ checker.checkString("Test2", nullptr);
checker.checkInteger(2, "int2");
- EXPECT_NONFATAL_FAILURE(checker.checkString("Test3", NULL), "");
- checker.checkString("Test2", NULL);
+ EXPECT_NONFATAL_FAILURE(checker.checkString("Test3", nullptr), "");
+ checker.checkString("Test2", nullptr);
}
{
TestReferenceData data(gmx::test::erefdataCompare);
TestReferenceChecker checker(data.rootChecker());
checker.checkInteger(1, "int1");
- checker.checkString("Test", NULL);
- checker.checkString("Test2", NULL);
+ checker.checkString("Test", nullptr);
+ checker.checkString("Test2", nullptr);
checker.checkInteger(2, "int2");
- EXPECT_NONFATAL_FAILURE(checker.checkString("Test3", NULL), "");
+ EXPECT_NONFATAL_FAILURE(checker.checkString("Test3", nullptr), "");
checker.checkInteger(1, "int1");
- checker.checkString("Test", NULL);
- checker.checkString("Test2", NULL);
- EXPECT_NONFATAL_FAILURE(checker.checkString("Test", NULL), "");
+ checker.checkString("Test", nullptr);
+ checker.checkString("Test2", nullptr);
+ EXPECT_NONFATAL_FAILURE(checker.checkString("Test", nullptr), "");
checker.checkInteger(2, "int2");
- EXPECT_NONFATAL_FAILURE(checker.checkString("Test3", NULL), "");
+ EXPECT_NONFATAL_FAILURE(checker.checkString("Test3", nullptr), "");
+ }
+}
+
+
+TEST(ReferenceDataTest, HandlesReadingValues)
+{
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkUChar('A', "char");
+ checker.checkInteger(1, "int");
+ checker.checkString("Test", "string");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ EXPECT_EQ('A', checker.readUChar("char"));
+ EXPECT_EQ(1, checker.readInteger("int"));
+ EXPECT_EQ("Test", checker.readString("string"));
}
}
}
}
+TEST(ReferenceDataTest, HandlesUpdateChangedWithRemovedEntries)
+{
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateAll);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkInteger(1, "int");
+ checker.checkString("Test", "string");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataUpdateChanged);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkInteger(2, "int");
+ }
+ {
+ TestReferenceData data(gmx::test::erefdataCompare);
+ TestReferenceChecker checker(data.rootChecker());
+ checker.checkInteger(2, "int");
+ }
+}
+
} // namespace
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
gmx::test::TestReferenceData data(gmx::test::erefdataCompare);
gmx::test::TestReferenceChecker checker(data.rootChecker());
gmx::StringInputStream sis(input);
- EXPECT_NONFATAL_FAILURE(checkXvgFile(&sis, &checker, XvgMatchSettings()), "absent");
+ EXPECT_NONFATAL_FAILURE(checkXvgFile(&sis, &checker, XvgMatchSettings()), "not used in test");
}
}
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* See \ref page_refdata for more details.
* - gmx::test::CommandLine and related classes (in cmdlinetest.h) provide
* utilities for constructing command line argument arrays for use in tests
- * that invoke actual commands.
+ * that invoke actual commands. The same header also provides
+ * gmx::test::CommandLineTestHelper and gmx::test::CommandLineTestBase
+ * for easily creating tests that execute essentially full command-line
+ * programs, including checking the output files produced.
* - gmx::test::StringTestBase provides a test fixture for tests that need to
* test long strings for correctness.
- * - gmx::test::IntegrationTestFixture provides a test fixture for tests that
- * execute legacy code where `stdin` reading etc. cannot be easily mocked.
+ * - gmx::test::StdioTestHelper provides a helper class for tests that need to
+ * execute legacy code where `stdin` reading cannot be easily mocked.
*
* Additionally, testinit.h and mpi-printer.h, and their corresponding source
* files, provide functionality that is not visible on the API level: they
/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2015, by the GROMACS development team, led by
+ * Copyright (c) 2015,2016,2017, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
//! Helper function to check a single xvg value in a sequence.
void checkXvgDataPoint(TestReferenceChecker *checker, const std::string &value)
{
- checker->checkRealFromString(value, NULL);
+ checker->checkRealFromString(value, nullptr);
}
} // namespace
&checkXvgDataPoint);
++dataRowCount;
}
- if (settings.testData)
- {
- dataChecker.checkPresent(false, formatString("Row%d", dataRowCount).c_str());
- }
+ dataChecker.checkUnusedEntries();
legendChecker.checkTextBlock(legendText, "XvgLegend");
}
#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2012,2013,2014,2015, by the GROMACS development team, led by
+# Copyright (c) 2012,2013,2014,2015,2016, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
set(REGRESSIONTEST_DOWNLOAD OFF CACHE BOOL "Tests already downloaded. Set to yes to download again" FORCE)
endif()
-if(REGRESSIONTEST_PATH AND (GMX_BLUEGENE OR CMAKE_CROSSCOMPILING OR CMAKE_CONFIGURATION_TYPES OR GMX_BUILD_MDRUN_ONLY))
- # TODO: It would be nicer to do these before potentially downloading the tests.
- # Bluegene requires us to compile both front-end and back-end binaries
- # (single build is insufficient)
+if(REGRESSIONTEST_PATH AND (CMAKE_CROSSCOMPILING OR CMAKE_CONFIGURATION_TYPES OR GMX_BUILD_MDRUN_ONLY))
+ # TODO: It would be nicer to do these checks before potentially downloading the tests.
+ # Cross-compiling toolchains require us to compile both front-end and
+ # back-end binaries to run gmxtest.pl.
# Testing an mdrun-only builds require supporting binaries from a full build
message(WARNING
"With cross-compiling, multi-configuration generators (e.g. Visual Studio), or with mdrun-only builds, running regressiontests from build system is not supported. Please run gmxtest.pl directly.")
ENVIRONMENT "PATH=${PATH}")
endforeach()
else()
- add_custom_target(regressiontests-notice
- ${CMAKE_COMMAND} -E echo "NOTE: Regression tests have not been run. If you want to run them from the build system, get the correct version of the regression tests package and set REGRESSIONTEST_PATH in CMake to point to it, or set REGRESSIONTEST_DOWNLOAD=ON."
- DEPENDS run-ctest
- COMMENT "Regression tests not available" VERBATIM)
- add_dependencies(check regressiontests-notice)
+ gmx_add_missing_tests_notice("Regression tests have not been run. If you want to run them from the build system, get the correct version of the regression tests package and set REGRESSIONTEST_PATH in CMake to point to it, or set REGRESSIONTEST_DOWNLOAD=ON.")
endif()
+gmx_create_missing_tests_notice_target()
include(CppCheck.cmake)
--- /dev/null
+#
+# This file is part of the GROMACS molecular simulation package.
+#
+# Copyright (c) 2014,2016, by the GROMACS development team, led by
+# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+# and including many others, as listed in the AUTHORS file in the
+# top-level source directory and at http://www.gromacs.org.
+#
+# GROMACS is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public License
+# as published by the Free Software Foundation; either version 2.1
+# of the License, or (at your option) any later version.
+#
+# GROMACS is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with GROMACS; if not, see
+# http://www.gnu.org/licenses, or write to the Free Software Foundation,
+# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+# If you want to redistribute modifications to GROMACS, please
+# consider that scientific software is very special. Version
+# control is crucial - bugs must be traceable. We will be happy to
+# consider code for inclusion in the official distribution, but
+# derived work must not be called official GROMACS. Details are found
+# in the README & COPYING files - if they are missing, get the
+# official version at http://www.gromacs.org.
+#
+# To help us fund GROMACS development, we humbly ask that you cite
+# the research papers on the package. Check out http://www.gromacs.org.
+
+# "tests" target builds all the separate test binaries.
+add_custom_target(tests)
+# "run-ctest" is an internal target that actually runs the tests.
+# This is necessary to be able to add separate targets that execute as part
+# of 'make check', but are ensured to be executed after the actual tests.
+add_custom_target(run-ctest
+ COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
+ COMMENT "Running all tests"
+ USES_TERMINAL VERBATIM)
+add_dependencies(run-ctest tests)
+# "check" target builds and runs all tests.
+add_custom_target(check DEPENDS run-ctest)
+
+# Global property for collecting notices to show at the end of the "check"
+# target.
+set_property(GLOBAL PROPERTY GMX_TESTS_NOTICE)
+
+function (gmx_add_missing_tests_notice TEXT)
+ set_property(GLOBAL APPEND PROPERTY GMX_TESTS_NOTICE ${TEXT})
+endfunction()
+
+function (gmx_create_missing_tests_notice_target)
+ get_property(_text GLOBAL PROPERTY GMX_TESTS_NOTICE)
+ set(_cmds)
+ foreach (_line ${_text})
+ list(APPEND _cmds COMMAND ${CMAKE_COMMAND} -E echo "NOTE: ${_line}")
+ endforeach()
+ add_custom_target(missing-tests-notice
+ ${_cmds}
+ DEPENDS run-ctest
+ COMMENT "Some tests not available" VERBATIM)
+ add_dependencies(check missing-tests-notice)
+endfunction()
--suppress=invalidscanf
--suppress=sizeofCalculation
--suppress=invalidscanf_libc
- --suppress=missingInclude:src/programs/mdrun/gmx_gpu_utils/gmx_gpu_utils.cu
--suppress=*:src/external/Random123-1.08/include/Random123/features/compilerfeatures.h
- --suppress=invalidPointerCast:src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
- --suppress=passedByValue:src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel.cuh
- --suppress=passedByValue:src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh
- --suppress=shiftTooManyBits:src/gromacs/gpu_utils/gpu_utils.cu
)
set(_cxx_flags
-D__cplusplus
--suppress=passedByValue:src/gromacs/simd/tests/*
--suppress=redundantAssignment:src/gromacs/simd/simd_math.h #seems to be a bug in cppcheck
--suppress=noExplicitConstructor # can't be selective about this, see http://sourceforge.net/p/cppcheck/discussion/general/thread/db1e4ba7/
+ --suppress=unusedStructMember:src/gromacs/onlinehelp/tests/helpmanager.cpp
+ --suppress=unusedStructMember:src/gromacs/commandline/cmdlinehelpmodule.cpp
+ --suppress=unusedStructMember:src/gromacs/selection/selhelp.cpp
+ --suppress=redundantPointerOp:src/gromacs/fileio/gmxfio-xdr.cpp
+ --suppress=passedByValue # See comment below
+ --suppress=shiftTooManyBits:src/gromacs/gpu_utils/gpu_utils.cu # CUDA kernel launch false positive
)
+ # Passing non-trivial objects by value is rarely a problem for
+ # GROMACS in performance-sensitive code, and shouldn't be
+ # enforced for types that are intended to be used like value
+ # types (e.g. SIMD wrapper types, ArrayRef) , nor for
+ # move-enabled types. cppcheck isn't sensitive to these
+ # subtleties yet.
# This list will hold the list of all files with cppcheck errors
# (one per input file)
set(_target_name cppcheck-${_filename}.${_outputext})
string(REPLACE "/" "_" _target_name ${_target_name})
list(APPEND _filelist ${_target_name})
- if (_filename MATCHES "\\.cpp$")
+ if (_filename MATCHES "\\.cpp$" OR _filename MATCHES "\\.cu$")
set(_lang CXX)
set(_lang_flags ${_cxx_flags})
else()
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff